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Seasonal H1N1 Sequences Co-circulating with Pandmeic H1N1 in South America Released
> Actually, the current pandemic was signaled in 2006/2007
you should have warned us.
Here is another which specifically says that many of the newly acquired polymorphisms trace back to swine (which is also quite obvious from the travel log listed)
ahh, and this all was foreseen by you in 2007 from that posted "travel-log"
In case you missed it, thr Nature abstract is below, with key statements on reassortment
In March and early April 2009, a new swine-origin influenza A (H1N1) virus (S-OIV) emerged in Mexico and the United States. During the first few weeks of surveillance, the virus spread worldwide to 30 countries (as of May 11) by human-to-human transmission, causing the World Health Organization to raise its pandemic alert to level 5 of 6. This virus has the potential to develop into the first influenza pandemic of the twenty-first century. Here we use evolutionary analysis to estimate the timescale of the origins and the early development of the S-OIV epidemic. We show that it was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak. A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that the reassortment of swine lineages may have occurred years before emergence in humans, and that the multiple genetic ancestry of S-OIV is not indicative of an artificial origin. Furthermore, the unsampled history of the epidemic means that the nature and location of the genetically closest swine viruses reveal little about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates. Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans.
In March and early April 2009, a new swine-origin influenza A (H1N1) virus (S-OIV) emerged in Mexico and the United States. During the first few weeks of surveillance, the virus spread worldwide to 30 countries (as of May 11) by human-to-human transmission, causing the World Health Organization to r …
this ** was created by reassortment, not recombination, right ?
I think a review is in order. Triple reassortants are called triple reassortants becasue they have flu genes from three different species, swine, birds, and human, The overall constellation of the 2009 pandemic strain is 1 human (PB1), 2 avian (PB2 and PA) and 5 swine. This constellation was formed by reasortment, but those events happened decades prior to the emergence of the pandemic strain. The PB1 in the pandemic strain, like the ealrier reassortants, has a human PB1 gene from 1993 H3N2. The two avian genes were also acquired in the 1990's. Thus, these reassortments are not proximal to the 2009 pandemic strain, which recently acquired the ability to transmit H2H.
When the sequences first came out, it was called a quadruple reassortant because although the H and N were swine, the H was North American swine and the N was Eurasian swine, which was said to have not been reported previously. However, it then became clear that quadruple reassortants had been circulating in Thailand, long before the H2H acquisition in 2009. That was followed by a report from Hong Kong showing that many of the most closley related genes could be found in swine in Hong Kong years ago. Thus, there is no evidence even hinting that the acquistion of efficient H2H transmission was linked to reassortment, becasue the efficient and sustaned H2H transmission is a recent event, and the reassortment events happened years or decades ago.
public sequences don't indicate increased virulence.
No officials or experts did hint for such changes either.
Well, except occasional Tamiflu-resistance if you want to count that.
The virus is stable so far, no reassortment.
The Cancun-substrain seems to dominate, that's the
strain which had infected New York in May,June - the biggest
well reported city outbreak so far.
There were only 900 reported hospitalizations and 50 deaths
in a city of 8M. Total number of deaths in NYC were smaller
than in the same period 2008.
It seems that Argentina has the same strain.
Other reasons are presumably responsible for increased
virulence there. (weather,genetics,nutrition,...)
Agreed. And it is certainly no surprise that humans and pigs trade influenza viruses with one another, leading to co-infections and the exchange of genetic material.
Re: Seasonal H1N1 Sequences Co-circulating with Pandmeic H1N1 in South America Released
> I think a review is in order. Triple reassortants are called triple
> reassortants becasue they have flu genes from three different
> species, swine, birds, and human, The overall constellation of
> the 2009 pandemic strain is 1 human (PB1), 2 avian (PB2 and PA)
> and 5 swine. This constellation was formed by reasortment, but
> those events happened decades prior to the emergence of the
> pandemic strain. The PB1 in the pandemic strain, like the ealrier
> reassortants, has a human PB1 gene from 1993 H3N2. The two
> avian genes were also acquired in the 1990's. Thus, these
> reassortments are not proximal to the 2009 pandemic strain,
> which recently acquired the ability to transmit H2H.
