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Old 12-11-2015, 11:19 AM   #26
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Old 02-03-2016, 08:43 AM   #27
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today 1508 sequences in total, many Avian H5n8,H1n8 etc. 2011-2014

120 human genomes from Thailand 19,13,24,24,17,19,4 from 2007,..,2013
80 H1N1 and 40 H3N2 (Thailand is a candidate where flu is year-round
and new strains, new mutations and reassortments may emerge -
between India and China)


[more later]

ftp://ftp.ncbi.nih.gov/genomes/INFLU...fluenza_na.dat


A/duck/Eastern China/S0131/2014/01/31/H5N2
matches the Korean H5N8 from Jan.2014 in segments
4,5,7

15 differences from the Korean index in segment 4, 8 of which
were also in previous Chinese samples
5 differences in segment 5, 2 of which were also in previous
Chinese samples
3 differences in segment 7, 2 of which were also in previous
Chinese samples

suggesting a common ancestor with the Korean [-->Europe,Taiwan,USA]
2014 H5N8-virus in these 3 segments of ~early 2013 in HA
and ~summer/fall 2013 in NP,MP

so it looks as if this one came again from Chinese ducks

----------2016/02/04
A/environment/Gainesville/08/2015/09/16(H1N1)
Mexflu in summer in Florida, Sept.16,2015
classroom air and environmental surfaces
["living",infective virus or just RNA ?]
http://www.ncbi.nlm.nih.gov/nuccore/KU509999
AUTHORS Lednicky,J.A. and Loeb,J.C.
TITLE Pandemic H1N1 influenza virus in classroom air and on environmental
surfaces in 2015
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1701)
AUTHORS Lednicky,J.A. and Loeb,J.C.
TITLE Direct Submission
JOURNAL Submitted (08-JAN-2016) Environmental and Global Health, University
of Florida - Gainesville, 1225 Center Drive, Room 4155,
Gainesville, FL 32610, USA
---------------------------------------------------
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Old 02-12-2016, 10:26 AM   #28
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US-human genomes from Sept. 2015,2014 (mostly H3N2)

so,... do they have the seasonal strains already in Sept. or do
they enter from Asia later

http://magictour.free.fr/sept32a.GIF
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Old 02-13-2016, 03:59 PM   #29
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>KU558903,A/turkey/Indiana/16-001403-1/2016,2016/01/13,USA,H7N8,Avian
>KU585905,A/turkey/Indiana/16-001573-2/2016,2016/01/15,USA,H7N8,Avian
>KU585913,A/turkey/Indiana/16-001574-7/2016,2016/01/,USA,H7N8,Avian

totally unrelated to the H5Nx from last year in all segments


5,5,7,-,5,12,1,8 differences to the H3N8NS2 bird index
4,4,5,-,3,(12),1,8 differences to the North American bird index

[to compare:
1918-flu had 8,7,10,-,9,-,7,5 differences
Qinghai-H5N1-2005 had 11,8,10,-,8,-,14,19 differences
Mexflu-H1N1-2009 had 17,23,17,-,28,-,16,51 differences
H7N9-2013 had 7,14,20,-,11,-,27,35 differences,
so this 2016-Indiana H7N8 is pretty close to mallard-index-flu,
probably evolving less than 10 years in poultry ]


Code:
>KU585913,A/turkey/Indiana/160015747/2016,2016/01/,USA,H7N8,Avian

----------segment 1------------- 
 104    5  477 12126 >KC492426,A/Northern pintail/Newfoundland/GR495/2011,2011/09/19,Canada,H12,Avian,1
 109   25 2280 12706 >CY186837,A/blue-winged teal/Ohio/12OS2106/2012,2012/09/01,USA,H4N6,Avian,1
 133   30 2247 7799 >CY035282,A/mallard/Minnesota/Sg-00169/2007,2007/09/16,USA,H3N8,Avian,1

----------segment 2------------- 
  52   12 2274 12773 >CY186435,A/bufflehead/Illinois/12OS4798/2012,2012/11/23,USA,N8,Avian,2
  70   16 2274 12440 >CY167246,A/American green-winged teal/Mississippi/12OS405/2012,2012/01/18,USA,H10N7,Avian,2
  79   18 2274 12419 >CY167173,A/mallard/Arkansas/12OS184/2012,2012/01/15,USA,H10N7,Avian,2
  87   20 2274 11509 >CY132655,A/mallard/Illinois/10OS3786/2010,2010/11/27,USA,H10N7,Avian,2
  87   20 2274 12754 >CY186995,A/northern shoveler/Ohio/12OS5647/2012,2012/11/10,USA,H2N3,Avian,2

----------segment 3------------- 
 125   27 2151 12250 >CY157523,A/northern pintail/California/2789/2011,2011/10/29,USA,H9N2,Avian,3
 130   28 2142 12504 >KJ413454,A/blue-winged teal/TX/AI12-801/2012,2012/03/07,USA,H10N3,Avian,3
 130   28 2151 12505 >KJ413462,A/blue-winged teal/TX/AI12-802/2012,2012/03/07,USA,H10N3,Avian,3
 139   30 2151 12278 >CY166725,A/mallard/Wisconsin/11OS4368/2011,2011/11/05,USA,H11N9,Avian,3

----------segment 4------------- 
 178   30 1683 1700 >KJ568345,A/blue-winged teal/Iowa/13OS2316/2013,2013/09/21,USA,H7N3,Avian,4
 213   36 1683 1699 >KJ567945,A/blue-winged teal/Ohio/13OS2037/2013,2013/09/16,USA,H7N1,Avian,4

----------segment 5------------- 
 113   17 1497 10139 >CY096973,A/bufflehead/Illinois/4016/2009,2009/11/28,USA,H4N8,Avian,5
 133   20 1497 11056 >CY132753,A/mallard/Wisconsin/10OS3166/2010,2010/10/29,USA,mixed,Avian,5
 133   20 1497 11337 >CY133696,A/American green-winged teal/Mississippi/11OS257/2011,2011/01/15,USA,H11N9,Avian,5
 140   21 1497 11746 >CY167105,A/blue-winged teal/Wisconsin/11OS2873/2011,2011/09/24,USA,H3N2,Avian,5

----------segment 6------------- 
  46    6 1289 1611 >CY186431,A/bufflehead/Illinois/12OS4798/2012,2012/11/23,USA,N8,Avian,6
  77   11 1413 1563 >CY167096,A/common goldeneye/Wisconsin/11OS4503/2011,2011/11/20,USA,H4N8,Avian,6
  77   11 1413 1564 >CY166404,A/common goldeneye/Wisconsin/11OS5764/2011,2011/12/04,USA,H4N8,Avian,6
  77   11 1413 1570 >CY134337,A/bufflehead/California/3118/2011,2011/12/07,USA,H4N8,Avian,6

----------segment 7------------- 
  81    8  982 12955 >CY166203,A/bufflehead/Wisconsin/11OS3570/2011,2011/10/30,USA,H4N8,Avian,7
  81    8  982 13016 >CY167095,A/common goldeneye/Wisconsin/11OS4503/2011,2011/11/20,USA,H4N8,Avian,7
  81    8  982 13487 >CY186430,A/bufflehead/Illinois/12OS4798/2012,2012/11/23,USA,N8,Avian,7
  91    9  982 13046 >CY166403,A/common goldeneye/Wisconsin/11OS5764/2011,2011/12/04,USA,H4N8,Avian,7
  91    9  982 13053 >CY134336,A/bufflehead/California/3118/2011,2011/12/07,USA,H4N8,Avian,7

----------segment 8------------- 
  59    5  838 13607 >CY186433,A/bufflehead/Illinois/12OS4798/2012,2012/11/23,USA,N8,Avian,8
  83    7  838 13385 >CY133133,A/common goldeneye/Wisconsin/10OS4202/2010,2010/12/02,USA,H7N6,Avian,8



2 of the 2016-Indiana H7s are lp (KTR) 1 is hp (KKRKTR)


cleavage sites Avian H7 , 2 main strains, 2500 out of 2800 H7s as of 2015/11/20

...P---GLFGAIA...

1500,KGR
448,KTR
251,KPR
59,KKR
10,KRR
8,KGK
7,KTR
7,KAR
4,KGR
3,RGR
3,KPR
2,RKR
2,KER
2,KGR
1,RKR
1,KTK
1,KG
1,GR
------------
2310



82,KGSRVRR Italy 1999/0
30,KRRKR Pakistan 2003/4
10,KRRRR NL,2003
9,KKREKR
6,KKRRKR
5,KTCSPLSRCRETR
5,KQAYRKRMTR
4,SKKRKKR
4,RKRKR
4,KDRKSRHRRTR
3,KTCSPLSRCRKTR
3,KRRERR
3,KKKKR
2,RRRKR
2,KRKRKR
2,KRKKR
2,KQAYQKRMTR
2,KQAYQKQMTR
2,KQAHQKRMTR
2,KKKKKKR
1,SKKREKR
1,RQAYRKRMTR
1,KTTKPRPRR
1,KTRRRR
1,KRRR
1,KRRNR
1,KQAYKKRMTR
1,KQAYHKRMTR
1,KQACQKRMTR
1,KPRGLFGIA
1,KKRKKR
1,KGRGLLGAIA
1,KGRGLFGVRV
1,KGRGL

1,KKRKTR Indiana,2016

------------------------
197

equine H7 [1956-1977] had THKQLTHHMRKKR
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Old 04-24-2016, 06:37 AM   #30
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904 Mexican swine sequences at genbank !
16 from 2010 , 92 from 2011 , 532 from 2012 , 224 from 2013 , 40 from 2014
unfortunately none from 2008

we were waiting for those since 2009


I found no precursor of the 2009 pandemic H1N1
in segments 1,2 (segments 3-8 were only briefly checked so far).

So it's still a mystery where that virus came from, where it did hide
from 2000-2009

========================================
2016/04/27 11 genomes H5Nx from Taiwan, early 2015
2016/04/29 8 Czech H1N1, early 2016 , segments 4,6,7
2 genomes H1N1,USA, Feb.2016
=====================================
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Old 06-29-2016, 09:34 AM   #31
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there is a paper now:
40-pages .pdf here: https://elifesciences.org/content/5/e16777-download.pdf
[this should have been done in 2009 ]

originated in pigs from a very small region in central Mexico

circulated for more than 10 years in pigs in Mexico before jumping into humans.

58 whole-genome sequences

the parent strains still exist in the pigs there today.

lack of any complete swIAV genomes from Mexico’s large swine populations
at the start of the pandemic,

the majority of swIAVs in previous analyses were collected in northern and eastern Mexico,
and no studies to date have included viruses from major swine-producing states in central Mexico,

samples from Sonora,Yucatan,Puebla,Jalisco,Guanajuato,Aguascali entes

(sequence accession numbers are available in the Dryad data repository under DOI: 10.5061/dryad.m550m)

viral introductions from US and European swine into Mexico have occurred periodically for
at least two decades

live swine imports into Mexico also were reported from several European countries during the
late 1990s, including the United Kingdom and Denmark

"genotype 1"

Guanajuato most closely to pdmH1N1 in PB2, PB1, H1,N1,NP
Jalisco in PA,MP,NP

highest in Mexico City (0.81), consistent with an origin of the pandemic outbreak in Mexico’s capital city

2010 (1), 2011 (6), 2012 (34), 2013 (14), 2014 (3)
All samples came from large commercial facilities

GenBank accession numbers of the 58 genomes are available in the Dryad data repository
under DOI: 10.5061/dryad.m550m

A large number of whole-genome sequences from swIAVs in European swine were published
by Watson et al., (Watson et al., 2015) after we completed our analysis.

