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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments
Infection, Genetics and Evolution, Volume 18, Year 2013
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Description
Recombination plays an important role in shaping the genetic diversity of a number of DNA and RNA viruses. Although some recent studies have reported bioinformatic evidence of mosaic sequences in a variety of influenza A viruses, it remains controversial as to whether these represent bona fide natural recombination events or laboratory artifacts. Importantly, mosaic genome structures can create significant topological incongruence during phylogenetic analyses, which can mislead additional phylogeny-based molecular evolutionary analyses such as molecular clock dating, the detection of selection pressures and phylogeographic inference. As a result, there is a strong need for systematic screenings for mosaic structures within the influenza virus genome database. We used a combination of sequence-based and phylogeny-based methods to identify 388 mosaic influenza genomic segments, of which 332 are previously unreported and are significantly supported by phylogenetic methods. It is impossible, however, to ascertain whether these represent natural recombinants. To facilitate the future identification of recombinants, reference sets of non-recombinant sequences were selected for use in an automatic screening protocol for detecting mosaic sequences. Tests using real and simulated mosaic sequences indicate that our screening protocol is both sensitive (average >90%) and accurate (average >77%) enough to identify a range of different mosaic patterns. The relatively high prevalence of mosaic influenza virus sequences implies that efficient systematic screens, such as that proposed here, should be performed routinely to detect natural recombinant strains, potential laboratory artifacts, and sequencing contaminants either prior to sequences being deposited in GenBank or before they are used for phylogenetic analyses. © 2013 Elsevier B.V.
Authors & Co-Authors
Lam, Tommy Tsan Yuk
United Kingdom, Oxford
University of Oxford
Chong, Yee Ling
Malaysia, Kota Samarahan
Universiti Malaysia Sarawak
Shi, Mang
Australia, Sydney
The University of Sydney School of Medicine
Hon, Chungchau
France, Paris
Institut Pasteur, Paris
Li, Jun
Hong Kong, Hong Kong
The University of Hong Kong
Martin, Darren Patrick
South Africa, Cape Town
University of Cape Town
Tang, Julians Wei Tze
Canada, Edmonton
University of Alberta
Mok, Chee Keng
Taiwan, Taoyuan
Chang Gung University
Shih, Shinru
Taiwan, Taoyuan
Chang Gung University
Yip, Chi Wai
Hong Kong, Hong Kong
The University of Hong Kong
Jiang, Jingwei
Hong Kong, Hong Kong
The University of Hong Kong
Hui, Raymond Kin Hei
Hong Kong, Hong Kong
The University of Hong Kong
Pybus, Oliver George
United Kingdom, Oxford
University of Oxford
Holmes, Edward C.
Australia, Sydney
The University of Sydney School of Medicine
United States, Bethesda
National Institutes of Health Nih
Leung, Frederick Chi Ching Chi Ching
Hong Kong, Hong Kong
The University of Hong Kong
Statistics
Citations: 15
Authors: 15
Affiliations: 9
Identifiers
Doi:
10.1016/j.meegid.2013.03.015
ISSN:
15671348
e-ISSN:
15677257
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study