OK with that. Referring to the triple reassortment in 1998 which since
then is common in American swine.
> When the sequences first came out, it was called a quadruple
> reassortant because although the H and N were avian,
> the H was North American avian and the N was Eurasian avian,
you mean swine
> which was said to have not been reported previously.
...in this constellation
> However, it then became clear that quadruple reassortants had
> been circulating in Thailand, long before the H2H acquisition in 2009.
however still not exactly the 2009-constellation. They had
AHASSsSS in Asia while ** is AHASSssS AFAIR
(S:American swine , s:Eurasian swine(1979 from birds))
> That was followed by a report from Hong Kong showing that many
> of the most closley related genes could be found in swine in
> Hong Kong years ago.
related by general type but still quite different. Many years of evolution
-probably in swine- are missing due to bad surveillance in pigs.
> Thus, there is no evidence even hinting that the acquistion of
> efficient H2H transmission was linked to reassortment,
it's reassorted,it's not been seen before in this constellation.
1957,1968,2003,1947 ,... and other severe flu epidemics and pandemics
resulted from reassortments. This pattern is also seen in swine
and birds.
> becasue the efficient and sustaned H2H transmission is a recent
> event, and the reassortment events happened years or decades
> ago.
probably not decades. The mixes in Asia were ~5 years ago.
Earliest is 1998, the year of the triple reassortent.
I think it more likely happened recently, else why no human
pandemic earlier, why no outbreak in swine ?
And where do you think that recombination and 2007-travel logs jump in ?
> I think a review is in order. Triple reassortants are called triple
> reassortants becasue they have flu genes from three different
> species, swine, birds, and human, The overall constellation of
> the 2009 pandemic strain is 1 human (PB1), 2 avian (PB2 and PA)
> and 5 swine. This constellation was formed by reasortment, but
> those events happened decades prior to the emergence of the
> pandemic strain. The PB1 in the pandemic strain, like the ealrier
> reassortants, has a human PB1 gene from 1993 H3N2. The two
> avian genes were also acquired in the 1990's. Thus, these
> reassortments are not proximal to the 2009 pandemic strain,
> which recently acquired the ability to transmit H2H.
OK with that. Referring to the triple reassortment in 1998 which since
then is common in American swine.
> When the sequences first came out, it was called a quadruple
> reassortant because although the H and N were avian,
> the H was North American avian and the N was Eurasian avian,
you mean swine
> which was said to have not been reported previously.
...in this constellation
> However, it then became clear that quadruple reassortants had
> been circulating in Thailand, long before the H2H acquisition in 2009.
however still not exactly the 2009-constellation. They had
AHASSsSS in Asia while ** is AHASSssS AFAIR
(S:American swine , s:Eurasian swine(1979 from birds))
> That was followed by a report from Hong Kong showing that many
> of the most closley related genes could be found in swine in
> Hong Kong years ago.
related by general type but still quite different. Many years of evolution
-probably in swine- are missing due to bad surveillance in pigs.
> Thus, there is no evidence even hinting that the acquistion of
> efficient H2H transmission was linked to reassortment,
it's reassorted,it's not been seen before in this constellation.
1957,1968,2003,1947 ,... and other severe flu epidemics and pandemics
resulted from reassortments. This pattern is also seen in swine
and birds.
> becasue the efficient and sustaned H2H transmission is a recent
> event, and the reassortment events happened years or decades
> ago.
probably not decades. The mixes in Asia were ~5 years ago.
Earliest is 1998, the year of the triple reassortent.
I think it more likely happened recently, else why no human
pandemic earlier, why no outbreak in swine ?
And where do you think that recombination and 2007-travel logs jump in ?
