First detection and complete genome analysis of porcine circovirus-like virus P1 and porcine circovirus-2 in yak in China

Abstract

Porcine circovirus-like virus P1, like porcine circovirus type 2 (PCV2), is a potential pathogen of post-weaning multisystemic wasting syndrome in swine. Yaks are a valuable species and an iconic symbol of the Tibet Plateau which is the highest and largest plateau in the world. In this study, a total of 105 yak diarrheal samples, collected from 13 farms in Linzhi in the Tibet Plateau from January 2019 to December 2021, that were screened for P1 and PCV2 by polymerase chain reaction, 10.48% (n = 11) were positive for P1, 4.76% (n = 5) for PCV2, and 5.71% (n = 6) were positive for coinfection of P1 and PCV2. In addition, the whole genomes of eight P1 strains and eight PCV2 strains were sequenced. Alignment of deduced amino acid sequences of P1 ORF1 and PCV2 ORF2 gene revealed that ON012566 had one unique amino acid mutation at residues 137 (T to P). This mutation has important implication for the study of virus virulence, tissue tropism, and immune response. Phylogenetic analysis shows that the yak-origin P1 strains in this study with cattle-origin P1 reference strains were grouped into one cluster. The yak-origin PCV2 (ON012566) and a buffalo-origin PCV2 (KM116514) reference strain clustered in the same branch in the PCV2b regions. Meanwhile, the remaining PCV2 strains and buffalo-origin PCV2 reference strain (ON012565) clustered in the PCV2d regions. To summarize, to our knowledge, this is the first report on the molecular prevalence and genome characteristics of P1 and PCV2 in yaks in the world and will contribute to further study of the molecular epidemiology, source, and evolution of P1 and PCV2 strains.

Keywords: phylogeny; porcine circovirus-2; porcine circovirus-like virus P1; sequencing; yak.

FIGURE 1

P1‐positive and porcine circovirus type 2 (PCV2)‐positives rate in yaks sampled in Linzhi from 2019 to 2021. All 105 clinical samples form yaks were screened for P1 and PCV2 by PCR, 10.48% (n = 11) were positive for P1 (red area), 4.76% (n = 5) for PCV2 (blue area) and 5.71% (n = 6) were positive for co‐infection of P1 and PCV2 (the intersecting part).

FIGURE 2

Analysis of nucleic acid sequence and amino acid sequence of P1 ORF1. The nucleotide sequence of P1 ORF1 (a) and the deduced amino acid sequence (b) were compared with the previously reported sequences and amino acid sequences of P1 ORF1 genes, respectively. This alignment included deduced nucleotide sequences of 8 P1 ORF1 sequences from this study and 13 P1 ORF1 reference sequences from Genbank. All the sequences were aligned in Clustal W and viewed in BioEdit sequence alignment editor tool. Mutant strains and mutant sites are marked with red underlines.

FIGURE 3

Alignment of deduced amino acid sequences of porcine circovirus type 2 (PCV2) ORF2 gene.This alignment included deduced amino acid sequences of ORF2 from 8 PCV2 sequences from this study and 15 PCV2 reference sequences of different genotypes from Genbank. All the sequences were aligned in Clustal W and viewed in BioEdit sequence alignment editor tool. Mutation sites marked with red underline or red box. Position 89, marked with a blue box, could differentiate PCV2a, PCV2b, and PCV2d, which harbored isoleucine (I), arginine (R), and leucine (L) residues, respectively.

FIGURE 4

Phylogenetic analysis of eight yak‐origin P1 strains in this study and other reference strains. The phylogenetic tree was constructed by the neighbor‐joining method using MEGA 11.0 software. Bootstrap replications were set by 1000. Note: Eight yak‐origin P1 strains in this study labeled by blue circles and two cattle‐origin P1 reference sequences were labeled using underlines.

FIGURE 5

Phylogenetic analysis of eight yak‐origin porcine circovirus type 2 (PCV2) strains in this study and other reference strains. The phylogenetic tree was constructed by the neighbor‐joining method using MEGA 11.0 software. Bootstrap replications were set by 1000. Note: Eight yak‐origin PCV2 strains in this study labeled by blue circles and two buffalo‐origin PCV2 reference sequences were labeled using underlines.