Today at GenBank

gsgs · Jul 1, 2012

2012.06.22 : genbank release 190.0 ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt

daily updates : ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/
2012.06.26 - US-swine 2009-2012
2012.06.27 - more US-swine , Netherland and Sweden mallards most from 2002
2012.06.28 - American H5N2 1995-2004
2012.06.29 - 222 swine H1N1 , HA1 , UK 2010.12.01 , European 1978 ,
2012.06.30 - 348 more UK-swine, same strain,date
2012.07.01 - 46 more UK-swine, same strain,date
2012.07.05 - more UK.swine , US-swine

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

European swine (1978) is the strain which
gave segments 6,7 to ****** and has the HA to which we have no immunity
and which may reassort into ****** or H3N2v and cause the next pandemic. (IMO)
So far that H1 only caused occasional mild disease in humans or even asymptomatic.
It's unusual that UK publishes swine sequences and 222 at once was never seen, AFAIR

UK had a severe early wave of ****** in Dec.2010, so maybe this was just
to test whether the swine would have it too - but all 222 samples were
the European swine H1N1 that went from birds to swine in the late 70s
as an entirely avian virus and since then stayed in Eurasia until 2009
when 2 segments appeared in Mexico and reassorted with 6 American swine segments
to cause the 2009 pandemic

Jun.30 : 562 UK partial HA1 swine now, all very similar , closest match at genbank is
A/Sw/England/195852/1992(H1N1)
to which is has 49 differences in 937 nucleotides = 5.2%
an earlier good match is A/Sw/France/WVL4/1985(H1N1) with 53 differences = 5.6%
88 differences to A/Sw/Germany/2/1981, one of the earliest available genomes from that strain
It's not similar to other swine sequences from Europe, so this evolved undetected
since 20 years, remembering us to ****** for which our best match is also more
than 10 years ago. Surveillance in swine is not good.

before that there were only 295 swine H1 sequences from Europe in total

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

the strain is similar to English swine strains from the mid 90s
(characterized by mutations C54T,T84C,C99T,G123A,C336T,G489A,T825C)
Showing that they succeeded to keep English swineflu viruses on the island
and continental ones outside.

sweus4z1.GIF

gsgs · May 15, 2013

Re: today at genbank

Re: today at genbank

big update today, 6507 flu sequences
ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2013-05-15/influenza_na.dat

H7N9(34),H3N2(381),H5N1(132),
Cuba(99),US,Iran(,

so many Alaska ducks,( 2802)
NJ+DE turnstones,(2230)

Arg.swine,

H7N9: F1,Z0,ZC,H1,HE,H2,H3,S5

two H11N9 environment genoms from Jiangxi,2009 close to the bird-index (-->mallard-like)
N9 has 60 differences to H7N9, (not so close, closer to Vietnam-duck,Australia-sandpipers)

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

and another big update on May,16 , this time mainly human sequences, USA,2011-2013

ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2013-05-16/influenza_na.dat

4445 sequences,
------------------------
2101 times H3N2 , USA season 2011/12 : ~400 times segments 4,6,7
1502 times H1N1
39 times H9N2
8 times H7N9 (S2-genome)
8 times H7N7
---------------------
1823 from 2011
2109 from 2012
10 from 2013

=====================================

genbank has now 5605 full avian flu genomes, up from ~5000 2 days ago.
3904 of these are from North America.

genbank now has 5293=245+246+246+1801+248+1141+1115+251
human flu sequences from 2011 or later from North America,
13+13+13+549+13+531+525+13 of these were in Yesterday's update.

gsgs · May 19, 2013

Re: today at genbank

Re: today at genbank

A/Ck/Zhejiang/C11/2013(H9N9)

NA only
0 differences from the H7N9-index

also 2 duck-H7N3 from 2013,Zhejiang,
but they are not closer to H7N9 than the 2011 ducks, that we already have

also a Ck-H9N2 ,2013, 8 segments, from Guangdong,
but it is not so close to H7N9

we still have no matching H9N2

gsgs · May 20, 2013

Re: today at genbank

Re: today at genbank

and now H10N9 from Jiangsu,2013 (in chicken !) full genome
(5,6,6,-,3,-,2,2) differences from the bird index, so this
is mallard-like in all segments.
compare:
A/duck/Zhejiang/10/2011(H7N3) has (4,7,4,-,5,-,2,1) differences
A/mallard/Korea/1242/2011(H10N6) has (2,2,-,-,2,-,2,1) differences
A/wild bird/Korea/A12/2010(H10N1) has (3,2,-,-,0,-,1,1) differences
A/wild bird/Korea/A13/2010(H10N1) has (2,1,-,-,0,-,1,1) differences
A/mallard/Czech/13438-29k/2011(H11N9) has (1,2,4,-,1,-,0,2) differences

only 17 differences to the H7N9-index in NA, replacing the
best match so far (mallard,Czech,36 differences)

distant in the other segments

http://www.ncbi.nlm.nih.gov/nuccore/KF006416
Complete Genome Sequence of a Novel H10N9 Influenza Virus Isolated
from a Live Poultry Market in Eastern China

Code:

   0    0 2280    1 >A/chicken/Jiangsu/RD5/2013(H10N9)
------------segment 1----------
 109   25 2280 6195 >A/duck/Zhejiang/10/2011,2011/06/,H7N3
 114   26 2280 6194 >A/duck/Zhejiang/11/2011,2011/06/,H7N3
 118   27 2280 6193 >A/duck/Zhejiang/12/2011,2011/06/,H7N3
 144   33 2280 6591 >A/duck/Jiangsu/10-d4/2011,2011/10/,H11N3
------------segment 2-----------
 171   39 2274 5659 >A/duck/Zhejiang/0607-13/2011,2011/06/,H1N2
 180   41 2274 6330 >A/duck/Zhejiang/12/2011,2011/06/,H7N3
 184   42 2274 5657 >A/duck/Zhejiang/0611-17/2011,2011/06/,H1N3
 184   42 2274 5716 >A/duck/Zhejiang/0611-24/2011,2011/06/,H1N3
 184   42 2274 5717 >A/duck/Zhejiang/0611-21/2011,2011/06/,H1N3
 184   42 2274 5718 >A/duck/Zhejiang/0611-19/2011,2011/06/,H1N3
 184   42 2274 5719 >A/duck/Zhejiang/0611-15/2011,2011/06/,H1N3
 193   44 2274 6332 >A/duck/Zhejiang/10/2011,2011/06/,H7N3
 193   44 2274 6333 >A/duck/Zhejiang/2/2011,2011/06/,H7N3
 197   45 2274 5658 >A/duck/Zhejiang/0611-8/2011,2011/06/,H1N3
 197   45 2274 5720 >A/duck/Zhejiang/0611-3/2011,2011/06/,H1N3
 206   47 2274 6736 >A/duck/Jiangsu/10-d4/2011,2011/10/,H11N3
 215   49 2274 6601 >A/duck/Zhejiang/5/2011,2011/06/,H3N3
 228   52 2274 6331 >A/duck/Zhejiang/11/2011,2011/06/,H7N3
-----------segment 3---------------
  92   20 2151 6131 >A/duck/Zhejiang/10/2011,2011/06/,H7N3
  97   21 2151 6132 >A/duck/Zhejiang/2/2011,2011/06/,H7N3
 111   24 2151 6675 >A/duck/Jiangsu/10-d4/2011,2011/10/,H11N3
 116   25 2151 5461 >A/duck/Zhejiang/0611-17/2011,2011/06/,H1N3
 116   25 2151 5519 >A/duck/Zhejiang/0611-24/2011,2011/06/,H1N3
 116   25 2151 5520 >A/duck/Zhejiang/0611-21/2011,2011/06/,H1N3
 116   25 2151 5521 >A/duck/Zhejiang/0611-19/2011,2011/06/,H1N3
 116   25 2151 5522 >A/duck/Zhejiang/0611-15/2011,2011/06/,H1N3
 125   27 2151 5462 >A/duck/Zhejiang/0611-8/2011,2011/06/,H1N3
 125   27 2151 5523 >A/duck/Zhejiang/0611-3/2011,2011/06/,H1N3
----------segment 4-----------------------------
 326   55 1686  273 >A/mallard/Korea/1242/2010,2010/12/,H10N6
 326   55 1686  275 >A/wild bird/Korea/A12/2010,2010/02/,H10N1
 344   58 1686  274 >A/wild bird/Korea/A13/2010,2010/02/,H10N1
 375    3   80  284 >A/mallard/Germany/NVP/Wv1677-81/03,2003//,H10N4
 385   44 1140  271 >A/mallard/Korea/1041/2010,2010/11/,H10N8
 388   19  489   17 >A/duck/IT/701/2005,2005//,H10N7
 391   66 1686  272 >A/mallard/Korea/1203/2010,2010/12/,H10N8
 415   70 1686  276 >A/wild bird/Korea/A02/2011,2011/02/,H10N4
 415   70 1686  277 >A/wild bird/Korea/A01/2011,2011/02/,H10N4
 427   72 1686   86 >A/mallard/Bavaria/3/2006,2006//,H10N7
------------segment 5---------------------------------
  73   11 1497 5461 >A/duck/Zhejiang/0611-8/2011,2011/06/,H1N3
  73   11 1497 5523 >A/duck/Zhejiang/0611-3/2011,2011/06/,H1N3
  86   13 1497 6304 >A/duck/Zhejiang/5/2011,2011/06/,H3N3
  93   14 1497 6148 >A/duck/Zhejiang/2/2011,2011/06/,H7N3
 100   15 1497 5460 >A/duck/Zhejiang/0611-17/2011,2011/06/,H1N3
 100   15 1497 5519 >A/duck/Zhejiang/0611-24/2011,2011/06/,H1N3
 100   15 1497 5520 >A/duck/Zhejiang/0611-21/2011,2011/06/,H1N3
 100   15 1497 5521 >A/duck/Zhejiang/0611-19/2011,2011/06/,H1N3
 100   15 1497 5522 >A/duck/Zhejiang/0611-15/2011,2011/06/,H1N3
 126   19 1497 6440 >A/duck/Jiangsu/10-d4/2011,2011/10/,H11N3
 153   23 1497 6145 >A/duck/Zhejiang/12/2011,2011/06/,H7N3
 153   23 1497 6259 >A/duck/Guangdong/E1/2012,2012/01/10,H10N8
 153   23 1497 7271 >A/muscovy duck/Vietnam/LBM189/2012,2012//,H3N2
 180   27 1497 5462 >A/duck/Zhejiang/0607-13/2011,2011/06/,H1N2
 180   27 1497 6146 >A/duck/Zhejiang/11/2011,2011/06/,H7N3
 187   28 1497 6147 >A/duck/Zhejiang/10/2011,2011/06/,H7N3
 187   28 1497 6360 >A/duck/Guangdong/W12/2011,2011/12/22,H3N2
-----------------segment 6-----------------
 121   17 1398    2 >A/Index/H7N9-China/2013/01/31,H7N9,China,throat-swab,65m,E1
 121   17 1398    3 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)
 247   35 1413  105 >A/Baikal teal/Hongze/14/2005,2005/02/,H11N9
 247   35 1413  213 >A/mallard/Czech Republic/13438-29K/2010,2010/09/09,H11N9
 276   39 1413   59 >A/duck/Hokkaido/W245/2004,2004//,H11N9
 276   39 1413   81 >A/sharp-tailed sandpiper/Australia/10/2004,2004//,H11N9
 276   39 1413  107 >A/duck/Tsukuba/164/2005,2005//,H11N9
 283   40 1413   78 >A/sharp-tailed sandpiper/Australia/6/2004,2004//,H11N9
 283   40 1413  108 >A/duck/Tsukuba/239/2005,2005//,H11N9
 297   42 1413  106 >A/duck/Tsukuba/441/2005,2005//,H11N9
-----------------segment 7---------------------
  40    4  982 6459 >A/duck/Zhejiang/0611-17/2011,2011/06/,H1N3
  40    4  982 6460 >A/duck/Zhejiang/0611-8/2011,2011/06/,H1N3
  40    4  982 6502 >A/duck/Zhejiang/0611-24/2011,2011/06/,H1N3
  40    4  982 6503 >A/duck/Zhejiang/0611-21/2011,2011/06/,H1N3
  40    4  982 6504 >A/duck/Zhejiang/0611-19/2011,2011/06/,H1N3
  40    4  982 6505 >A/duck/Zhejiang/0611-15/2011,2011/06/,H1N3
  40    4  982 6506 >A/duck/Zhejiang/0611-3/2011,2011/06/,H1N3
  40    4  982 7137 >A/duck/Zhejiang/12/2011,2011/06/,H7N3
  40    4  982 7138 >A/duck/Zhejiang/11/2011,2011/06/,H7N3
  40    4  982 7139 >A/duck/Zhejiang/10/2011,2011/06/,H7N3
  40    4  982 7140 >A/duck/Zhejiang/2/2011,2011/06/,H7N3
  50    5  982 7309 >A/duck/Zhejiang/5/2011,2011/06/,H3N3
  61    6  982 7486 >A/duck/Jiangsu/10-d4/2011,2011/10/,H11N3
 132   13  982 7247 >A/duck/Guangdong/E1/2012,2012/01/10,H10N8
 132   13  982 8377 >A/muscovy duck/Vietnam/LBM189/2012,2012//,H3N2
 162   16  982 6461 >A/duck/Zhejiang/0607-13/2011,2011/06/,H1N2
------------segment 8--------------------------
  83    7  838 5766 >A/duck/Zhejiang/12/2011,2011/06/,H7N3
  83    7  838 5767 >A/duck/Zhejiang/11/2011,2011/06/,H7N3
  83    7  838 5768 >A/duck/Zhejiang/10/2011,2011/06/,H7N3
  83    7  838 5769 >A/duck/Zhejiang/2/2011,2011/06/,H7N3
  83    7  838 6009 >A/duck/Jiangsu/10-d4/2011,2011/10/,H11N3
  95    8  838 5171 >A/duck/Zhejiang/0611-17/2011,2011/06/,H1N3
  95    8  838 5172 >A/duck/Zhejiang/0611-8/2011,2011/06/,H1N3
  95    8  838 5173 >A/duck/Zhejiang/0607-13/2011,2011/06/,H1N2
  95    8  838 5229 >A/duck/Zhejiang/0611-24/2011,2011/06/,H1N3
  95    8  838 5230 >A/duck/Zhejiang/0611-21/2011,2011/06/,H1N3
  95    8  838 5231 >A/duck/Zhejiang/0611-19/2011,2011/06/,H1N3
  95    8  838 5232 >A/duck/Zhejiang/0611-15/2011,2011/06/,H1N3
  95    8  838 5233 >A/duck/Zhejiang/0611-3/2011,2011/06/,H1N3
 178   15  838 5876 >A/duck/Zhejiang/5/2011,2011/06/,H3N3

gsgs · May 23, 2013

Re: today at genbank

Re: today at genbank

5,4,8,3,0,2,22,0,A/Taiwan/S02076/2013(H7N9)
3,4,4,3,4,2,21p,0p,A/Taiwan/T02081/2013(H7N9)

2,0,4,0,4,0,0,0, to each other

3,4,4,3,0,2,22,0, Taiwan_index

KF018042
KF018050

http://www.ncbi.nlm.nih.gov/nuccore/KF018042
http://www.ncbi.nlm.nih.gov/nuccore/KF018050

http://www.ncbi.nlm.nih.gov/nuccore/KC896770
http://www.ncbi.nlm.nih.gov/nuccore/KC896778

2,10,3,3,4,1,20,2,A/environment(poultry cage)/Nanjing/2913/2013/03/29(H7N9)
5,16,1,3,15,6,20,1,A/Nanjing/1/throat_swab/2013/03/28(H7N9)

gsgs · Jun 22, 2013

Re: today at genbank

Re: today at genbank

lots of H3N2 from USA (NY,CA) from Apr,May 2009
presumably found when they did lots of sampling to detect pH1N1

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

2013/06/24 : 267273 flu-sequences at genbank, 272342 including lab-strains
60 on 2013/06/24,672 on 2013/06/23(all flu-B), 266 on 2013/06/22, 0 on 2013/06/21,0 on 2013/06/20

while ftp/updates gives 3 on 2013/06/24,2065 on 2013/06/23, 1528 on 2013/06/22,
8 on 2013/06/21, 48 on 2013/06/20, 16 on 2013/06/19, 16 on 2013/06/18, 0 on 2013/06/17,
385 on 2013/06/16

-------------------------------------------
272630 on Jul.3.2013

gsgs · Jul 3, 2013

Re: today at genbank

Re: today at genbank

23 genomes from Hunan ducks, 2011-2012, different serotypes

ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2013-07-03/influenza_na.dat
http://www.ncbi.nlm.nih.gov/nuccore/CY146610

Deng,G., Tan,D., Shi,J., Cui,P., Jiang,Y., Liu,L., Tian,G., Kawaoka,Y., Li,C. and Chen,H.
Complex reassortment of multiple subtypes in domestic ducks at the Dongting Lake region
http://jvi.asm.org/content/early/2013/06/20/JVI.00776-13.abstract

Harbin lab ; farmed,domestic ducks

http://www.eurekalert.org/pub_releases/2013-04/scp-sio042213.php
The NA gene of the novel H7N9 virus isolates shared highest homology (97.3&#56033;&#57293;.9%)
with NA genes from H4N9 or H11N9 influenza viruses isolated from ducks,
and environmental samples from duck farms, located in the Dongting Lake region.

so, what kind is this domestic duck farm business in China ?
Does it exist in other countries ?

domestic ducks could be the "mixing vessel" between mallards and chickens

waterborne in mallards (dabbling)
respiratory or foodborne in domestic ducks ?

