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.
Highlights
Continuous epidemiological surveillance of emerging viruses is crucial to control widespread.[1]
We found that all the Porcine circovirus 3 (PCV3) strains were closely related to the clade 1 bat CVs with a high confidence
We discovered that canine CVs are closely related to clade 2 bat CVs and porcine circovirus 1 (PCV1) and PCV2 strains
Summary
Continuous epidemiological surveillance of emerging viruses is crucial to control widespread.[1]. A novel circovirus was identified by generation sequence (NGS) analysis of aborted fetuses of sows and named PCV3.[21,22] The newly discovered virus was associated with PDNS.[23] PCV3 infection might contribute to PDNS and reproductive failure, cardiac, and multisystemic inflammation.[10,21,24] It has been shown that PCV3 found in aborted fetuses is the result of vertical transmission.[21] Like PCV2, there are two major open reading frames (ORFs) in the genome of PCV3: ORF1 encodes proteins involved in viral replication (Rep) and ORF2 encodes a major structural protein, the capsid protein (Cap).[25] PCV3 sequences were detected widely in the USA,[21] China,[26,27,28] Brazil,[29] Thailand,[30] Korea,[23] and many European countries,[22,31,32,33,34] including Poland, Italy, Spain, Denmark, Germany, the UK among others. Our results provide a global view of the origin, genetic divergence, and evolutionary dynamics of PCV3 and indicate positive selection and high evolutionary rate, supporting the ongoing genotype shift and outbreaks
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