Abstract
Swine have often been considered as a mixing vessel for different influenza strains. In order to assess their role in more detail, we undertook a retrospective sequencing study to detect and characterize the reassortants present in European swine and to estimate the rate of reassortment between H1N1, H1N2 and H3N2 subtypes with Eurasian (avian-like) internal protein-coding segments. We analysed 69 newly obtained whole genome sequences of subtypes H1N1–H3N2 from swine influenza viruses sampled between 1982 and 2008, using Illumina and 454 platforms. Analyses of these genomes, together with previously published genomes, revealed a large monophyletic clade of Eurasian swine-lineage polymerase segments containing H1N1, H1N2 and H3N2 subtypes. We subsequently examined reassortments between the haemagglutinin and neuraminidase segments and estimated the reassortment rates between lineages using a recently developed evolutionary analysis method. High rates of reassortment between H1N2 and H1N1 Eurasian swine lineages were detected in European strains, with an average of one reassortment every 2–3 years. This rapid reassortment results from co-circulating lineages in swine, and in consequence we should expect further reassortments between currently circulating swine strains and the recent swine-origin H1N1v pandemic strain.
Highlights
The major reservoir for influenza A viruses comprises avian hosts, primarily waterfowl, from which certain strains occasionally cross the species barrier to infect mammals, including swine, humans and horses (Webster et al, 1992)
We combined these with complete genome sequences from 41 H1N1 avian-like Eurasian swine isolates reported in another study by our consortium (Bhatt et al, 2012), to make a total of 69 complete genome sequences taken from Belgium, the Czech Republic, France, Italy, Poland, Spain and the UK
As well as the major H1N1, H1N2 and H3N2 strains, we found examples of inter-lineage reassortment including two H3N1 strains
Summary
The major reservoir for influenza A viruses comprises avian hosts, primarily waterfowl, from which certain strains occasionally cross the species barrier to infect mammals, including swine, humans and horses (Webster et al, 1992). These events can lead to epizootic and epidemic outbreaks, and establishment of new viral lineages in the recipient host. Time-resolved trees were generated for each internal protein-coding segment of the complete genome COSI sequences together with the other human, swine and avian background sequences (448 sequences per segment, Table S3) using BEAST via BEAUTi (version 1.6.1) XML input files (Drummond & Rambaut, 2007). Time-resolved trees were generated for each subtype of HA and NA separately (i.e. HA-H1, HA-H3, NA-N1, NAN2)
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