We excluded nine triple reassortant Mexican swIAVs (e.g., A/swine/Mexico/Mex19/2010(H1N1),
Figure 3--figure supplement 1) that had shorter branch lengths than expected given their year of
sampling, an indication of possible errors in sequencing or assembly.

Figure 2. 12 genotypes in Mexican swine herds during 2010-2014.


I didn't find anything at "datadryad"
However, when the sequences are uploaded to genbank, I'll probably notice that.

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

OK, these are viruses from April, mentioned above.

I had found no (direct) precursor of the pandemic strain in Mexican swine when I looked
at it briefly in April.
But there seem to be precursors who separated early, in ~2003 or such.
So we are down from the 10 years gap to a 6 years gap in some segments,
with an early reassortment of American and Eurasian viruses.

the best evidence are these 6 viruses from 2012:
>A/Sw/Mexico/AVX27/2012,2012/08/02,H1N1
>A/Sw/Mexico/AVX39/2012,2012/11/15,H1N1
>A/Sw/Mexico/AVX43/2012,2012/11/26,H1N1
>A/Sw/Mexico/AVX44/2012,2012/11/26,H1N1
>A/Sw/Mexico/AVX45/2012,2012/12/19,H1N1
>A/Sw/Mexico/AVX46/2012,2012/12/19,H1N1

http://www.ncbi.nlm.nih.gov/nuccore/KU976672
http://www.ncbi.nlm.nih.gov/nuccore/KU976900
http://www.ncbi.nlm.nih.gov/nuccore/KU976808
http://www.ncbi.nlm.nih.gov/nuccore/KU976661
http://www.ncbi.nlm.nih.gov/nuccore/KU976848
http://www.ncbi.nlm.nih.gov/nuccore/KU976663


(is it their genotype 1 ? from Central Mexico ? genbank just says "Mexico" )

they share some (about half ?) of the mexflu mutations in segments 1,2,4,6,7
(as compared to triple-reassortant+H1 in 1,2,3,4,5,8 or
Euroswine(H1N1,1979) in segments 6,7 respectively)

I'll compare it with the "smoking pig" A/Swine/4/Mexico/... later

-----------------------------------
another paper from Sept.2015 :
http://currents.plos.org/outbreaks/a...ico-and-chile/
(Mexico and Chile, Swine, only HA
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Old 06-29-2016, 11:14 PM   #32
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there are 679=77+76+78+135+79+76+79+79 Mexican swine sequences at genbank
It is clear, that there is lots of swine influenza in Mexico. Many different strains and reassortments
that are not seen in USA or elsewhere. The combination with Eurasian swine viruses was
successfully kept out of USA and Canada, presumably by import regulations and controls.
Not so in Mexico.
here a mutations-picture: http://magictour.free.fr/mxsw16.GIF

--------edit-----------
I'm making the bigger pictures now, involving all related viruses, not only Mexican ones

on 2016/06/30 there are 48718=4148+4129+4191+10715+4353+8781+8019+4382
swine flu-A sequences at genbank.



now, while searching systematically through all genbank swine sequences, I found some other
sequences which could be considered precursors of mexflu-2009

i.e. A/swine/Missouri/A01047968/2010,2010/12/14,H3N2 , segment 2

but these could be sequencing errors, they often sequence several viruses in one run
and then they make mistakes in associating the partials to the correct viruses
and then concatenating the short partials into the whole segment.

mexflu segment 2 acquired 72 mutations on its way from triple-reassortant(1998) until 2009.
MO10 segment 2 acquired only 62 mutations 1998-2010
But 25 of these mutations coincide with the mexflu ones ! Very unlikely that this is
coincidence with 2274 mutation-positions in segment 2, 1/3 of which are 3rd-position
and thus ~4-times more likely to mutate.

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

viruses with mexflu precursor mutations: (AVX=A/Sw/Mexico/AVX...)

segment 1: AVX,27,39,43,44,45,46 ; AVX,4,13,16 ;
AVX,3,5,6,7,8,9,11,12,14,17,18,19,23,24,26,35,36,3 7,38,40,41,42,53,54,57,60,62,63

segment 2: JQ689106,A/Sw/MO/A01047968/2010, (looks like a sequencing error, since it has also 27
mutations from another strain)
H3N2 ; JQ689114, same day
AVX,27,39,43,44,45,46 ;

segment 3:
CY067685,M26080

AVX,3,4,5,6,7,8,9,11,12,13,14,16,17,18,19,23,24,26 ,35,36,37,38,40,41,42,53,54,57,60,62,63
KF026721,KC779029,JX099404,KM389163,KM389163 look also like sequencing errors

segment 4:
AVX,27,39,43,44,45,46 ;

AVX,3,9,11,12,23,24,40,41,42,54,62,63, 9557133, 9762101,9783445,9800323,
EU139827, 8935602,AVX30

segment 5:
JX239982,KC261907,KJ528300,KC471434
AVX,3,4,5,6,7,8,9,11,12,13,14,16,17,18,19,20,23,24 ,26,27,35,36,37,38,39,40,41,42,43,44,45,46,53,54,5 7,60,62,63
KM361365

segment 6:
AVX,27,39,43,44,45,46 ;

segment 7:
AVX,5,6,7,8,17,18

segment 8:
KM489609,KR859444,KJ413932


A/swine/Mexico/AVX27/2012(H1N1))
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Old 07-05-2016, 06:04 AM   #33
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now I'm speculating that the triple-reassortant swine had also come from Mexico !
I think there are some hints from the epizootic timing and the mutations in the viruses for that.

-----------------------short history of American swine flu-------------------------
Swine flu was first seen in 1918, parallel with the human pandemic.
Later it was established that the swine and human H1N1 strains had probably jumped from
birds to mammals between 1880 and 1918 and had reassorted (= combined,mixed) in the 8 segments.
The human and swine strains had separated in 1900-1915, depending on segment.
The human H1N1 reassorted with Avian strains and formed the pandemics of 1957(H2N2)
and 1968(H2N3).
Then, in 1976, when the swine and human lineages were already pretty much different,
some recruits in Fort Dix had caught the swine flu and died and all of USA got vaxed because
they feared a recurrence of 1918.

Then in 1998 a new swine flu virus emerged, the so called "triple-reassortant", it was
first seen in Nebraska, March,19,1998 . It had segments 5,7,8 from classical(1918) swine,
segments 2,4,6 from human seasonal H3N2 (since 1968) and segments 1,3 were Avian,
as seen in Canadian mallards 1993. So they called it triple-reassortant, but it likely
was 2 consecutive normal reassortments , which may have occurred years apart.

This new strain had dominated the American swine-flus since then and the classical
swine-H1N1 is rare now.
Then in 2009 or 2008 a descendent of that triple-reassortant swine strain reassorted with an
European Swine virus, which was never seen in USA or Canada before,
and formed the Mexican pandemic H1N1 virus.
This jumped to humans and starting from Mexico a human pandemic emerged,
which was thankfully not as lethal as predicted.
(only 12000 deaths in USA,2009 rather than the predicted 60000)
--------------------------------------------------------------------------------------------------------


----------------------------edit-------------------------------
but I want to make clear that at this point this is speculative.
So far I have no clear evidence from mutations analysis to
demonstrates this. The mutation analysis is inconclusive , unclear
for me so far. It neither supports nor rejects that theory.
I just base this on the information and analysis which the others
also have, but I am allowed to speak out what the funded
scientists in their papers maybe wouldn't.

### How likely is it, that TA (triple-reassortant-swine-flu,1998) went early in 1998
from USA to Mexico so to serve as the precursor of the strains AVX27 and
pandemic H1N1, but then there was no other introduction from USA to Mexico
of TA since 1999 ?

### How likely is it, that the human[swine or avian-swine TA-precursors had circulated
for years and remained undetected in USA, despite their advanced surveillance ?

### How likely is it, that we had no European swine sequences in USA in thousands
of samples, but then we had several in just a few samples from Mexico ?
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Old 07-28-2016, 02:16 AM   #34
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> A/chinstrap penguin/Antarctica/B04/2015,2015/01/16,Antarctica,H5N5,Avian

segments 4 and 6 , aligning ... more later


I remember, this was once (2006?) an April-1-joke at curevents,
penguins with H5N1, H5N1 spreading to Antarctica


Code:
   0    0 1466    1 >KX458006,A/chinstrap penguin/Antarctica/B04/2015,2015/01/16,Antarctica,H5N5,Avian,6

--------------------------segment 4--------------------------
 273   18  657  937 >CY093742,A/northern shoveler/California/8855/2008,2008/11/05,USA,H5N2,Avian,4
 302   51 1688 1389 >CY133909,A/northern shoveler/California/2815/2011,2011/10/29,USA,H5N2,Avian,4
 319   54 1688 3753 >CY033444,A/American green-winged teal/California/HKWF609/2007,2007/11/10,USA,H5N2,Avian,4
 337   57 1688 1565 >CY133153,A/American green-winged teal/Wisconsin/10OS3127/2010,2010/10/20,USA,H5N2,Avian,4
 337   57 1688 2588 >CY096704,A/blue-winged teal/Guatemala/CIP049-08/2010,2010/01/31,Guatemala,H5N3,Avian,4
...
 367   62 1688 1364 >CY194148,A/mallard/Southcentral Alaska/12ML00985/2014,2014/09/22,USA,mixedÞH5,Avian,4

-------------------------segment 6------------------------
 321   46 1430   10 >JX679163,A/wild duck/Korea/SH12-7/2008,2008/11/,South Korea,H10N5,Avian,6
 380   55 1445  215 >AB593481,A/duck/Vietnam/G18/2009,2009/01/,Viet Nam,H12N5,Avian,6
 434   62 1426  276 >CY041404,A/mallard/Netherlands/11/2007,2007//,Netherlands,H6N5,Avian,6
 437   62 1416  257 >FN386470,A/Anas plathyrhynchos/Spain/1252/2007,2007/09/26,Spain,H6N5,Avian,6
 444   63 1416  445 >CY186278,A/mallard/Sweden/79389/2008,2008/11/15,Sweden,mixedÞN5,Avian,6
 462   63 1363   96 >KR862702,A/mallard/Netherlands/16/2008,2008/09/20,Netherlands,H4N5,Avian,6
...
 532   76 1426    4 >CY185619,A/black-headed gull/Republic of Georgia/9/2012,2012/02/22,Georgia,H2N5,Avian,6
...
 615   88 1430  198 >AB270599,A/duck/Mongolia/149/03,2003//,Mongolia,H10N5,Avian,6
 615   88 1430  199 >AB270600,A/duck/Hokkaido/24/04,2004//,Japan,H10N5,Avian,6
...
1030  147 1426  237 >CY075927,A/common murre/Oregon/19497-004/2005,2005/07/25,USA,H9N5,Avian,6

so, segment 4 is American and segment 6 is Eurasian, quite unusual.
And both are quite recent, from 2008

------------------edit-------------------

ahh, we already had flu in penguins in 2013 (H11N2).
In Adelie Penguins, it presumably went to Antarctica in the 1970s.
I must have posted about it in 2014 , I completely forgot.

