Metagenomic characterization of the porcine respiratory virome on farms in northern Kazakhstan.

Studies of the porcine respiratory virome are essential for understanding the complex viral communities in the porcine respiratory tract and their roles in health and disease. Characterizing the respiratory virome provides insights into the diversity, prevalence, and dynamics of pathogenic and commensal viruses, thereby facilitating the identification of emerging and previously unrecognized respiratory pathogens. Metagenomic next-generation sequencing (mNGS) is a method for analyzing viral communities, enabling comprehensive monitoring of circulating and co-detected pathogens in animals. In this study, mNGS on the Illumina platform was used to characterize the porcine respiratory virome in Kazakhstan. The study included 150 nasopharyngeal swabs collected from commercial pig farms in northern Kazakhstan. Viral sequences were assigned to the families Parvoviridae, Herpesviridae, Picornaviridae, Astroviridae, and Anelloviridae. High coverage was achieved for Porcine cytomegalovirus, Porcine parvovirus 5, and Porcine parvovirus 7, including reconstruction of a nearly complete PPV7 genome. Significant variability in mapped read counts and sequencing depth was observed across samples, reflecting heterogeneity in the detection of viral nucleic acids within the sampled population. Phylogenetic analysis showed that all identified viruses belong to globally circulating evolutionary lineages and do not form new divergent clusters. Moreover, respiratory and gastrointestinal virus sequences were often detected simultaneously in nasopharyngeal samples, indicating a complex composition of viral nucleic acids in the upper respiratory tract of pigs. Pigs are important reservoirs and intermediate hosts for zoonotic viruses. Metagenomic studies contribute not only to animal health and disease control but also to One Health initiatives by strengthening early warning systems for pathogens with epidemic or pandemic potential. The results demonstrate the high viral diversity in domestic pigs in Kazakhstan and confirm the effectiveness of mNGS as a tool for epizootiological surveillance and molecular monitoring of viral infections in livestock.