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Article: Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

TitleUse of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections
Authors
Issue Date2010
PublisherInforma Healthcare. The Journal's web site is located at http://www.tandf.co.uk/journals/titles/10408363.asp
Citation
Critical Reviews In Clinical Laboratory Sciences, 2010, v. 47 n. 1, p. 5-49 How to Cite?
AbstractSince DNA sequencing techniques first became available almost 30 years ago, the amount of nucleic acid sequence data has increased enormously. Phylogenetics, which is widely applied to compare and analyze such data, is particularly useful for the analysis of genes from rapidly evolving viruses. It has been used extensively to describe the molecular epidemiology and transmission of the human immunodeficiency virus (HIV), the origins and subsequent evolution of the severe acute respiratory syndrome (SARS)-associated coronavirus (SCoV), and, more recently, the evolving epidemiology of avian influenza as well as seasonal and pandemic human influenza viruses. Recent advances in phylogenetic methods can infer more in-depth information about the patterns of virus emergence, adding to the conventional approaches in viral epidemiology. Examples of this information include estimations (with confidence limits) of the actual time of the origin of a new viral strain or its emergence in a new species, viral recombination and reassortment events, the rate of population size change in a viral epidemic, and how the virus spreads and evolves within a specific population and geographical region. Such sequence-derived information obtained from the phylogenetic tree can assist in the design and implementation of public health and therapeutic interventions. However, application of many of these advanced phylogenetic methods are currently limited to specialized phylogeneticists and statisticians, mainly because of their mathematical basis and their dependence on the use of a large number of computer programs. This review attempts to bridge this gap by presenting conceptual, technical, and practical aspects of applying phylogenetic methods in studies of influenza, HIV, and SCoV. It aims to provide, with minimal mathematics and statistics, a practical overview of how phylogenetic methods can be incorporated into virological studies by clinical and laboratory specialists. © 2010 Informa UK Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/182374
ISSN
2015 Impact Factor: 4.167
2015 SCImago Journal Rankings: 1.668
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorLam, TTYen_US
dc.contributor.authorHon, CCen_US
dc.contributor.authorTang, JWen_US
dc.date.accessioned2013-04-23T08:21:11Z-
dc.date.available2013-04-23T08:21:11Z-
dc.date.issued2010en_US
dc.identifier.citationCritical Reviews In Clinical Laboratory Sciences, 2010, v. 47 n. 1, p. 5-49en_US
dc.identifier.issn1040-8363en_US
dc.identifier.urihttp://hdl.handle.net/10722/182374-
dc.description.abstractSince DNA sequencing techniques first became available almost 30 years ago, the amount of nucleic acid sequence data has increased enormously. Phylogenetics, which is widely applied to compare and analyze such data, is particularly useful for the analysis of genes from rapidly evolving viruses. It has been used extensively to describe the molecular epidemiology and transmission of the human immunodeficiency virus (HIV), the origins and subsequent evolution of the severe acute respiratory syndrome (SARS)-associated coronavirus (SCoV), and, more recently, the evolving epidemiology of avian influenza as well as seasonal and pandemic human influenza viruses. Recent advances in phylogenetic methods can infer more in-depth information about the patterns of virus emergence, adding to the conventional approaches in viral epidemiology. Examples of this information include estimations (with confidence limits) of the actual time of the origin of a new viral strain or its emergence in a new species, viral recombination and reassortment events, the rate of population size change in a viral epidemic, and how the virus spreads and evolves within a specific population and geographical region. Such sequence-derived information obtained from the phylogenetic tree can assist in the design and implementation of public health and therapeutic interventions. However, application of many of these advanced phylogenetic methods are currently limited to specialized phylogeneticists and statisticians, mainly because of their mathematical basis and their dependence on the use of a large number of computer programs. This review attempts to bridge this gap by presenting conceptual, technical, and practical aspects of applying phylogenetic methods in studies of influenza, HIV, and SCoV. It aims to provide, with minimal mathematics and statistics, a practical overview of how phylogenetic methods can be incorporated into virological studies by clinical and laboratory specialists. © 2010 Informa UK Ltd.en_US
dc.languageengen_US
dc.publisherInforma Healthcare. The Journal's web site is located at http://www.tandf.co.uk/journals/titles/10408363.aspen_US
dc.relation.ispartofCritical Reviews in Clinical Laboratory Sciencesen_US
dc.subject.meshAnimalsen_US
dc.subject.meshEvolution, Molecularen_US
dc.subject.meshHost-Pathogen Interactionsen_US
dc.subject.meshHumansen_US
dc.subject.meshMolecular Epidemiologyen_US
dc.subject.meshPhylogenyen_US
dc.subject.meshVirus Diseases - Geneticsen_US
dc.subject.meshViruses - Geneticsen_US
dc.titleUse of phylogenetics in the molecular epidemiology and evolutionary studies of viral infectionsen_US
dc.typeArticleen_US
dc.identifier.emailLam, TTY: ttylam@hku.hken_US
dc.identifier.authorityLam, TTY=rp01733en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.3109/10408361003633318en_US
dc.identifier.pmid20367503-
dc.identifier.scopuseid_2-s2.0-77952508826en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-77952508826&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume47en_US
dc.identifier.issue1en_US
dc.identifier.spage5en_US
dc.identifier.epage49en_US
dc.identifier.isiWOS:000280850400002-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridLam, TTY=36775821700en_US
dc.identifier.scopusauthoridHon, CC=7003617137en_US
dc.identifier.scopusauthoridTang, JW=35273734900en_US

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