Since its emergence in early 2009 [1] the pandemic influenza A(H1N1) virus has remained closely related to one of the earliest viruses detected, A/California/7/2009, with little change in the viruses' genetic makeup in even the most variable genes, haemagglutinin (HA) and neuraminidase (NA). This lack of drift was reflected in the World Health Organization's (WHO) Vaccine formulation decisions which recommended an A/California/7/2009-like pandemic influenza A(H1N1) virus for both the southern hemisphere 2010 and the northern hemisphere 2010-11 influenza vaccines [2]. While some genetic variants have been reported such as the D222G (D239G numbering if starting at the first methionine) HA mutation which was linked with more severe outcomes following pandemic influenza virus infection [3] and a more commonly seen E391K change in the HA gene [4] during late 2009, no clear variant has predominated in a country or region and no vaccine update has been forthcoming. This report, however, describes the recent emergence in Singapore and subsequent spread of a genetic variant of the pandemic influenza A(H1N1) virus to Australia and New Zealand during their 2010 winter influenza season, where it now predominates and has been detected in some vaccine breakthroughs and fatal cases.
Genetic characterisation of the pandemic influenza A(H1N1) variant
We sequenced the HA, NA and other genes of 2010 pandemic influenza A(H1N1) viruses from Singapore, Australia, New Zealand and elsewhere using conventional Sanger sequencing. Viruses early in 2010 (January to April) from Singapore and Australia showed the E391K (numbering beginning at the first methionine in HA; equivalent to E374K if starting after the signal peptide sequence in HA at DTLC) change in the HA but were scattered throughout the phylogenetic trees for HA (Figure 1) and the whole genome (Figure 2).
Figure 1. Phylogenetic analysis of haemagglutinin sequences from recent pandemic influenza A(H1N1) viruses
Figure 2. Full genome maximum likelihood phylogenetic analysis of pandemic influenza A(H1N1) variants from Singapore, Australia and New Zealand and other non-redundant (<80% identity) strains 
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