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Article: Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic
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TitleOrigins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic
 
AuthorsSmith, GJD1
Vijaykrishna, D1
Bahl, J1
Lycett, SJ4
Worobey, M2
Pybus, OG3
Ma, SK1
Cheung, CL1
Raghwani, J4
Bhatt, S3
Peiris, JSM1
Guan, Y1
Rambaut, A4
 
Issue Date2009
 
PublisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/nature
 
CitationNature, 2009, v. 459 n. 7250, p. 1122-1125 [How to Cite?]
DOI: http://dx.doi.org/10.1038/nature08182
 
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about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates.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.
 
ISSN0028-0836
2013 Impact Factor: 42.351
 
DOIhttp://dx.doi.org/10.1038/nature08182
 
ISI Accession Number IDWOS:000267636700042
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.

 
ReferencesReferences in Scopus
 
GrantsControl of Pandemic and Inter-pandemic Influenza
 
DC FieldValue
dc.contributor.authorSmith, GJD
 
dc.contributor.authorVijaykrishna, D
 
dc.contributor.authorBahl, J
 
dc.contributor.authorLycett, SJ
 
dc.contributor.authorWorobey, M
 
dc.contributor.authorPybus, OG
 
dc.contributor.authorMa, SK
 
dc.contributor.authorCheung, CL
 
dc.contributor.authorRaghwani, J
 
dc.contributor.authorBhatt, S
 
dc.contributor.authorPeiris, JSM
 
dc.contributor.authorGuan, Y
 
dc.contributor.authorRambaut, A
 
dc.date.accessioned2010-05-31T03:49:10Z
 
dc.date.available2010-05-31T03:49:10Z
 
dc.date.issued2009
 
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.
 
dc.description.naturelink_to_subscribed_fulltext
 
dc.identifier.citationNature, 2009, v. 459 n. 7250, p. 1122-1125 [How to Cite?]
DOI: http://dx.doi.org/10.1038/nature08182
 
dc.identifier.citeulike4832143
 
dc.identifier.doihttp://dx.doi.org/10.1038/nature08182
 
dc.identifier.eissn1476-4687
 
dc.identifier.epage1125
 
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dc.identifier.isiWOS:000267636700042
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.

 
dc.identifier.issn0028-0836
2013 Impact Factor: 42.351
 
dc.identifier.issue7250
 
dc.identifier.openurl
 
dc.identifier.pmid19516283
 
dc.identifier.scopuseid_2-s2.0-67649538978
 
dc.identifier.spage1122
 
dc.identifier.urihttp://hdl.handle.net/10722/59392
 
dc.identifier.volume459
 
dc.languageeng
 
dc.publisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/nature
 
dc.publisher.placeUnited Kingdom
 
dc.relation.ispartofNature
 
dc.relation.projectControl of Pandemic and Inter-pandemic Influenza
 
dc.relation.referencesReferences in Scopus
 
dc.subject.meshAnimals
 
dc.subject.meshDisease Outbreaks
 
dc.subject.meshEvolution, Molecular
 
dc.subject.meshGenome, Viral - genetics
 
dc.subject.meshHumans
 
dc.subject.meshInfluenza A Virus, H1N1 Subtype - classification - genetics
 
dc.subject.meshInfluenza, Human - epidemiology - virology
 
dc.subject.meshMolecular Sequence Data
 
dc.subject.meshOrthomyxoviridae Infections - epidemiology - veterinary - virology
 
dc.subject.meshPhylogeny
 
dc.subject.meshReassortant Viruses - classification - genetics
 
dc.subject.meshSwine
 
dc.subject.meshSwine Diseases - virology
 
dc.subject.meshTime Factors
 
dc.titleOrigins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic
 
dc.typeArticle
 
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Author Affiliations
  1. The University of Hong Kong
  2. University of Arizona
  3. University of Oxford
  4. University of Edinburgh