A question about recombination (could contamination be an issue?)

[gsgs]

Re: A question about recombination (could contamination be an issue?)

that thread was from May 2007.

Meanwhile we have a paper from Worobey, claiming that the Sibirian-ice-flu
and the 1917-flu and probably many others were lab-contaminations.

Also the recent paper by Boni et.al with two possible
recombinants, but rejected because of assumed contamination.

Then some other examples of supposed recombination, where
the donor-sequence is many years old.
This is strange and rare and suggests some irregularity too.
If both, recombination and preservation of sequences
is rare, then occurrance of both in the same examples
should be _very_ rare.

The Wisconsin/66 sequence got my attention recently
with another issue:
compare e.g. Brevig/18,WI/66,TR/Minn/3/92(H5N2)
distances in PB2 are 242,243,98 which doesn't match.
18-->92 (242) could be a direct line (3.36 per year),
but then where to place 66 ?

 

[HenryN]

Re: A question about recombination (could contamination be an issue?)

that thread was from May 2007.

Meanwhile we have a paper from Worobey, claiming that the Sibirian-ice-flu
and the 1917-flu and probably many others were lab-contaminations.

Also the recent paper by Boni et.al with two possible
recombinants, but rejected because of assumed contamination.

Then some other examples of supposed recombination, where
the donor-sequence is many years old.
This is strange and rare and suggests some irregularity too.
If both, recombination and preservation of sequences
is rare, then occurrance of both in the same examples
should be _very_ rare.

The Wisconsin/66 sequence got my attention recently
with another issue:
compare e.g. Brevig/18,WI/66,TR/Minn/3/92(H5N2)
distances in PB2 are 242,243,98 which doesn't match.
18-->92 (242) could be a direct line (3.36 per year),
but then where to place 66 ?

The ice study never made sense because sequences where human and from the 1930's.

However, the vast majority of acquisitions by recombination are quite real and widespread.

 

[Oracle]

Re: A question about recombination (could contamination be an issue?)

Come on, Henry.

There was a marked warming of the highest latitdues in the 1920s-30s (studied foremost in Greenland, an temporal cluster of warm temp records set early in this century), followed by a prolonged cooling period. The permafrost could very well have refrozen, sequestering viral samples for decades.

Instead of inferring contamination (which the authors clearly demonstrate they worked hard to avoid in paper 2, after paper 1 critics loudly denounced the experiments as flawed), try.......

See, it makes sense when you read about strains that 'suddenly' re-emerge into extant circulation, 'startling' the experts, who then draw the inane conclusion that it was a research lab freezer escapee.

 

[HenryN]

Re: A question about recombination (could contamination be an issue?)

Come on, Henry.

There was a marked warming of the highest latitdues in the 1920s-30s (studied foremost in Greenland, an temporal cluster of warm temp records set early in this century), followed by a prolonged cooling period. The permafrost could very well have refrozen, sequestering viral samples for decades.

Instead of inferring contamination (which the authors clearly demonstrate they worked hard to avoid in paper 2, after paper 1 critics loudly denounced the experiments as flawed), try.......

See, it makes sense when you read about strains that 'suddenly' re-emerge into extant circulation, 'startling' the experts, who then draw the inane conclusion that it was a research lab freezer escapee.

They said the human sequences from the 30's were avian. The original paper had MANY problems.

 

[Oracle]

Re: A question about recombination (could contamination be an issue?)

Papers referred to:

Zhang et al., Evidence of Influenza A Virus RNA in Siberian Lake Ice

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1676296

Refutation paper by Worobey, Phylogenetic Evidence against Evolutionary Stasis and Natural Abiotic Reservoirs of Influenza A Virus.

http://jvi.asm.org/cgi/content/abstract/82/7/3769

Tell me, Niman. Where do you think these influenza viruses reside in the environment, eh?

 

[HenryN]

Re: A question about recombination (could contamination be an issue?)

Papers referred to:

Zhang et al., Evidence of Influenza A Virus RNA in Siberian Lake Ice

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1676296

Refutation paper by Worobey, Phylogenetic Evidence against Evolutionary Stasis and Natural Abiotic Reservoirs of Influenza A Virus.

http://jvi.asm.org/cgi/content/abstract/82/7/3769

Tell me, Niman. Where do you think these influenza viruses reside in the environment, eh?

Birds

 

[HenryN]

Re: A question about recombination (could contamination be an issue?)

Papers referred to:

Zhang et al., Evidence of Influenza A Virus RNA in Siberian Lake Ice

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1676296

Refutation paper by Worobey, Phylogenetic Evidence against Evolutionary Stasis and Natural Abiotic Reservoirs of Influenza A Virus.

http://jvi.asm.org/cgi/content/abstract/82/7/3769

Tell me, Niman. Where do you think these influenza viruses reside in the environment, eh?

