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PLoS One. 2016 Aug 5;11(8):e0160510. doi: 10.1371/journal.pone.0160510. eCollection 2016.

Novel Sequence-Based Mapping of Recently Emerging H5NX Influenza Viruses Reveals Pandemic Vaccine Candidates.

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New York Influenza Center of Excellence, David Smith Center for Immunology and Vaccine Biology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America.
Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, United States of America.


Recently, an avian influenza virus, H5NX subclade, emerged and spread to North America. This subclade has frequently reassorted, leading to multiple novel viruses capable of human infection. Four cases of human infections, three leading to death, have already occurred. Existing vaccine strains do not protect against these new viruses, raising a need to identify new vaccine candidate strains. We have developed a novel sequence-based mapping (SBM) tool capable of visualizing complex protein sequence data sets using a single intuitive map. We applied SBM on the complete set of avian H5 viruses in order to better understand hemagglutinin protein variance amongst H5 viruses and identify any patterns associated with this variation. The analysis successfully identified the original reassortments that lead to the emergence of this new subclade of H5 viruses, as well as their known unusual ability to re-assort among neuraminidase subtypes. In addition, our analysis revealed distinct clusters of variants that would not be covered by existing strains in the H5 vaccine stockpile. The results suggest that our method may be useful for pandemic candidate vaccine virus selection.

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