Discussion: Seasonal Reassortment of Influenza A virus

[Laidback Al]

Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus

http://pathogens.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.ppat.0020125

Synopsis

A comparative analysis of 413 complete genomes of the H3N2 subtype of human influenza A virus sampled from New York State, United States, the largest and first population-based study of its kind, reveals that viral evolution within epidemic seasons is dominated by the random importation of genetically different viral strains from other geographic areas, rather than by natural selection favoring local strains able to escape the human immune response. Multiple clades of genetically distinct viral strains cocirculate across the entire state within any season and occasionally exchange genes through reassortment. Both genetic diversity and geographic viral ?traffic? are extensive within epidemics. Therefore, the evolution of influenza A virus is strongly shaped by random migration and reassortment and is far harder to predict than previously realized. Consequently, intensive sampling and whole-genome sequencing are essential for selecting viral strains for future vaccine production.

Hat-tip to Solitaire

 

[wetDirt]

Re: Discussion: Seasonal Reassortment of Influenza A virus

Yet another nail in the coffin of random mutation. Although they don't say it, the only way that they could get the results they do is if a) random mutations are rare and b) dual or multiple infections are common). If they look into the remaining single-nucleotide changes, they will discover they are due to recombination. A fine start.

 

[gsgs]

Re: Discussion: Seasonal Reassortment of Influenza A virus

strange, wetdirt that you see this as a confirmation of frequent
recombination. They don't even mention recombination.

Strange also, that they consider 11 reassortment events in 9 years
with 500 examined genomes as "frequent".
They should specify "frequent" by a probability estimation.
How many reassortment events per flu-season in humans
do we estimate ?
Defining reassortment as exchange of segments between viruses
whose ancestors were not in the same infection of the same host.

I guess, there are maybe 30 reassortments then in USA per season
or 1 per million flu-infections. I wouldn't consider this "frequent".
I'd like to see the estimates from the authors of that paper
or from other people here.

They didn't search for recombinations, but I estimate they are almost
as frequent as reassortments, maybe 1-10fold rarer I guess.

But as I said, it's hard to discuss these things when authors hide
behind formulations like "fequent" without specifying what they mean
with this.

Just checking - I couldn't find these clear examples of recombination
in H3N2 as I found earlier with H5N1 and H1N1