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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JOURNAL Unpublished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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