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A/Shanghai/60T/2009(H1N1) released 6/22

AlaskaDenise

AlaskaDenise

In Memoriam
PB2 released Mon. 6/22/09:
GQ290434 2280 Human 1 H1N1 China 2009/05/28 Influenza A virus (A/Shanghai/60T/2009(H1N1)


LOCUS GQ290434 2280 bp cRNA linear VRL 22-JUN-2009
DEFINITION Influenza A virus (A/Shanghai/60T/2009(H1N1)) segment 1 polymerase
PB2 (PB2) gene, complete cds.
ACCESSION GQ290434
VERSION GQ290434.1 GI:241149115
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Shanghai/60T/2009(H1N1))
ORGANISM Influenza A virus (A/Shanghai/60T/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 2280)
AUTHORS Hu,Y., Song,Z., Tian,D., He,J., Zhou,Z., Zhang,X., Guan,W., Yin,K.,
Wu,M., Chen,Z., Zhang,X., Lu,H., Zhang,Z. and Yuan,Z.
TITLE Genetic Characterization of Swine-Origin 2009 A (H1N1) Influenza
Viruses Isolated in Shanghai
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 2280)
AUTHORS Hu,Y., Song,Z., Tian,D., He,J., Zhou,Z., Zhang,X., Guan,W., Yin,K.,
Wu,M., Chen,Z., Zhang,X., Lu,H., Zhang,Z. and Yuan,Z.
TITLE Direct Submission
JOURNAL Submitted (21-JUN-2009) Research Unit, Shanghai Public Health
Clinical Center Affiliated to Fudan University, Caolang Road 2901,
Shanghai 201508, China
COMMENT Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009.
FEATURES Location/Qualifiers
source 1..2280
/organism="Influenza A virus (A/Shanghai/60T/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Shanghai/60T/2009"
/serotype="H1N1"
/host="Homo sapiens"
/db_xref="taxon:654419"
/segment="1"
/country="China"
/collection_date="28-May-2009"
/note="lineage: swl"
gene 1..2280
/gene="PB2"
CDS 1..2280
/gene="PB2"
/codon_start=1
/product="polymerase PB2"
/protein_id="ACS66827.1"
/db_xref="GI:241149116"
/translation="MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPA
LRMKWMMAMRYPITADKRIMDMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRN
GPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDTNPGHADLSAKEAQ
DVIMEVVFPNEVGARILTSESQLAITKEKKEELQDCKIAPLMVAYMLERELVRKTRFL
PVAGGTGSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRAAVSADP
LASLLEMCHSTQIGGVRMVDILRQNPTEEQAVDICKAAIGLRISSSFSFGGFTFKRTS
GSSVKKEEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQ
SIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWG
IESIDNVMGMIGILPDMTPSTEMSLRGIRVSKMGVDEYSSTERVVVSIDRFLRVRDQR
GNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWEIVKIQWSQ
DPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAA
PPEQSRMQFSSLTVNVRGSGLRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEG
TSGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRD
SSILTDSQTATKRIRMAIN"
ORIGIN
1 atggagagaa taaaagaact gagagatcta atgtcgcagt cccgcactcg cgagatactc
61 actaagacca ctgtggacca tatggccata atcaaaaagt acacatcagg aaggcaagag
121 aagaaccccg cactcagaat gaagtggatg atggcaatga gatacccaat tacagcagac
181 aagagaataa tggacatgat tccagagagg aatgaacaag gacaaaccct ctggagcaaa
241 acaaacgatg ctggatcaga ccgagtgatg gtatcacctc tggccgtaac atggtggaat
301 aggaatggcc caacaacaag tacagttcat taccctaagg tatataaaac ttatttcgaa
361 aaggtcgaaa ggttgaaaca tggtaccttc ggccctgtcc acttcagaaa tcaagttaaa
421 ataaggagga gagttgatac gaaccctggc catgcagatc tcagtgccaa ggaggcacag
481 gatgtgatta tggaagttgt tttcccaaat gaagtggggg caagaatact gacatcagag
541 tcacagctgg caataacaaa agagaagaaa gaagagctcc aggattgtaa aattgctccc
601 ttgatggtgg cgtacatgct agaaagagaa ttggtccgta aaacaaggtt tctcccagta
661 gccggcggaa caggcagtgt ttatattgaa gtgttgcact taacccaagg gacgtgctgg
721 gagcagatgt acactccagg aggagaagtg agaaatgatg atgttgacca aagtttgatt
781 atcgctgcta gaaacatagt aagaagagca gcagtgtcag cagacccatt agcatctctc
841 ttggaaatgt gccacagcac acagattgga ggagtaagga tggtggacat ccttagacag
901 aatccaactg aggaacaagc cgtagacata tgcaaggcag caatagggtt gaggattagc
961 tcatctttca gttttggtgg gttcactttc aaaaggacaa gcggatcatc agtcaagaaa
1021 gaagaagaag tgctaacggg caacctccaa acactgaaaa taagagtaca tgaagggtat
1081 gaagaattca caatggttgg gagaagagca acagctattc tcagaaaggc aaccaggaga
1141 ttgatccagt tgatagtaag cgggagagac gagcagtcaa ttgctgaggc aataattgtg
1201 gccatggtat tctcacaaga ggattgcatg atcaaggcag ttaggggcga tctgaacttt
1261 gtcaataggg caaaccagcg gctgaacccc atgcaccaac tcttgaggca tttccaaaaa
1321 gatgcaaaag tgcttttcca gaactgggga attgaatcca tcgacaatgt gatgggaatg
1381 atcggaatac tgcccgacat gaccccaagc acggagatgt cgctgagagg gataagagtc
1441 agcaaaatgg gagtagatga atactccagc acggagagag tggtagtgag tattgaccga
1501 tttttaaggg ttagagatca aagagggaac gtactattgt ctcccgaaga agtcagtgaa
1561 acgcaaggaa ctgagaagtt gacaataact tattcgtcat caatgatgtg ggagatcaat
1621 ggccctgagt cagtgctagt caacacttat caatggataa tcaggaactg ggaaattgtg
1681 aaaattcaat ggtcacaaga tcccacaatg ttatacaaca aaatggaatt tgaaccattt
1741 cagtctcttg tccctaaggc aaccagaagc cggtacagtg gattcgtaag gacactgttc
1801 cagcaaatgc gggatgtgct tgggacattt gacactgtcc aaataataaa acttctcccc
1861 tttgctgctg ctccaccaga acagagtagg atgcaatttt cctcattgac tgtgaatgtg
1921 agaggatcag ggttgaggat actggtaaga ggcaattctc cagtattcaa ttacaacaag
1981 gcaaccaaac gacttacagt tcttggaaag gatgcaggtg cattgactga agatccagat
2041 gaaggcacat ctggggtgga gtctgctgtc ctgagaggat ttctcatttt gggcaaagaa
2101 gacaagagat atggcccagc attaagcatc aatgaactga gcaatcttgc aaaaggagag
2161 aaagctaatg tgctaattgg gcaaggggac gtagtgttgg taatgaaacg aaaacgggac
2221 tctagcatac ttactgacag ccagacagcg accaaaagaa ttcggatggc catcaattag
//
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

