Real-time characterization of the molecular epidemiology of an influenza pandemic.
Identifieur interne : 000979 ( PubMed/Curation ); précédent : 000978; suivant : 000980Real-time characterization of the molecular epidemiology of an influenza pandemic.
Auteurs : J. Hedge [Royaume-Uni] ; S J Lycett ; A. RambautSource :
- Biology letters [ 1744-957X ] ; 2013.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Virus de la grippe A.
- épidémiologie : Grippe humaine.
- Humains, Épidémiologie moléculaire.
English descriptors
- KwdEn :
- MESH :
- epidemiology : Influenza, Human.
- genetics : Influenza A virus.
- Humans, Molecular Epidemiology.
Abstract
Early characterization of the epidemiology and evolution of a pandemic is essential for determining the most appropriate interventions. During the 2009 H1N1 influenza A pandemic, public databases facilitated widespread sharing of genetic sequence data from the outset. We use Bayesian phylogenetics to simulate real-time estimates of the evolutionary rate, date of emergence and intrinsic growth rate (r0) of the pandemic from whole-genome sequences. We investigate the effects of temporal range of sampling and dataset size on the precision and accuracy of parameter estimation. Parameters can be accurately estimated as early as two months after the first reported case, from 100 genomes and the choice of growth model is important for accurate estimation of r0. This demonstrates the utility of simple coalescent models to rapidly inform intervention strategies during a pandemic.
DOI: 10.1098/rsbl.2013.0331
PubMed: 23883574
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Hedge</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK. jessica.hedge@ndm.ox.ac.uk</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh</wicri:regionArea></affiliation></author><author><name sortKey="Lycett, S J" sort="Lycett, S J" uniqKey="Lycett S" first="S J" last="Lycett">S J Lycett</name></author><author><name sortKey="Rambaut, A" sort="Rambaut, A" uniqKey="Rambaut A" first="A" last="Rambaut">A. 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IdType="pubmed">23883574</ArticleId><ArticleId IdType="pii">rsbl.2013.0331</ArticleId><ArticleId IdType="doi">10.1098/rsbl.2013.0331</ArticleId><ArticleId IdType="pmc">PMC3971669</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Philos Trans R Soc Lond B Biol Sci. 2013 Mar 19;368(1614):20120314</Citation><ArticleIdList><ArticleId IdType="pubmed">23382432</ArticleId></ArticleIdList></Reference><Reference><Citation>Influenza Other Respir Viruses. 2009 Nov;3(6):267-76</Citation><ArticleIdList><ArticleId IdType="pubmed">19903209</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Comput Biol. 2011 Aug;7(8):e1002136</Citation><ArticleIdList><ArticleId IdType="pubmed">21901082</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2012 Sep;29(9):2157-67</Citation><ArticleIdList><ArticleId IdType="pubmed">22403239</ArticleId></ArticleIdList></Reference><Reference><Citation>Philos Trans R Soc Lond B Biol Sci. 1994 Jun 29;344(1310):403-10</Citation><ArticleIdList><ArticleId IdType="pubmed">7800710</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2004 Jan 16;303(5656):327-32</Citation><ArticleIdList><ArticleId IdType="pubmed">14726583</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2009 Jun 19;324(5934):1557-61</Citation><ArticleIdList><ArticleId IdType="pubmed">19433588</ArticleId></ArticleIdList></Reference><Reference><Citation>CMAJ. 2010 Feb 9;182(2):131-6</Citation><ArticleIdList><ArticleId IdType="pubmed">19959592</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2007 Mar;24(3):845-52</Citation><ArticleIdList><ArticleId IdType="pubmed">17218639</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Biol. 2006 May;4(5):e88</Citation><ArticleIdList><ArticleId IdType="pubmed">16683862</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2012 Aug;29(8):1969-73</Citation><ArticleIdList><ArticleId IdType="pubmed">22367748</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2008 Jul;25(7):1459-71</Citation><ArticleIdList><ArticleId IdType="pubmed">18408232</ArticleId></ArticleIdList></Reference><Reference><Citation>MMWR Morb Mortal Wkly Rep. 2009 Apr 24;58(15):400-2</Citation><ArticleIdList><ArticleId IdType="pubmed">19390508</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Microbiol. 2008 Jun;6(6):477-87</Citation><ArticleIdList><ArticleId IdType="pubmed">18533288</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2005 May;22(5):1185-92</Citation><ArticleIdList><ArticleId IdType="pubmed">15703244</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Biol Sci. 2007 Feb 22;274(1609):599-604</Citation><ArticleIdList><ArticleId IdType="pubmed">17476782</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):228-33</Citation><ArticleIdList><ArticleId IdType="pubmed">23248286</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Curr. 2009 Aug 18;1:RRN1003</Citation><ArticleIdList><ArticleId IdType="pubmed">20025195</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2009 Jun 25;459(7250):1122-5</Citation><ArticleIdList><ArticleId IdType="pubmed">19516283</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2009 Dec;183(4):1421-30</Citation><ArticleIdList><ArticleId IdType="pubmed">19797047</ArticleId></ArticleIdList></Reference><Reference><Citation>J R Soc Interface. 2012 Aug 7;9(73):1797-808</Citation><ArticleIdList><ArticleId IdType="pubmed">22337627</ArticleId></ArticleIdList></Reference><Reference><Citation>Syst Biol. 2012 Jan;61(1):170-3</Citation><ArticleIdList><ArticleId IdType="pubmed">21963610</ArticleId></ArticleIdList></Reference><Reference><Citation>N Engl J Med. 2009 Dec 31;361(27):2619-27</Citation><ArticleIdList><ArticleId IdType="pubmed">20042753</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Evol Biol. 2007;7:214</Citation><ArticleIdList><ArticleId IdType="pubmed">17996036</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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