=======================================================

amino acid differences from the bird-index:

Code:

  1 >A/Index/birds/2000(H3N8a)  

 1:  0,  0,  0,  0,  0,  0,  0,  0
 2:  0,  0,  0,  0,  0,  0,  0, 89
 3:  1,  4,  8,481,  2,395,  0,  2
 4:  1,  1,  5,481,  2,395,  1,  2
 5:  3,  6,  1,475,  3,387,  4,  2
 6:  6,  4,  2,481,  2,399,  1,  3
 7:  6,  3,  5,481,  3,398,  2,  8
 8:  7,  3,  3,481,  2,398,  1,  8
11:  4,  4,  7,481,  4,398,  3,  5
13:  3,  6,  3,489,  2,396,  3,  4
24:  3,  6,  3,478,  3,397,  5,  1
 9:  6,  6,  4,479, 10,395,  3,  3
14:  1,  3,  4,480, 29,398,  0,  1
20:  1,  4,  5,480, 29,398,  0,  1
25:  1,  3,  5,480, 27,397,  1,  2
18:  2,  5,  8,488, 28,395,  9, 28
19:  3,  6,  7,487, 28,395,  9, 26
16:  4,  5,  7,488, 29,395, 10, 26
12:  8,  9, 11,484,  9,393,  9, 24
17:  6, 12, 19,483, 10,392, 25, 31
15: 14, 10, 18,491,  7,373, 15, 24
21: 13, 10,  8,491,  5,374, 13, 24
22: 13, 11, 15,490,  7,372, 13, 25
23: 14,  9, 13,491,  6,372, 23, 31

10:  3,  2,  3,489,  1,392,  2, 90

most are close to the index, mallard-like
some poultry segments have come in, (or evolved ?) i.e. segments 5,8

N9 has 23 nucleotide differences to H7N9 and not the deletion. --> common ancester ~3 years ago

4 are H5N1, one of them with a new segment 7
10 more share segments 1 and 8 with H5N1
3 more share segment 8 only

gsgs · Jul 14, 2013

Re: today at genbank

Re: today at genbank

Vetnam avian genomes 2011-2013

ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2013-07-14/influenza_na.dat

gsgs · Jul 20, 2013

Re: today at genbank

Re: today at genbank

2013.07.20
Mexico genomes from 2008/9 , no new early pH1N1=****** , afaics

many new non-human H7N9 genomes

lots with a new segment 2 and 5

gsgs · Aug 20, 2013

Re: today at genbank

Re: today at genbank

13 H1N1 genomes from India , 2011-2013 update:3 of them available in genbank-format on Aug.30

3 H7N9 genomes Jiangsu1(2),Jiangsu2

-----------------------------
2013/08/30
278254 nucleotide sequences
1281 WRAIR
886 China released Aug.2013
24 India released 2013

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

number of genbank sequences released 2013/08/21... until 2013/08/31:
2634,401,401,209,209,209,209,193,13,9
--> 2233 on 2013/08/21
the update on 2013/08/23 had 2262 new sequences (most from the new H7N7-paper)

gsgs · Sep 19, 2013

Re: today at genbank

Re: today at genbank

~129 H3N2 genomes from Boston , most from Dec.2012-Jan.2013

most are similar to the Texas viruses, no dramatic new reassortments

so why was it so bad in 2012/13 when almost the same thing was so mild in 2011/12 ?

yesterday ~20-50 H1N1 viruses from USA, segments 4,6,7 , quite some from summer 2013

most recent H1:

Code:

>KF500960,A/India/LKOS-415/2013,2013/05/12,India,H1N1,Human,4,7,61-905,7,
  A538C,A579G,G605C,T658A,G817A,A819T,G891A
>KF648223,A/Hawaii/01/2013,2013/05/28,USA,H1N1,Human,4,26,1-1701,26,
  G43A,C195T,C273T,G340A,T465C,A538C,A579G,T588C,G605C,T658A,G675A,G817A,C839T,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,G1546A,T1653C,G1683A
>KF648217,A/Kentucky/06/2013,2013/06/07,USA,H1N1,Human,4,25,1-1701,25,
  T30C,G159A,C273T,G340A,G375A,C537A,A538G,A579G,G605C,T658A,C672T,G751A,A898G,A966G,T1013C,T1041C,T1056C,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,G1496A,G1546A
>KF648022,A/Florida/18/2013,2013/06/15,USA,H1N1,Human,4,23,1-1701,23,
  T17C,C273T,G340A,T465C,A538C,A579G,G605C,T658A,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,G1496A,A1538G,G1546A,T1653C
>KF647939,A/Florida/16/2013,2013/06/19,USA,H1N1,Human,4,21,1-1701,21,
  G159T,C273T,G340A,T465C,A538C,A579G,G605C,T658A,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,G1546A,T1653C
>KF647949,A/Florida/16/2013,2013/06/19,USA,H1N1,Human,4,22,1-1701,22,
  G159T,C273T,G340A,T465C,A538C,A579G,G605C,T658A,A716G,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,G1546A,T1653C
>KF647993,A/Wisconsin/11/2013,2013/06/23,USA,H1N1,Human,4,25,1-1701,25,
  T30C,C273T,G340A,A579G,G605C,T658A,G751A,C867T,A898G,A907C,A966G,T1041C,T1056C,T1101G,G1125A,G1158A,G1171A,A1230G,C1249T,A1386G,G1403A,C1408T,G1546A,T1590C,G1630A
>KF500967,A/India/LKO3828/2013,2013/06/24,India,H1N1,Human,4,7,60-906,7,
  A579G,G605C,G607A,T658A,G751A,G891A,T906A
>KF647985,A/Kentucky/05/2013,2013/06/27,USA,H1N1,Human,4,23,1-1701,23,
  C273T,G340A,T465C,C534T,A538C,A579G,G605C,T658A,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,C1249T,A1386G,G1403A,C1408T,A1468G,G1546A,T1653C
>KF647947,A/Massachusetts/10/2013,2013/06/30,USA,H1N1,Human,4,21,1-1701,21,
  T30C,C273T,G340A,A540C,A579G,G605C,T658A,G751A,A898G,A966G,T985C,T1041C,T1056C,G1158A,G1171A,A1230G,G1266A,A1386G,G1403A,C1408T,G1546A
>KF647957,A/Florida/19/2013,2013/07/02,USA,H1N1,Human,4,21,1-1701,21,
  C273T,G340A,T465C,A538C,A579G,G605C,T658A,G817A,A898G,C945T,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,G1546A,T1653C
>KF648044,A/Indiana/12/2013,2013/07/03,USA,H1N1,Human,4,23,1-1701,23,
  G193T,C273T,G340A,T465C,A538C,A579G,T594C,G605C,T658A,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,C1362T,A1386G,G1403A,C1408T,G1546A,T1653C
>KF648018,A/Connecticut/02/2013,2013/07/06,USA,H1N1,Human,4,23,1-1701,23,
  G268T,C273T,G340A,T465C,A510G,A538C,A579G,G605C,T658A,C748T,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,G1546A,T1653C
>KF648021,A/Connecticut/02/2013,2013/07/06,USA,H1N1,Human,4,25,1-1701,25,
  C44Y,G268T,C273T,G340A,T465C,A510G,A538C,A579G,G605C,C622M,T658A,C748T,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,G1546A,T1653C
>KF648020,A/Florida/20/2013,2013/07/07,USA,H1N1,Human,4,28,1-1701,28,
  T30C,G159A,C273T,G340A,G450A,C467A,A539T,A579G,A597G,G605C,T658A,A750G,G751A,G759A,A898G,A966G,T1041C,T1056C,C1098T,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,G1465R,G1546A,T1686C
>KF648015,A/South Carolina/01/2013,2013/07/10,USA,H1N1,Human,4,24,1-1701,24,
  A155G,C273T,G340A,T465C,G505A,A510G,A538C,A579G,G605C,T658A,C748T,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,G1546A,T1653C
>KF495196,A/swine/Illinois/A01397807/2013,2013/07/10,USA,H1N1,Swine,4,25,1-1701,25,
  T30C,G190A,C273T,G340A,A363G,T462C,A516G,A579G,G605C,T658A,G751A,A898G,A966G,T1041C,T1056C,G1080A,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,C1488T,A1512G,G1546A
>KF648052,A/Indiana/20/2013,2013/07/15,USA,H1N1,Human,4,23,1-1701,23,
  G193T,C273T,G340A,T465C,A538C,A579G,T594C,G605C,T658A,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,C1362T,A1386G,G1403A,C1408T,G1546A,T1653C
>KF648129,A/Texas/13/2013,2013/07/21,USA,H1N1,Human,4,25,1-1701,25,
  C102T,C273T,G340A,T465C,A538C,A579G,T588C,G605C,T658A,G675A,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,G1330A,A1386G,G1403A,C1408T,G1546A,T1653C,G1683A
>KF648085,A/Nevada/06/2013,2013/07/23,USA,H1N1,Human,4,24,1-1701,24,
  C261T,C273T,G340A,T465C,A538C,A579G,G605C,T658A,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,G1173A,T1191C,A1230G,A1386G,G1403A,C1408T,C1539T,G1546A,T1653C
>KF648120,A/Nevada/06/2013,2013/07/23,USA,H1N1,Human,4,26,1-1701,26,
  C261T,C273T,G340A,T465C,A538C,A579G,T598Y,G605C,C622M,T658A,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,G1173A,T1191C,A1230G,A1386G,G1403A,C1408T,C1539T,G1546A,T1653C
>KF537364,A/swine/Illinois/A01398316/2013,2013/07/23,USA,H1N1,Swine,4,24,1-1701,24,
  T30C,G190A,C273T,G340A,A363G,T462C,A516G,A579G,G605C,T658A,G751A,A898G,A966G,T1041C,T1056C,G1080A,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,A1512G,G1546A
>KF648080,A/North Carolina/08/2013,2013/07/24,USA,H1N1,Human,4,25,1-1701,25,
  C261T,C273T,G340A,T465C,A538C,A579G,G605C,T658A,G715A,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,T1191C,A1215R,A1230G,A1386G,G1403A,C1408T,C1539T,G1546A,T1653C
>KF648032,A/Delaware/09/2013,2013/08/02,USA,H1N1,Human,4,27,1-1701,27,
  T30C,A179G,C273T,G340A,A399G,A579G,G605C,T658A,G665A,G751A,C870T,A898G,A907G,A966G,T1041C,T1056C,G1158A,G1171A,T1179C,A1230G,A1255R,C1352Y,A1386G,G1403A,C1408T,C1455T,G1546A
>KF648118,A/Wisconsin/12/2013,2013/08/04,USA,H1N1,Human,4,23,1-1701,23,
  A192G,C273T,G340A,T465C,A538C,A579G,G605C,T658A,G817A,G871A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,G1524A,G1546A,T1653C
>KF648128,A/Wisconsin/12/2013,2013/08/04,USA,H1N1,Human,4,22,1-1701,22,
  A192G,C273T,G340A,T465C,A538C,A579G,G605C,T658A,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,G1524A,G1546A,T1653C
>KF648169,A/California/24/2013,2013/08/08,USA,H1N1,Human,4,21,1-1701,21,
  G37A,C273T,G340A,T465C,A538C,A579G,G605C,T658A,G817A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,G1546A,T1653C
>KF648170,A/Indiana/22/2013,2013/08/13,USA,H1N1,Human,4,22,1-1701,22,
  T30C,C273T,G340A,A540C,A564G,A579G,G605C,G607A,T658A,G751A,A898G,A966G,T1041C,T1056C,G1158A,G1171A,A1230G,A1386G,G1403A,C1408T,A1542G,G1546A
>KF648172,A/Texas/15/2013,2013/08/15,USA,H1N1,Human,4,28,1-1701,28,
  G19A,G43A,C273T,G302A,G340A,T465C,A538C,A579G,G605C,T658A,C777T,G817A,C867T,A898G,A966G,T1041C,T1056C,T1132C,G1158A,G1171A,A1230G,G1338A,A1386G,G1403A,C1408T,G1497A,G1546A,T1653C

almost all have the (nucleotide-) mutations at (coding-region-numbering)
340,579,605,658,1056,1171,1386,1403,1408
which made (one of) the England-strains from Nov/Dec 2010

also almost all have additional mutations at
273,898,966,1041,1158,1230,1546
5 of these (273,898,966,1041,1546) were first seen in India, Sept.2011
the other 2 of these in Washington, July 2012

about half of them have additional mutations at
465,538,817,1653
465 was also in WA,July 2012 - the other 3 in PA,Dec.2012

again a new successful,dominant,surviving strain that probably(IMO) formed in India
>KF280663,A/India/P1114854/2011,2011/09/23,India,H1N1,Human,4,16,1-1701
C273T,G340A,A357G,A579G,G605C,T658A,A898G,A966G,
A1026G,T1041C,T1056C,G1171A,A1386G,G1403A,C1408T,G1546A

(positions divisible by 3 are usually synonymous)

gsgs · Sep 26, 2013

Re: today at genbank

Re: today at genbank

119 H1N1 genomes from Finland , Jan.2013 , uploaded on 2013/09/25
36 bird genomes from Iceland , ~2011 , uploaded on 2013/09/26
A/black headed gull/Iceland/1298/2011(H10N5) has an Eurasian segment 1
but American segments 2,3,5,7,8
A/glaucous gull/Iceland/1444/2011(H2N5) has American segments 1,2,3,5,7,8

gsgs · Oct 23, 2013

Re: today at genbank

Re: today at genbank

2013/10/23
full chicken genome from 1925
HA was available before, but now all 8 segments

A/Ck/Japan/1925/H7N7

(4,10,12,-,8,-,6,12)

Code:

   0    0 2280    1 >A/chicken/Japan/1925(H7N7)
----------segment 1------------- 
 701  160 2280 1175 >A/chicken/Brescia/1902,1902//,H7N7
 706  161 2280 4409 >A/chicken/Brescia/1902,1902//,H7N7
 719  164 2280   13 >A/fowl/Weybridge,1934//,H7N7
 723  165 2280 1170 >A/fowl/Dobson/1927,1927//,H7N7
 789  180 2280 1174 >A/chicken/Rostock/45/1934,1934//,H7N1
 903  206 2280 4059 >A/duck/Czech Republic/1/1956,1956/06/11,H4N6
 916  209 2280   10 >A/ruddy turnstone/New Jersey/47/1985,1985//,H4N6
 929  212 2280 1133 >A/duck/England/1/1956,1956//,H11N6
 956  218 2280 1132 >A/chicken/Germany/N/1949,1949//,H10N7
 964  220 2280 4642 >A/chicken/Scotland/1959,1959//,H5N1
 969  221 2280  696 >A/quail/Italy/1117/1965,1965//,H10N8
 978  223 2280 6102 >A/shearwater/Australia/2/1972,1972/06/11,H10N8
1000  228 2280  300 >A/duck/Zhejiang/11/2000,2000//,H5N1
1000  228 2280 8435 >A/turkey/England/1963,1963//,H7N3
1004  229 2280  824 >A/duck/Hong Kong/7/1975,1975//,H3N2
1008  230 2280 2889 >A/turkey/England/N28/73,1973//,H5N2
1009  228 2258 1803 >A/duck/Hong Kong/23/1976,1976//,H5N3
1009  228 2258 3021 >A/turkey/England/N28/1973,1973//,H5N2
1022  233 2278 6635 >A/whooper swan/Mongolia/1-14/2007,2007/09/,H3N8
1026  234 2280  934 >A/duck/Taiwan/0526/72,1972//,H6N1
----------segment 2------------- 
 628  143 2274 1142 >A/chicken/Rostock/45/1934,1934//,H7N1
 751  171 2274 1136 >A/fowl/Dobson/1927,1927//,H7N7
 751  171 2274 4429 >A/chicken/Brescia/1902,1902//,H7N7
 751  171 2274 8372 >A/FPV/Dutch/1927,1927//,H7N7
 760  173 2274 1095 >A/duck/England/1/1956,1956//,H11N6
 791  180 2274 4716 >A/duck/Czechoslovakia/1956,1956//,H4N6
 844  192 2274  679 >A/quail/Italy/1117/1965,1965//,H10N8
 844  192 2274 1094 >A/chicken/Germany/N/1949,1949//,H10N7
 844  192 2274 6144 >A/shearwater/Australia/2/1972,1972/06/11,H10N8
 861  196 2274 4777 >A/turkey/Canada/1963,1963//,H6N8
 866  197 2274 1144 >A/turkey/England/1963,1963//,H7N3
 866  197 2274 1146 >A/chicken/Scotland/1959,1959//,H5N1
 879  200 2274 1093 >A/turkey/Wisconsin/1/1966,1966//,H9N2
 905  206 2274  812 >A/duck/Ukraine/1/1963,1963/12/12,H3N8
 905  206 2274 4674 >A/Canada goose/Wisconsin/902/1975,1975//,H5N2
----------segment 3------------- 
 604  130 2151 1102 >A/chicken/Rostock/45/1934,1934//,H7N1
 632  136 2151 1103 >A/chicken/Brescia/1902,1902//,H7N7
 650  140 2151 1096 >A/fowl/Dobson/1927,1927//,H7N7
 697  150 2151 1062 >A/chicken/Germany/N/1949,1949//,H10N7
 729  157 2151 1063 >A/duck/England/1/1956,1956//,H11N6
 739  159 2151  779 >A/duck/Czechoslovakia/1956,1956//,H4N6
 748  161 2151 1107 >A/chicken/Scotland/1959,1959//,H5N1
 771  166 2151 1105 >A/turkey/England/1963,1963//,H7N3
 776  167 2151  761 >A/duck/Hong Kong/365/1978,1978//,H4N6
 776  167 2151 5835 >A/duck/Hokkaido/5/1977,1977//,H3N2
 781  168 2151  575 >A/blue-winged teal/ALB/221/1978,1978/08/07,H7N2
 785  169 2151 1095 >A/tern/South Africa/1961,1961//,H5N3
 785  169 2151 2757 >A/mallard/WI/42/1975,1975//,H5N2
 790  170 2151  538 >A/mallard/ALB/60/1976,1976/08/12,H12N5
 790  170 2151  673 >A/pintail/ALB/303/1977,1977/09/03,H10N7
 790  170 2151  686 >A/pintail/ALB/86/1976,1976/08/13,H3N2
 790  170 2151  738 >A/mallard/ALB/302/1977,1977/08/31,H10N7
 790  170 2151 7237 >A/black duck/New Jersey/1580/1978,1978/02/04,H2N3
 790  170 2151 7945 >A/duck/Alberta/60/1976,1976/08/12,H12N5
 790  170 2151 8301 >A/duck/Alberta/60/1976,1976//,H12N5
 794  171 2151  635 >A/shearwater/Australia/1/1973,1973//,H6N5
 794  171 2151  670 >A/mallard/ALB/57/1976,1976/08/12,H5N2
 794  171 2151  763 >A/duck/Hong Kong/293/1978,1978//,H7N2
 794  171 2151 5528 >A/shearwater/Australia/1/1972,1972//,H6N5
 794  171 2151 7186 >A/mallard/New York/6750/1978,1978//,H2N2
----------segment 4------------- 
 792  131 1653  664 >A/chicken/Brescia/1902,1902//,H7N7,Italy
 798  132 1653 1951 >A/fowl/Dobson/1927,1927//,H7N7,USA
 973  161 1653 1099 >A/chicken/Rostock/45/1934,1934//,H7N1,Germany
1445  239 1653 1205 >A/chicken/Victoria/1976,1976/01/,H7N7,Australia
1524  252 1653 4776 >A/starling/Victoria/1985,1985//,H7N7,Australia
1663  275 1653 1068 >A/chicken/Pakistan/34669/1995,1995//,H7N3,Pakistan
----------segment 5------------- 
 574   86 1497    9 >A/chicken/Rostock/8/1934,1934//,H7N1
 614   92 1497 1303 >A/chicken/Germany/N/1949,1949//,H10N7
 641   96 1497 1343 >A/tern/South Africa/1961,1961//,H5N3
 647   97 1497 1344 >A/fowl/Dobson/1927,1927//,H7N7
 647   97 1497 1351 >A/chicken/Brescia/1902,1902//,H7N7
 647   97 1497 4503 >A/tern/South Africa/1959,1959//,H5N3
 647   97 1497 8086 >A/FPV/Dutch/1927,1927//,H7N7
 654   98 1497   17 >A/fowl/Dobson/'Dutch'/1927,1927//,H7N7
 654   98 1497   39 >A/tern/South Africa/1961,1961//,H5N3
 654   98 1497 1355 >A/chicken/Scotland/1959,1959//,H5N1
 654   98 1497 8087 >A/turkey/England/1963,1963//,H7N3
 660   92 1393 4504 >A/tern/South Africa/1961,1961//,H5N3
 661   99 1497 1353 >A/turkey/England/1963,1963//,H7N3
 668  100 1497   18 >A/duck/England/1/1956,1956//,H11N6
 674  101 1497 1299 >A/duck/Czechoslovakia/1956,1956//,H4N6
 674  101 1497 2006 >A/duck/Hong Kong/698/1979,1979//,H5N3
 682   84 1230 4468 >A/chicken/Scotland/1959,1959//,H5N1
 684   96 1402 4529 >A/turkey/England/35013/1963,1963//,H7N3
 688  103 1497 1375 >A/duck/Hokkaido/8/1980,1980//,H3N8
 694  104 1497 1307 >A/duck/Chabarovsk/1610/1972 ,1972//,H3N8
 694  104 1497 5885 >A/duck/Hokkaido/5/1977,1977//,H3N2
 694  104 1497 7310 >A/mallard/Stralsund/45-6/1981,1981//,H2N3
 701  105 1497   35 >A/duck/Ukraine/2/1960,1960//,H11N8
 708  106 1497  992 >A/duck/Hong Kong/365/1978,1978//,H4N6
 714  107 1497 4431 >A/quail/Italy/39403/1965,1965//,H10N8
 714  107 1497 5946 >A/shearwater/Australia/2/1972,1972/06/11,H10N8
----------segment 6------------- 
   0    0 1311    1 >A/chicken/Japan/1925(H7N7)
  22    3 1311 2149 >A/duck/Taiwan/Ya103/1993,1993//,H7N7
  45    6 1311 2148 >A/duck/Taiwan/33/1993,1993//,H7N7
1586  208 1311 5543 >A/chicken/Brescia/1902,1902//,H7N7
1594  209 1311 10205 >A/FPV/Dutch/1927,1927//,H7N7
1595  209 1310 1592 >A/fowl/Dobson/1927,1927//,H7N7
1601  140  874 8017 >A/shoveler/Italy/2698-27/2006,2006/01/18,H7N7
1685  221 1311 2082 >A/chicken/Germany/N/1949,1949//,H10N7
2006  263 1311 5800 >A/northern pintail/Akita/1367/2008,2008//,H7N7
----------segment 7------------- 
 407   40  982 1630 >A/chicken/Brescia/1902,1902//,H7N7
 417   41  982 1583 >A/chicken/Germany/N/1949,1949//,H10N7
 437   43  982 1272 >A/duck/Ukraine/1/1963,1963/12/12,H3N8
 437   43  982 8970 >A/FPV/Dutch/1927,1927//,H7N7
 448   44  981 4217 >A/duck/Hong Kong/15/1976,1976//,H10N5
 448   44  981 4226 >A/duck/Munich/523/1981,1981//,H4N2
 448   44  982   15 >A/fowl/Dobson/1927,1927//,H7N7
 468   46  981 4207 >A/duck/Ukraine/1/1960,1960//,H11N9
 478   47  982 1587 >A/duck/Chabarovsk/1610/1972 ,1972//,H3N8
 478   47  982 1632 >A/turkey/England/1963,1963//,H7N3
 478   47  982 4067 >A/mallard/Netherlands/3/2005,2005//,H3N8
 478   47  982 6734 >A/mallard/PT/27972-B139/2007,2007/09/06,H9N2
----------segment 8------------- 
   0    0  838    1 >A/chicken/Japan/1925(H7N7)
  36    3  830    9 >A/chicken/Japan/1924,1924//,H7N7
 477   40  838    4 >A/Brevig Mission/1/1918,1918//,H1N1
 489   41  838    8 >A/chicken/Rostock/8/1934,1934//,H7N1
 501   42  838 1275 >A/chicken/Brescia/1902,1902//,H7N7
 513   43  838 1271 >A/fowl/Dobson/1927,1927//,H7N7
 513   43  838 6890 >A/FPV/Dutch/1927,1927//,H7N7
 525   44  838 1281 >A/turkey/Ontario/7732/1966,1966//,H5N9
 536   45  838 1237 >A/turkey/Ontario/6118/1968,1968//,H8N4
 536   45  838 5145 >A/turkey/Ontario/6213/1966,1966/06/11,mixed
 548   38  693  693 >A/quail/Italy/4610/03,2003//,H7N3
 548   38  693 2368 >A/shorebird/Korea/S285/2006,2006//,H10N4
 548   38  693 5698 >A/mallard/Sanjiang/390/2007,2007/10/,H1N1
 548   46  838  554 >A/duck/PA/69,1969//,H6
 548   46  838  848 >A/mallard/ALB/676/1979,1979/08/13,H3N6
 548   46  838  933 >A/duck/Czechoslovakia/1956,1956//,H4N6
 548   46  838 2782 >A/duck/PA/486/1969,1969//,H6N1
 560   47  838   55 >A/chicken/Scotland/1959,1959//,H5N1
 562   39  693  646 >A/tree sparrow/Henan/1/2004,2004//,H5N1
 562   39  693  649 >A/tree sparrow/Henan/4/2004,2004//,H5N1
 570   47  824 4696 >A/wild duck/Korea/YS44/2004,2004/11/,H1N2