using the new tracking tool that Toaster showed us (http://mammalia.gsc.riken.jp/swine_influenza/),

we can look directly at position 627 in the mutation frame.

Below the title "[PB2 of A/Shanghai/60T/2009(H1N1) : GQ290434] Mutation information - Multiple alignment against 52 PB2 sequences of swine influenza [H1N1]"

We can scroll down to position 627, where we find:

627E K GQ253501
Click to expand...

To rephrase the explanation from their HELP menu:

This frame includes the mutation information for this protein.
The amino acid residues that the mutation was observed in other strains of swine influenza are listed.

For example, {627E - K - GQ253501 } indicates that the 627th resides (Glutamic acid) this protein was mutated to Lysine on the sequence of GQ253501.
Click to expand...

GQ253501 is Shanghai/70T - the one we know carries 627K

.
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

what maybe you wanted to say :

it has 627E, not the mutation of Shanghai/71T

nor any other of the potetially dangerous mutations in the end-area of PB2 which
we saw in Shanghai/71T
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

I didn't say it was like Shanghai/71T!

I was copying directly from the Japanese site.

Their HELP menu for the mutation frame (on the useable page), is what I copied, substituting the actual contents of their mutation comparisons.

If you use the site, you'll understand the meaning. What their chart is saying is: - compared to the 627E present in the new Shanghai/60T sample, these are the other values in other PB2s and it names their associated sequence numbers. In this case they pointed to the "K" in Shanghai/70T

I was trying to show how anyone could use the tool to find differences between sequences.

have you used the site?

.
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

I've looked at it a bit, but I'm using my own programs, as you know.
I may look again at it later and try more.

When I want to find other viruses with a certain mutation,
then I usually just look at my mutation tables
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

Good that you have some tools you're comfortable with. For people with a less-than-in-depth understanding of the genetics here, some of these pre-programmed tools are very helpful.

I don't understand it all yet, but it's nice to learn a little more.

The Japanese researchers did a great job and it is fantastic that they are releasing their work to the global community.

