Retrospective study of porcine circovirus 3 infection in China

Significant Detection of Porcine Circovirus 3 and Porcine Circovirus 4 in Wild Boars from Mid-Western Spain Without Apparent Sanitary Consequences

PCV-3 and PCV-4 are novel viruses that can infect domestic pigs and wild boars. Both viruses are associated with multiple disorders in domestic pigs (reproductive failure, respiratory damage, etc.). However, the clinical impact on wild boars remains unknown. This study aimed to assess the presence of these viruses in wild boars from mid-western Spain and their sanitary impact on the species. A total of 166 submandibular lymph nodes were collected from hunted wild boars, along with available information about their reproductive status, lung injuries, body condition, and tuberculosis status. The samples were used to detect PCV-3 and PCV-4 using real-time PCR. In total, 84.9% of the sampled animals were positive for PCV-3, and 33.7% were positive for PCV-4. The detection of PCV-4 was more frequent in wild boars that had received supplementary feeding, suggesting that the direct contact favored by this practice could increase the transmission of this virus in wild boar populations. The infections did not seem to influence the body condition, reproductive status, lung lesions, or TB lesion severity patterns in the studied animals. Thus, although these viruses have been widely detected throughout wild boar populations from the studied area, they do not seem to be a health threat to this species. Nevertheless, their monitoring in wild boars is recommended, as they are often in contact with extensively reared pigs, which are susceptible to these viruses.

Epidemiologic Investigation and Genetic Variation Analysis of PRRSV, PCV2, and PCV3 in Guangdong Province, China from 2020 to 2022

Recently, the emergence of HP-PRRSV (Highly Pathogenic porcine reproductive and respiratory syndrome virus) and the exacerbation of mixed infections of PRRSV and PCV have resulted in significant economic losses for the Chinese pig industry. This study collected a total of 226 samples suspected of infection with the aforementioned viruses from diverse pig farms in seven urban districts of central and northern Guangdong Province between 2020 and 2022. The positive rates of PRRSV, PCV2, and PCV3 in the samples were 33.2%, 37.6%, and 7.5%, respectively, and there were various mixed-infection scenarios present in the samples. This study successfully isolated multiple strains of PRRSV2 and PCV2 from their positive samples, and obtained the gene sequences of six PCV3 (ORF1 + ORF2) from samples. The associated sequences obtained were subjected to bioinformatic analysis and revealed the following:Predominantly prevalent strains of PRRSV in Guangdong Province include HP-PRRSV and NADC30-like variants, whereas PCV2 is primarily represented by the 2b and 2d subtypes. Specifically, the amino acid variation patterns exhibited by the PRRSV GP5 and NSP2 proteins of the strains sg_2108, qy_2008, and fs_2108 under environmental selective pressure are remarkably similar to the characteristics of Highly Pathogenic PRRSV; thus, it is inferred that they may possess higher virulence. The detected PCV3 strains were predominantly concentrated within the PCV3a-IM branch. All PRRSV strains involved in this study are wild-type-PRRSV (wt-PRRSV), comprising three recombinant strains and seven highly virulent strains. Among these strains, the ORF1a gene exhibited the highest variability in their genomes. Environmental selective pressure may enhance the virulence and immune evasion capabilities of PRRSV and drive mutations in the Cap proteins of PCV2 and PCV3. Conversely, PCV2 and PCV3 strains demonstrated greater stability in genetic evolution. In conclusion, this study enhances the epidemiological data regarding PRRSV, PCV2, and PCV3 in Guangdong Province, China, and is significant for the surveillance, prevention, and active control of these three diseases.

Molecular detection and genetic characteristics of porcine circovirus 3 and porcine circovirus 4 in central China

Porcine circoviruses (PCVs) are a significant cause of concern for swine health, with four genotypes currently recognized. Two of these, PCV3 and PCV4, have been detected in pigs across all age groups, in both healthy and diseased animals. These viruses have been associated with various clinical manifestations, including porcine dermatitis and nephropathy syndrome (PDNS) and respiratory and enteric signs. In this study, we detected PCV3 and PCV4 in central China between January 2022 and February 2023. We tested fecal swabs and tissue samples from growing-finishing and suckling pigs with or without respiratory and systemic manifestations and found the prevalence of PCV3 to be 15.15% (15/99) and that of PCV3/PCV4 coinfection to be 4.04% (4/99). This relatively low prevalence might be attributed to the fact that most of the clinical samples were collected from pigs exhibiting respiratory signs, with only a few samples having been obtained from pigs with diarrhea. In some cases, PCV2 was also detected, and the coinfection rates of PCV2/3, PCV2/4, and PCV2/3/4 were 6.06% (6/99), 5.05% (5/99), and 3.03% (3/99), respectively. The complete genomic sequences of four PCV3 and two PCV4 isolates were determined. All four of the PCV3 isolates were of subtype PCV3b, and the two PCV4 isolates were of subtype PCV4b. Two mutations (A24V and R27K) were found in antibody recognition domains of PCV3, suggesting that they might be associated with immune escape. This study provides valuable insights into the molecular epidemiology and evolution of PCV3 and PCV4 that will be useful in future investigations of genotyping, immunogenicity, and immune evasion strategies.

Pathogenicity and immune modulation of porcine circovirus 3

Porcine circoviruses (PCVs) are members of the genus Circovirus of the family Circoviridae, and four species of PCVs have been discovered and named PCV1-PCV4, respectively. With the first report of PCV3 in America in 2016, the pathogenic variant was found to be associated with various clinical features, called porcine circovirus associated disease (PCVAD), including multisystemic inflammation, porcine dermatitis and nephropathy syndrome (PDNS), reproductive disorders, respiratory or digestive disorders. Increasing experimental data have shown that PCV3 is widespread around the world, but the failure of virus isolation and propagation has put obstacles in the way of PCV3 research. Moreover, a large number of reports demonstrate that PCV3 usually co-infects with other pathogens in pigs. Thus, whether PCV3 alone causes clinical manifestations needs to be fully discussed. In addition, the host cell immune response was activated during PCV3 infection, and PCV3-encoded proteins may regulate immune responses to facilitate its replication. An in-depth understanding of PCV3 pathogenesis and immune regulation strategies is critical for PCVAD prevention. In this review, the advances in pathogenicity and innate immune modulation of PCV3 were summarized, which could deepen the understanding of this virus and PCV3-related diseases.

