Analysis of all complete genome sequences of the pandemic influenza A(H1N1)v virus available as of 10 September 2009 revealed that two closely related but distinct clusters were circulating in most of the affected countries at the same time. The characteristic differences are located in genes encoding the two surface proteins – haemagglutinin and neuraminidase – and four internal proteins – the polymerase PB2 subunit, nucleoprotein, matrix protein M1 and the non-structural protein NS1. Phylogenetic inference was demonstrated by neighbour joining, maximum likelihood and Bayesian trees analyses of the involved genes and by tree construction of concatenated sequences.


Following the worldwide spread of the pandemic influenza A(H1N1)v virus after its emergence in the United States (US) and Mexico in March 2009, the World Health Organization (WHO) raised the influenza pandemic alert level to phase 6 on 11 June 2009. It is expected that this new influenza virus will continue to circulate and spread due to efficient human to human transmission. Data on the genetic composition of the virus became available very early in the pandemic [1], and until 10 September 2009, more than 3,500 individual gene sequences had been deposited in public databases such as GISAID and GenBank. The influenza A(H1N1)v virus, which is a unique combination of gene segments from both North American and Eurasian swine influenza viruses [2], has a high mean evolutionary rate for individual segments and the whole genome (3.66 x 10-3 substitutions per site per year) [3].

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