Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States.
To determine the spatial and temporal dynamics of influenza A virus during a single epidemic, we examined whole-genome sequences of 284 A/H1N1 and 69 A/H3N2 viruses collected across the continental United States during the 2006-2007 influenza season, representing the largest study of its kind undertaken to date. A phylogenetic analysis revealed that multiple clades of both A/H1N1 and A/H3N2 entered and co-circulated in the United States during this season, even in localities that are distant from major metropolitan areas, and with no clear pattern of spatial spread. In addition, co-circulating clades of the same subtype exchanged genome segments through reassortment, producing both a minor clade of A/H3N2 viruses that appears to have re-acquired sensitivity to the adamantane class of antiviral drugs, as well as a likely antigenically distinct A/H1N1 clade that became globally dominant following this season. Overall, the co-circulation of multiple viral clades during the 2006-2007 epidemic season revealed patterns of spatial spread that are far more complex than observed previously, and suggests a major role for both migration and reassortment in shaping the epidemiological dynamics of human influenza A virus.
Nelson
Martha I
MI
Department of Biology, Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America.
Edelman
Laurel
L
Spiro
David J
DJ
Boyne
Alex R
AR
Bera
Jayati
J
Halpin
Rebecca
R
Sengamalay
Naomi
N
Ghedin
Elodie
E
Miller
Mark A
MA
Simonsen
Lone
L
Viboud
Cecile
C
Holmes
Edward C
EC
D016679:Genome, Viral; D049674:History, 21st Century; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics*; D053122:Influenza A Virus, H3N2 Subtype / Q000235:genetics*; D007251:Influenza, Human / Q000453:epidemiology* / Q000235:genetics*; D017720:Molecular Epidemiology; D010802:Phylogeny; D014481:United States / Q000453:epidemiology