Skip to main content
ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Virus and Prion Research » Research » Publications at this Location » Publication #357251

Research Project: Intervention Strategies to Control Endemic and New and Emerging Viral Diseases of Swine

Location: Virus and Prion Research

Title: Spatial and temporal patterns of swine IAV gene constellations in the USA from 2010 to 2018

item CHANG, JENNIFER - Orise Fellow
item Anderson, Tavis
item Baker, Amy

Submitted to: Research Workers in Animal Diseases Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 10/15/2018
Publication Date: 11/30/2018
Citation: Chang, J., Anderson, T.K., Vincent, A.L. 2018. Spatial and temporal patterns of swine IAV gene constellations in the USA from 2010 to 2018 [abstract]. Research Workers in Animal Diseases Conference Proceedings. p. none assigned.

Interpretive Summary:

Technical Abstract: Objectives Since 2009, USDA monitors swine in the United States for influenza A virus (IAV) with a focus on strain subtyping and segment sequencing from clinical respiratory cases. Regular temporal or spatial analysis of the genetic diversity (e.g. subtype counts, gene constellation prevalence) can help inform control efforts and improve animal health. Expanding from previous work from our group [1, 2], our goal was to: 1) quantify and describe the temporal and spatial patterns in whole genome constellation diversity from 2010 to 2018; and 2) determine hotspots of IAV genomic reassortment in U.S. swine. Methods A comprehensive phylogenetic analysis of publicly available PB2, PB1, PA, NP, MP, and NS genes generated by the USDA surveillance system was conducted on samples collected in a 2-year timespan (April 2016 – March 2018) and an 8-year time span (April 2010 to March 2018). Internal genes were classified as T (TRIG) or P (Pandemic) using MAFFT [3] and FastTree [4]. One letter codes (T=TRIG or P=Pandemic) for each internal gene was used to designate the genetic constellation of a strain. Gene constellations were then partitioned by state or region and clustered by several distance metrics to identify temporal and spatial patterns. Results The dominant gene constellations detected during the 2-year timespan (April 2016 – March 2018) were TTTTPT (41.5% total, H3-hulike_2010.1/N2-2002 12.9% dominant), TTTPPT (22.9% total, H1- '/N1-classical 5.9% dominant) and TTPPPT (21.5% total, H1-'/N1-classical 16.3% dominant), but 8 other minor constellations were also maintained. Partitioning the data into 5 spatial zones revealed that gene constellations varied at the state, region and national level. Conclusions Our data suggest that vaccine composition and control efforts should consider IAV diversity within swine production regions in addition to aggregated national patterns. Genetic variation other than subtype (e.g. gene constellation patterns) may supplement the HA/NA subtypes to improve targeting and control efforts. 1. Walia, R.R., T.K. Anderson, and A.L. Vincent, Regional patterns of genetic diversity in swine influenza A viruses in the United States from 2010 to 2016. Influenza Other Respir Viruses, 2018. 2. Gao, S., et al., The genomic evolution of H1 influenza A viruses from swine detected in the United States between 2009 and 2016, in J Gen Virol. 2017. p. 2001-10. 3. Katoh, K. and D.M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol, 2013. 30(4): p. 772-80. 4. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments. 2018.