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Abstract
In 1977, H1N1 influenza A virus reappeared after a 20-year absence. Genetic analysis indicated that this strain was missing decades of nucleotide sequence evolution, suggesting an accidental release of a frozen laboratory strain into the general population. Recently, this strain and its descendants were included in an analysis attempting to date the origin of pandemic influenza virus without accounting for the missing decades of evolution. Here, we investigated the effect of using viral isolates with biologically unrealistic sampling dates on estimates of divergence dates. Not accounting for missing sequence evolution produced biased results and increased the variance of date estimates of the most recent common ancestor of the re-emergent lineages and across the entire phylogeny. Reanalysis of the H1N1 sequences excluding isolates with unrealistic sampling dates indicates that the 1977 re-emergent lineage was circulating for approximately one year before detection, making it difficult to determine the geographic source of reintroduction. We suggest that a new method is needed to account for viral isolates with unrealistic sampling dates.
Highlights
Phylogenetic inference is an important tool for understanding the origin and evolution of emerging pathogens [1]
This outbreak marked the return of a seasonal H1N1 human influenza virus after a nearly 20-year absence following its displacement during the 1957 H2N2 pandemic
The amount of evolutionary time missing from the branch leading to the re-emergent H1N1 clade was inferred by examining the discrepancy between the root-to-tip genetic distance and sampling-year in the re-emergent H1N1 clade
Summary
Phylogenetic inference is an important tool for understanding the origin and evolution of emerging pathogens [1]. If frozen laboratory strains escape into the general population, they will be missing years of nucleotide sequence evolution, and the date of isolation can be misleading. In a recent paper estimating the age of human pandemic influenza, Smith et al [9] included the re-emergent H1N1 sequences in their analysis without correcting for the missing years of evolution.
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