A Retrospective Analysis of Porcine Circovirus Type 3 in Samples Collected from 2008 to 2021 in Mexico

Porcine circovirus type 3 (PCV3) is a nonenveloped virus of the Circoviridae family. This virus has been identified in pigs of different ages and pigs with several clinical manifestations of the disease or even in apparently healthy pigs. While PCV3 was first reported in 2015, several retrospective studies have reported the virus before that year. The earliest report indicates that PCV3 has been circulated in swine farms since 1996. In this study, we evaluated the presence of PCV3 in samples collected in Mexico in 2008, 2015, 2020, and 2021. This study assessed PCV3 DNA by qPCR and antibodies against CAP protein by indirect ELISA. The results showed that PCV3 (DNA and anti-CAP antibodies) was detected in the samples collected from 2008 to 2021. The highest prevalence was in 2008 (100%), and the lowest was in 2015 (negative). Genetic analysis of ORF2 showed that the virus identified belonged to genotype a, as most of the viruses identified thus far. PCV3 was detected in samples from piglets with respiratory signs and growth retardation, sows with reproductive failure, or asymptomatic piglets and sows. Pigs with respiratory signs, growth retardation, or reproductive failure had a higher prevalence of antibodies and qPCR-positive samples. In conclusion, this study showed that PCV3 has been circulating in Mexico since 2008 and that PCV3 DNA and antibodies were more prevalent in samples from pigs with clinical manifestations of diseases.

Revisiting Porcine Circovirus Infection: Recent Insights and Its Significance in the Piggery Sector

Porcine circovirus (PCV), a member of the Circoviridae family within the genus Circovirus, poses a significant economic risk to the global swine industry. PCV2, which has nine identified genotypes (a-i), has emerged as the predominant genotype worldwide, particularly PCV2d. PCV2 has been commonly found in both domestic pigs and wild boars, and sporadically in non-porcine animals. The virus spreads among swine populations through horizontal and vertical transmission routes. Despite the availability of commercial vaccines for controlling porcine circovirus infections and associated diseases, the continuous genotypic shifts from a to b, and subsequently from b to d, have maintained PCV2 as a significant pathogen with substantial economic implications. This review aims to provide an updated understanding of the biology, genetic variation, distribution, and preventive strategies concerning porcine circoviruses and their associated diseases in swine.

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

The increasing detection of Porcine circovirus 3 (PCV3, family Circoviridae) in clinically ill pigs worldwide has raised concerns on the implications of the virus on porcine health and the pork industry. Although pork production constitutes an important component of the livestock economy and is a major source of animal protein in the Caribbean Islands, there are no reports on PCV3 in pigs from the region so far. In the present study, PCV3 was detected in 21% (21/100) of diarrheic pigs (sampled at three farms) from the Caribbean nation of the Dominican Republic (DR). Although the sample size varied between porcine age groups, the highest PCV3 detection rates (35.3% each, respectively) were observed in piglets and growers. Co-infections with PCV2 and porcine adenovirus were observed in 38.09% and 9.52% of the PCV3 positive samples, respectively. The complete genomes of 11 DR PCV3 strains were analyzed in the present study, revealing a unique deletion (corresponding to nucleotide residue at position 1165 of reference PCV3 sequences) in one of the DR PCV3 sequences. Based on sequence identities and phylogenetic analysis (open reading frame 2 and complete genome sequences), the DR PCV3 strains were assigned to genotype PCV3a, and shared high sequence homologies (>98% identities) between themselves and with those of other PCV3a (Clade-1) strains, corroborating previous observations on the genetic stability of PCV3 worldwide. To our knowledge, this is the first report on the detection and molecular characterization of PCV3 in pigs from the Caribbean region, providing important insights into the expanding global distribution of the virus, even in isolated geographical regions (the Island of Hispaniola). Our findings warrant further investigations on the molecular epidemiology and economic implications of PCV3 in pigs with diarrhea and other clinical conditions across the Caribbean region.

Histopathological Changes and Inflammatory Response in Specific Pathogen-Free (SPF) with Porcine Circovirus Type 3 Infection

Since the first report of PCV3 virus infection in 2016, it has been linked to multisystemic inflammation, reproductive failure, cardiac pathology, and clinical indications resembling porcine dermatitis and nephropathy syndrome (PDNS). However, the pathogenesis and clinical significance of PCV3 is still unclear. In this study, a PCV3 infection model was created using SPF pigs, and histopathology and fluorescence quantitative PCR were utilized to examine PCV3's pathogenicity. Reductions in body weight gain and fever were observed during this study. However, other clinical signs such as Dermatitis and Nephropathy Syndrome were not observed through the study. Viremia was detected in the PCV3-inoculated group from 17 days post-inoculation (p.i.) until the end of the study. Nasal shedding was detected from 21 to 35 dpi and fecal shedding was detected during 25-33 days and 39 days, respectively. Gross lesions and histological evaluation were detected in various tissues and organs, including the lung, heart, kidney, lymph nodes, spleen, liver, small intestine, and testis. The heart, lung, liver, kidney, lymph nodes, and spleen showed pathological changes. The pathological features include swelling, inflammation, cell degeneration, necrosis, and hemorrhage. The lesions are consistent with multisystemic inflammation. Tissue viral load results showed only heart, lung, liver, kidney, lymph nodes, and spleen was positive by qRT-PCR. Moreover, the pro-inflammation cytokines in serum increased a lot in the PCV3-inoculated group compared to the control group, demonstrating that the induced inflammation response may be the cause of tissue damage in PCV3-infection. This study demonstrated that PCV3 can produce mild pathological damage to multiple organs, especially multisystemic inflammatory cell infiltration and prolonged viremia, viral shedding in nasal secretions. This is the first in vivo characterization of PCV3 infection in the SPF piglets model using isolated PCV3 strain, and this is also the first time to show the gross and pathological lesion with all tissue and organs in the PCV3-inoculated group. Our findings might serve as a starting point for more investigation into PCV3's pathogenic mechanism.

Retrospective assessment of porcine circovirus 3 (PCV-3) in formalin-fixed, paraffin-embedded tissues from pigs affected by different clinical-pathological conditions

BACKGROUND

Porcine circovirus 3 (PCV-3) is a recently discovered pathogen of swine that has been associated with several conditions. However, many questions remain unanswered regarding its infection, especially in terms of pathogenesis and disease impact. The aim of the present study was to retrospectively investigate the presence of PCV-3 genome by real time quantitative PCR (qPCR) and in situ hybridization (ISH) on selected formalin-fixed paraffin-embedded tissues of pigs affected by different clinical conditions and histological lesions.

MATERIALS AND METHODS

Conditions investigated included porcine dermatitis and nephropathy syndrome (PDNS), periweaning failure-to-thrive syndrome (PFTS), congenital tremors type AII, reproductive disorders, and pigs affected by systemic periarteritis/arteritis, myocarditis, or encephalitis. Studied cases (n = 587) were investigated from a diagnostic database (n = 4162) that comprised samples collected within the period 1998-2021. From each condition/lesion, 10 to 12 cases were subsequently selected and tested by qPCR and ISH (72 cases total).

