MERS-sequences

[gsgs]

I'm posting here, as I develop things ...
maybe these posts are edited and removed or relocated
later by the more readable results and updates


------------------------------------------------

I haven't been doing MERS-sequence analysis yet


"Christian's" webpage just goes to http://www.virology-bonn.de/

there is no possibility of commenting or discussion, afaics

it would be nice to have a computer-readable file with all the aligned
MERS-sequences, locations and dates and patient-data.

that everyone can easily check and discuss

are all sequences at genbank or do the MERS-people have some
GISAID-like semi-secret database ?


do we have the one MERS-index sequence ?
----edit--- attached to this post as i_mers.txt
what's the mutation rate
----edit----, see below ~1e-3 nucleotide mutations
per position per year

----------------------------------------

Rambaut (U.of Edinburgh) has threads and comments, but requires log in
and there is no button for registering, so that seems to be a closed group

http://epidemic.bio.ed.ac.uk/node/63

---------------------------------------------

http://epidemic.bio.ed.ac.uk/

> This is a website for collaborative analysis and discussion about the emergence,
> evolution and epidemiology of novel human viral pathogens. The site is divided into
> sections for different viruses. The aim is to present new analyses as data becomes
> available. All content is publically viewable but adding content, comments or blog
> entries is restricted to account holders.

----------------------------------------------
Rambaut wrote at http://epidemic.bio.ed.ac.uk/node/58 :

> KSA has been consistently less forthcoming with details of individual cases

------------------------------------------------------

for the 3 sequences at Bonn I get: (ignoring positions behind ~26000)
29915 nucleotides when aligned with MAFFT, 29133-29705 filled nucleotides
index = average of the 3 , starting with CTTCCCCTCGTT...

>MERS-CoV/Jeddah_2014_C7770,2014/04/07,6,1-29748
C1657T,C1759T,C18498T

>MERS-CoV/Jeddah_2014_C7569,2014/04/05,167,1-29915,167,

>MERS-CoV/Jeddah_2014_C7149,2014/04/03,213,1-29750,213,
G6745A

----------------------------------------------
I get 289 hits at genbank for middle east respiratory syndrome
http://www.ncbi.nlm.nih.gov/nuccore/...atory+syndrome

OK, I figured you can click "send to" and make a fasta-file from them

289 sequences , 204 - 30177 nucleotides , 2.2MB

aligning now ... allocation error ...splitting the big file ... still very slow with MAFFT

-------------------------------------------
http://epidemic.bio.ed.ac.uk/coronavirus_analysis
Fri, 2013-06-14 10:26
There are now >70 published complete or partial genome sequences from MERS-CoV cases
both of humans and, recently, camels
http://epidemic.bio.ed.ac.uk/MERS_sequences
rate of molecular evolution : 1.12*10^(-3) subst/site/year (flu-A has ~ double that)
most recent common ancestor : mid-2011

28 complete or partial genomes sampled from April 2012 to late 2013
-----------------------------------------------------
The virus MERS-CoV is a new member of the beta group of coronavirus, Betacoronavirus,
lineage C. MERS-CoV genomes are phylogenetically classified into two clades, clade A and B.
The earliest cases of MERS were of clade A clusters (EMC/2012 and Jordan-N3/2012),
and new cases are genetically distinct (clade B).[4]
MERS-CoV is distinct from SARS and distinct from the common-cold coronavirus and
known endemic human betacoronaviruses HCoV-OC43 and HCoV-HKU1.[5

http://wwwnc.cdc.gov/eid/article/20/6/14-0299_article.htm

SARS-MERS = 11782/27579=43% differences
SARS-2cn3=43%
SARS-OC43=46%
MERS-2cn3=0.3%
MERS-OC43=45%


----------------------------------------------------------------------
http://mbio.asm.org/content/5/3/e01146-14
MERS genomes from camels, identical to human MERS
more than one genomic variant in individual camels

Partial
KSA-344-Taif-2
KSA-409-Tabuk-26.

http://www.ncbi.nlm.nih.gov/nuccore/JX869059
KSA-363-Taif-21, http://www.ncbi.nlm.nih.gov/nuccore/KJ713298 (not yet available)
KSA-378-Taif-36, http://www.ncbi.nlm.nih.gov/nuccore/KJ713296
KSA-376-Taif-34, http://www.ncbi.nlm.nih.gov/nuccore/KJ713299
KSA-503-Taif-45, http://www.ncbi.nlm.nih.gov/nuccore/KJ713297
KSA-505-Taif-47, http://www.ncbi.nlm.nih.gov/nuccore/KJ713295

-------------------------------------------------

-----------------edit 2014/05/23 -----------------------
321 sequences now at
http://www.ncbi.nlm.nih.gov/nuccore/?term=middle+east+respiratory+syndrome
51 of them are longer than 22222 nucleotides
3 of those 51 are a different strain of betacoronavirus,
that leaves 48 mers long mers sequences as of May,23,2014

-------------edit---------ebola:~200 full sequences of ~18000 nucleotides-------------------------

 

[gsgs]

Re: MERS-sequences

my first attempt has 177 sequences, most short,partial ones,
that I would classify as the standard strain, then there is
some gap towards the next relatives

it would be useful to assign the FT-casenumbers and exact dates
and locations to the sequences !

genbank access codes are included as first parameter

e.g.
http://www.ncbi.nlm.nih.gov/nuccore/KF600648.1


mutation picture:

the attached file mers1.gz contains the sequences, aligned with MAFFT, after filtering
out the more distant sequences