Code:
   0    0 2280    1 >KJ729356,A/Adelie penguin/Antarctica/184/2013(H11N2)
----------segment 1------------- 
 442  101 2280 2795 >A/mallard/WI/169/1975,1975//,H5N3
 657  150 2280 1164 >A/mallard duck/New York/90/1982,1982/12/01,H6N8
 657  150 2280 1181 >A/chicken/Pennsylvania/1370/1983,1983//,H5N2
----------segment 2------------- 
 996   75  753 8856 >A/semi-palmated sandpiper/New Jersey/237/1990,1990/05/26,H3N6
1474  182 1234 8812 >A/mallard/New Zealand/449-68/2004,2004//,H1N2
1509  218 1444 8871 >A/American black duck/New Brunswick/03532/2009,2009/09/10,H4N6
1525  347 2274    2 >A/Brevig Mission/1/1918(H1N1)
1539  350 2274 3443 >A/blue goose/WI/711/1975,1975//,H5N2
1556  354 2274  595 >A/blue-winged teal/ALB/286/1977,1977/08/10,H3N6
----------segment 3------------- 
 953  205 2151 1097 >A/chicken/Chile/184240-4322/2002,2002//,H7N3
 953  205 2151 7892 >A/chicken/Chile/184240-1/2002,2002//,H7N3
 962  207 2151  213 >A/chicken/Chile/4957/02,2002//,H7N3
 962  207 2151 1012 >A/cinnamon teal/Bolivia/4537/2001,2001//,H7N3
 962  207 2151 4289 >A/semipalmated sandpiper/Delaware/2144/2000,2000//,H11N6
 971  208 2142  214 >A/chicken/Chile/4322/02,2002//,H7N3
 971  209 2151  212 >A/chicken/Chile/176822/02,2002//,H7N3
1055  227 2151 6276 >A/rosy-billed pochard/Argentina/CIP051-269/2007,2007/05/13,H6N8
1073  231 2151 7155 >A/rosy-billed pochard/Argentina/CIP051-559/2007,2007//,H9N2
1075   63  586 2539 >A/kelp gull/Argentina/LDC4/2006,2006//,H13N9
1078  232 2151 5222 >A/rosy-billed pochard/Argentina/CIP051-557/2007,2007/05/,H6N2
1083  233 2151 5224 >A/rosy-billed pochard/Argentina/CIP051-925/2008,2008/02/,H6N2
1087  234 2151 5223 >A/rosy-billed pochard/Argentina/CIP051-575/2007,2007/05/,H6N8
1109  211 1901 3698 >A/red-winged tinamou/Argentina/MP1/2008,2008/04/,H1N1
1115  240 2151 6275 >A/rosy-billed pochard/Argentina/CIP051-1977/2010,2010/06/29,H6N2
1263  198 1567 8771 >A/mallard/New Zealand/1613-39/2004,2004//,H2N7
1306  281 2151 1058 >A/turkey/Massachusetts/3740/1965,1965//,H6N2
1306  281 2151 3873 >A/whiskered tern/Egypt/04/2004,2004/12/05,H6N2
1306  281 2151 8293 >A/turkey/Massachusetts/3740/1965,1965//,H6N2
1311  282 2151 5881 >A/turkey/Massachusetts/3740/1965,1965/06/11,H6N2
1311  282 2151 6206 >A/duck/Egypt/053/2005,2005/02/05,H6N2
1315  283 2151 4405 >A/chicken/Alabama/1975,1975//,H4N8
----------segment 4------------- 
2188  371 1695 4426 >A/ruddy turnstone/Delaware/2762/1987,1987/05/20,H11N2,USA
2525  427 1691 4790 >A/tern/Australia/752/1975,1975//,H11N9,Australia
2613  443 1695 4425 >A/ruddy turnstone/Delaware/2589/1987,1987/05/20,H11N1,USA
2625  445 1695 2193 >A/herring gull/Delaware Bay/2610/1987,1987/05/20,H11N1,USA
----------segment 5------------- 
 414   62 1497 2936 >A/turkey/CO/118899/1972,1972//,H5N2
 447   67 1497   13 >A/gull/Maryland/5/1977,1977//,H11N9
 460   69 1497  863 >A/gull/Maryland/19/1977,1977/04/04,H2N9
 460   69 1497 2844 >A/gull/Maryland/19/1977,1977//,H2N9
 460   69 1497 7356 >A/gull/Maryland/18/1977,1977/08/01,H2N9
 627   94 1497  706 >A/sanderling/New Jersey/766/1986,1986/05/12,H2N7
----------segment 6------------- 
 943  133 1410 10194 >A/turkey/Wisconsin/1/1966,1966//,H9N2
 950  134 1410 1196 >A/duck/Hong Kong/293/1978,1978//,H7N2
 950  134 1410 2400 >A/duck/Hong Kong/301/1978,1978//,H7N2
 950  134 1410 7488 >A/duck/Hokkaido/5/1977,1977//,H3N2
1000  141 1410  947 >A/mallard/ALB/250/1978,1978/08/07,H6N2
1000  141 1410  952 >A/pintail/ALB/367/1978,1978/08/10,H6N2
1000  141 1410 1136 >A/mallard/Alberta/354/1978,1978/08/10,H4N2
1000  141 1410 1531 >A/mallard/Alberta/205/1978,1978/08/10,H6N2
1000  141 1410 1541 >A/duck/Hong Kong/784/1979,1979/10/10,H9N2
1007  140 1389  795 >A/turkey/Wisconsin/1/1966,1966//,H9N2
----------segment 7------------- 
 121    1   82 5943 >A/northern waterthrush/Maine/CTR-AIV21/2006,2006/08/05,
 185    2  108 5931 >A/western wood-pewee/Washington/CTR-AIV09/2006,2006/07/26,
 305   30  981  502 >A/blue-winged teal/Alberta/96/76 ,1976//,H4N8
 305   30  981 1197 >A/mallard/ALB/210/1977,1977/08/30,H4N8
 316   31  981 1195 >A/redhead duck/ALB/74/1977,1977/08/08,H4N6
 326   32  981   48 >A/turkey/Oregon/71,1971//,H7N3
 326   32  981 1044 >A/mallard/ALB/25/1976,1976/08/11,H3N1
 326   32  981 1166 >A/mallard/ALB/676/1979,1979/08/13,H3N6
 326   32  981 1198 >A/mallard/ALB/161/1977,1977/09/03,H4N6
 326   32  981 8510 >A/turkey/Oregon/1971,1971/03/,H7N3
 336   33  981 1548 >A/turkey/Oregon/1971,1971//,H7N3
 336   33  981 3331 >A/duck/PA/486/1969,1969//,H6N1
 336   33  981 6712 >A/turkey/Oregon/1/1971,1971/06/11,mixed
 346   34  981 1074 >A/gadwall duck/Alberta/291/1977,1977/09/01,H7N3
 346   34  981 1219 >A/blue-winged teal/ALB/295/1977,1977/09/01,H7N3
 346   34  981 1220 >A/widgeon/Alberta/284/1977,1977/09/01,H7N3
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Old 09-15-2016, 11:05 AM   #35
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Hong Kong Swine , 1977-1999
Alaska birds , 2005-2010
France 2014/5, HP Avian
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Old 01-06-2017, 04:53 PM   #36
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A/lion/Hubei/1-2/2016(H5N1)
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Old 02-24-2017, 08:35 AM   #37
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human sequences from USA, 37 States, this season at genbank !

76 full genomes H3N2 : http://magictour.free.fr/32-2427b.GIF
25 full genomes H1N1
79 full genomes B
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Old 03-24-2017, 12:37 PM   #38
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the first public sequences from the European H5N8 outbreak 2016/7
are now at genbank.
All the previous sequences went to GISAID only, where I have no access
and whose sequences may not be published.
Thanks to Czechia for the genbank upload !


>KY621531,A/chicken/Czech Republic/206-17_2/2017,2017/01/06,Czech Republic,H5N8,Avian



amino-acid differences from the bird-index
(wild birds, mallards usually have these amino-acid sequences
in the inner segments 1,2,3,5,7,8. When it goes to poultry the
amino-acid mutations start to accumulate again, so by this
you can see how long the virus evolved already in poultry)

08,05,09,--,01,74,06,23 Europe H5N8,2016
01,03,02,--,01,68,00,17 best matches, see below

02,07,19,--,02,67,19,13 Korea H5N8,2014

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

best genbank-neighbors, fewest nucleotide-mutations in the 8 segments

Eastern China , H5N8, 2014 is close in 3 major segments
this is quite different from what we had 2014 in Europe and what
America had in 2015. It is another variation that did split in
~early 2014 and developed in Asia, until it reassorted with some new
wild-bird segments and went to Mongolia,Sibiria,Europe.


Code:
A: differences in 1/100 percent of nucleotides
B: total number of differences
C: number of available,sequenced nucleotides
D: number in my database
E: sequence name

   A    B    C     D          E
 236   54 2280 14198 >CY185408,A/common coot/Republic of Georgia/1/2010,2010/01/21,Georgia,H6N2,Avian,1
 114   26 2274 2656 >LC121338,A/duck/Mongolia/211/2015,2015/08/31,Mongolia,H3N8,Avian,2
 176   38 2151 3525 >AB916666,A/muscovy duck/Vietnam/LBM529/2013,2013/11/04,Viet Nam,H3N8,Avian,3
  99   17 1704 7130 >KP732646,A/duck/Eastern China/S1109/2014,2014/11/09,China,H5N8,Avian,4
 173   26 1497 1706 >CY185580,A/mallard/Republic of Georgia/13/2011,2011/11/26,Georgia,H6N2,Avian,5
 134   19 1413  749 >KP732686,A/duck/Eastern China/S1109/2014,2014/11/09,China,H5N8,Avian,6
 173   17  981 2825 >LC121383,A/duck/Mongolia/499/2015,2015/08/31,Mongolia,H10N7,Avian,7
 131   11  838 3225 >KP732726,A/duck/Eastern China/S1109/2014,2014/11/09,China,H5N8,Avian,8


Code:
amino-acid-index-distances:
132-3-12,A/common coot/Republic of Georgia/1/2010/01/21,H6N2
332-2-13,A/duck/Mongolia/211/2015/08/31,H3N8
322-0-00,A/muscovy duck/Vietnam/LBM529/2013/11/04,H3N8
82(25)-4-(22)(17),A/duck/Eastern China/S1109/2014/11/09,H5N8
041-1-21,A/mallard/Republic of Georgia/13/2011/11/26,H6N2
A/duck/Eastern China/S1109/2014/11/09,H5N8
145-1-04,A/duck/Mongolia/499/2015/08/31,H10N7
A/duck/Eastern China/S1109/2014/11/09,H5N8
in segments 1,2,3,7 this is similar to the 1918-human virus ,
which probably went from wild birds to mammals years/decades before.
Segment 5 is still more wild, more recent, segments 4,6,8
are from the Eastern China , poultry - H5 - virus .
Segments 1,2,3,7 have 29 amino-acid-differences from the index,
their closest neighbors , wild birds, had 7 differences only.
It's not clear in which species these differences=mutations
were accumulated,
Chinese half-domestic ducks ?, geese/swans ?
Since Eurasian mallards or similar ducks usually don't accumulate
these amino-acid mutations in the inner segments.
It would be interesting to examine the sequences from
early 2016 from Uvs-lake or Qinghai-lake , but these are
only at GISAID, nonpublic , and researchers in the papers
usually don't report these differences from the
amino-acid-bird-index = avian consensus virus.
Instead they usually give the phylogenetic trees, which don't show this,
they show the genetic distance, nucleotides - not amino-acids.
https://en.wikipedia.org/wiki/Phylogenetic_tree
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Old 04-24-2017, 02:19 AM   #39
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A/feline/New York/16-040082-1/2016(H7N2)) , 2016/12/06

https://www.ncbi.nlm.nih.gov/nuccore/KY888121

> First Detection of Low Pathogenic Avian Lineage H7N2 in
> Felis catus Genome Announc (2017) In press

all 8 segments , genbank April 20

analysis later today

distance to the bird-index : 20,17,18,--,12,--,17,24*

first mammalean flu with the 2nd type of segment 8 , AFAIR (?)
{ahh, no, 2 people had that strain in 2002/2003, according to CDC}
[16 types of HA , 9 types of NA , 2 types of NS for avian influenza]


best neighbors [ at least one per available year]