.
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

they should give a list of mutations (from the calculated index)
with each released sequence, or even instead of that sequence
(the sequence can be constructed from it)

Also the count, how often that mutation occurred already
and on request(clicking) a list of other mutations
that occurred together with that mutation and how often.
Also on click a list of closest related sequences
sorted by #of differences

It can be done and isn't so difficult.
But it's rather specific and doesn't easily apply to other
(non-flu) sequences, so there is not so much interest,
I assume
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

To clarify and credit the site Toaster2 referenced:

location: http://mammalia.gsc.riken.jp/swine_influenza/

credits:

References
Ogata K. and Umeyama H., J. Mol. Graph. Model 18, 258-272, 305-306 (2000)
Terashi G, Takeda-Shitaka M, Kanou K, Iwadate M, Takaya D, Hosoi A, Ohta K, Umeyama H, Proteins., 69 Suppl 8, 98-107 (2007)
Takeda-Shitaka M, Terashi G, Takaya D, Kanou K, Iwadate M, Umeyama H., Proteins., 61 Suppl 7, 122-7 (2005)

URL http://mammalia.gsc.riken.jp/swine_influenza/

Title Swine influenza (H1N1) protein structure model database
Kazuhiko Kanou,a Yuuki Nakamura,a Genki Terashi,a Mitsuo Iwadate,b,c Daisuke Takaya,b Takehisa Matsumoto,b Mayuko Takeda-Shitaka,a,b and Hideaki Umeyamaa,b

aSchool of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
bRIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
cDepartment of Biological Sciences, Faculty of Science and Engineering, Chuo University; Kasuga 1-13-27, Bunkyo-ku, Tokyo 112-8551, Japan
Click to expand...

.
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

AlaskaDenise said:
using the new tracking tool that Toaster showed us (http://mammalia.gsc.riken.jp/swine_influenza/),

we can look directly at position 627 in the mutation frame.

Below the title "[PB2 of A/Shanghai/60T/2009(H1N1) : GQ290434] Mutation information - Multiple alignment against 52 PB2 sequences of swine influenza [H1N1]"

We can scroll down to position 627, where we find:



To rephrase the explanation from their HELP menu:



GQ253501 is Shanghai/70T - the one we know carries 627K

.
Click to expand...
Speaking of 70T, the PB1 travel log for 60T below contains a number of Shanghai isolates, which adds to the evidence that E627K is on a Shanghai backbone and therefore was acquired in Shanghai (and not in NY or Hong Kong) - 60T isn't listed because it is new and not in the search database yet

gb|GQ253500.1| Influenza A virus (A/Shanghai/71T/2009(H1N1)) ... 34.2 2.8
gb|GQ253490.1| Influenza A virus (A/Shanghai/37T/2009(H1N1)) ... 34.2 2.8
gb|GQ225355.1| Influenza A virus (A/Shanghai/1/2009(H1N1)) se... 34.2 2.8
gb|GQ200234.1| Influenza A virus (A/Georgia/01/2009(H1N1)) se... 34.2 2.8
gb|GQ166208.2| Influenza A virus (A/Bayern/63/2009(H1N1)) seg... 34.2 2.8
gb|GQ168887.1| Influenza A virus (A/Ohio/07/2009(H1N1)) segme... 34.2 2.8
gb|CY040360.1| Influenza A virus (A/Hong Kong/HKU77/2005(H3N2... 34.2 2.8
gb|CY040048.1| Influenza A virus (A/New York/3007/2009(H1N1))... 34.2 2.8
gb|GQ160544.1| Influenza A virus (A/Ohio/07/2009(H1N1)) segme... 34.2 2.8
gb|GQ132180.1| Influenza A virus (A/Canada-ON/RV1526/2009(H1N... 34.2 2.8
gb|CY023718.1| Influenza A virus (A/chicken/Guangxi/187/2005(... 34.2 2.8
gb|CY023702.1| Influenza A virus (A/chicken/Guangxi/2441/2004... 34.2 2.8
gb|CY023694.1| Influenza A virus (A/chicken/Guangxi/1857/2004... 34.2 2.8
gb|EF551051.1| Influenza A virus (A/swine/North Carolina/2003... 34.2 2.8
gb|CY021771.1| Influenza A virus (A/South Australia/53/2005(H... 34.2 2.8
gb|CY017923.1| Influenza A virus (A/Queensland/28/2002(H3N2))... 34.2 2.8
gb|EF101748.1| Influenza A virus (A/Philippines/344/2004(H1N2... 34.2 2.8
gb|CY015682.1| Influenza A virus (A/Western Australia/13/2001... 34.2 2.8
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