                                                                                   0000000000000000000000000000000000000111111111111111111111112222222222222222222223333333333333333333333333344444444444444444444455555555555555555555566666666666666666666667777777777777788888888888888888888899999999990000000000000000011111111111112222222222222222333333333334444444444455555556666666666667777777777778888888888889999999999999999900000000000000000000001111111111111111111111111222222222222222222222222222222233333333333333333334444444444444444444444444455555555555555555555555555566666666666666666666666667777777777777788888888888888888888889999999999999999999999999999999999999999999999999999999999999999999999999999999999999999000 
                                                                                   0000000000000000000111133345556677889112223344455666777888890001122233344456677880011112233333444555556677801122333455777789999900111234455567889999901111123334455566678990002335567789901111111222334556678801133679990011133455667888934455566677991223444466788888000012346690133346678901677891223344579990134566778990222444556790011122233445589901222224445556678888990011224555556778888899999000111122333333334777777888999903444555667777788991111222333555666666777889900000111234444555677777889901111234456788888888889990222446688889900123345556677778899990112566666666666666666666666666666666666666666666666666677777777777777777777777777777888001 
                                                                                   1113344444444555777002504874782237097272222812511038689122331470723917855901466280411337722469457002487901530977289139013941449935125002316957020356710566870395718967870090057492572242931445589015033011876817879578895733535805454337863923338908886590022818001136012908910680445714416249005177484701120115018812893994027678127633736857844131945909222445893992880477058958293233670290225723669337146658122235585245569239057855045047491235708551199059558116034559004062235679233065679199705889112655667453887602278888886689028571324791956864743773736771845891453422223333333444445555566666666677777777888888899999900000000111111122222222233333155390 
                                                                                   6788912346789037025017711162174678607483696880414415979439389046948582426044458447709496704937144064297275943619287808803379155612825597268384280290900679975272659760038751966013020106884230533708530287107546545995685036419652258354539203411984476794058664797866212641629336376104560306767434727474130493312846846586889050469346565922767883807961078797748399620824532717023312907617389177356459685660912646791465600445081167671420804186243341817719233450247096240636722094456842951407146781096887176617323861550125796742993984439457378505581252374281018268737356790123689013480134612345678923456789023567912468902456789012468901345678901237114006 
-codon-position--------------------------------------------------------------------12 2 2 1212 122 1  121112 2212 22122222222 221222222222222    1 11  22212 2112211122221 12 1 1 1 2222122211222212222 21 2222 1 1   11 2 22 1 2 22112 11 21 12212221  12211221 122221121  12 1212 22212  1121222222222122222222 121122 2222 2 12 222 221221122 1 221222  21  1211 211111121111111111121   1211 21 112111111111  11 11111112111  2 211211121 12 2  1 11111111 1111111111 12 1 2 1 11 1 2 2 2 21222212 2 1 22  122 1212 112 2 212222 22 2 12 122 2212212221222  22222  212221222 22 2 1  12  11    11122122 21121 1221 2 22211 1211 112 1   1121   2  2222 22122222 1212 12212 1 1212121 12 12 122 12 12 1 1 121 1 212 212 12 12 21 12 2 12 12 12 1 11  1 
---Index---------------------------------------------------------------------------CTTGTCTCTGCAGATATAATTTACCCGAATTGTGGCATCTCCACTTTATCCCCCTGACCGAATTACCGTTCCTCGACACGTAACTTCGTCGCGCTAACCATAAGTCCACCGAGTGCGGCCCCTGCTAACTCACGAACGCACTCCCCCTTTCCGACGCTCCGTATCGGGTCGCTACTTTTTTCGGCCCACATTATCTTTACTTGAGTGGGCACTCACTGCAGCGATCTCTCTTGGGCACACCATACTTTCAATAGTTACCGCTAGTCACCTTGAGGTACCGCTTTTTCCTGCTCCCGGCTCTCCAACCTCACTCGCTTGGGACACCTCGGTTGTCTGAATCGACCTGACAAAAGCCTCTTCTCTCTTTGTCCTGCGTTTCCTGCACCGTGTATCCCTGCACTCTATCGGTTGGCCTACTCCCATGTTGTTCCCTGCCCCGAGGGTGGTTCCCGGACTCCCTGACCCTGGCCGCCCCTCTTCGCCCCTCCCCGTCACGGCACGGCATTCTGGTCCGTCTTCCCCCCTACTCAACCGTCTACACTCCACGCTCTGTCCGCCCGAATTTGATCACAAACCCTAGAAAGAAACAAGGCACCAAAGAGAACACGCAAAGCTGAACCTCAAGAGCGCGTGTGCAAGGCCCCCC 
   1 >MERS-Index,2011                                                              ......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................        0      0 ,      0      0       1:>MERS-Index,2011                                                              
   2 >KF600648.1| AlHasa_9a_2013                                                   ---..A...........................................................................................................-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      537    537 ,      1      1       2:>KF600648.1| AlHasa_9a_2013                                                   
   3 >KF600614.1| AlHasa_10e_2013                                                  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T.......C......................C........C..............C...----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      592    592 ,      5      5       3:>KF600614.1| AlHasa_10e_2013                                                  
   4 >|KJ156872.1| AlHasa_26c_2013 ORF1ab gene;                                    -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.....................C........C..............C.........C........A.......................................T......T..............C......TT.........................T..T............................C...........................................................................................---      375    375 ,     13     13       4:>|KJ156872.1| AlHasa_26c_2013 ORF1ab gene;                                    
   5 >KF600632.1| AlHasa_19_2013                                                   ..................................................................................................................T..................T.................................................A...................................G.................T..........T...............................................T..................C.........................................C......................C........C..............C.........C........A.......................................T......T..............C......TT.........................T..T............................C..............................................................................................       22     22 ,     22     22       5:>KF600632.1| AlHasa_19_2013                                                   
   6 >KF600651.1| AlHasa_18_2013                                                   ..................................................................................................................T..................T.................................................A...................................G............................T..................................................................C.........................................C......................C........C..............C.........C........A.......................................T......T..............C......TT.........................T..T..........................................................................................................................-       20     20 ,     19     19       6:>KF600651.1| AlHasa_18_2013                                                   
   7 >|KJ156866.1| AlHasa_25_2013, complete genome                                 --------------....................................................................................................T..................T.................................................A.......C...........................G............................T..................................................................C.........................................C......................C........C..............C.........C........A.......................................T......T..............C......TT.........................T..T.........T................................................................................................................-       36     36 ,     21     21       7:>|KJ156866.1| AlHasa_25_2013, complete genome                                 
   8 >KF186564.1| AlHasa_4_2013                                                    ---.....C.........................................................................................................T..................T.................................................A...................................G............................T..................................................................C.........................................C......................C........C..............C.........C........A.......................................T......T..............C......TT.........................T..T...........................................................................................................................       23     23 ,     20     20       8:>KF186564.1| AlHasa_4_2013                                                    
   9 >KF600634.1| AlHasa_21_2013                                                   -------...........................................................................................................T..................T.................................................A...................................G............................T..................................................................C.........................................C......................C........C..............C.........C........A....................................T..T......T..............C......TT.....................T...T..T..........................................................................................................................-       29     29 ,     21     21       9:>KF600634.1| AlHasa_21_2013                                                   
  10 >KF186567.1| AlHasa_1_2013                                                    ..................................................................................................................T..................T.................................................A...................................G............................T..................................................................C.........................................C......................C........C..............C.........C........A.......................................T......T..............C......TT.........................T..T...........................................................................................................................       19     19 ,     19     19      10:>KF186567.1| AlHasa_1_2013                                                    
  11 >KF186566.1| AlHasa_2_2013                                                    ..................................................................................................................T..................T.................................................A...................................G............................T..................................................................C.........................................C.T....................C........C..............C.........C........A.......................................T......T..............C......TT.........................T..T...........................................................................................................................       20     20 ,     20     20      11:>KF186566.1| AlHasa_2_2013                                                    
  12 >|KJ156919.1| AlHasa_24b_2013 ORF1a gene                                      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.......................G...---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      620    620 ,      1      1      12:>|KJ156919.1| AlHasa_24b_2013 ORF1a gene                                      
  13 >KF600641.1| AlHasa_10d_2013                                                  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------...A...-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      640    640 ,      1      1      13:>KF600641.1| AlHasa_10d_2013                                                  
  14 >KF600646.1| AlHasa_11b_2013                                                  --------------------------------------------------------------------------------------------------------------------.............Y...T.................................................A...................................G............................T..................A.....A------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      495    495 ,      7      7      14:>KF600646.1| AlHasa_11b_2013                                                  
  15 >|KJ156950.1| Madinah_3a_2013 ORF1a gene                                      --------------.......C.T..AG..C..A.......T....C.C...A.....A....A------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      608    608 ,     12     12      15:>|KJ156950.1| Madinah_3a_2013 ORF1a gene                                      
  16 >|KJ156942.1| Riyadh_8b_2013, partial genome                                  -------------------------------------------------------------------------...................T......................................................C.....C.................A................................................................................................T............................................................................................A........T.....C.........T........C.....................C......C.......G...............................T...T..............T.............T.......................T...........A............T..............................................................................................T....       94     94 ,     21     21      16:>|KJ156942.1| Riyadh_8b_2013, partial genome                                  
  17 >|KJ156887.1| AlHasa_28a_2013 ORF1a gene                                      --------------------------------------....C............T.......-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      623    623 ,      2      2      17:>|KJ156887.1| AlHasa_28a_2013 ORF1a gene                                      
  18 >|KJ156875.1| AlHasa_24c_2013 ORF1ab and ORF1a genes                          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......T.......................----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      617    617 ,      1      1      18:>|KJ156875.1| AlHasa_24c_2013 ORF1ab and ORF1a genes                          
  19 >KF600656.1| AlHasa_13d_2013                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..G.G.A........C........----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      626    626 ,      4      4      19:>KF600656.1| AlHasa_13d_2013                                                  
  20 >|KJ156933.1| ORF4a and ORF4b genes; and ORF5 gene                            -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......T.....G.A...............T.---------------------------------------------------------------------------------------------------------------------------      618    618 ,      4      4      20:>|KJ156933.1| ORF4a and ORF4b genes; and ORF5 gene                            
  21 >|KJ156902.1| AlHasa_24g_2013 N protein and ORF8b genes                       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.........................................................................................................-      541    541 ,      0      0      21:>|KJ156902.1| AlHasa_24g_2013 N protein and ORF8b genes                       
  22 >KF600620.1| Bisha_1_2012                                                     ----------..........C...A.........T....................................................A................................................................................................................C.........G............G.......C...T..G......................C...................G......C.....................T.........GY.T....A........G..T....................A...........................................................G......................................................................T..........................T..............................................................................................................................       34     34 ,     24     24      22:>KF600620.1| Bisha_1_2012                                                     
  23 >|KF600612.1| Riyadh_1_2012, complete genome                                  -----.............T.C...A.........T....................................................A................................................................................................................C.........G............G.......C...T..G......................C...................G......C.....................T.........G..T....A........G..T....................A...........................................................G......................................................................T..........................T..............................................................................................................................       29     29 ,     24     24      23:>|KF600612.1| Riyadh_1_2012, complete genome                                  
  24 >KJ396766.1| strain KSA_378 ORF1ab and S protein genes                        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..........A.............................................-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      591    591 ,      1      1      24:>KJ396766.1| strain KSA_378 ORF1ab and S protein genes                        
  25 >MERSCoV/Jeddah_2014_C7770,2014/04/07                                         ---.............................C..................T.T...................T.............A.T.............T....................................T...................A.......................................C.........GT...........................T.......C.................................G.........C..................T.T.......G..T....A........G.....T.................A.................................................................C.TT....T.T.G...C..CC....................T..............T.............T.......-----------.....T...........A....GGT-----..A.CC......................................................................T.................------       70     70 ,     45     45      25:>MERSCoV/Jeddah_2014_C7770,2014/04/07                                         
  26 >KJ396763.1| strain KSA_364 spike protein gene                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.................................-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      613    613 ,      0      0      26:>KJ396763.1| strain KSA_364 spike protein gene                                
  27 >Index/                                                                       ---.............................C........................................T.............A.T.............T....................................T...................A.......................................C.........GT...........................T.......C.................................G.........C..................T.T.......G.......A........G.....T.................A.................................................................C.TT....T.T.G...C..CC....................T..............T.............T.......-----------.....T...........A..............A.CC......................................................................T.................------       59     59 ,     39     39      27:>Index/                                                                       
  28 >MERSCoV/Jeddah_2014_C7569,2014/04/05                                         ---.............................C........................................T.............A.T.............T....................................T...................A.......................................C.........GT...........................T.......C.................................G.........C..................T.T.......G.......A........G.....T.................A.................................................................C.TT....T.T.G...C..CC....................T..............T...........---------------------.....T...........A..............A.CC......................................................................T..................-----       67     67 ,     38     38      28:>MERSCoV/Jeddah_2014_C7569,2014/04/05                                         
  29 >KJ396760.1| strain KSA_378 spike protein gene                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.................................-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      613    613 ,      0      0      29:>KJ396760.1| strain KSA_378 spike protein gene                                
  30 >|KJ156944.1| Riyadh_5_2013, complete genome                                  --------------..........................T..........T....G..............T...............A.T................................C..CG..............................C.........................................TC...T...A.G.......T.A..........C...T..G..........................................G............................T.........G.......A........G.....T.T...............A................T................................................C.TT....T.......C..CC...AC.........G.....T..............T.....A.A...................T.........T........G..A.....................TT.................................................................T..................T....       65     65 ,     51     51      30:>|KJ156944.1| Riyadh_5_2013, complete genome                                  
  31 >|KJ156921.1| Taif_3e_2013 S protein gene                                     -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AC.........G.....T..............T..----------------------------------------------------------------------------------------------------------------------------------------------------------------      616    616 ,      5      5      31:>|KJ156921.1| Taif_3e_2013 S protein gene                                     
  32 >KJ556336.1| Jeddah_1_2013                                                    -----------------------............................T...................T......T........A.....T..........C.................C...G..................T...........CT........................................TC.........G....T..T.A..........C...T..G..........................................G............................T.........G.......A........G....TT.................A.................................................................C.TT....T.......C..CC...AC.........G.....T..............T.....A.A........T..........T.........T...........A.....................TT.................................................................T..................T....       73     73 ,     50     50      32:>KJ556336.1| Jeddah_1_2013                                                    
  33 >|KJ156883.1| Asir_1d_2013 N protein and ORF8b genes                          -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------................TT.................................................................T..................T..--      545    545 ,      4      4      33:>|KJ156883.1| Asir_1d_2013 N protein and ORF8b genes                          
  34 >KF600637.1| AlHasa_13c_2013                                                  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T....................A..C..-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      622    622 ,      3      3      34:>KF600637.1| AlHasa_13c_2013                                                  
  35 >|KJ156945.1| Asir_2f_2013 ORF1ab and S protein genes                         -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------...A.............CT.......................C.........YW.C.......T.C.................................YM.....G...........-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      540    540 ,     12     12      35:>|KJ156945.1| Asir_2f_2013 ORF1ab and S protein genes                         
  36 >|KJ156889.1| AlHasa_28c_2013 ORF1ab and ORF1a genes                          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.T.......................--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      622    622 ,      1      1      36:>|KJ156889.1| AlHasa_28c_2013 ORF1ab and ORF1a genes                          
  37 >|KJ156869.1| Riyadh_9_2013, complete genome                                  --------------.............................................................C..............A......T..................................T...............................T.............C..............................................................G......T.........................K......G.................................C..........T.....................................................C........C..............C.....C...C...T............................................T..........................T.T..............CT............T...........A.T.........T.................................................................G...........................T...T..       44     44 ,     30     30      37:>|KJ156869.1| Riyadh_9_2013, complete genome                                  