RESULTS

A total of 587 cases fulfilled inclusion criteria of the different studied conditions and were distributed among the seven groups. For the further selected cases, PCV-3 genome was found by qPCR in 12/12 periarteritis, 5/10 reproductive disease, 5/10 PFTS, 3/10 myocarditis, 1/10 encephalitis and 1/10 congenital tremor cases. PCV-3 was not found in any of the PDNS cases assessed. In periarteritis cases, tissues more commonly affected were mesenteric arteries and kidney. Reproductive disease cases associated to PCV-3 genome consistently displayed myocarditis. The lesions and labelling distribution of PFTS cases with presence of PCV-3 genome were comparable to those of the periarteritis group. qPCR and ISH yielded similar results within each studied case and were statistically comparable.

CONCLUSION

Our results suggest that periarteritis is the hallmark lesion of PCV-3-SD, and that mesenteric lymph node and kidney appeared to be the most reliable organs to confirm the presence of PCV-3 genome in cases with periarteritis.

Epidemiological and genetic characteristics of porcine circovirus 3 in 15 provinces and municipalities of China between 2016 and 2020

Porcine circovirus 3 (PCV3) is a newly emerging virus and has been found associated with porcine dermatitis and nephropathy syndrome in pigs. Compared with PCV2, research into PCV3 cap gene sequencing is deficient. To investigate the prevalence and genotype distribution of PCV3, we collected 1291 samples from 211 pig farms throughout 15 provinces and municipalities. 312 out of 1291 samples were tested positive by PCR. We further sequenced and analyzed 164 PCR-positive samples. The majority (61.8%) of isolates we sequenced belong to genotype PCV3c. PCV3c is also the dominant genotype in Hubei, Hunan, Hebei province and Chongqing city. We found 3 sites under positive selection and located in predicted epitope peptide, revealing that the pig’s immunity may be a reason those sites are undergoing highly positive selection.

Frequency of porcine circovirus 3 detection and histologic lesions in clinical samples from swine in the United States

Porcine circovirus 3 (PCV3) is widespread in pigs worldwide. Diverse clinical signs and lesions have been associated with PCV3, but the role of PCV3 as a cause of disease in swine remains unclear. We investigated the association of PCV3 with clinical signs and histologic lesions in 730 diagnostic swine cases between February 2016 and January 2018. The cases contained 2,177 samples submitted from 474 sites located in 21 states in the United States. PCR assay results were positive for PCV3 for 577 of 2,177 (27%) samples, 255 of 730 (35%) cases, 181 of 474 (38%) sites, and 17 of 21 (81%) states. We detected PCV3 in 19 of 28 specimen types and in pigs of all ages and clinical presentations, including healthy pigs, with the highest detection rate in adult pigs. PCV3 detection was not associated with respiratory, gastrointestinal, or CNS signs, weight loss, or sudden death. Of 58 types of histologic lesions evaluated, PCV3 detection was associated with myocarditis, cardiac vasculitis, and interstitial pneumonia in growing pigs. A high PCV3 detection rate was observed in aborted fetuses.

The Prevalence and Genetic Diversity of PCV3 and PCV2 in Colombia and PCV4 Survey during 2015–2016 and 2018–2019

Four genotypes of circovirus have been recognized in swine, with PCV2 and PCV3 being the most associated with clinical manifestations, while PCV4 does not have a defined disease. In addition, PCV2 is associated with different syndromes grouped as diseases associated with porcine circovirus (PCVAD), while PCV3 causes systemic and reproductive diseases. In the present study, we retrospectively detected PCV2, PCV3, and PCV4 in Colombia during two periods: A (2015–2016) and B (2018–2019). During period A, we evaluated stool pools from the 32 Colombian provinces, finding a higher prevalence of PCV3 compared to PCV2 as well as PCV2/PCV3 co-infection. Furthermore, we determined that PCV3 had been circulating since 2015 in Colombia. Regarding period B, we evaluated sera pools and tissues from abortions and stillborn piglets from the five provinces with the highest pig production. The highest prevalence found was for PCV3 in tissues followed by sera pools, while PCV2 was lower and only in sera pools. In addition, PCV2/PCV3 co-infection in sera pools was also found for this period. The complete genome sequences of PCV3 and PCV3-ORF2 placed the Colombian isolates within clade 1 as the majority in the world. For PCV2, the predominant genotype currently in Colombia is PCV2d. Likewise, in some PCV3-ORF2 sequences, a mutation (A24V) was found at the level of the Cap protein, which could be involved in PCV3 immunogenic recognition. Regarding PCV4, retrospective surveillance showed that there is no evidence of the presence of this virus in Colombia.

Phylogenetic analysis of porcine circovirus 3 circulating in Canadian pigs

Introduction

Porcine circovirus 3 (PCV3) has been detected in pigs worldwide and associated with several clinical signs.

Methods

To investigate the genetic diversity of PCV3 strains circulating in Canada, 44 PCV3 positive samples from Saskatchewan (2/44), Manitoba (2/44), Quebec (4/44), Alberta (11/44) and Ontario (25/44) submitted to diagnostic laboratories in Canada between 2019 and 2021 were sequenced and analyzed.

Results

Phylogenetic analysis of capsid genes showed that all of the 44 Canadian strains classified into PCV3a and segregated into seven lineages with common amino acid changes observed at A24V, R27K, N56D, T77S, Q98R, L150I (F) and R168K positions.

Conclusion

Future studies are required to determine whether the polymorphisms in capsid proteins, as revealed in this study, could be associated with differences in the pathogenicity or antigenicity of PCV3 strains. This is the first phylogenetic analysis of PCV3 strains among different provinces in Canada.

Novel Porcine Circoviruses in View of Lessons Learned from Porcine Circovirus Type 2-Epidemiology and Threat to Pigs and Other Species

Porcine circovirus type 2 (PCV2) plays a key role in PCV2-associated disease (PCVAD) etiology and has yielded significant losses in the pig husbandry in the last 20 years. However, the impact of two recently described species of porcine circoviruses, PCV3 and PCV4, on the pork industry remains unknown. The presence of PCV3 has been associated with several clinical presentations in pigs. Reproductive failure and multisystemic inflammation have been reported most consistently. The clinical symptoms, anatomopathological changes and interaction with other pathogens during PCV3 infection in pigs indicate that PCV3 might be pathogenic for these animals and can cause economic losses in the swine industry similar to PCV2, which makes PCV3 worth including in the differential list as a cause of clinical disorders in reproductive swine herds. Moreover, subsequent studies indicate interspecies transmission and worldwide spreading of PCV3. To date, research related to PCV3 and PCV4 vaccine design is at early stage, and numerous aspects regarding immune response and virus characteristics remain unknown.

