Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans

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Although a large number of immune epitopes have been identified in the influenza A virus (IAV) hemagglutinin (HA) protein using various experimental systems, it is unclear which are involved in protective immunity to natural infection in humans. We developed a data mining approach analyzing natural H1N1 human isolates to identify HA protein regions that appear to be targeted by the human immune system and can predict the evolution of IAV.

We identified sixteen amino acid sites experiencing diversifying selection during the evolution of pre-pandemic seasonal H1N1 strains and found that eleven of these sixteen diversified sites were located in experimentally-determined B-cell/Ab epitopes, including three previously characterized Caton epitopes: Sa, Sb and Ca2. We predicted that these diversified epitope regions would be the targets of mutation as the 2009 H1N1 pandemic (pH1N1) lineage evolves in response to the development of population-level protective immunity in humans.

Using a chi-squared goodness-of-fit test we identified ten amino acid sites that significantly differed between the 2009 pandemic outbreak isolates and isolates from the recent 2012-2013 and 2013-2014 flu seasons. Of these ten mutated sites, three were located in the same diversified B-cell/Ab epitope regions identified in the pre-pandemic analysis, including Sa and Sb. As predicted, hemagglutination inhibition (HI) assays using human serum from subjects vaccinated with the initial 2009 outbreak isolate demonstrated reduced reactivity against 2013-2014 isolates. Taken together, these results suggest that diversifying selection analysis can identify key immune epitopes responsible for protective immunity to influenza virus in humans and thereby predict virus evolution.

Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans.
Journal of virology. 2015-05-01; 89.10: 5427-40.
PMID: 25741011

This work is funded by the National Institute of Allergy and Infectious Diseases (NIH/DHHS) under contract no. HHSN272201200005C and HHSN272201400028C.