Can H1N1 and H5N1 share genetic material?

[Pert]

Has anyone looked at the probabilities that H1N1 and H5N1 might share genetic material in a future mutation?

Does any agency have a plan for an outbreak of this type?

 

[gsgs]

Re: Can H1N1 and H5N1 share genetic material?

yes, avian H1N1, not the current swine flu.

You would need humans, who have both - more likely with birds.

H5N1 has exchanged genetic material with H9N2,H6N1
in the past, that's how it became what it is.

I'm not so much concerned about H5N1-swine flu combinations,
more about swine-flu + seasonal flu combinations(=exchange of genetic material)

 

[Mingus]

Re: Can H1N1 and H5N1 share genetic material?

I aggree with GS that it is more likely to exchange genetic information with the seasonal flu but considering that human can transmit it back to pig, it is perfectly possible that H5N1 can encounter this 2009 human & swine H1N1 in a same host, possibly pigs somewhere in asia.

From that point, nobody know what can happen and we can only speculate uselessly.

 

[gsgs]

Re: Can H1N1 and H5N1 share genetic material?

hi Mingus !!

why should H5N1 use pigs, when birds are so much "nearer" ?

reassortment of pig viruses and avian viruses is rare.

What are we concerned about ? the H5-HA going into humans ?

It would find a virus which was in swine since...
I'll examine

------edit1---------

distance
32 >A/California/04/2009-04-01/(H1N1)
A/Bar-h Gs/Qinghai/62/05(H5N1)
in the 8 segments:

153,145,110,361,170,149, 88,158

 

[HenryN]

Re: Can H1N1 and H5N1 share genetic material?

H5N1 has been reported in swine in China and Indonesia. Genetic exchanges are likely.

 

[Mingus]

Re: Can H1N1 and H5N1 share genetic material?

Viruses don't follow rules written by humans nor they have the will to do something logical.

They simply exchange genetic material (by reassortment or by recombination) when they have the chance to be in the same host at the same time. It can produce a better adapted strain or it may not too.

This novel H1N1 will be widespread in Human AND Pigs over the nexts years.
H5N1 is widespread in birds but have been asymtomaticaly seen in pigs many times, you know it gs.

So if it is possible that both strain can meet each other, they will they will.

Our hope is that it give noting beneficial for each strain.

 

[AlexanderSJones]

Re: Can H1N1 and H5N1 share genetic material?

Yes.

They can share material through reassortment and recombination.

This needs to occur through coinfection, most likely in pigs. We already know the new swine flu is highly infectious in both humans and pigs, based on the fact a farmer in Alberta, CA infected his animals. Remember, Coinfection in a host selects for higher virulence. Coinfection in a population also selects for higher virulence. See Evolutionary Dynamics, by Dr. Robert Nowak.

http://www.amazon.com/Evolutionary-Dynamics-Exploring-Equations-Life/dp/0674023382


There could be a possible reassortment with H5N1, where the swine flu H1N1 strain gets an HA segment, containing the poly-basic cleavage site, a property would allow the virus to become pantrophic (infect most any tissue). There could also be recombination , or even simple mutation. The possibilities are endless, really... there are 256 reassortments possible per genome per coinfected cell (8 RNA segments x 8 RNA segments, aka 2^8 combinations).

What is most likely to occur first are A) SNPs from the existing polymerase and B) reassortment or recombination with H1N1 human flu. Reassortment/recombination with H5N1 may occur later, in places where H5N1 is present in swine.

While the margin of error is high, initial data from myself, gsgs/Germany, and Andrew Rembaut/UK , suggest that the new 'swine flu' virus already has an antigenic drift rate which exceeds double the rate of seasonal flu. It appears to be mutating twice as fast , due to an error prone RNA polymerase. Additionally, initial data also suggests that swine flu has double the infectivity of normal flu, but both these possibilities will need to be statistically confirmed with more sequences.


Now is the time to get prepared, as I expect a highly virulent strain (poly-basic cleavage site or not) to emerge in a second wave later this year.

 

[Mingus]

Re: Can H1N1 and H5N1 share genetic material?

I don't believe H1 could acquire a polybasic cleavage site.
All HA serotype can be found in ducks and aquatic bird and only H5 and H7 so far ever evolve in a highly virulent polybasic cleavage site format.

But who knows if H5 may reassort into the H1N1 internal frame ?

The difference between now and 1918 is that we don't know wich influenza subtype was widespread before 1918.

Maybe the population now is not so immunonaïve to the the novel H1N1 than it was in 1918, thanks to the russian H1N1 lab accident of 1977.

http://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H1N1
Russian flu

<dl><dd>See Influenza A virus subtype H2N2#Russian flu for the 1889–1890 Russian flu</dd></dl> The more recent Russian flu was a 1977–1978 flu epidemic caused by strain Influenza A/USSR/90/77 (H1N1). It infected mostly children and young adults under 23 because a similar strain was prevalent in 1947–57, causing most adults to have substantial immunity. Some have called it a flu pandemic but because it only affected the young it is not considered a true pandemic. The virus was included in the 1978–1979 influenza vaccine.<sup class="reference" id="cite_ref-9">[10]</sup><sup class="reference" id="cite_ref-10">[11]</sup><sup class="reference" id="cite_ref-11">[12]</sup><sup class="reference" id="cite_ref-12">[13]</sup>

 

[nomadic wench]

Re: Can H1N1 and H5N1 share genetic material?

