tetano
Editor, Senior Moderator
First published October 2011, doi: 10.1128/JVI.05347-11 J. Virol. January 2012 vol. 86 no. 1 11-18
Evolutionary Dynamics of Local Pandemic H1N1/2009 Influenza Virus Lineages Revealed by Whole-Genome Analysis
Gregory J. Bailliea,
Monica Galianob,
Paul-Michael Agapowb,
Richard Myersb,
Rachael Chiama,
Astrid Galla,
Anne L. Palsera,
Simon J. Watsona,
Jessica Hedgec,
Anthony Underwoodb,
Steven Plattb,
Estelle McLeanb,
Richard G. Pebodyb,
Andrew Rambautc,d,
Jonathan Greenb,
Rod Danielse,
Oliver G. Pybusf,
Paul Kellama and
Maria Zambonb
+ Author Affiliations
aWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
bCentre for Infections, Health Protection Agency, London, United Kingdom
cInstitute of Evolutionary Biology, Ashworth Laboratories, Edinburgh, United Kingdom
dFogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
eDivision of Virology, National Institute for Medical Research, London, United Kingdom
fDepartment of Zoology, University of Oxford, Oxford, United Kingdom
ABSTRACT
Virus gene sequencing and phylogenetics can be used to study the epidemiological dynamics of rapidly evolving viruses. With complete genome data, it becomes possible to identify and trace individual transmission chains of viruses such as influenza virus during the course of an epidemic. Here we sequenced 153 pandemic influenza H1N1/09 virus genomes from United Kingdom isolates from the first (127 isolates) and second (26 isolates) waves of the 2009 pandemic and used their sequences, dates of isolation, and geographical locations to infer the genetic epidemiology of the epidemic in the United Kingdom. We demonstrate that the epidemic in the United Kingdom was composed of many cocirculating lineages, among which at least 13 were exclusively or predominantly United Kingdom clusters. The estimated divergence times of two of the clusters predate the detection of pandemic H1N1/09 virus in the United Kingdom, suggesting that the pandemic H1N1/09 virus was already circulating in the United Kingdom before the first clinical case. Crucially, three clusters contain isolates from the second wave of infections in the United Kingdom, two of which represent chains of transmission that appear to have persisted within the United Kingdom between the first and second waves. This demonstrates that whole-genome analysis can track in fine detail the behavior of individual influenza virus lineages during the course of a single epidemic or pandemic.
http://jvi.asm.org/content/86/1/11.short?rss=1
Evolutionary Dynamics of Local Pandemic H1N1/2009 Influenza Virus Lineages Revealed by Whole-Genome Analysis
Gregory J. Bailliea,
Monica Galianob,
Paul-Michael Agapowb,
Richard Myersb,
Rachael Chiama,
Astrid Galla,
Anne L. Palsera,
Simon J. Watsona,
Jessica Hedgec,
Anthony Underwoodb,
Steven Plattb,
Estelle McLeanb,
Richard G. Pebodyb,
Andrew Rambautc,d,
Jonathan Greenb,
Rod Danielse,
Oliver G. Pybusf,
Paul Kellama and
Maria Zambonb
+ Author Affiliations
aWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
bCentre for Infections, Health Protection Agency, London, United Kingdom
cInstitute of Evolutionary Biology, Ashworth Laboratories, Edinburgh, United Kingdom
dFogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
eDivision of Virology, National Institute for Medical Research, London, United Kingdom
fDepartment of Zoology, University of Oxford, Oxford, United Kingdom
ABSTRACT
Virus gene sequencing and phylogenetics can be used to study the epidemiological dynamics of rapidly evolving viruses. With complete genome data, it becomes possible to identify and trace individual transmission chains of viruses such as influenza virus during the course of an epidemic. Here we sequenced 153 pandemic influenza H1N1/09 virus genomes from United Kingdom isolates from the first (127 isolates) and second (26 isolates) waves of the 2009 pandemic and used their sequences, dates of isolation, and geographical locations to infer the genetic epidemiology of the epidemic in the United Kingdom. We demonstrate that the epidemic in the United Kingdom was composed of many cocirculating lineages, among which at least 13 were exclusively or predominantly United Kingdom clusters. The estimated divergence times of two of the clusters predate the detection of pandemic H1N1/09 virus in the United Kingdom, suggesting that the pandemic H1N1/09 virus was already circulating in the United Kingdom before the first clinical case. Crucially, three clusters contain isolates from the second wave of infections in the United Kingdom, two of which represent chains of transmission that appear to have persisted within the United Kingdom between the first and second waves. This demonstrates that whole-genome analysis can track in fine detail the behavior of individual influenza virus lineages during the course of a single epidemic or pandemic.
http://jvi.asm.org/content/86/1/11.short?rss=1