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Article: Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic

TitleOrigins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic
Authors
Issue Date2009
PublisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/nature
Citation
Nature, 2009, v. 459 n. 7250, p. 1122-1125 How to Cite?
AbstractIn March and early April 2009, a new swine-origin influenza A (HlNl) virus (S-OIV) emerged in Mexico and the United States'. During the first few weeks of surveillance, the virus spread worldwide to 30 countries (as of May 11 ) by human-to-human transmission, causing the World Health Organization to raise its pandemic alert to level 5 of 6. This virus has the potential to develop into the first influenza pandemic of the twenty-first century. Here we use evolutionary analysis to estimate the timescale of the origins and the early development of the S-OIV epidemic. We show that it was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak. A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that, the reassortment of swine lineages may have occurred years before emergence in humans, and that the multiple genetic ancestry of S-OIV is not indicative of an artificial origin. Furthermore, the unsampled history of the epidemic means that the nature and location of the genetically closest swine viruses reveal little about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates. Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans2. ©2009 Macmillan Publishers Limited. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/59392
ISSN
2014 Impact Factor: 41.456
2014 SCImago Journal Rankings: 17.313
ISI Accession Number ID
Funding AgencyGrant Number
The Royal Society of London
National Institute of Allergy and Infectious Diseases ( NIAID)
Biotechnology and Biological Sciences Research Council ( BBSRC)
David and Lucile Packard Foundation
Interdisciplinary Centre for Human and Avian Influenza Research ( ICHAIR)
National Institutes of HealthHHSN266200700005C
Area of Excellence Scheme of the University Grants Committee of the Hong Kong SAR GovernmentAoE/M-12/06
Funding Information:

We thank E. C. Holmes for comments and encouragement. We acknowledge support from The Royal Society of London ( A. R. and O. G. P.), the National Institute of Allergy and Infectious Diseases ( NIAID) ( G. J. D. S. and M. W.), the Biotechnology and Biological Sciences Research Council ( BBSRC) ( S. J. L.), and the David and Lucile Packard Foundation ( M. W.). A. R. works as a part of the Interdisciplinary Centre for Human and Avian Influenza Research ( ICHAIR). This study was supported by the National Institutes of Health ( NIAID contract HHSN266200700005C) and the Area of Excellence Scheme of the University Grants Committee ( grant AoE/M-12/06) of the Hong Kong SAR Government.

References
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DC FieldValueLanguage
dc.contributor.authorSmith, GJDen_HK
dc.contributor.authorVijaykrishna, Den_HK
dc.contributor.authorBahl, Jen_HK
dc.contributor.authorLycett, SJen_HK
dc.contributor.authorWorobey, Men_HK
dc.contributor.authorPybus, OGen_HK
dc.contributor.authorMa, SKen_HK
dc.contributor.authorCheung, CLen_HK
dc.contributor.authorRaghwani, Jen_HK
dc.contributor.authorBhatt, Sen_HK
dc.contributor.authorPeiris, JSMen_HK
dc.contributor.authorGuan, Yen_HK
dc.contributor.authorRambaut, Aen_HK
dc.date.accessioned2010-05-31T03:49:10Z-
dc.date.available2010-05-31T03:49:10Z-
dc.date.issued2009en_HK
dc.identifier.citationNature, 2009, v. 459 n. 7250, p. 1122-1125en_HK
dc.identifier.issn0028-0836en_HK
dc.identifier.urihttp://hdl.handle.net/10722/59392-
dc.description.abstractIn March and early April 2009, a new swine-origin influenza A (HlNl) virus (S-OIV) emerged in Mexico and the United States'. During the first few weeks of surveillance, the virus spread worldwide to 30 countries (as of May 11 ) by human-to-human transmission, causing the World Health Organization to raise its pandemic alert to level 5 of 6. This virus has the potential to develop into the first influenza pandemic of the twenty-first century. Here we use evolutionary analysis to estimate the timescale of the origins and the early development of the S-OIV epidemic. We show that it was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak. A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that, the reassortment of swine lineages may have occurred years before emergence in humans, and that the multiple genetic ancestry of S-OIV is not indicative of an artificial origin. Furthermore, the unsampled history of the epidemic means that the nature and location of the genetically closest swine viruses reveal little about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates. Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans2. ©2009 Macmillan Publishers Limited. All rights reserved.en_HK
dc.languageengen_HK
dc.publisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/natureen_HK
dc.relation.ispartofNatureen_HK
dc.subject.meshAnimalsen_HK
dc.subject.meshDisease Outbreaksen_HK
dc.subject.meshEvolution, Molecularen_HK
dc.subject.meshGenome, Viral - geneticsen_HK
dc.subject.meshHumansen_HK
dc.subject.meshInfluenza A Virus, H1N1 Subtype - classification - geneticsen_HK
dc.subject.meshInfluenza, Human - epidemiology - virologyen_HK
dc.subject.meshMolecular Sequence Dataen_HK
dc.subject.meshOrthomyxoviridae Infections - epidemiology - veterinary - virologyen_HK
dc.subject.meshPhylogenyen_HK
dc.subject.meshReassortant Viruses - classification - geneticsen_HK
dc.subject.meshSwineen_HK
dc.subject.meshSwine Diseases - virologyen_HK
dc.subject.meshTime Factorsen_HK
dc.titleOrigins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemicen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0028-0836&volume=459&spage=1122&epage=1125&date=2009&atitle=Origins+and+evolutionary+genomics+of+the+2009+swine-origin+H1N1+influenza+A+epidemicen_HK
dc.identifier.emailSmith, GJD: gjsmith@hkucc1.hku.hken_HK
dc.identifier.emailPeiris, JSM: malik@hkucc.hku.hken_HK
dc.identifier.emailGuan, Y: yguan@hkucc.hku.hken_HK
dc.identifier.authoritySmith, GJD=rp00444en_HK
dc.identifier.authorityPeiris, JSM=rp00410en_HK
dc.identifier.authorityGuan, Y=rp00397en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1038/nature08182en_HK
dc.identifier.pmid19516283-
dc.identifier.scopuseid_2-s2.0-67649538978en_HK
dc.identifier.hkuros157950en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-67649538978&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume459en_HK
dc.identifier.issue7250en_HK
dc.identifier.spage1122en_HK
dc.identifier.epage1125en_HK
dc.identifier.eissn1476-4687-
dc.identifier.isiWOS:000267636700042-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.f10001162111-
dc.relation.projectControl of Pandemic and Inter-pandemic Influenza-
dc.identifier.scopusauthoridSmith, GJD=8344015800en_HK
dc.identifier.scopusauthoridVijaykrishna, D=12752817700en_HK
dc.identifier.scopusauthoridBahl, J=35308668200en_HK
dc.identifier.scopusauthoridLycett, SJ=26664832200en_HK
dc.identifier.scopusauthoridWorobey, M=6603603024en_HK
dc.identifier.scopusauthoridPybus, OG=6701390795en_HK
dc.identifier.scopusauthoridMa, SK=35215973500en_HK
dc.identifier.scopusauthoridCheung, CL=34975244700en_HK
dc.identifier.scopusauthoridRaghwani, J=26664986400en_HK
dc.identifier.scopusauthoridBhatt, S=26658840800en_HK
dc.identifier.scopusauthoridPeiris, JSM=7005486823en_HK
dc.identifier.scopusauthoridGuan, Y=7202924055en_HK
dc.identifier.scopusauthoridRambaut, A=7004230842en_HK
dc.identifier.citeulike4832143-

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