Genetic characterization of three porcine circovirus‐like viruses in pigs with diarrhoea in China

In this study, we detected a circular replication‐associated protein (Rep)‐encoding single‐stranded (CRESS) DNA virus (named Po‐Circo‐like (PCL) virus) in intestinal tissue samples of pigs, and the complete genome sequences of three strains (named PCL viruses GX14, GX15 and GX19) were obtained. Unlike PCL virus strains 21 and 22, whose genome sequences have 3,912 and 3,923 nucleotides (nt), respectively, the strains revealed in this study have a circular genome with 3,944 nt and five major open reading frames (ORFs). Among these ORFs, ORF1 encodes the Rep and not the typical capsid protein encoded in PCV. Furthermore, the strains in this study share 79.2%–96.0% nucleic acid identity and 83.0%–98.1% amino acid identity with ORF1 of the reference strains. Moreover, the Rep of the PCL virus in this study shared 19.9%–22.2% (30%) identity of its amino acid sequence with sequences of five proteins that are expressed by the family Kirkoviridae. [Correction added on 24 December 2020 after first online publication: The preceding sentence has been corrected in this version.] Interestingly, the stem loop of the PCL virus has one nucleotide substitution, T1328G. The Bo‐Circo‐like CH strain shares high nucleic acid and amino acid similarity (>80%) with the PCL virus. Moreover, Bo‐Circo‐like CH and GX‐19 had similar stem‐loop sequences. The PCL virus might therefore be transmitted to non‐porcine hosts by cross‐species transmission routes. Phylogenetic analysis classified the PCL virus into the new family Kirkoviridae and indicated its close relationship with the Bo‐Circo‐like virus. A phylogenetic divergence analysis based on the rep gene classified all PCL virus strains into two genotypes (PCLa and PCLb). In conclusion, the present study is the first detailed report of the PCL virus, which is a potential new virus in pigs that might be involved in cross‐species transmission. Further investigation is needed to determine the pathogenesis of this virus and its epidemiologic impact.