Phylogenetic Inference of H3N2 Canine Influenza A Outbreak in Ontario, Canada in 2018

J Scott Weese,Katherine Handel,Davor Ojkic,Oliver Lung,Wanhong Xu,Yohannes Berhane

doi:10.1038/s41598-020-63278-z

Abstract

The first Canadian H3N2 canine influenza A outbreak involving an Asian-origin H3N2 canine influenza virus (CIV) began in southwestern Ontario, Canada, in late December 2017. More H3N2 CIV cases were identified in central and eastern Ontario between March and October 2018. Based on epidemiological investigation, 5 clusters were identified (C1, C2, C3a, C3b, and C4); however, the origin of infection has only been revealed for epidemiological cluster C1. Here, we use phylogenetic analyses to unravel the links of virus transmission between the 5 epidemiological clusters and the origin of infection for all epidemiological clusters. Our results demonstrate that the Canadian H3N2 CIV sequences were grouped into four distinct phylogenetic clusters with minimal genetic diversity between these clusters. Large scale phylogenetic analysis of H3N2 CIV from around the globe showed that the Canadian CIVs formed a distinct new clade along with CIVs that have been circulating in the USA since 2017–2018 and in China since 2017. This clade shares a common ancestor of Asian origin. This study concludes that the H3N2 CIV outbreak in Ontario was driven by multiple introductions of South Korean/Chinese-origin H3N2 CIVs over 10 months.

Highlights

Avian-origin canine influenza virus (CIV) H3N2 emerged in dogs in China and South Korea around 20051–3
Out of twenty-seven amino acid mutations that differentiate the current H3N2 CIV isolates from other avian influenza viruses (AIVs) reported in a previous study[14], twenty of these amino acids remained unchanged in this study (Table 1), suggesting these amino acids were important for dog adaptation
Our findings from 21 H3N2 CIV genomes sampled in Ontario over 10 months during the 2018 H3N2 CIV outbreak in Canada demonstrate the value of phylogenetic analysis

Summary

Introduction

Avian-origin canine influenza virus (CIV) H3N2 emerged in dogs in China and South Korea around 20051–3. To gain a better understanding of H3N2 CIV emergence in Ontario and the evolutionary dynamics of this outbreak, 21 samples from five epidemiological clusters were randomly selected for full genome sequencing. Both Maximum Likelihood (ML) and Bayesian approaches were used to infer phylogenetic relatedness. We provide an analysis of the complete coding-region of eight gene segments of 21 H3N2 CIV strains that were sampled from infected dogs in Ontario, Canada in 2018 We compared their full genomes to 162 H3N2 CIV full genomes that were available in the GenBank database. We used this combined data set to better understand the molecular evolution of H3N2 CIV, including the nucleotide substitution rate and selection pressure

Methods

Results

Conclusion