You are correct about H and N. The summary has been corrected to read swine. The recombination happens all the time and frequently involves (or ends up involving) single nucleotide polymorphisms (SNPs). That is why the Sao Paulo HA sequence only has three new polymorphisms and all three trace to different sources, although 2 of the 3 are in one of the Hong Kong swine isolates. The travel logs I posted several years ago on seasonal 2006/2007 isolates showed that many of the new polymorphisms traced to swine isolates, indicating significant interactions, which would signal dual infections. The data posted in 2007 was supported further by the travel logs on this thread which was based on 2009 polymorphisms in South America (as seen in the recent sequences deposited by the CDC at GISAID). Those polymorphsism also trace back to seasonal flu from 2006/2007, but the polymorphisms were acquired much closer to the time the swine flu jumped to humans and as a result the polymorphism are found in a large number of 2009 sequences create a tracel log that is quite long and jumps from seasonal 2006/2007 to pandemic 2009 (as well as 2009 seasonal from South America - there are still huge gaps in the seasoanl flu database from South America).
The presence of these polymorphisms in seasonal 2006/2007 and pandemic 2009 is NOT a coincidence or due to recent copy errors.
ahh, and this all was foreseen by you in 2007 from that posted "travel-log"
The "commentaries" first mentioned the dangers of swine flu in humans in 2004 - with Dr.Niman's clear concern about the WSN/33-like genes in Korean swine flu.
Also, from a October 25, 2007 commentary:
The movement of human influenza into swine, as well as swine influenza into humans is cause for concern. The human sequences in swine evolve more slowly and acquire swine polymorphisms. These infections can act as a reservoir of early human as well as swine polymorphisms which can move into seasonal flu via recombination. Similarly, the acquisition of human polymorphisms in swine increases regions of identity, which can facilitate additional recombination.
The 1918 pandemic H1N1 was a recombinant with human H1N1 and swine H1N1 sequences, which raises concerns about the increased movement of swine and human sequences between the two species.
"The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation
The "commentaries" first mentioned the dangers of swine flu in humans in 2004 - with Dr.Niman's clear concern about the WSN/33-like genes in Korean swine flu.
> Actually, the current pandemic was signaled in 2006/2007
you should have warned us.
I agree with gsgs.
An real needed warning means to be submited as an scientifical prove of an incipient human pandemic to the health authorities plus WHO, which must than be re-warned at least to the structures, and they must conduct an early blanketing/quarantine policy as a result of this warning.
Concerns of maybe-to-be events, not picked up by the healths machineries, could not represent an real warning espected by the worldwide citizens.
From the readings here at FT, almost all speculations rotate over bird flu humanization possibilities, with some suspects at the time of the something changed human seasonal flu epidemics, but no real citizen awareness came before the famous march events.
Posterior rationalizations represents only scientific debates, now similar to the ones about the climatic change (the scientists agreed when the damage was already visible by plain eyes).
I remember the many cases of "atypical pneumonias" and cases without temperatures, at the begining of this year, which didn't drove to any warnings worldwide. "Only ILI's, or similar ...
If indeed the health structures which have all the data, were well aware of this pandemic months before mid march 2009, and they didn't conducted any blanketing/quarantines at the very begining, than that could be a material for judgments.
Re: Seasonal H1N1 Sequences Co-circulating with Pandmeic H1N1 in South America Released
I'm not sure any 'blanket' or 'quarantine' policy would ever have a chance of stopping an emergent strain of influenza. When I look at the history of H274Y appearing on multiple genetic backgrounds I think of Einsteins 'spooky action at a distance'. It's 'spooky' but has never been disproven.
It seems to me the influenza virus is a part of a complex adaptive system which includes all influenza viruses, all clades, sub-clades, the human host, all the other host species...the whole danged biosphere, in short. A complex adaptive system is quite capable of emergent behavior and self-organization, and re-organization.
What makes us puny humans think we can stiffle an evolutionary process that has a successful history that goes back 4.5 billion years?
In that sense, Henry Niman is right....this virus does know what it's doing.
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