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**gsgs** · April 2, 2010, 08:27 AM

Re: slow evolution in Chinese birds

Waterborne transmission from inoculated sparrows to contact chickens was absent, while 25% of sparrows were infected via waterborne transmission from chickens. The viral shedding and susceptibility to infection we observed in sparrows, coupled with their presence in poultry houses, could facilitate virus spread among poultry and wild birds in the face of an H5N1 influenza virus outbreak.

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http://www.hubmed.org/display.cgi?uids=20089659

**gsgs** · December 17, 2011, 06:58 AM

Re: slow evolution in Chinese birds

A/environment/Guizhou/2/2009/01/16(H5N1) http://www.ncbi.nlm.nih.gov/nuccore/CY098796?
has only 6 differences in PB1 to
A/Anhui/1/2005/11/2005/11/01(H5N1)

TITLE Indications that Live Poultry Markets Are a Major Source of Human
H5N1 Influenza Virus Infection in China
JOURNAL J. Virol. 85 (24), 13432-13438 (2011)

Guizhou and Anhui are Southern China, so quite warm.
Still it seems that H5N1 can survive in the environment
of live poultry markets for prolonged time
More then double as long as it resides inside cells, at least.

Indications that live poultry markets are a major source of human H5N1 influenza virus infection in China - PubMed

http://www.ncbi.nlm.nih.gov/pubmed/21976646

Human infections of H5N1 highly pathogenic avian influenza virus have continued to occur in China without corresponding outbreaks in poultry, and there is little conclusive evidence of the source of these infections. Seeking to identify the source of the human infections, we sequenced 31 H5N1 viruse …

**gsgs** · May 2, 2012, 04:34 PM

Re: slow evolution in Chinese birds

Genetic relationship of H3 subtype avian influenza viruses isolated from domestic ducks and wild birds in Korea and their pathogenic potential in chickens and ducks - PubMed

http://www.ncbi.nlm.nih.gov/pubmed/21955449

The H3 subtype avian influenza virus (AIV) is one of the most frequently isolated subtypes in domestic ducks, live poultry markets, and wild birds in Korea. In 2002-2009, a total of 45 H3 subtype AIVs were isolated from the feces of clinically normal domestic ducks (n=28) and wild birds (n=17). The …

Influenza A virus (A/environment/Korea/SH142/2007(H3N8)) segment 1 pol - Nucleotide - NCBI

http://www.ncbi.nlm.nih.gov/nuccore/JN087301

A/environment/Korea/SH142/2007/12/17

PB2 similar to A/Dk/HK/562/1979(H10N9)
and A/Dk/Nanchang/1681/1992/12/01(H3N8)
and A/Dk/Zhejiang/11/2000(H5N1)

A/slaty backed gull/Shandong/38/2004(H5N1)
A/Dk/HK/394/1978(H5N3)

A/Sw/KU/16/2001(H7N2)
A/Dk/HK/293/1978(H7N2)

31 mutations in 26 years
44 in 15 years
39 in 28 years
26 in 21 years

and this is confirmed by more than one sequence

and it changed evolution : the PB2 is now in almost all H5N1

Code:

