Friday, May 3, 2013

Pro-MED: Avian influenza, human (71): China H7N9 update

Published Date: 2013-05-03 14:42:36 --  A ProMED-mail post
ProMED-mail is a program of the
International Society for Infectious Diseases
Archive Number: 20130503.1689649
In this update:

[1] Genetic diversity
[2] Origin unresolved
[3] 27th death

[1] Genetic diversity
Date: Wed 1 May 2013
Source; The Lancet, Early Online Publication, doi:10.1016/S0140-6736(13)60938-1Cite or Link Using DOI [edited]

Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural, and coalescent analyses.
Authors: Di Liu et al.

On 30 Mar 2013, a novel avian influenza A H7N9 virus that infects human beings was identified. This virus had been detected in 6 provinces and municipal cities in China as of 18 Apr 2013. We correlated genomic sequences from avian influenza viruses with ecological information and did phylogenetic and coalescent analyses to extrapolate the potential origins of the virus and possible routes of reassortment events.

We downloaded H7N9 virus genome sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database and public sequences used from the Influenza Virus Resource. We constructed phylogenetic trees and did 1000 bootstrap replicates for each tree. Two rounds of phylogenetic analyses were done. We used at least 100 closely related sequences for each gene to infer the overall topology, removed suspicious sequences from the trees, and focused on the closest clades to the novel H7N9 viruses. We compared our tree topologies with those from a bayesian evolutionary analysis by sampling trees (BEAST) analysis. We used the bayesian Markov chain Monte Carlo method to jointly estimate phylogenies, divergence times, and other evolutionary parameters for all 8 gene fragments. We used sequence alignment and homology-modelling methods to study specific mutations regarding phenotypes, specifically addressing the human receptor binding properties.

The novel avian influenza A H7N9 virus originated from multiple reassortment events. The HA gene might have originated from avian influenza viruses of duck origin, and the NA gene might have transferred from migratory birds infected with avian influenza viruses along the east Asian flyway. The 6 internal genes of this virus probably originated from 2 different groups of H9N2 avian influenza viruses, which were isolated from chickens. Detailed analyses also showed that ducks and chickens probably acted as the intermediate hosts leading to the emergence of this virulent H7N9 virus. Genotypic and potential phenotypic differences imply that the isolates causing this outbreak form 2 separate subclasses.

The novel avian influenza A H7N9 virus might have evolved from at least 4 origins. Diversity among isolates implies that the H7N9 virus has evolved into at least 2 different lineages. Unknown intermediate hosts involved might be implicated; extensive global surveillance is needed, and domestic-poultry-to-person transmission should be closely watched in the future.

Funding: China Ministry of Science and Technology Project 973, National Natural Science Foundation of China, China Health and Family Planning Commission, Chinese Academy of Sciences.

communicated by:
Ryan McGinnis

[Perhaps the most surprising outcome of this analysis is the discovery that the H7N9 viruses may already have diverged into 2 distinct lineages. - Mod.CP]

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