Molecular surveillance of coronaviruses in livestock in northern Vietnam

Coronavirus (CoV) infections continue to pose a significant challenge to global public health and food security. The COVID-19 pandemic has underscored the importance of One Health approaches and improved surveillance systems. This is due to the considerable potential of CoVs to infect a broad spectrum of hosts and cause respiratory diseases. The present study investigated CoVs circulating in livestock in northern Vietnam using molecular detection and phylogenetic analysis. A total of 412 samples collected from livestock were analysed for the presence of CoVs, and we detected infectious bronchitis virus (IBV), porcine haemagglutinating encephalomyelitis virus (PHEV), and avian Gamma-CoV. Nearly full-length genomes of IBV and PHEV were obtained in this study. Phylogenetic analysis inferred that the IBV strains detected in this study were GI-13 vaccine-like strains. Furthermore, this study provides the first genome sequences of Vietnamese PHEV strains. The viruses were closely related to the respiratory-variant lineage detected in China, suggesting that the viruses may have entered Vietnam from China; however, further analysis of PHEVs would likely be necessary for a more detailed characterization. Moreover, avian Gamma-CoVs were inferred to be related to migratory birds, thereby suggesting the risk of transmission from migratory birds to livestock. In summary, this study provides insights into the diversity of CoVs in livestock in northern Vietnam. Therefore, continuous surveillance is necessary to prevent further spread of CoVs among livestock.