PA travel log

gb|GQ290436.1| Influenza A virus (A/Shanghai/60T/2009(H1N1)) ... 38.2 0.18
gb|GQ267855.1| Influenza A virus (A/Shiga/1/2009(H1N1)) segme... 38.2 0.18
gb|GQ253496.1| Influenza A virus (A/Shanghai/37T/2009(H1N1)) ... 38.2 0.18
gb|GQ253488.1| Influenza A virus (A/Zhejiang/2/2009(H1N1)) se... 38.2 0.18
gb|GQ225356.1| Influenza A virus (A/Shanghai/1/2009(H1N1)) se... 38.2 0.18
gb|EU148425.1| Influenza A virus (A/chicken/Nigeria/1071-22/2... 38.2 0.18
gb|EU148409.1| Influenza A virus (A/chicken/Nigeria/1071-10/2... 38.2 0.18
gb|EF597400.1| Influenza A virus (A/duck/Hong Kong/394/1978(H... 38.2 0.18
gb|CY021530.1| Influenza A virus (A/turkey/Italy/1258/2005(H5... 38.2 0.18
gb|CY017280.1| Influenza A virus (A/mallard/Ohio/265/1987(H1N... 38.2 0.18
gb|DQ280199.2| Influenza A virus (A/swine/Alberta/56626/03(H1... 38.2 0.18
gb|CY005820.1| Influenza A virus (A/duck/Czechoslovakia/1956(... 38.2 0.18
gb|CY005817.1| Influenza A virus (A/duck/UKR/1/1963(H3N8)) se... 38.2 0.18
gb|AF156450.1|AF156450 Influenza A virus (A/Chicken/Hong Kong... 38.2 0.18
gb|M55473.1|FLAPAB Influenza A virus (A/swine/1976/1931(H1N1)... 38.2 0.18
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

71T is different from the other Shanghai-viruses, which I think
came from Australia.

this Ohio,Bayern group of 7 has 2 additional markers
of which 71T has G1161A(2) but lacks G1282A(4).

But it also lacks C1140T(4) and A742G(6) from the 11 standard
Cancun-markers.

This is strange and made me speculate about reassortment,
but that can't explain it either


no Shanghai background IMO
more likely one certain hotel or place in Cancun, mid April
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

Code: 
                                           00112222222 1 00 00111 000000111 00000000111 0000 00000 
                                           34280011122 1 06 67024 127888112 35666779222 4679 23457 
                                           04873300644 6 43 51080 195015444 18999453258 9027 96842 
                                           31192818349 1 00 86128 781436368 68789270163 2033 17979 
-codon-position----------------------------   11112  2   1  12211  11  1    1 12 11  22    1  1 1  
---Index-----------------------------------GAAGGGGGGGC G GT TAGGC CGGAAGGAG GTTGTATGTGG GGGG AAAGG 
  2 >A/Shanghai/1/2009/05/23               .GG.....R.. A A. A..AT .A....A.A A....G..... AA.. GGGAA       20     20 ,     20     20      2:>A/Shanghai/1/2009/05/23               
  6 >A/Shanghai/60T/2009/05/28             .GG.....A.. A A. ----- .A....A.A ----------- AA.. GG..A       29     29 ,     13     13      6:>A/Shanghai/60T/2009/05/28             
  3 >A/Shanghai/37T/2009/05/24             AGG.....A.. A A. A..AT TA....A.A A.GTGGAT... AAA. GG..A       26     26 ,     26     26      3:>A/Shanghai/37T/2009/05/24             
  1 >A/Shanghai/71T/2009/05/31             ...AAAAAA.. A .. A.... .A.GTAAGA AC......CAA AA.. .G...       23     23 ,     23     23      1:>A/Shanghai/71T/2009/05/31             
  5 >A/Newflu/Cancun-NY/Index/2009-04-15   ........A.. . .. A...T .A....A.A A....G..... AA.. .G...       11     11 ,     11     11      5:>A/Mexflu/Cancun-NY/Index/2009-04-15   
  7 >A/Bayern/63/2009//                    ........ATA A .. A..AT .A....A.A A....G..... AA.C .G...       16     16 ,     16     16      7:>A/Bayern/63/2009//                    
  8 >A/Ohio/07/2009/04/24                  ........A.. A .. A.A-- .AA...A.A A....G..... AA.. .G...       15     15 ,     13     13      8:>A/Ohio/07/2009/04/24                  
  9 >A/NY/3007/2009/04/27                  ........A.. A .. A..AT .A....A.A A....G..... AA.. .G...       13     13 ,     13     13      9:>A/NY/3007/2009/04/27                  
 10 >A/Georgia/01/2009/04/27               ........A.. A -- AG.AT .A....A.A A....G..... AA.. .G...       16     16 ,     14     14     10:>A/Georgia/01/2009/04/27               
 11 >A/Canada-ON/RV1526/2009//             ........A.. A .C W..AT .A....A.A A....G..... AA.. .G...       14     14 ,     14     14     11:>A/Canada-ON/RV1526/2009//             
  4 >A/Newflu/index/2009-02-01             ........... . .. ..... ......... ........... .... .....        0      0 ,      0      0      4:>A/Mexflu/index/2009-02-01
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

