Evolutionary dynamics of local pandemic H1N1/2009 influenza virus lineages revealed by whole-genome analysis.
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.
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom.
Gregory J
GJ
Baillie
Monica
M
Galiano
Paul-Michael
PM
Agapow
Richard
R
Myers
Rachael
R
Chiam
Astrid
A
Gall
Anne L
AL
Palser
Simon J
SJ
Watson
Jessica
J
Hedge
Anthony
A
Underwood
Steven
S
Platt
Estelle
E
McLean
Richard G
RG
Pebody
Andrew
A
Rambaut
Jonathan
J
Green
Rod
R
Daniels
Oliver G
OG
Pybus
Paul
P
Kellam
Maria
M
Zambon
D000293:Adolescent; D000328:Adult; D002648:Child; D019143:Evolution, Molecular; D016679:Genome, Viral; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D007251:Influenza, Human / Q000453:epidemiology / Q000821:virology*; D008969:Molecular Sequence Data; D058873:Pandemics; D010802:Phylogeny; D006113:United Kingdom; D055815:Young Adult