Code:

nucleotide differences in promille, 8 segments

  1 >A/chicken/Japan/1925(H7N7)                                                      2280 2274 2151 1653 1497 1311  982  838   

  9: 78, 62, 60, 97, 58,474, 51, 48   CY077417,A/chicken/Rostock/45/1934,1934//,Germany,H7N1,Avian,1                  2280 2277 2151 1697 1497 1347  982  838
  6: 70, 75, 63, 79, 64, 99, 41, 51   GU186784,A/chicken/Brescia/1902,1902//,Italy,H7N7,Avian,1                       2280 2277 2151 1697 1497 1416  982  838
  5: 72, 75, 65, 79, 64,101, 43, 51   CY130149,A/FPV/Dutch/1927,1927//,United Kingdom,H7N7,Avian,1                    2280 2277 2151 1697 1497 1416  982  838
  7: 95, 84, 69,355, 61,111, 41,300   CY014678,A/chicken/Germany/N/1949,1949//,Germany,H10N7,Avian,1                  2280 2277 2151 1686 1497 1416  982  838
 10: 96, 86, 74,468, 65,472, 51, 57   CY015088,A/chicken/Scotland/1959,1959//,United Kingdom,H5N1,Avian,1             2280 2277 2151 1703 1497 1413  982  838

  2:117,106,100,158, 93,161, 62, 65   A/Netherlands/219/03(H7N7)                                                      2280 2274 2151 1689 1497 1416  982  838
  4:135,155, 77,354, 78,231, 72, 56   KF435062,A/duck/Manitoba/1953,1953//,Canada,H10N7,Avian,1                       2280 2277 2151 1686 1497 1413  982  838
 12:106, 95, 91,425, 69,494, 47,294   CY130133,A/duck/Chabarovsk/1610/1972 ,1972//,Russia,H3N8,Avian,1                2280 2277 2151 1703 1497 1415  982  838
 14: 93, 76, 73,495, 68,386, 49, 71   CY130069,A/duck/England/1/1956,1956//,United Kingdom,H11N6,Avian,1              2280 2277 2151 1715 1497 1420  982  838
 15:102,103, 90,492, 87,482, 49,294   DQ376870,A/duck/Taiwan/0526/72,1972//,Taiwan,H6N1,Avian,1                       2280 2277 2151 1706 1497 1413  982  838
 17:107, 90, 81,429, 73,494, 43, 63   CY130021,A/duck/Ukraine/1/1963,1963//,Ukraine,H3N8,Avian,1                      2280 2277 2151 1703 1497 1415  982  838
 20:114,100, 92,469, 77,455, 50,296   CY116850,A/mallard/MT/Y61 ,//,Russia,H2N2,Avian,1                               2280 2274 2151 1697 1497 1407  982  838
 22: 96, 84, 90,352, 71,497, 56, 60   CY087839,A/quail/Italy/1117/1965,1965/06/11,Italy,H10N8,Avian,1                 2280 2277 2151 1686 1497 1415  982  838
 24:109, 95, 79,487, 77,480, 55, 61   CY130045,A/shearwater/Australia/1/1973,1973//,Australia,H6N5,Avian,1            2280 2277 2151 1706 1497 1409  982  838
 25: 97, 84, 90,352, 71,497, 56, 60   CY087767,A/shearwater/Australia/2/1972,1972/06/11,Australia,H10N8,Avian,1       2280 2277 2151 1686 1497 1415  982  838
 26:107, 95, 78,466, 64,478, 52, 65   CY014991,A/tern/South Africa/1961,1961//,South Africa,H5N3,Avian,1              2280 2277 2151 1715 1497 1410  982  838
 27:141, 96,125,468,100,448, 63, 69   EU743085,A/turkey/CO/118899/1972,1972//,USA,H5N2,Avian,1                        2280 2277 2151 1700 1497 1407  982  838
 29: 99, 86, 77,129, 65,468, 47, 58   CY130157,A/turkey/England/1963,1963//,United Kingdom,H7N3,Avian,1               2280 2277 2151 1694 1497 1326  982  838
 31:136, 95, 85,478, 90,439, 86, 58   CY130037,A/turkey/Massachusetts/3740/1965,1965//,USA,H6N2,Avian,1               2280 2277 2151 1709 1497 1407  982  838
 34:140,160,123,492, 89,497, 65, 54   CY130053,A/turkey/Ontario/6118/1968,1968//,Canada,H8N4,Avian,1                  2280 2277 2151 1704 1497 1416  982  838
 35:133,159, 79,465, 88,483, 66, 53   CY087815,A/turkey/Ontario/6213/1966,1966/06/11,Canada,mixed,Avian,1             2280 2277 2151 1703 1497 1413  982  838
 37:146, 87,125,482, 88,445, 66, 57   CY087831,A/turkey/Wisconsin/1/1966,1966/06/11,USA,H9N2,Avian,1                  2280 2277 2151 1691 1497 1407  982  838
 41:117,106,100,158, 93,161, 62, 65   A/Netherlands/219/03(H7N7)                                                      2280 2274 2151 1689 1497 1416  982  838

(about 2.5-3 promille per year is normal, so the most recent common ancester
to the 1934 Rostock virus is ~1917 in segments 2,3,5)

gsgs · Oct 31, 2013

Re: today at genbank

Re: today at genbank

2013/10/30
big update , 1131 sequences
33 H3N2 from India segments 4,6 , 2013 , 2011 [I should check for original mutations]
spg, h1n1,2009
USA,mallards,2012 [I should check for 17g-strain ----done,none found----]
176 Sweden mallards , 19 genomes
the obligatory H3N2v in swine from USA

gsgs · Nov 7, 2013

Re: Today at GenBank

2013/11/07
H3N2 from USA, season 2012/3 , from all states, mainly segments 4,6,7

Code:

     17,Alabama/
     58,Alaska/
      9,Arizona/
     18,Arkansas
     42,Californ
     21,Colorado
      6,Connecti
     30,Delaware
      9,District
     30,Florida/
     15,Georgia/
     36,Hawaii/
     21,Idaho/
      6,Illinois
     12,Indiana/
     18,Iowa/
     18,Kansas/
     18,Kentucky
     18,Louisian
     12,Maine/
     27,Maryland
     27,Massachu
     28,Michigan
     15,Minnesot
     12,Mississi
     15,Missouri
     15,Montana/
     18,Nebraska
     24,Nevada/
     18,New Hamp
     15,New Jers
     27,New Mexi
     42,New York
     21,North Ca
     15,North Da
     15,Ohio/
     21,Oklahoma
     15,Oregon/
     18,Pennsylv
     12,Rhode Is
     12,South Ca
     21,South Da
      9,Tennesse
     39,Texas/
     12,Utah/
     15,Vermont/
     18,Virginia
     32,Washingt
     18,West Vir
     21,Wisconsi
     12,Wyoming/

Code:

                                                            0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111111111111111111111111 
                                                            0000000000000000000001111111111111112222222222222233333333334444444444444444455555555555556666666666666677777777777777788888888888999999999999900000000000111111111111122222222223333333333334444444444455555555555666666666 
                                                            0122233334445557778990334445667888990011223477888901124556990111233456677789900111234466990001223448889900011122336668812333477889013456777889900111345888011123566799901345567892234456667891123445789900112455677112356778 
                                                            9812836793582570284368594676251027155609287069125130685784035389005760823822814689870314163596399032790345904516262584569037303271359446258383459147276037103551867314508654795160384732351923687398451479384547958344732013 
-codon-position---------------------------------------------   11  1 1  11 1       1 2      212 12        2    111  11   212 1   1 1212     2        2 2 122 111 2  2 12 11  1   12 122     2    2     21 1 1        1   2   2    1                 1           1   1 1        2 12  2   
---Index----------------------------------------------------TTGAAATCGTCTACTACGGTGACACAATTTGGGTCTGATGCTCCTTGCCTCGCTTGGGACGAAGCAACCGAAGAATAGTCTAAAGCTAGAGGGGTTAGTGATCGCTCCAGACCAAGAAATCGGGCTCTACTCAGCCTTGACATACATATCGGAGCGTAGATCATGTAGGACCAGTATCGCGCTTCACGTGGGCTCCGACAGCGAAGCGGAGTATCCCAAG 
   1 >Index/2009/Egypt/Iowa                                 ............................................................................................................................................................................................................................        0      0 ,      0      0       1:>Index/2009/Egypt/Iowa                                 
   2 >KF790169,A/Oklahoma/04/2012(H3N2)                     ..........T..........G..............A..T.........C...C....C.A........T........................A...G...T......AG..G.A............C...............A.....T....A..............T...........C....................G.A..............       30     24 ,     30     24       2:>KF790169,A/Oklahoma/04/2012(H3N2)                     
   3 >KF790050,A/Florida/68/2012(H3N2)                      .....................G..............A............C...CC..................................T........G...T..........G..............C...............A.....T........G......................C...T................G.A..............       18     17 ,     18     17       3:>KF790050,A/Florida/68/2012(H3N2)                      
   4 >KF789819,A/Virginia/16/2012(H3N2)                     .....................G..............A....C.......C...CC.................................AT........G...T..C..G....G..............C.C.............A.....T...T....G......................C...T...............TG.A.....C........       25     25 ,     25     25       4:>KF789819,A/Virginia/16/2012(H3N2)                     
   5 >KF789670,A/Virginia/15/2012(H3N2)                     .....................G..............A....C.......C...CC.................................A.........G...T..C..G....G..............C.C.............A.....T...T....G......................C...T...............TG.A.....C........       24     24 ,     24     24       5:>KF789670,A/Virginia/15/2012(H3N2)                     
   6 >KF789706,A/Tennessee/18/2012(H3N2)                    .....................G..............A....C.......C...CC.................................A.........G...T..C..G....G..............C.C.............A.....T...T....G......................C...T...............TG.A.....C........       25     24 ,     25     24       6:>KF789706,A/Tennessee/18/2012(H3N2)                    
   7 >KF789804,A/Virginia/16/2012(H3N2)                     .....................G..............A....C.......C...CC.................................A.........G...T..C..G....G..............C.C.............A.....T...T....G......................C...T...............TG.A.....C........       24     24 ,     24     24       7:>KF789804,A/Virginia/16/2012(H3N2)                     
   8 >KF789782,A/Michigan/33/2012(H3N2)                     .....................G..............A....C.......C...CC.................................A.........G...T..C..G....G..............C.C.............A.....T...T....G......................C...T...............TG.A.....C........       24     24 ,     24     24       8:>KF789782,A/Michigan/33/2012(H3N2)                     
   9 >KF790488,A/South Carolina/22/2012(H3N2)               .....................G..............A............C...CC.................................A.........G...T..C..G....G..............C.C.............A.....T...T....G......................C...T...............TG.A.....C........       23     23 ,     23     23       9:>KF790488,A/South Carolina/22/2012(H3N2)               
  10 >KF790479,A/South Carolina/24/2012(H3N2)               .....................G..............A............C...CC.................................A.........G...T..C.TG....G..............C.C.............A.....T...T....G......................C...T...............TG.A.....C........       24     24 ,     24     24      10:>KF790479,A/South Carolina/24/2012(H3N2)               
  11 >KF789707,A/Kentucky/18/2012(H3N2)                     .....................G..............A............C...CC.................................A.........G...T..C..G....G..............C.C.............A.....T...T....G......................C...T...............TG.A.....C........       23     23 ,     23     23      11:>KF789707,A/Kentucky/18/2012(H3N2)                     
  12 >KF790495,A/Tennessee/10/2012(H3N2)                    .....................G..............A............C...CC.................................A.........G...T..C..G....G..............C.C.............A.....T...T....G......................C...T...............TG.A.....C.C......       25     24 ,     25     24      12:>KF790495,A/Tennessee/10/2012(H3N2)                    
  13 >KF789604,A/Kentucky/17/2012(H3N2)                     .....................G..............A............C...CC.................................A.........G...T..C..G....G..............C.C.............A.....T...T....G......................C...T...............TG.A.....C........       23     23 ,     23     23      13:>KF789604,A/Kentucky/17/2012(H3N2)                     
  14 >KF790048,A/South Carolina/24/2012(H3N2)               .....................G..............A............C...CC.................................A..T......G...T.YC..G....G..............C.C.............A.....T...T....G......................C...T...............TG.A.....C........       25     25 ,     25     25      14:>KF790048,A/South Carolina/24/2012(H3N2)               
  15 >KF789899,A/Kentucky/24/2012(H3N2)                     .....................G..............A............C...CC.................................A.........G...T.YC..G....G..............C.C.............A.....T...T....G......................C...T...............TG.A.....C........       25     24 ,     25     24      15:>KF789899,A/Kentucky/24/2012(H3N2)                     
  16 >KF790491,A/Louisiana/11/2012(H3N2)                    ..............C......G..............A............C...C.....T...................T..............C...G...T..........G.........A....C.........A.....A.....T....A...G......................C....................G.A........T.....       26     22 ,     26     22      16:>KF790491,A/Louisiana/11/2012(H3N2)                    
  17 >KF790063,A/Delaware/23/2012(H3N2)                     C.......A...G..G.....G.G............A............C...C.........................T......................T..........G...C.....A....C........C......A..............G......................C..................T.G.A..............       23     22 ,     23     22      17:>KF790063,A/Delaware/23/2012(H3N2)                     
  18 >KF790081,A/Delaware/23/2012(H3N2)                     C.......A...G..G.....G.G............A............C...C.........................T......................T..........G.........A....C........C......A..............G......................C..................T.G.A..............       21     21 ,     21     21      18:>KF790081,A/Delaware/23/2012(H3N2)                     
  19 >KF789534,A/California/55/2012(H3N2)                   C.......A.T.G..G.A...GA.......A.....A............C...C........................................C.......T..........G..............C........C......A..............G....A.................C..................T.G.A..............       24     24 ,     24     24      19:>KF789534,A/California/55/2012(H3N2)                   
  20 >KF789944,A/Florida/01/2013(H3N2)                      C.......A.T.G..G.....G........A.....A............C...C................................................T...M......G..G...........C........C......A..............G......................C..................T.G.A..............       25     22 ,     25     22      20:>KF789944,A/Florida/01/2013(H3N2)                      
  21 >KF790287,A/South Carolina/16/2012(H3N2)               C.......A.T.G..G.....G........A.....A............C...C................................................T..........G..............C........C......A..............G......................C..................T.G.A..............       20     20 ,     20     20      21:>KF790287,A/South Carolina/16/2012(H3N2)               
  22 >KF790212,A/Alaska/02/2013(H3N2)                       C.......A.T.G..G.....G........A.....A............C...C................................................T..........G..............C........C......A........A.....G......................C..................T.G.A..............       21     21 ,     21     21      22:>KF790212,A/Alaska/02/2013(H3N2)                       
  23 >KF790407,A/Alaska/02/2013(H3N2)                       C.......A.T.G..G.....G........A.....A............C...C................................................T..........G..............C........C......A........A.....G......................C..................T.G.A..............       21     21 ,     21     21      23:>KF790407,A/Alaska/02/2013(H3N2)                       
  24 >KF789805,A/Georgia/22/2012(H3N2)                      C.......A.T.G..G.....G........A.....A............C...C................................................T.......R..G..............C........C......A..............G......................C..................T.G.A..............       21     21 ,     21     21      24:>KF789805,A/Georgia/22/2012(H3N2)                      
  25 >KF789665,A/Georgia/16/2012(H3N2)                      C....T..A...G..G.....G..............A........C...C...C.................GA........G....................T.......G..G..........T...C........C......A..............G.T....................C..................T.G.A.A............       27     27 ,     27     27      25:>KF789665,A/Georgia/16/2012(H3N2)                      
  26 >KF789690,A/Georgia/15/2012(H3N2)                      C....T..A...G..G.....G..............A........C...C...C.................GA........G....................T.......G..G..........T...C........C......A..............G.T....................C..................T.G.A.A............       27     27 ,     27     27      26:>KF789690,A/Georgia/15/2012(H3N2)                      
  27 >KF789983,A/Florida/39/2012(H3N2)                      C.......A...G..G.....G..............A............C..AC.A..............................................T.......G..GGA............C........C......A..............G......................C..................T.G.A..............       26     23 ,     26     23      27:>KF789983,A/Florida/39/2012(H3N2)                      
  28 >KF789748,A/Louisiana/16/2012(H3N2)                    C.......A...G..G.....G..............A............C..AC.A..............................................T....Y.....G.A............C........C......A..............G......................C..................T.G.A..............       23     22 ,     23     22      28:>KF789748,A/Louisiana/16/2012(H3N2)                    
  29 >KF790278,A/New York/40/2012(H3N2)                     C.......A...G..G.....G..............A............C..AC.A..............................................T..........G.A............C........C......A..............G......................C..................T.G.A..............       21     21 ,     21     21      29:>KF790278,A/New York/40/2012(H3N2)                     
  30 >Index/32g12f1.c2,55-62                                C.......A...G..G.....G...G..........A............C..AC.............................................A..T..........G.A.......A....C........C......A....T.........G......................C..................T.G.A..............       24     24 ,     24     24      30:>Index/32g12f1.c2,55-62                                
  31 >KF790178,A/Vermont/16/2012(H3N2)                      C.......A...G..G.....G..............A............C...C................................................T..........G.A............C........C......A..............G......................C................G.T.G.A..............       21     20 ,     21     20      31:>KF790178,A/Vermont/16/2012(H3N2)                      
  32 >KF789680,A/Virginia/14/2012(H3N2)                     C.......A...G..G.....G..............A............C...C................................................T..........G.A............C.....T..C......A..G...........G............G.........C..................T.G.A..............       22     22 ,     22     22      32:>KF789680,A/Virginia/14/2012(H3N2)                     
  33 >KF789674,A/Maryland/43/2012(H3N2)                     C.......A...G..G.....G..............A............C...C................................................T..........G.A............C.....T..C......A..G...........G............G.........C..................T.G.A..............       23     22 ,     23     22      33:>KF789674,A/Maryland/43/2012(H3N2)                     
  34 >KF789912,A/Alabama/35/2012(H3N2)                      C.......A...G..G.....G..............A............C...C................................................T..........G.A............C.....T..C......A..G...........G............G.........C..................T.G.A..............       22     22 ,     22     22      34:>KF789912,A/Alabama/35/2012(H3N2)                      
  35 >KF790242,A/Nevada/26/2012(H3N2)                       C.......A...G..G.....G..............A............C...C.................................G..............T....M.....G..............C........C......A..............G......................C..................T.G.A....A.........       23     21 ,     23     21      35:>KF790242,A/Nevada/26/2012(H3N2)                       
  36 >KF790209,A/Mississippi/12/2012(H3N2)                  C.....C.A...G.CG.....G..............A............C...C..............G.................................T..........G..............C........C.....GA..............G......................C..................T.G.A..............       22     22 ,     22     22      36:>KF790209,A/Mississippi/12/2012(H3N2)                  
  37 >KF790093,A/Wisconsin/37/2012(H3N2)                    C.....C.A...G.CG.....G..............A............C...C................................................T..........G..............C........C.....GA..............G......................C..................T.G.A..............       22     21 ,     22     21      37:>KF790093,A/Wisconsin/37/2012(H3N2)                    
  38 >KF790402,A/Nebraska/04/2013(H3N2)                     C.....C.A...G.CG.....G..............A............C...C................................................T..........G..............C........C......A......A.......G......................C..................T.G.A..............       22     21 ,     22     21      38:>KF790402,A/Nebraska/04/2013(H3N2)                     
  39 >KF790265,A/Mississippi/13/2012(H3N2)                  C.......A...G..G.....G..............A............C...C................................................T..........G..............C........C......A...Y..........G......................C..................T.G.A..............       20     19 ,     20     19      39:>KF790265,A/Mississippi/13/2012(H3N2)                  
  40 >KF789596,A/Colorado/20/2012(H3N2)                     C.......A...G........G..............A............C...C................................................T..........G.........A....C........C......A..............G......................C..................T.G.A..............       18     18 ,     18     18      40:>KF789596,A/Colorado/20/2012(H3N2)                     
  41 >Index/H3N3-2011-reassortedEI/2011(H3N2)               .....................G..............A............C...C................................................T..........G..............C...............A..............G......................C....................G.A..............       12     12 ,     12     12      41:>Index/H3N3-2011-reassortedEI/2011(H3N2)               
  42 >Index/H3N2-2011-normalEI/2011(H3N2)                   C......................................T...................................................................................................G.............A..................................................................        7      4 ,      7      4      42:>Index/H3N2-2011-normalEI/2011(H3N2)                   
  43 >KC892570,A/Pennsylvania/09/2012(H3N2)                 .......T........T........G......AAT.................................T........A...................T...........A.................G...........G..........................C....A............T................T..................       16     16 ,     16     16      43:>KC892570,A/Pennsylvania/09/2012(H3N2)                 
  44 >KF789697,A/Pennsylvania/09/2012(H3N2)                 .......T........T........G......AAT.................................T........A.................C.T.....A.....A.................G...........G..........................C....A............T................T..................       18     18 ,     18     18      44:>KF789697,A/Pennsylvania/09/2012(H3N2)                 
  45 >KF789838,A/Wisconsin/06/2013(H3N2)                    ................T........G......A.T.............T................G..T..G..G..A...................T...........AR................G...........G..........................C....A....A...........................G...............       20     19 ,     20     19      45:>KF789838,A/Wisconsin/06/2013(H3N2)                    
  46 >KF789767,A/New Mexico/11/2013(H3N2)                   C...............T........G......A.T.............T................G..T..G..G.GA...................T...........AR.....G..........G...........G..........................CA...A....A.........................A.G.............G.       26     25 ,     26     25      46:>KF789767,A/New Mexico/11/2013(H3N2)                   
  47 >KF789567,A/Idaho/03/2013(H3N2)                        C...............T........G......A.T.............T................G..T..G..G..A...................T...........A......G..........G...........G..........................CA...A....A.........................A.G.............G.       23     23 ,     23     23      47:>KF789567,A/Idaho/03/2013(H3N2)                        
  48 >KF790514,A/Arizona/11/2012(H3N2)                      C...............T........G......A.T.............T................G..TT.G..G..A...................T...........A......G..........G...........G..........................CA...A....A.........................A.G.............G.       25     24 ,     25     24      48:>KF790514,A/Arizona/11/2012(H3N2)                      
  49 >KF790408,A/Texas/11/2013(H3N2)                        ................T........G......A.T.............T................G..TT.G..G..A...................T...........A.................G...T.......G..........................C....A....A...........................G.............G.       21     21 ,     21     21      49:>KF790408,A/Texas/11/2013(H3N2)                        
  50 >KF790027,A/Massachusetts/07/2013(H3N2)                ................T........G......A.T.......T.....T................G..TT.G..G..A...................T...........A.................G...........G.............A............C.A..A....A...........................G.............G.       25     23 ,     25     23      50:>KF790027,A/Massachusetts/07/2013(H3N2)                
  51 >KF789585,A/Florida/46/2012(H3N2)                      ...........C....T...A....G......A.T.......T.....T................G..T..G..G..A...................T...........A.................G...........G..........................C....A....A...........................G.............G.       22     22 ,     22     22      51:>KF789585,A/Florida/46/2012(H3N2)                      
  52 >KF789889,A/Wisconsin/51/2012(H3N2)                    ................T...A....G......A.T.......T.....T................G..T..G..G..A...................T...........A.................G...........G..........................C....A....A...........................G.............G.       21     21 ,     21     21      52:>KF789889,A/Wisconsin/51/2012(H3N2)                    
  53 >KF789895,A/New Hampshire/21/2012(H3N2)                ................T...A....G......A.T.......T.....T................G..T..G..G..A...................T...........A.................G...........G..........................C....A....A...........................G.............G.       22     21 ,     22     21      53:>KF789895,A/New Hampshire/21/2012(H3N2)                
  54 >KF790411,A/Massachusetts/05/2013(H3N2)                ................T........G......A.T.......T.....T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       21     21 ,     21     21      54:>KF790411,A/Massachusetts/05/2013(H3N2)                
  55 >KF790310,A/Massachusetts/04/2013(H3N2)                ................T........G......A.T.......T.....T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       23     21 ,     23     21      55:>KF790310,A/Massachusetts/04/2013(H3N2)                
  56 >KF790482,A/Florida/09/2013(H3N2)                      ................T........G......A.T.......T.....T................G..T..G..G..A...................T...........A.................G...........G.............A............C....G....A...........................G.............G.       22     21 ,     22     21      56:>KF790482,A/Florida/09/2013(H3N2)                      
  57 >KF789954,A/Rhode Island/02/2013(H3N2)                 ................T........G......A.T.............T...............TG..T..G..G..A...................T.......C...A.................G...........G.............A............C....G....A...........................G.............G.       23     22 ,     23     22      57:>KF789954,A/Rhode Island/02/2013(H3N2)                 
  58 >KF789731,A/New Mexico/06/2013(H3N2)                   ................T........G......A.T.............T...............TG..T..G..G..A...................T...........A.................G...........G.............A............C....G....A...........................G.............G.       21     21 ,     21     21      58:>KF789731,A/New Mexico/06/2013(H3N2)                   
  59 >KF790148,A/Arkansas/03/2013(H3N2)                     ................T........GG.....A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....G....A...........................G.....T.......G.       22     22 ,     22     22      59:>KF790148,A/Arkansas/03/2013(H3N2)                     
  60 >KF790144,A/Arkansas/13/2013(H3N2)                     ................T........GG.....A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....G....A...........................G.....T.......G.       23     22 ,     23     22      60:>KF790144,A/Arkansas/13/2013(H3N2)                     
  61 >KF790136,A/Arkansas/07/2013(H3N2)                     ................T........GG.....A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....G....A...........................G.....T.......G.       22     22 ,     22     22      61:>KF790136,A/Arkansas/07/2013(H3N2)                     
  62 >KF789970,A/Arkansas/06/2013(H3N2)                     ................T........GG.....A.T.............T................G..T..G..G..A...................T.........Y.A.................G...........G.............A............C....G....A...........................G.....T.......G.       24     23 ,     24     23      62:>KF789970,A/Arkansas/06/2013(H3N2)                     
  63 >KF789975,A/Arkansas/04/2013(H3N2)                     ................T........GG.....A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....G....A...........................G.....T.......G.       22     22 ,     22     22      63:>KF789975,A/Arkansas/04/2013(H3N2)                     
  64 >KF789560,A/Florida/06/2013(H3N2)                      ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       20     20 ,     20     20      64:>KF789560,A/Florida/06/2013(H3N2)                      
  65 >KF790362,A/New York/06/2013(H3N2)                     ................T........G......A.T.............T......A.........G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       21     21 ,     21     21      65:>KF790362,A/New York/06/2013(H3N2)                     
  66 >KF790302,A/New Jersey/02/2013(H3N2)                   ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       20     20 ,     20     20      66:>KF790302,A/New Jersey/02/2013(H3N2)                   
  67 >KF790404,A/Iowa/02/2013(H3N2)                         ................T........G......A.T.............T................G..T..G..G..A...................C...........AR................G...........G.............A............C....A....A..........A................G.............G.       23     22 ,     23     22      67:>KF790404,A/Iowa/02/2013(H3N2)                         
  68 >KF789635,A/Texas/09/2013(H3N2)                        ................T........G......A.T.............T................G..T..G..G..A...................T...........AG................G...........G.............A............C....A....A...........................G.............G.       21     21 ,     21     21      68:>KF789635,A/Texas/09/2013(H3N2)                        
  69 >KF789842,A/North Carolina/06/2013(H3N2)               ................T........G......A.T.............T................G..T..G..G..A...................T...........AG................G...........G.............A............C....A....A...........................G.............G.       21     21 ,     21     21      69:>KF789842,A/North Carolina/06/2013(H3N2)               
  70 >KF790147,A/Texas/14/2013(H3N2)                        ................T........G......A.T.............T................G..T..G..G..A..C................T...........AG................G...........G.............A............C....A....A..........................GG.............G.       24     23 ,     24     23      70:>KF790147,A/Texas/14/2013(H3N2)                        
  71 >KF789965,A/Massachusetts/12/2013(H3N2)                ................T........G......A.T.............T................G..T..G..G..A..C................T...........A.................G...........G.............A............C....A....A..................T........G.............G.       24     22 ,     24     22      71:>KF789965,A/Massachusetts/12/2013(H3N2)                
  72 >KF790297,A/Massachusetts/13/2013(H3N2)                .........C......T........G......A.T.............T................G..T..G..GC.A..C................T...........A.................G.........C.G.............A............C....A....A...........................G.............G.       25     24 ,     25     24      72:>KF790297,A/Massachusetts/13/2013(H3N2)                
  73 >KF789849,A/Utah/07/2013(H3N2)                         ................T........G......A.T.............T................G..T..G..GC.A..C................T...........A.................G...........G.........T...A............C....A....A...........................G.............G.       23     23 ,     23     23      73:>KF789849,A/Utah/07/2013(H3N2)                         
  74 >KF790427,A/Missouri/05/2013(H3N2)                     ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.........A...A............C....A....AT..........................G.............G.       22     22 ,     22     22      74:>KF790427,A/Missouri/05/2013(H3N2)                     
  75 >KF790384,A/New Mexico/24/2012(H3N2)                   ................T........G......A.T.............T................G..T..G..G..A...................T...........AG................G...........G..........................C....A....AT..........................G.............G.       21     21 ,     21     21      75:>KF790384,A/New Mexico/24/2012(H3N2)                   
  76 >KF790137,A/Oklahoma/03/2013(H3N2)                     ................T........G......A.T.............T.........T......G..T..G..G..A...G...............T...........AG................G...........G..........................C....A..C.A...........................G.............G.       24     23 ,     24     23      76:>KF790137,A/Oklahoma/03/2013(H3N2)                     
  77 >KF790129,A/Virginia/06/2013(H3N2)                     C.......T.......T........G......A.T.............T.........T......G..T..G..G..A...................T...........A..T..............G...........G..........................C....A..C.A..................T........G.............G.       25     25 ,     25     25      77:>KF790129,A/Virginia/06/2013(H3N2)                     
  78 >KF790119,A/Louisiana/04/2013(H3N2)                    ................T.A......G......A.T.............T.........T......G..T..G..G..A...................T...........A.................G...........G..........................C....A..C.A...........................G.............G.       26     22 ,     26     22      78:>KF790119,A/Louisiana/04/2013(H3N2)                    
  79 >KF790201,A/North Carolina/01/2013(H3N2)               .........................G......A.T.............T.........T.....TG..T..G..G..A...................T...........A.................G...........G..........................C....A..C.A...........................G.............G.       22     21 ,     22     21      79:>KF790201,A/North Carolina/01/2013(H3N2)               
  80 >KF789829,A/Connecticut/13/2012(H3N2)                  ................T........G......A.T.............T...............T...T..G..G..A...................T...........A.................G..........AG........C.................C....A....A......C....................G.............G.       22     22 ,     22     22      80:>KF789829,A/Connecticut/13/2012(H3N2)                  
  81 >KF790118,A/Alaska/03/2013(H3N2)                       ................T........G.C....A.T.............T................GG.T..G..G..A...................T...........A....G............G...........G........C.................C....A....A...........................G.............G.       24     23 ,     24     23      81:>KF790118,A/Alaska/03/2013(H3N2)                       
  82 >KF789562,A/Massachusetts/06/2013(H3N2)                ................T........G.C....A.T.............T................GG.T..G..G..A...................T...........A.................G...........G........C.................C....A....A...........................G.............G.       22     22 ,     22     22      82:>KF789562,A/Massachusetts/06/2013(H3N2)                
  83 >KF789891,A/Kansas/16/2012(H3N2)                       ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G........C.................C....A....A...........................G.............G.       20     20 ,     20     20      83:>KF789891,A/Kansas/16/2012(H3N2)                       
  84 >KF790053,A/Wyoming/01/2013(H3N2)                      ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G........C.................C....A....A...........................G..........S..G.       22     21 ,     22     21      84:>KF790053,A/Wyoming/01/2013(H3N2)                      
  85 >KF790225,A/Texas/82/2012(H3N2)                        ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G..........................C....A....A...........................G.............G.       19     19 ,     19     19      85:>KF790225,A/Texas/82/2012(H3N2)                        
  86 >KF790414,A/Nebraska/03/2013(H3N2)                     ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G..........................C....A....A...........................G.............G.       21     19 ,     21     19      86:>KF790414,A/Nebraska/03/2013(H3N2)                     
  87 >KF790311,A/Nebraska/15/2012(H3N2)                     ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G..........................C....A....A...........................G.............G.       19     19 ,     19     19      87:>KF790311,A/Nebraska/15/2012(H3N2)                     
  88 >KF789810,A/Iowa/22/2012(H3N2)                         ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G.T.........G..........................C....A....A...........................G.............G.       20     20 ,     20     20      88:>KF789810,A/Iowa/22/2012(H3N2)                         
  89 >KF789966,A/Rhode Island/06/2013(H3N2)                 ................T........G......A.T.............T................G..T..G..G..A.........G....A....T...........A.................A.T.........G..........................C....A....A...........................G...............       23     21 ,     23     21      89:>KF789966,A/Rhode Island/06/2013(H3N2)                 
  90 >KF790180,A/New York/37/2012(H3N2)                     ................T........G......A.T.............T................G..T..G..G..A.........G.........T...........A.................A.T.........G..........................C....A....A...........................G.............G.       21     21 ,     21     21      90:>KF790180,A/New York/37/2012(H3N2)                     
  91 >KF789958,A/West Virginia/01/2013(H3N2)                ................T........G......A.T.............TY...............G..T..G..G..A.........GR........T...........A.................A.T.........G..........................C....A....A...........................G.............G.       23     23 ,     23     23      91:>KF789958,A/West Virginia/01/2013(H3N2)                
  92 >KF790258,A/New York/39/2012(H3N2)                     ................T........G......A.T.............T................G..T..G..G..A.........G.........T...........A.................A.T.........G..........................C....A....A...........................G.............G.       21     21 ,     21     21      92:>KF790258,A/New York/39/2012(H3N2)                     
  93 >KF789872,A/Hawaii/02/2013(H3N2)                       ................T........G......A.T.............T................G..T..G..G..A.........G.........T.........T.AG................A.T.........G..........................C....A....A...........................G.............G.       23     23 ,     23     23      93:>KF789872,A/Hawaii/02/2013(H3N2)                       
  94 >KF790224,A/Rhode Island/08/2012(H3N2)                 ................T........G......A.T.............T................G..T..G..G..A.........G.........T...........A.................A.T.........G..........................C....A....A...........................G.............G.       21     21 ,     21     21      94:>KF790224,A/Rhode Island/08/2012(H3N2)                 
  95 >KF790277,A/New York/39/2012(H3N2)                     ................T........G......A.T.............T................G..T..G..G..A.........G...K.....T......M....A.................A.T.........G..........................C....A....A...........................G.............G.       24     23 ,     24     23      95:>KF790277,A/New York/39/2012(H3N2)                     
  96 >KF789774,A/Massachusetts/11/2013(H3N2)                ................T........G......A.T...........A.T................G..T..G..G..A...................T...........A.................G...........G.......G..................C....A....A...........................G.............G.       22     21 ,     22     21      96:>KF789774,A/Massachusetts/11/2013(H3N2)                
  97 >KF790232,A/Iowa/14/2012(H3N2)                         ................T........G......A.T.............T................G..T..G..G..A...................T...Y.......A.................G...........G..........................C....A....A...........................G.............G.       20     20 ,     20     20      97:>KF790232,A/Iowa/14/2012(H3N2)                         
  98 >KF789841,A/New Jersey/03/2013(H3N2)                   ................T........G......A.T.............T................G..T..G..G..A..............A....T...........A.................G...........G..........................C....A....A...........................G.............G.       20     20 ,     20     20      98:>KF789841,A/New Jersey/03/2013(H3N2)                   
  99 >KF790416,A/Iowa/01/2013(H3N2)                         ................T........G......A.T.............T........A.......G..T..G..G..A...................T...........A.................G...........G..........................C....A....A...........................G.............G.       21     20 ,     21     20      99:>KF790416,A/Iowa/01/2013(H3N2)                         
 100 >KF790248,A/Iowa/15/2012(H3N2)                         ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G..........................C....A....A...........................G.............G.       19     19 ,     19     19     100:>KF790248,A/Iowa/15/2012(H3N2)                         
 101 >KF790459,A/North Dakota/01/2013(H3N2)                 ..........T.....T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G..........................C....A....A...........................G.............G.       21     20 ,     21     20     101:>KF790459,A/North Dakota/01/2013(H3N2)                 
 102 >KF790483,A/West Virginia/11/2013(H3N2)                .........A......T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G..........................C....A....A........G..C...............G.............G.       22     22 ,     22     22     102:>KF790483,A/West Virginia/11/2013(H3N2)                
 103 >KF789974,A/West Virginia/05/2013(H3N2)                .........A......T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G..........................C....A....A........G..C...............G.............G.       22     22 ,     22     22     103:>KF789974,A/West Virginia/05/2013(H3N2)                