Gosh, the things you learn on this site! What Russian lab accident I wondered... anyway ....just for those as new to all this stuff as me...

The suggestion is clear: the virus was frozen in a laboratory freezer since 1950, and was released, either by intent or accident, in 1977. This possibility has been denied by Chinese and Russian scientists, but remains to this day the only scientifically plausible explanation.

http://www.virology.ws/2009/03/02/origin-of-current-influenza-h1n1-virus/

And that wikipedia link is interesting too.

From October 2004 to February 2005, approximately 3,700 test kits of the 1957 H2N2 virus were accidentally spread around the world from the College of American Pathologists (CAP). CAP assists laboratories in accuracy by providing unidentified samples of viruses; private contractor Meridian Bioscience in Cincinnati, U.S., chose the 1957 strand instead of one of the less deadly avian influenza virus subtypes. "CAP spokesman Dr. Jared Schwartz said Meridian knew what the virus was but believed it was safe. In selecting it, the company had determined that the virus was classified as a biosafety level 2 (BSL-2) agent, which meant it could legally be used in the kits. [...] Before the problem came to light, the CDC had made a recommendation that the H2N2 virus be reclassified as a BSL-3 agent, Gerberding said. She promised to speed up the reclassification. The CDC determines the classifications in collaboration with the National Institutes of Health. In BSL-3 labs, agents are handled with equipment designed to prevent any airborne contamination and resulting respiratory exposure."[10] The 1957 H2N2 virus is considered deadly and the U.S. government called for the vials containing the strain to be destroyed.

"CDC officials reported on 21 April that 99% of the samples had already been destroyed. News reports on 25 April said the last samples outside the United States had been destroyed at the American University of Beirut in Lebanon, after they were found at the Beirut airport. Earlier reports said H2N2 samples were sent to 3,747 labs under CAP auspices and to about another 2,700 labs certified by other organizations. All but about 75 labs that received the CAP samples were in the United States."[11]

"In the United States, there is no government regulation over the 1957 flu strain. In fact, federal officials at the CDC do not even know how many U.S. laboratories keep this deadly strain in their viral libraries."[12]

That last paragraph is a bit alarming. Happens a lot does it, these accidental spills of lethal viruses?

 

[gsgs]

Re: Can H1N1 and H5N1 share genetic material?

the chances for human+H5 reassortment have not increased
by the emergence of the new novel H1N1
I can't see why the new virus should be more potent to reassort with H5N1
It may kill old H1N1 and H3N2 in the next years

 

[Mingus]

Re: Can H1N1 and H5N1 share genetic material?

This Novel H1N1can replicate itself AND is efficiently transmitted in two species. Human & Swine.

It's like (it's juste an analogy) there is a gate that have been open there.

Before it, there was the possibility that

1- H5N1 pass directly to the human population
2- H5 reassort with the seasonal human H3N2
3- H5 reassort with the seasonal human H1N1

now there is more possibility

4- H5 could reassort with the novel H1N1 in human.
5- H5 could reassort with the novel H1N1 in pigs and then bring it back to human.
6- H5 could reassort with the swine H3N2 stay there some time before it reassort with some novel H1N1 component then pass to human.
7- This novel H1N1 may pass back from pigs to birds and bring to H5N1 the little kick it lacked to spark some more in the human population who know.

If there is more possible scenario, there is more chance don't you think.

 

[Mathematician]

Re: Can H1N1 and H5N1 share genetic material?

the chances for human+H5 reassortment have not increased
by the emergence of the new novel H1N1
I can't see why the new virus should be more potent to reassort with H5N1
It may kill old H1N1 and H3N2 in the next years

Surely the probability of reassortment between H5N1 and a human flu, in a given time period, is proportional to the number of individuals infected with a human flu in that time period, and proportional to the number of individuals infected with H5N1 in that time period. The former number may well be in the process of increasing dramatically: whether you think worldwide or just in H5N1-infested environments, the number of individuals (human and pig) infected with human flu will be much larger over the coming year or two than over the past year or two. Therefore it seems reasonable to me to think that the probability of such a reassortment is indeed increasing - unless, for reasons we don't understand, it was exactly 0 before, in which case it's still 0. We can hope.

 

[gsgs]

Re: Can H1N1 and H5N1 share genetic material?

it's not only the number of infected persons, it's also the diversity
of the involved viruses. Diversity in swineflu is currently small.

If it turns out that H5N1 can't reasonably reassort with -say- H3N2
then increasing the opportunities won't help much.