I commented on this in 2006

http://www.curevents.com/vb/showpost.php?p=570990&postcount=3

 

[Oracle]

Re: A question about recombination (could contamination be an issue?)

Zhang et al published a correction ot the misattribution of human isolates (Wilson Smiths early 30s (heavily passaged) strains. I did obtain a copy of Worobey's paper and read it carefully quite some time ago. He sticks to his guns that evolutionary clock mutation rate is obvious for influenza; however, he can't discount the fact that birds overwinter in high arctic wetlands, on permafrost. The adjacent nesting grounds thaw and refreeze yearly, but freezing and thaw dates have changed, while photoperiod activated migration dates haven't shifted nearly as much.

Permafrost melt rate has now descended to depths of dozens of feet (thirty or more) due to climate shift. Heave cracking on from deep ice wedges is a well known cause of tundral soils degradation, documented to have occurred as far back as 8-10K BP (years before present), in the first major warming of the global climate after the end of the last ice age (15-12,000 BP) - in Greenland, Siberia and Far East Asia.

While we wouldn't expect to find human influenza strains (and I applaud Woberleys careful explanation and provision of contamination evidence), finding avian isolates that are decades or older is plausible, provided you knew how to be very careful in your sampling and sample processing and avoided nested PCR.

You would NOT, however, find the 1918 pandemic virus in such a location, because thaw horizons in permafrost have receded well below that of early 1900s soil horizon - presuming virus was released from body fluids of hastily interred Northern Alaska and Canada First Nations influenza victims. In fact, if you read the published records of the US Congress, you will find that there weren't enough funds to cover the cost of medical personnel, never mind the cost of burial (estimated at $30 per corpse) for native Alaskan in distant settlements inland. The dead were abandoned by their surviving clans, and they presumably were scavenged.

Nor would you expect to find evidence of the pre-epidemic viral strains from migrating waterfowl, because the virulent strains did not arise in the holoactic in avians.

Where might we look for avian influenza strains in the environment?

You really do not want to sample water and ice per se of you are looking for intact samples of influenza virus, but rather look for a aquatic rhizosphere environment along migration routes and in tundra heave ice in holoactic breeding sites.

 

[gsgs]

Re: A question about recombination (could contamination be an issue?)

Worobey :
> Many putative examples of evolutionary stasis in influenza A
> virus appear to be due to laboratory artifacts.


why not look in ice directly ? I remember, they found some methods
to sample water from lakes recently.
Or better look for frozen sediments, some sequences from sediments
are at genbank already.

Frozen droppings from birds frequenting an ancient lake,
which then did freeze and remained frozen.
Or maybe bird droppings conserved in Bernstein ?

 

[gsgs]

Re: A question about recombination (could contamination be an issue?)

or something like the story below with one of the soldiers
havind flu from the 1st wave 1918


http://209.85.135.104/search?q=cach...tory=555135&hl=de&ct=clnk&cd=1&gl=de&ie=UTF-8

'Ice man' experts get Great War soldierThey were hanging upside down like three bats, their frozen heads dangling in the icy air, ice-encrusted uniforms still cladding their mummified bodies, glued toa wall of ice. They were soldiers of the Austro-Hungarian empire who died inbattle on 3 September 1918; 12,000ft up in the Italian Alps. The first intact, mummified casualties of the war between Austria and Italy forcontrol of the Alps to come to light were discovered last Friday by Maurizio Vicenzi, 42. He and a group of friends had already brought back rifles, machine guns, bombsand other items from the battlefield. But this discovery dwarfs the rest. One of the three soldiers had lost his head, and all had lost their nails and bodyhair, but otherwise they were perfectly preserved. It is believed they died onPunta San Matteo, in one of many fierce battles fought along a 50-mile front. The bodies were brought down from the mountain on Sunday by helicopter. OnTuesday they were accorded a funeral attended by 300 people, with full military honours. Two of the soldiers were then buried, but the third was transferred to a hospitalin Bolzano. Three of the top experts on Otzi, the ice man who died in thesemountains 5,300 years ago and was discovered in 1991, have been given three months to examine him. One of the experts, Dr Alex Susanna, director of the South Tyrol ArcheologicalMuseum in Bolzano, where Otzi is displayed, said: "Until now all comparativestudies have been between Otzi and artificial mummies. Now we have a natural mummy, preserved like Otzi above 3,000 metres, in very low temperatures and with strong winds and in humid conditions. We want to compare the body tissueof the two mummies." They are also curious to discover why Otzi retained his hair and nails for 5,300 years, while the Austrians lost theirs in less than 90.

