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Article: Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments

TitleSystematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments
Authors
KeywordsInfluenza A virus
Mosaic pattern
Recombination
Mosaic screening protocol
Issue Date2013
Citation
Infection, Genetics and Evolution, 2013, v. 18, p. 367-378 How to Cite?
AbstractRecombination 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.
Persistent Identifierhttp://hdl.handle.net/10722/190372
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorLam, TYen_US
dc.contributor.authorChong, YLen_US
dc.contributor.authorShi, Men_US
dc.contributor.authorHon, CCen_US
dc.contributor.authorLI, Jen_US
dc.contributor.authorMartin, DPen_US
dc.contributor.authorTang, JWTen_US
dc.contributor.authorMok, CKen_US
dc.contributor.authorShih, SRen_US
dc.contributor.authorYip, CWen_US
dc.contributor.authorJiang, Jen_US
dc.contributor.authorHui, RKHen_US
dc.contributor.authorPybus, OGen_US
dc.contributor.authorHolmes, ECen_US
dc.contributor.authorLeung, FCCen_US
dc.date.accessioned2013-09-17T15:21:37Z-
dc.date.available2013-09-17T15:21:37Z-
dc.date.issued2013en_US
dc.identifier.citationInfection, Genetics and Evolution, 2013, v. 18, p. 367-378en_US
dc.identifier.urihttp://hdl.handle.net/10722/190372-
dc.description.abstractRecombination 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.-
dc.languageengen_US
dc.relation.ispartofInfection, Genetics and Evolutionen_US
dc.subjectInfluenza A virus-
dc.subjectMosaic pattern-
dc.subjectRecombination-
dc.subjectMosaic screening protocol-
dc.titleSystematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segmentsen_US
dc.typeArticleen_US
dc.identifier.emailHui, RKH: rkhhui@hkucc.hku.hken_US
dc.identifier.emailLeung, FCC: fcleung@hkucc.hku.hken_US
dc.identifier.authorityHui, RKH=rp00711en_US
dc.identifier.authorityLeung, FCC=rp00731en_US
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1016/j.meegid.2013.03.015-
dc.identifier.pmid23548803-
dc.identifier.hkuros222935en_US
dc.identifier.volume18en_US
dc.identifier.spage367en_US
dc.identifier.epage378en_US
dc.identifier.isiWOS:000324660900048-

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