Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

Abstract

Porcine circovirus 3 (PCV3) is a novel virus associated with acute PDNS (porcine dermatitis and nephropathy syndrome)‐like clinical signs identified by metagenomic sequencing from swine. Its high occurrence may pose a potential threat to the swine industry worldwide. The processes resulting in the emergence and spread of PCV3 remain poorly understood. Herein, the possible origin, genotypes, and evolutionary dynamics of PCV3 based on available genomic sequences are determined. The closest ancestor of PCV3 is found to be within the clade 1 bat CVs. Using different phylogenetic methods, two major genotypes are identified, PCV3a and PCV3b. It is found that the effective population size of PCV3 increased rapidly during late 2013 to early 2014 and this is associated with the diversification of PCV3a and PCV3b. A relatively high effective reproductive number (Re) value and higher evolutionary rate were found compared to other single‐stranded DNA viruses, and positive selection on codons 122 and 320 (24 of ORF2) is identified. It is hypothesized that this, together with the prediction of a potential change of an antigenic epitope at position 320, might have allowed PCV3 to escape from the host immune response. Overall, this study has important implications for understanding the ongoing PCV3 cases worldwide and will guide future efforts to develop effective preventive and control measures.

Etiology and genetic evolution of canine coronavirus circulating in five provinces of China, during 2018–2019

“…Therefore, further investigations still need to clarify the specific functions of these non-synonymous substitutions. Cross-host transmission frequently occurred in animal virus, such as porcine circovirus (PCV3) [51], and pseudorabies virus (PRV) [52] in DNA virus, influenza A viruses (IAVs) [53][54][55] and coronavirus [7,[56][57][58] in RNA virus. One of the most notable is coronavirus.…”

An epidemiological investigation of porcine circovirus 3 infection in dogs in the Guangxi Province from 2015 to 2017, China

“…Currently, there is controversy about the classification of PCV3. In general, most scholars have divided PCV3 into two genotypes (Ha et al, 2018;Li et al, 2018), but there is no consensus on the best classification method. In the present study, we referred to the method described by Li et al, which also divided PCV3 into two different genotypes, PCV3a and PCV3b.…”

COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives

“…Yet, from [42,43]. This is not unprecedented since bat viruses have been shown to 'jump' the species barrier frequently to infect new species [44][45][46][47][48][49][50]. However, since bats were in hibernation when the outbreak occurred, and it was uncertain whether bats were sold at the market, the virus is more likely to have been transmitted via members have been shown to transfer long chain fatty acids to cysteine residues of cellular and viral proteins.…”