 104 >KF789858,A/West Virginia/10/2013(H3N2)                .........A......T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G..........................C....A....A........G..C...............G.............G.       22     22 ,     22     22     104:>KF789858,A/West Virginia/10/2013(H3N2)                
 105 >KF789978,A/West Virginia/06/2013(H3N2)                .........A......T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G..........................C....A....A........G..C...............G.............G.       22     22 ,     22     22     105:>KF789978,A/West Virginia/06/2013(H3N2)                
 106 >KF790419,A/New York/60/2012(H3N2)                     ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G..........................C....A....A...........................G.............G.       19     19 ,     19     19     106:>KF790419,A/New York/60/2012(H3N2)                     
 107 >KF789736,A/Montana/03/2013(H3N2)                      ................T........G......A.T.............T................G..T..G..G..A...................T...........A...............C.G...........G..........................C....A....A...........................G.............G.       22     20 ,     22     20     107:>KF789736,A/Montana/03/2013(H3N2)                      
 108 >KF789770,A/North Carolina/28/2012(H3N2)               ................T........G......A.T.............T................G..TK.G..G..A...................T...........A...............C.G...........G..........................C....A....A...........................G.............G.       22     21 ,     22     21     108:>KF789770,A/North Carolina/28/2012(H3N2)               
 109 >KF790339,A/Delaware/06/2013(H3N2)                     ................T...............A.T.............T................G..TK.G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       24     22 ,     24     22     109:>KF790339,A/Delaware/06/2013(H3N2)                     
 110 >KF789637,A/Idaho/24/2012(H3N2)                        ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     110:>KF789637,A/Idaho/24/2012(H3N2)                        
 111 >KF789828,A/Idaho/38/2012(H3N2)                        ................T...............A.T.............T................G..T..G..G..A....G..............T...........AR................G...........G..........................C..G.A....A.A.........................G.............G.       23     22 ,     23     22     111:>KF789828,A/Idaho/38/2012(H3N2)                        
 112 >KF789541,A/Colorado/02/2013(H3N2)                     ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     112:>KF789541,A/Colorado/02/2013(H3N2)                     
 113 >KF790127,A/Colorado/27/2012(H3N2)                     ................T...............A.T.............T................G..T..G..G..A.T..G..............T...........A.................G...........G.........M................C..G.A....A.A.........................G.............G.       23     23 ,     23     23     113:>KF790127,A/Colorado/27/2012(H3N2)                     
 114 >KF789544,A/Washington/06/2013(H3N2)                   ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     114:>KF789544,A/Washington/06/2013(H3N2)                   
 115 >KF790418,A/New Hampshire/03/2013(H3N2)                ................TA..............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       23     22 ,     23     22     115:>KF790418,A/New Hampshire/03/2013(H3N2)                
 116 >KF789627,A/California/16/2013(H3N2)                   ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     116:>KF789627,A/California/16/2013(H3N2)                   
 117 >KF789847,A/Washington/07/2013(H3N2)                   ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       23     21 ,     23     21     117:>KF789847,A/Washington/07/2013(H3N2)                   
 118 >KF789753,A/Washington/60/2012(H3N2)                   ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     118:>KF789753,A/Washington/60/2012(H3N2)                   
 119 >KF789799,A/Idaho/37/2012(H3N2)                        ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       24     21 ,     24     21     119:>KF789799,A/Idaho/37/2012(H3N2)                        
 120 >KF789947,A/Alaska/01/2013(H3N2)                       ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     120:>KF789947,A/Alaska/01/2013(H3N2)                       
 121 >KF790527,A/Minnesota/17/2012(H3N2)                    ................T...............A.T.............T..........T.....G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       22     22 ,     22     22     121:>KF790527,A/Minnesota/17/2012(H3N2)                    
 122 >KF790348,A/Utah/03/2013(H3N2)                         ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     122:>KF790348,A/Utah/03/2013(H3N2)                         
 123 >KF790503,A/Nevada/03/2013(H3N2)                       ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.............T...........G.............G.       23     22 ,     23     22     123:>KF790503,A/Nevada/03/2013(H3N2)                       
 124 >KF790329,A/Nevada/36/2012(H3N2)                       ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.............T...........G.............G.       22     22 ,     22     22     124:>KF790329,A/Nevada/36/2012(H3N2)                       
 125 >KF789915,A/Delaware/24/2012(H3N2)                     ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     125:>KF789915,A/Delaware/24/2012(H3N2)                     
 126 >KF790065,A/Minnesota/01/2013(H3N2)                    C...............T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.....A.......G.       23     23 ,     23     23     126:>KF790065,A/Minnesota/01/2013(H3N2)                    
 127 >KF789957,A/Montana/01/2013(H3N2)                      ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     127:>KF789957,A/Montana/01/2013(H3N2)                      
 128 >KF790214,A/Idaho/23/2012(H3N2)                        ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     128:>KF790214,A/Idaho/23/2012(H3N2)                        
 129 >KF790330,A/Maryland/01/2013(H3N2)                     ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       23     21 ,     23     21     129:>KF790330,A/Maryland/01/2013(H3N2)                     
 130 >KF790001,A/Washington/50/2012(H3N2)                   ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     130:>KF790001,A/Washington/50/2012(H3N2)                   
 131 >KF790077,A/Oregon/15/2012(H3N2)                       ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G......C...................C..G.A....A.A.........................G.............G.       22     22 ,     22     22     131:>KF790077,A/Oregon/15/2012(H3N2)                       
 132 >KF789818,A/Washington/61/2012(H3N2)                   ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     132:>KF789818,A/Washington/61/2012(H3N2)                   
 133 >KF790438,A/Utah/27/2012(H3N2)                         ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..................A.......C..G.A....A.A.........................G.............G.       22     22 ,     22     22     133:>KF790438,A/Utah/27/2012(H3N2)                         
 134 >KF789590,A/Nevada/27/2012(H3N2)                       ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     134:>KF789590,A/Nevada/27/2012(H3N2)                       
 135 >KF790331,A/Washington/04/2013(H3N2)                   ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       22     21 ,     22     21     135:>KF790331,A/Washington/04/2013(H3N2)                   
 136 >KF789539,A/Michigan/01/2013(H3N2)                     ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     136:>KF789539,A/Michigan/01/2013(H3N2)                     
 137 >KF790516,A/Washington/53/2012(H3N2)                   ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       22     21 ,     22     21     137:>KF790516,A/Washington/53/2012(H3N2)                   
 138 >KF790307,A/Missouri/02/2013(H3N2)                     ................T...............A.T.............T................G..T..G..G..A....G..............T...........A.................G...........G..........................C..G.A....A.A.........................G.............G.       21     21 ,     21     21     138:>KF790307,A/Missouri/02/2013(H3N2)                     
 139 >KF790076,A/Nebraska/02/2013(H3N2)                     ................T...............A.T.............T................G..T..G..G..A....G.............GT...........A.................G...........G.................T........C..G.A....A.A.........................G.............G.       24     23 ,     24     23     139:>KF790076,A/Nebraska/02/2013(H3N2)                     
 140 >KF789623,A/Kentucky/03/2013(H3N2)                     ................T........G......A.T.............T...........A....G..T..G..G..A..................GT...........A.................G......T....G..........................C....A....A...........................G.............G.       23     22 ,     23     22     140:>KF789623,A/Kentucky/03/2013(H3N2)                     
 141 >KF789597,A/Alabama/24/2012(H3N2)                      ................T........G......A.T.............T...........A....G..T..G..G..A..................GT...........A.................G......T....G..........................C....A....A...........................G.............G.       22     22 ,     22     22     141:>KF789597,A/Alabama/24/2012(H3N2)                      
 142 >KF790114,A/Alabama/17/2012(H3N2)                      ................T........G......A.T.............T...........A....G..T..G..G..A..................GT...........A.................G......T....G..........................C....A....A...........................G.............G.       22     22 ,     22     22     142:>KF790114,A/Alabama/17/2012(H3N2)                      
 143 >KF789600,A/Montana/13/2012(H3N2)                      ................T........G......A.T.............T...........A....G..T..G..G..A..................GT...........A.................G......T....G..........................C....A....A...........................G.............G.       23     22 ,     23     22     143:>KF789600,A/Montana/13/2012(H3N2)                      
 144 >KF790351,A/Kentucky/01/2013(H3N2)                     ................T........G......A.T.............T...........A....G..T..G..G..A..................GT...........A.................G......T....G..........................C....A....A...........................G.............G.       22     22 ,     22     22     144:>KF790351,A/Kentucky/01/2013(H3N2)                     
 145 >KF790257,A/Alabama/18/2012(H3N2)                      ................T........G......A.T.............T...........A....G..T..G..G..A..................GT...........A.................G......T....G..........................C....A....A...........................G.............G.       23     22 ,     23     22     145:>KF790257,A/Alabama/18/2012(H3N2)                      
 146 >KF789662,A/Alabama/17/2012(H3N2)                      ................T........G......A.T.............T...........A....G..T..G..G..A..................GT...........A.................G......T....G..........................C....A....A...........................G.............G.       22     22 ,     22     22     146:>KF789662,A/Alabama/17/2012(H3N2)                      
 147 >KF789949,A/New York/04/2013(H3N2)                     ......C.........T........G......A.T.............T...........A....G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.........T...G.       23     23 ,     23     23     147:>KF789949,A/New York/04/2013(H3N2)                     
 148 >KF789879,A/Virginia/03/2013(H3N2)                     ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       20     20 ,     20     20     148:>KF789879,A/Virginia/03/2013(H3N2)                     
 149 >KF790010,A/Wisconsin/08/2013(H3N2)                    ................T........G......A.T.............T....C...........G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       22     21 ,     22     21     149:>KF790010,A/Wisconsin/08/2013(H3N2)                    
 150 >KF790389,A/Minnesota/04/2013(H3N2)                    ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       22     20 ,     22     20     150:>KF790389,A/Minnesota/04/2013(H3N2)                    
 151 >KF789968,A/Florida/21/2013(H3N2)                      ................T........G......A.T.............T................G..T..G..G..A......A............T...........A.................G...........G.............A............C....A....A...........................G.............G.       22     21 ,     22     21     151:>KF789968,A/Florida/21/2013(H3N2)                      
 152 >KF790032,A/Florida/08/2013(H3N2)                      ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       20     20 ,     20     20     152:>KF790032,A/Florida/08/2013(H3N2)                      
 153 >KF790037,A/North Dakota/02/2013(H3N2)                 ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A.A..............C..........G.............G.       22     22 ,     22     22     153:>KF790037,A/North Dakota/02/2013(H3N2)                 
 154 >KF789840,A/California/18/2013(H3N2)                   ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A................C..........G.............G.       21     21 ,     21     21     154:>KF789840,A/California/18/2013(H3N2)                   
 155 >KF789874,A/Massachusetts/15/2012(H3N2)                ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       21     20 ,     21     20     155:>KF789874,A/Massachusetts/15/2012(H3N2)                
 156 >KF789888,A/New Jersey/05/2013(H3N2)                   ............G...T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       21     21 ,     21     21     156:>KF789888,A/New Jersey/05/2013(H3N2)                   
 157 >KF790256,A/Pennsylvania/20/2012(H3N2)                 ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       20     20 ,     20     20     157:>KF790256,A/Pennsylvania/20/2012(H3N2)                 
 158 >KF790403,A/Delaware/08/2013(H3N2)                     ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       21     20 ,     21     20     158:>KF790403,A/Delaware/08/2013(H3N2)                     
 159 >KF789822,A/New York/47/2012(H3N2)                     ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       20     20 ,     20     20     159:>KF789822,A/New York/47/2012(H3N2)                     
 160 >KF789630,A/Wyoming/03/2013(H3N2)                      ................T.A......G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       21     21 ,     21     21     160:>KF789630,A/Wyoming/03/2013(H3N2)                      
 161 >KF790039,A/New York/05/2013(H3N2)                     ................T........G......A.T.............T................G..T..G..G..A...................T...........A.................G...........G.............A............C....A....A.........T...............A.G.............G.       22     22 ,     22     22     161:>KF790039,A/New York/05/2013(H3N2)                     
 162 >KF789660,A/Maryland/06/2013(H3N2)                     ................T........G......A.T.............T................G..T..G..G..A...................T.........T.A.................G...........G..........................C....A....A.........T.................G.............G.       24     21 ,     24     21     162:>KF789660,A/Maryland/06/2013(H3N2)                     
 163 >KF789591,A/New Jersey/04/2012(H3N2)                   ................T........G......A.T.............T.T.................T..G..G..A...................T...........A.................G...........G..........................C....A....A...........................GA.......C....G.       21     21 ,     21     21     163:>KF789591,A/New Jersey/04/2012(H3N2)                   
 164 >KF789671,A/New Jersey/08/2012(H3N2)                   ................T........G......A.T.............T...................T..G..G..A...................T...........A.................G...........G.............A............C....A....A...........................G.............G.       20     19 ,     20     19     164:>KF789671,A/New Jersey/08/2012(H3N2)                   
 165 >KC892601,A/Alaska/04/2012(H3N2)                       ................T..G.....G......A.T.............T..................TT.....G.GA...................T...........A.................G...........G..........................C....A...G..................T.........G.............G.       21     21 ,     21     21     165:>KC892601,A/Alaska/04/2012(H3N2)                       
 166 >KF790088,A/Alaska/04/2012(H3N2)                       ................T..G.....G......A.T.............T..................TT.....G.GA.............T.....T...........A........G........G...........G..........................C....A...G..................T.........G.............G.       24     23 ,     24     23     166:>KF790088,A/Alaska/04/2012(H3N2)                       
 167 >KF790275,A/Arizona/09/2012(H3N2)                      ................T........G..C...A.T........T....T...................T.....G..A.............TT....T...........A.....A..S........G...A.......G......C...................C....A................................G.............G.       24     24 ,     24     24     167:>KF790275,A/Arizona/09/2012(H3N2)                      
 168 >KF790270,A/Arizona/09/2012(H3N2)                      ................T........G..C...A.T........T....T...................T.....G..A..............T....T...........A.....A...........G...A.......G......C...................C....A................................G.............G.       22     22 ,     22     22     168:>KF790270,A/Arizona/09/2012(H3N2)                      
 169 >KF790286,A/Indiana/161/2012(H3N2)                     ................T........G..C...A.T........T....T...................T.....G..A..............T....T...........AG....A...........G...A.......G......C...................C....A................................G.............G.       24     23 ,     24     23     169:>KF790286,A/Indiana/161/2012(H3N2)                     
 170 >KF789871,A/Michigan/02/2013(H3N2)                     ................T........G......A.T........T....T...................TT....GC.A........C..........T...........AG....A...........G...A.......G......C...................C....A................................GA............G.       26     25 ,     26     25     170:>KF789871,A/Michigan/02/2013(H3N2)                     
 171 >KF790011,A/Oklahoma/08/2013(H3N2)                     ................T........G......A.T........T....T...................T.....G..A........C..........T...........A.....A...........G...A.......G......C...................C....A................................G.............G.       23     21 ,     23     21     171:>KF790011,A/Oklahoma/08/2013(H3N2)                     
 172 >KF790345,A/Indiana/01/2013(H3N2)                      ................T........G......A.T........T....T...................T.....G..A........C..........T...........A.....A...........G...A.......G......C...................C....A................................G.............G.       22     21 ,     22     21     172:>KF790345,A/Indiana/01/2013(H3N2)                      
 173 >KF789998,A/Montana/10/2012(H3N2)                      ................T........G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G......C...........A.......C....A.............G..................G.............G.       22     22 ,     22     22     173:>KF789998,A/Montana/10/2012(H3N2)                      
 174 >KF789613,A/North Carolina/04/2013(H3N2)               ................T....G...G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G......C...................C....A................................G.............G.       22     21 ,     22     21     174:>KF789613,A/North Carolina/04/2013(H3N2)               
 175 >KF790378,A/Alaska/05/2013(H3N2)                       ................T........G......A.T........T....T...................T.....G..A...................T...G.......A.....A...........G...A.......G......C...................C....A................................G.............G.       21     21 ,     21     21     175:>KF790378,A/Alaska/05/2013(H3N2)                       
 176 >KF790109,A/Delaware/10/2012(H3N2)                     ................T........G......A.T........T....T...................T.....G..A.......T...........T...........A.....A...........G...A.......G......C...................C....A................................G.............G.       21     21 ,     21     21     176:>KF790109,A/Delaware/10/2012(H3N2)                     
 177 >KF790429,A/Delaware/11/2012(H3N2)                     ................T........G......A.T........T....T...................T.....G..A.......T...........T...........A.....A...........G...A.......G......C...................C....A................................G.............G.       21     21 ,     21     21     177:>KF790429,A/Delaware/11/2012(H3N2)                     
 178 >KF789701,A/Delaware/01/2013(H3N2)                     ................T........G......A.T........T....T...................T.....G..A.......T...........T...........A.....A...........G...A.......G......C...................C....A................................G.............G.       21     21 ,     21     21     178:>KF789701,A/Delaware/01/2013(H3N2)                     
 179 >KF790440,A/Delaware/15/2012(H3N2)                     ................T........G......A.T........T....T...................T.....G..A.......T...........T...........A.....A...........G...A.......G......C...................C....A................................G.............G.       21     21 ,     21     21     179:>KF790440,A/Delaware/15/2012(H3N2)                     
 180 >KF789569,A/Alaska/06/2013(H3N2)                       ................T........G......A.T........T....T....C..............T.....G..A...................T...........A.....A...........G...A.......G......C...................C....A................................G.............G.       21     21 ,     21     21     180:>KF789569,A/Alaska/06/2013(H3N2)                       
 181 >KF790167,A/Washington/52/2012(H3N2)                   ................T........G......A.T........T....T....C..............T.....G..A...................T...........A.....A...........G...A.......G..........................C....A................................G.............G.       20     20 ,     20     20     181:>KF790167,A/Washington/52/2012(H3N2)                   
 182 >KF789780,A/Kansas/14/2012(H3N2)                       ................T........G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G.G........................C....A................................G.............G.       20     20 ,     20     20     182:>KF789780,A/Kansas/14/2012(H3N2)                       
 183 >KF790464,A/Oklahoma/05/2013(H3N2)                     ................T........G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G.G........................C....A................................G.............G.       20     20 ,     20     20     183:>KF790464,A/Oklahoma/05/2013(H3N2)                     
 184 >KF790360,A/Oklahoma/05/2013(H3N2)                     ................T........G......A.T........T....T...................T.....G..A.............T.....T......Y....A.....A...........G...A.......G.G........................C....A................................G.............G.       22     22 ,     22     22     184:>KF790360,A/Oklahoma/05/2013(H3N2)                     
 185 >KF790197,A/Florida/40/2012(H3N2)                      ................T........G......A.T........T....T..A................T.....G..A.A...........T.....T...........A.....A...........G...A.......G..........................C....A................................G.............G.       23     22 ,     23     22     185:>KF790197,A/Florida/40/2012(H3N2)                      
 186 >KF789661,A/Hawaii/24/2012(H3N2)                       ................T........G......A.T........T....T..A................T.....G..A...................T.........Y.A.....A...........G...A.......G..........................C....A................................G.............G.       22     21 ,     22     21     186:>KF789661,A/Hawaii/24/2012(H3N2)                       
 187 >KF790064,A/Vermont/28/2012(H3N2)                      ...G............T........G......A.T........T....T..A................T.....G..A.................C.T...........A.....A...........G...A.......G..........................C....A................................G.............G.       23     22 ,     23     22     187:>KF790064,A/Vermont/28/2012(H3N2)                      
 188 >KF790084,A/Vermont/28/2012(H3N2)                      ...G............T........G......A.T........T....T..A................T.....G..A...................T...........AR....A...........G...A.......G..........................C....A................................G.............G.       22     22 ,     22     22     188:>KF790084,A/Vermont/28/2012(H3N2)                      
 189 >KF789714,A/Texas/91/2012(H3N2)                        ................T........G......A.T........T....T.T.................T.....G..A...................T...........AG....A...........G...A.......G..........................C....A................................G.............G.       21     21 ,     21     21     189:>KF789714,A/Texas/91/2012(H3N2)                        
 190 >KF789614,A/Maryland/03/2013(H3N2)                     ................T........G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G..........................C....A.................A..............G.............G.       21     20 ,     21     20     190:>KF789614,A/Maryland/03/2013(H3N2)                     
 191 >KF790356,A/Utah/02/2013(H3N2)                         ................T........G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G..........................C....A................................G.............G.       20     19 ,     20     19     191:>KF790356,A/Utah/02/2013(H3N2)                         
 192 >KF790153,A/California/04/2013(H3N2)                   ................T........G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G..........................C....A................................G.............G.       20     19 ,     20     19     192:>KF790153,A/California/04/2013(H3N2)                   
 193 >KF790457,A/New Mexico/05/2013(H3N2)                   ................T........G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G..........................C....A................................G.............G.       19     19 ,     19     19     193:>KF790457,A/New Mexico/05/2013(H3N2)                   
 194 >KF789684,A/Rhode Island/09/2012(H3N2)                 ................T........G......A.T........T....T........A..........T.....G..A...................T.........M.A.....A...........G...A.......G..........................C....A................................G.............G.       21     21 ,     21     21     194:>KF789684,A/Rhode Island/09/2012(H3N2)                 
 195 >KF789547,A/Pennsylvania/03/2013(H3N2)                 ................T........G......A.T........T....T........A..........T.....G..A...................T...........A.....A.....A.....G...A.......G..........................C....A................................G.............G.       22     21 ,     22     21     195:>KF789547,A/Pennsylvania/03/2013(H3N2)                 
 196 >Index/32g12f1.c2,10-37                                ................T........G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G..........................C....A................................G.............G.       19     19 ,     19     19     196:>Index/32g12f1.c2,10-37                                
 197 >KF789752,A/Oregon/12/2012(H3N2)                       ................T........G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G..........................C....A................................G.............G.       22     19 ,     22     19     197:>KF789752,A/Oregon/12/2012(H3N2)                       
 198 >KF790532,A/Maryland/05/2013(H3N2)                     .............A..T........G......A.T........T....T...................T..G..G..A...................T...........A.....A....A......G...A.......G..........................C....A................................G.............G.       22     22 ,     22     22     198:>KF790532,A/Maryland/05/2013(H3N2)                     
 199 >KF790316,A/District Of Columbia/02/2012(H3N2)         .............A..T........G......A.T...C....T....T...................T..G..G..A...................T........A..A.....A....A......G...A.......G..........................C....A................................G.............G.       24     24 ,     24     24     199:>KF790316,A/District Of Columbia/02/2012(H3N2)         
 200 >KF790361,A/Florida/12/2013(H3N2)                      .............A..T........G......A.T........T....T...................T.....G..A...................T...........A.....A....A......G...A.......G........C.................C....A................................G.............G.       22     22 ,     22     22     200:>KF790361,A/Florida/12/2013(H3N2)                      
 201 >KF789618,A/Nebraska/06/2013(H3N2)                     .............A..T........G......A.T........T....T...................T.....G..A...................T...........A.....A....A......G...A.......G..........................C....A................................G.............G.       22     21 ,     22     21     201:>KF789618,A/Nebraska/06/2013(H3N2)                     
 202 >KF790106,A/Kentucky/16/2012(H3N2)                     ......C......A..T........G......A.T........T....T...................T.....G..A...................T...........A.....A....A......G...A.......G..........................C....A................................G.............G.       22     22 ,     22     22     202:>KF790106,A/Kentucky/16/2012(H3N2)                     
 203 >KF790059,A/Texas/111/2012(H3N2)                       ................T........G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G..........................C....A................................G.............G.       19     19 ,     19     19     203:>KF790059,A/Texas/111/2012(H3N2)                       
 204 >KF790060,A/Texas/81/2012(H3N2)                        ................T........G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G.............A............C....A................................G.............G.       20     20 ,     20     20     204:>KF790060,A/Texas/81/2012(H3N2)                        
 205 >KF790448,A/California/42/2012(H3N2)                   ................T........G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G.............A............C....A................................G.............G.       21     20 ,     21     20     205:>KF790448,A/California/42/2012(H3N2)                   
 206 >KF789535,A/California/15/2013(H3N2)                   ................T........G......A.T........T...AT...................T.G...G..A...................T...........A.....A...........G...A.......G..........................C....A................................G..A..........G.       22     22 ,     22     22     206:>KF789535,A/California/15/2013(H3N2)                   
 207 >KF789725,A/Montana/14/2012(H3N2)                      ................T........G......A.T........T...AT...................T.G...G..A...................T...........A.....A...........G...A.......G..........................C....A................................G..A..........G.       22     22 ,     22     22     207:>KF789725,A/Montana/14/2012(H3N2)                      
 208 >KF789982,A/New York/35/2012(H3N2)                     ................T........G......A.T........T....T...................T.....G..A...................T...........A.....A...........G...A.......G..........................C....A................................G.............G.       22     19 ,     22     19     208:>KF789982,A/New York/35/2012(H3N2)                     
 209 >KF790049,A/Texas/01/2013(H3N2)                        ................T........G......A.T.............T...................TT....G..A...................T...........A.....A...........G...A.......G..........................C....A................................G...............       18     18 ,     18     18     209:>KF790049,A/Texas/01/2013(H3N2)                        
 210 >KF790524,A/Maryland/33/2012(H3N2)                     ................T........G......A.T.............T...................T.....G..A...................T...........A.................G......T....G..................A.....A.C....A................................G.............G.       22     19 ,     22     19     210:>KF790524,A/Maryland/33/2012(H3N2)                     
 211 >KF790325,A/Delaware/07/2013(H3N2)                     ................T........G......T.T.............T...................T...A.G..A...................T...........AR................G...........G..........................C....A................................G.............G.       18     18 ,     18     18     211:>KF790325,A/Delaware/07/2013(H3N2)                     
 212 >KF789664,A/Maryland/29/2012(H3N2)                     ................T........G......A.T.............T...................T.....G..A...................T...........A.................G...........G..........................C....A...........................G....G.............G.       18     17 ,     18     17     212:>KF789664,A/Maryland/29/2012(H3N2)                     
 213 >Index/32g12f1.c2,38-41                                ................T........G......A.T....A........T..............A....T.....G..A..............A....T...........A.................G...........G..........................C....A...............................GG.............G.       23     20 ,     23     20     213:>Index/32g12f1.c2,38-41                                
 214 >KF790138,A/North Carolina/02/2013(H3N2)               ................T........G......A.T..G..........T...................T.....G..A...................T...........A.................G....C......G..........................C....A...............................GG.............G.       20     19 ,     20     19     214:>KF790138,A/North Carolina/02/2013(H3N2)               
 215 >KF789615,A/Oklahoma/06/2013(H3N2)                     ................T........G......A.T...........A.T...................T.....G..A...................T...........A.................G....C......G..........................C....A...............................GG............GG.       20     20 ,     20     20     215:>KF789615,A/Oklahoma/06/2013(H3N2)                     
 216 >KF790019,A/New Mexico/08/2013(H3N2)                   ................T........G......A.T.............T...................T.....G..A...................T...........A.................G....C......G..........................C....A...............................GG............GG.       21     19 ,     21     19     216:>KF790019,A/New Mexico/08/2013(H3N2)                   
 217 >KF790398,A/District Of Columbia/01/2013(H3N2)         ................T........G......A.T.............T...................T.....G..A...................T...........A.................G...........G.........................CC....A...............................GG.............G.       20     18 ,     20     18     217:>KF790398,A/District Of Columbia/01/2013(H3N2)         
 218 >KF789571,A/Alabama/07/2013(H3N2)                      ................T........G...C..A.T.........C...T...................T.....G..A...................T.....A.....A.................G...........G.....G.G.T................C....A.A............................AGG...........A.G.       26     26 ,     26     26     218:>KF789571,A/Alabama/07/2013(H3N2)                      
 219 >KF789550,A/Nevada/04/2013(H3N2)                       ................T........G...C..A.T.........C...T...................T.....G..A...................T.....A.....A.........C.......G...........G.....G...T................C....A.A............................AGG...........A.G.       30     26 ,     30     26     219:>KF789550,A/Nevada/04/2013(H3N2)                       
 220 >KF789579,A/Indiana/164/2012(H3N2)                     ................T........G...C..A.T.............T...................T.....G..A...................T.....A.....A.........G.......G...........G.....G...T................C....A.A......................A.....AGG...........A.G.       26     26 ,     26     26     220:>KF789579,A/Indiana/164/2012(H3N2)                     
 221 >KF790244,A/Indiana/162/2012(H3N2)                     ................T........G...C..A.T.............T...................T.....G..A...................T.....A.....A.........G.......G...........G.....G...T................C....A.A......................A.....AGG...........A.G.       28     26 ,     28     26     221:>KF790244,A/Indiana/162/2012(H3N2)                     
 222 >KF790205,A/Colorado/18/2012(H3N2)                     ..........T.....T........G...C..A.T.............T...................T.....G..A.............T.....T.....A.....A.................G...........G.........T................C....A...............A..............AGG...........A.G.       26     25 ,     26     25     222:>KF790205,A/Colorado/18/2012(H3N2)                     
 223 >KF790104,A/Colorado/18/2012(H3N2)                     ..........T.....T........G...C..A.T.............T...................T.....G..A...................T.....A.....A.................G...........G.........T................C....A...............A..............AGG...........A.G.       24     24 ,     24     24     223:>KF790104,A/Colorado/18/2012(H3N2)                     
 224 >KF789582,A/North Carolina/24/2012(H3N2)               ................T........G...C..A.T.............T...................T.....G..A...................T.....A.....A.................G...........G..........................C....A..............................AGG.............G.       22     20 ,     22     20     224:>KF789582,A/North Carolina/24/2012(H3N2)               
 225 >KF790452,A/South Dakota/01/2013(H3N2)                 ..A.............T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AGG...T......A..GA       26     26 ,     26     26     225:>KF790452,A/South Dakota/01/2013(H3N2)                 
 226 >KF789923,A/North Dakota/08/2012(H3N2)                 ..A.............T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AGG...T..........A       25     24 ,     25     24     226:>KF789923,A/North Dakota/08/2012(H3N2)                 
