A Retrospective Study of Prevalence of Porcine Parvoviruses 6 in Guangxi, China and Its Co-Infection with Porcine Circovirus

Abstract Background Parvovirus can infect human and a variety of animals (such as pigs, dogs, cats, etc.). Porcine parvovirus is characterized by infertility, mummified fetuses, early embryonic death, and stillbirths. Worldwide, many porcine parvoviruses (PPVs) have been linked to porcine circovirus (PCV) associated disease (PCVAD). Results By PCR amplification and sequencing, the total PPV6-positive rate was 12.5% (62/497) and the positive rate of PPV6 ranged from 12.0–17.6% in differently city. Meanwhile, we found that the positive rate of PPV6 co-infection with PCV (69.4%) was significantly higher than that of PPV6 infection alone (30.6%) (p < 0.01). The positive rate of PPV6 co-infected with PCV2 was significantly higher than that of PPV6 co-infection with PCV3 and PCV4. Of ten PPV6 isolates, six isolates were 6112 nt in length and four isolates were 6111 nucleotides (nt) in length. Compared with the reference strains, we found that the 3' UTRs of ten strains are lacked 14 and 15 bases, respectively, which leads to significant changes in the RNA secondary structure. Within the VP1 unique region, compared with PPV1, PPV2 and PPV3, the motifs of the Ca2+ binding loop (YTGPR) and the catalytic residues (HDIRY) of putative secretory PLA2 were very conserved without amino acid mutation. Phylogenetic analysis of the NS1 gene showed that all PPV6 isolates were located in the genus Copiparvovirus together with PPV4 and PPV5. Phylogenetic analysis of the VP1 gene showed that all PPV6 strains isolated from China clustered in group B, except for the three Chinese strains that clustered in group A. Combined with the results of multiple sequence alignment and genetic evolution, we found a total of 14 amino acid mutation related to phylogenetic tree branches (R14K/Q, I116L/K/T, N788S, R789/M, S/T791H, M792H, A815S, D873G, N919S, R938K, S941T, R1013H, T1038N, T1042D/Y). Compared with PPV6 sequences in different geographic regions, the VP1 gene is more prone to mutation than NS1 gene. From which, two adaptive mutations were found in NS1 (Q3H, P20H) and VP1 (A619T, Q730E), respectively. In addition, we predicted the B cell and T lymphoid epitopes of the NS1 and VP1 genes of 10 PPV6 strains, respectively, and speculated that compare with VP1, the NS1 gene is more suitable as an epitope vaccine target. Conclusion In summary, our findings provide new insight into the prevalence of PPV6 in Guangxi, China, as well as lay the foundation for the study of virus infection mechanism.