Code:
>A/feline/New York/16-040082-1/2016,H7N2,2016/12/06

----------segment 1------------- 
 204   46 2251 11333 >CY035776,A/avian/New York/Sg-00349/2000,2000//,USA,H7N2,Avian,1
 221   50 2253 11455 >CY036326,A/avian/New York/Sg-00362/2001,2001//,USA,H7N2,Avian,1
 235   53 2251 11314 >CY035701,A/avian/New York/Sg-00328/1999,1999//,USA,H7N2,Avian,1
 236   54 2280 7438 >EU742982,A/chicken/NJ/16224-6/1999,1999//,USA,H7N2,Avian,1
 240   54 2247 11318 >CY035716,A/chicken/New Jersey/Sg-00333/1999,1999//,USA,H7N2,Avian,1
 298   68 2280 12749 >CY014900,A/chicken/Pennsylvania/143586/2002,2002//,USA,H7N2,Avian,1
 302   68 2247 11294 >CY035615,A/chicken/New York/Sg-00306/1998,1998//,USA,H7N2,Avian,1
 342   77 2246 11286 >CY035588,A/chicken/New York/Sg-00298/1997,1997//,USA,H7N2,Avian,1
 377   86 2280 8525 >EU084907,A/chicken/New York/3112-1/1995,1995//,USA,H7N2,Avian,1
 380   86 2258 11274 >CY035543,A/duck/New Jersey/Sg-00286/1996,1996//,USA,H7N2,Avian,1
 381   87 2280 14825 >EU742942,A/chicken/RI/4328-1/1995,1995//,USA,H7N2,Avian,1
 438  100 2280 7433 >EU742951,A/chicken/New York/13142-5/1994,1994//,USA,H7N2,Avian,1

----------segment 2------------- 
 242   55 2264 11390 >CY036295,A/avian/New York/Sg-00353/2000,2000//,USA,H7N2,Avian,2
 243   55 2263 11398 >CY036327,A/avian/New York/Sg-00362/2001,2001//,USA,H7N2,Avian,2
 256   58 2263 11430 >CY036456,A/avian/New York/Sg-00396/2002,2002//,USA,H7N2,Avian,2
 283   64 2261 11248 >CY035724,A/duck/New Jersey/Sg-00335/1999,1999//,USA,H7N2,Avian,2
 322   73 2261 11222 >CY035616,A/chicken/New York/Sg-00306/1998,1998//,USA,H7N2,Avian,2
 402   91 2262 11215 >CY035589,A/chicken/New York/Sg-00298/1997,1997//,USA,H7N2,Avian,2
 413   94 2274 1604 >EU980467,A/chicken/NY/3202-7/1996,1996//,USA,H7N2,Avian,2
 426   97 2274 8035 >CY116993,A/guinea fowl/New Jersey/6322-8/1995,1994/11/07,USA,mixed,Avian,2
 430   98 2274 8039 >CY117025,A/guinea fowl/New Jersey/7290-19/1994,1994/12/19,USA,H2N2,Avian,2

----------segment 3------------- 
 209   45 2151 8037 >CY036340,A/avian/New York/Sg-00365/2001,2001//,USA,H7N2,Avian,3
 211   45 2131 11205 >CY035774,A/avian/New York/Sg-00348/2000,2000//,USA,H7N2,Avian,3
 237   51 2151 8062 >CY036439,A/guinea fowl/New Jersey/Sg-00391/2002,2002//,USA,H7N2,Avian,3
 244   52 2129 11188 >CY035703,A/avian/New York/Sg-00328/1999,1999//,USA,H7N2,Avian,3
 283   61 2151 8076 >CY036497,A/avian/New York/Sg-00406/2003,2003//,USA,H7N2,Avian,3
 292   63 2151 8071 >CY036477,A/avian/New York/Sg-00401/2003,2003//,USA,H7N2,Avian,3
 311   67 2151 8098 >CY036595,A/chicken/New Jersey/Sg-00431/2004,2004//,USA,H7N2,Avian,3
 330   71 2151 1591 >EU980466,A/chicken/NY/3202-7/1996,1996//,USA,H7N2,Avian,3
 336   71 2113 11159 >CY035590,A/chicken/New York/Sg-00298/1997,1997//,USA,H7N2,Avian,3
 357   77 2151 18263 >CY024831,A/chicken/New York/11678-5/2005,2005/02/02,USA,H7N2,Environment,3
 367   79 2151 14800 >EU742940,A/chicken/RI/4328-1/1995,1995//,USA,H7N2,Avian,3

----------segment 4-------------
 294   48 1632 1760 >CY035752,A/quail/New Jersey/Sg-00342/2000,2000//,USA,H7N2,Avian,4
 304   50 1641 1767 >CY035779,A/avian/New York/Sg-00349/2000,2000//,USA,H7N2,Avian,4
 312   51 1634 1754 >CY035730,A/chicken/New Jersey/Sg-00336/1999,1999//,USA,H7N2,Avian,4
 321   53 1648 1792 >CY036317,A/avian/New York/Sg-00358/2001,2001//,USA,H7N2,Avian,4
 365   60 1641 1726 >CY035614,A/chicken/New York/Sg-00305/1998,1998//,USA,H7N2,Avian,4
 379   63 1659 1113 >EU743261,A/turkey/VA/158512/2002,2002//,USA,H7N2,Avian,4
 379   63 1659 2151 >AY240896,A/chicken/NY/22409-4/99,1999//,USA,H7N2,Avian,4
 390   64 1641 1723 >CY035591,A/chicken/New York/Sg-00298/1997,1997//,USA,H7N2,Avian,4
 401   66 1642 1825 >CY036498,A/avian/New York/Sg-00406/2003,2003//,USA,H7N2,Avian,4
 416   69 1656 2127 >AF072394,A/Guinea Fowl/Pennsylvania/7777-1/96,1996//,USA,H7N2,Avian,4
 440   73 1659 2031 >AY831670,A/chicken/MD/MinhMa/2004,2004//,USA,H7N2,Avian,4
 462   76 1645 1704 >CY035504,A/chicken/New York/Sg-00274/1995,1995//,USA,H7N2,Avian,4
 468   77 1642 1850 >CY036635,A/chicken/New Jersey/Sg-00441/2005,2005//,USA,H7N2,Avian,4
 473   76 1605 2037 >AF071775,A/chicken/Jalisco/1994,1994//,Mexico,H7,Avian,4

----------segment 5------------- 
 213   32 1497 16253 >EU182288,A/chicken/PA/143586/2001,2001//,USA,H7N2,Avian,5
 213   32 1497 17394 >CY014898,A/chicken/Pennsylvania/143586/2002,2002//,USA,H7N2,Avian,5
 233   35 1497 10168 >EU743268,A/goose/NY/8600-3/1998,1998//,USA,H7N2,Avian,5
 260   39 1497 15686 >EU742884,A/unknown/NY/85161/2000,2000//,USA,H7N2,,5
 267   40 1497 12949 >EU742944,A/chicken/PA/11767/1997,1997//,USA,H7N2,Avian,5
 273   41 1497 8016 >HQ541723,A/chicken/MD/MinhMa/2004,2004//,USA,H7N2,Avian,5
 280   42 1497 12948 >EU742953,A/chicken/New York/13833-7/1995,1995//,USA,H7N2,Avian,5
 287   43 1497 10183 >EU742998,A/chicken/CT/260413-2/2003,2003//,USA,H7N2,Avian,5
 287   43 1497 9610 >EU982304,A/turkey/VA/55/2002,2002//,USA,H7N2,Avian,5
 300   45 1497 1601 >EU980465,A/chicken/NY/3202-7/1996,1996//,USA,H7N2,Avian,5
 307   46 1497 9785 >FJ517327,A/chicken/NY/21586-8/1999,1999//,USA,H7N2,Avian,5
 313   47 1497 10085 >CY031654,A/Guinea fowl/New York/22071/2005,2005/03/03,USA,H7N2,Avian,5
 313   47 1497 7279 >CY117022,A/guinea fowl/New Jersey/7290-19/1994,1994/12/19,USA,H2N2,Avian,5

----------segment 6------------
 363   49 1349 3496 >CY054398,A/avian/New York/Sg-00353/2000,2000//,USA,H7N2,Avian,6
 365   49 1340 3491 >CY054393,A/avian/New York/Sg-00348/2000,2000//,USA,H7N2,Avian,6
 373   50 1340 3494 >CY054396,A/avian/New York/Sg-00351/2000,2000//,USA,H7N2,Avian,6
 378   51 1349 3495 >CY054397,A/chicken/New York/Sg-00352/2000,2000//,USA,H7N2,Avian,6
 380   51 1340 3497 >CY054399,A/avian/New York/Sg-00354/2000,2000//,USA,H7N2,Avian,6
 382   52 1360 4475 >CY014897,A/chicken/Pennsylvania/143586/2002,2002//,USA,H7N2,Avian,6
 382   52 1360 4526 >AY254130,A/chicken/PA/143586/2001,2001//,USA,H7N2,Avian,6
 392   53 1349 3541 >CY054444,A/avian/New York/Sg-00399/2003,2003//,USA,H7N2,Avian,6
 408   55 1345 3478 >CY054380,A/duck/New Jersey/Sg-00335/1999,1999//,USA,H7N2,Avian,6
 437   59 1348 3567 >CY054473,A/avian/New York/Sg-00428/2004,2004//,USA,H7N2,Avian,6
 448   61 1360 3965 >CY034832,A/Guinea fowl/New York/101276-1/2005,2005/08/19,USA,H7N2,Avian,6
 454   61 1342 3455 >CY054353,A/chicken/New York/Sg-00305/1998,1998//,USA,H7N2,Avian,6
 485   65 1340 3448 >CY054346,A/chicken/New York/Sg-00298/1997,1997//,USA,H7N2,Avian,6
 492   67 1360 4521 >AY254125,A/chicken/NY/3202-7/1996,1996//,USA,H7N2,Avian,6
 500   68 1360 2399 >CY028582,A/chicken/New York/8391-2/2006,2006//,USA,H7N2,Avian,6
 522   71 1360 5870 >CY028533,A/environment/New York/3181-1/2006,2006//,USA,H7N2,Environment,6
 530   72 1357 3424 >CY054321,A/guinea fowl/New York/Sg-00272/1995,1995//,USA,H2N2,Avian,6
 558   76 1362 2841 >CY116901,A/duck/New Jersey/7872-27/1995,1994/11/18,USA,mixedÞ N2,Avian,6
 639   36  563 3025 >CY099620,A/sooty tern/Western Australia/7666/1984,1984//,Australia,mixedÞN2,Avian,6
 690   94 1362 2845 >CY116933,A/chicken/Pennsylvania/24825/1991,1991/04/12,USA,H2N2,Avian,6
 712   97 1362 1789 >AB745485,A/guinea fowl/New York/3070/1991,1991//,USA,H2N2,Avian,6
 748  102 1362 2844 >CY116925,A/guinea fowl/New Jersey/26146/1990,1990/04/05,USA,H2N2,Avian,6
 792  108 1362 4472 >CY014874,A/black duck/New York/184/1988,1988//,USA,H5N2,Avian,6
 814  111 1362 4478 >CY016150,A/mallard/Ohio/94/1989,1989/10/19,USA,H4N2,Avian,6
 877  118 1344 1442 >CY180318,A/mallard/Wisconsin/619/1983,1983//,USA,H4N2,Avian,6
 881  120 1362 1813 >CY136648,A/coot/Alberta/134/1987,1987/08/13,Canada,H6N2,Avian,6
 888  121 1362 1416 >CY178649,A/mallard/Saskatchewan/17/1981,1981//,Canada,H5N2,Avian,6
 888  121 1362 1814 >CY136656,A/mallard/Alberta/186/1987,1987/08/19,Canada,H6N2,Avian,6
 895  122 1362 1413 >CY178569,A/mallard/Wisconsin/280/1982,1982//,USA,H4N2,Avian,6
 932  127 1362 4440 >CY004621,A/pintail duck/ALB/627/1979,1979/08/13,Canada,H3N2,Avian,6
 961  131 1362 4743 >CY004102,A/pintail duck/Alberta/1360/1979,1979/08/25,Canada,H6N2,Avian,6
 973  131 1346 5031 >KF188340,A/goose/Minnesota/5733-1243/1980,1980//,USA,H9N2,Avian,6
 998  136 1362  229 >KX377332,A/greater white-fronted goose/Alaska/81081/2008,2008/05/22,USA,H9N2,Avian,6
1027  140 1362   63 >CY202638,A/mallard/Maryland/08OS1392/2008,2008/08/27,USA,H6N2,Avian,6
1027  140 1362 1437 >CY180141,A/green-winged teal/Wisconsin/228/1976,1976//,USA,H9N2,Avian,6
1027  140 1362 6075 >CY097255,A/environment/Indiana/3607/2009,2009/11/13,USA,H5N2,Environment,6
1035  141 1362 4888 >CY097592,A/mallard/Missouri/129/2009,2009/12/07,USA,H6N2,Avian,6
1042  142 1362  476 >CY139329,A/American black duck/New Brunswick/00867/2010,2010/09/13,Canada,H5N2,Avian,6
1042  142 1362 1289 >KJ567867,A/blue-winged teal/Wisconsin/13OS3463/2013,2013/09/29,USA,H3N2,Avian,6
1042  142 1362 5039 >KF188322,A/turkey/Minnesota/511/1978,1978//,USA,H9N2,Avian,6

