Genomic and Antigenic Analysis of Seasonal H3N2 Influenza a Virus From 2012-2013

Haley Hochstein1, Karla M. Stucker1, Seth Schobel2, Xudong Lin1, Randall J. Olsen3, Anju Subba1, Rebecca A. Halpin1, Asmik Akopov1, Nadia Fedorova1, Timothy B. Stockwell2, James M. Musser3, Suman R. Das1, David E. Wentworth1
1Virology Group and 2Informatics Department, J. Craig Venter Institute, Rockville, MD 20850
3Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, TX 77030


Influenza is an acute viral infection of the upper respiratory system that accounts for 3-5 million hospitalizations and 250,000-500,000 deaths annually worldwide (WHO). Influenza A virus is a segmented, negative-sense RNA virus that is classified into various subtypes based on its two main surface glycoproteins, hemagluttinin (HA) and neuraminidase (NA). The two influenza A subtypes that annually circulate in humans are seasonal H1N1 and seasonal H3N2. The 2012-2013 influenza season resulted in a severe epidemic of H3N2 viruses. We hypothesize that this epidemic resulted from genetic changes in the HA that resulted in significant drift and aim to prove this by analyzing 145 human nasopharyngeal isolates that were collected from The Methodist Hospital System in Houston, Texas from November, 2012 through February, 2013. Full influenza genomic sequencing was performed on all samples using the Ion Torrent next-generation sequencing platform to identify nucleotide substitutions important in the epidemic strain. The complete genome analysis suggested that the most important changes in this strain were in the HA gene. Using the HA sequence data from these samples, as well as from other publically available clinical and vaccine sequences, we performed an alignment and inferred a maximum-likelihood phylogenetic tree. Based on these analyses, 12 clinical isolates of interest were chosen for viral isolation and in vitro antigenic analyses. The combined genomic and antigenic analyses of these samples demonstrate biologically significant antigenic drift among H3N2 viruses from the 2012-2013 influenza season in Texas, which provides important information for the upcoming vaccine selection decisions.