Detection and genetic characteristics of porcine circovirus type 2 and 3 in Henan province of China

PCV2 is one of the most economically important viral agents in swine worldwide. Recently, PCV3 has been frequently reported, and the co-infection of PCV2 and PCV3 is common in China. In order to explore the distribution, epidemiology and genetic diversity of PCV2 and PCV3, a total of 1,760 clinical tissue samples were randomly collected from 18 different regions in Henan province of China from October 2018 to September 2019 and screened for the presence of PCV2 and PCV3 by a duplex real-time PCR assay. The results showed that the positive rates of PCV2 and PCV3 were 72.90% and 5.17% respectively, and the co-infection rate of the two viruses was 3.64%. PCV2 and PCV3 are prevalent all year round. The prevalence of PCV2 in diseased pigs was 83.98%, higher than that in slaughterhouse pigs, while the prevalence of PCV3 in diseased pigs was 2.16%, slightly lower than that in slaughterhouse pigs. Furthermore, the complete genomes of 14 PCV2 and 3 PCV3 strains were obtained, among which 1 belonged to PCV2a, 5 belonged to PCV2b and 8 belonged to PCV2d. A new variant strain (XX2) might escape the host immune system. The phylogenetic analysis of PCV3 showed high nucleotide identity (>98%) between sequences obtained in this study and reference sequences. The results of this study might enrich the epidemiological data of PCV2 and PCV3 in Henan province and provide reference information for the comprehensive prevention and control of PCVAD.

Prevalence and Genetic Analysis of Porcine Circovirus 3 in China From 2019 to 2020

Porcine circovirus type 3 (PCV3), a virus belonging to the Circoviridae family, is considered to be associated with respiratory and neurological signs, cardiac and multisystemic inflammation, reproductive failure, and porcine dermatitis and nephropathy syndrome-like disease in pigs (Sus scrofa). In this study, epidemiological and serological investigations of PCV3 in clinically healthy pigs from different regions of China were performed. Overall, 42.87% (1,101/2,568) of pigs were positive for PCV3 Cap antibody via indirect enzyme-linked immunosorbent assay, with a higher prevalence of PCV3 in multiparous sows (62.22%, 881/1,416) and fattening pigs (28.96%, 159/549) than in suckling piglets (8.96%, 32/357) and nursery pigs (11.79%, 29/246). Of the 2,568 samples, 255 were further tested for PCV3 DNA using real-time polymerase chain reaction, and 63.14% of these were positive, with nearly half having <10 virus copies. The PCV3 DNA and antibody positivity rates were high in the pig serum samples; however, the virus titers and antibody levels were both low, indicating that the humoral immune response of PCV3-infected pigs was weak or lagging, and persistent or repeated infections could occur. Additionally, the complete genomes of 23 PCV3 strains were sequenced and analyzed, which showed nucleotide identities of 98.5~100.0%, 98.6~100.0%, and 99.2~100.0% in the complete genome, open reading frame (ORF)2, and ORF1 sequences, respectively, and amino acid identities of 96.7~100.0% and 99.3~100.0% in the capsid and replicase proteins, respectively. Phylogenetic analysis based on ORF2 nucleotide sequences indicated that the PCV3 strains obtained in the present study could be classified into three sub-clades, with most strains clustered into clade 3c, indicating that PCV3c is the dominant subtype in the regions of China investigated. In general, the present study revealed a high prevalence and high genetic divergence of PCV3 among Chinese pig herds, and indicated that the potential effect of PCV3 on the pig industry may be a concern.

Recent Progress on Epidemiology and Pathobiology of Porcine Circovirus 3

The recently discovered porcine circovirus 3 (PCV3) belongs to the Circovirus genus of the Circoviridae family together with the other three PCVs, PCV1, PCV2, and PCV4. As reported, PCV3 can infect pig, wild boar, and several other intermediate hosts, resulting in single or multiple infections in the affected animal. The PCV3 infection can lead to respiratory diseases, digestive disorders, reproductive disorders, multisystemic inflammation, and immune responses. Up to now, PCV3 infection, as well as the disease caused by PCV3, has been reported in many swine farms worldwide with high positive rates, which indicates that the virus may be another important pathogen in the swine industry. Therefore, we reviewed the current progress on epidemiology and pathobiology of PCV3, which may provide the latest knowledge of the virus and PCV3-related diseases.

Detection and molecular characterization of two canine circovirus genotypes co-circulating in Vietnam

Background

Canine circovirus is reported in dogs in many countries, including the USA, China and Thailand. It has been detected in healthy dogs and dogs with diarrhea, hemorrhagic gastroenteritis, and vasculitis. It comprises five genotypes and is frequently found as a coinfection with canine parvovirus-2 (CPV-2).

Aim

To characterize canine circovirus genotypes co-circulating with CPV-2 in Vietnam.

Method

PCR assessment of 81 CPV-2-positive fecal samples from Vietnamese diarrheic dogs up to seven months of age for other viral enteric pathogens, including canine bocavirus, canine adenovirus, paramyxovirus, canine coronavirus, porcine circovirus-3 and canine circovirus. In addition, eight selected full genome sequences of Vietnamese canine circovirus were analyzed and used for phylogeny.

Results

In total 19.8% of samples were found to be positive for canine circovirus. Phylogeny revealed that the Vietnamese canine circovirus strains were clustered in two different genotypes (genotype-1 and -3). The genetic diversity among Vietnamese canine circovirus was 86.0–87.2%. The nucleotide discrepancy among both genotypes altered the deduced amino acid sequence in 14 and ten residues of the replicase and capsid proteins, respectively. Genetic recombination analysis revealed that the Vietnamese canine circovirus-6 strain has the American and Chinese canine circovirus as its major and minor parents, respectively. Only a single dog revealed triple detections of CPV-2c, Canine circovirus and canine adenovirus (1.2%).

Conclusion

The co-circulation of two different genotypes of canine circovirus and CPV-2c in dogs in Vietnam has been illustrated.

Clinical relevance

The mortality rate with CPV-2 only (22%) doubled in dogs with canine circovirus and CPV-2 co-infection.

PCV3 in Thailand: Molecular epidemiology and relationship with PCV2

Porcine circovirus type 3 has been circulating throughout the world and since their first report, various clinical signs and disease developments have been documented. The virus is similar to the closely related PCV2 and is associated with several clinical signs called porcine circovirus-associated diseases (PCVAD). PCV2 or PCV3 is occasionally reported with clinical signs such as PDNS, respiratory signs and reproductive failure. Retrospective research conducted in Thailand revealed that both PCV2 and PCV3 have been circulation for decades. However, awareness about PCV3 infection has just arisen in recent years because of the similarities observed in disease circulation and clinical signs that have led to concerns. This study was conducted to find the relationship between the quantity of PCV2 and PCV3 in Thai pigs displaying the clinical signs related to PCVAD. A total of 479 serum samples with different production phases and clinical signs were sent to Kamphaeng Saen Veterinary Diagnostic Center (KVDC) for qPCR to detect the presence of PCV2 or PCV3. There was no relationship between the PCV3 and PCVAD-related clinical signs. Also, the relationship between PCV2 and PCV3 with no clinical signs suggested that both viruses might come from the same reservoir or have been circulating in Thailand for a long time, leading to common incidents in finding. The viral load of PCV2 was significantly different among the pig groups with and without clinical signs. The capsid sequence analysis of PCV3 revealed that 22 capsid sequences obtained from this study were found as clusters within PCV3a with a minor variation. Additional control measures are further needed to reduce the findings of the viruses. A future study with a control experiment may be needed to clarify the pathogenesis of PCV3.