----------segment 7------------- 
 219    2   91 10105 >HM355895,A/hermit thrush/Washington/CTR-AIV08/2006,2006/06/16,USA,,Avian,7
 234   23  982 1641 >AY241617,A/guineafowl/MA/148081-11/02,2002//,USA,H7N2,Avian,7
 250    5  200 18888 >EU087173,unidentified influenza virus,//,USA,,Environment,7
 251   23  913 10542 >CY053453,A/guinea fowl/Massachusetts/Sg-00390/2002,2002//,USA,H7N2,Avian,7
 253   23  908 10640 >CY055128,A/avian/New York/Sg-00398/2002,2002//,USA,H7N2,Avian,7
 254   25  982 1645 >AY241623,A/turkey/VA/55/2002,2002//,USA,H7N2,Avian,7
 264   26  982 1621 >AY241595,A/chicken/NJ/16224-6/1999,1999//,USA,H7N2,Avian,7
 270   25  923 10512 >CY053423,A/avian/New York/Sg-00339/2000,2000//,USA,H7N2,Avian,7
 274   27  982 8954 >AY241608,A/chicken/PA/143586/2001,2001//,USA,H7N2,Avian,7
 275   24  870 2371 >CY048669,A/blue-winged teal/Texas/Sg-00173/2007,2007/09/16,USA,H4N8,Avian,7
 276   25  903 10552 >CY053464,A/avian/New York/Sg-00411/2003,2003//,USA,H7N2,Avian,7
 277    3  108 10104 >HM355894,A/MacGillivray's warbler/Idaho/CTR-AIV07/2006,2006/06/05,USA,,Avian,7
 277   25  900 2372 >CY048670,A/mallard/Minnesota/Sg-00176/2007,2007/09/16,USA,H4N6,Avian,7
 282   25  885 2363 >CY048658,A/blue-winged teal/Louisiana/Sg-00165/2007,2007/09/15,USA,H4N6,Avian,7
 288   26  900 2375 >CY048673,A/mallard/Minnesota/Sg-00179/2007,2007/09/25,USA,H11N9,Avian,7
 297   27  908 2447 >CY048746,A/chicken/New York/Sg-00305/1998,1998//,USA,H7N2,Avian,7
 305   30  982 12211 >CY031117,A/chicken/New York/30732-6/2005,2005/03/23,USA,H7N2,Avian,7
 335   31  923 2440 >CY048739,A/chicken/New York/Sg-00298/1997,1997//,USA,H7N2,Avian,7

----------segment 8------------- 
 178   15  838 16676 >EU742908,A/unknown/NY/120485-5/2001,2001//,USA,H7N2,,8
 190   16  838 15480 >AY241626,A/avian/NY/76247-3/00,2000//,USA,H7N2,Avian,8
 214   18  838 15487 >AY241633,A/chicken/NJ/16224-6/1999,1999//,USA,H7N2,Avian,8
 250   21  838 16198 >AY241654,A/guineafowl/MA/148081-11/02,2002//,USA,H7N2,Avian,8
 298   25  838 15490 >AY241636,A/chicken/NJ/9777-7/98,1998//,USA,H7N2,Avian,8
 298   25  838 18232 >AF001410,A/chicken/NY/13202-7/1996,1996//,USA,H7N2,Avian,8
 310   26  838 15501 >AY241649,A/chicken/PA/9701524/97,1997//,USA,H7N2,Avian,8
 322   27  838 18967 >GU186489,A/environment/NY/241365-18/2003,2003//,USA,H7N2,Environment,8
 346   29  838 15904 >HQ541722,A/chicken/MD/MinhMa/2004,2004//,USA,H7N2,Avian,8
 357   30  838 17497 >CY117015,A/guinea fowl/New York/4449-12/1994,1994/11/29,USA,H2N2,Avian,8
 369   31  838 16668 >CY036747,A/environment/New York/88291-3/2005,2005/07/20,USA,H7N2,Environment,8

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

46+55+45+48+32+49+23+15=313 nucleotide-mutations in 16 years
~20 mutations per year, while ~40 would be normal.
So, this is another one of the rare examples of slow influenza-nucleotide-evolution.

The virus may have survived 8 years in some freezer but then had evolved
for another 8 years in poultry ?!?
Or bats ? We do not yet know, how fast flu evolves in bats


amino-acid mutations in the inner segments :
20,17,18,--,12,--,17,24* feline/2016
13,11,08,--,06,--,10,19* best neighbor/2000

so, quite some new amino-acid mutations, away from the bird-index.


it would be interesting to see whether that virus can
still infect poultry.


mammalean influenza at genbank with type-2 NS (segment 8) :
>KJ889419,A/swine/Kazakhstan/106/1985,1985//,Kazakhstan,H3N6,Swine,8
>CY067690,A/swine/KU/16/2001,2001//,South Korea,H7N2,Swine,8
>FJ461600,A/swine/Korea/C12/2008,2008/01/,South Korea,H5N2,Swine,8
>FJ461601,A/swine/Korea/C13/2008,2008/02/,South Korea,H5N2,Swine,8
>M65020,A/equine/Jilin/1/1989,1989//,China,H3N8,Equine,8
>GU052363,A/muskrat/Buryatiya/1944/2000,2000//,Russia,H4N6,Muskrat,8

muskrats in NY: https://www.nytimes.com/2016/05/01/n...krat.html?_r=0

hmm, muskrats as the source of the mysterical 17G -virus (A/duck/LA/17G/1987(H3N8)) ?
Lots in Mississippi (segment 5), none in Florida.
http://www.cfr.msstate.edu/wildlife/...df/muskrat.pdf
Code:
>A/duck/LA/17G/1987,1987//,H3N8
>KT887300,A/blue-winged teal/Louisiana/UGAI14-179/2014,2014/03/30,USA,H10N3,Avian,5
>KT887348,A/blue-winged teal/Louisiana/UGAI14-430/2014,2014/04/04,USA,H10N3,Avian,5
>KT887356,A/blue-winged teal/Louisiana/UGAI14-453/2014,2014/04/04,USA,H10N3,Avian,5
>KT887403,A/blue-winged teal/Louisiana/UGAI14-821/2014,2014/04/12,USA,H10N3,Avian,5
>KX960407,A/Northern shoveler/Guatemala/CIP049HT114-14/2013,2013/01/19,Guatemala,H3N8,Avian,5
>KX960442,A/Northern shoveler/Guatemala/CIP049H112-79/2012,2012/12/21,Guatemala,H4N2,Avian,5
>KX960484,A/American wigeon/Guatemala/CIP049H112-03/2012,2012/12/21,Guatemala,H4N2,Avian,5
>KM244115,A/turkey/Minnesota/16423-3/2014,2014/05/21,USA,H4N2,Avian,5
>CY097162,A/American coot/Illinois/3405/2009,2009/10/31,USA,H10N3,Avian,5
>CY076016,A/cinnamon teal/California/44287-325/2007,2007/01/27,USA,H3N8,Avian,5
>CY053824,A/pekin duck/California/P30/2006,2006/03/06,USA,H4N2,Avian,5
>FJ520131,A/northern pintail/California/44291-259/2007,2007/03/18,USA,H10N3,Avian,5
>CY076096,A/American coot/California/20181-006/2007,2007/03/02,USA,H10N3,Avian,5
>CY076168,A/American coot/Oregon/20589-007/2007,2007/12/17,USA,H3N8,Avian,5
>CY079407,A/American coot/Mississippi/09OS615/2009,2009/01/24,USA,H10N3,Avian,5
>CY097681,A/American green-winged teal/Mississippi/285/2010,2010/01/14,USA,H3N8,Avian,5
>CY097705,A/mallard/Mississippi/354/2010,2010/01/16,USA,H3N8,Avian,5
>CY097713,A/mallard/Mississippi/360/2010,2010/01/16,USA,H3N8,Avian,5
>CY097721,A/mallard/Mississippi/386/2010,2010/01/17,USA,H3N8,Avian,5
>CY097729,A/mallard/Mississippi/390/2010,2010/01/17,USA,H3N8,Avian,5
>CY186727,A/northern shoveler/Illinois/12OS5294/2012,2012/11/10,USA,H10N3,Avian,5
>KJ413566,A/blue-winged teal/LA/AI13-1334/2013,2013/03/20,USA,H4N2,Avian,5
>EU871831,A/duck/LA/17G/1987,1987//,USA,H3N8,Avian,5
>KF648925,A/environment/Mexico/CPA-04740/2011,2011/02/28,Mexico,H4N2,Environment,5
>CY032721,A/northern pintail/California/HKWF792/2007,2007/11/28,USA,H3N8,Avian,5

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

By analyzing virological data obtained in the study area between 2003 and 2011, the H2N2 antigenic subtype resulted to be prevalent in 2003 in wildlife species, including muskrat (Ondatra zibethicus),
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4074073/

a/common muskrat/chany lake/226/05 h2n2 ...
http://www.findpatent.ru/patent/260/2606030.html

