Evolutionary Dynamics and Emergence of Panzootic H5N1 Influenza Viruses

[mixin]

Evolutionary Dynamics and Emergence of Panzootic H5N1 Influenza Viruses
Dhanasekaran Vijaykrishna1,2, Justin Bahl1,2, Steven Riley3, Lian Duan1,2, Jin Xia Zhang1,2, Honglin Chen1,2, J. S. Malik Peiris1, Gavin J. D. Smith1,2*, Yi Guan1,2*

Abstract
The highly pathogenic avian influenza (HPAI) H5N1 virus lineage has undergone extensive genetic reassortment with viruses from different sources to produce numerous H5N1 genotypes, and also developed into multiple genetically distinct sublineages in China. From there, the virus has spread to over 60 countries. The ecological success of this virus in diverse species of both poultry and wild birds with frequent introduction to humans suggests that it is a likely source of the next human pandemic. Therefore, the evolutionary and ecological characteristics of its emergence from wild birds into poultry are of considerable interest.

Here, we apply the latest analytical techniques to infer the early evolutionary dynamics of H5N1 virus in the population from which it emerged (wild birds and domestic poultry). By estimating the time of most recent common ancestors of each gene segment, we show that the H5N1 prototype virus was likely introduced from wild birds into poultry as a non-reassortant low pathogenic avian influenza H5N1 virus and was not generated by reassortment in poultry.

In contrast, more recent H5N1 genotypes were generated locally in aquatic poultry after the prototype virus (A/goose/Guangdong/1/96) introduction occurred, i.e., they were not a result of additional emergence from wild birds. We show that the H5N1 virus was introduced into Indonesia and Vietnam 3?6 months prior to detection of the first outbreaks in those countries. Population dynamics analyses revealed a rapid increase in the genetic diversity of A/goose/Guangdong/1/96 lineage viruses from mid-1999 to early 2000.

Our results suggest that the transmission of reassortant viruses through the mixed poultry population in farms and markets in China has selected HPAI H5N1 viruses that are well adapted to multiple hosts and reduced the interspecies transmission barrier of those viruses.

Author Summary
H5N1 influenza virus has been responsible for poultry outbreaks over the last 12 years?the longest recorded example of highly pathogenic avian influenza (HPAI) circulation in poultry. The ecological success of this virus in diverse species of both poultry and wild birds with sporadic introduction to humans suggests that it is a likely source of the next human pandemic. Genome sequences of H5N1 viruses reveal extensive genetic reassortment (mixing) with other influenza subtypes to produce many H5N1 genotypes that have developed into multiple genetically distinct clades, some of which have spread to affect over 60 countries.

Here, we analyze all available sequence data of avian influenza viruses from Eurasia and show that the original HPAI H5N1 virus (referred to as A/goose/Guangdong/1/96) was likely introduced directly into poultry as an intact virus particle from wild aquatic birds. In contrast, H5N1 genotypes were generated in aquatic poultry populations after the introduction of A/goose/Guangdong/1/96 virus.

Our results suggest that the transmission of reassortant viruses through the diverse poultry populations in farms and markets in China has selected H5N1 viruses that are well-adapted to multiple hosts and reduced the interspecies transmission barrier of those viruses.

http://www.plospathogens.org/articl...1;jsessionid=0CE958A39B9EB849559DB817DAC12A17

 

[gsgs]

Re: Evolutionary Dynamics and Emergence of Panzootic H5N1 Influenza Viruses

you have to distinguish the segments, each segment has its own evolution.
Earlier this was done by "genotypes", I once saw a good graphics -
unfortunately I didn't bookmark the link.
Now they use "clades" , where some use it for whole viruses,
some only for HA. It's confusing.

One question is : was the assumed transition from LP to HP
done in wild birds or poultry ?

-----edit1------
I printed it now. ...reading...
my substitution rates for Qinghai-H5N1 : ~3.5*10^-3 , much more
than what they list. OTOH we had a phase of slow mutation in some

the genotypes table which I remembered was similar to the one on page 6,
but with colors it's bad to distinguish, better use letters or digits
and no example-viruses are given

 

[mixin]

Re: Evolutionary Dynamics and Emergence of Panzootic H5N1 Influenza Viruses

One question is : was the assumed transition from LP to HP
done in wild birds or poultry ?

From the study: "...H5N1 prototype virus was likely introduced from wild birds into poultry as a non-reassortant low pathogenic avian influenza H5N1 virus and was not generated by reassortment in poultry."

First, AIV (of different subtypes) from the natural gene pool in wild birds are introduced into domestic duck. In domestic duck, these viruses undergo regular reassortment with endemic H5N1 viruses. Subsequently, transmission of these reassortant viruses within large highly connected populations of duck and other poultry species results in frequent interspecies transmission and genetic drift. Therefore, it is likely that this process selects for relatively fit viruses with a broad host range which are subsequently exported to other geographical regions.

It is interesting to note that further reassortment has not been observed once those H5N1 viruses were transmitted out of China. We suggest that host population structures elsewhere may not result in the same intense multi-species transmission we observe in southern China. I wish they would have discussed this. Why would reassortment stop once the virus left China?