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Article: Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus

TitleCodon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus
Authors
Issue Date2010
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcevolbiol/
Citation
Bmc Evolutionary Biology, 2010, v. 10 n. 1 How to Cite?
AbstractBackground. The influenza A virus is an important infectious cause of morbidity and mortality in humans and was responsible for 3 pandemics in the 20 th century. As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission. A better understanding of viral evolution and host adaptive responses might help control this disease. Results. Relative Synonymous Codon Usage (RSCU) values of the genes from segment 1 to segment 6 of avian and human influenza viruses, including pandemic H1N1, were studied via Correspondence Analysis (CA). The codon usage patterns of seasonal human influenza viruses were distinct among their subtypes and different from those of avian viruses. Newly isolated viruses could be added to the CA results, creating a tool to investigate the host origin and evolution of viral genes. It was found that the 1918 pandemic H1N1 virus contained genes with mammalian-like viral codon usage patterns, indicating that the introduction of this virus to humans was not through in toto transfer of an avian influenza virus. Many human viral genes had directional changes in codon usage over time of viral isolation, indicating the effect of host selection pressures. These changes reduced the overall GC content and the usage of G at the third codon position in the viral genome. Limited evidence of translational selection pressure was found in a few viral genes. Conclusions. Codon usage patterns from CA allowed identification of host origin and evolutionary trends in influenza viruses, providing an alternative method and a tool to understand the evolution of influenza viruses. Human influenza viruses are subject to selection pressure on codon usage which might assist in understanding the characteristics of newly emerging viruses. © 2010 Wong et al; licensee BioMed Central Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/135268
ISSN
2015 Impact Factor: 3.406
2015 SCImago Journal Rankings: 2.053
PubMed Central ID
ISI Accession Number ID
Funding AgencyGrant Number
University Grants CommitteeAoE/M-12/06
Research Grant Council of Hong KongHKU 773408M
Funding Information:

We thank Ms. K.M. Wu for technical support. This work was supported by the Area of Excellence Scheme of the University Grants Committee (Grant AoE/M-12/06); and the Research Grant Council of Hong Kong (HKU 773408M).

References
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DC FieldValueLanguage
dc.contributor.authorWong, EHMen_HK
dc.contributor.authorSmith, DKen_HK
dc.contributor.authorRabadan, Ren_HK
dc.contributor.authorPeiris, Men_HK
dc.contributor.authorPoon, LLMen_HK
dc.date.accessioned2011-07-27T01:30:55Z-
dc.date.available2011-07-27T01:30:55Z-
dc.date.issued2010en_HK
dc.identifier.citationBmc Evolutionary Biology, 2010, v. 10 n. 1en_HK
dc.identifier.issn1471-2148en_HK
dc.identifier.urihttp://hdl.handle.net/10722/135268-
dc.description.abstractBackground. The influenza A virus is an important infectious cause of morbidity and mortality in humans and was responsible for 3 pandemics in the 20 th century. As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission. A better understanding of viral evolution and host adaptive responses might help control this disease. Results. Relative Synonymous Codon Usage (RSCU) values of the genes from segment 1 to segment 6 of avian and human influenza viruses, including pandemic H1N1, were studied via Correspondence Analysis (CA). The codon usage patterns of seasonal human influenza viruses were distinct among their subtypes and different from those of avian viruses. Newly isolated viruses could be added to the CA results, creating a tool to investigate the host origin and evolution of viral genes. It was found that the 1918 pandemic H1N1 virus contained genes with mammalian-like viral codon usage patterns, indicating that the introduction of this virus to humans was not through in toto transfer of an avian influenza virus. Many human viral genes had directional changes in codon usage over time of viral isolation, indicating the effect of host selection pressures. These changes reduced the overall GC content and the usage of G at the third codon position in the viral genome. Limited evidence of translational selection pressure was found in a few viral genes. Conclusions. Codon usage patterns from CA allowed identification of host origin and evolutionary trends in influenza viruses, providing an alternative method and a tool to understand the evolution of influenza viruses. Human influenza viruses are subject to selection pressure on codon usage which might assist in understanding the characteristics of newly emerging viruses. © 2010 Wong et al; licensee BioMed Central Ltd.en_HK
dc.languageengen_US
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcevolbiol/en_HK
dc.relation.ispartofBMC Evolutionary Biologyen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.rightsBMC Evolutionary Biology. Copyright © BioMed Central Ltd.-
dc.subject.meshCluster Analysis-
dc.subject.meshCodon-
dc.subject.meshEvolution, Molecular-
dc.subject.meshGenome, Viral-
dc.subject.meshInfluenza A virus - genetics-
dc.titleCodon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virusen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1471-2148&volume=10, article no. 253&spage=253&epage=&date=2010&atitle=Codon+usage+bias+and+the+evolution+of+influenza+A+viruses.+Codon+Usage+Biases+of+Influenza+Virus.-
dc.identifier.emailPeiris, M: malik@hkucc.hku.hken_HK
dc.identifier.emailPoon, LLM: llmpoon@hkucc.hku.hken_HK
dc.identifier.authorityPeiris, M=rp00410en_HK
dc.identifier.authorityPoon, LLM=rp00484en_HK
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/1471-2148-10-253en_HK
dc.identifier.pmid20723216-
dc.identifier.pmcidPMC2933640-
dc.identifier.scopuseid_2-s2.0-77956395148en_HK
dc.identifier.hkuros188530en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-77956395148&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume10en_HK
dc.identifier.issue1en_HK
dc.identifier.isiWOS:000282767900002-
dc.publisher.placeUnited Kingdomen_HK
dc.relation.projectControl of Pandemic and Inter-pandemic Influenza-
dc.relation.projectCodon biases of avian and human influenza A viruses-
dc.identifier.scopusauthoridWong, EHM=36464610000en_HK
dc.identifier.scopusauthoridSmith, DK=36464390700en_HK
dc.identifier.scopusauthoridRabadan, R=15071174300en_HK
dc.identifier.scopusauthoridPeiris, M=7005486823en_HK
dc.identifier.scopusauthoridPoon, LLM=7005441747en_HK
dc.identifier.citeulike7686723-

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