 227 >KF790135,A/New York/03/2013(H3N2)                     ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AGG...T...........       22     22 ,     22     22     227:>KF790135,A/New York/03/2013(H3N2)                     
 228 >KF789769,A/Ohio/102/2012(H3N2)                        ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AGG...T.........G.       24     23 ,     24     23     228:>KF789769,A/Ohio/102/2012(H3N2)                        
 229 >KF789546,A/California/13/2013(H3N2)                   ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AG....T.........G.       22     22 ,     22     22     229:>KF789546,A/California/13/2013(H3N2)                   
 230 >KF789689,A/Nebraska/11/2012(H3N2)                     ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AGG...T.........G.       23     23 ,     23     23     230:>KF789689,A/Nebraska/11/2012(H3N2)                     
 231 >KF789722,A/Ohio/97/2012(H3N2)                         ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.....A...........G...........G..........................C....A.........T....................AGG...T.........G.       25     24 ,     25     24     231:>KF789722,A/Ohio/97/2012(H3N2)                         
 232 >KF789709,A/Missouri/04/2013(H3N2)                     ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.....A...........G...........G..........................C....A.........T....................AGG...T.........G.       24     24 ,     24     24     232:>KF789709,A/Missouri/04/2013(H3N2)                     
 233 >KF789605,A/West Virginia/20/2012(H3N2)                ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.....A...........G...........G..........................C....A.........T.C..................AGG...T.........G.       25     25 ,     25     25     233:>KF789605,A/West Virginia/20/2012(H3N2)                
 234 >KF790125,A/Missouri/04/2013(H3N2)                     ................T........G......A.T.......T.....T...................TT....G..A..........A......C.T.....A.....A.....A...........G...........G..........................C....A.........T....................AGG...T.........G.       26     26 ,     26     26     234:>KF790125,A/Missouri/04/2013(H3N2)                     
 235 >KF789728,A/North Carolina/05/2013(H3N2)               ................T........G......A.T.......T.....T...................TT....G..A..........A........T.....A.....AG................G...........G...............A..........C....A.........T....................AGG...T.........G.       29     26 ,     29     26     235:>KF789728,A/North Carolina/05/2013(H3N2)               
 236 >KF790323,A/New Mexico/23/2012(H3N2)                   ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....AG................G...........G..........................C....A.........T....................AGG...T.........G.       26     24 ,     26     24     236:>KF790323,A/New Mexico/23/2012(H3N2)                   
 237 >KF790190,A/Michigan/25/2012(H3N2)                     ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....AG................G...........G..........................C....A.........T....................AGG...T.........G.       24     24 ,     24     24     237:>KF790190,A/Michigan/25/2012(H3N2)                     
 238 >KF789732,A/Vermont/19/2012(H3N2)                      ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AGG...T.........G.       23     23 ,     23     23     238:>KF789732,A/Vermont/19/2012(H3N2)                      
 239 >KF789646,A/Idaho/02/2013(H3N2)                        ................T........G......A.T.......T.....T..............A....T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AGG...T.........G.       25     24 ,     25     24     239:>KF789646,A/Idaho/02/2013(H3N2)                        
 240 >KF790054,A/California/46/2012(H3N2)                   ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AGG...T.........G.       23     23 ,     23     23     240:>KF790054,A/California/46/2012(H3N2)                   
 241 >KF790454,A/Nevada/02/2013(H3N2)                       ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AGG...T.........G.       25     23 ,     25     23     241:>KF790454,A/Nevada/02/2013(H3N2)                       
 242 >KF789953,A/Ohio/01/2013(H3N2)                         ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AGG...T.........G.       23     23 ,     23     23     242:>KF789953,A/Ohio/01/2013(H3N2)                         
 243 >KF790509,A/California/11/2013(H3N2)                   ................T........G......A.T.......T.....T...................T.....G..A..........A........T...C.A.....A.................G...........G..........................C....A.........T....................AGG...T.........G.       26     24 ,     26     24     243:>KF790509,A/California/11/2013(H3N2)                   
 244 >KF790213,A/Iowa/13/2012(H3N2)                         ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AGG...T.........G.       23     23 ,     23     23     244:>KF790213,A/Iowa/13/2012(H3N2)                         
 245 >KF790512,A/Idaho/01/2013(H3N2)                        ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AGG.T.T.........G.       25     24 ,     25     24     245:>KF790512,A/Idaho/01/2013(H3N2)                        
 246 >KF789826,A/Washington/62/2012(H3N2)                   ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G...........G..........................C....A.........T....................AGG...T.........G.       23     23 ,     23     23     246:>KF789826,A/Washington/62/2012(H3N2)                   
 247 >KF790446,A/Wyoming/20/2012(H3N2)                      ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G.....A.....G..........................C....A.........T....................AGG...T.........G.       24     24 ,     24     24     247:>KF790446,A/Wyoming/20/2012(H3N2)                      
 248 >KF789775,A/South Dakota/12/2012(H3N2)                 ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G.....A.....G..........................C....A.........T....................AGG...T.........G.       24     24 ,     24     24     248:>KF789775,A/South Dakota/12/2012(H3N2)                 
 249 >KF789688,A/South Dakota/10/2012(H3N2)                 ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G.....A.....G..........................C....A.........T....................AGG...T.........G.       24     24 ,     24     24     249:>KF789688,A/South Dakota/10/2012(H3N2)                 
 250 >KF789791,A/South Dakota/14/2012(H3N2)                 ................T........G......A.T.......T.....T...................T.....G..A..........A........T.....A.....A.................G.....A.....G..........................C....A.........T....................AGG...T.........G.       24     24 ,     24     24     250:>KF789791,A/South Dakota/14/2012(H3N2)                 
 251 >KF789794,A/South Dakota/12/2012(H3N2)                 ................T........G......A.T.......T.....T...................T.....G..A..........A..T.....T.....A.....A........G........G.....A.....G..........................C....A.........T....................AGG...T.........G.       26     26 ,     26     26     251:>KF789794,A/South Dakota/12/2012(H3N2)                 
 252 >KF790051,A/South Dakota/15/2012(H3N2)                 ................T........G......A.T.......T.....T...................T........A..........A..T.....T.....AA....A.................G.....A.....G..........................C....A.........T....................AGG...T.........G.       25     25 ,     25     25     252:>KF790051,A/South Dakota/15/2012(H3N2)                 
 253 >KF790373,A/Ohio/01/2013(H3N2)                         ................T........G......A.T.......T.....T...................T.....G..A.A........A..T.....T.....A.....A.......M.........G...........G..........................C....A.........T....................AGG...T.........G.       26     26 ,     26     26     253:>KF790373,A/Ohio/01/2013(H3N2)                         
 254 >KF790009,A/South Dakota/16/2012(H3N2)                 ................T........G......A.T.......T.....T...................T.....G..A.M........A..T.R...T.....A.....A........R........G...........G..........................C....A.........T....................AGG...T.........G.       27     27 ,     27     27     254:>KF790009,A/South Dakota/16/2012(H3N2)                 
 255 >KF790141,A/Georgia/03/2013(H3N2)                      ................T........G......A.T.............T...................T.....G..A.............T.....T.....A.A...A........M........G...........G..C.......................C....A.................A........A...AGG.............G.       25     25 ,     25     25     255:>KF790141,A/Georgia/03/2013(H3N2)                      
 256 >KF789884,A/Georgia/03/2013(H3N2)                      ................T........G......A.T.............T...................T.....G..A...................T.....A.A...A.................G...........G..C.......................C....A.................A........A...AGG.............G.       23     23 ,     23     23     256:>KF789884,A/Georgia/03/2013(H3N2)                      
 257 >KF790115,A/Kansas/04/2013(H3N2)                       ................T........G......A.T.............T...................T.....G..A..............A....T.....A.....AR................G...........G..C........A.A............C....A........................T.A...AGG.............G.       28     26 ,     28     26     257:>KF790115,A/Kansas/04/2013(H3N2)                       
 258 >KF790023,A/New Mexico/09/2013(H3N2)                   ................T........G......A.T.............T...................T.....G..A..............A....T.....A.....AG................G...........G..........................C....A..........................A...AGG.............G.       22     22 ,     22     22     258:>KF790023,A/New Mexico/09/2013(H3N2)                   
 259 >KF790333,A/District Of Columbia/01/2012(H3N2)         ................T........G......A.T.............T...................T........A............A......T.....A.....A.................G...........G..........A.........C.....C....A.........................GA...AGG..A..........G.       25     24 ,     25     24     259:>KF790333,A/District Of Columbia/01/2012(H3N2)         
 260 >KF789759,A/Nevada/28/2012(H3N2)                       ................T........G......A.T.....T.......T...................T.....G..AC...........A......T.....A.....A...............C.G...........G..........A.......A.C....CC....A.........................GA...AGG..A..........G.       31     30 ,     31     30     260:>KF789759,A/Nevada/28/2012(H3N2)                       
 261 >KF790455,A/California/10/2013(H3N2)                   ................T........G......A.T.....T.......T...................T.....G..A............A......T.....A.....A......G..........G...........G........C.A.........C.....C....A.........................GA...AGG..A..........G.       30     28 ,     30     28     261:>KF790455,A/California/10/2013(H3N2)                   
 262 >KF790066,A/Colorado/01/2013(H3N2)                     ................T........G......A.T.....T.......T...................T.....G..A............A......T.....A.....A.....A...........G...........G..........A.........C.....C....A.........................GA...AGG..A..........G.       27     27 ,     27     27     262:>KF790066,A/Colorado/01/2013(H3N2)                     
 263 >KF789716,A/Colorado/21/2012(H3N2)                     ................T........G......A.T.....T.......T...................T.....G.GA............A......T.....A.....AR....A...........G...........G..........A.........C.....C....A...............A..........A...AGG.............G.       28     28 ,     28     28     263:>KF789716,A/Colorado/21/2012(H3N2)                     
 264 >KF789812,A/Illinois/15/2012(H3N2)                     ................T........G......A.T.....T.......T...................T.....G..A............A......T.....A.....AG................G...........G..........A.........C.....C....A..........................A...AGG.............G.       25     25 ,     25     25     264:>KF789812,A/Illinois/15/2012(H3N2)                     
 265 >KF790230,A/North Dakota/05/2012(H3N2)                 ................T........G......A.T.....T.......T...................T.....G..A............A......T.....A.....AG................G...........G..........A.........C.....C....A..........................A...AGG...............       24     24 ,     24     24     265:>KF790230,A/North Dakota/05/2012(H3N2)                 
 266 >KF789640,A/Vermont/02/2013(H3N2)                      ................T........G......A.T.....T.......T...................T.....G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       24     24 ,     24     24     266:>KF789640,A/Vermont/02/2013(H3N2)                      
 267 >KF790368,A/Ohio/92/2012(H3N2)                         ................T........G......A.T.....T.......T.......A...........T.....G..A............A......T.....A.....A..........A......G...........G..........A.........C.....C....A..........................A...AGG.............G.       26     26 ,     26     26     267:>KF790368,A/Ohio/92/2012(H3N2)                         
 268 >KF789656,A/Oregon/01/2013(H3N2)                       ................T........G......A.T.....T.......T...................T.....G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       24     24 ,     24     24     268:>KF789656,A/Oregon/01/2013(H3N2)                       
 269 >KF790028,A/Michigan/03/2013(H3N2)                     ................T........G......A.T.....T.......T...................T..G..G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       26     25 ,     26     25     269:>KF790028,A/Michigan/03/2013(H3N2)                     
 270 >KF789740,A/Minnesota/03/2013(H3N2)                    ................T........G......A.T.....T.......T..........G........T.....G..A............A......T.....A.....A.................G...........G..........A.........C..C..C....A..........................A...AGG.............G.       26     26 ,     26     26     270:>KF789740,A/Minnesota/03/2013(H3N2)                    
 271 >KF790473,A/New Mexico/04/2013(H3N2)                   ................TT.......G......A.T.....T.......T...................T.....G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       26     25 ,     26     25     271:>KF790473,A/New Mexico/04/2013(H3N2)                   
 272 >KF789628,A/Kansas/02/2013(H3N2)                       ................T........G......A.T.....T.......T...................T.....G..A.......T....A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       26     25 ,     26     25     272:>KF789628,A/Kansas/02/2013(H3N2)                       
 273 >KF789952,A/Illinois/01/2013(H3N2)                     ................T........G......A.T.....T.......T...................T.....G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       26     24 ,     26     24     273:>KF789952,A/Illinois/01/2013(H3N2)                     
 274 >KF790357,A/Mississippi/01/2013(H3N2)                  ................T........G......A.T.....T.......T......A............T.....G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       25     25 ,     25     25     274:>KF790357,A/Mississippi/01/2013(H3N2)                  
 275 >KF790334,A/Pennsylvania/02/2013(H3N2)                 ................T........G......A.T.....T.......T...................T.....G..A.....G......A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       25     25 ,     25     25     275:>KF790334,A/Pennsylvania/02/2013(H3N2)                 
 276 >KF790478,A/Louisiana/01/2013(H3N2)                    ................T........G......A.T.....T.......T...................T.....G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       25     24 ,     25     24     276:>KF790478,A/Louisiana/01/2013(H3N2)                    
 277 >KF789906,A/California/14/2013(H3N2)                   ................T........G......A.T.....T.......T...................T.....G..A............A......T.....A.....A.................G...........G.G........A.........C.....C....A..........................A...AGG.............G.       25     25 ,     25     25     277:>KF789906,A/California/14/2013(H3N2)                   
 278 >KF790439,A/Wisconsin/41/2012(H3N2)                    ................T........G.....AA.T.....T.......T...................T.....G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       25     25 ,     25     25     278:>KF790439,A/Wisconsin/41/2012(H3N2)                    
 279 >KF790413,A/Wisconsin/05/2013(H3N2)                    ................T........G.....AA.T.....T.......T...................T.....G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       26     25 ,     26     25     279:>KF790413,A/Wisconsin/05/2013(H3N2)                    
 280 >KF789673,A/Missouri/13/2012(H3N2)                     ................T........G.....AA.T.....T.......T...................T.....G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       25     25 ,     25     25     280:>KF789673,A/Missouri/13/2012(H3N2)                     
 281 >KF789619,A/Connecticut/01/2013(H3N2)                  ................T........G......A.T.....T.......T...................T.....G..A......A.....A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       25     25 ,     25     25     281:>KF789619,A/Connecticut/01/2013(H3N2)                  
 282 >KF790160,A/Wisconsin/38/2012(H3N2)                    ................T........G......A.T.....T.......T...................T.....G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       24     24 ,     24     24     282:>KF790160,A/Wisconsin/38/2012(H3N2)                    
 283 >KF789977,A/Oregon/01/2013(H3N2)                       ................T........G......A.T.....T.......T...................TT....G..A............A....C.T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       26     26 ,     26     26     283:>KF789977,A/Oregon/01/2013(H3N2)                       
 284 >KF790041,A/Kansas/01/2013(H3N2)                       ................T........G......A.T.....T.......T...................T.....G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       24     24 ,     24     24     284:>KF790041,A/Kansas/01/2013(H3N2)                       
 285 >KF789633,A/Louisiana/02/2013(H3N2)                    ................T........G......A.T.....T.......T...................T.....G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG..........T..G.       25     25 ,     25     25     285:>KF789633,A/Louisiana/02/2013(H3N2)                    
 286 >KF789741,A/Tennessee/02/2013(H3N2)                    ................T........G......A.T.....T.......T...................T.....G..A............A......T.....A.....A.................G...........G..........A.........C.....C....A..........................A...AGG.............G.       24     24 ,     24     24     286:>KF789741,A/Tennessee/02/2013(H3N2)                    
 287 >KF789885,A/Maine/11/2012(H3N2)                        ................T........G......A.T.....T.......T...................T.....G..A...................T.....A.....A.T...............G...........G..........A.G.......C.....C....A..........................A...AGG.............G.       25     25 ,     25     25     287:>KF789885,A/Maine/11/2012(H3N2)                        
 288 >KF789650,A/Mississippi/02/2013(H3N2)                  ................T........G......A.T.....T.......T...................T.....G..A...................T.....A.....A.T...............G...........G..........A.G.......C.....C....A..........................A...AGG.............G.       25     25 ,     25     25     288:>KF789650,A/Mississippi/02/2013(H3N2)                  
 289 >KF790517,A/California/12/2013(H3N2)                   C...............T........G......A.T.....T.......T...................T.....G..A...................T.....A.....A.T...............G...........G..........A.G.......C.....C....A..........................A...AGG.............G.       26     26 ,     26     26     289:>KF790517,A/California/12/2013(H3N2)                   
 290 >KF789787,A/Michigan/32/2012(H3N2)                     ................T........G......A.T.....T.......T...................T.....G..A...................T.....A.....A.T...............G...........G..........A.G.......C.....C....A..........................A...AGG.............G.       25     25 ,     25     25     290:>KF789787,A/Michigan/32/2012(H3N2)                     
 291 >KF790155,A/Minnesota/05/2013(H3N2)                    ................T........G......A.T..G..........T...................T.....G..A...................T.....A.....A.................G..........AG..........................C....A..........................A...AGG.............G.       25     22 ,     25     22     291:>KF790155,A/Minnesota/05/2013(H3N2)                    
 292 >KF789739,A/California/22/2013(H3N2)                   ................T........G......A.T.............TC..................T.....G..A.....G.............T.....A.....A.................G...........G.................T........C....A.......................T..A...AGG.............G.       24     24 ,     24     24     292:>KF789739,A/California/22/2013(H3N2)                   
 293 >KF790391,A/Alaska/04/2013(H3N2)                       ................T........G......A.T.............T...................T.....G..A...................T.....A.....A.................G...........G..........................C....A..........................A...AGG.............G.       22     20 ,     22     20     293:>KF790391,A/Alaska/04/2013(H3N2)                       
 294 >KF790036,A/Nevada/05/2013(H3N2)                       ................T........G......A.T.............T...................T.....G..A...................T.....A.....A.................G...........G..........................C....A..........................A...AGG.............G.       20     20 ,     20     20     294:>KF790036,A/Nevada/05/2013(H3N2)                       
 295 >KF790500,A/Kansas/11/2012(H3N2)                       ................T........G......A.T.............T.......A...........T.....G..A...................T.....A.....A.................G...........G..........................C....A..........................A...AGG.............G.       22     21 ,     22     21     295:>KF790500,A/Kansas/11/2012(H3N2)                       
 296 >KF790100,A/Wyoming/18/2012(H3N2)                      ................T........G......A.T.............T...A...............T.....G..A...................T...........A.................G...........G..........................C....A..................A............GG.............G.       21     19 ,     21     19     296:>KF790100,A/Wyoming/18/2012(H3N2)                      
 297 >KF789667,A/Maryland/30/2012(H3N2)                     ................T........G......A.T.................................T.....G..A..............T....T.....T.....A..T..............G...........G..........................C....A..................A.....................G.....G.       20     19 ,     20     19     297:>KF789667,A/Maryland/30/2012(H3N2)                     
 298 >KF790432,A/Oregon/11/2012(H3N2)                       ....T...........T........G......A.T.................................T.....G..A...................T.....T.....A..T..............G...........G..........................C....A..................A.....................G.....G.       21     19 ,     21     19     298:>KF790432,A/Oregon/11/2012(H3N2)                       
 299 >KF790229,A/Oklahoma/05/2012(H3N2)                     ....T...........T........G......A.T.................................T.....G..A...................T.....T.....A..T..............G...........G..........................C....A..................A.....................G.....G.       19     19 ,     19     19     299:>KF790229,A/Oklahoma/05/2012(H3N2)                     
 300 >A/Czech Republic/121/2012,2012/03/06,Czech Republic   ................T........G......A.T......C.....................A....T........A...................T...........A.T...............G...........G..........................C....A..............................................G.       18     16 ,     18     16     300:>A/Czech Republic/121/2012,2012/03/06,Czech Republic   
 301 >KF790228,A/Hawaii/30/2012(H3N2)                       ........A.......T........G......A.T.................................T........A..C................T........T..A.................G...........G.............A..C.........C...TA..............................................G.       19     19 ,     19     19     301:>KF790228,A/Hawaii/30/2012(H3N2)                       
 302 >KF790430,A/Massachusetts/07/2012(H3N2)                ........A.......T........G......A.T.................................T........A..C................T........S..AR................G...........G.........T...A..C.........C...TA..............................................G.       23     21 ,     23     21     302:>KF790430,A/Massachusetts/07/2012(H3N2)                
 303 >KF790502,A/Pennsylvania/21/2012(H3N2)                 ........A.......T........G......A.T.................................T........A..C................T...........A.................G..C........G.........T...A..C.........C...TA..............................................G.       20     20 ,     20     20     303:>KF790502,A/Pennsylvania/21/2012(H3N2)                 
 304 >KF790461,A/New Mexico/03/2013(H3N2)                   ........A.......T........G......A.T.................................T........A..C................T.........Y.A.................G..C........G.........T...A..C.........C...TA..............................................G.       23     21 ,     23     21     304:>KF790461,A/New Mexico/03/2013(H3N2)                   
 305 >KF790262,A/New Hampshire/12/2012(H3N2)                ........A.......T........G......A.T.................................T........A..C................T...........A.................G..C........G.........T...A..C.........C...TA..............................................G.       20     20 ,     20     20     305:>KF790262,A/New Hampshire/12/2012(H3N2)                
 306 >KF789668,A/New Hampshire/11/2012(H3N2)                ........A.......T........G......A.T.................................T........A..C................T...........A.................G...........G.........T...A..C.........C...TA..............................................G.       19     19 ,     19     19     306:>KF789668,A/New Hampshire/11/2012(H3N2)                
 307 >KF790236,A/New York/38/2012(H3N2)                     ........A.......T........G......A.T.................................T........A..C..............C.T...........A.................G...........G.........T...A..C.........C...TA..............................................G.       20     20 ,     20     20     307:>KF790236,A/New York/38/2012(H3N2)                     
 308 >KF789870,A/New Hampshire/11/2012(H3N2)                ........A.......T........G......A.T.................................T........A..C..............C.T...........A.................G...........G.........T...A..C.........C...TA..............................................G.       20     20 ,     20     20     308:>KF789870,A/New Hampshire/11/2012(H3N2)                
 309 >KF790282,A/New York/38/2012(H3N2)                     ........A.......T........G......A.T.................................T........A..C................T...........A.................G...........G.........T...A..C.........C...TA..............................................G.       19     19 ,     19     19     309:>KF790282,A/New York/38/2012(H3N2)                     
 310 >KF789989,A/Hawaii/26/2012(H3N2)                       ........A.......T........G......A.T.................................T........A..C................T...........A.................G...........G.............A..C.........C...TA..............................................G.       18     18 ,     18     18     310:>KF789989,A/Hawaii/26/2012(H3N2)                       
 311 >KF790171,A/Hawaii/28/2012(H3N2)                       ........A.......T........G......A.T.................................T........A..C................T...........A.................G...........G.............A..C.........C...TA..............................................G.       19     18 ,     19     18     311:>KF790171,A/Hawaii/28/2012(H3N2)                       
 312 >KF789941,A/Hawaii/45/2012(H3N2)                       ........A.......T........G......A.T.................................T........A..C................T...........A.................G...........G.............A..C.........C...TA..............................................G.       18     18 ,     18     18     312:>KF789941,A/Hawaii/45/2012(H3N2)                       
 313 >KF790223,A/Hawaii/29/2012(H3N2)                       ........A.......T........G......A.T.................................T........A..C................T...........A.................G...........G.............A..C.........C...TA..............................................G.       19     18 ,     19     18     313:>KF790223,A/Hawaii/29/2012(H3N2)                       
 314 >KF789927,A/California/49/2012(H3N2)                   ........A.......T........G......A.T.................................T........A..C................T...........A.................G...........G.............A..C.........C...TA..............................................G.       18     18 ,     18     18     314:>KF789927,A/California/49/2012(H3N2)                   
 315 >KF789990,A/Hawaii/25/2012(H3N2)                       ........A.......T........G......A.T...........................G.....T........A..C................T...........A.................G...........G.............A..C.........C...TA..............................................G.       19     19 ,     19     19     315:>KF789990,A/Hawaii/25/2012(H3N2)                       
 316 >KF789993,A/Hawaii/25/2012(H3N2)                       ........A.......T........G......A.T...........................G.....T........A..C..........T.....T......T....A.................G...........G.............A..C.........C...TA..............................................G.       21     21 ,     21     21     316:>KF789993,A/Hawaii/25/2012(H3N2)                       
 317 >KF789999,A/Hawaii/26/2012(H3N2)                       ........A.......T........G......A.T.................................T........A..C..........T.R...T......Y....A.................G...........G.............A..C.........C...TA..............................................G.       21     21 ,     21     21     317:>KF789999,A/Hawaii/26/2012(H3N2)                       
 318 >KF789587,A/New Hampshire/16/2012(H3N2)                ................T........G......A.T.................................T........A.............T.....T...........A.................G...........G..........................C....A.....T............................T.......T...G.       20     17 ,     20     17     318:>KF789587,A/New Hampshire/16/2012(H3N2)                
 319 >KF789696,A/Maine/05/2012(H3N2)                        .C...........A..T........G......A.T..........................G......T........A....G..............T...........A.................G...........G..........................C....A.......A...........................A..........G.       21     19 ,     21     19     319:>KF789696,A/Maine/05/2012(H3N2)                        
 320 >KC893164,A/Maine/05/2012(H3N2)                        .C...........A..T........G......A.T..........................G......T........A....G..............T...........A.................G...........G..........................C....A.......A...........................A..........G.       19     19 ,     19     19     320:>KC893164,A/Maine/05/2012(H3N2)                        
 321 >KF790394,A/New York/61/2012(H3N2)                     ......................................C...................................G......................T...........A.............................G.......................C..C.................................A......A..........G.       13     10 ,     13     10     321:>KF790394,A/New York/61/2012(H3N2)                     
 322 >KF789877,A/Arkansas/05/2012(H3N2)                     .............A....A...T............CA................................K...GG.........A...............G........A................A...................................T...............T.A............C......A........G..........       18     18 ,     18     18     322:>KF789877,A/Arkansas/05/2012(H3N2)                     
 323 >KF790184,A/Alaska/23/2012(H3N2)                       .............A........T.A..........CA..................................G.GG.........A......T........G........A........G.......A.........C................A........T.................A............C......A........G..........       21     21 ,     21     21     323:>KF790184,A/Alaska/23/2012(H3N2)                       
 324 >KF790196,A/Alaska/22/2012(H3N2)                       .............A........T.A..........CA..................................G.GG.........A...............G........A................A.........C................A........T.................A............C......A........G..........       20     19 ,     20     19     324:>KF790196,A/Alaska/22/2012(H3N2)                       
 325 >KF790195,A/Alaska/23/2012(H3N2)                       .............A........T.A..........CA..................................G.GG.........A...............G........A................A.........C................A........T.................A............C......A........G..........       19     19 ,     19     19     325:>KF790195,A/Alaska/23/2012(H3N2)                       
 326 >KF789796,A/Alaska/31/2012(H3N2)                       .............A........T.A..........CA..................................G.GG.........A...............G........A................A.........C................A........T.................A............C......A........G..........       20     19 ,     20     19     326:>KF789796,A/Alaska/31/2012(H3N2)                       
 327 >KF790255,A/Alaska/24/2012(H3N2)                       .............A........T.A..........CA..................................G.GG.........A...............G........A................A.........C................A........T.................A............C......A........G..........       19     19 ,     19     19     327:>KF790255,A/Alaska/24/2012(H3N2)                       
 328 >KF790238,A/Alaska/24/2012(H3N2)                       .............A........T.A..........CA..................................G.GG.........A..........C....G........A................A.........C................A........T.................A............C......A........G..........       20     20 ,     20     20     328:>KF790238,A/Alaska/24/2012(H3N2)                       
 329 >KF790216,A/Alaska/22/2012(H3N2)                       .............A........T.A..........CA..................................G.GG.........A..........C....G........A................A.........C................A........T.................A............C......A........G..........       20     20 ,     20     20     329:>KF790216,A/Alaska/22/2012(H3N2)                       
 330 >KF789606,A/North Dakota/07/2012(H3N2)                 .............A........T............CA.....T..............................GG...C.....A...............G........A................A...................................T.....A...........A............C......A........G..........       19     18 ,     19     18     330:>KF789606,A/North Dakota/07/2012(H3N2)                 
 331 >KF790370,A/Hawaii/27/2012(H3N2)                       .............A...........................................................GG.....C...A...............G........A............A...A.............T.......................................A............C......A........G.....T....       16     15 ,     16     15     331:>KF790370,A/Hawaii/27/2012(H3N2)                       
 332 >KF790343,A/Hawaii/27/2012(H3N2)                       .............A...........................................................GG.....C...A......T........G........A.......M....A...A.............T.......................................A............C......A........G.....T....       17     17 ,     17     17     332:>KF790343,A/Hawaii/27/2012(H3N2)                       
 333 >KF790425,A/Texas/83/2012(H3N2)                        ........A..C.............................................................GG........................TG........A...........A....A........T............................................A.........AA.C......A...................       16     15 ,     16     15     333:>KF790425,A/Texas/83/2012(H3N2)                        
 334 >Index/32g12f1.c2,42-53                                ........A..C.............................................................GG........................TG........A...........A....A........T............................................A.........AA.C......A...................       15     15 ,     15     15     334:>Index/32g12f1.c2,42-53                                
 335 >KF790187,A/Maryland/32/2012(H3N2)                     ...........C.............................................................GG........................TG........A................A........T............................................A.........AA.C......A...................       14     13 ,     14     13     335:>KF790187,A/Maryland/32/2012(H3N2)                     
 336 >KF790185,A/Louisiana/09/2012(H3N2)                    ................................A........................................GG.........................G........A................A........T............................................A............C......A...................       15     10 ,     15     10     336:>KF790185,A/Louisiana/09/2012(H3N2)                    
 337 >KF790227,A/Maine/08/2012(H3N2)                        .......................................................................G.GG.........................GC........................A........T............................................A...........TC......A...................       17     11 ,     17     11     337:>KF790227,A/Maine/08/2012(H3N2)                        
                                                                                                                                                                                                                                                                                         