KR052701

The strain proposed as an invention is a unique avian variant of the H2N2 subtype
influenza virus isolated from the mammalian muskrat (Ondatra zibethicus). .
The new influenza virus was isolated from the waterbird species that lives in
close contact with the carrier birds. It is most likely that this version of the virus
circulating in wild waterfowl has crossed the species barrier, is entrenched in a
new host, has the ability to replicate in the lungs of mammals and cause
pathological changes.

distance from the bird index: 02,03,03,--,04,--,02,03
best neighbors:

>KR052701,A/muskrat/Russia/63/2014,2014/08/30,Russia,H2N2,Muskrat
109 25 2274 18112 >JN087009,A/environment/Korea/CSM3/2002,2002//,South Korea,H3N6,Environment,1
92 21 2274 14075 >CY184013,A/mallard/Sweden/366/2002,2002/11/01,Sweden,H11N9,Avian,2
153 33 2151 9573 >HM145362,A/mallard/Jiangxi/12147/2005,2005//,China,H6N2,Avian,3
213 36 1689 289 >CY122300,A/mallard/Netherlands/12/2008,2008//,Netherlands,H2N3,Avian,4
190 28 1471 8822 >GU396905,A/wild duck/Taiwan/WB904/2006,2006/01/,Taiwan,H4N6,Avian,5
63 9 1410 5211 >CY184119,A/mallard/Sweden/4932/2004,2004/10/30,Sweden,H9N2,Avian,6
50 5 982 9689 >CY076961,A/mallard/Sweden/90/2005,2005//,Sweden,H11N9,Avian,7
60 5 831 6762 >EU599315,A/teal/Egypt/912908/2005,2005//,Egypt,H10N7,Avian,8
--------------
162 , slow evolution !

https://en.wikipedia.org/wiki/Lake_Chany
freezes Nov - May.

the slow evolution could be specific to Lake Chany (freezing ) rather than the muskrat species
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Old 06-08-2017, 09:48 AM   #40
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3 European H5N8 genomes at genbank today.
All from Belgium , Feb. 2017

So, with the Czech genome above, that makes 4.

One of the 3 is similar to the Czech sequences, except segment 2.
The other 2 are almost identical (peacock and chicken),
their closest neighbors are being examine and posted later

>MF073914,A/Cygnus olor/Belgium/1567/2017,2017/02/21,Belgium,H5N8,Avian
>MF073898,A/chicken/Belgium/807/2017,2017/02/01,Belgium,H5N8,Avian
>KY621531,A/chicken/Czech Republic/206-17_2/2017,2017/01/06,Czech Republic,H5N8,Avian
>MF073906,A/peacock/Belgium/1017/2017,2017/02/08,Belgium,H5N8,Avian


not related to a paper in a journal :
https://www.ncbi.nlm.nih.gov/nuccore/MF073914
https://www.ncbi.nlm.nih.gov/nuccore/MF073898
https://www.ncbi.nlm.nih.gov/nuccore/MF073906


http://www.patologiaviare.org/informative-da-promed.php
24-02-2017
AVIAN INFLUENZA (58): EUROPE (BELGIUM, CZECH REPUBLIC) WILDFOWL, POULTRY, SPREAD
In this posting:
[1] Belgium (Oud-Heverlee, Flemish Brabant): wildfowl, H5N8
[2] Czech Republic: poultry, H5

...
03-02-2017
AVIAN INFLUENZA (42): BELGIUM (EAST FLANDERS) ORNAMENTAL BIRDS, HPAI H5N8
Belgian authorities found the H5N8 bird flu virus at a farm north of Brussels on [Wed 1 Feb 2017] and imposed measures to contain the spread of the highly contagious virus, the Belgian agriculture ministry said on its website on [Thu 2 Feb 2017]


best neigbors in the 8 segments of
>MF073906,A/peacock/Belgium/1017/2017,2017/02/08,Belgium,H5N8,Avian

Code:
---------before 2015-------------------
 210   48 2280 4536 >LC121257,A/duck/Mongolia/118/2015,2015/08/30,Mongolia,H4N6,Avian,1
 233   53 2274 6557 >KU160817,A/chicken/Hunan/S1267/2010,2010/03/03,China,H4N6,Avian,2
 209   45 2151  490 >LC132919,A/duck/Mongolia/129/2015,2015/08/30,Mongolia,H3N3,Avian,3
 105   18 1704 7128 >KP732646,A/duck/Eastern China/S1109/2014,2014/11/09,China,H5N8,Avian,4
 213   32 1497 1435 >KX979542,A/mallard duck/Netherlands/15/2011,2011/09/14,Netherlands,H6N8,Avian,5
 134   19 1413  747 >KP732686,A/duck/Eastern China/S1109/2014,2014/11/09,China,H5N8,Avian,6
 203   20  981 2823 >LC121383,A/duck/Mongolia/499/2015,2015/08/31,Mongolia,H10N7,Avian,7
  95    8  838 3223 >KP732726,A/duck/Eastern China/S1109/2014,2014/11/09,China,H5N8,Avian,8
-----------------recent---------------------------------------------
 105   24 2280  652 >KY635499,A/duck/Bangladesh/26920/2015,2015/12/09,Bangladesh,H3N6,Avian,1
 250   57 2274  682 >KY635797,A/duck/Bangladesh/26918/2015,2015/12/09,Bangladesh,H3N6,Avian,2
 251   54 2151  656 >KY635496,A/black-tailed godwit/Bangladesh/24734/2015,2015/02/22,Bangladesh,H7N5,Avian,3
  52    9 1704    2 >KY621531,A/chicken/Czech Republic/206-17_2/2017,2017/01/06,Czech Republic,H5N8,Avian
 247   37 1497  262 >KY320435,A/Mallard/Sweden/816/2014,2014/12/15,Sweden,H1N1,Avian,5
  84   12 1413    3 >KY621531,A/chicken/Czech Republic/206-17_2/2017,2017/01/06,Czech Republic,H5N8,Avian
  91    9  981    4 >KY621531,A/chicken/Czech Republic/206-17_2/2017,2017/01/06,Czech Republic,H5N8,Avian
  59    5  838    4 >KY621531,A/chicken/Czech Republic/206-17_2/2017,2017/01/06,Czech Republic,H5N8,Avian
----------------------duck Bangldesh----------------------------------------
 109   25 2280  656 >KY635524,A/duck/Bangladesh/26918/2015,2015/12/09,Bangladesh,H3N6,Avian,1
 250   57 2274  682 >KY635797,A/duck/Bangladesh/26918/2015,2015/12/09,Bangladesh,H3N6,Avian,2
 278   60 2151  670 >KY635609,A/duck/Bangladesh/26918/2015,2015/12/09,Bangladesh,H3N6,Avian,3
-------
 320   48 1497  689 >KY635636,A/duck/Bangladesh/26918/2015,2015/12/09,Bangladesh,H3N6,Avian,5
-------
 530   52  981  696 >KY635602,A/duck/Bangladesh/26918/2015,2015/12/09,Bangladesh,H3N6,Avian,7
 440   30  681  550 >KY635490,A/duck/Bangladesh/26918/2015,2015/12/09,Bangladesh,H3N6,Avian,8

 214   21  981  705 >KY635683,A/duck/Bangladesh/24704/2015,2015/02/22,Bangladesh,H15N9,Avian,7
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Old 06-08-2017, 12:28 PM   #41
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H5N8 is a virus on the move.
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Old 06-24-2017, 05:38 AM   #42
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seems that Indonesia finally uploads H5N1 sequences to genbank again
after a 10 year's break.

20 full avian genomes from 2016

ftp://ftp.ncbi.nih.gov/genomes/INFLU...fluenza_na.dat


e.g. : https://www.ncbi.nlm.nih.gov/nuccore/KY614909
Reassortant highly pathogenic avian influenza (H5N1) virus in Indonesia
Unpublished
This virus isolate was sequenced on behalf of The Directorate
General of Livestock and Animal Health Services, The Indonesian
Ministry of Agriculture(DGLAHS-MOA). Please acknowledge the
DGLAHS-MOA if the virus sequence is used in a publication and other
molecular studies.



>A/quail/Deliserdang/01160025/2016,2016/01/22
is still the old Indonesian H5N1 from 2003-2007, in all 8 segments

>A/chicken/Subang/08160018-002/2016,2016/01/08
>A/eagle/Jakarta Timur/20616-206-III/2016,2016/03/07
>A/chicken/Majalengka/08160070-001/2016,2016/03/25
>A/chicken/Kuningan/08160178-003/2016,2016/03/18
>A/muscovy duck/Pekalongan/04160460/2016,2016/04/04

are the old H5N1 in segments 1,7,8 only

all the others are new, Fujian-type H5N1


the 2016 quail virus is most similar to a chicken from West Java
and the cat from 2006
[remember how Andrew Jerimijenko described here how he found
that kitten in mid-North Java while looking for sick chickens
in a small village]

Code:
>A/quail/Deliserdang/01160025/2016,2016/01/22,Indonesia,H5N1,Avian

----------segment 1------------- 
 488   84 1719 2099 >KR732579,A/chicken/WestJava/TASIKO B/2006,2006//,Indonesia,H5N1,Avian,1
 494   85 1719 17965 >CY014317,A/feline/Indonesia/CDC1/2006,2006/01/22,Indonesia,H5N1,Cat,1
 494   85 1719 7902 >DQ492819,A/chicken/Magetan/BBVW/2005,2005//,Indonesia,H5N1,Avian,1
 498   43  862 7906 >DQ492823,A/quail/Boyolali/BPPV4/2004,2004//,Indonesia,H5N1,Avian,1
 500   86 1719 11014 >GQ122436,A/quail/Yogjakarta/UT1023/2004,2004/01/15,Indonesia,H5N1,Avian,1

----------segment 2------------- 
 425   34  799 12840 >AY651651,A/chicken/Indonesia/BL/2003,2003//,Indonesia,H5N1,Avian,2
 435   35  803 10925 >GQ122425,A/chicken/West Java/UT1001/2003,2003/10/20,Indonesia,H5N1,Avian,2
 435   35  803 10926 >GQ122431,A/chicken/East Java/UT1006/2003,2003/11/15,Indonesia,H5N1,Avian,2
 435   35  803 10928 >GQ122443,A/chicken/East Kalimantan/UT1035/2004,2004/02/16,Indonesia,H5N1,Avian,2
 435   35  803 7806 >DQ366328,A/chicken/Guangxi/12/2004,2004//,China,H5N1,Avian,2
 439   35  796 11604 >CY029180,A/chicken/Shantou/4059/2002,2002//,China,H5N1,Avian,2

----------segment 3------------- 
 460   99 2151 17846 >CY116653,A/ferret/Indonesia/5-F1/2005,2005//,Indonesia,H5N1,Ferret,3
 460   99 2151 17910 >CY014318,A/feline/Indonesia/CDC1/2006,2006/01/22,Indonesia,H5N1,Cat,3
 483  104 2151 2101 >KR732561,A/chicken/WestJava/SMI-PAT/2006,2006//,Indonesia,H5N1,Avian,3