Here is the full PB1 travel log (which shows that 60T, and 71T, are with the other Shanghai sequences)

gb|GQ290435.1| Influenza A virus (A/Shanghai/60T/2009(H1N1)) ... 32.2 11 28-May-2009
gb|GQ253500.1| Influenza A virus (A/Shanghai/71T/2009(H1N1)) ... 32.2 11
gb|GQ253490.1| Influenza A virus (A/Shanghai/37T/2009(H1N1)) ... 32.2 11 24-May-2009
gb|GQ225355.1| Influenza A virus (A/Shanghai/1/2009(H1N1)) se... 32.2 11 23-May-2009 30M
gb|GQ200234.1| Influenza A virus (A/Georgia/01/2009(H1N1)) se... 32.2 11 27-April
gb|GQ166208.2| Influenza A virus (A/Bayern/63/2009(H1N1)) seg... 32.2 11
gb|GQ168887.1| Influenza A virus (A/Ohio/07/2009(H1N1)) segme... 32.2 11 24-Apr-2009 9M
gb|GQ160544.1| Influenza A virus (A/Ohio/07/2009(H1N1)) segme... 32.2 11
gb|GQ132180.1| Influenza A virus (A/Canada-ON/RV1526/2009(H1N... 32.2 11
gb|CY039173.1| Influenza A virus (A/Hong Kong/HKU24/2004(H3N2... 32.2 11
gb|CY040360.1| Influenza A virus (A/Hong Kong/HKU77/2005(H3N2... 32.2 11
gb|CY040048.1| Influenza A virus (A/New York/3007/2009(H1N1))... 32.2 11 27-Apr-2009 33Y
gb|CY039173.1| Influenza A virus (A/Hong Kong/HKU24/2004(H3N2... 32.2 11
gb|CY037861.1| Influenza A virus (A/Ohio/UR07-0023/2008(H3N2)... 32.2 11
gb|CY037525.1| Influenza A virus (A/Ohio/UR07-0031/2008(H3N2)... 32.2 11
gb|EF551051.1| Influenza A virus (A/swine/North Carolina/2003... 32.2 11
gb|CY021771.1| Influenza A virus (A/South Australia/53/2005(H... 32.2 11
gb|CY017923.1| Influenza A virus (A/Queensland/28/2002(H3N2))... 32.2 11
gb|EF101748.1| Influenza A virus (A/Philippines/344/2004(H1N2... 32.2 11
gb|CY015682.1| Influenza A virus (A/Western Australia/13/2001... 32.2 11
gb|CY000071.1| Influenza A virus (A/New York/45/2003(H3N2)) s... 32.2 11
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

