Prevalence and genetic analysis of porcine circovirus-like virus in pigs with diarrhea between 2016 and 2021 in Henan and Shanxi Provinces of China

Porcine circovirus-like virus (Po-Circo-like virus, PCLV), as a recently discovered virus, may be associated with diarrhea in pigs. To investigate the epidemic profile and genetic characteristics of the virus, one hundred and seventy-five clinical samples (141 intestinal samples, 17 blood samples and 17 fecal samples) were collected from diseased piglets during outbreaks of diarrhea on 33 pig farms in 19 cities of Henan and Shanxi Provinces of China between 2016 and 2021, and were screened by PCR for the presence of PCLV. The results showed that 32% (56/175) of diarrheal piglets were positive for PCLV, and 60.6% (20/33) of the pig farms and 57.9% (11/19) of the cities were positive for PCLV, which varied from 5.88–44.12% between 2016 and 2021. It was also found that PCLV might be co-infected with PRRSV, PCV2, PCV3, PCV4, and PEDV, but no nucleic acids were detected for TGEV, PDCoV and PRoV in piglets with diarrhea. Notably, only PCLV was detected in 13 diarrheal piglets from four of these farms, whereas other pathogens were negative. The findings suggest that PCLV has been circulating in piglets in Henan and Shanxi Provinces of China, and may be a diarrheal virus. The complete genomes of thirteen PCLV strains were sequenced, and these strains shared 35.4–91.0% genome nucleotide identity with those available in GenBank. Phylogenetic analysis demonstrated that the 13 PCLV strains in this study were clustered in Group 1, which closely related to 8 Chinese PCLV strains, Bo-Circo-like virus CH, two American strains 21 and 22, and two Hungary strains 288_4 and 302_4, but differed genetically from 7 other foreign PCLV strains. In addition, the whole genome and Rep gene of 13 PCLV strains in this study were 72.2% − 82% and 83.8% − 89.7% identity with those of Bo-Circo-like virus CH strain respectively, which provided further evidence for the hypothesis that PCLV is a novel virus in pigs that may be involved in cross-species transmission. Furthermore, a cross-recombination event was found in the genome and Rep region of the sequenced 13 PCLV strains. This research enriched the epidemiological data of PCLV infection in pigs in China and laid a foundation for further study on the pathogenesis of PCLV.