Everybody is Kung-Flu Fighting: Deep Sequencing of Clinical Influenza A Virus Reveals Patterns of Emerging/ Re-emerging Amino Acid Substitutions

Emma Roth, Brian Aevermann, Vinita Puri, Nadia Fedorova, Susmita Shrivastava, Lihui Wu, Paolo Amedeo, Rafael Medina, Gene Tan, Brett E. Pickett

J. Craig Venter Institute, La Jolla, CA

Infection by influenza A virus (IAV) can occur in birds or swine, and results in approximately 700,000 hospitalizations and 56,000 human deaths each year. Although vaccines exist and are reformulated each year, the rapid mutation rates (antigenic drift) and reassortment (antigenic shift) across the viral subtypes make it difficult to prevent or treat infection consistently. In this study, we examined deep sequencing data of IAV samples collected between 2011-2013 from Santiago, Chile to determine whether amino acid substitutions emerging/re-emerging at the global scale could be identified by observing minor variants in the genomes isolated from multiple patients. We created a workflow that visualizes the locations of minor variants across each segment for these genomes, calculates mutations that stray from the consensus amino acid in that location across all GenBank sequence data for each year, and determines whether the amino acid positions that contain a minor variant are located in known epitope regions from a reference genome. Phylogenetic tree reconstruction based on the consensus sequences for the hemagglutinin segment reveals that the sequences lie within the expected topology of influenza and cluster primarily by year of isolation. Patterns identified in this analysis have the potential to improve our ability to understand how the virus is adapting to immune pressures within its host, and to detect any substitutions that change immune epitopes to increase virus fitness. Overall, these results can be applied at a larger scale to sequences of future epidemic strains and thus improve the efficacy of the influenza vaccine.


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