PB2 travel log

gb|GQ290434.1| Influenza A virus (A/Shanghai/60T/2009(H1N1)) ... 40.1 0.046
gb|GQ253489.1| Influenza A virus (A/Shanghai/37T/2009(H1N1)) ... 40.1 0.046
gb|GQ225354.1| Influenza A virus (A/Shanghai/1/2009(H1N1)) se... 40.1 0.046
gb|EU980493.1| Influenza A virus (A/mallard/MD/865/2002(H5N2)... 40.1 0.046
gb|EU980501.1| Influenza A virus (A/mallard/MD/898/2002(H5N2)... 40.1 0.046
gb|EU980508.1| Influenza A virus (A/mallard/MD/185/2003(H5N2)... 40.1 0.046
gb|CY029936.1| Influenza A virus (A/blue-winged teal/Ohio/186... 40.1 0.046
gb|EU050626.1| Influenza A virus (A/chukkar/Shantou/1530/2005... 40.1 0.046
gb|EU050621.1| Influenza A virus (A/chukkar/Shantou/89/2005(H... 40.1 0.046
gb|EU050619.1| Influenza A virus (A/chukkar/Shantou/7964/2004... 40.1 0.046
gb|EU050615.1| Influenza A virus (A/chukkar/Shantou/6865/2004... 40.1 0.046
gb|EU050613.1| Influenza A virus (A/quail/Shantou/6651/2004(H... 40.1 0.046
gb|EU050610.1| Influenza A virus (A/quail/Shantou/6060/2004(H... 40.1 0.046
gb|EU050609.1| Influenza A virus (A/guinea fowl/Shantou/6042/... 40.1 0.046
gb|EU050608.1| Influenza A virus (A/chukkar/Shantou/5651/2004... 40.1 0.046
gb|EU050606.1| Influenza A virus (A/partridge/Shantou/5028/20... 40.1 0.046
gb|EU050600.1| Influenza A virus (A/guinea fowl/Shantou/3431/... 40.1 0.046
gb|EU050591.1| Influenza A virus (A/guinea fowl/Shantou/2418/... 40.1 0.046
gb|EU050550.1| Influenza A virus (A/quail/Shantou/1811/2001(H... 40.1 0.046
gb|CY023317.1| Influenza A virus (A/chicken/Shantou/2402/2004... 40.1 0.046
gb|EU026013.1| Influenza A virus (A/mallard/Maryland/887/2002... 40.1 0.046
gb|CY021596.1| Influenza A virus (A/mallard/Maryland/899/2002... 40.1 0.046
gb|CY020868.1| Influenza A virus (A/blue-winged teal/Ohio/907... 40.1 0.046
gb|CY020860.1| Influenza A virus (A/mallard/Ohio/664/2002(H6N... 40.1 0.046
gb|CY011119.1| Influenza A virus (A/mallard/Maryland/881/2002... 40.1 0.046
gb|CY020820.1| Influenza A virus (A/mallard/Maryland/470/2002... 40.1 0.046
gb|CY020804.1| Influenza A virus (A/mallard/Ohio/671/2002(H4N... 40.1 0.046
gb|CY020780.1| Influenza A virus (A/mallard/Ohio/655/2002(H4N... 40.1 0.046
gb|CY014525.2| Influenza A virus (A/mallard/Ohio/657/2002(H4N... 40.1 0.046
gb|CY020772.1| Influenza A virus (A/black duck/Maryland/834/2... 40.1 0.046
gb|CY020740.1| Influenza A virus (A/mallard/Maryland/750/2002... 40.1 0.046
gb|EF063554.1| Influenza A virus (A/quail/Dubai/303/2000(H9N2... 40.1 0.046
gb|EF063553.1| Influenza A virus (A/quail/Dubai/302/2000(H9N2... 40.1 0.046
gb|EF063552.1| Influenza A virus (A/quail/Dubai/301/2000(H9N2... 40.1 0.046
gb|CY017732.1| Influenza A virus (A/pintail/Ohio/25/1999(H1N1... 40.1 0.046
gb|CY017724.1| Influenza A virus (A/green-winged teal/Ohio/72... 40.1 0.046
gb|CY016962.1| Influenza A virus (A/mallard/Ohio/66/1999(H1N1... 40.1 0.046
gb|CY014805.1| Influenza A virus (A/turkey/Minnesota/1012/199... 40.1 0.046
gb|CY014701.1| Influenza A virus (A/gull/Maryland/704/1977(H1... 40.1 0.046
gb|CY012831.1| Influenza A virus (A/mallard/Ohio/56/1999(H1N1... 40.1 0.046
gb|AY619970.1| Influenza A virus (A/swine/Ontario/42729A/01(H... 40.1 0.046
gb|AY619962.1| Influenza A virus (A/swine/Ontario/K01477/01(H... 40.1 0.046
gb|AF508647.1| Influenza A virus (A/Pheasant/Ireland/PV18/97(... 40.1 0.046
gb|CY005071.1| Influenza A virus (A/laughing gull/DE/2838/198... 40.1 0.046
gb|CY004567.1| Influenza A virus (A/herring gull/DE/712/1988(... 40.1 0.046
gb|CY004457.1| Influenza A virus (A/herring gull/NJ/782/1986(... 40.1 0.046
gb|CY003901.1| Influenza A virus (A/herring gull/DE/475/1986(... 40.1 0.046
gb|CY005865.1| Influenza A virus (A/gull/Minnesota/945/1980(H... 40.1 0.046
gb|CY005858.1| Influenza A virus (A/shoveler/Netherlands/19/1... 40.1 0.046
gb|CY004880.1| Influenza A virus (A/herring gull/DE/665/1988(... 40.1 0.046
gb|CY004389.1| Influenza A virus (A/herring gull/New Jersey/7... 40.1 0.046
gb|M73525.1|FLAH13N6B Influenza A virus (A/gull/Maryland/704/... 40.1 0.046
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

The above travel logs show that the three earlier Shanghai sequences are from the same sub-clade. For PB1 the defining polymorphism is also in 71T, suggesting the E627K in PB2 has a Shanghai origin.

It is also worth noting that the defining PB1 polymorphism is also in human H3N2 (and PB1 traces back to human H3N2 PB1), while the defining polymorphism in PB2 is shared with avian isolates and PB2 originated in avian.