----------segment 4------------- 
 240   41 1704 7261 >KP742944,A/environment/Bekasi/0813321-013/2013,2013/09/,Indonesia,H5N1,Environment,4
 246   42 1707 7248 >KP742931,A/environment/Jakarta Pusat/0813129-008/2013,2013/04/,Indonesia,H5N1,Environment,4
 251   43 1707 7250 >KP742933,A/environment/Jakarta Timur/0813129-029/2013,2013/05/,Indonesia,H5N1,Environment,4
 252   43 1704 7257 >KP742940,A/environment/Jakarta Utara/0813207-026/2013,2013/07/,Indonesia,H5N1,Environment,4
 252   43 1704 7265 >KP742948,A/environment/Jakarta Selatan/0813321-034/2013,2013/09/,Indonesia,H5N1,Environment,4
 257   44 1707 1571 >KP742891,A/chicken/Karimun/BPPVII 719-11/2012,2012/11/,Indonesia,H5N1,Avian,4
 258   44 1704 7262 >KP742945,A/environment/Kota Tangerang/0813321-018/2013,2013/06/,Indonesia,H5N1,Environment,4
 258   44 1704 7263 >KP742946,A/environment/Kota Depok/0813321-020/2013,2013/06/,Indonesia,H5N1,Environment,4
 269   46 1707 7249 >KP742932,A/environment/Jakarta Timur/0813129-027/2013,2013/05/,Indonesia,H5N1,Environment,4
 273   29 1062 7267 >KP742950,A/environment/Kota Surabaya/0414283-046/2013,2013/06/,Indonesia,H5N1,Environment,4
 275   47 1704 7244 >KP742927,A/environment/Kota Bekasi/081489-004/2013,2013/10/,Indonesia,H5N1,Environment,4
 281   48 1707 1540 >KP742850,A/chicken/Padang/BPPVRII-62-2/2011,2011/02/,Indonesia,H5N1,Avian,4
 299   51 1704 7245 >KP742928,A/environment/Tangerang Selatan/081489-008/2013,2013/10/,Indonesia,H5N1,Environment,4
 305   52 1704 7255 >KP742938,A/environment/Kota Depok/0813207-020/2013,2013/08/,Indonesia,H5N1,Environment,4
 310   53 1707 1553 >KP742873,A/chicken/Padang/BPPVRII-51-2/2011,2011/02/,Indonesia,H5N1,Avian,4
 333   57 1707 7225 >KP742859,A/environment/Bekasi/BPPVRVIII-344-08/2010,2010/12/,Indonesia,H5N1,Environment,4
 339   58 1707 7226 >KP742860,A/environment/East Jakarta/BPPVRVIII-344-25/2010,2010/12/,Indonesia,H5N1,Environment,4
 345   59 1707 7224 >KP742858,A/environment/South Jakarta/BPPVRVIII-344-20/2010,2010/12/,Indonesia,H5N1,Environment,4
 345   59 1707 7232 >KP742866,A/environment/East Jakarta/BPPVRVIII-492-CM/2011,2011/09/,Indonesia,H5N1,Environment,4
 361   41 1133 1132 >KR078232,A/chicken/West Java/M35/2010,2010//,Indonesia,H5N1,Avian,4
 369   63 1707 3098 >AB621353,A/chicken/Indonesia/D10014/2010,2010/06/,Indonesia,H5N1,Avian,4
 369   63 1707 7228 >KP742862,A/environment/South Jakarta/BPPVRVIII-52-99/2010,2010/01/,Indonesia,H5N1,Environment,4
 372   61 1637 3403 >JF302895,A/chicken/Indonesia/SmiWN18/2009,2009/11/22,Indonesia,H5N1,Avian,4
 373   13  348 6758 >KR987692,A/chicken/Bangli/06/2005,2005/10/20,Indonesia,H5N1,Avian,4
 395   53 1339 6558 >JF970241,A/chicken/Indonesia/Tanggerang_1/2007,2007/12/,Indonesia,H5N1,Avian,4
 404   69 1707 7223 >KP742857,A/environment/West Jakarta/BPPVRVIII-344-19/2010,2010/12/,Indonesia,H5N1,Environment,4
 404   69 1707 7227 >KP742861,A/environment/South Jakarta/BPPVRVIII-52-84/2010,2010/05/,Indonesia,H5N1,Environment,4
 414   47 1133 1124 >KR078224,A/chicken/Banten/M15/2009,2009//,Indonesia,H5N1,Avian,4
 414   47 1133 1126 >KR078226,A/chicken/Central Java/M22/2009,2009//,Indonesia,H5N1,Avian,4
 421   72 1707 1554 >KP742874,A/chicken/Sarolangun/BPPVRII-187/2009,2009/03/,Indonesia,H5N1,Avian,4
 432   49 1133 1123 >KR078223,A/chicken/East Java/M14/2009,2009//,Indonesia,H5N1,Avian,4
 437   25  571 3590 >JN032397,A/chicken/Indonesia/Ambon_4/2006,2006//,Indonesia,H5N1,Avian,4
 437   25  571 3592 >JN032399,A/chicken/Indonesia/Timika_1/2006,2006//,Indonesia,H5N1,Avian,4
 439   75 1707 1557 >KP742877,A/chicken/Pekanbaru/BPPVRII-91-3/2011,2011/03/,Indonesia,H5N1,Avian,4
 441   50 1133 1122 >KR078222,A/chicken/East Java/M12/2009,2009//,Indonesia,H5N1,Avian,4
 449   19  423 7450 >KR987706,A/canine/Buleleng/21/2006,2006/10/20,Indonesia,H5N1,Canine,4
 467   53 1133 1125 >KR078225,A/chicken/East Java/M19/2009,2009//,Indonesia,H5N1,Avian,4
 468   25  534 3591 >JN032398,A/chicken/Indonesia/Ambon_5/2006,2006//,Indonesia,H5N1,Avian,4
 481   82 1704 6986 >GU183461,A/chicken/Banten/Srg-Fadh/2008,2008/01/,Indonesia,H5N1,Avian,4
 488   17  348 6757 >KR987691,A/duck/Karangasem/04/2005,2005/10/15,Indonesia,H5N1,Avian,4
 496   21  423 6764 >KR987704,A/chicken/Klungkung/19/2006,2006/10/20,Indonesia,H5N1,Avian,4
 503   86 1707 7229 >KP742863,A/environment/East Jakarta/BPPVRVIII-413-AD/2011,2011/09/,Indonesia,H5N1,Environment,4
 509   87 1707 1542 >KP742852,A/chicken/Melak/BPPVRV-32-1/2011,2011/01/,Indonesia,H5N1,Avian,4
 511   58 1133 1127 >KR078227,A/chicken/West Java/M25/2009,2009//,Indonesia,H5N1,Avian,4
 515   88 1707 1541 >KP742851,A/chicken/Bartim/BPPVRV-126-4/2011,2011/04/,Indonesia,H5N1,Avian,4
 515   88 1707 3097 >AB621352,A/tree sparrow/Indonesia/D10013/2010,2010/05/,Indonesia,H5N1,Avian,4
 516   11  213 4795 >EU542781,A/chicken/Turkey/Carsamba 1037/2006,2006//,Turkey,H5N1,Avian,4
 516   11  213 4863 >EU542849,A/chicken/Turkey/Silivri ist962/2006,2006//,Turkey,H5N1,Avian,4
 520   59 1133 1128 >KR078228,A/chicken/South Kalimantan/M28/2010,2010//,Indonesia,H5N1,Avian,4
 520   59 1133 1129 >KR078229,A/chicken/South Kalimantan/M29/2010,2010//,Indonesia,H5N1,Avian,4
 520   59 1133 1130 >KR078230,A/chicken/West Java/M30/2010,2010//,Indonesia,H5N1,Avian,4
 526   21  399 6761 >KR987695,A/chicken/Jembrana/09/2006,2006/07/23,Indonesia,H5N1,Avian,4
 526   21  399 6762 >KR987696,A/chicken/Jembrana/10/2006,2006/08/01,Indonesia,H5N1,Avian,4
 527   90 1707 7230 >KP742864,A/environment/East Jakarta/BPPVRVIII-392-3/2011,2011/09/,Indonesia,H5N1,Environment,4
 527   90 1707 7231 >KP742865,A/environment/East Jakarta/BPPVRVIII-447-AU/2011,2011/09/,Indonesia,H5N1,Environment,4
 528   90 1704 3613 >GU183455,A/Muscovy duck/West Java/Bks3/2007,2007/01/,Indonesia,H5N1,Avian,4
 529   60 1133 1131 >KR078231,A/chicken/West Java/M34/2010,2010//,Indonesia,H5N1,Avian,4
 533   91 1707 1537 >KP742847,A/chicken/Tabanan/BBVD-0178-3/2011,2011/03/,Indonesia,H5N1,Avian,4
 533   91 1707 1543 >KP742853,A/chicken/Sukoharjo/BBVW-218-03/2011,2011/03/,Indonesia,H5N1,Avian,4
 536   89 1659 7302 >CY014208,A/feline/Indonesia/CDC1/2006,2006/01/22,Indonesia,H5N1,Cat,4
 538   92 1707 1538 >KP742848,A/chicken/Tabanan/BBVD-0212-4/2011,2011/04/,Indonesia,H5N1,Avian,4
 538   92 1707 1539 >KP742849,A/chicken/Bangli/BBVD-0245A-4/2011,2011/04/,Indonesia,H5N1,Avian,4
 538   92 1707 1545 >KP742855,A/chicken/Sukoharjo/BBVW-1148-07/2011,2011/07/,Indonesia,H5N1,Avian,4
 538   92 1707 1561 >KP742881,A/quail/Blitar/BBVW-790-05/2011,2011/05/,Indonesia,H5N1,Avian,4
 538   92 1707 1562 >KP742882,A/chicken/Buleleng/BBVD-0224B-4/2011,2011/04/,Indonesia,H5N1,Avian,4
 538   92 1707 1563 >KP742883,A/chicken/Karangasem/BBVD-0209-4/2011,2011/04/,Indonesia,H5N1,Avian,4
 538   92 1707 1564 >KP742884,A/chicken/Klungkung/BBVD-0259-5/2011,2011/05/,Indonesia,H5N1,Avian,4
 538   92 1707 5090 >EU124151,A/Chicken/West Java/TASIKSOL/2006,2006/08/01,Indonesia,H5N1,Avian,4
 539   92 1704 7247 >KP742930,A/environment/Kota Bekasi/0813129-003/2013,2013/11/,Indonesia,H5N1,Environment,4
 544   93 1707  651 >KR732514,A/chicken/WestJava/TASIKO B/2006,2006//,Indonesia,H5N1,Avian,4
 544   93 1707 1546 >KP742856,A/chicken/Gorontalo/BBVM-228-10/2011,2011/03/,Indonesia,H5N1,Avian,4
 544   93 1707 1565 >KP742885,A/chicken/Tabanan/BBVD-0149-3/2011,2011/03/,Indonesia,H5N1,Avian,4
 544   93 1707 3245 >CY091794,A/chicken/Tabanan/BBVD-461/2007,2007/08/21,Indonesia,H5N1,Avian,4
 544   93 1707 3247 >CY091796,A/chicken/Bangli/BBVD-343/2007,2007/07/11,Indonesia,H5N1,Avian,4
 544   93 1707 3256 >CY091805,A/chicken/Jembrana/BBVD-298b/2007,2007/06/18,Indonesia,H5N1,Avian,4
 544   93 1707 3263 >CY091812,A/chicken/Badung/BBVD-205/2007,2007/05/15,Indonesia,H5N1,Avian,4
 544   93 1707 3264 >CY091813,A/chicken/Badung/BBVD-216/2007,2007/05/22,Indonesia,H5N1,Avian,4

----------segment 5------------- 
 280   42 1497 15747 >CY014254,A/feline/Indonesia/CDC1/2006,2006/01/22,Indonesia,H5N1,Cat,5
 280   42 1497 16351 >KR732538,A/chicken/WestJava/TASIKO B/2006,2006//,Indonesia,H5N1,Avian,5
 287   43 1497 16354 >KR732556,A/chicken/Garut/BBVW-223/2007,2007//,Indonesia,H5N1,Avian,5
 293   44 1497 16358 >KR732575,A/chicken/WestJava/SMI-PAT/2006,2006//,Indonesia,H5N1,Avian,5
 293   44 1497 16467 >KR732428,A/chicken/West Java/Sbg-29/2007,2007//,Indonesia,H5N1,Avian,5
 293   44 1497 16471 >KR732464,A/chicken/West Java/TJA/2008,2008//,Indonesia,H5N1,Avian,5
 300   45 1497 18101 >CY116687,A/ferret/Indonesia/5-F6/2005,2005//,Indonesia,H5N1,Ferret,5
 307   46 1497 18097 >CY116655,A/ferret/Indonesia/5-F1/2005,2005//,Indonesia,H5N1,Ferret,5

----------segment 6------------- 
 243   31 1275 2650 >GU183474,A/Muscovy duck/West Java/Bks3/2007,2007/01/,Indonesia,H5N1,Avian,6
 245   32 1303  935 >KM892800,A/chicken/Bali/U8661/2009,2009/06/01,Indonesia,H5N1,Avian,6
 250   32 1275 2648 >GU183476,A/chicken/Inhu/BPPVRII/2007,2007/06/18,Indonesia,H5N1,Avian,6
 256   33 1288 3707 >EU124217,A/Chicken/Indonesia/Siak1631-2/2006,2006//,Indonesia,H5N1,Avian,6
 258   32 1236 1139 >KC831537,A/chicken/Padang Pariaman/BPPVRII-698/2007,2007/12/03,Indonesia,H5N1,Avian,6
 258   33 1275 2643 >GU183481,A/chicken/Banten/Srg-Fadh/2008,2008/01/,Indonesia,H5N1,Avian,6
 260   34 1303 1065 >KC831462,A/chicken/Ponorogo/BBVW-197b/2007,2007/04/19,Indonesia,H5N1,Avian,6
 260   34 1303 1116 >KC831514,A/pigeon/Bukittinggi/BPPVRII-178-B/2007,2007/03/26,Indonesia,H5N1,Avian,6
 260   34 1303 1117 >KC831515,A/chicken/Bukittinggi/BPPVRII-178-C/2007,2007/03/26,Indonesia,H5N1,Avian,6
 260   34 1303 1118 >KC831516,A/chicken/Padang/BPPVRII-151/2007,2007/03/26,Indonesia,H5N1,Avian,6
 260   34 1303 1119 >KC831517,A/Muscovy duck/Bukittinggi/BPPVRII-178-M/2007,2007/03/26,Indonesia,H5N1,Avian,6
 260   34 1303 1120 >KC831518,A/swan/Bukittinggi/BPPVRII-178-S/2007,2007/03/26,Indonesia,H5N1,Avian,6
 260   34 1303 1121 >KC831519,A/duck/Padang/BPPVRII-151/2007,2007/03/28,Indonesia,H5N1,Avian,6
 260   34 1303 1122 >KC831520,A/chicken/Batam/BPPVRII-188/2007,2007/04/02,Indonesia,H5N1,Avian,6
 260   34 1303 1131 >KC831529,A/chicken/Pariaman/BPPVRII-370/2007,2007/06/15,Indonesia,H5N1,Avian,6
 260   34 1303 1138 >KC831536,A/chicken/Agam/BPPVRII-694/2007,2007/11/28,Indonesia,H5N1,Avian,6
 263   34 1290 3706 >EU124216,A/Chicken/Indonesia/Padang1631-1/2006,2006//,Indonesia,H5N1,Avian,6
 263   34 1290 3708 >EU124218,A/Chicken/Indonesia/Agam1631-3/2006,2006/06/01,Indonesia,H5N1,Avian,6
 263   34 1290 3709 >EU124219,A/Pigeon/Indonesia/Rokhit1631-6/2006,2006/10/01,Indonesia,H5N1,Avian,6
 263   34 1290 3710 >EU124220,A/Chicken/Indonesia/Pekenbaru1631-11/2006,2006/12/01,Indonesia,H5N1,Avian,6
 266   34 1275 2644 >GU183480,A/chicken/West Java/Smi-Acul/2008,2008/01/18,Indonesia,H5N1,Avian,6
 266   34 1275 2649 >GU183475,A/chicken/Pessel/BPPVRII/2007,2007/03/07,Indonesia,H5N1,Avian,6
 268   35 1303 1115 >KC831513,A/chicken/Pesisir Selatan/BPPVRII-119/2007,2007/03/07,Indonesia,H5N1,Avian,6
 268   35 1303 1123 >KC831521,A/chicken/Solok Selatan/BPPVRII-217/2007,2007/04/08,Indonesia,H5N1,Avian,6
 268   35 1303 1124 >KC831522,A/chicken/Kerinci/BPPVRII-262-C/2007,2007/04/23,Indonesia,H5N1,Avian,6
 268   35 1303 1125 >KC831523,A/duck/Kerinci/BPPVRII-262-D/2007,2007/04/23,Indonesia,H5N1,Avian,6
 268   35 1303 1128 >KC831526,A/chicken/Payakumbuh/BPPVRII-307/2007,2007/05/22,Indonesia,H5N1,Avian,6
 276   36 1303 1127 >KC831525,A/chicken/Sawahlunto/BPPVRII-273/2007,2007/05/07,Indonesia,H5N1,Avian,6
 276   36 1303 1130 >KC831528,A/chicken/Tanah Datar/BPPVRII-365/2007,2007/06/14,Indonesia,H5N1,Avian,6
 276   36 1303 2234 >AB685457,A/chicken/EastKalimantan/UT511/2010,2010/04/,Indonesia,H5N1,Avian,6
 276   36 1303 2235 >AB685458,A/chicken/South Kalimantan/UT521/2010,2010/07/,Indonesia,H5N1,Avian,6
 280   35 1249 3687 >EU124120,A/Chicken/Murao Jambi/BPPV11/2005,2005//,Indonesia,H5N1,Avian,6
 282   36 1275 2653 >GU183471,A/chicken/West Java/Smi-Hay/2005,2005/02/,Indonesia,H5N1,Avian,6
 283   37 1303 1052 >KC831449,A/chicken/West Java/Sbg-08/2006,2006/01/20,Indonesia,H5N1,Avian,6
 283   37 1303 1053 >KC831450,A/chicken/West Java/Sbg-09/2006,2006/02/26,Indonesia,H5N1,Avian,6
 283   37 1303 1055 >KC831452,A/chicken/West Java/Drd-20/2007,2007/03/04,Indonesia,H5N1,Avian,6
 283   37 1303 1133 >KC831531,A/chicken/Bengkalis/BPPVRII-532/2007,2007/09/03,Indonesia,H5N1,Avian,6
 283   37 1303 1141 >KC831539,A/chicken/West Java Tangerang/PTB6/2008,2008/02/22,Indonesia,H5N1,Avian,6
 283   37 1303 2233 >AB685456,A/chicken/EastKalimantan/UT498/2010,2010/04/,Indonesia,H5N1,Avian,6
 283   37 1303 2236 >AB685459,A/chicken/Riau/UT531/2010,2010/07/,Indonesia,H5N1,Avian,6
 283   37 1303 2453 >CY091965,A/duck/Bantul/BBVW-78-22210/2008,2008/01/30,Indonesia,H5N1,Avian,6
 285   36 1261 3715 >EU124225,A/Chicken/Indonesia/Lampung1631-23/2006,2006/09/01,Indonesia,H5N1,Avian,6
 286   37 1290 3714 >EU124224,A/Chicken/Indonesia/Rejang Lebong1631-22/2006,2006/07/01,Indonesia,H5N1,Avian,6
 288   37 1284 5579 >CY014234,A/feline/Indonesia/CDC1/2006,2006/01/22,Indonesia,H5N1,Cat,6
 291   38 1303  648 >KR732533,A/chicken/Garut/BBVW-223/2007,2007//,Indonesia,H5N1,Avian,6
 291   38 1303 1059 >KC831456,A/chicken/Sumenep/BBVW-165/2007,2007/04/03,Indonesia,H5N1,Avian,6
 291   38 1303 1068 >KC831465,A/chicken/Bantul/BBVW-218/2007,2007/05/13,Indonesia,H5N1,Avian,6
 291   38 1303 1069 >KC831466,A/chicken/Garut/BBVW-223/2007,2007/05/05,Indonesia,H5N1,Avian,6
 291   38 1303 1070 >KC831467,A/Muscovy duck/Garut/BBVW-223/2007,2007/05/05,Indonesia,H5N1,Avian,6
 291   38 1303 1079 >KC831477,A/chicken/Klaten/BBVW-290/2007,2007/05/30,Indonesia,H5N1,Avian,6

----------segment 7------------- 
 274   27  982 10572 >GU183442,A/chicken/West Java/Smi-Acul/2008,2008/01/18,Indonesia,H5N1,Avian,7
 285   28  982 10571 >GU183443,A/chicken/Banten/Srg-Fadh/2008,2008/01/,Indonesia,H5N1,Avian,7
 295   29  982 10578 >GU183436,A/Muscovy duck/West Java/Bks3/2007,2007/01/,Indonesia,H5N1,Avian,7
 325   32  982 2210 >KR732557,A/chicken/WestJava/TASIKO B/2006,2006//,Indonesia,H5N1,Avian,7
 325   32  982 4036 >KM892801,A/chicken/Bali/U8661/2009,2009/06/01,Indonesia,H5N1,Avian,7
 346   34  982 19032 >CY014221,A/feline/Indonesia/CDC1/2006,2006/01/22,Indonesia,H5N1,Cat,7
 346   34  982 2791 >KR732494,A/chicken/Pekalongan/BBVW/2007,2007//,Indonesia,H5N1,Avian,7

----------segment 8------------- 
 280   23  821 12891 >KR732545,A/chicken/WestJava/TASIKO B/2006,2006//,Indonesia,H5N1,Avian,8
 292   24  821 13759 >GU183423,A/chicken/Banten/Srg-Fadh/2008,2008/01/,Indonesia,H5N1,Avian,8
 304   25  821 12755 >CY014260,A/feline/Indonesia/CDC1/2006,2006/01/22,Indonesia,H5N1,Cat,8
 316   26  821 13766 >GU183416,A/Muscovy duck/West Java/Bks3/2007,2007/01/,Indonesia,H5N1,Avian,8
 341   28  821 11757 >GQ122470,A/chicken/Bali/UT2091/2005,2005//,Indonesia,H5N1,Avian,8
 341   28  821 11758 >GQ122476,A/chicken/Bali/UT2092/2005,2005//,Indonesia,H5N1,Avian,8
 341   28  821 11764 >GQ122513,A/chicken/East Java/UT6021/2006,2006/11/,Indonesia,H5N1,Avian,8
 341   28  821 13767 >GU183415,A/duck/Jakarta/Slmt306/2006,2006/09/,Indonesia,H5N1,Avian,8
 341   28  821 15033 >CY116658,A/ferret/Indonesia/5-F1/2005,2005//,Indonesia,H5N1,Ferret,8
 341   28  821 15034 >CY116666,A/ferret/Indonesia/5-F2/2005,2005//,Indonesia,H5N1,Ferret,8
__________________
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Last edited by gsgs; 06-24-2017 at 08:53 AM.
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