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Meta-Analysis
. 2008 Apr;82(7):3769-74.
doi: 10.1128/JVI.02207-07. Epub 2008 Jan 30.

Phylogenetic evidence against evolutionary stasis and natural abiotic reservoirs of influenza A virus

Michael Worobey  1
Affiliations
Meta-Analysis

Phylogenetic evidence against evolutionary stasis and natural abiotic reservoirs of influenza A virus

Michael Worobey. J Virol. 2008 Apr.

Abstract

Zhang et al. (G. Zhang, D. Shoham, D. Gilichinsky, S. Davydov, J. D. Castello, and S. O. Rogers, J. Virol. 80:12229-12235, 2006) have claimed to have recovered influenza A virus RNA from Siberian lake ice, postulating that ice might represent an important abiotic reservoir for the persistence and reemergence of this medically important pathogen. A rigorous phylogenetic analysis of these influenza A virus hemagglutinin gene sequences, however, indicates that they originated from a laboratory reference strain derived from the earliest human influenza A virus isolate, WS/33. Contrary to Zhang et al.'s assertions that the Siberian "ice viruses" are most closely related either to avian influenza virus or to human influenza virus strains from Asia from the 1960s (Zhang et al., J. Virol. 81:2538 [erratum], 2007), they are clearly contaminants from the WS/33 positive control used in their laboratory. There is thus no credible evidence that environmental ice acts as a biologically relevant reservoir for influenza viruses. Several additional cases with findings that seem at odds with the biology of influenza virus, including modern-looking avian influenza virus RNA sequences from an archival goose specimen collected in 1917 (T. G. Fanning, R. D. Slemons, A. H. Reid, T. A. Janczewski, J. Dean, and J. K. Taubenberger, J. Virol. 76:7860-7862, 2002), can also be explained by laboratory contamination or other experimental errors. Many putative examples of evolutionary stasis in influenza A virus appear to be due to laboratory artifacts.

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Figures

FIG. 1.
FIG. 1.
The majority-rule consensus tree summarizing the results from the BMCMC analysis of partial influenza A virus HA genes. The branch lengths are drawn to scale and represent the mean value observed for that branch among the post-burn-in sampled trees. Posterior probabilities greater than or equal to 0.95 are indicated for each node, and bootstrap percentages greater than or equal to 70 are given in parentheses. The potentially problematic sequences discussed in the main text are labeled in red. LP, Lake Park “ice virus.” The estimated maximum likelihood phylogeny was very consistent with the Bayesian results, though on the ML tree the clade including the Brant goose/Alaska 1917 and Ohio 1999 sequences was characterized by branch lengths equal to zero, reflecting the 100% identity between these sequences in the region of overlap. The slightly longer branch length of the Brant goose sequence on the Bayesian consensus tree is possibly due to the fact that only 139 nucleotides were available for analysis. As with the Bayesian result, the swine/Iowa/15/30 sequences were also paraphyletic in the ML tree, most likely representing a minor phylogenetic error in the placement of the branch leading to the remaining swine sequences; however, a significant proportion of bootstrap replicates (87%) supported monophyly for this group.
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