Now, in a pandemic we expect that the new H1N1 will replace
other seasonal flu-A

 

[gsgs]

Re: Can H1N1 and H5N1 share genetic material?

well, it seems that H5N1 is closer to swineflu than to seasonal.
Reassortment should be more likely among similar viruses

 58 >A/Bar-h Gs/Qinghai/62/05(H5N1)                      
 10:153,144,110,359,170,148, 87,158   A/swine-flu/index/2009-02-01(H1N1)
 26:158,133, 95,404,174,212,134,147   A/Wisconsin/10/98(H1N1)
 38:152,170,147,353,142,171,111,123   A/swine/1931(H1N1)
 40:153,158,139,358,136,173, 94, 89   A/Brevig Mission/1/1918(H1N1)
 47:176,182,165,373,167,218,121,139   A/Kansas/UR06-0068/2007(H1N1)
 49:170,138,167,496,189,491,125,135   A/Texas/UR06-0356/2007(H3N2)

from that pov the best candidates for H5N1-human reassortment are
PB1(sw,H3N2),PA(sw),NA(sw),M(sw),NS(H3N2,H1N1)

 

[LMonty]

Re: Can H1N1 and H5N1 share genetic material?

it's not only the number of infected persons, it's also the diversity
of the involved viruses. Diversity in swineflu is currently small.

gs- I'm not sure I follow you. i'd like to understand better what your thinking is on this subject. Let me explain what I am thinking so I can see if I understand you.

Why do you consider diversity of the virus an issue? I'm assuming "opportunities for reassortment/recombination" are directly related to the number of individual (human, swine, avian or other) hosts with coinfections, each one creating large numbers (Mingus, anybody? How many cells might carry both virus in a coinfection? hundreds, thousands, millions?)

I may not be following you gs, because I may not understand what you mean by diversity. By diversity, do you mean how unstable the current strain is, and how many viable variants of it are developing and spreading? that is what it means to me.

I have to agree with Mathemetician, I think the chances of H5 and H1 meeting up and H1 picking up more lethal genes or polymorphisms is a math issue the greater the opportunity for both viruses to meet, the greater the chance of reassorment/recombination.

One of the recognized characteristics of a pandemic strain is the greater number of infections in the population due to lack of or limited prior exposure to the novel H and the lack of circulating antibodies. IIRC, some estimates taken from flu researchers work on tracking anitbodies in the aging population exposed to 1918 H1N1 was that up to 50% of the population exhibited antibodies.

Many of those were probably asymptomatic infections, but they do influence attack rate data, indicating that with flu, what we see is not all of what we get. IIRC actively infected but asymptomatic individuals can shed live virus, but in numbers smaller than symptomatic ones.

Also, the greater the number of infections with the pandemic strain, the greater the chance of drift from errors in viral replication. I agree those will be much less likely to develop a polybasic cleavage site- but I would consider the possibility greater than zero, only because we know that at least two H strains in avians have it. Where did it come from? at least once in the shadowy past of the influenza virus, a strain developed it through one of the methods of genetic change. Wether both strains have one common ancestor seems plausible but AFAIK not proven.

If its done it once, it could do it again. I consider that unlikely, with an amazingly small probability, but have no way to assess it since we have inadequate data to attempt that.

SO I have to say that with a pandemic strain, due to the unique higher attack rates than seasonal flu, I believe that the opportunities for dual infection, reassorment and recombiation, and even indiidual infections with drift are dramatically increased.

 

[LMonty]

Re: Can H1N1 and H5N1 share genetic material?

Pert, to answer your second question, heres my take on it- generic pandemic planning would address whatever strain and whatever lethality develops.

If a highly lethal strain causes social disruption, then appropriate entities would need to activate their planning for those scenarios, and they would likely be specific to the locality and level of disruption.

 

[marcovth]

Re: Can H1N1 and H5N1 share genetic material?

Does it look like H5N1 is getting out of control in Egypt ?

Edit ... This is partially answering my question ...
http://www.almasry-alyoum.com/article2.aspx?ArticleID=210586

 

[gsgs]

Re: Can H1N1 and H5N1 share genetic material?

diversity = how much different the viruses are.

Suppose you have one H5N1 together with 100 seasonal H1N1
and 100 seasonal H3N2 in dual infection of 200 humans

and then you have the same H5N1 together with 200 seasonal
H1N1 in dual infection of 200 humans

double chance (H1N1 plus H3N2) in the first case


increasing the number in the 2nd case is not supposed to help much.
There are biological constraints, configurations (=viruses) where just no
reassortment is viable, no matter how many opportunities.

 

[Shannon Bennett]

Re: Can H1N1 and H5N1 share genetic material?

H5N1 is in the wild bird populations all along the Nile. Sick wild bird meets domestic chicken and you have infection. The government in Egypt has worked hard to educate its people. But, it is one of the hot spots where pigs, humans, chickens and H5N1 infected birds are all mixing freely. It isn't the only place, however. China, Indonesia, and Southeast Asia all have the same problem. Any one of those places could provide the breeding ground for the next pandemic flu.

 

[deerskie]

Re: Can H1N1 and H5N1 share genetic material?

If most of the world population becomes infected with H1N1 (swine flu) over the next year, and then H1N1 and H5N1 combine, wouldn't that provide the population with some immunity to the recombined avian/swine flu?