No evidence for intra-segment recombination of 2009 H1N1 influenza virus in swine

Abstract

Hao (2011) reported that the PB2 genes of three swine influenza A viruses were likely generated through homologous recombination between two closely related parental strains. However, we show that Hao's observation is an artifact of incorrect taxon sampling arising through the lack of an appropriate evolutionary context. Through rigorous phylogenetic analyses we explain the evolutionary origins of these stains and confirm the lack of any statistical support for intra-segmental recombination.

Fig. 1

Lack of evidence for intra-segment recombination in the PB2 segment of 2009 pandemic influenza A viruses isolated from swine in Hong Kong. The alignment shows the variable nucleotides in the PB2 gene of swine influenza A viruses compared to a 99% consensus of 2009 human pandemic viruses (n>2000) (A). Maximum likelihood phylogenies of nucleotide regions 1–1197 (B) and 1198–2277 (C) of the coding region of the PB2 gene were generated using the best-fit nucleotide substitution model in RAxML (Stamatakis, 2006; Stamatakis et al., 2008). Putative parental strains are colored in red and blue, while the putative recombinant viruses are shaded in gray. Scale bars represent nucleotide substitutions per site. Bootstrap values generated from 500 maximum likelihood bootstrap replicates are shown at branch nodes.

Fig. 2

Maximum likelihood phylogenies of the two putative regions of the PB2 gene of the 32 pandemic influenza A viruses isolated from swine in Hong Kong. Both trees inferred with RAxML using 1000 bootstrap replicates (Stamatakis, 2006; Stamatakis et al., 2008). Red and blue sequences are the parental clades P1 and P2, respectively, as described by Hao (2011).