  38 >KF600629.1| AlHasa_11a_2013                                                  ---CGTCTCTGCAG...................................................-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      595    595 ,     11     11      38:>KF600629.1| AlHasa_11a_2013                                                  
  39 >|KJ156916.1| Madinah_3b_2013, partial genome                                 ----------------------------------------------------------------............................T.......C..............................................C.....M.................A...C...............................................................T............................T...............................................................................G............A........T.....CY........TY.......C.....................C......C.......G.......A.........Y.............T...TT.............T.............T................Y......T...........A............T..............................................................................................T....       95     95 ,     31     31      39:>|KJ156916.1| Madinah_3b_2013, partial genome                                 
  40 >|KJ156917.1| Madinah_1c_2013                                                 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------...........T..............................................................................................T....      537    537 ,      2      2      40:>|KJ156917.1| Madinah_1c_2013                                                 
  41 >|KJ396770.1| strain KSA_376 ORF1ab and S protein genes                       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.A...T............................T.............T....C..-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      595    595 ,      5      5      41:>|KJ396770.1| strain KSA_376 ORF1ab and S protein genes                       
  42 >|KJ156922.1| Taif_3c_2013 ORF1ab and ORF1a genes                             -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..........C...T.TGT.........................T...............G................C-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      576    576 ,      8      8      42:>|KJ156922.1| Taif_3c_2013 ORF1ab and ORF1a genes                             
  43 >KF600619.1| AlHasa_22d_2013                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.A.G.....C...---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      636    636 ,      3      3      43:>KF600619.1| AlHasa_22d_2013                                                  
  44 >|KJ156861.1| HafrAlBatin_4d_2013                                             ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.......G..T.....................................................................................................      536    536 ,      2      2      44:>|KJ156861.1| HafrAlBatin_4d_2013                                             
  45 >KF600615.1| AlHasa_14a_2013                                                  -------------------------------------------------------------------------------------------------------------------------------------------------------................................A...................................G............................T...........--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      540    540 ,      3      3      45:>KF600615.1| AlHasa_14a_2013                                                  
  46 >KF600645.1| AlHasa_15_2013                                                   -------------.....................................................................................................T..................T.................................................A...................................G............................T..................................................................C......................C..................Y......................C........Y..............C.........C........A.......................................T......T..............C......TT.........................T..T...........................................................................................................................       33     33 ,     20     20      46:>KF600645.1| AlHasa_15_2013                                                   
  47 >KF600616.1| AlHasa_13b_2013                                                  --------------------------------------------------------------------------------------------------------------------.................T.................................................A............------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      568    568 ,      2      2      47:>KF600616.1| AlHasa_13b_2013                                                  
  48 >KF493885.1| Bat Coronavirus Taper/CII_KSA_287/Bisha/Saudi Arabia/2012        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      646    646 ,      1      1      48:>KF493885.1| Bat Coronavirus Taper/CII_KSA_287/Bisha/Saudi Arabia/2012        
  49 >KJ396764.1| strain KSA_459 spike protein gene                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....................C.........C..-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      615    615 ,      2      2      49:>KJ396764.1| strain KSA_459 spike protein gene                                
  50 >KF600630.1| Buraidah_1_2013                                                  ---............C........................................................................................................................................................................................C.........G............................T.........................................G......................................................................A...................................................C.........C..........................................................TT.................T.......................C..T.....G...............G.....................................................................................................T..       19     19 ,     16     16      50:>KF600630.1| Buraidah_1_2013                                                  
  51 >KJ396768.1| strain KSA_459 ORF1ab and S protein genes                        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.A...................................................C..-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      592    592 ,      2      2      51:>KJ396768.1| strain KSA_459 ORF1ab and S protein genes                        
  52 >KJ650295.1| KFUHKU 13                                                        .........................T.......................T.................................T.........................T..................................................A..C....................................C.........G......................................................................G................................T.C........C..........................A...................................................C.........CG...............T....T.A...............T............T........T...............T...C....A........C........T.....................G.A......................................................................................................       29     29 ,     29     29      52:>KJ650295.1| KFUHKU 13                                                        
  53 >KJ650296.1| KFUHKU 19Dam                                                     .........................T.......................T.................................T.........................T..................................................A..C....................................C.........G......................................................................G................................T.C........C..........................A...................................................C.........CG...............T....T.A...............T............T........T...............T...C....A........C........T.....................G.A......................................................................................................       29     29 ,     29     29      53:>KJ650296.1| KFUHKU 19Dam                                                     
  54 >KJ650297.1| KFUHKU 1                                                         .........................T.......................T.................................T.........................T..................................................A..C....................................C.........G......................................................................G................................T.C........C..........................A...................................................C.........CG...............T....T.A...............T............T........T...............T...C....A........C........T.....................G.A......................................................................................................       29     29 ,     29     29      54:>KJ650297.1| KFUHKU 1                                                         
  55 >|KJ156900.1| Asir_2d_2013 ORF1ab gene                                        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......................-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      624    624 ,      0      0      55:>|KJ156900.1| Asir_2d_2013 ORF1ab gene                                        
  56 >gi|496838675|ref|NC_019843.2|                                                .......................................................................................A................................................................................................................C.........G....................C...T..G...A......................................G......C.....................T.........G.......A........G..T....................A...................................................T......T......C..T....T.......C..CC...AC.........G.....T..............T.............T.......................T....................................................................................................T.....T..........-.T....       34     34 ,     33     33      56:>gi|496838675|ref|NC_019843.2|                                                
  57 >KJ477103.1| NRCEHKU270 RNAdependent RNA polymerase gene                      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      645    645 ,      0      0      57:>KJ477103.1| NRCEHKU270 RNAdependent RNA polymerase gene                      
  58 >KF600644.1| AlHasa_16_2013                                                   ------............................................................................................................T..................T.................................................A...................................G............................T..................................................................C...................C.....................C......................C........C..............C.........C........A.......................................T......T..............C......TT.....Y...................T..T...A.......................................................................................................................       28     28 ,     22     22      58:>KF600644.1| AlHasa_16_2013                                                   
  59 >KF600627.1| AlHasa_12_2013                                                   ------............................................................................................................T..................T.................................................A...................................G............................T..................................................................C.........................................C......................C........C..............C.........C........A.......................................T......T..............C......TT.........................T..T...........................................................................................................................       25     25 ,     19     19      59:>KF600627.1| AlHasa_12_2013                                                   
  60 >KF186565.1| AlHasa_3_2013                                                    -------------.....................................................................................................T..................T.................................................A...................................G............................T..................................................................C.........................................C......................C........C..............C.........C........A.......................................T......T..............C......TT.........................T..T..........................................................................................................................A       33     33 ,     20     20      60:>KF186565.1| AlHasa_3_2013                                                    
  61 >|KJ156870.1| AlHasa_24e_2013 S protein gene                                  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....C.........C........A...........................---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      598    598 ,      3      3      61:>|KJ156870.1| AlHasa_24e_2013 S protein gene                                  
  62 >KF600647.1| AlHasa_17_2013                                                   ...................................................................................................G..............T..................T.................................................A...................................G.................T..........T..................................................................C..............C.....G....................C......................C........C..............C.........C........A.......................................T......T..............C......TT.........................T..T...........................................................................................................................       23     23 ,     23     23      62:>KF600647.1| AlHasa_17_2013                                                   
  63 >|KJ156885.1| AlHasa_24d_2013 ORF1ab gene                                     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.......................C..----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      621    621 ,      1      1      63:>|KJ156885.1| AlHasa_24d_2013 ORF1ab gene                                     
  64 >|KJ396769.1| strain KSA_364 ORF1ab and S protein genes                       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..........AC.....C..Y...................................-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      594    594 ,      4      4      64:>|KJ396769.1| strain KSA_364 ORF1ab and S protein genes                       
  65 >|KJ156926.1| Riyadh_12a_2013 ORF1ab gene; and ORF1a gene                     --------------..................C.....................................................................G...................................T................................A.................................C.................................T............................T.......................................................----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      343    343 ,      7      7      65:>|KJ156926.1| Riyadh_12a_2013 ORF1ab gene; and ORF1a gene                     
  66 >|KJ156930.1| AlHasa_28f_2013 ORF1ab and S protein genes                      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------........C......................C........C..............C.........C........A...........................---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      550    550 ,      6      6      66:>|KJ156930.1| AlHasa_28f_2013 ORF1ab and S protein genes                      
  67 >|KJ156896.1| Taif_2a_2013 ORF1ab gene; and ORF1a gene                        --------------...................................T..................................A...................................T.............T.........................A.......................................C.........G......................................................................G.........C......................T....---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      351    351 ,     10     10      67:>|KJ156896.1| Taif_2a_2013 ORF1ab gene; and ORF1a gene                        
  68 >KF933384.1| ORF4b gene                                                       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C.T...........-----------------------------------------------------------------------------------------------------------------------------------------      634    634 ,      2      2      68:>KF933384.1| ORF4b gene                                                       
  69 >|KJ156908.1| Riyadh_6d_2013 ORF1ab and S protein genes                       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------................A........T.....C.............................T..........C......C.......G.................T................-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      532    532 ,      8      8      69:>|KJ156908.1| Riyadh_6d_2013 ORF1ab and S protein genes                       
  70 >|KJ156899.1| Asir_2b_2013 ORF1a gene                                         --------------------------------------------------------------------------------------------------------------.V..................T...........T.........................C....-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      587    587 ,      4      4      70:>|KJ156899.1| Asir_2b_2013 ORF1a gene                                         
  71 >KJ396765.1| strain KSA_464 spike protein gene                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....................C............-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      614    614 ,      1      1      71:>KJ396765.1| strain KSA_464 spike protein gene                                
  72 >|KJ156867.1| AlHasa_24a_2013 ORF1a gene                                      --------------------------------------------------------------------------------------------------------------....T..................T.........................-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      599    599 ,      2      2      72:>|KJ156867.1| AlHasa_24a_2013 ORF1a gene                                      
  73 >KF600639.1| AlHasa_9e_2013                                                   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C...............................................................................................................      535    535 ,      1      1      73:>KF600639.1| AlHasa_9e_2013                                                   
  74 >KF600638.1| AlHasa_8b_2013                                                   -------------------------------------------------------------------------------------------------------------------------------------------------------TA..............................A.............................T...A.G............................T.------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      554    554 ,      7      7      74:>KF600638.1| AlHasa_8b_2013                                                   
  75 >|KJ156906.1| Taif_3g_2013                                                    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......................T.................................................................T..................T...-      538    538 ,      3      3      75:>|KJ156906.1| Taif_3g_2013                                                    
  76 >|KJ156949.1| Taif_1_2013, complete genome                                    --------------.....................T...............T............G......T...............A.....T..........C.................C...G..................T...........CT........................................TC.........G.......T.A..........C...T.TG..........................T...............G............................T.........G.......A........G.T.......T.....T.......A.................................................................C.TT....T.......C..CC...AC.........G.....T..............T.....A.A...................T.........T...........A......................T.................................................................T..................T....       65     65 ,     51     51      76:>|KJ156949.1| Taif_1_2013, complete genome                                    
  77 >|KJ156868.1| Taif_3d_2013 ORF1ab and S protein genes                         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------...T.......A..............................................----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      590    590 ,      2      2      77:>|KJ156868.1| Taif_3d_2013 ORF1ab and S protein genes                         
  78 >|KJ156909.1| AlHasa_28h_2013 N protein and ORF8b genes                       -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------............C.............................................................................................-      541    541 ,      1      1      78:>|KJ156909.1| AlHasa_28h_2013 N protein and ORF8b genes                       
  79 >|KJ156948.1| Asir_1a_2013 ORF1a gene                                         -------------------------------------------------------------------------------------------------------------.....................T...........T.................A....T..................................C........TG............---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      539    539 ,      7      7      79:>|KJ156948.1| Asir_1a_2013 ORF1a gene                                         
  80 >|KJ156864.1| HafrAlBatin_4c_2013 S protein gene                              ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.................C......C.......G.................T..-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      597    597 ,      4      4      80:>|KJ156864.1| HafrAlBatin_4c_2013 S protein gene                              
  81 >KF600628.1| HafrAlBatin_1_2013                                               .....................C....AG..C.......T.......C.C.........A..............................................................................................C.................A................................................................................................T............................................................................................A........T.....C.........T..............................C......C.......G.................T.................T..............T.............T.......................T...........A...........................................................................................................T...-       26     26 ,     25     25      81:>KF600628.1| HafrAlBatin_1_2013                                               
  82 >KF933380.1| ORF1a gene                                                       -----------------------------------------------------------------------------------------------------------------------------------------------------------------------....A.....-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      637    637 ,      1      1      82:>KF933380.1| ORF1a gene                                                       
  83 >KF961221.1| Qatar3                                                           ---....................T..AG..C...............C.C.........A.................................................Y...T...........T............................C.................A...............................G..............................................R.................T....................................T.......................Y.RY............................A.T.....MT.....C.......................................TC......C.......G.................T.......T......C..T..............TT............T.......................T...........A....................T...T..................................................................................T....       43     43 ,     40     40      83:>KF961221.1| Qatar3                                                           
  84 >KF961222.1| Qatar4                                                           .......................T..AG..C...............C.C.........A.....................................................T...........T............................C.................A...............................G................................................................T....................................T.......................................................A.T......T.....C.......................................TC......C.......G.................T.......T......C..T..............TT............T.......................T...........A........................T..................................................................................T...-       34     34 ,     33     33      84:>KF961222.1| Qatar4                                                           