---Index----------------------------------------------------TTGAAATCGTCTACTACGGTGACACAATTTGGGTCTGATGCTCCTTGCCTCGCTTGGGACGAAGCAACCGAAGAATAGTCTAAAGCTAGAGGGGTTAGTGATCGCTCCAGACCAAGAAATCGGGCTCTACTCAGCCTTGACATACATATCGGAGCGTAGATCATGTAGGACCAGTATCGCGCTTCACGTGGGCTCCGACAGCGAAGCGGAGTATCCCAAG 
-codon-position---------------------------------------------   11  1 1  11 1       1 2      212 12        2    111  11   212 1   1 1212     2        2 2 122 111 2  2 12 11  1   12 122     2    2     21 1 1        1   2   2    1                 1           1   1 1        2 12  2   
                                                            0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111111111111111111111111 
                                                            0000000000000000000001111111111111112222222222222233333333334444444444444444455555555555556666666666666677777777777777788888888888999999999999900000000000111111111111122222222223333333333334444444444455555555555666666666 
                                                            0122233334445557778990334445667888990011223477888901124556990111233456677789900111234466990001223448889900011122336668812333477889013456777889900111345888011123566799901345567892234456667891123445789900112455677112356778 
                                                            9812836793582570284368594676251027155609287069125130685784035389005760823822814689870314163596399032790345904516262584569037303271359446258383459147276037103551867314508654795160384732351923687398451479384547958344732013