Porcine circovirus 3 in North and South America: Epidemiology and genetic diversity

Porcine circovirus 3 (PCV3) is a recently discovered virus that has been detected in the swine population worldwide. PCV3 infection has been associated with several signs, but its pathogenicity is currently uncertain. This review article aimed to analyse the PCV3 strains that circulate in different countries in North and South America. We demonstrated the main regions of polymorphisms in the capsid protein structure. Furthermore, we found that PCV3 has at least six different lineages circulating in the Americas. Additional studies are required to determine the role of PCV3 in different clinical syndromes and its epidemiology in swine herds in North and South American countries.

Porcine circovirus 3 (PCV-3) as a causal agent of disease in swine and a proposal of PCV-3 associated disease case definition

Porcine circovirus 3 (PCV‐3) was discovered in 2015 using next‐generation sequencing (NGS) methods. Since then, the virus has been detected worldwide in pigs displaying several clinical–pathological outcomes as well as in healthy animals. The objective of this review is to critically discuss the evidence existing so far regarding PCV‐3 as a swine pathogen. In fact, a significant number of publications claim PCV‐3 as a disease causal infectious agent, but very few of them have shown strong evidence of such potential causality. The most convincing proofs of disease association are those that demonstrate a clinical picture linked to multisystemic lymphoplasmacytic to lymphohistiocytic perivascular inflammation and presence of viral nucleic acid within these lesions. Based on these evidence, individual case definitions for PCV‐3‐reproductive disease and PCV‐3‐systemic disease are proposed to standardize diagnostic criteria for PCV‐3‐associated diseases. However, the real frequency of these clinical–pathological conditions linked to the novel virus is unknown, and the most frequent outcome of PCV‐3 infection is likely subclinical based on its worlwide distribution.

What do we know about porcine circovirus 3 (PCV3) diagnosis so far?: A review

Porcine circovirus 3 (PCV3) was first discovered in 2016, almost concomitantly by two groups of researchers in the United States. The novel case was reported in a group of sows with chronic reproductive problems with clinical presentation alike porcine dermatitis and nephropathy syndrome (PDNS), where metagenomic sequencing revealed a genetically divergent porcine circovirus designated PCV3. The discovery of PCV3 in a PDNS case, which used to be considered as part of PCVAD attributed to PCV2 (porcine circovirus 2), has garnered attention and effort in further research of the novel virus. Just when an infectious molecular DNA clone of PCV3 has been developed and successfully used in an in vivo pathogenicity study, yet another novel PCV strain surfaced, designated PCV4 (porcine circovirus 4). So far, PCV3 has been reported in domestic swine population globally at low to moderate prevalence, from almost all sample types including organ tissues, faecal, semen and colostrum samples. PCV3 has been associated with a myriad of clinical presentations, from PDNS to porcine respiratory disease complex (PRDC). This review paper summarizes the studies on PCV3 to date, with focus on diagnosis.

Detection of Porcine circovirus 3 from captured wild boars in Korea

Porcine circovirus 3 (PCV3) is a newly discovered ssDNA virus. The virus was first reported in pigs suffering from several clinical syndromes, including porcine dermatitis and nephropathy syndrome, reproductive disorders, respiratory disease and myocarditis. PCV3 was recently reported in wild boars with high prevalence as well. In this study, 266 wild boar anal swab, feces, nasal swab and whole blood samples were collected from three mainland provinces and one island province (Chungbuk, Gangwon, Gyeonggi, Jeju) of South Korea between 2019 and 2020 including 119 from male, 142 from female and 5 undetermined. PCV3 was diagnosed targeting conserved rep (replication associated protein) gene region using Direct PCR and sequencing. Out of 266 tested samples, 15 were positive for PCV3 with detection frequency at 5.6%. Among 266 samples tested, we obtained 14 partial rep gene sequences and one complete genome sequence of PCV3 with a genome size of 2000nt. Here we present the evidence of PCV3 circulation in Korean wild boars.

Porcine Circovirus 3a Field Strains in Free-Living Wild Boars in Paraná State, Brazil

Simple Summary

Porcine circovirus 3 (PCV-3) was first identified in pigs in the USA and was subsequently detected in several other countries, including Brazil. PCV-3 can be associated with diseases in pigs. To date, there are only a few reports of PCV-3 in wild boars worldwide. This study aimed to investigate the presence of PCV-3 in wild boars in Paraná state, Brazil. The results revealed that PCV-3 was present in the serum and lungs of the sampled boars. The complete genome of the PCV-3a strain was determined and compared with other PCV-3 strains around the world. Phylogenetic analysis has shown a close relationship to the strains already described in domestic and wild pigs. At this moment, there is no evidence that PCV-3 causes disease in wild boars. However, the monitoring of circulation of PCV-3 in wild boars is important for pig industry biosecurity because these animals share pathogens with domestic pigs.

Abstract

Porcine circovirus 3 (PCV-3) was identified in domestic pigs worldwide. Although PCV-3 has also been detected in wild boars, information regarding its circulation in this free-living animal species is scarce. To investigate PCV-3 occurrence in free-living wild boars in Brazil, 70 serum samples collected between January 2017 and June 2019 in Paraná state, Brazil were analyzed by PCR assay. Amplicons measuring 330 bp in length were amplified in seven (10.0%) of the serum samples and confirmed to be PCV3-specific by nucleotide (nt) sequencing. As the amplified products from the serum samples yielded only intermediate levels of viral DNA, lung samples from the seven PCR-positive wild boars were also evaluated by PCR. Of these samples, five lung samples were positive and provided high levels of viral DNA. The three lung samples that presented the highest levels of viral DNA were selected for amplification and sequencing of the whole PCV-3 genome. The three full-length sequences obtained were grouped in PCV-3 clade “a”, and the sequences exhibited 100% nucleotide similarity among them. The PCV-3 field strains of this study showed nucleotide and amino acid similarities of 98.5–99.8% and 98.8–100%, respectively, with whole-genome PCV-3 sequences from around the world.