  85 >KF933381.1| ORF1a gene                                                       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..........----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      636    636 ,      0      0      85:>KF933381.1| ORF1a gene                                                       
  86 >KF745068.1,MERS,2013/05/07                                                   ---------------------..........................G.T.......T...............................................................T.....................................TA.G..................T..................C.........G..................................................................T...G............T........G..........T...............................C.....A...........C..................T................C...C.........C.............................T......................T........................T.................C........TT....................G....................................................................................................T---       54     54 ,     30     30      86:>KF745068.1,MERS,2013/05/07                                                   
  87 >KF745068.1| FRA/UAE                                                          ---------------------..........................G.T.......T...............................................................T.....................................TA.G..................T..................C.........G..................................................................T...G............T........G..........T...............................C.....A...........C..................T................C...C.........C.............................T......................T........................T.................C........TT....................G....................................................................................................T---       54     54 ,     30     30      87:>KF745068.1| FRA/UAE                                                          
  88 >|KJ156928.1| M protein gene                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------........--------------------------------------------------------------------------------------------------------------      638    638 ,      0      0      88:>|KJ156928.1| M protein gene                                                  
  89 >KJ477102.1|                                                                  ---------------............G.CCA.....C..........C.T...G.....TG...TT.C.T.A...T..A.....C.ACT.T..CGG.T.C......G.....G..T.....C....GT..G...T.A...C.T..T..C....TT.C........A......GT.....G...T.T.....CCTCCC..CC....TA..G.C.........T.C..T.TG...A.........T........T.CGT.TT...C.....CA...CG.T..GCC..TT....T.......GT........TC.....T.T..C.T............G...G.TC......G..TG....C............T.C................T....TT.........CC.T.T...........CA.C.T..CTT.....TTC.TC....A.....T...GG...T....T.....C.T.T............T.......T.C.T..T..TT............................T....T.T...T.....A.......................C........................................................TT.---      165    165 ,    147    147      89:>KJ477102.1|                                                                  
  90 >KF933382.1| ORF1b gene                                                       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..............------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      632    632 ,      0      0      90:>KF933382.1| ORF1b gene                                                       
  91 >|KJ156878.1| Riyadh_15c_2013 ORF1ab and S protein genes                      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------............A........T.....C....C....K...........--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      602    602 ,      5      5      91:>|KJ156878.1| Riyadh_15c_2013 ORF1ab and S protein genes                      
  92 >|KJ156877.1| Riyadh_15b_2013 ORF1a gene                                      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..C.........G..........T.---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      624    624 ,      3      3      92:>|KJ156877.1| Riyadh_15b_2013 ORF1a gene                                      
  93 >|KJ156876.1| Taif_2b_2013 ORF1ab gene                                        GAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..A...................................................C.........C....................................................T..........C.............T.........................AT.....................G........................................................................................................      359    359 ,     12     12      93:>|KJ156876.1| Taif_2b_2013 ORF1ab gene                                        
  94 >|KJ156937.1| Riyadh_7a_2013 ORF1ab gene; and ORF1a gene                      --------------.......C.T..AG..C...............C.C.........A...............................................T...........T..................................C.................A................................................................................................T..........................................................T.......-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      339    339 ,     14     14      94:>|KJ156937.1| Riyadh_7a_2013 ORF1ab gene; and ORF1a gene                      
  95 >KJ396759.1| strain KSA_376 spike protein gene                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.T.............T....C..T......C..-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      618    618 ,      5      5      95:>KJ396759.1| strain KSA_376 spike protein gene                                
  96 >|KJ156879.1| Riyadh_6a_2013 ORF1a gene                                       ---------------------------------------------------.......A.......................G..........................---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      590    590 ,      2      2      96:>|KJ156879.1| Riyadh_6a_2013 ORF1a gene                                       
  97 >|KJ156904.1| Madinah_1b_2013 S protein gene                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....C.........T........C..--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      623    623 ,      3      3      97:>|KJ156904.1| Madinah_1b_2013 S protein gene                                  
  98 >|KJ156936.1| Riyadh_10b_2013 ORF1ab gene; and S protein gene                 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------...................A........T.....C.........T........C.....................C......C.......G.................Y.............T...TT.............T......------------------------------------------------------------------------------------------------------------------------------------------------------------      511    511 ,     13     13      98:>|KJ156936.1| Riyadh_10b_2013 ORF1ab gene; and S protein gene                 
  99 >|KJ156918.1| Riyadh_17a_2013 ORF1ab gene; and ORF1a gene                     --------------.......C.T..AG..C..A............C.C...A.....AR................................T......................................................C.......................A...................................................................T............................T.................................................R.....----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      353    353 ,     17     17      99:>|KJ156918.1| Riyadh_17a_2013 ORF1ab gene; and ORF1a gene                     
 100 >|KJ156915.1| ORF4a, ORF4b, ORF5, and E protein genes                         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A..A.A...................T.........T..........------------------------------------------------------------------------------------------------------------------      605    605 ,      5      5     100:>|KJ156915.1| ORF4a, ORF4b, ORF5, and E protein genes                         
 101 >|KJ156895.1| HafrAlBatin_4b_2013 ORF1ab and ORF1a genes                      -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..C....G...W........G......................K.......G.............T...--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      584    584 ,      7      7     101:>|KJ156895.1| HafrAlBatin_4b_2013 ORF1ab and ORF1a genes                      
 102 >KF600631.1| AlHasa_22e_2013                                                  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......C......................C........C..............C.........C........A...........................--------G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      552    552 ,      7      7     102:>KF600631.1| AlHasa_22e_2013                                                  
 103 >KF600655.1| AlHasa_7a_2013                                                   --------------..............R.....................................................................................T..................T.................................................A...................................G................G...........T..................................................................C........----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      344    344 ,      8      8     103:>KF600655.1| AlHasa_7a_2013                                                   
 104 >KJ396761.1| strain KSA_371 spike protein gene                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.................................-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      613    613 ,      0      0     104:>KJ396761.1| strain KSA_371 spike protein gene                                
 105 >MERSCoV/Jeddah_2014_C7149,2014/04/03                                         ---.............................C........................................T.............A.T.............T....................................T...................A......A................................C.........GT...........................T.......C.................................G.........C..................T.T.......G.......A........G.....T.................A.................................................................C.TT....T.T.G...C..CC....................T..............T.............T.......................T...........A..............A.CC........CTCCCATCTGTCCCTGACGATTCATGTTGTTTACAGTGCATAGGATTTACC.TAATTGATAGTTCTTTTTAAAGTGTGT-------      127    127 ,    117    117     105:>MERSCoV/Jeddah_2014_C7149,2014/04/03                                         
 106 >KJ396756.1| strain KSA_363 spike protein gene                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.................................-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      613    613 ,      0      0     106:>KJ396756.1| strain KSA_363 spike protein gene                                
 107 >|KJ156881.1| WadiAdDawasir_1_2013, complete genome                           --------------.....................................T.................C.T...............A.....T...........T................C...G..............................C........................A................TC.........G.......T.A..........C.A.T..G......C...................................G........T...................T.........G.......A........G.......................A...C.............................................................C.TT....T.......C..CC...AC.........G.....T...........C..T...TTA.A.............................T.T...C.....A......................T.................................................................T..................T....       66     66 ,     52     52     107:>|KJ156881.1| WadiAdDawasir_1_2013, complete genome                           
 108 >|KJ156871.1| Taif_4b_2013                                                    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......................T.................................................................T..................T....      537    537 ,      3      3     108:>|KJ156871.1| Taif_4b_2013                                                    
 109 >|KJ156952.1| Riyadh_4_2013, complete genome                                  --------------..............................G..........................T...............A...........................T......C.................................................C...........................C.........G....................C...T..G.T........................................G..C.........................T.........G.......A........G.......................A.......................................................C.T.......................C..CC...AC.........G.....T..............T.....A.A.............................T...........A......................T.................................................................T..................T...-       51     51 ,     36     36     109:>|KJ156952.1| Riyadh_4_2013, complete genome                                  
 110 >|KJ156952.1| Riyadh_4_2013, complete genome                                  --------------..............................G..........................T...............A...........................T......C.................................................C...........................C.........G....................C...T..G.T........................................G..C.........................T.........G.......A........G.......................A.......................................................C.T.......................C..CC...AC.........G.....T..............T.....A.A.............................T...........A......................T.................................................................T..................T...-       51     51 ,     36     36     110:>|KJ156952.1| Riyadh_4_2013, complete genome                                  
 111 >|KJ156952.1| Riyadh_4_2013, complete genome                                  --------------..............................G..........................T...............A...........................T......C.................................................C...........................C.........G....................C...T..G.T........................................G..C.........................T.........G.......A........G.......................A.......................................................C.T.......................C..CC...AC.........G.....T..............T.....A.A.............................T...........A......................T.................................................................T..................T...-       51     51 ,     36     36     111:>|KJ156952.1| Riyadh_4_2013, complete genome                                  
 112 >KJ556338.1| Jeddah_Camel1_2013 ORF3 gene                                     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......T.....A.A...-------------------------------------------------------------------------------------------------------------------------------------------------------      631    631 ,      3      3     112:>KJ556338.1| Jeddah_Camel1_2013 ORF3 gene                                     
 113 >KF600613.1| Riyadh_3_2013                                                    ------.................................C...........................A....A.A............A.T......G.........................C.............T..G.................C...C.......................T.............TC.........G.......T.A..........C...T..G..........................................G.................T..........T..A......G.......A........G.......................A.................Y...............................................C.TT....T.......C..CC...ACG.......TG.....T...T..C.......T.....A.A.............................T...........A..C...................T...............................................T.................T..................T...-       62     62 ,     55     55     113:>KF600613.1| Riyadh_3_2013                                                    
 114 >KF933383.1| Spike gene                                                       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.......---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      639    639 ,      0      0     114:>KF933383.1| Spike gene                                                       
 115 >KF600617.1| AlHasa_22a_2013                                                  ----------------...........................T....................------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      599    599 ,      1      1     115:>KF600617.1| AlHasa_22a_2013                                                  
 116 >|KJ156894.1| AlHasa_23b_2013 ORF1ab and ORF1a genes                          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......G.....Y....................................TT.................G.......T.......A............------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      556    556 ,      7      7     116:>|KJ156894.1| AlHasa_23b_2013 ORF1ab and ORF1a genes                          
 117 >KF600635.1| AlHasa_8d_2013                                                   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......................................................................................................................A.      527    527 ,      1      1     117:>KF600635.1| AlHasa_8d_2013                                                   
 118 >|KJ156863.1| Asir_2a_2013 ORF1a gene                                         --------------.....C.............................T...............................T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      581    581 ,      3      3     118:>|KJ156863.1| Asir_2a_2013 ORF1a gene                                         
 119 >|KJ156905.1| Riyadh_7b_2013 ORF1ab gene;                                     -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------........................A........T.....C............................T...........C......C.......G...............................T...T..............T.............T.......................TT..........A..................C......---------------------------------------------------------------------------------------      439    439 ,     15     15     119:>|KJ156905.1| Riyadh_7b_2013 ORF1ab gene;                                     
 120 >KF600642.1| AlHasa_10b_2013                                                  --------------------------------------------------------------------------------------------------------------T...T..................T...................................A.............A..............T---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      563    563 ,      6      6     120:>KF600642.1| AlHasa_10b_2013                                                  
 121 >KJ396758.1| strain KSA_370 spike protein gene                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....A............................-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      614    614 ,      1      1     121:>KJ396758.1| strain KSA_370 spike protein gene                                
 122 >|KJ156935.1| Madinah_1a_2013 ORF1a gene                                      ----------------------------------------------------------------............................T......................................................C.....M.................A.....Y...........WK....-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      522    522 ,      7      7     122:>|KJ156935.1| Madinah_1a_2013 ORF1a gene                                      
 123 >|KJ156892.1| M proteinlike gene                                              -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..G..----------------------------------------------------------------------------------------------------------      642    642 ,      1      1     123:>|KJ156892.1| M proteinlike gene                                              
 124 >|KJ156891.1| Riyadh_10a_2013 ORF1ab gene; and ORF1a gene                     --------------.......C.T..AG..C..A............C.C...A.....A...Y.............................T......................................................C.....M.................A...................................................................T............................T...............................................................--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      345    345 ,     17     17     124:>|KJ156891.1| Riyadh_10a_2013 ORF1ab gene; and ORF1a gene                     
 125 >|KJ156873.1| Riyadh_13b_2013 ORF1ab gene;                                    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.....A...........................A........T.....C........................................C......C.......G...............................T...T.....T.......TT.............T.......................T..C...Y....A.T.......................---------------------------------------------------------------------------------------      433    433 ,     18     18     125:>|KJ156873.1| Riyadh_13b_2013 ORF1ab gene;                                    
 126 >|KJ156880.1| Riyadh_8a_2013 ORF1a gene                                       --------------.......C.T..AG..C...............C.C.........A.....------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      604    604 ,      8      8     126:>|KJ156880.1| Riyadh_8a_2013 ORF1a gene                                       
 127 >KF600654.1| AlHasa_9b_2013                                                   -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------...........................T...C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      616    616 ,      2      2     127:>KF600654.1| AlHasa_9b_2013                                                   
 128 >KF933385.1| ORF1a gene                                                       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------................AG...-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      627    627 ,      2      2     128:>KF933385.1| ORF1a gene                                                       
 129 >KF600625.1| AlHasa_22b_2013                                                  ----------------------------------------------------------------------------------------------....................T..................T...-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      605    605 ,      2      2     129:>KF600625.1| AlHasa_22b_2013                                                  
 130 >KF600621.1| AlHasa_22f_2013                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------................................................................................................................      534    534 ,      0      0     130:>KF600621.1| AlHasa_22f_2013                                                  
 131 >KF600652.1| Riyadh_2_2012                                                    ---......................................................................................................................................................................................................................................................................................G..........................................................................................................................C.........C.......C.....................................................................T..........................T...........T..................................................................................................................       10     10 ,      7      7     131:>KF600652.1| Riyadh_2_2012                                                    
 132 >|KJ156925.1| Asir_1b_2013 ORF1ab and ORF1a genes                             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------............................G----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      618    618 ,      1      1     132:>|KJ156925.1| Asir_1b_2013 ORF1ab and ORF1a genes                             
 133 >KJ396767.1| strain KSA_464 ORF1ab and S protein genes                        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.A........A..........................................C..-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      593    593 ,      3      3     133:>KJ396767.1| strain KSA_464 ORF1ab and S protein genes                        
 134 >|KJ156924.1| HafrAlBatin_5b_2013 ORF1ab and ORF1a genes                      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..R.W..............W.T..........TT.----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      617    617 ,      6      6     134:>|KJ156924.1| HafrAlBatin_5b_2013 ORF1ab and ORF1a genes                      
 135 >|KJ156911.1| Riyadh_11b_2013 ORF1ab gene;                                    -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..............A........T.....C.......T.T........C.....................C......C.......G...............................T...T..............T.............T.......................T...........A............T............---------------------------------------------------------------------------------------      450    450 ,     16     16     135:>|KJ156911.1| Riyadh_11b_2013 ORF1ab gene;                                    