 

[HenryN]

Re: A question about recombination (could contamination be an issue?)

Zhang et al published a correction ot the misattribution of human isolates (Wilson Smiths early 30s (heavily passaged) strains. I did obtain a copy of Worobey's paper and read it carefully quite some time ago. He sticks to his guns that evolutionary clock mutation rate is obvious for influenza; however, he can't discount the fact that birds overwinter in high arctic wetlands, on permafrost. The adjacent nesting grounds thaw and refreeze yearly, but freezing and thaw dates have changed, while photoperiod activated migration dates haven't shifted nearly as much.

Permafrost melt rate has now descended to depths of dozens of feet (thirty or more) due to climate shift. Heave cracking on from deep ice wedges is a well known cause of tundral soils degradation, documented to have occurred as far back as 8-10K BP (years before present), in the first major warming of the global climate after the end of the last ice age (15-12,000 BP) - in Greenland, Siberia and Far East Asia.

While we wouldn't expect to find human influenza strains (and I applaud Woberleys careful explanation and provision of contamination evidence), finding avian isolates that are decades or older is plausible, provided you knew how to be very careful in your sampling and sample processing and avoided nested PCR.

You would NOT, however, find the 1918 pandemic virus in such a location, because thaw horizons in permafrost have receded well below that of early 1900s soil horizon - presuming virus was released from body fluids of hastily interred Northern Alaska and Canada First Nations influenza victims. In fact, if you read the published records of the US Congress, you will find that there weren't enough funds to cover the cost of medical personnel, never mind the cost of burial (estimated at $30 per corpse) for native Alaskan in distant settlements inland. The dead were abandoned by their surviving clans, and they presumably were scavenged.

Nor would you expect to find evidence of the pre-epidemic viral strains from migrating waterfowl, because the virulent strains did not arise in the holoactic in avians.

Where might we look for avian influenza strains in the environment?

You really do not want to sample water and ice per se of you are looking for intact samples of influenza virus, but rather look for a aquatic rhizosphere environment along migration routes and in tundra heave ice in holoactic breeding sites.

The ice paper had major problems. They were looking for avian and found human at multiple locations. The human was similar to the lab strain, and therefore was likely to have NOTHING to do with flu sequences in Siberian ice.

 

[HenryN]

Re: A question about recombination (could contamination be an issue?)

Zhang et al published a correction ot the misattribution of human isolates (Wilson Smiths early 30s (heavily passaged) strains. I did obtain a copy of Worobey's paper and read it carefully quite some time ago. He sticks to his guns that evolutionary clock mutation rate is obvious for influenza; however, he can't discount the fact that birds overwinter in high arctic wetlands, on permafrost. The adjacent nesting grounds thaw and refreeze yearly, but freezing and thaw dates have changed, while photoperiod activated migration dates haven't shifted nearly as much.

Permafrost melt rate has now descended to depths of dozens of feet (thirty or more) due to climate shift. Heave cracking on from deep ice wedges is a well known cause of tundral soils degradation, documented to have occurred as far back as 8-10K BP (years before present), in the first major warming of the global climate after the end of the last ice age (15-12,000 BP) - in Greenland, Siberia and Far East Asia.

While we wouldn't expect to find human influenza strains (and I applaud Woberleys careful explanation and provision of contamination evidence), finding avian isolates that are decades or older is plausible, provided you knew how to be very careful in your sampling and sample processing and avoided nested PCR.

You would NOT, however, find the 1918 pandemic virus in such a location, because thaw horizons in permafrost have receded well below that of early 1900s soil horizon - presuming virus was released from body fluids of hastily interred Northern Alaska and Canada First Nations influenza victims. In fact, if you read the published records of the US Congress, you will find that there weren't enough funds to cover the cost of medical personnel, never mind the cost of burial (estimated at $30 per corpse) for native Alaskan in distant settlements inland. The dead were abandoned by their surviving clans, and they presumably were scavenged.

Nor would you expect to find evidence of the pre-epidemic viral strains from migrating waterfowl, because the virulent strains did not arise in the holoactic in avians.

Where might we look for avian influenza strains in the environment?

You really do not want to sample water and ice per se of you are looking for intact samples of influenza virus, but rather look for a aquatic rhizosphere environment along migration routes and in tundra heave ice in holoactic breeding sites.

Human genes in swine reduces the evolution of the human polymorphisms, so older human polymorphisms can be found in live animals, not Siberian ice. There hasn'gt been any re-emerged 1918 sequences and no evidence that any earlier sequences are viable or contribute to flu evolution.

 

[gsgs]

Re: A question about recombination (could contamination be an issue?)

for a list of candidates see here:

http://www.setbb.com/fluwiki2/viewtopic.php?t=187&mforum=fluwiki2