This association linked to newly acquired polymorphisms is NOT a coincidence, and these acquisitions are NOT due to random de novo mutations created by a "sloppy" polymerase, as described in dogma cited by WHO and its band of consultants.
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

Here is the other PB2 polymorphism found in the three Shanghai sequences, which also traces back to avian (in Asia)

gb|GQ290434.1| Influenza A virus (A/Shanghai/60T/2009(H1N1)) ... 40.1 0.046
gb|GQ253489.1| Influenza A virus (A/Shanghai/37T/2009(H1N1)) ... 40.1 0.046
gb|GQ225354.1| Influenza A virus (A/Shanghai/1/2009(H1N1)) se... 40.1 0.046
gb|DQ485213.2| Influenza A virus (A/chicken/China/Guangxi14/2... 40.1 0.046
gb|EU086333.1| Influenza A virus (A/swine/Guangxi/S15/2005(H9... 40.1 0.046
gb|EU086301.1| Influenza A virus (A/bird/Guangxi/A1/2006(H9N2... 40.1 0.046
gb|EU086262.1| Influenza A virus (A/duck/Guangxi/51/2005(H9N2... 40.1 0.046
gb|EU086244.1| Influenza A virus (A/chicken/Guangxi/6/2000(H9... 40.1 0.046
gb|EU081871.1| Influenza A virus (A/chicken/Guangxi/4/1999(H9... 40.1 0.046
gb|DQ366319.1| Influenza A virus (A/duck/Vietnam/8/05(H5N1)) ... 40.1 0.046
gb|DQ366311.1| Influenza A virus (A/goose/Vietnam/3/05(H5N1))... 40.1 0.046
gb|DQ366303.1| Influenza A virus (A/duck/Vietnam/1/2005(H5N1)... 40.1 0.046
gb|DQ485221.1| Influenza A virus (A/chicken/China/Guangxi17/2... 40.1 0.046
gb|AF258846.1| Influenza A virus (A/Hong Kong/97/98(H5N1)) RN... 40.1 0.046
gb|AF258845.1| Influenza A virus (A/Hong Kong/542/97(H5N1)) R... 40.1 0.046
gb|AF258844.1| Influenza A virus (A/Hong Kong/538/97(H5N1)) R... 40.1 0.046
gb|AF258843.1| Influenza A Virus (A/Hong Kong/532/97(H5N1)) R... 40.1 0.046
gb|AF258840.1| Influenza A virus (A/Hong Kong/486/97(H5N1)) R... 40.1 0.046
gb|AF258839.1| Influenza A Virus (A/Hong Kong/483/97(H5N1)) R... 40.1 0.046
gb|AF258838.1| Influenza A virus (A/Hong Kong/482/97(H5N1)) R... 40.1 0.046
gb|AF258837.1| Influenza A virus (A/Hong Kong/481/97(H5N1)) R... 40.1 0.046
gb|AF258836.1| Influenza A virus (A/Hong Kong/1074/99(H9N2)) ... 40.1 0.046
gb|AF258835.1| Influenza A virus (A/Hong Kong/1073/99(H9N2)) ... 40.1 0.046
gb|DQ064569.1| Influenza A virus (A/chicken/Shenzhen/9/97(H9N... 40.1 0.046
gb|DQ064557.1| Influenza A virus (A/chicken/Henan/26/00(H9N2)... 40.1 0.046
gb|DQ064555.1| Influenza A virus (A/chicken/Heilongjiang/35/0... 40.1 0.046
gb|DQ064553.1| Influenza A virus (A/chicken/Guangxi/9/99(H9N2... 40.1 0.046
gb|DQ064552.1| Influenza A virus (A/chicken/Guangxi/10/99(H9N... 40.1 0.046
gb|DQ064551.1| Influenza A virus (A/chicken/Guangdong/6/97(H9... 40.1 0.046
gb|AF508659.1| Influenza A virus (A/Chicken/Shenzhen/9/97(H9N... 40.1 0.046
gb|AF508656.1| Influenza A virus (A/Chicken/Sichuan/5/97(H9N2... 40.1 0.046
gb|AF508654.1| Influenza A virus (A/Chicken/Henan/62/00(H9N2)... 40.1 0.046
gb|AF508642.1| Influenza A virus (A/Chicken/Pakistan/5/99(H9N... 40.1 0.046
gb|AF508641.1| Influenza A virus (A/Chicken/Pakistan/4/99(H9N... 40.1 0.046
gb|AY043030.1| Influenza A virus (A/Guangzhou/333/99(H9N2)) p... 40.1 0.046
gb|AF250476.1|AF250476 Influenza A virus (A/Teal/Hong Kong/W3... 40.1 0.046
gb|AF115291.1|AF115291 Influenza A virus (A/Hong Kong/486/97(... 40.1 0.046
gb|AF115290.1|AF115290 Influenza A virus (A/Hong Kong/481/97(... 40.1 0.046
gb|AF084263.1|AF084263 Influenza A virus (A/HongKong/485/97(H... 40.1 0.046
gb|AF084262.1|AF084262 Influenza A virus (A/HongKong/483/97(H... 40.1 0.046
gb|AF084261.1|AF084261 Influenza A virus (A/HongKong/482/97(H... 40.1 0.046
gb|AF046093.1| Influenza A virus (A/Hong Kong/156/97(H5N1)) p... 40.1 0.046
gb|AF046086.1| Influenza A virus (A/Chicken/Hong Kong/220/97 ... 40.1 0.046
emb|AJ427305.1| Influenza A virus (A/pheasant/Hong Kong/FY294... 40.1 0.046
emb|AJ410501.1| Influenza A virus genomic RNA for polymerase ... 40.1 0.046
emb|AJ410499.1| Influenza A virus genomic RNA for polymerase ... 40.1 0.046
emb|AJ410498.1| Influenza A virus genomic RNA for polymerase ... 40.1 0.046
emb|AJ410497.1| Influenza A virus genomic RNA for polymerase ... 40.1 0.046
emb|AJ410496.1| Influenza A virus genomic RNA for polymerase ... 40.1 0.046
emb|AJ410495.1| Influenza A virus genomic RNA for polymerase ... 40.1 0.046
dbj|AB049154.1| Influenza A virus (A/parakeet/Narita/92A/98(H... 40.1 0.046
dbj|AB049153.1| Influenza A virus (A/parakeet/Chiba/1/97(H9N2... 40.1 0.046
emb|AJ291395.1| Influenza A virus (A/Chicken/Pakistan/2/99 (H... 40.1 0.046
emb|AJ404632.1| Influenza A virus pb2 gene for polymerase Pb2... 40.1 0.046
emb|AJ404631.1| Influenza A virus pb2 gene for polymerase Pb2... 40.1 0.046
emb|AJ404630.1| Influenza A virus pb2 gene for polymerase Pb2... 40.1 0.046
gb|AF098584.1|AF098584 Influenza A virus (A/Goose/Hong Kong/w... 40.1 0.046
gb|AF098583.1|AF098583 Influenza A virus (A/Duck/Hong Kong/y2... 40.1 0.046
gb|AF098582.1|AF098582 Influenza A virus (A/Duck/Hong Kong/p4... 40.1 0.046
gb|AF098581.1|AF098581 Influenza A virus (A/Chicken/Hong Kong... 40.1 0.046
gb|AF098580.1|AF098580 Influenza A virus (A/Chicken/Hong Kong... 40.1 0.046
gb|AF098579.1|AF098579 Influenza A virus (A/Chicken/Hong Kong... 40.1 0.046
gb|AF098578.1|AF098578 Influenza A virus (A/Chicken/Hong Kong... 40.1 0.046
gb|AF098577.1|AF098577 Influenza A virus (A/Chicken/Hong Kong... 40.1 0.046
gb|AF156435.1|AF156435 Influenza A virus (A/Quail/Hong Kong/G... 40.1 0.046
gb|AF036363.1|AF036363 Influenza A virus (A/HongKong/156/97(H... 40.1 0.046
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