 136 >|KJ156907.1| Riyadh_10c_2013                                                 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.......T.......................T...........A............T...........----------------------------------------------------------------------------------------      582    582 ,      4      4     136:>|KJ156907.1| Riyadh_10c_2013                                                 
 137 >|KJ156914.1| Riyadh_15a_2013 ORF1a gene                                      --------------------------------------------------------------------..................A....................................K....................T.....M......C............T........Y................------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      525    525 ,      7      7     137:>|KJ156914.1| Riyadh_15a_2013 ORF1a gene                                      
 138 >KJ396757.1| strain KSA_349 spike protein gene                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..........T......................-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      614    614 ,      1      1     138:>KJ396757.1| strain KSA_349 spike protein gene                                
 139 >|KJ156940.1| AlHasa_28b_2013 ORF1a gene                                      ----------------------------------------------------------------..................................................T....T.............T..............G..................................A...................................G.............-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      483    483 ,      6      6     139:>|KJ156940.1| AlHasa_28b_2013 ORF1a gene                                      
 140 >|KJ156882.1| AlHasa_26a_2013 ORF1a gene                                      --------------C.................................................------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      597    597 ,      1      1     140:>|KJ156882.1| AlHasa_26a_2013 ORF1a gene                                      
 141 >|KJ156865.1| Riyadh_17c_2013                                                 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.......T.......................T...........A............T..............................................................................................T....      495    495 ,      5      5     141:>|KJ156865.1| Riyadh_17c_2013                                                 
 142 >|KJ156941.1| AlHasa_26b_2013 ORF1ab gene                                     ----------------------------------------------------------------..................................................T..................T.................................................A...................................G.................T..........T...............................................T..................C.........................................C.-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      360    360 ,      9      9     142:>|KJ156941.1| AlHasa_26b_2013 ORF1ab gene                                     
 143 >|KJ156932.1| Asir_2g_2013                                                    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......G........................................................................................................      536    536 ,      1      1     143:>|KJ156932.1| Asir_2g_2013                                                    
 144 >KJ396762.1| strain KSA_356 spike protein gene                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.T.............T....C..T......C..-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      618    618 ,      5      5     144:>KJ396762.1| strain KSA_356 spike protein gene                                
 145 >|KJ156884.1| AlHasa_28e_2013 ORF1ab gene                                     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..T..................C........----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      618    618 ,      2      2     145:>|KJ156884.1| AlHasa_28e_2013 ORF1ab gene                                     
 146 >KF600623.1| AlHasa_7b_2013                                                   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------........C......................C........C..............C.........C........A.......................................T......T..............C......TT.........................T..T....................................---------------------------------------------------------------------------------------      449    449 ,     13     13     146:>KF600623.1| AlHasa_7b_2013                                                   
 147 >KF600622.1| AlHasa_9d_2013                                                   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------...............T......T..............C......TT.........................T..T.--------------------------------------------------------------------------------------------------------------------------      577    577 ,      7      7     147:>KF600622.1| AlHasa_9d_2013                                                   
 148 >|KJ156946.1| Riyadh_11a_2013 ORF1ab gene; and ORF1a gene                     --------------.......C.T..AG..C...............C.C.........A.................................T......................................................C.....M.................A................................................................................................T........................T......................................--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      342    342 ,     14     14     148:>|KJ156946.1| Riyadh_11a_2013 ORF1ab gene; and ORF1a gene                     
 149 >|KJ156939.1| AlHasa_27b_2013 ORF1ab gene;                                    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------........C......................C........C..............C.........C........A.......................................T......T..............C......TT.........................T..T............................C.............................................................................................-      364    364 ,     14     14     149:>|KJ156939.1| AlHasa_27b_2013 ORF1ab gene;                                    
 150 >|KJ156931.1| HafrAlBatin_4a_2013 ORF1a gene                                  --------------..WR..............C...W.................................................................G...................................T..............M.....-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      508    508 ,      7      7     150:>|KJ156931.1| HafrAlBatin_4a_2013 ORF1a gene                                  
 151 >KF600649.1| AlHasa_9c_2013                                                   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.C......C......................C........C..............C...----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      592    592 ,      5      5     151:>KF600649.1| AlHasa_9c_2013                                                   
 152 >|KJ156897.1| Taif_3b_2013 ORF1a gene                                         --------------------------------------------------------------------------------------------------------------------------------------------------------.....CT.......................................----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      602    602 ,      2      2     152:>|KJ156897.1| Taif_3b_2013 ORF1a gene                                         
 153 >|KJ156886.1| Taif_4a_2013 ORF1a gene                                         ----------------------------------------------------------------.......T...............A.....T..........C.................C...G..................T...........CT.....................................------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      523    523 ,      9      9     153:>|KJ156886.1| Taif_4a_2013 ORF1a gene                                         
 154 >|KJ156913.1| HafrAlBatin_5d_2013                                             ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.......G..T.....................................................................................................      536    536 ,      2      2     154:>|KJ156913.1| HafrAlBatin_5d_2013                                             
 155 >|KJ156943.1| AlHasa_27a_2013 ORF1ab gene; and ORF1a gene                     --------------........G...........................................................................................T..................T.................................................A...................................G.................T..........T...............................................T..................C........----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      345    345 ,      9      9     155:>|KJ156943.1| AlHasa_27a_2013 ORF1ab gene; and ORF1a gene                     
 156 >KF600640.1| AlHasa_13e_2013                                                  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......C.T....................C.T......C......C.--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      605    605 ,      6      6     156:>KF600640.1| AlHasa_13e_2013                                                  
 157 >|KJ156951.1| HafrAlBatin_5a_2013 ORF1a gene                                  ----------------------------------------------------------------................Y...........K.........G...................................T..............M.................A.................................C....................C.....A......T......----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      474    474 ,     10     10     157:>|KJ156951.1| HafrAlBatin_5a_2013 ORF1a gene                                  
 158 >|KJ156862.1| AlHasa_23e_2013 N protein and ORF8b genes                       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..............................W...........................................................................---      541    541 ,      1      1     158:>|KJ156862.1| AlHasa_23e_2013 N protein and ORF8b genes                       
 159 >|KJ396771.1| strain KSA_363 ORF1ab and S protein genes                       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.A...................T...............................C..-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      593    593 ,      3      3     159:>|KJ396771.1| strain KSA_363 ORF1ab and S protein genes                       
 160 >|KJ156860.1| AlHasa_23a_2013 ORF1a gene                                      -----------------------------------------------------------------..................................R..............T..................T..........................................G...................------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      519    519 ,      4      4     160:>|KJ156860.1| AlHasa_23a_2013 ORF1a gene                                      
 161 >|KJ156929.1| AlHasa_23c_2013 ORF1ab and S protein genes                      ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....................................................T......C.........C...................................----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      544    544 ,      3      3     161:>|KJ156929.1| AlHasa_23c_2013 ORF1ab and S protein genes                      
 162 >|KJ156927.1| ORF4b, ORF5, E protein, M protein, N protein, and ORF8b genes   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....T.......................T...........A.......................T...................................................................................T....      498    498 ,      5      5     162:>|KJ156927.1| ORF4b, ORF5, E protein, M protein, N protein, and ORF8b genes   
 163 >KJ556340.1| Jeddah_Camel1_2013 ORF1ab and S protein genes                    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......................G...------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      621    621 ,      1      1     163:>KJ556340.1| Jeddah_Camel1_2013 ORF1ab and S protein genes                    
 164 >|KJ156859.1| Riyadh_15d_2013 S protein gene                                  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.....R.............C......C.....------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      617    617 ,      3      3     164:>|KJ156859.1| Riyadh_15d_2013 S protein gene                                  
 165 >KF600633.1| AlHasa_22c_2013                                                  ------------------------------------------------------------------------------------------------------------------------------------------.............................................A..............----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      587    587 ,      1      1     165:>KF600633.1| AlHasa_22c_2013                                                  
 166 >|KJ156938.1| Taif_3a_2013 ORF1a gene                                         --------------.....................T.........G.....T............G......T..--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      591    591 ,      5      5     166:>|KJ156938.1| Taif_3a_2013 ORF1a gene                                         
 167 >|KJ156920.1| Riyadh_17b_2013 ORF1ab gene; and S protein gene                 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..........G..........................A........T.....C.........T........C.....................C......C.......G.................T.............T...TT.............T......------------------------------------------------------------------------------------------------------------------------------------------------------------      494    494 ,     14     14     167:>|KJ156920.1| Riyadh_17b_2013 ORF1ab gene; and S protein gene                 
 168 >|KJ156947.1| Riyadh_6b_2013 ORF1a gene                                       --------------------------------------------------------------------------------------------------------------.......T.....................................................A.................................................................................---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      505    505 ,      2      2     168:>|KJ156947.1| Riyadh_6b_2013 ORF1a gene                                       
 169 >|KJ156954.1| HafrAlBatin_5c_2013 ORF1ab and S protein genes                  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------............A........T.....C.........T..............................C......C.......G..................---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      551    551 ,      7      7     169:>|KJ156954.1| HafrAlBatin_5c_2013 ORF1ab and S protein genes                  
 170 >|KJ156912.1| Asir_2c_2013 ORF1a gene                                         -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------........RSWK.........C........TG............---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      609    609 ,      7      7     170:>|KJ156912.1| Asir_2c_2013 ORF1a gene                                         
 171 >|KJ156903.1| Asir_1c_2013 ORF1ab and S protein genes                         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.A.............CT.......................C............C.......T.C........-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      581    581 ,      7      7     171:>|KJ156903.1| Asir_1c_2013 ORF1ab and S protein genes                         
 172 >|KJ156953.1| Riyadh_15f_2013 N protein and ORF8b genes                       -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......................................................................................................T....      540    540 ,      1      1     172:>|KJ156953.1| Riyadh_15f_2013 N protein and ORF8b genes                       
 173 >KF192507.1|                                                                  .......................................................................T.....G.........A.............T....................C.................................T...........................................C.........G.....C..............C...T..G..........................................G............................T.........G.......A........G....................C..A............A..................T.......................C............T....T.......C..CC...AC...T.....G.............................T.....C..............................................................................................................................................T....       34     34 ,     34     34     173:>KF192507.1|                                                                  
 174 >KF600653.1| AlHasa_10a_2013                                                  ------------------------------------............................------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      618    618 ,      0      0     174:>KF600653.1| AlHasa_10a_2013                                                  
 175 >|KJ156910.1| HafrAlBatin_2_2013, complete genome                             --------------..................C.....................................................................G...................................T..............M.................A.................................C.................................T............................T............................................................................................A........T.....C.........T..............................C......C.......G.................Y.................T..............T.............T...................C...........G...........G..T.....................................................................................................       37     37 ,     23     23     175:>|KJ156910.1| HafrAlBatin_2_2013, complete genome                             
 176 >|KJ156874.1| HafrAlBatin_6_2013, complete genome                             --------------..................C.....................................................................G...................................T..............M.................A.................................C.................................T............................T............................................................................................A........T.....C.........T..............................C......C.......G...................................T..............T.............T...................C...........G...........G..T.....................................................................................................       36     36 ,     22     22     176:>|KJ156874.1| HafrAlBatin_6_2013, complete genome                             
 177 >|KJ156901.1| Riyadh_12b_2013 ORF1ab gene;                                    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------............A........T.....C.........T..............................C......C.......G...................................T..............T.............T...................C...........G...........G..T.....................................................................................................      363    363 ,     14     14     177:>|KJ156901.1| Riyadh_12b_2013 ORF1ab gene;                                    
 178 >|KJ156888.1| Riyadh_13a_2013 ORF1ab gene; and ORF1a gene                     --------------.......C.T..AG..C...............C.C.........A...........................A.........................................................T............C............T.............................C.........G..........T......C..............G........................T.......................................T...........G.....--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      354    354 ,     20     20     178:>|KJ156888.1| Riyadh_13a_2013 ORF1ab gene; and ORF1a gene                     
 179 >|KJ156934.1| Riyadh_14_2013, complete genome                                 --------------.......C.T..AG..C...............C.C.........A...........................A.........................................................T............C............T.............................C.........G..........T......C.......................................T.......................................T...........G......T.................................A........T.....C........................................C......C.......G.................Y.............T...T.............TT.............T.......................T...........A.T.........................................................................................................T....       50     50 ,     36     36     179:>|KJ156934.1| Riyadh_14_2013, complete genome                                 
 180 >KF600624.1| AlHasa_10c_2013                                                  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..............-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      632    632 ,      0      0     180:>KF600624.1| AlHasa_10c_2013                                                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
---Index---------------------------------------------------------------------------CTTGTCTCTGCAGATATAATTTACCCGAATTGTGGCATCTCCACTTTATCCCCCTGACCGAATTACCGTTCCTCGACACGTAACTTCGTCGCGCTAACCATAAGTCCACCGAGTGCGGCCCCTGCTAACTCACGAACGCACTCCCCCTTTCCGACGCTCCGTATCGGGTCGCTACTTTTTTCGGCCCACATTATCTTTACTTGAGTGGGCACTCACTGCAGCGATCTCTCTTGGGCACACCATACTTTCAATAGTTACCGCTAGTCACCTTGAGGTACCGCTTTTTCCTGCTCCCGGCTCTCCAACCTCACTCGCTTGGGACACCTCGGTTGTCTGAATCGACCTGACAAAAGCCTCTTCTCTCTTTGTCCTGCGTTTCCTGCACCGTGTATCCCTGCACTCTATCGGTTGGCCTACTCCCATGTTGTTCCCTGCCCCGAGGGTGGTTCCCGGACTCCCTGACCCTGGCCGCCCCTCTTCGCCCCTCCCCGTCACGGCACGGCATTCTGGTCCGTCTTCCCCCCTACTCAACCGTCTACACTCCACGCTCTGTCCGCCCGAATTTGATCACAAACCCTAGAAAGAAACAAGGCACCAAAGAGAACACGCAAAGCTGAACCTCAAGAGCGCGTGTGCAAGGCCCCCC 
-codon-position--------------------------------------------------------------------12 2 2 1212 122 1  121112 2212 22122222222 221222222222222    1 11  22212 2112211122221 12 1 1 1 2222122211222212222 21 2222 1 1   11 2 22 1 2 22112 11 21 12212221  12211221 122221121  12 1212 22212  1121222222222122222222 121122 2222 2 12 222 221221122 1 221222  21  1211 211111121111111111121   1211 21 112111111111  11 11111112111  2 211211121 12 2  1 11111111 1111111111 12 1 2 1 11 1 2 2 2 21222212 2 1 22  122 1212 112 2 212222 22 2 12 122 2212212221222  22222  212221222 22 2 1  12  11    11122122 21121 1221 2 22211 1211 112 1   1121   2  2222 22122222 1212 12212 1 1212121 12 12 122 12 12 1 1 121 1 212 212 12 12 21 12 2 12 12 12 1 11  1 
                                                                                   0000000000000000000000000000000000000111111111111111111111112222222222222222222223333333333333333333333333344444444444444444444455555555555555555555566666666666666666666667777777777777788888888888888888888899999999990000000000000000011111111111112222222222222222333333333334444444444455555556666666666667777777777778888888888889999999999999999900000000000000000000001111111111111111111111111222222222222222222222222222222233333333333333333334444444444444444444444444455555555555555555555555555566666666666666666666666667777777777777788888888888888888888889999999999999999999999999999999999999999999999999999999999999999999999999999999999999999000 
                                                                                   0000000000000000000111133345556677889112223344455666777888890001122233344456677880011112233333444555556677801122333455777789999900111234455567889999901111123334455566678990002335567789901111111222334556678801133679990011133455667888934455566677991223444466788888000012346690133346678901677891223344579990134566778990222444556790011122233445589901222224445556678888990011224555556778888899999000111122333333334777777888999903444555667777788991111222333555666666777889900000111234444555677777889901111234456788888888889990222446688889900123345556677778899990112566666666666666666666666666666666666666666666666666677777777777777777777777777777888001 
                                                                                   1113344444444555777002504874782237097272222812511038689122331470723917855901466280411337722469457002487901530977289139013941449935125002316957020356710566870395718967870090057492572242931445589015033011876817879578895733535805454337863923338908886590022818001136012908910680445714416249005177484701120115018812893994027678127633736857844131945909222445893992880477058958293233670290225723669337146658122235585245569239057855045047491235708551199059558116034559004062235679233065679199705889112655667453887602278888886689028571324791956864743773736771845891453422223333333444445555566666666677777777888888899999900000000111111122222222233333155390 
                                                                                   6788912346789037025017711162174678607483696880414415979439389046948582426044458447709496704937144064297275943619287808803379155612825597268384280290900679975272659760038751966013020106884230533708530287107546545995685036419652258354539203411984476794058664797866212641629336376104560306767434727474130493312846846586889050469346565922767883807961078797748399620824532717023312907617389177356459685660912646791465600445081167671420804186243341817719233450247096240636722094456842951407146781096887176617323861550125796742993984439457378505581252374281018268737356790123689013480134612345678923456789023567912468902456789012468901345678901237114006

