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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Virus and Prion Research » Research » Publications at this Location » Publication #361844

Research Project: Intervention Strategies to Control Influenza A Virus Infection in Swine

Location: Virus and Prion Research

Title: Spatial and temporal patterns of swine IAV gene constellations and reassortment in the USA from 2009 to 2019

item CHANG, JENNIFER - Oak Ridge Institute For Science And Education (ORISE)
item Anderson, Tavis
item Baker, Amy

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/17/2019
Publication Date: 6/24/2019
Citation: Chang, J., Anderson, T.K., Vincent, A.L. 2019. Spatial and temporal patterns of swine IAV gene constellations and reassortment in the USA from 2009 to 2019 [abstract] . CEIRS Network Meeting. p. none assigned.

Interpretive Summary:

Technical Abstract: Since 2009, the USDA influenza A virus (IAV) in swine surveillance system has reported on swine IAV in the United States with strain subtyping and segment sequencing from clinical respiratory cases. Regular temporal or spatial analysis of the genetic diversity can inform control efforts and improve animal health. Our goals were to: 1) quantify and describe temporal and spatial patterns in whole genome constellation diversity from 2009 to 2019; and 2) determine hotspots of IAV genomic reassortment in U.S. swine. Comprehensive phylogenetic analyses were conducted on publicly available PB2, PB1, PA, NP, MP, and NS genes, as well as HA and NA genes, generated by the USDA surveillance system. A one letter code (T=TRIG, P=Pandemic or V=Vaccine) for each internal gene, following the order of the aforementioned genes, was used to designate the genetic constellation of a strain and paired with HA and NA phylogenetic clade combinations. For 2017-2018, the dominant HA clade was H1-gamma (29.2%) and exhibited 6 different gene constellations, with a preference for a TTPPPT gene constellation. In contrast, H3 human-like 2010.1 and H1 delta1a, the next two most predominant HA clades, displayed a preference for a TTTTPT gene constellation. Constellations were partitioned by state and clustered by distance metrics to identify temporal and spatial patterns, revealing that gene constellation profiles in Iowa were highly variable across time whereas North Carolina had low variability across time. A blast-based method was developed to identify gene reassortment events among strains within the same clade. Across 2009 to 2018, high rates of reassortment were preliminarily identified in North Carolina, Michigan, and South Dakota. Our data suggest that there are spatial and temporal patterns in gene constellation diversity and that control efforts within swine production systems should consider local IAV diversity in addition to aggregated national patterns.