Epidemiologic and Genomic Characterizations of Porcine Kobuviruses in Diarrheic and Healthy Pigs

SIMPLE SUMMARY: Enteric diseases pose huge threats to the global swine industry. Porcine kobuvirus (PKV) is a newly emerging enteric virus, but the role of PKV in causing enteric diseases is unclear. Here, we evaluated the up-to-date prevalence and evolution of PKV in both diarrheic and healthy pigs. Our results showed that PKV was highly prevalent in Chinese swine herds during 2018–2022. In addition, PKV is frequently co-infected with porcine epidemic diarrhea virus (PEDV). Most PKV and PEDV double-positive pigs were clinically diseased, while most PKV-positive but PEDV-negative pigs were clinically healthy, suggesting that PKV is unlikely to be a direct gastroenteritis-causing virus but a potential opportunistic pathogen. Furthermore, three PKV genomes were obtained and submitted for evolutionary evaluation. The results indicated that Chinese PKV has evolved into three groups, and SH-W-CHN-like viruses are predominant. Moreover, even though mutations frequently occurred during the evolution of PKV in China, large amounts of them are nonsense and strong negative selection seems to play a critical role in maintaining the antigenic stability. Overall, this study not only provides an epidemiological clue on the role of PKV in enteric diseases, but also the evolutionary status of PKV in both diarrheic and healthy pigs in China. ABSTRACT: Porcine kobuvirus (PKV) is an enteric virus commonly detected in both diarrheic and healthy pigs. Little is known about the role of PKV in enteric diseases. In this study, an epidemiological investigation based on 324 intestinal samples collected from six provinces of China during the period of 2018 to 2022 was performed, and showed that PKV has an overall 65.43% (212/324) positive rate. Noticeably, 89.47% (17/19) of PKV and porcine epidemic diarrhea virus (PEDV) double-positive pigs were clinically diseased, while 91.71% (177/193) of PKV-positive but PEDV-negative pigs were clinically healthy, suggesting that PKV infection in itself is unlikely to cause enteric diseases. In addition, three PKV genomes were obtained from both diseased and healthy pigs. Phylogenetic analysis showed that Chinese PKV strains could be divided into three groups (SH-W-CHN-like, S-1-HUN-like and JXAT2015-like strains). All three obtained PKV genomes belong to SH-W-CHN-like strains and JSYZ1806-158 was detected as a recombinant virus. Furthermore, multiple comparisons showed that nucleotide similarities are clearly lower than amino acid similarities for PKV polyproteins. Selective pressure analysis indicated that Chinese PKV polyproteins are predominantly under negative selection. Overall, this study provided new insights into the prevalence and evolution of PKV in both diarrheic and healthy pigs in China.