sorted by distance from the index in promille:

   0    0  358  114 >KF933383.1| Spike gene
   0    0  381   57 >KJ477103.1| NRCEHKU270 RNAdependent RNA polymerase gene
   0    0  390   88 >|KJ156928.1| M protein gene
   0    0  586   85 >KF933381.1| ORF1a gene
   0    0  793   90 >KF933382.1| ORF1b gene
   0    0 1044   26 >KJ396763.1| strain KSA_364 spike protein gene
   0    0 1044   29 >KJ396760.1| strain KSA_378 spike protein gene
   0    0 1044  104 >KJ396761.1| strain KSA_371 spike protein gene
   0    0 1044  106 >KJ396756.1| strain KSA_363 spike protein gene
   0    0 1195  174 >KF600653.1| AlHasa_10a_2013
   0    0 1577   21 >|KJ156902.1| AlHasa_24g_2013 N protein and ORF8b genes
   0    0 1752  180 >KF600624.1| AlHasa_10c_2013
   0    0 1857   55 >|KJ156900.1| Asir_2d_2013 ORF1ab gene
   0    0 2042  130 >KF600621.1| AlHasa_22f_2013
   0    0 30128    1 >MERS-Index,2011
   2    1 4327    2 >KF600648.1| AlHasa_9a_2013
   2    2 8258  168 >|KJ156947.1| Riyadh_6b_2013 ORF1a gene
   2    7 30082  131 >KF600652.1| Riyadh_2_2012
   3    1 2880  165 >KF600633.1| AlHasa_22c_2013
   3    7 18570   65 >|KJ156926.1| Riyadh_12a_2013 ORF1ab gene; and ORF1a gene
   4    1 2009   24 >KJ396766.1| strain KSA_378 ORF1ab and S protein genes
   4    1 2036  143 >|KJ156932.1| Asir_2g_2013
   4    1 2044   73 >KF600639.1| AlHasa_9e_2013
   4    1 2087   63 >|KJ156885.1| AlHasa_24d_2013 ORF1ab gene
   4    1 2101  115 >KF600617.1| AlHasa_22a_2013
   4    1 2116  140 >|KJ156882.1| AlHasa_26a_2013 ORF1a gene
   4    1 2199   12 >|KJ156919.1| AlHasa_24b_2013 ORF1a gene
   4    1 2350  132 >|KJ156925.1| Asir_1b_2013 ORF1ab and ORF1a genes
   4    1 2381   18 >|KJ156875.1| AlHasa_24c_2013 ORF1ab and ORF1a genes
   4    1 2489  117 >KF600635.1| AlHasa_8d_2013
   4    3 6673   45 >KF600615.1| AlHasa_14a_2013
   4    8 18505  103 >KF600655.1| AlHasa_7a_2013
   4    9 18500  155 >|KJ156943.1| AlHasa_27a_2013 ORF1ab gene; and ORF1a gene
   4    9 18545  142 >|KJ156941.1| AlHasa_26b_2013 ORF1ab gene
   5    1 1671  172 >|KJ156953.1| Riyadh_15f_2013 N protein and ORF8b genes
   5    1 1714   78 >|KJ156909.1| AlHasa_28h_2013 N protein and ORF8b genes
   5    1 1783   36 >|KJ156889.1| AlHasa_28c_2013 ORF1ab and ORF1a genes
   5    2 3787   47 >KF600616.1| AlHasa_13b_2013
   5   10 18266   67 >|KJ156896.1| Taif_2a_2013 ORF1ab gene; and ORF1a gene
   5   16 30081   50 >KF600630.1| Buraidah_1_2013
   6    1 1641  158 >|KJ156862.1| AlHasa_23e_2013 N protein and ORF8b genes
   6    4 6064  160 >|KJ156860.1| AlHasa_23a_2013 ORF1a gene
   6    6 9023  139 >|KJ156940.1| AlHasa_28b_2013 ORF1a gene
   6   19 30076   59 >KF600627.1| AlHasa_12_2013
   6   19 30105    6 >KF600651.1| AlHasa_18_2013
   6   19 30117   10 >KF186567.1| AlHasa_1_2013
   6   20 30069   60 >KF186565.1| AlHasa_3_2013
   6   20 30071   46 >KF600645.1| AlHasa_15_2013
   6   20 30081    8 >KF186564.1| AlHasa_4_2013
   6   20 30112   11 >KF186566.1| AlHasa_2_2013
   6   21 30054    7 >|KJ156866.1| AlHasa_25_2013, complete genome
   6   21 30063    9 >KF600634.1| AlHasa_21_2013
   7    3 4274  161 >|KJ156929.1| AlHasa_23c_2013 ORF1ab and S protein genes
   7    7 9625   14 >KF600646.1| AlHasa_11b_2013
   7   14 19140  148 >|KJ156946.1| Riyadh_11a_2013 ORF1ab gene; and ORF1a gene
   7   14 19266   94 >|KJ156937.1| Riyadh_7a_2013 ORF1ab gene; and ORF1a gene
   7   21 27630   16 >|KJ156942.1| Riyadh_8b_2013, partial genome
   7   22 30055  176 >|KJ156874.1| HafrAlBatin_6_2013, complete genome
   7   22 30078   58 >KF600644.1| AlHasa_16_2013
   7   22 30108    5 >KF600632.1| AlHasa_19_2013
   7   23 30055  175 >|KJ156910.1| HafrAlBatin_2_2013, complete genome
   7   23 30115   62 >KF600647.1| AlHasa_17_2013
   7   24 30051   22 >KF600620.1| Bisha_1_2012
   7   24 30063   23 >|KF600612.1| Riyadh_1_2012, complete genome
   8    2 2228  145 >|KJ156884.1| AlHasa_28e_2013 ORF1ab gene
   8    2 2258  152 >|KJ156897.1| Taif_3b_2013 ORF1a gene
   8    2 2500   96 >|KJ156879.1| Riyadh_6a_2013 ORF1a gene
   8   17 19165  124 >|KJ156891.1| Riyadh_10a_2013 ORF1ab gene; and ORF1a gene
   8   25 30104   81 >KF600628.1| HafrAlBatin_1_2013
   9    1 1044   71 >KJ396765.1| strain KSA_464 spike protein gene
   9    1 1044  121 >KJ396758.1| strain KSA_370 spike protein gene
   9    1 1044  138 >KJ396757.1| strain KSA_349 spike protein gene
   9    2 2009   51 >KJ396768.1| strain KSA_459 ORF1ab and S protein genes
   9    2 2033   40 >|KJ156917.1| Madinah_1c_2013
   9    2 2043   44 >|KJ156861.1| HafrAlBatin_4d_2013
   9    2 2043  154 >|KJ156913.1| HafrAlBatin_5d_2013
   9    2 2101  129 >KF600625.1| AlHasa_22b_2013
   9    2 2146   77 >|KJ156868.1| Taif_3d_2013 ORF1ab and S protein genes
   9    2 2147   72 >|KJ156867.1| AlHasa_24a_2013 ORF1a gene
   9    2 2218  127 >KF600654.1| AlHasa_9b_2013
   9    7 7745  116 >|KJ156894.1| AlHasa_23b_2013 ORF1ab and ORF1a genes
   9   17 18515   99 >|KJ156918.1| Riyadh_17a_2013 ORF1ab gene; and ORF1a gene
   9   29 30099   53 >KJ650296.1| KFUHKU 19Dam
   9   29 30100   52 >KJ650295.1| KFUHKU 13
   9   29 30105   54 >KJ650297.1| KFUHKU 1
   9   30 30055   37 >|KJ156869.1| Riyadh_9_2013, complete genome
  10    1  958  163 >KJ556340.1| Jeddah_Camel1_2013 ORF1ab and S protein genes
  10    3 2975  118 >|KJ156863.1| Asir_2a_2013 ORF1a gene
  10    7 6369  150 >|KJ156931.1| HafrAlBatin_4a_2013 ORF1a gene
  10   10 9951  157 >|KJ156951.1| HafrAlBatin_5a_2013 ORF1a gene
  10   20 18853  178 >|KJ156888.1| Riyadh_13a_2013 ORF1ab gene; and ORF1a gene
  10   30 29901   86 >KF745068.1,MERS,2013/05/07
  10   30 29901   87 >KF745068.1| FRA/UAE
  10   33 30086   84 >KF961222.1| Qatar4
  10   33 30111   56 >gi|496838675|ref|NC_019843.2|
  11    4 3374  136 >|KJ156907.1| Riyadh_10c_2013
  11    5 4303  141 >|KJ156865.1| Riyadh_17c_2013
  11    7 5990  137 >|KJ156914.1| Riyadh_15a_2013 ORF1a gene
  11    7 6071  122 >|KJ156935.1| Madinah_1a_2013 ORF1a gene
  11    7 6169   74 >KF600638.1| AlHasa_8b_2013
  11    7 6308   79 >|KJ156948.1| Asir_1a_2013 ORF1a gene
  11   31 27973   39 >|KJ156916.1| Madinah_3b_2013, partial genome
  11   34 30123  173 >KF192507.1|
  11   36 30054  109 >|KJ156952.1| Riyadh_4_2013, complete genome
  11   36 30054  110 >|KJ156952.1| Riyadh_4_2013, complete genome
  11   36 30054  111 >|KJ156952.1| Riyadh_4_2013, complete genome
  11   36 30055  179 >|KJ156934.1| Riyadh_14_2013, complete genome
  12    5 4159  162 >|KJ156927.1| ORF4b, ORF5, E protein, M protein, N protein, and ORF8b genes
  12    8 6324   42 >|KJ156922.1| Taif_3c_2013 ORF1ab and ORF1a genes
  12   12 9861   93 >|KJ156876.1| Taif_2b_2013 ORF1ab gene
  13    1  752   82 >KF933380.1| ORF1a gene
  13   38 29133   28 >MERSCoV/Jeddah_2014_C7569,2014/04/05
  13   39 29592   27 >Index/
  13   40 30090   83 >KF961221.1| Qatar3
  14    3 2009  133 >KJ396767.1| strain KSA_464 ORF1ab and S protein genes
  14    3 2009  159 >|KJ396771.1| strain KSA_363 ORF1ab and S protein genes
  14    3 2024   75 >|KJ156906.1| Taif_3g_2013
  14    3 2043  108 >|KJ156871.1| Taif_4b_2013
  14    3 2102   61 >|KJ156870.1| AlHasa_24e_2013 S protein gene
  14    3 2110   92 >|KJ156877.1| Riyadh_15b_2013 ORF1a gene
  14    4 2757   70 >|KJ156899.1| Asir_2b_2013 ORF1a gene
  14    6 4174  120 >KF600642.1| AlHasa_10b_2013
  14    6 4237   66 >|KJ156930.1| AlHasa_28f_2013 ORF1ab and S protein genes
  14    7 5000  101 >|KJ156895.1| HafrAlBatin_4b_2013 ORF1ab and ORF1a genes
  14    9 6110  153 >|KJ156886.1| Taif_4a_2013 ORF1a gene
  14   13 9142  146 >KF600623.1| AlHasa_7b_2013
  14   13 9202    4 >|KJ156872.1| AlHasa_26c_2013 ORF1ab gene;
  14   14 9861  149 >|KJ156939.1| AlHasa_27b_2013 ORF1ab gene; and S protein, ORF3, ORF4a, ORF4b, ORF5, E protein, M protein, N protein, and ORF8b genes
  14   14 9863  177 >|KJ156901.1| Riyadh_12b_2013 ORF1ab gene;
  14   15 10013  119 >|KJ156905.1| Riyadh_7b_2013 ORF1ab gene;
  15    3 1935   34 >KF600637.1| AlHasa_13c_2013
  15   45 29410   25 >MERSCoV/Jeddah_2014_C7770,2014/04/07
  16    7 4162  169 >|KJ156954.1| HafrAlBatin_5c_2013 ORF1ab and S protein genes
  16    8 4861   69 >|KJ156908.1| Riyadh_6d_2013 ORF1ab and S protein genes
  16   50 29890   32 >KJ556336.1| Jeddah_1_2013
  16   51 30055   30 >|KJ156944.1| Riyadh_5_2013, complete genome
  16   51 30055   76 >|KJ156949.1| Taif_1_2013, complete genome
  17    4 2245   80 >|KJ156864.1| HafrAlBatin_4c_2013 S protein gene
  17    7 4099  102 >KF600631.1| AlHasa_22e_2013
  17   16 9161  135 >|KJ156911.1| Riyadh_11b_2013 ORF1ab gene;
  17   18 10327  125 >|KJ156873.1| Riyadh_13b_2013 ORF1ab gene;
  17   52 30055  107 >|KJ156881.1| WadiAdDawasir_1_2013, complete genome
  18   55 30064  113 >KF600613.1| Riyadh_3_2013
  19    2 1044   49 >KJ396764.1| strain KSA_459 spike protein gene
  19    4 2009   64 >|KJ396769.1| strain KSA_364 ORF1ab and S protein genes
  19   14 7144  167 >|KJ156920.1| Riyadh_17b_2013 ORF1ab gene; and S protein gene
  20    5 2442  166 >|KJ156938.1| Taif_3a_2013 ORF1a gene
  21    2  940  128 >KF933385.1| ORF1a gene
  21    2  945   17 >|KJ156887.1| AlHasa_28a_2013 ORF1a gene
  22    1  449  123 >|KJ156892.1| M proteinlike gene
  22    3 1326  164 >|KJ156859.1| Riyadh_15d_2013 S protein gene
  22    5 2188  100 >|KJ156915.1| ORF4a, ORF4b, ORF5, and E protein genes
  22    6 2640  134 >|KJ156924.1| HafrAlBatin_5b_2013 ORF1ab and ORF1a genes
  22    7 3138  147 >KF600622.1| AlHasa_9d_2013
  22   13 5893   98 >|KJ156936.1| Riyadh_10b_2013 ORF1ab gene; and S protein gene
  23    4 1678   19 >KF600656.1| AlHasa_13d_2013
  23    5 2150  151 >KF600649.1| AlHasa_9c_2013
  23    5 2151    3 >KF600614.1| AlHasa_10e_2013
  23    7 3031  171 >|KJ156903.1| Asir_1c_2013 ORF1ab and S protein genes
  24    4 1633   20 >|KJ156933.1| ORF4a and ORF4b genes; and ORF5 gene
  24    4 1638   33 >|KJ156883.1| Asir_1d_2013 N protein and ORF8b genes
  24    5 2009   41 >|KJ396770.1| strain KSA_376 ORF1ab and S protein genes
  24    7 2853  170 >|KJ156912.1| Asir_2c_2013 ORF1a gene
  25    2  773   68 >KF933384.1| ORF4b gene
  25    5 1961   91 >|KJ156878.1| Riyadh_15c_2013 ORF1ab and S protein genes
  25   12 4748   35 >|KJ156945.1| Asir_2f_2013 ORF1ab and S protein genes
  27    1  361   13 >KF600641.1| AlHasa_10d_2013
  34    3  871   97 >|KJ156904.1| Madinah_1b_2013 S protein gene
  34    3  881   43 >KF600619.1| AlHasa_22d_2013
  34    6 1752  156 >KF600640.1| AlHasa_13e_2013
  37    8 2117  126 >|KJ156880.1| Riyadh_8a_2013 ORF1a gene
  39    5 1258   31 >|KJ156921.1| Taif_3e_2013 S protein gene
  39  117 29705  105 >MERSCoV/Jeddah_2014_C7149,2014/04/03
  42    3  708  112 >KJ556338.1| Jeddah_Camel1_2013 ORF3 gene
  47    5 1044   95 >KJ396759.1| strain KSA_376 spike protein gene
  47    5 1044  144 >KJ396762.1| strain KSA_356 spike protein gene
  49  147 29908   89 >KJ477102.1|
  50   11 2169   38 >KF600629.1| AlHasa_11a_2013
  57   12 2077   15 >|KJ156950.1| Madinah_3a_2013 ORF1a gene
m=180 n=30130 pivot=1 year0=0


