Evidence for influenza A virus RNA in Siberian lake ice

[aardvark]

http://jvi.asm.org/cgi/content/abstract/JVI.00986-06v1

Greetings all -- I'm a newly registered user, but have been periodically reading this forum for some time.

I thought this item was intriguing because, among other things, it would seem to present an alternate mechanism to account for observed (but unexpected according to dogmatic reasoning) sequence fidelity in viral isolates that are greatly separated in time.

 

[hawkeye]

Re: Evidence for influenza A virus RNA in Siberian lake ice

welcom aardvark. Thank you for the link.

Abstract For the link above

Influenza A infects a large proportion of the human population annually, sometimes leading to the deaths of millions. The biotic cycles of infection are well characterized, and include studies among populations of humans, poultry, swine, and migratory waterfowl. However, there are few studies of abiotic reservoirs for this virus. Here, we report the preservation of influenza A genes in ice and water from high latitude lakes that are visited by large numbers of migratory birds. The lakes are along the migratory flight paths of birds flying into Asia, North America, Europe, and Africa. The data suggest that influenza A virus deposited as the birds begin their autumn migration can be preserved in lake ice. As birds return in the spring, the ice melts releasing the viruses. Therefore, temporal gene flow is facilitated between the viruses shed during the previous year, and the newly-acquired viruses contracted by the birds during the winter months spent in the south. Above the Arctic Circle, the cycles of entrapment in the ice and release by melting can be variable in length, because some ice persists for several years, decades, or longer. This type of temporal gene flow might be a feature common to viruses that can survive entrapment in environmental ice and snow.

 

[christian]

Re: Evidence for influenza A virus RNA in Siberian lake ice

http://jvi.asm.org/cgi/content/abstract/JVI.00986-06v1

Greetings all -- I'm a newly registered user, but have been periodically reading this forum for some time.

I thought this item was intriguing because, among other things, it would seem to present an alternate mechanism to account for observed (but unexpected according to dogmatic reasoning) sequence fidelity in viral isolates that are greatly separated in time.

"Above the Arctic Circle, the cycles of entrapment in the ice and release by melting can be variable in length, because some ice persists for several years, decades, or longer. This type of temporal gene flow might be a feature common to viruses that can survive entrapment in environmental ice and snow."

Plausibility combined with simplicity - great observation.

By the way, welcome

 

[Mingus]

Re: Evidence for influenza A virus RNA in Siberian lake ice

Hi aardvark, Good find!
_____________________
Hawkeye, you did the same at the same time lol

 

[sharon sanders]

Re: Evidence for influenza A virus RNA in Siberian lake ice

Welcome Aardvark. Great find. Thanks.

 

[HenryN]

Re: Evidence for influenza A virus RNA in Siberian lake ice

The sequences detected are mammalian, although the paper calls the closest huma sequences avian (WS/33 - the first human flu ever isolated named after Wilson Smith, is called avian in the text and figure).

The other sequence listed is H2N2, although the tree says it is H1.

Paper has some major problems.

 

[HenryN]

Re: Evidence for influenza A virus RNA in Siberian lake ice

H1 probes were used:

"The H1 from Lake Park ice and Lake Edoma water are closest to avian strains isolated in Asia in 1933 and 1967.

Also, they were related to strains from 1938 and 1939 isolated form swine in the United Kingdom. These are embedded within a large clade that includes a wide range of H1 sequences isolated from humans from the 1930's to the present."

The "avian" sequences referenced above are WS/33 (1st human flu isolate) and A/Tokyo/3/67 (listed as H2N2 at Genbank and Los Alamos).

As noted above, the other close sequences were swine.

The sequences were not given, but phylogenetic tree indicates the sequences were mammalian, not avian.​

 

[HenryN]

Re: Evidence for influenza A virus RNA in Siberian lake ice

The "Asian' "avian" isolate, WS/33 was actually isoalted from Christopher Matthewes in Wilson Smith's lab in Cambridge, England in 1933.

It is neither avian nor Asian.

 

[HenryN]

Re: Evidence for influenza A virus RNA in Siberian lake ice

Figure 2​

​

Neighbor-Joining phylogram of the influenza heamagglutinin H1 gene
sequences isolated from Lake Park ice (collected in March, 2002) and Lake
Edoma water (collected in September, 2001). Numbers indicate sequences from clones derived from RT-PCR reactions. The number before the decimal point indicates the RT-PCR reaction number, while the number after the decimal point indicates each unique clone from the reaction. Sequences from the control virus (A/WS/33, clone p1.9) and from the Brevig Mission, Alaska H1 (accession number AF116575), also are shown. The Brevig Mission sequence was used as the outgroup. LPI indicates cloned sequences from Lake Park ice, while LEW indicates the one clone from Lake Edoma water.
​

Figure 3​

​

Maximum Parsiomony phylogram of a wide selection of haemagglutinin
H1 gene sequences, including selected sequences from this study. Gaps were scored as a fifth base. There were more than two thousand most parsimonious trees, varying in placement of several of the sequences. Primarily, very closely related sequences shifted relative to one another. However, the relationships of the influenza A H1 sequences from this study with the other sequences were consistent in all of the trees. The tree shown has 1128 steps, with CI = 0.5417, HI = 0.4583, RI = 0.8562, and RC = 0.4638. The H1 from Lake Park ice and
Lake Edoma water are closest to avian strains isolated in Asia in 1933 and 1967. Also, they were related to strains from 1938 and 1939 isolated form swine in the United Kingdom. These are embedded within a large clade that includes a wide range of H1 sequences isolated from humans from the 1930's to the present. There is a more distant relationship with the H1 from the 1918 H1 influenza A (upper clade) and avian strains from 1976 through 1985 (lower ingroup clade).
Sequences from H6 influenza strains were used as representatives of the
outgroup. Sources are: Av = avian; Hu = human; Sw = swine.​

 

[HenryN]

Re: Evidence for influenza A virus RNA in Siberian lake ice

In BLAST searches of NCBI (National Center for Biotechnology Information,​

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http://www.ncbi.nlm.nih.gov/) databases, the H1 gene amplicons were most​

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similar to those previously isolated with neuraminidase gene subtypes N1, N2,​

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and N5. Phylogenetic analyses indicated that while the viruses exhibit genetic​

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diversity (Fig. 2), they form a monophyletic cluster (Fig. 3) when compared with​

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other H1 sequences. Comparison with a wide variety of H1 gene sequences​

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indicates that the population in the Lake Park ice is most closely related to​

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subtypes that were isolated from both avian and porcine hosts in the 1930's and
the 1960's (Fig. 3). They are distantly related to the H1 subtype
1 from the 1918
2 pandemic.​

ACCEPTED​

 

[LMonty]

Re: Evidence for influenza A virus RNA in Siberian lake ice

welcome, aardvark! glad to have you join us, very interesting find.