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Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest

View ORCID ProfileCrystal M. Hepp, Jill Hager Cocking, Michael Valentine, Steven J. Young, Dan Damien, Krystal Sheridan, Viacheslav Y. Fofanov, Joseph D. Busch, Daryn E. Erickson, Ryan C. Lancione, Kirk Smith, James Will, John Townsend, Paul S. Keim, David M. Engelthaler
doi: https://doi.org/10.1101/223503
Crystal M. Hepp
1School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United Sates of America
2The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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  • ORCID record for Crystal M. Hepp
  • For correspondence: crystal.hepp@nau.edu
Jill Hager Cocking
1School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United Sates of America
2The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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Michael Valentine
3Translational Genomics Research Institute North, Flagstaff, Arizona, United States of America
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Steven J. Young
5Maricopa County Environmental Services Department Vector Control Division, Phoenix, Arizona, United States of America
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Dan Damien
4Maricopa County Environmental Services Department Office of Enterprise Technology, Phoenix, Arizona, United States of America
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Krystal Sheridan
2The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
3Translational Genomics Research Institute North, Flagstaff, Arizona, United States of America
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Viacheslav Y. Fofanov
1School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United Sates of America
2The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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Joseph D. Busch
2The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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Daryn E. Erickson
1School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United Sates of America
2The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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Ryan C. Lancione
1School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United Sates of America
2The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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Kirk Smith
5Maricopa County Environmental Services Department Vector Control Division, Phoenix, Arizona, United States of America
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James Will
5Maricopa County Environmental Services Department Vector Control Division, Phoenix, Arizona, United States of America
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John Townsend
5Maricopa County Environmental Services Department Vector Control Division, Phoenix, Arizona, United States of America
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Paul S. Keim
2The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
3Translational Genomics Research Institute North, Flagstaff, Arizona, United States of America
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David M. Engelthaler
3Translational Genomics Research Institute North, Flagstaff, Arizona, United States of America
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Abstract

West Nile Virus (WNV) has been detected annually in Maricopa County, Arizona, since 2003. With this in mind, we sought to determine if contemporary strains are established within the county or are annually imported. As part of this effort, we developed a new protocol for tiled amplicon sequencing of WNV to efficiently attain greater than 99% coverage of 14 WNV genomes collected directly from positive mosquito pools distributed throughout Maricopa County between 2014 and 2017. Bayesian phylogenetic analyses revealed that the contemporary genomes fall within two major lineages, NA/WN02 and SW/WN03. We found that all of the Arizona strains possessed a mutation known to be under positive selection (NS5-K314R), which has arisen independently four times. The SW/WN03 strains exhibited transient behavior, with at least 10 separate introductions into Arizona when considering both historical and contemporary strains. However, NA/WN02 strains are geographically differentiated and appear to be established in Arizona, with likely origins in New York. The clade of New York and Arizona strains looks to be the most ancestral extant lineage of WNV still circulating in the United States. The establishment of WNV strains in Maricopa County provides the first evidence of local overwintering by a WNV strain over the course of several years in Arizona.

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Posted November 22, 2017.
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Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest
Crystal M. Hepp, Jill Hager Cocking, Michael Valentine, Steven J. Young, Dan Damien, Krystal Sheridan, Viacheslav Y. Fofanov, Joseph D. Busch, Daryn E. Erickson, Ryan C. Lancione, Kirk Smith, James Will, John Townsend, Paul S. Keim, David M. Engelthaler
bioRxiv 223503; doi: https://doi.org/10.1101/223503
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Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest
Crystal M. Hepp, Jill Hager Cocking, Michael Valentine, Steven J. Young, Dan Damien, Krystal Sheridan, Viacheslav Y. Fofanov, Joseph D. Busch, Daryn E. Erickson, Ryan C. Lancione, Kirk Smith, James Will, John Townsend, Paul S. Keim, David M. Engelthaler
bioRxiv 223503; doi: https://doi.org/10.1101/223503

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