distance in promille
number of nucleotide differences
number of nucleotides available
number in my list (sorted with seq1 h9999 H99)
access-code and name

 

[gsgs]

Re: MERS-sequences

removing the partials leaves 42 full genomes

---------edit----------
KJ477102 is the Camel from Egypt, and the mutations are evenly scattered,not concentrated in an area
so probably neither recombination nor sequencing errors, 148 mutations from the index (which I now think
was in 2012, maybe another introduction in 2011, I'm not sure yet)
so the common ancestor of the Camel and the humans would be in ~2009
-----------------------------------------------------------

I'd identify 5 substrains

........................  1:>MERS-Index,2011
...............GCTTATTA.  2:>KJ156934.1, Riyadh_14_2013
.................TTATTA.  3:>KF961221.1, Qatar3
.................TTATTA-  4:>KF961222.1, Qatar4
.................TTATTA-  5:>KF600628.1, HafrAlBatin_1_2013
.................TTATTA.  6:>KJ156942.1, Riyadh_8b_2013
.................TTATTA.  7:>KJ156916.1, Madinah_3b_2013
....................TTA.  8:>KJ156910.1, HafrAlBatin_2_2013
....................TTA.  9:>KJ156874.1, HafrAlBatin_6_2013
.....CCTCTCCT.G...TA.... 10:>KJ156869.1, Riyadh_9_2013
ACTATCCTCTCCTT.......... 11:>KF186564.1, AlHasa_4_2013
ACTATCCTYTCCTT.......... 12:>KF600645.1, AlHasa_15_2013
ACTATCCTCTCCTT.........- 13:>KF600651.1, AlHasa_18_2013
ACTATCCTCTCCTT.......... 14:>KF600644.1, AlHasa_16_2013
ACTATCCTCTCCTT.......... 15:>KF600627.1, AlHasa_12_2013
ACTATCCTCTCCTT.......... 16:>KF600632.1, AlHasa_19_2013
ACTATCCTCTCCTT.......... 17:>KF600647.1, AlHasa_17_2013
ACTATCCTCTCCTT.........- 18:>KJ156866.1, AlHasa_25_2013
ACTATCCTCTCCTT.........A 19:>KF186565.1, AlHasa_3_2013
ACTATCCTCTCCTT.......... 20:>KF186566.1, AlHasa_2_2013
ACTATCCTCTCCTT.........- 21:>KF600634.1, AlHasa_21_2013
ACTATCCTCTCCTT.......... 22:>KF186567.1, AlHasa_1_2013
..........CCTTG......... 23:>KF600652.1, Riyadh_2_2012
..........CCTTGGC....... 24:>KJ650295.1, KFUHKU 13
..........CCTTGGC....... 25:>KJ650296.1, KFUHKU 19Dam
..........CCTTGGC....... 26:>KJ650297.1, KFUHKU 1
..........CCTTGGC......- 27:>KF745068.1, FRA/UAE same as 28
..........CCTTGGC....... 29:>KF600630.1, Buraidah_1_2013
............TTGGC.....A. 30:>KF600612.1, Riyadh_1_2012
............TTGGC.....A. 31:>KF600620.1, Bisha_1_2012
............T.GGCT....A. 32:>KF192507.1, MERS
..............GGCTTATTA- 33:>KJ156952.1, Riyadh_4_2013
..............GGCTTATTA. 34:>KJ156881.1, WadiAdDawasir_1_2013
..............GGCTTATTA. 35:>KJ156949.1, Taif_1_2013
..............GGCTTATTA. 36:>KJ556336.1, Jeddah_1_2013
..............GGCTTATTA. 37:>KJ156944.1, Riyadh_5_2013
..............GGCTTATTA- 38:>KF600613.1, Riyadh_3_2013
..............GGCTT.TTA. 39:>NC_019843.2,MERS
..............GGC-TATTA- 40:>MERSCoV/Jeddah_2014_C7149,2014/04/03
..............GGC-TATTA- 41:>MERSCoV/Jeddah_2014_C7569,2014/04/05
..............GGC-TATTA- 42:>MERSCoV/Jeddah_2014_C7770,2014/04/07
..............GGCT.....- 43:>KJ477102.1, MERS

http://www.ncbi.nih.gov/nuccore/KJ156934.1
http://www.ncbi.nih.gov/nuccore/KF961221.1
http://www.ncbi.nih.gov/nuccore/KF961222.1
http://www.ncbi.nih.gov/nuccore/KF600628.1
http://www.ncbi.nih.gov/nuccore/KJ156942.1
http://www.ncbi.nih.gov/nuccore/KJ156916.1
http://www.ncbi.nih.gov/nuccore/KJ156910.1
http://www.ncbi.nih.gov/nuccore/KJ156874.1
http://www.ncbi.nih.gov/nuccore/KJ156869.1
http://www.ncbi.nih.gov/nuccore/KF186564.1
http://www.ncbi.nih.gov/nuccore/KF600645.1
http://www.ncbi.nih.gov/nuccore/KF600651.1
http://www.ncbi.nih.gov/nuccore/KF600644.1
http://www.ncbi.nih.gov/nuccore/KF600627.1
http://www.ncbi.nih.gov/nuccore/KF600632.1
http://www.ncbi.nih.gov/nuccore/KF600647.1
http://www.ncbi.nih.gov/nuccore/KJ156866.1
http://www.ncbi.nih.gov/nuccore/KF186565.1
http://www.ncbi.nih.gov/nuccore/KF186566.1
http://www.ncbi.nih.gov/nuccore/KF600634.1
http://www.ncbi.nih.gov/nuccore/KF186567.1
http://www.ncbi.nih.gov/nuccore/KF600652.1
http://www.ncbi.nih.gov/nuccore/KJ650295.1
http://www.ncbi.nih.gov/nuccore/KJ650296.1
http://www.ncbi.nih.gov/nuccore/KJ650297.1
http://www.ncbi.nih.gov/nuccore/KF745068.1
http://www.ncbi.nih.gov/nuccore/KF600630.1
http://www.ncbi.nih.gov/nuccore/KF600612.1
http://www.ncbi.nih.gov/nuccore/KF600620.1
http://www.ncbi.nih.gov/nuccore/KF192507.1
http://www.ncbi.nih.gov/nuccore/KJ156952.1
http://www.ncbi.nih.gov/nuccore/KJ156881.1
http://www.ncbi.nih.gov/nuccore/KJ156949.1
http://www.ncbi.nih.gov/nuccore/KJ556336.1
http://www.ncbi.nih.gov/nuccore/KJ156944.1
http://www.ncbi.nih.gov/nuccore/KF600613.1
http://www.ncbi.nih.gov/nuccore/NC_019843.2
http://www.ncbi.nih.gov/nuccore/KJ477102.1


