Genetic diversity and prevalence of porcine circovirus type 3 (PCV3) and type 2 (PCV2) in the Midwest of the USA during 2016–2018

Abstract

In recent years, reports indicated that PCV3 may be involved in porcine dermatitis and nephropathy syndrome (PDNS)-like disease similar to that linked to PCV2.A total of 2,125 porcine samples from 910 cases were collected during 2016-2018 and tested for presence of PCV3 and PCV2 by real-time PCR assays. Results showed high prevalence of PCV3 and PCV2: 28.4% samples from 41.2% cases were PCV3 positive and 16.4% samples from 16.7% cases were PCV2 positive. The overall coinfection rate was 5.4% and 8.4% at the sample and case level, respectively. Temporal analysis indicated that PCV3 positive case rate increased from 31.6% in 2016, 40.9% in 2017, to 55.6% in 2018. Although its prevalence was lower, PCV2-positive case rate in 2018 (28.8%) doubled that in 2017 (14.4%). The coinfection case rate also increased from 3.4% in 2016, 8.0% in 2017 to 16.1% in 2018. The high positive rate of PCV3 (56.9%) and PCV2 (33.8%) in oral fluids, PCV3 in foetuses (57.1%) and PCV2 in tonsils (54.8%) implied viral transmission route and tissue tropism. In phylogenetic analysis, two small PCV3 clusters (1 and 2) were separated but others were clustered with low bootstrapping values indicating overall low genetic diversity. Genotypes, PCV2a-h, were confirmed by analysing 2,944 strains, with a new genotype proposed as PCV2i. In this study, 61 PCV3 unique whole genomes were sequenced; 12 belonged to a separate cluster that were characterized by five consistent amino acid changes in the capsid protein (24V, 27K, 56D, 98R and 168K) and may be associated with potential differences in immunogenicity. Among the 43 unique PCV2 whole genomes sequenced, 31 belonged to PCV2d, 7 to PCV2a and 5 to PCV2b. Thus, our study demonstrates that PCV2d is the predominant genotype and PCV3 is widely circulating in the Midwest of the USA. K E Y W O R D Sgenetic diversity, genotype, PCV2, PCV3, prevalence | 1285 WANG et Al.

Development of a differential multiplex real-time PCR assay for porcine circovirus type 2 (PCV2) genotypes PCV2a, PCV2b and PCV2d

“…Based on our previous study ( Wang et al, 2019b ), PCV2 strains were separated into 12 clusters, namely Cluster 1–12, by phylogenetic analysis; Cluster 8, Cluster 3 and Cluster 1 corresponded to genotypes, PCV2a, PCV2b and PCV2d, respectively. The three genotypes were identified as common strains currently circulating in the USA ( Wang et al, 2019b ; Xiao et al, 2016 ). An unrooted phylogenetic tree generated with PCV2 ORF2 sequences indicated that the three genotypes grouped into three separate clusters ( Fig.…”

“…The sequence dataset was established from our previous study ( Wang et al, 2019b ). Briefly, all available PCV2 ORF2 sequences were downloaded from the GenBank database (https://www.ncbi.nlm.nih.gov/genbank/).…”

“…With a high substitution rate, 5 major genotypes of PCV2 have been identified based on ORF2 sequences: PCV2a, PCV2b, PCV2c, PCV2d and PCV2e ( Davies et al, 2016 ). Among the five genotypes, PCV2a, PCV2b and PCV2d are the most commonly circulating genotypes in the USA ( Wang et al, 2019b ; Xiao et al, 2016 ), in China ( Hou et al, 2019 ; Lv et al, 2020 ) and in European countries ( Saporiti et al, 2020 ). There are two major genotype shifting events that have occurred globally: PCV2b replaced PCV2a as the dominant genotype around 2003, and PCV2d became the most prevalent genotype beginning in 2012 ( Xiao et al, 2016 ).…”

“…ORF2-targeted gene sequencing is widely used as a gold standard for genotyping of PCV2 strains ( Wang et al, 2019b ). Other methods are developed as well for the differentiation of PCV2a and PCV2b strains, such as real time PCR, loop-mediated isothermal amplification method (LAMP) and restriction fragment length polymorphism (RFLP) ( Guo et al, 2010 ; Qiu et al, 2012 ; Wozniak et al, 2019 ; Xiao et al, 2016 ).…”

The Monoclonal Antibody Recognized the Open Reading Frame Protein in Porcine Circovirus Type 2-Infected Peripheral Blood Mononuclear Cells

“…At least four commercial PCV2a vaccines have been widely used to reduce viremia and PCV2 infectious pressure in swine herds [12][13][14][15]. That might have caused the global trend shift from PCV2a to PCV2b first [16][17][18][19], and then PCV2d (PCV2b mutant strain) has become a predominant genotype globally [20][21][22][23][24][25][26][27].…”