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Article: Phylodynamics of H5N1 avian influenza virus in Indonesia

TitlePhylodynamics of H5N1 avian influenza virus in Indonesia
Authors
Keywordsagriculture
ecology
evolution
influenza
phylodynamics
phylogeography
Issue Date2012
PublisherBlackwell Publishing Ltd. The Journal's web site is located at http://www.blackwellpublishing.com/journals/MEC
Citation
Molecular Ecology, 2012, v. 21 n. 12, p. 3062-3077 How to Cite?
Abstract
Understanding how pathogens invade and become established in novel host populations is central to the ecology and evolution of infectious disease. Influenza viruses provide unique opportunities to study these processes in nature because of their rapid evolution, extensive surveillance, large data sets and propensity to jump species boundaries. H5N1 highly pathogenic avian influenza virus (HPAIV) is a major animal pathogen and public health threat. The virus is of particular importance in Indonesia, causing severe outbreaks among poultry and sporadic human infections since 2003. However, little is known about how H5N1 HPAIV emerged and established in Indonesia. To address these questions, we analysed Indonesian H5N1 HPAIV gene sequences isolated during 2003-2007. We find that the virus originated from a single introduction into East Java between November 2002 and October 2003. This invasion was characterized by an initially rapid burst of viral genetic diversity followed by a steady rate of lineage replacement and the maintenance of genetic diversity. Several antigenic sites in the haemagglutinin gene were subject to positive selection during the early phase, suggesting that host-immune-driven selection played a role in host adaptation and expansion. Phylogeographic analyses show that after the initial invasion of H5N1, genetic variants moved both eastwards and westwards across Java, possibly involving long-distance transportation by humans. The phylodynamics we uncover share similarities with other recently studied viral invasions, thereby shedding light on the ecological and evolutionary processes that determine disease emergence in a new geographical region. © 2012 Blackwell Publishing Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/153210
ISSN
2013 Impact Factor: 5.840
ISI Accession Number ID
Funding AgencyGrant Number
Strategic Research Theme of Infection and Immunology, HKU
European Union278433
ERC260864
Newton International Fellowship
Royal Society, UK
Funding Information:

We gratefully thank the Indonesian and other scientists, including those who collected the specimens and sequenced and shared the influenza virus genomes in public sequence databases. We also thank Endang R. Sedyaningsih (MoH, Indonesia) and David Mulyono for useful discussions. We thank Joseph T. Wu (SPH, HKU), the editor and the three anonymous reviewers for important suggestions. The research was supported by funding from the Strategic Research Theme of Infection and Immunology, HKU (to FCL), and the European Union Seventh Framework Programme [FP7/2007-2013] under Grant Agreement no. 278433 and ERC Grant agreement no. 260864 (to PL). TTL is supported by the Newton International Fellowship and both TTL and OGP are supported by Royal Society, UK. We also acknowledge the support of BIOSUPPORT and HPCPOWER projects (HKU) for providing computational resources. We also thank W. K. Kwan and Frankie Cheung for their technical assistance.

References

 

Author Affiliations
  1. Rega Institute for Medical Research
  2. The University of Hong Kong
  3. John E. Fogarty International Center for advanced study in the health sciences
  4. Pennsylvania State University
  5. University of Oxford
DC FieldValueLanguage
dc.contributor.authorLam, TTYen_HK
dc.contributor.authorHon, CCen_HK
dc.contributor.authorLemey, Pen_HK
dc.contributor.authorPybus, OGen_HK
dc.contributor.authorShi, Men_HK
dc.contributor.authorTun, HMen_HK
dc.contributor.authorLi, Jen_HK
dc.contributor.authorJiang, Jen_HK
dc.contributor.authorHolmes, ECen_HK
dc.contributor.authorLeung, FCCen_HK
dc.date.accessioned2012-07-16T09:59:51Z-
dc.date.available2012-07-16T09:59:51Z-
dc.date.issued2012en_HK
dc.identifier.citationMolecular Ecology, 2012, v. 21 n. 12, p. 3062-3077en_HK
dc.identifier.issn0962-1083en_HK
dc.identifier.urihttp://hdl.handle.net/10722/153210-
dc.description.abstractUnderstanding how pathogens invade and become established in novel host populations is central to the ecology and evolution of infectious disease. Influenza viruses provide unique opportunities to study these processes in nature because of their rapid evolution, extensive surveillance, large data sets and propensity to jump species boundaries. H5N1 highly pathogenic avian influenza virus (HPAIV) is a major animal pathogen and public health threat. The virus is of particular importance in Indonesia, causing severe outbreaks among poultry and sporadic human infections since 2003. However, little is known about how H5N1 HPAIV emerged and established in Indonesia. To address these questions, we analysed Indonesian H5N1 HPAIV gene sequences isolated during 2003-2007. We find that the virus originated from a single introduction into East Java between November 2002 and October 2003. This invasion was characterized by an initially rapid burst of viral genetic diversity followed by a steady rate of lineage replacement and the maintenance of genetic diversity. Several antigenic sites in the haemagglutinin gene were subject to positive selection during the early phase, suggesting that host-immune-driven selection played a role in host adaptation and expansion. Phylogeographic analyses show that after the initial invasion of H5N1, genetic variants moved both eastwards and westwards across Java, possibly involving long-distance transportation by humans. The phylodynamics we uncover share similarities with other recently studied viral invasions, thereby shedding light on the ecological and evolutionary processes that determine disease emergence in a new geographical region. © 2012 Blackwell Publishing Ltd.en_HK
dc.languageengen_US
dc.publisherBlackwell Publishing Ltd. The Journal's web site is located at http://www.blackwellpublishing.com/journals/MECen_HK
dc.relation.ispartofMolecular Ecologyen_HK
dc.rightsThe definitive version is available at www.blackwell-synergy.com-
dc.subjectagricultureen_HK
dc.subjectecologyen_HK
dc.subjectevolutionen_HK
dc.subjectinfluenzaen_HK
dc.subjectphylodynamicsen_HK
dc.subjectphylogeographyen_HK
dc.titlePhylodynamics of H5N1 avian influenza virus in Indonesiaen_HK
dc.typeArticleen_HK
dc.identifier.emailLam, TTY: ttylam@hku.hken_HK
dc.identifier.emailLeung, FCC: fcleung@hkucc.hku.hken_HK
dc.identifier.authorityLam, TTY=rp01733en_HK
dc.identifier.authorityLeung, FCC=rp00731en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1111/j.1365-294X.2012.05577.xen_HK
dc.identifier.pmid22574738en_HK
dc.identifier.scopuseid_2-s2.0-84861998642en_HK
dc.identifier.hkuros200940en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-84861998642&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume21en_HK
dc.identifier.issue12en_HK
dc.identifier.spage3062en_HK
dc.identifier.epage3077en_HK
dc.identifier.isiWOS:000304903100021-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridLam, TTY=36775821700en_HK
dc.identifier.scopusauthoridHon, CC=7003617137en_HK
dc.identifier.scopusauthoridLemey, P=6602704841en_HK
dc.identifier.scopusauthoridPybus, OG=6701390795en_HK
dc.identifier.scopusauthoridShi, M=25951822000en_HK
dc.identifier.scopusauthoridTun, HM=38062179300en_HK
dc.identifier.scopusauthoridLi, J=54881403300en_HK
dc.identifier.scopusauthoridJiang, J=35310401200en_HK
dc.identifier.scopusauthoridHolmes, EC=35433598300en_HK
dc.identifier.scopusauthoridLeung, FCC=7103078633en_HK

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