                                                            000000000000000000000000000000
                                                            111111112222333333444555556667
                                                            000113994777033489588012374663
                                                            589674579456178090305811958121
                                                            ------------------------------
                                                            TTVKTHDKEADPNSVRRDPVVRVTIMLATV
>A/duck/Zhejiang/11/2000,2000//,H5N1,China                  ...............K..............
>A/duck/Hong Kong/7/1975,1975//,H3N2,Hong Kong              ...............K..............
>A/duck/Hong Kong/562/1979,1979//,H10N9,Hong Kong           ..L............K......I.......
>A/environment/Korea/SH142/2007,2007/12/17,H3N8,South Korea ...............K..............
>A/duck/Nanchang/1681/1992,1992/12/01,H3N8,China            ...............K........VV..I.
>A/duck/Hong Kong/24/1976,1976//,H4N2,Hong Kong             ...............K..............
>A/goose/HK/10/1976,1976/11/11,H3N2,Hong Kong               A........T.....K..............
>A/duck/Hong Kong/293/1978,1978//,H7N2,Hong Kong            ....P..........KGN............
>A/swine/KU/16/2001,2001//,H7N2,South Korea                 ....P.........IKGN.....I......
>A/duck/Hubei/126/1985,1985//,H7N8,China                    .A...Y.R.......K..S.I.........
>A/duck/Hong Kong/366/78,1978//,H9N2,Hong Kong              ----------GS...K..............
>A/duck/Hong Kong/698/1979,1979//,H5N3,Hong Kong            ..I...N.....S..K...........T.-
>A/duck/Hong Kong/784/1979,1979/10/10,H9N2,Hong Kong        ........G......K..............
>A/slaty-backed gull/Shandong/38/04,2004//,H5N1,China       ...............K..........F..M
>A/duck/Hong Kong/394/1978,1978//,H5N3,Hong Kong            ...R.........A.K...I.L........
>A/Index/birds/2000(H3N8a)                                  ..............................

taking only viruses that did spread , where we have multiple similar samples at genbank

(low)mutations in promille in PB2 :

H5N1 (Henan/16/2004 <-- one of the main strains) -(HK/7/1975) : 28 in 29 years
H5N1 (Henan/16 <-- HK/562/1979) : 30 in 25 years
H5N1 (Henan/16 <-- ~5 other examples from HK) : ~35 in 25 years
H5N1 (Henan/16 <-- UK/1/1956) : 57 in 48 years

human H3N2 : 52 in 35 years
equine H3N8 : 61 in 45 years
human H1N1 : 85 in ~62 years
swine H1N1 : 73 in 29 years

**Amish Country** · May 3, 2012, 06:06 AM

Re: low mutation rates in flu-viruses

Originally posted by gsgs View Post

it's not really about recombination (IMO)
recombination-theory can't explain this either.
I had speculated that vaccine strains might have become wild
or frozen viruses might have escaped from a lab.

For how long and at what temperatures do flu viruses remain viable when frozen? I know this sounds like the plot out of an old 1950 era B sifi movie but with all the glacial melting around the world and in the Arctic and Antarctic is it possible that some older strains preserved in the ice are resurfacing? Possibly picked up as ground nesting birds are find new homes that were formerly under ice or were carried in the frigid melt waters?

**gsgs** · May 3, 2012, 07:22 AM

Re: slow evolution in Chinese birds

this had been examined but none were found ("Sibirian Ice")
the 1918 virus was recovered from a permafrost-burial,
but only in small parts, broken into many pieces.

We have one example however with the 1977 virus that
"slept" for ~25 years and presumably escaped from a (Russian?) lab.

But labs use liquid nitrogene, which is much colder than just
water-ice. Hmm, they should try it in a lab : try to recover
infectable flu from water ice after ~1,2,..,5 years - looks doable.

When it is waterborne, stays in water for some months - then into a duck
for some weeks, then into water ... ,for years ... then it would only
spend half of the time in ducks where it can mutate.
But, even if this would happen, it must still be rare.

It could also maybe survive inside some special cells or maybe
in immunodeficient ducks where it just stays for prolonged time without
replicating, protected from degrading, - until it is reactivated.
Other viruses are doing this, AFAIK.
Some even insert their RNA or DNA into host-DNA where it is preserved.
But flu won't do that

**gsgs** · August 29, 2013, 02:11 AM

Re: slow evolution in Chinese birds

A/chicken/Hubei/119/1983//,H10N5
A/duck/Hubei/126/1985//,H7N8
A/duck/Hubei/137/1985//,H10N4

Influenza A virus (A/chicken/Hubei/119/1983(H10N5)) polymerase PB2 (PB - Nucleotide - NCBI

http://www.ncbi.nlm.nih.gov/nuccore/EU559256

He,X., Tang,S., Li,Y., Kou,Z., Wu,Y., Chen,S. and Li,T.
The Role of LPAI Viruses in Origin and Spread of HPAI Virus Genes:
Implication from Three LPAI Viruses Isolated from Poultry in Hubei
Province of Southern China in mid-1980s

unpublished

--------------------------------------------------
to each other:

