Abstract
BackgroundData about molecular diversity of commonly circulating type A influenza viruses in Ontario swine are scarce. Yet, this information is essential for surveillance of animal and public health, vaccine updates, and for understanding virus evolution and its large-scale spread.MethodsThe study population consisted of 21 swine herds with clinical problems due to respiratory disease. Nasal swabs from individual pigs were collected and tested by virus isolation in MDCK cells and by rtRT-PCR. All eight segments of 10 H3N2 viruses were sequenced using high-throughput sequencing and molecularly characterized.ResultsWithin-herd prevalence ranged between 2 and 100%. Structurally, Ontario H3N2 viruses could be classified into three different groups. Group 1 was the most similar to the original trH3N2 virus from 2005. Group 2 was the most similar to the Ontario turkey H3N2 isolates with PB1 and NS genes originating from trH3N2 virus and M, PB2, PA and NP genes originating from the A(H1N1)pdm09 virus. All Group 3 internal genes were genetically related to A(H1N1)pdm09. Analysis of antigenic sites of HA1 showed that Group 1 had 8 aa changes within 4 antigenic sites, A(1), B(3), C(2) and E(2). The Group 2 viruses had 8 aa changes within 3 antigenic sites A(3), B(3) and C(2), while Group 3 viruses had 4 aa changes within 3 antigenic sites, B(1), D(1) and E(2), when compared to the cluster IV H3N2 virus [A/swine/Ontario/33853/2005/(H3N2)].ConclusionsThe characterization of the Ontario H3N2 viruses clearly indicates reassortment of gene segments between the North American swine trH3N2 from cluster IV and the A(H1N1)pdm09 virus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-014-0194-z) contains supplementary material, which is available to authorized users.
Highlights
Data about molecular diversity of commonly circulating type A influenza viruses in Ontario swine are scarce
Viruses from eleven out of 16 positive herds were typed as H3N2, from 3 herds were typed as H1N1, and in 2 herds, subtyping was not successful
The 4 Group 2 viruses were most similar to the Ontario turkey H3N2 variants with PB1 and NS genes originating from triple-reassortant H3N2 (trH3N2) virus and M, PB2, PA, and NP
Summary
Data about molecular diversity of commonly circulating type A influenza viruses in Ontario swine are scarce This information is essential for surveillance of animal and public health, vaccine updates, and for understanding virus evolution and its large-scale spread. After initial detection of the trH3N2 virus in 2005, there were no further scientific publications about molecular diversity of influenza viruses circulating in Canadian swine until 2009 [4] This information has been limited in Ontario. According to a recent statistic from 2012 and 2013, Ontario is the province with the second largest number of pigs on farms in Canada, and with the largest number of farms with pigs [5] This information is important for surveillance of influenza viruses and informing animal and public health decisions, vaccine updates, and for understanding virus evolution and its large-scale spread. The objective of this study was to determine which H3N2 influenza A viruses circulated in Ontario swine in 2011 and 2012
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