Abstract
BackgroundMost previous evolutionary studies of influenza A have focussed on genetic drift, or reassortment of specific gene segments, hosts or subtypes. We conducted a systematic literature review to identify reported claimed reassortant influenza A lineages with genomic data available in GenBank, to obtain 646 unique first-report isolates out of a possible 20,781 open-access genomes.ResultsAfter adjusting for correlations, only: swine as host, China, Europe, Japan and years between 1997 and 2002; remained as significant risk factors for the reporting of reassortant viral lineages. For swine H1, more reassortants were observed in the North American H1 clade compared with the Eurasian avian-like H1N1 clade. Conversely, for avian H5 isolates, a higher number of reported reassortants were observed in the European H5N2/H3N2 clade compared with the H5N2 North American clade.ConclusionsDespite unavoidable biases (publication, database choice and upload propensity) these results synthesize a large majority of the current literature on novel reported influenza A reassortants and are a potentially useful prerequisite to inform further algorithmic studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-015-1298-9) contains supplementary material, which is available to authorized users.
Highlights
Most previous evolutionary studies of influenza A have focussed on genetic drift, or reassortment of specific gene segments, hosts or subtypes
Whole genome restriction and suspected duplicate removal The 209 articles identified in the literature search made reference to 876 isolates that were available in GenBank with some sequence data available for at least two gene segments
We identified 85 duplicates (55 of which were initially reported as having the same genotype as one another in the same research article)
Summary
Most previous evolutionary studies of influenza A have focussed on genetic drift, or reassortment of specific gene segments, hosts or subtypes. An increase in the number of publicly available genomes of influenza A across all hosts and subtypes has motivated an expanding literature on the algorithmic detection and classification of reassortant viruses [20,21,22,23,24,25,26,27], through phylogenetic analysis or via statistical models of genetic distance. These methods can be very computationally intensive and are only tested on small subsets of available data. The dataset collated in this study could be viewed as a training set from which existing and new algorithmic methods could be refined, developed and validated
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