gsgs · Nov 19, 2013

Re: Today at GenBank

17 H9N2 genomes, China 2010
42 H3N2,HA,Canada Jan,2013 , 40=CZ-strain

gsgs · Jan 22, 2014

Re: Today at GenBank

A/Florida/38/2013(H1N1)2013/08/20
A/Utah/08/2013(H1N1)2013/08/05
A/Wisconsin/13/2013(H1N1)2013/09/05
A/North Carolina/09/2013(H1N1)2013/08/27
A/wild boar/Brazil/214-11-13D/2011(H1N2))
A/wild waterfowl/Dongting/PC2560/2012(H9N2))

gsgs · Jan 31, 2014

Re: Today at GenBank

726 human sequences from India ! 13 complete, 713 partial , 360 H3N2 , 366 B
123 times segment 4 with 914 nucleotides in average
and 903 times segment 6 with 966 nucleotides in average

(you probably know already that I suspect India being the main reservoir
for seasonal flu and the source of most successful human seasonal strains,
so I'm eager to look at the mutations and whether they reappeared
later in seasonal strains, as we saw before)

also:
China,2013/11/04,A/Guangdong/02/2013(H7N9) segments 1,2,3,4,5,6,7,8
China,2013/08/08,A/Huizhou/01/2013(H7N9) segments 1,2,3,4,5,6,7,8
China,2013/04/26,A/environment/Guangdong/25/2013(H7N9) segments 1,3,4,5,6,7,8
China,2013/04/26,A/environment/Guangdong/30/2013(H7N9) segments 4,5,6,7,8

South Korea,2008/12,A/wild duck/SH17-1/2008(H2N3) segments 1,2,3,4,5,6,7,8
South Korea,2008/12,A/wild duck/SH17-34/2008(H2N3) segments 1,2,3,4,5,6,7,8
South Korea,2010/03,A/wild duck/SH38-26/2010(H2N8)
South Korea,2010/03,A/wild duck/SH38-28/2010(H2N8)
South Korea,2010/03,A/wild duck/SH38-51/2010(H2N8)
A/wild duck/SH38-56/2010(H2N8)
A/wild duck/SH38-60/2010(H2N8)),,,c
A/wild duck/SH38-64/2010(H2N8)),,,c

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

the India sequences :
segment,serotype,count 2003,...,2011
4,B,0,1,14,2,0,29,0,0,0
6,B,0,1,17,7,1,36,20,191,47
4,H3N2,0,0,13,9,10,45,0,0,0
6,H3N2,16,5,16,10,11,66,119,20,20
----------------------------------

gsgs · Feb 4, 2014

Re: Today at GenBank

>KF997838|A/Shanghai/5190T/2013(H7N9) , 8 segments , 8 "clones"

~100 Russian H1N1,2013

>KJ023067|A/Guangdong/03/2013(H7N9) , 5 segments
>KJ023072|A/Guangdong/04/2013(H7N9) , 7 segments
>KJ023079|A/Guangdong/05/2013(H7N9) , 7 segments

>KJ128362|A/pigeon/Shanghai/JC1/2013(H9N2) 8 segments

Code:

KJ023067 Human 4 H7N9 China 2013/12/15 1711 A/Guangdong/03/2013(H7N9))   c
KJ023072 Human 2 H7N9 China 2013/12/16 2313 A/Guangdong/04/2013(H7N9))   p
KJ023079 Human 1 H7N9 China 2013/12/17 2314 A/Guangdong/05/2013(H7N9))   c
KF997846 Human 1 H7N9 LAB NON 2281 A/Shanghai/5190T/2013(H7N9))   c
KJ128369 Avian 1 H9N2 China 2013/04 2280 Influenza A virus (A/pigeon/Shanghai/JC1/2013(H9N2))   c

KF998212 Avian 4 H9N2 Egypt 2012/04/17 1683 (A/chicken/Egypt/BSU-BS-K7/2012(H9N2))   c
DQ845348 Avian 4 H5N1 Laos 2006 1719 Influenza A virus (A/duck/Laos/3295/2006(H5N1))   c

gsgs · Feb 11, 2014

Re: Today at GenBank

28 HAs from Spain Dec.2013, 11 H1 and 17 H3

Code:

                                              0000000000000001111 
                                              0123345555668890000 
                                              3674963777051961455 
                                              0830058069587867106 
-codon-position-------------------------------   1  1   2111      
---Index--------------------------------------TGCGGTACGAGTGAAGTTT 
   1 >A/******/index/2009/02/01               ................... 
   2 >KJ144625,A/Andalucia/1584/2013(H1N1)    -.TAACC.AGCAAGGAC.C 
   3 >KJ144626,A/Andalucia/1586/2013(H1N1)    -.TAACC.AGCAAGGAC.C 
   4 >KJ144641,A/Navarra/1564/2013(H1N1)      -.TAACCT.GCAAGGAC.C 
   5 >KJ144642,A/Pais Vasco/1567/2013(H1N1)   -.TAACC..GCAAGGAC.C 
   6 >KJ144643,A/Pais Vasco/1568/2013(H1N1)   -.TAACC..GCAAGGAC.C 
   7 >KJ144644,A/Pais Vasco/1570/2013(H1N1)   -.TAACC..GCAAGGAC.C 
   8 >KJ144645,A/Pais Vasco/1571/2013(H1N1)   C.TAACC..GCAAGGAC.C 
   9 >KJ144649,A/Pais Vasco/1530/2013(H1N1)   -.TAACC..GCAAGGAC.C 
  10 >KJ144650,A/Pais Vasco/1533/2013(H1N1)   -.TAACC..GCAAGGAC.C 
  11 >KJ144651,A/Pais Vasco/1534/2013(H1N1)   -.TAACC..GCAAGGACAC 
  12 >KJ144652,A/Pais Vasco/1536/2013(H1N1)   -ATAACC..GCAAGGAC.C

C273T,G340A,G390A,T465C,A538C,A579G,G605C,T658A,G817A,A898G,A966G,G1017A,T1041C,T1056C

G340A,A579G,G605C,T658A,T1056C is the Ohio/Denmark variant from 2010/2011
C273T,G390A,T465C,A538C,G817A,A898G,A966G,G1017A,T1041C

first seen in A/PA/25/2012/11/23
an American strain survived summer ? That could be a feature of new H1, we suspected it before
with the "Chi"-strains

Code:

                                                            0000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111 
                                                            0000000000111111111122222222233333444444444455555556666666666777777778888899999900000111112233444555555556 
                                                            0234456677014478899901234488911225113577888801225690012446889122369993378801267800458338995945124001244677 
                                                            9696820402842632601659820305168387290628012318279516952020270569655890732735365359737015574643683798458081 
-codon-position--------------------------------------------- 2 1 1 11   1222 1211  1  1  1 21 121 11 12  2 211    11  1  1  1   12   2  2  2 1  12  1        1         
---Index----------------------------------------------------TAGGTATAACACGATGCACGGGTGCAGCTCAATGAGACAATAATGTCAACGTGGAGAAGACGCTAGGTCGGCTATCACTAACCAGGAGAACTGTGGTGCAAGCAGA 
   4 >Index/2009/Egypt/Iowa                                 .......................................................................................................... 
   1 >2007/02/06,14278,AUS,A/Brisbane/10/07                 ...A..C.......................C............C..A..A...T...CA....C..........C.....G..C.T...G.C...........CA. 
   2 >Index/Brisbane-like/2007                              ..............................C............C..A..A...TG..CA....C................G..C.T...G.C...........CA. 
   3 >Index/Perth-like/2009                                 .......................A......C.........A..C.........A...CA.....................G..C..................T... 
   5 >Index/USA-2007                                        ..............................C............C..A..A...T...CA....C................G..C.T...G.C...........CA. 
   6 >Index/H3N3-2011-reassortedEI/2011(H3N2)               ..........G.........A.......C...C...........................T...G........C.......A....G......C.....G.A.... 
   7 >Index/H3N2-2011-normalEI/2011(H3N2)                   C................G...T.........G...............................................G....A..A.................. 
   9 >A/Czech Republic/121/2012,2012/03/06,Czech Republic   .........T...G.A..TA..C............A.T......A...G......T.....AT.........G......G........C.A..............G 
  10 >Index/32g12f1.c2,10-37                                .........T...G.A..T.....T..T.........T....G.A..........T.....A...A......G..A...G........C.A.........G....G 
  11 >Index/32g12f1.c2,38-41                                .........T...G.A..T..A...G.T.......A.T....G.A......CA..T.....A..........G...G..G........C.A........GG....G 
  12 >Index/32g12f1.c2,42-53                                ..A.C..................................G..G...............TG.A.......A.A.....T..............A.AACA........ 
  13 >Index/32g12f1.c2,55-62                                C.A..G..G.G..G......A.......CA..C.........................A.T...GA....A..C....C..AT...G......C....TG.A.... 
  14 >KJ144627|A/Aragon/1548/2013(H3N2)                     .........T...G.AT.T........T......G.GTG...G.AC.........T.....A..........G......G....---------------------- 
  15 >KJ144628|A/Baleares/1520/2013(H3N2)                   .........T...G.A..T........T........GTG...G.A..........T.....A..........G......G....---------------------- 
  16 >KJ144629|A/Baleares/1521/2013(H3N2)                   .........T...G.A..T........T........GTG..GG.A..........T.....A..........G......G....---------------------- 
  17 >KJ144630|A/Baleares/1580/2013(H3N2)                   -........T...G.A..T........T........GTG...G.A..........T.....A..........G......G....---------------------- 
  18 >KJ144631|A/Baleares/1581/2013(H3N2)                   -........T...G.A..T........T........GTG...G.A..........T.....A..........G......G....---------------------- 
  19 >KJ144632|A/Baleares/1582/2013(H3N2)                   .........T...G.A..T........T........GTG...G.A..........T.....A..........G......G....---------------------- 
  20 >KJ144633|A/Baleares/1583/2013(H3N2)                   .........T...G.A..T.................GTG...G.A..........T.....A..........G......G....---------------------- 
  21 >KJ144634|A/Navarra/1528/2013(H3N2)                    .........T...G.A..T.......AT........GTG...G.A..G.......T.....A....A.....G......G....---------------------- 
  22 >KJ144635|A/Navarra/1552/2013(H3N2)                    .........T...G.AT.T........T......G.GTG...G.AC.........T.....A..........G......G....---------------------- 
  23 >KJ144636|A/Navarra/1553/2013(H3N2)                    .........T...G.AT.T........T......G.GTG...G.AC.........T.....A..........G......G....---------------------- 
  24 >KJ144637|A/Navarra/1554/2013(H3N2)                    -........T...G.A..T........T........GTG...G.A..........T.....A..........G......G....---------------------- 
  25 >KJ144638|A/Navarra/1565/2013(H3N2)                    .........T...G.AT.T........T......G.GTG...G.AC.........T.....A..........G......G....---------------------- 
  26 >KJ144639|A/Navarra/1576/2013(H3N2)                    -........T..AG.AT.T........T......G.GTG...G.AC.........T.....A..........G....----------------------------- 
  27 >KJ144640|A/Navarra/1578/2013(H3N2)                    .......G.T...G.AT.T........T......G.GTG...G.AC.........T.....A......T...G......G....---------------------- 
  28 >KJ144646|A/Pais Vasco/1573/2013(H3N2)                 .........T...G.A..T........T.....A..GTG...G.A..G.......T.....A..........G......G....---------------------- 
  29 >KJ144647|A/Baleares/1440/2013(H3N2)                   .G.......T.T.GWA..T........T..G.....GTG...G.A.....A....TG....A.....C....G......G....---------------------- 
  30 >KJ144648|A/Baleares/1441/2013(H3N2)                   .G.......T.T.G.A..T........T..G.....GTG...G.A.....A....TG....A.....C....G......G....---------------------- 
                                                                                                                                                                       
---Index----------------------------------------------------TAGGTATAACACGATGCACGGGTGCAGCTCAATGAGACAATAATGTCAACGTGGAGAAGACGCTAGGTCGGCTATCACTAACCAGGAGAACTGTGGTGCAAGCAGA 
-codon-position--------------------------------------------- 2 1 1 11   1222 1211  1  1  1 21 121 11 12  2 211    11  1  1  1   12   2  2  2 1  12  1        1         
                                                            0000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111 
                                                            0000000000111111111122222222233333444444444455555556666666666777777778888899999900000111112233444555555556 
                                                            0234456677014478899901234488911225113577888801225690012446889122369993378801267800458338995945124001244677 
                                                            9696820402842632601659820305168387290628012318279516952020270569655890732735365359737015574643683798458081

same H3 as last season, new mutations: A430G,A472G , first seen in
A/Boston/DOA2-162/2012/01/10(H3N2)

Today at GenBank

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