Histological Lesions and Replication Sites of PCV3 in Naturally Infected Pigs

Simple Summary

Diagnosing porcine circovirus type 3 (PCV3) is a challenge in pig production. Although the virus has been recently isolated, the patterns of PCV3-associated histological lesions are still to be elucidated. The present study describes the association of PCV3 mRNA by in situ hybridization within histological lesions and PCV3 DNA detected by real-time PCR in naturally infected pigs. The main histologic lesions associated with PCV3 mRNA detection were lymphoplasmacytic myocarditis and lymphoplasmacytic interstitial pneumonia, in heart and lung, respectively. Our findings offer robust guidance of microscopic lesions associated with PCV3, which may have a key role in PCV3 diagnosis.

Abstract

Porcine circovirus type 3 (PCV3) has been recently described as a potential cause of abortions and systemic vasculitis in pigs. Although the virus has been detected by real-time PCR in several porcine tissues from countries worldwide, PCV3-associated diseases have not been satisfactorily clarified. The objective of this study was to investigate the association between the presence of PCV3 mRNA detected by in situ hybridization (ISH) within histological lesions and PCV3 DNA detected by real-time PCR in naturally infected pigs. A total of 25 PCV3 PCR-positive cases were analyzed. Formalin-fixed tissues from these cases were evaluated for histologic lesions and for ISH-RNA positive signals for PCV3. The most frequent tissue type with histopathologic lesions was heart, 76.2%, with lymphoplasmacytic myocarditis and epicarditis as the most frequent lesions observed. Lymphoplasmacytic interstitial pneumonia was also a frequent finding, 47.6%. There were also lesions in kidney, liver, spleen and lymph nodes. PCV3-ISH-RNA positive signals were mostly observed in association with lymphoplasmacytic inflammatory infiltrate in various tissues, including arteries. Based on our results, the minimum set of specimens to be submitted for histopathology and mRNA in situ hybridization to confirm or exclude a diagnosis of PCV3 are heart, lung and lymphoid tissues (i.e., spleen and lymph nodes), especially for differential diagnosis related with PCV2-associated diseases.

Porcine circovirus type 3 capsid protein induces NF-κB activation and upregulates pro-inflammatory cytokine expression in HEK-293T cells

Porcine circovirus type 3 (PCV3) has been widely detected throughout the world since it was first discovered on pig farms in 2015. PCV3 is closely associated with cardiac and multisystem inflammation, respiratory disease, congenital tremors, myocarditis, diarrhea, encephalitis and neurologic disease, and periarteritis. However, there have been few reports on the relationship between PCV3 and inflammatory pathways. The NF-κB signaling pathway plays an important role in the defense against viral infection. Here, we demonstrate that the capsid protein (Cap) of PCV3 plays a key role in the activation of NF-κB signaling in HEK-293T cells. Furthermore, PCV3 Cap promotes the mRNA expression of the pro-inflammatory cytokines IL6 and TNFα. In addition, PCV3 Cap promotes RIG-I and MDA5 mRNA expression in RIG-like receptor (RLR) signaling and MyD88 mRNA expression in Toll-like receptor (TLR) signaling but does not influence TRIF mRNA expression in TLR signaling. These results show that PCV3 Cap activates NF-κB signaling, possibly through the RLR and the TLR signaling pathways. This work illustrates that PCV3 Cap activates NF-κB signaling and thus may provide a basis for the pathogenesis of PCV3 and the innate immunity of the host.

Retrospective surveillance of porcine circovirus 4 in pigs in Inner Mongolia, China, from 2016 to 2018

A novel circovirus designated "porcine circovirus type 4" (PCV4) was recently reported in pigs with severe clinical disease in Hunan Province, China. Relatively little is known about the molecular epidemiology of this recently discovered virus. In order to assess the prevalence of PCV4 infection in pigs and to analyze its genomic characteristics, 1683 clinical samples were collected in Inner Mongolia, China, from 2016 to 2018. The overall infection rate of PCV4 was 1.6% (27/1683) at the sample level and 21.6% (11/51) at the farm level, with rates ranging from 3.2% (1/31) to 20.0% (6/30) on different PCV4-positive pig farms. In addition, the PCV4 infection rates at both the sample and farm level increased from 2016 to 2018. This also showed that PCV4 was present in pigs in 2016 in China and therefore did not arrive later than this date. Additionally, our findings showed that PCV4 infections had no association with PCV2 or PCV3 infections. We sequenced the complete genomes of three PCV4 strains and found that the PCV4 strains had a high degree of genetic stability but shared less than 80% sequence identity with other circoviruses. We identified six amino acid mutations in the Rep protein and seven in the Cap protein. Phylogenetic analysis based on Cap and Rep sequences confirmed that the PCV4 strains grouped in an independent branch. Our findings provide important information about the prevalence and genetic characteristics of PCV4 strains.

Pathogenicity and immune response against porcine circovirus type 3 infection in caesarean-derived, colostrum-deprived pigs

Recently, a novel PCV species (PCV3) has been detected in cases associated with sow mortality, lesions consistent with porcine dermatitis and nephropathy syndrome, reproductive failure and multisystemic inflammation. The pathogenesis and clinical significance of PCV3 is still unclear. In this study, we investigated the immunopathogenesis of PCV3 in CD/CD pigs. Four treatment groups, PCV3 (n=6), PCV3-KLH (n=6), control (n=3) and control-KLH (n=3), were included with PCV3-positive tissue homogenate (gc=3.38×10¹² ml^-1 and gc=1.04×10¹¹ ml^-1), confirmed by quantitative PCR (qPCR) and next-generation sequencing. Clinical signs, viremia, viral shedding, systemic cytokines, humoral (IgG) and T-cellular response were evaluated for 42 days. At necropsy, tissues were collected for histological evaluation and PCV3 detection by qPCR and in situ hybridization. No significant clinical signs were observed through the study. Viremia was detected in both PCV3-inoculated groups from 3 days post-inoculation (p.i.) until the end of the study. Nasal shedding was detected from 3 to 28 days p.i. and faecal shedding was transient. PCV3 induced an early (7 days p.i.) and sustained (42 days p.i.) IgG response. No significant T-cell response was observed. Histological evaluation demonstrated lesions consistent with multisystemic inflammation and perivasculitis. All tissues evaluated were positive by qPCR and virus replication was confirmed by positive in situ hybridization. This study demonstrated the potential role of PCV3 in subclinical infection, producing a mild, multisystemic inflammatory response, prolonged viremia detectable for 42 days p.i., presence of IgG humoral response and viral shedding in nasal secretions. More research is required to understand and elucidate potential co-factors necessary in the manifestation and severity of clinical disease.

