Detection and Complete Genome Analysis of Porcine Circovirus 2 (PCV2) and an Unclassified CRESS DNA Virus from Diarrheic Pigs in the Dominican Republic: First Evidence for Predominance of PCV2d from the Caribbean Region

Abstract

We report here high rates (47.5%, 48/101) of detection of porcine circovirus 2 (PCV2) in diarrheic pigs from three pig farms in the Dominican Republic. Seventeen of the PCV2 positive samples, representing the three pig farms, different age groups and sampling periods (2020–2021), were amplified for the complete PCV2 genome. Based on analysis of open reading frame 2 and complete genome sequences, the 17 PCV2 strains were assigned to the PCV2d genotype. Significant differences were observed in PCV2 detection rates between the vaccinated (20% (10/50)) and unvaccinated (62.5% (10/16) and 80% (28/35)) farms, corroborating previous observations that PCV2a-based vaccines confer protection against heterologous PCV2 genotypes. The present study is the first to report detection and molecular characterization of PCV2 from the Dominican Republic, warranting large-scale molecular epidemiological studies on PCV2 in pig farms and backyard systems across the country. For the first time, PCV2d was identified as the predominant PCV2 genotype in a study from the Caribbean region, suggesting that a genotype shift from PCV2b to PCV2d might be happening in the Caribbean region, which mirrored the current PCV2 genotype scenario in many other parts of the world. Besides PCV2, we also identified a pigeon circovirus-like virus, and a circular Replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus, which was characterized for the complete genome. The CRESS DNA virus shared a similar genomic organization and was related to unclassified CRESSV2 DNA viruses (belonging to the Order Cirlivirales) from porcine feces in Hungary, indicating that related unclassified CRESS DNA viruses are circulating among pigs in different geographical regions, warranting further studies on the epidemiology and biology of these novel viruses.

Detection and Complete Genomic Analysis of Porcine circovirus 3 (PCV3) in Diarrheic Pigs from the Dominican Republic: First Report on PCV3 from the Caribbean Region

“…On the other hand, co-infections might be due to the widespread occurrence of other major porcine pathogens, such as PCV2, devoid of any association with PCV3 [ 9 , 28 , 33 ]. In previous studies, we screened the 100 porcine fecal samples from the Dominican Republic for PCV2 (detection rates of 48%, 48/100 fecal samples) and porcine adenovirus (PAdV) (26%, 26/100 fecal samples) DNA, and Rotavirus-A (RVA) RNA (0%, 0/100 fecal samples) [ 21 , 34 ]. In the present study, the fecal samples were also screened for the presence of porcine coronaviruses (PDCoV, PEDV, and TGEV) using a pan-coronavirus RT-PCR assay as described previously [ 25 ].…”

“…The present study was based on archival fecal samples that were obtained from 100 diarrheic pigs for a previous research project on porcine enteric viruses (PCV2, PAdV, and RVA) in the Dominican Republic [ 21 ]. During August-November 2020, 34 and 16 fecal samples were obtained from diarrheic pigs at a farm in the municipality of Cabrera (housing ~300 pigs) and Pedro Brand (~100 pigs), respectively, and in January–February 2021, 50 fecal samples were collected from a pig farm in the municipality of Villa Mella (~500 pigs) ( Supplementary Figure S1 ).…”

“…The complete genomes of PCV3 strains were investigated for potential recombination events by the RDP4 program with default parameters and were recognized as recombinants if supported by 2 or >2 detection methods (3Seq, CHIMAERA, BOOTSCAN, MAXCHI, GENECONV, RDP, and SISCAN) with a highest acceptable p -value of p < 0.01 after Bonferroni’s correction, as previously described [ 21 , 26 ]. Phylogenetic analyses were performed by the MEGA7 software using the maximum-likelihood method with the Hasegawa–Kishino–Yano (HKY) model plus Gamma (G) distribution, and supported with 1000 bootstrap replicates, as described previously [ 7 , 18 , 23 , 27 ].…”

“…Several economically important porcine viral diseases (African swine fever, classical swine fever, porcine circovirus 2 (PCV2), porcine epidemic diarrhea (PED), porcine reproductive and respiratory syndrome (PRRS), porcine teschovirus-1, rabies, and swine influenza) have been reported in pigs from the Dominican Republic, although many of these reports were based on preliminary data [ 20 ]. Among the porcine circoviruses, to date, the molecular epidemiology of only PCV2 has been studied in the Dominican Republic [ 21 ] and in two other Caribbean islands (Cuba, and Saint Kitts and Nevis) [ 20 , 22 ]. On the other hand, although PCV3 has been increasingly detected in clinically ill pigs from different parts of the world, and the possible economic implications of PCV3 infections on pig farming are growing concerns, there are no reports on PCV3 in pigs from the Caribbean region so far [ 2 , 23 ].…”

Genotype Detection of Circovirus Type 2 (PCV2) in Swine Clinical Samples from Brazil

“…Previous studies have shown a shift in the most prevalent genotypes in pig production over the years [17] from the PCV2a genotype to PCV2b in 2002 [48], [49], and in 2012, a shift occurred from PCV2b to PCV2d [34], [50]. Since then, PCV2d has become the most prevalent in various regions of the world, such as China [37], South Korea [51], Austria [42], the United States [13], Colombia [52], and the Dominican Republic [53].…”