1 >EU559256,A/chicken/Hubei/119/1983,1983//,China,H10N5
2280 2274 2151 1686 1497 1419 982 693
2 >EU559257,A/duck/Hubei/126/1985,1985//,China,H7N8
2280 2274 2151 1683 1497 1413 982 693
3 >EU559263,A/duck/Hubei/137/1985,1985//,China,H10N4
2280 2274 2151 1686 1497 1413 759 693

Code:

 1-2:112, 58, 60,725, 50,695, 20,289
 2-3:108, 56, 62,727, 51,744, 22,283
 1-3:  5,  3, 21, 94,  2,664,  1, 33

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

A/tree sparrow/3/Henan/2004,H5N1:

Hb119: 15, 9, 8,768, 2,562, 5, 4
Hb126:247,126,131,767, 77,556, 23,199
Hb137: 9, 5, 49,765, 5,452, 6, 19

very closely related

so some animal picked up a 10-20 years-old LP flu-virus
reassorted it with a then-circulating H5N1 and gave it
to the sparrows in Hunan ?

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

A/chicken/Hubei/wx/1997//,H5N1 ; x in {h,i,j,k,l,m}

h2: 431 98 2273 800 >A/duck/Hong Kong/7/1975,1975//,H3N2
h3: 246 53 2151 596 >A/mallard/Astrakhan/244/1982,1982//,H14N6
h5: 222 33 1483 18 >A/duck/Beijing/1/1978,1978//,H3N6
h7: 132 10 757 3172 >A/duck/Hubei/137/1985,1985//,H10N4
h8: 405 34 838 1239 >A/duck/Germany/1215/1973,1973//,H2N3

i1: 171 39 2280 2633 >A/chicken/Hubei/119/1983,1983//,H10N5
i2: 140 23 1632 2631 >A/duck/Hubei/137/1985,1985//,H10N4
153 25 1632 2633 >A/chicken/Hubei/119/1983,1983//,H10N5
i3: 195 42 2151 2577 >A/chicken/Hubei/119/1983,1983//,H10N5
i5: 33 5 1497 2848 >A/chicken/Hubei/119/1983,1983//,H10N5
i7: 0 0 982 3174 >A/chicken/Hubei/119/1983,1983//,H10N5
i8: 303 21 692 2713 >A/chicken/Hubei/119/1983,1983//,H10N5

j1: 178 27 1512 90 >A/goose/Hong Kong/17/77 ,1977//,H6N4
j2: 387 88 2271 3042 >A/turkey/England/N28/1973,1973//,H5N2
j3: 177 38 2143 1731 >A/duck/Hong Kong/312/1978,1978//,H5N3
j5: 146 22 1497 840 >A/duck/Hong Kong/d134/1977,1977//,H6N2
j7: 91 9 982 1260 >A/duck/Hong Kong/365/1978,1978//,H4N6
j8: 131 11 838 800 >A/duck/Hong Kong/147/1977,1977//,H9N6

k1: 429 65 1512 90 >A/goose/Hong Kong/17/77 ,1977//,H6N4
k2: 26 6 2274 2631 >A/duck/Hubei/137/1985,1985//,H10N4
k3: 162 35 2151 2575 >A/duck/Hubei/137/1985,1985//,H10N4
k5: 33 5 1497 2848 >A/chicken/Hubei/119/1983,1983//,H10N5
k7: 92 7 759 3172 >A/duck/Hubei/137/1985,1985//,H10N4
k8: 115 8 693 2712 >A/duck/Hubei/137/1985,1985//,H10N4

l1: 364 83 2280 675 >A/duck/Hong Kong/342/78,1978//,H5N2
l5: 247 37 1497 2848 >A/chicken/Hubei/119/1983,1983//,H10N5
l7: 91 9 981 2283 >A/goose/Hong Kong/23/1978,1978//,H5N3
l8: 131 11 838 800 >A/duck/Hong Kong/147/1977,1977//,H9N6

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slow evolution in Chinese birds

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