Porcine Circovirus Type 3 in Pig Farms Experiencing Diarrhea in Jiangxi, China: Prevalence, Genome Sequence and Pathogenicity

Simple Summary

Porcine circovirus 3 (PCV3) is a new species of PCV that was associated with porcine dermatitis and nephropathy syndrome (PDNS), respiratory disease, cardiac and multisystem inflammation in nursery and finishing pigs, and reproductive failure problems, including abortion, mummified fetuses, and stillbirth in sows. To date, the reports on the PCV3 present in diarrhea pigs are limited and the genetic characteristics of PCV3 from diarrheal pigs and pathogenicity on pigs were inconsistent. This study aimed to investigate the prevalence of PCV3 in pigs with/without diarrhea, to analyze the genome sequence of PCV3 from diarrheal pigs, and to inquire into the associated pathogenicity of PCV3 to piglets experimentally infected with PCV3-positive intestinal contents. The results demonstrated that PCV3 was widely circulating in diarrheal suckling and weaned piglets. Clinical signs, gross lesions, and histological changes were observed in suckling piglets inoculated with PCV3. The complete genome of a PCV3a strain was determined and two mutations (V24A and K27R) were present when compared with PCV3b strains. The findings of this study increase the knowledge of the epidemiology, viral genetics, pathogenicity, and pathogenesis of PCV3.

Abstract

Porcine circovirus 3 (PCV3) infections have been reported in different clinical presentations. However, the prevalence and pathogenicity of PCV3 associated with diarrhea in piglets have been limited. Herein, we present an investigation and genome analyses of PCV3 in piglets experiencing diarrhea, and observed clinical signs, gross lesions, and histological changes in pigs negative for all known pathogens associated with diarrhea but positive for PCV3 alone. Among the feces (n = 141) tested, 16.31% (23/141) were positive for PCV3. Of which, 27.28% (15/55) and 14.29% (5/35) were present in diarrheal samples from suckling and weaned piglets, respectively. Moderate to severe atrophic villi was confined in duodenum, jejunum, and ileum, and significantly decreased average heights of villi, and the depths of crypt were observed in PCV3-infected piglets. The complete genome of a representative strain of PCV3, designated as JX/CH/2018, was determined. Multialignment analysis indicated that JX/CH/2018 had 97.7–99.7% nucleotide identity at the complete genome level, and 97.2–100% at the amino acid level of the capsid protein when compared with reference PCV3 strains. Phylogenetic analysis showed that the PCV3 strain identified in this study belonged to PCV3a lineage. The present study demonstrated that PCV3 is a common virus in diarrheal suckling and weaned piglets.

Detection and phylogenetic analysis of porcine circovirus 3 in part of northern China from 2016 to 2018

Porcine circovirus 3 (PCV3) is a recently identified virus that is associated with reproductive failure, porcine dermatitis and nephropathy syndrome, and multi-systemic inflammation. To investigate the molecular epidemic characteristics and genetic evolution of PCV3 in northern China, a commercial TaqMan-based real-time quantitative PCR kit was used to detect PCV3 in 435 tissue specimens collected from pigs with various clinical signs from 105 different swine farms in northern China. The results showed that 48 out of 105 (45.7%) farms and 97 out of 435 (22.3%) samples tested positive for PCV3. Of the 97 PCV3-positive samples, 80 (82.5%) tested positive for other pathogens. PCV3 was found more frequently in pigs with reproductive failure than in those with other clinical signs. This study is the first to detect PCV3 in Tianjin. The complete genome sequences of six PCV3 isolates and the capsid (Cap) protein gene sequences of 11 isolates were determined. Based on the predicted amino acids at positions 24 and 27 of the Cap protein and their evolutionary relationships, the 17 PCV3 strains obtained from northern China and 49 reference strains downloaded from the GenBank database were divided into four major groups (3a-3d). An analysis of selection pressure and polymorphism indicated that the PCV3 Cap protein seems to be evolving under balancing selection, that the population is in dynamic equilibrium, and that no population expansion occurred during the study period. Our results provide new information about the molecular epidemiology and evolution of PCV3.

A molecular survey and phylogenetic analysis of porcine circovirus type 3 using oral fluid, faeces and serum

Background

Porcine circovirus type 3 is the most recently discovered porcine circovirus, and an emerging pathogen. In this study the status of its presence on some Slovenian farms is reported. The effectiveness of the vaccine against porcine circovirus type 2 was assessed against porcine circovirus type 3.

Group samples of oral fluid, faeces and individual serum samples were taken from six different pig categories and tested for presence of viral DNA, using both real time and conventional PCR. Positive samples were subjected to direct Sanger sequencing. Nucleotide sequences were analyzed and compared to GenBank PCV3 sequences.

Results

Positive samples were sent for genome sequencing, which confirmed the presence of virus in all different pig categories on five farms. A high to moderate correlation of strong statistical significance was found between individual serum samples, oral fluid and faeces. Slovenian PCV3 was found to be distributed in a way similar to that of other countries. Slovenian PCV3 nt sequences are highly related, sharing more than 99.5% nt identity. On one farm a commercially available vaccine against porcine circovirus type 2 was used on 3-week-old pigs. It did not affect the presence of porcine circovirus type 3 in oral fluid or sera of any of the seven age groups of pigs, each with two control groups.

Conclusions

The results constitute the first discovery of the virus in Slovenia. Genome sequencing has revealed a high degree of similarity between Slovenian and GenBank isolates.

Major swine viral diseases: an Asian perspective after the African swine fever introduction

Asia is a major pig producer of the world, and at present, African swine fever virus (ASFV) continues to significantly impact the Asian pig industry. Since more than 50% of the world’s pig population is in Asia, ASFV outbreaks in Asia will affect the global pig industry. Prior to the introduction of ASF, several outbreaks of major swine viruses occurred in Asia over the last two decades, including porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV) and foot and mouth disease virus (FMDV). The rapid spreading of those viruses throughout Asia involve many factors such as the various pig production systems and supply chains ranging from back-yard to intensive industrial farms, animal movement and animal product trading within and among countries, and consumer behaviors. ASF has notoriously been known as a human-driven disease. Travelers and international trading are the major ASFV-carriers for the transboundary transmission and introduction to naïve countries. Globalization puts the entire pig industry at risk for ASF and other infectious diseases arising from Asian countries. Disease control strategies for the various pig production systems in Asia are challenging. In order to ensure future food security in the region and to prevent the deleterious consequences of ASF and other major viral disease outbreaks, disease control strategies and production systems must be improved and modernized.