>index,MERS,2011//
>KJ156934.1, Riyadh_14_2013,2013/08/15
>KF961221.1, Qatar3,2013/10/13
>KF961222.1, Qatar4,2013/10/17
>KF600628.1, HafrAlBatin_1_2013,2013/06/04
>KJ156942.1, Riyadh_8b_2013,2013/07/17
>KJ156916.1, Madinah_3b_2013,2013/09/11
>KJ156910.1, HafrAlBatin_2_2013,2013/08/05
>KJ156874.1, HafrAlBatin_6_2013,2013/08/28
>KJ156869.1, Riyadh_9_2013,2013/07/17
>KF186564.1, AlHasa_4_2013,2013/05/01
>KF600645.1, AlHasa_15_2013,2013/05/11
>KF600651.1, AlHasa_18_2013,2013/05/23
>KF600644.1, AlHasa_16_2013,2013/05/12
>KF600627.1, AlHasa_12_2013,2013/05/13
>KF600632.1, AlHasa_19_2013,2013/05/23
>KF600647.1, AlHasa_17_2013,2013/05/13
>KJ156866.1, AlHasa_25_2013,2013/05/02
>KF186565.1, AlHasa_3_2013,2013/04/22
>KF186566.1, AlHasa_2_2013,2013/04/21
>KF600634.1, AlHasa_21_2013,2013/05/30
>KF186567.1, AlHasa_1_2013,2013/05/09
>KF600652.1, Riyadh_2_2012,2013/10/30
>KJ650295.1, KFUHKU 13,2013/11/30
>KJ650296.1, KFUHKU 19Dam,2013/12/30
>KJ650297.1, KFUHKU 1,2013/12/30
>KF745068.1, FRA/UAE,2013/05/07
>KF600630.1, Buraidah_1_2013,2013/05/13
>KF600612.1, Riyadh_1_2012,2012/10/23
>KF600620.1, Bisha_1_2012,2012/06/19
>KF192507.1, MERS/UAR,2013/05/
>KJ156952.1, Riyadh_4_2013,2013/03/01
>KJ156881.1, WadiAdDawasir_1_2013,2013/06/12
>KJ156949.1, Taif_1_2013,2013/06/12
>KJ556336.1, Jeddah_1_2013,2013/11/06
>KJ156944.1, Riyadh_5_2013,2013/07/02
>KF600613.1, Riyadh_3_2013,2013/02/05
>NC_019843.2,MERS/England-1,2012/09/11
>MERSCoV/Jeddah_2014_C7149,2014/04/03
>MERSCoV/Jeddah_2014_C7569,2014/04/05
>MERSCoV/Jeddah_2014_C7770,2014/04/07
>KJ477102.1, MERS/Camel?/Egypt,2013//

 

[gsgs]

Re: MERS-sequences

mutations over time since 2011/01/01 for these 42 genomes :

 

[gsgs]

Re: MERS-sequences

I can spot (at least) one possible recombination :

Riyadh_4 has 24514A,24515C,24740G
Jeddah_7149 has 23504C,23570T,23648T,23756T

and then Taif_1 (and others) have all these 7


remember, we had this with flu, pairs of positions (p1,p2)
and viruses V1,V2 and V3 where
V1 has the mutation at p1 but not at p2
V2 has the mutation at p2 but not at p1
V3 has both mutations at p1 and p2


this unlikely happens with normal evolution.

And here we have even 3 and 4 neighboring mutations
showing this.
Suggesting that the parts containing these mutations
were swapped in recombination.

(or sequencing errors, e.g. when combining the reads
from partial scans)

full MERS-genomes, positions 20000-25000 only
                                                    222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222   
                                                    000000000000000000111111111111112222222222222222222233333333333333333334444444444444444444444   
                                                    012224445566788899125555567789990011233477777888999903444555667777788991111222355566667778899   
                                                    092225893928804705822336702922363746513524569239057855045047491235708551199059811604550040622   
                                                    610787748396208453703129076187755986694146500445081167671420804186243341817719345027092406367   
                                                                                                                                                    
---Index--------------------------------------------TGACAAGCCTTTCTCCTTCCCGTTTCCTAGTTCCTCATTTTGGCTACTCCCATGTTGTTCCCTGCCCCGAGGGTGGTTCGGACCCCGACCCTG   
   1 >index,MERS,2011//                             .............................................................................................   
   2 >KJ156869.1, Riyadh_9_2013,2013/07/17          ...........................C...C......C..C..C...T........................................T...   
   3 >KF186564.1, AlHasa_4_2013,2013/05/01          ..........C................C...C......C.....C........A...................................T...   
   4 >KF600645.1, AlHasa_15_2013,2013/05/11         ..........Y................C...Y......C.....C........A...................................T...   
   5 >KF600651.1, AlHasa_18_2013,2013/05/23         ..........C................C...C......C.....C........A...................................T...   
   6 >KF600644.1, AlHasa_16_2013,2013/05/12         ..........C................C...C......C.....C........A...................................T...   
   7 >KF600627.1, AlHasa_12_2013,2013/05/13         ..........C................C...C......C.....C........A...................................T...   
   8 >KF600632.1, AlHasa_19_2013,2013/05/23         ..........C................C...C......C.....C........A...................................T...   
   9 >KF600647.1, AlHasa_17_2013,2013/05/13         ..........C................C...C......C.....C........A...................................T...   
  10 >KJ156866.1, AlHasa_25_2013,2013/05/02         ..........C................C...C......C.....C........A...................................T...   
  11 >KF186565.1, AlHasa_3_2013,2013/04/22          ..........C................C...C......C.....C........A...................................T...   
  12 >KF186566.1, AlHasa_2_2013,2013/04/21          ..........C.T..............C...C......C.....C........A...................................T...   
  13 >KF600634.1, AlHasa_21_2013,2013/05/30         ..........C................C...C......C.....C........A................................T..T...   
  14 >KF186567.1, AlHasa_1_2013,2013/05/09          ..........C................C...C......C.....C........A...................................T...   
  15 >KF600652.1, Riyadh_2_2012,2012/10/30          ......................................C.....C.......C........................................   
  16 >KJ650295.1, KFUHKU 13,2013/11/30              ......A...............................C.....CG...............T....T.A.............T..........   
  17 >KJ650296.1, KFUHKU 19Dam,2013/12/30           ......A...............................C.....CG...............T....T.A.............T..........   
  18 >KJ650297.1, KFUHKU 1,2013/12/30               ......A...............................C.....CG...............T....T.A.............T..........   
  19 >KF745068.1, FRA/UAE,2013/05/07                ..C...A.........C...........T........CC.....C.............................T..................   
  20 >KF600630.1, Buraidah_1_2013,2013/05/13        ......A...............................C.....C................................................   
  21 >KF600612.1, Riyadh_1_2012,2012/10/23          ..............A....................................G.........................................   
  22 >KF600620.1, Bisha_1_2012,2012/06/19           ..............A....................................G.........................................   
  24 >KJ156952.1, Riyadh_4_2013,2013/03/01          ..............A................................C.T.......................C..CC.AC.......G....
  23 >KF192507.1, MERS/UAR,2013/05/                 ...........C..A......A...........T.............C............T....T.......C..CC.AC..T....G....   
  25 >KJ156881.1, WadiAdDawasir_1_2013,2013/06/12   ..............A..C.......................................C.TT....T.......C..CC.AC.......G....   
  26 >KJ156949.1, Taif_1_2013,2013/06/12            ...T...T......A..........................................C.TT....T.......C..CC.AC.......G....   
  27 >KJ556336.1, Jeddah_1_2013,2013/11/06          ..............A..........................................C.TT....T.......C..CC.AC.......G....   
  28 >KJ156944.1, Riyadh_5_2013,2013/07/02          .T............A..........T...............................C.TT....T.......C..CC.AC.......G....   
  29 >KF600613.1, Riyadh_3_2013,2013/02/05          ..............A...........Y..............................C.TT....T.......C..CC.ACG.....TG....   
  30 >NC_019843.2,MERS/England-1,2012/09/11         ..............A............................T......T......C..T....T.......C..CC.AC.......G....   
  31 >MERSCoV/Jeddah_2014_C7149,2014/04/03          ..............A..........................................C.TT....T.T.G...C..CC...............   
  32 >MERSCoV/Jeddah_2014_C7569,2014/04/05          ..............A..........................................C.TT....T.T.G...C..CC...............   
  33 >MERSCoV/Jeddah_2014_C7770,2014/04/07          ..............A..........................................C.TT....T.T.G...C..CC...............   
  34 >KJ156910.1, HafrAlBatin_2_2013,2013/08/05     ..............A....T...C.....T.................C......C.......G...............Y..............   
  35 >KJ156874.1, HafrAlBatin_6_2013,2013/08/28     ..............A....T...C.....T.................C......C.......G..............................   
  36 >KJ156934.1, Riyadh_14_2013,2013/08/15         ..............A....T...C.......................C......C.......G...............Y...........T..   
  37 >KF961221.1, Qatar3,2013/10/13                 ..............AT..MT...C......................TC......C.......G...............T......T.....C.   
  38 >KF961222.1, Qatar4,2013/10/17                 ..............AT...T...C......................TC......C.......G...............T......T.....C.   
  39 >KF600628.1, HafrAlBatin_1_2013,2013/06/04     ..............A....T...C.....T.................C......C.......G...............T..............   
  40 >KJ156942.1, Riyadh_8b_2013,2013/07/17         ..............A....T...C.....T....C............C......C.......G...........................T..   
  41 >KJ156916.1, Madinah_3b_2013,2013/09/11        ....G.........A....T...CY....TY...C............C......C.......G.......A.......Y...........T..   
  42 >KJ477102.1, MERS/Camel?/Egypt,2013//          C....G..TG...C......T.C.........T..TT..CC.TT...........CA.C.T..CTT.....TTC.TC..A....T..GG...T   
                                                                                                                                                    
---Index--------------------------------------------TGACAAGCCTTTCTCCTTCCCGTTTCCTAGTTCCTCATTTTGGCTACTCCCATGTTGTTCCCTGCCCCGAGGGTGGTTCGGACCCCGACCCTG   
                                                                                                                                                    
                                                    222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222   
                                                    000000000000000000111111111111112222222222222222222233333333333333333334444444444444444444444   
                                                    012224445566788899125555567789990011233477777888999903444555667777788991111222355566667778899   
                                                    092225893928804705822336702922363746513524569239057855045047491235708551199059811604550040622   
                                                    610787748396208453703129076187755986694146500445081167671420804186243341817719345027092406367   
                                                                                                                                                    
  24 >KJ156952.1, Riyadh_4_2013,2013/03/01          ..............A................................C.T.......................C..CC.AC.......G....
  26 >KJ156949.1, Taif_1_2013,2013/06/12            ...T...T......A..........................................C.TT....T.......C..CC.AC.......G....   
  31 >MERSCoV/Jeddah_2014_C7149,2014/04/03          ..............A..........................................C.TT....T.T.G...C..CC...............

------------edit---------------------------------
only synonymous mutations are involved , so a change in virus properties by this seems less likely

 

[gsgs]

Re: MERS-sequences

--------------update-----------------
49 full MERS from genbank , 2014/05/23
attached files:
mers50.gz : aligned and sorted sequences in fasta-format (compressed with gzip)
mers50.txt : mutation-table
mers50c.gif : mutation-picture


mutation picture: