Homologous recombination as an evolutionary force in the avian influenza A virus

[Hanshilinzuo]

Research Article
Homologous recombination as an evolutionary force in the avian influenza A virus
Cheng-Qiang He1,*, Zhi-Xun Xie2,*, Guan-Zhu Han1, Jian-Bao Dong2, Dong Wang1, Jia-Bo Liu2, Le-Yuan Ma1, Xiao-Fei Tang2, Xi-Ping Liu1, Yao-Shan Pang2 and Guo-Rong Li1

1 College of Life Science, Shandong Normal University, Jinan, China 250014
2 Guangxi Veterinary Research Institute, Nanning, China 530001

* Corresponding authors: Cheng-Qiang He, College of Life Science, Shandong Normal University, Shandong Province, China 250014, Tel.: 86-531-8618-0745, E-mail: hchqiang@yahoo.com.cn ; Zhi-Xun Xie, Guangxi Veterinary Research Institute, Nanning, China 530001, Tel.: 86-771-3105702, Email: xiezhixun@126.com.

Received for publication August 7, 2008. Revision received September 27, 2008. Revision received October 8, 2008. Accepted for publication October 12, 2008.

Avian influenza A viruses (AIVs), including the H5N1, H9N2 and H7N7 subtypes, have been directly transmitted to humans, raising concerns over the possibility of a new influenza pandemic. To prevent a future avian influenza pandemic, it is very important to fully understand the molecular basis driving the change in AIV virulence and host tropism. Although virulent variants of other viruses have been generated by homologous recombination, the occurrence of homologous recombination within AIV segments is controversial and far from proven. This study reports three circulating H9N2 AIVs with similar mosaic PA genes descended from H9N2 and H5N1. Additionally, many homologous recombinants are also found deposited in GenBank. Recombination events can occur in PB2, PB1, PA, HA and NP segments and between lineages of the same/different serotype. These results collectively demonstrate that intragenic recombination plays a role in driving the evolution of AIVs, potentially resulting in effects on AIV virulence and host tropism changes.

MBE Advance Access published on October 17, 2008.
doi:10.1093/molbev/msn238

 

[Hanshilinzuo]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

This paper is published in Mol Biol Evol by a group that pay their attention in recombination recently. Mol Biol Evol is a top journal in Evolution.

 

[sharon sanders]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

Thank you Hanshilinzuo.

 

[gsgs]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

lots of Chinese H9N2 uploaded recently, I haven't checked it yet

 

[AlaskaDenise]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

This article requires a subscription to view. See:
http://mbe.oxfordjournals.org/cgi/content/abstract/msn238

.

 

[HenryN]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

H9N2 recombination also seen in isolates from Korea

http://www.recombinomics.com/phylo/H9N2_NA.html

 

[HenryN]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

More recombinant serotypes in Korea

http://www.recombinomics.com/News/09120801/Human_Avian_Recombinants.html

 

[AlaskaDenise]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

More recombinant serotypes in Korea

http://www.recombinomics.com/News/09120801/Human_Avian_Recombinants.html

Commentary

Human / Avian Influenza Recombinants in Korean Swine
Recombinomics Commentary 19:39
September 12, 2008

Complete sequences for all eight gene segments from swine isolates in South Korea were recently released at Genbank (see list here). The twenty isolates represented all three serotypes currently in circulation in seasonal flu (H3N2, H1N2, H1N1). Like many swine sequences in circulation, including the Canadian swine sequences, all isolates had a human PB1. In the <?XML:NAMESPACE PREFIX = ST1 /><ST1:COUNTRY-REGION w:st="on"><ST1LACE w:st="on">Korea</ST1LACE></ST1:COUNTRY-REGION> swine, the PB1 was most closely related to human isolates from the mid-nineties. The other gene segments were swine, but five of the sequences had segments representing 1/3 to 1/2 of the gene, which were identical or closely related to avian sequences. Many of the avian sequences matched low path isolates, but clade 2.2 H5N1 was present in one isolate, which also had regions of identity with clade 1 H5N1 also.

These regions of obvious homologous recombination represented several combinations. Two of the isolates, A/swine/Korea/CY07/2007(H3N2) and A/swine/Korea/CY08/2007(H1N2) had the same wild bird sequence in the first half of PA. The H1N2 isolate also had long segments of avian sequences in PB2.

However, recombination was also present in the human PB1 sequence. One isolate, A/swine/Korea/CY09/2007(H3N2) had long regions of identity with wild bird sequences. In contrast, the other isolates, A/swine /Korea/CAS05/2004(H3N2) had clade 2.2 H5N1 sequences in its human PB1 sequences. In addition, there were clade 1 H5N1 sequences in PB2 for this isolate.

The examples of PB1 recombination represent the first reported human / avian recombinants, which are cause for concern. Swine are mixing vessels that lead to reassortment and recombination. When H5N1 emerged in humans in southeast Asia in 2004, many of the isolates had mammalian polymorphisms that would be frequently found in swine. Some of these polymorphisms were also present in wild birds. These recent sequences help explain both of those observations.

These recombinants also support earlier results with Canadian swine, which had examples of recombination with earlier swine sequences. The most striking examples in the Canadian swine were in PB2 and PA, as was also seen in the Korean swine. Similarly, sequences with clear examples of recombination were seen in isolates from live markets in <ST1:COUNTRY-REGION w:st="on"><ST1LACE w:st="on">Korea</ST1LACE></ST1:COUNTRY-REGION> in 2003.

The latest recombinants highlight the role of swine as mixing vessels as well as evolution in mammalian flu genes, including the human sequences in PB1. This extensive evolution between avian and mammalian flu sequences remain a cause for concern.


.

 

[gsgs]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

> the occurrence of homologous recombination within AIV segments is controversial and far from proven
> This study reports three circulating H9N2 AIVs with similar mosaic PA genes descended
> from H9N2 and H5N1... These results collectively demonstrate that intragenic recombination
> plays a role in driving the evolution of AIVs

this remains unclear.
Apparantly they have just 3 avian samples which are recombinants of H5N1 and H9N2 PA.
They don't say which viruses from genbank are involved.

they "demonstrate intragenic recombination" but say that "homologous recombination
is far from proven".

To prove the claim we need a recombinant virus, which survives,replicates,continues to spread.
When recombinant viruses zwar appear but then disappear soon,
then they hardly play a role in influenza evolution.

 

[HenryN]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

> the occurrence of homologous recombination within AIV segments is controversial and far from proven
> This study reports three circulating H9N2 AIVs with similar mosaic PA genes descended
> from H9N2 and H5N1... These results collectively demonstrate that intragenic recombination
> plays a role in driving the evolution of AIVs

this remains unclear.
Apparantly they have just 3 avian samples which are recombinants of H5N1 and H9N2 PA.
They don't say which viruses from genbank are involved.

they "demonstrate intragenic recombination" but say that "homologous recombination
is far from proven".

To prove the claim we need a recombinant virus, which survives,replicates,continues to spread.
When recombinant viruses zwar appear but then disappear soon,
then they hardly play a role in influenza evolution.

Please. If a virus recombines with distantly related sequences and survives, then it recombines much more frequently with closely related sequences, as seen with the MANY examples of SNP's, which are VERY common and are the key to influenza evolution.

 

[AlaskaDenise]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

Is there a particular reason that certain AI's can infect humans (H1, H2, H3, H5, H7, & H9), and others don't? Or do they all have the potential to infect humans?

.

 

[HenryN]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

Is there a particular reason that certain AI's can infect humans (H1, H2, H3, H5, H7, & H9), and others don't? Or do they all have the potential to infect humans?

.

Serotypes are used to classify influenza. All have the potential of infecting humans. A few receptor binding domain changes go a long way toward infectivity.

 

[gsgs]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

just reformatting the Author names so FT-search will find them


> These results collectively demonstrate that intragenic recombination plays a role in driving
> the evolution of avian flu

I haven't yet seen a recombined segment, that establishes and spreads

--------------------------------------------------------------------------
http://mbe.oxfordjournals.org/cgi/content/abstract/26/1/177

MBE Advance Access originally published online on October 17, 2008
Molecular Biology and Evolution 2009 26(1):177-187; doi:10.1093/molbev/msn238

Homologous Recombination as an Evolutionary Force in the Avian Influenza A Virus
Cheng-Qiang He
Zhi-Xun Xie , Guan-Zhu Han , Jian-Bao Dong , Dong Wang , Jia-Bo Liu ,
Le-Yuan Ma , Xiao-Fei Tang , Xi-Ping Liu , Yao-Shan Pang
and Guo-Rong Li


E-mail: hchqiang@yahoo.com.cn
Accepted for publication October 12,2008 .
Avian influenza A viruses (AIVs), including the H5N1, H9N2, and H7N7 subtypes,
have been directly transmitted to humans, raising


Key Words: Avain influenza virus homologous recombination evolution


{ I can't find any mentioning of the recombination in the pika/BI }


Homologous Recombination as an Evolutionary Force in the Avian Influenza A Virus
Mol. Biol. Evol. 26(1):177–187. 2009

 

[gsgs]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

free full text available now:

http://mbe.oxfordjournals.org/cgi/c...actfulltext=and&searchid=1&resourcetype=HWCIT



we analyzed roughly 9,000 complete segments of AIVs deposited in GenBank and found the evidence of recombination in these genes. Moreover, several mosaic viruses were also found to be able to circulate in the field.
A/chicken/Guangxi/14/00 and A/chicken/Guangxi/17/00 were collected in November, whereas A/chicken/Guangxi/1/00 was collected in March

segments used: http://mbe.oxfordjournals.org/cgi/content/full/26/1/177/TBL1

recombinations found: http://mbe.oxfordjournals.org/cgi/content/full/26/1/177/TBL2

A/chicken/Jilin/hh/2002(H5N1)   | pb2
A/chicken/Hubei/wh/1997(H5N1)   | pb2
A/chicken/jilin/53/01(H9N2)     | pb2
A/chicken/Hebei/718/2001(H5N1)  | pb2
A/chicken/Hubei/wj/1997(H5N1)   | pb2
A/chicken/Henan/wu/2004(H5N1)   | pb2
A/chicken/Henan/210/2004(H5N1)  | pb2
A/tree sparrow/Henan/1/04(H5N1) | pb2
A/chicken/Jilin/hj/2003(H5N1)   | pb2
A/chicken/Jilin/hq/2003(H5N1)   | pb2
A/chicken/Guangxi/1/00(H9N2)    | pb2
A/duck/Hubei/wg/2002(H5N1)      | PB2
A/tree sparrow/Henan/4/04(H5N1) | pb2

A/goose/Jilin/hb/2003(H5N1)     | pb1
A/chicken/Beijing/ne/1999(H9N2) | pb1
A/chicken/Jilin/9/2004(H5N1)    | pb1
A/chicken/Jilin/he/2002(H5N1)   | pb1
A/chicken/Jiangsu/nf/02(H9N2)   | pb1
A/chicken/Jilin/hd/2002(H5N1)   | pb1
A/chicken/Hubei/wf/2002(H5N1)   | pb1
A/chicken/Hebei/718/2001(H5N1)  | pb1

A/duck/Zhejiang/bj/2002(H5N1)   | pa 
A/chicken/Guiyang/1655/06(H5N1) | pa 
A/chicken/Guangxi/17/00(H9N2)   | pa 
A/chicken/Guangxi/14/00(H9N2)   | pa 
A/chicken/Guangxi/1/00(H9N2)    | pa 
A/chicken/Jilin/ha/2003(H5N1)   | pa 
A/chicken/jilin/hg/02(H5N1)     | pa 
A/goose/Jilin/hb/2003(H5N1)     | pa 
A/chicken/Hubei/wl/1997(H5N1)   | pa 
A/SCk/HK/YU100/2002(H5N1)       | pa 
A/chicken/Hebei/108/02(H5N1)    | pa 
A/chicken/jilin/hj/03(H5N1)     | pa 
A/mallard/ohio/1801/2005/(H3N8) | pa 
A/chicken/Hubei/wi/1997(H5N1)   | pa 

A/chicken/Gansu/1/99(H9N2)      | ha 
A/chicken/Tianjing/1/96(H9N2)   | ha 
A/CK/HongKong/NT142/03(H9N2)    | ha 
A/duck/Vietnam/8/05(H5N1) Arch  | ha 

A/chicken/Jilin/9/2004(H5N1)    | np 
A/chicken/Jilin/hd/2002(H5N1)   | np 
A/chicken/Jilin/hq/2003(H5N1)   | np 
A/chicken/Jilin/hn/2003(H5N1)   | np 
A/Ck/HK/37.4/2002(H5N1)         | np 

A/chieken/hebei/718/01(H5N1)    | na

Interestingly, almost all recombinants were isolated in China

We have also found that the recombination can occur between human and swine influenza viruses (He et al. 2008).

In conclusion, this study provides evidence demonstrating that recombination can occur in AIVs and plays a role in the evolution of the virus


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


see here my list :
http://www.setbb.com/fluwiki2/viewtopic.php?t=243&mforum=fluwiki2
with p-values

and Kuller-pictures:
http://magictour.free.fr/panflu/reco0.l5

update from Jan.2009: (time to do my 2010 - list ....)
with 81 homologous recombination candidates
http://magictour.free.fr/panflu/re9a1.txt
PB2 only, (I was lazy in 2008)


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

so many examples of homologous recombination, yet whether they play a role
in the evolution os influenza cannot be shown.
Apparantly none of these recombined virus did spread and produce preogeny
which was recognized and sampled.
The paper doesn't address this phenomenon (at least I didn't find it),
despite their title.

 

[gsgs]

Re: Homologous recombination as an evolutionary force in the avian influenza A virus

most recombination in PB2 is in China poultry or DE,NJ ruddy turnstones
But turnstones are only a small part of the flu database, most wild birds
are mallards.
turning stones shuffles genes ? Nuclear Plant in DE,NJ ? Same lab ?



non-China recombinations in PB2 of wild birds

whistling swan/Shimone/499/1983(H5N3)   mallard/Sweden/49/2002(H5N9) 
shorebird/DE/22/2006(H7N3)              ruddy turnstone/NJ/195/2006(H7)
ruddy turnstone/NJ/Sg-00476/2008(H12N5) mallard/Minnesota/Sg-00579/2008(H1N1) 
ruddy turnstone/NJ/196/2006(H7N3)       ruddy turnstone/NJ/569/2006(H7N3) 
ruddy turnstone/DE/752/2006(H7N7)       ruddy turnstone/DE/892/2006(H7N7) 
mallard/Minnesota/195/99(H4N6)          mallard/Minnesota/212/99(H4N8) 
mallard/Montana/458328-5/2006(H5N3)     bufflehead/CA/HKWF205/2007(H4N8)
ruddy turnstone/DE/669/2002(H2N1)       ruddy turnstone/NJ/1315/2002(H2N9) 
ruddy turnstone/DE/1444/2000(H12N5)     laughing gull/DE/94/2000(H12N4)
red knot/DE/1269/00(H10N7)              shorebird/DE/236/03(H11N9)
mallard/Ohio/667/2002(H4N6)             mallard/MD/185/2003(H5N2)
pintail/Alaska/211/2005(H3N8)           mallard/Alaska/256/2005(H3N8)

>A/whistling swan/Shimone/499/1983(H5N3) 
>A/mallard/Sweden/49/2002(H5N9) 
.................o.......................................... 1 
.........................................o..o............... 2 
..............o..o.................o....................o... 4 
.....o..............o.......................o..............o 4 
..............o........o........o..........................o 4 
..o...........o.....o.....o..............o........o......... 6 
.....o..o..o..o..o...........o..............o..o.....o...... 9 
........o..........o........................................ 2 
..............o..............o.....o..............o......... 4 
........o..........................o......o....o........o... 5 
.......................o...........o.....o.................o 4 
........o..........................o..o..................... 3 
..............o..o.................o...........o...........o 5 
..............o................................o..o........o 4 
.................o...........o..o.o.........o............... 5 
...................................o.................o...... 2 
..........................o........o........................ 2 
..o...........o..............o.................o.....o...... 5 
.................o..o.......................o............... 3 
.....o...o.......o........o.....o..o........o.....o..o..o..o 11 
..o.....o..............o........o.....o..o..o.....oo....o..o 11 
..o..o..o..o.....o........o..o............o................. 8 
........o...o.o..o.......................o........o.....o... 7 
.....o........o...........o..o..o........o.....o...o.o...... 9 
.....o........o........o.....o..o..oo.o..o..o..o.....o..o..o 14 
..o.....o..o.....o..o...........o..o..o..o...........o.....o 11 
.....o..oo.o......o....o..o..o.....o..o..o..............o..o 13 
.....o..o..o...o.o..o..o..o..o.............................. 9 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
-- 167 

>A/ostrich/South Africa/9508103/1995(H9N2)
>A/Ck/Victoria/9306-04-0930/1992(H7N3) 
..................o......o.o.......o.....o.....o...........o 7 
..........................o................................. 1 
...........o..o..o.....o..........................o..o.....o 7 
.....o........o........o.......................o..o........o 6 
..o..o.....o..o..o...o.oo.o.....o..o..o..o........o........o 15 
..o.....o..o..........................o..o........o..o.....o 8 
.....o................................o..o...o....o........o 6 
...o.o..oo.............o..o........o..o...........o..o...... 10 
o....o........o..o....................o..o......o.o..o..o..o 11 
..o...o..........o........o..o.....o..............o.....o..o 9 
........o.........o.o..o..o..oo..........o..o........o..o... 11 
..o..o..o.................o.....o..............o.....o...... 7 
..o..o........o.....o..o...........o.....o.....o..o..oo.o..o 13 
..o..o.....o.....o..o..o........o........o..o.....o.....o... 11 
o....o...........o.....o..............o...o.o..o.....o...... 9 
...........o..o................................o............ 3 
..................................................o......... 1 
..........................................o................. 1 
............................................................ 0 
.........................................o......ooo......... 4 
...................................................o........ 1 
..o.....o.................o........o........................ 4 
....................................o.......o............... 2 
.....o.................o...........o........................ 3 
..........................o..o.................o............ 3 
.......................o......o.........................o... 3 
...........................................o...............o 2 
.................o.......................................... 1 
.......................o........o..............o............ 3 
.........................................o.................. 1 
..............o...o..................o...................... 3 
..............o...o......................................... 2 
........................................................o... 1 
.................o..o..................o..........o......... 4 
..........................o...........o..................... 2 
....................................o....................... 1 
.........................................o.................. 1 
............................................................ 0 
-- 177 


>A/shorebird/Delaware/22/2006(H7N3) 
>A/ruddy turnstone/New Jersey/195/2006(H7)
............................................................ 0 
............................................................ 0 
............................................................ 0 
.....o...................................................... 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
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............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
.......................o....................o............... 2 
...........o.........................o............o......... 3 
...........o..o........o......o...................o......... 5 
.............................o.....oo.o..o.....o.....o...... 7 
...........o..o......o.......o..o...........o............... 6 
........o..o.....o........o........o........................ 5 
........o.....o...........o...........o........o...........o 6 
.................o..o.....o.....o.....o....................o 6 
................................o........o..............o... 3 
.....o....................o..o.......................o.....o 5 
...........o.......................o.........o.............. 3 
..o....................o.....o........o.................o... 5 
..o..o........o.......................o..................... 4 
..o...........o..o............o.o..............o............ 6 
..........................o........o.................o...... 3 
............................................................ 0 
............................................................ 0 
-- 70 


>A/ruddy turnstone/New Jersey/Sg-00476/2008(H12N5)
>A/mallard/Minnesota/Sg-00579/2008(H1N1) 
...........................................................o 1 
..............o...........o....................o..o......... 4 
........o..o...........o..........................o........o 5 
...o................o.................o..o..o..o..o......... 7 
.....o..o.....o............................................. 3 
..o..............o...........o..o........................... 4 
.....o......o.o.......................o..o........o........o 7 
..............o........o..o..o..o..o....................o... 7 
.....o........o.....o..o..........................o..o...... 6 
....................o..o..........................o..o...... 4 
o.........................o...........o..o........o.....o... 6 
....................o..................o.o........o......... 4 
.....o.....o..o..o.....o........o..o........o.....o.....o... 10 
..o................................o........................ 2 
.......................o.....o..o........................... 3 
....................o..............o..............o......... 3 
.....o...........o...........o..o........o..o........o....o. 8 
........o..........................o......o................. 3 
..............o.................o..........................o 3 
o........................................................... 1 
............................................................ 0 
..............o............................................. 1 
............................................................ 0 
............................................................ 0 
.........................................o.................. 1 
............................................................ 0 
............................................................ 0 
....................................o.o..................... 2 
..........................o................................. 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
........................o................................... 1 
..................o......................................... 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
-- 98 


>A/ruddy turnstone/New Jersey/196/2006(H7N3)
>A/ruddy turnstone/New Jersey/569/2006(H7N3) 
...........................o................................ 1 
........o.............................o........o............ 3 
........o.....o........o..........................o........o 5 
..oo.........................o........o...........o......... 5 
.....o........o........................o.......o............ 4 
.................o......o.......o..o.....o.................. 5 
.....oo....o..........................o........o............ 5 
......o.o.....o...........o..o..oo.......................... 7 
..............o..o..o..o..............o....o......o..o...... 8 
....................o........o....................o..o...... 4 
o...................o.....o...........o..o..o..o..o......... 8 
..o.................o.......................o.....o......... 4 
.....o........o.................o..o........o.....o......... 6 
..o........o.................o.............................. 3 
....o............o.....o.....o..o.........o................. 6 
....................o...o.......o..o..............o......... 5 
.................o.......................o..o............... 3 
.............................................o.............. 1 
...........o................................................ 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
................................o........................... 1 
............................................................ 0 
............................................................ 0 
...........................................................o 1 
.......................o................................o... 2 
..o..o...................................................... 2 
...............................................o............ 1 
..........................o................................. 1 
............................................................ 0 
............................................................ 0 
-- 92 


>A/ruddy turnstone/Delaware/752/2006(H7N7)
>A/ruddy turnstone/Delaware/892/2006(H7N7) 
...........................o................................ 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
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............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
................................o..o.......................o 3 
........o..............o.................................... 2 
...........o...........o........o..o........o.....oo........ 7 
.......................o....................o............... 2 
..o..................................o............o......... 3 
..o........o..o........o......o...................o......... 6 
.............................o.....oo.o..o.....o.....o...... 7 
...........o..o......o.......o..o...........o............... 6 
o.......o..o.....o........o........o........................ 6 
........o.....o...........o...........o........o.......o...o 7 
.................o....................o....................o 3 
.........................................o..............o... 2 
..........................o.................o........o...... 3 
...................................o........................ 1 
..o......................................................... 1 
............................................................ 0 
..o......................................................... 1 
..............o............................................. 1 
............................................................ 0 
............................................................ 0 
-- 62 


>A/mallard/Minnesota/195/99(H4N6)
>A/mallard/Minnesota/212/99(H4N8) 
...................................o.....o.....o............ 3 
..o...................................o..............o...... 3 
.....o......................................o............... 2 
.......................o..............o..................... 2 
...........o..o........o....................o.....o......... 5 
........o..o........o.....o.....o........o.................. 6 
.......................o.................................... 1 
.............................o..o................o.......... 3 
.....o..............o..............o.....o...........o...... 5 
.....................................................o..o..o 3 
........o.......................o...........o..o..o......... 5 
....................o............o..........o.....o......... 4 
..........................................o.o.........o.o..o 5 
........o...........o.................o....................o 4 
............................................o...........o... 2 
.....o.................o........................o....o...... 4 
.................o..o....................o.....o............ 4 
.....o........o......................................o..o... 4 
..o........o.....o..............o...........o............... 5 
.........o................o..o.....o....................o... 5 
...........o.......................o......o.o......o.o...... 6 
.......................o..o........o..............o......... 4 
........o..............o..........................o......... 3 
...........o.....o...........o..o...o..........o...........o 7 
....................o....................................... 1 
..o......................................................... 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
....................o....................................... 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
-- 98 


>A/mallard/Montana/458328-5/2006(H5N3)
>A/bufflehead/CA/HKWF205/2007(H4N8)
............................................................ 0 
......................o..................................... 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
.................o.......................................... 1 
...o........................................................ 1 
........o................................................... 1 
............................................................ 0 
............................................................ 0 
......................................o..................... 1 
............................................................ 0 
............................................................ 0 
.........o..............................................o... 2 
....................o....o......o..o..o..................... 5 
.......................o.................................... 1 
...........o...........o..o.....o...........o.....o......... 6 
..............o........o..................o....o............ 4 
.....o..............o.............................o......... 3 
..................................................o......... 1 
..............o..............o......o.o........o.....o..o... 7 
...........o..o...........o..o..oo.......o..o.....o......... 9 
........oo.o..o..o........o.............................o... 7 
........o.....o..............o........o................o.... 5 
....................o.....o.....o.....o....................o 5 
................................o........o..............o... 3 
.............................o.......................o..o... 3 
...........o.................................o.............. 2 
..o....................o.....o........o.................o... 5 
..............o...........o................................. 2 
........o........o............o.o..............o............ 5 
...................................o........o........o...... 3 
.................o..............o........................... 2 
......................................o..................... 1 
-- 86 


>A/ruddy turnstone/Delaware/669/2002(H2N1)
>A/ruddy turnstone/New Jersey/1315/2002(H2N9) 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
.......................o.................................... 1 
............................................................ 0 
............................................................ 0 
........................................................o... 1 
........o...........o.....o...........o.....o.....o......... 6 
........o...........o..o.................o..o............... 5 
.....o........o........o........o....................oo....o 7 
...........o....................o...............o..........o 4 
.....o.....o..o.................o...........o.....o......... 6 
....................o..o.......................o..o......... 4 
..............o..o.................o........o..o.....o...... 6 
..............o..................o...................o...... 3 
.....o...........o.................o....................o... 4 
.........o.........................o...........o............ 3 
...........o............o................oo.o...........o... 6 
.....o..o...........o..o..o..o....................o........o 8 
..o..............o..o..o..........................o......... 5 
.....o...o.......o........o..o..o...o.o........o............ 9 
..o..o...........................................o.......... 3 
.....o.....o..........o......o..o........o..o.....o.....o... 9 
...........o......o......................................... 2 
..o.....o..o..oo............................o..o.....o...... 8 
....................o..............o........................ 2 
................................o........................... 1 
............................................................ 0 
............................................................ 0 
..o.....................................................o... 2 
.....o..o................................................... 2 
.................o...........o.................o............ 3 
............................................................ 0 
............................................................ 0 
............................................................ 0 
-- 110 


>A/ruddy turnstone/DE/1444/2000(H12N5)
>A/laughing gull/DE/94/2000(H12N4)
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
................................o........................... 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
.........o...........................................o...... 2 
.....o...........o....o.....................o...........o..o 6 
.........o.........................o...........o............ 3 
...........o..............o...............o.............o... 4 
......o.............o..o..o..o.....o..............o........o 8 
.................o..o..o.......o...o...........o..o......... 7 
.....o...o.......o...........o..o...o.o........o............ 8 
.....o.....o.......................o..o....................o 5 
.....o..o.............o.........o........o..o..............o 7 
...........o......o................o........................ 3 
...........o..oo..o....o.......................o.....o...... 7 
..............o..o..o.....o........o.....o...........o.....o 8 
........o.....o..o.........o....o..............o............ 6 
.....o....................o..............o.................o 4 
.......................o..............o..o..oo.............. 5 
............................................o............... 1 
..o..o...........o.....o.....o..............o..o.....o...... 8 
.....o..o.....o..o...........oo.o........................... 7 
.......................o...........o........................ 2 
................................o........................... 1 
............................................................ 0 
-- 103 


>A/red knot/Delaware/1269/00(H10N7)
>A/shorebird/DE/236/03(H11N9)
..............o................................o............ 2 
.....o..............o..............o..o...........o.....o..o 7 
.................o.........................................o 2 
..o....................o..o...........o...........o......... 5 
.....o.....o..o................................o............ 4 
........o....................o.....o.....o..............o... 5 
..............o.....o..o...................................o 4 
......o....o......................................o.....o..o 5 
..o..o..o.............................o..o.................o 6 
.....oo....o........o..o.....o..o..o..o.....o........o..o..o 13 
..o.....o...........o..o.....o.....o....o......o.....o...... 9 
........o...........o...o...................o............... 4 
.....o...........o.....o........o....................oo....o 7 
........o..o..o.................o.....o.........o..........o 7 
.....o.....o..o.............................o.....o...o..... 6 
.....o........o........o.......................o..o......... 5 
..............o.....o........o.....o........o..o.....o....o. 8 
..............o......................................o...... 2 
.....o...........o....o.....................o...........o..o 6 
.........o.................................................. 1 
............................................................ 0 
......o..................................o.................. 2 
....................................o....................... 1 
............................................................ 0 
............................................................ 0 
.............................o.............................. 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
.......................o.............................o...... 2 
..........................o................................. 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
-- 115 


>A/mallard/Ohio/667/2002(H4N6)
>A/mallard/MD/185/2003(H5N2)
...................................o.....o.....o...........o 4 
..............o......................................o...... 2 
........o........o.....o....................o........o..o... 6 
..o...........o........o..o.................o...........o... 6 
.....o........o...........o..............o.....o............ 5 
..o...........o..o.......................o........o..o..o... 7 
..o..o........o.....o.................o........o..o.....o... 8 
......o.o..o....................o.......................o... 5 
.........................................o..............o... 2 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
...........o................................................ 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
......................................o..................... 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
.........................................o.................. 1 
............................................................ 0 
...............................................o............ 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
-- 49 


>A/pintail/Alaska/211/2005(H3N8)
>A/mallard/Alaska/256/2005(H3N8) 
............................................................ 0 
............................................................ 0 
........................................o............o...... 2 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
..................................................o......... 1 
.............................o........o..................... 2 
........o................................................... 1 
............................................................ 0 
...........o................................................ 1 
............................................................ 0 
............................................................ 0 
.................o.............................o..........o. 3 
.................................o.............o.....o...... 3 
.....o.................o........o..o....................o... 5 
.....o..o..............o..o..o.....o...........o........o... 8 
..........................................o.o..o...........o 4 
....................oo....o..o.............................o 5 
........o...........o....................................... 2 
.....o...................................oo.......o......... 4 
..o..o..............o...........o...........o.....o..o...... 7 
........o..o.....o........o..o..o........o..o............... 8 
.....o..o..........................o........................ 3 
..............oo...............................o............ 3 
..o..............o..o.....o........o..o..............o...... 7 
........oo.......o.........o......................o......... 5 
..o........o..............o..............o.................o 5 
.....o..............o..o...........o........oo.............. 6 
.................o...o.o................................o... 4 
.....o.....o...........o.....oo....o.....o..o.........o.o... 10 
.................o.....o.....oo.o...........o..o............ 7 
.......................o...........oo......................o 4 
...........o.....o.......................................... 2 
............................................................ 0 
-- 112