look at the other markers. That mutation in PB1 is an exception
(or contamination ?)

------edit---------
ahh, better: look at the timing and travel histories of the cases.
That PB1-mutation emerged in Cancun mid April, then spread to Ohio,Georgia,...
Not the St.Francis introduction but another one (still Cancun presumably)
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

gsgs said:
look at the other markers. That mutation in PB1 is an exception
(or contamination ?)
Click to expand...
All recent isolates with that acquistion are from Shanghai (no lab error required - the isolate was cloned and sequenced again with IDENTICAL results).
Reality check - sequences that don't follow the random mutation dogma are NOT lab errors, no matter how many times lab error is cited or how vigorously hands are waved).
 
Re: A/Shanghai/60T/2009(H1N1) released 6/22

PB1 in the Shanghai isolates has a silent mutation: AAG387AAA

which is present in those isolates of the h1n1 outbreak (and those only):
A/Canada-ON/RV1526/2009(H1N1)
A/Georgia/01/2009(H1N1)
A/New York/3007/2009(H1N1)
A/Ohio/07/2009(H1N1)
A/Shanghai/1/2009(H1N1)
A/Shanghai/37T/2009(H1N1)
A/Shanghai/60T/2009(H1N1)
A/Shanghai/71T/2009(H1N1)
Click to expand...

On the other hand the shanghai isolates have two silent mutations in PB2 that 71T doesn't have : ACA147ACG and CGA427CGG.

Those two mutations are only found in the shanghai sequences :
A/Shanghai/1/2009(H1N1)
A/Shanghai/37T/2009(H1N1)
A/Shanghai/60T/2009(H1N1)
Click to expand...
 
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