A systematic review of reported reassortant viral lineages of influenza A. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Pinsent, Amy; Fraser, Christophe; Ferguson, Neil; Riley, Steven
• Is Part Of: BMC infectious diseases. Volume 16:Issue 1(2016)
• Page Start: 1
• Page End: 13
• Publication Date: 2015-12
• Subjects: Influenza -- Reassortment -- Reassortant -- Evolution -- Genomic data -- Reporting -- Pandemic; Communicable diseases -- Periodicals; Sexually Transmitted Diseases -- Periodicals; 616.905
• DOI: 10.1186/s12879-015-1298-9
• Languages: English
• ISSNs: 1471-2334

Abstract

Abstract Background Most 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. Results After 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. Conclusions Despite 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.