An emerging H1N2 sub-cluster within the alpha H1 cluster of influenza A viruses of swine in Canada

Over the last 15 years, genetically and antigenically distinct groups of influenza A viruses in swine (IAV-S) have emerged. The 2009 pandemic H1N1 virus and variant H3N2 viruses of swine-origin underscore the threat that IAV-S pose to public health. Consequently, there is greater need for increased IAV-S surveillance globally. This is particularly important in regions where there is very little historical sequence data available. In this study, IAV-S surveillance was conducted to examine H1N1 and H1N2 sequences from Western Canada.

Diagnostic samples of lung tissue and nasal swabs were collected from pigs in Alberta (AB), Saskatchewan (SK) and Manitoba (MB). Samples were screened for IAV-S by CFIA or USDA certified Matrix PCR tests. Positive samples were subtyped and virus isolation and sequencing of the hemagglutinin (HA) gene was attempted on 443 viruses. Whole-genome sequencing was performed on 169 of these viruses. Phylogenetic analyses were conducted in MEGA 6 using Neighbor-Joining and Maximum Composite Likelihood methods with bootstrapping.

Phylogenetic analysis of the HA genes revealed that the Western Canadian H1 viruses (2012-2015) were within the pH1N1 and H1α clusters. Within the H1α cluster there were two distinct sub-clusters. These included the H1N1α viruses known to previously circulate in this region and a new cluster of H1N2 alpha viruses first detected in MB in the fall of 2013. Most of the H1N2α viruses contained the same 2 amino acid (AA) deletion (amino acid positions 129 and 130 in the H1 numbering system), which is similar to the 1AA human-like deletion observed in the H1 delta-cluster viruses. This H1N2 strain containing a unique deletion at amino acid positions 129 and 130 continues to be the dominant IAV-S detected in Western Canada 2015. Whole genome analysis revealed the same phylogenetic pattern for the other 7 genes of these H1N2α viruses. While 17/36 virus sequences are from the 6 farms in one MB system, 12 are from unrelated farms in MB, 1 unrelated farm in SK and 6 farms in the United States. Additionally, one strain from AB and two strains from MB are within the H1N2 alpha sub-cluster, but do not contain this deletion.

The results highlight the importance of IAV-S surveillance within overlooked regions, and is thus crucial for understanding the ecology and spatial dissemination of swine diseases. In order to develop effective control strategies for emerging influenza strains, we need to know what types of viruses are circulating. We also need to know the genetic relationships of these viruses to each other, as well as their relationship to viruses in other regions.

Disclosure of Interest: None Declare.