Prevalence, pathogenesis, and evolution of porcine circovirus type 3 in China from 2016 to 2019

Porcine circovirus type 3 (PCV3) infection causes substantial economic losses in pig populations since its discovery in 2016. However, PCV3 molecular epidemiology remains need further study. In order to assess the prevalence of PCV3 infection in China, 4094 clinical samples from 271 pig farms in 10 provinces of China were evaluated by PCR. It was shown that the overall prevalence of PCV3 infection was 29.3 % (1200/4094) and 74.2 % (201/271) at sample and farm levels respectively, suggesting that PCV3 infection is prevalent in China. Furthermore, a statistical analysis showed PCV3 might exacerbate PCV2 and PRRSV infection rate and have a potential association with pig clinical disease. In addition, we sequenced the entire genome of 57 PCV3 strains; homology analysis showed that PCV3 strains have more than 96 % similarities at the nucleotide level, and PCV3 shares less than 60 % similarities with other circoviruses. By comparing the total 673 PCV3 strains from the NCBI GenBank, we found the major of amino acid mutations are located in predicted epitope regions and the mutations ratio changed during PCV3 evolution. Phylogenetic analysis revealed that all isolates belonged to PCV3a and PCV3b, and increasing PCV3a and decreasing PCV3b trends were observed during PCV3 evolution. Overall, this study provides important insights for understanding PCV3 prevalence, pathogenesis, and evolution and will guide future efforts to develop effective preventive and control measures.

Fine mapping of linear B cell epitopes on capsid protein of porcine circovirus 3

Porcine circovirus type 3 (PCV3) is an emerging swine pathogen associated with acute porcine dermatitis and nephropathy syndrome (PDNS)-like clinical signs, reproductive failure, and multisystemic inflammation. Current evidence shows that PCV3 is spread worldwide, and its high incidence may pose a threat to the global pig industry. Capsid (Cap) protein is the sole structural protein which plays an important role in inducing protective immunity against PCV3 infection. In this study, monoclonal antibodies (mAbs) against Cap protein of PCV3 were produced by the hybridoma technique. Subsequently, 12 serial overlapping peptides (P1 to P12) spanning the entire region of Cap were synthesized to determine the B cell epitope regions using the mAbs. Results from dot-blot and peptide ELISA identified that P3, P9, and P10 were the major B cell antigenic regions. Fine mapping by shorter N- and C-terminal truncated peptides confirmed that the motifs ⁵⁷NKPWH⁶¹, ¹⁴⁰KHSRYFT¹⁴⁶, and ¹⁶¹QSLFFF¹⁶⁶ were linear B cell epitopes, which were highly conserved among different PCV3 strains. Interestingly, we found that the motif ¹⁴⁰KHSRYFT¹⁴⁶ was highly conserved in all reported types of PCVs (i.e., PCV1, PCV2, PCV3, and PCV4), except for the substitution (Y → K → R) of the first residue. This is the first research to identify B cell epitopes of PCV3 Cap, and these findings may lead to a better understanding of the antibody-antigen interaction and provide some guidance for PCV3 vaccine design.Key points• The recombinant Cap protein of PCV3 was expressed and purified in soluble form. • PCV3 Cap-specific mAbs prepared in this study had no cross-reactivity with PCV1/PCV2 Cap. • This is the first report of three conserved linear B cell epitopes on PCV3 Cap. • The minimal residues of the epitopes were 57-61 aa, 140-146 aa, and 161-166 aa.

Detection and genotyping of Porcine circovirus 2 (PCV-2) and detection of Porcine circovirus 3 (PCV-3) in sera from fattening pigs of different European countries

PCV‐2 is considered one of the most economically important viral agents in swine worldwide. Recently, PCV‐3 has been found in pigs affected by different disorders and in healthy animals. The objective of this epidemiological work was to describe the frequency of detection of PCV‐2 and PCV‐3 in pig farms of 9 European countries. Moreover, a second aim was to assess the most frequent PCV‐2 genotypes found in the studied farms. Sera from 5 to 10 pigs per farm were collected from 2 to 11 farms per studied country. A total of 624 sera of fattening pigs (10–25 week old) from 64 farms from Spain (n = 11), Belgium (n = 10), France (n = 8), Germany (n = 8), Italy (n = 7), Denmark (n = 8), the Netherlands (n = 5), Ireland (n = 5) and Sweden (n = 2) were analysed by conventional PCR. In addition, one or two PCV‐2‐positive samples per farm were genotyped by sequencing the ORF2 gene. PCV‐3 PCR‐positive samples with relatively low Ct values were also sequenced and phylogenetically analysed. PCV‐2 DNA was detected in pig sera from all European tested countries, but Sweden. A total of 132 out of 624 (21%) sera were positive for PCV‐2 PCR, corresponding to 30 out of the 64 (47%) tested farms. PCV‐3 DNA was detected in 52 out of 624 (8%) sera, corresponding also to 30 out of the 64 (47%) studied farms from all tested countries. A total of 48 PCV‐2 PCR‐positive samples were successfully sequenced and genotyped, being PCV‐2d the most frequently genotype found (n = 28), followed by PCV‐2b (n = 11) and PCV‐2a (n = 9). These results pointed out PCV‐2d as the most prevalent genotype currently in Europe. The PCV‐3 phylogenetic analysis showed high identity (>98%) among sequences from all the analysed countries. The relatively low co‐infection (3%), likely suggest an independent circulation patterns of PCV‐2 and PCV‐3.

Retrospective study of porcine circovirus 3 (PCV3) in swine tissue from Brazil (1967-2018)

In this study, we report the molecular diagnosis and retrospective study of porcine circovirus 3 (PCV3) in frozen and formalin-fixed paraffin-embedded swine tissues (FFPE) collected from 1967 to 2018 in southeastern Brazil (Espírito Santo and Rio de Janeiro states). Frozen tissues from 35 pigs and FFPE tissues from 143 pigs were tested by nested PCR, targeting the PCV3 partial capsid gene. Bidirectional sequencing of 16 positive samples was performed, followed by sequence analysis and haplotype networks. A total of 26/178 samples (14.6%) tested positive for PCV3: 14/35 (40%) frozen tissue and 12/143 (8.4%) FFPE tissue. PCV3 was detected in the 1960s, 1970s, 2000s, and 2010s with the characterization of types PCV3a and PCV3b. A star-like distribution was observed in the grid of haplotypes, with a low haplotype diversity and more recent dispersal of the virus. A total of 40% of asymptomatic animals considered fit for slaughter tested positive for PCV3. In conclusion, PCV3 DNA was detected over 51 years of study, prior to initial reports and, so far, the sample detected in 1967 is the oldest partial capsid sequence described. The circulation of two different genotypes was reported, suggesting more than one introduction event of this virus into Brazil. Moreover, taken together, our studies indicated an ancient origin of PCV3 and its circulation in asymptomatic animals in Brazilian herds.

Simultaneous detection of classical swine fever virus and porcine circovirus 3 by SYBR green I-based duplex real-time fluorescence quantitative PCR

In the present study, the SYBR green I-based duplex quantitative polymerase chain reaction (qPCR) was developed for simultaneous detection of classical swine fever virus (CSFV) and porcine circovirus 3 (PCV3). The assay was used to detect both CSFV and PCV3 in one sample by their distinct melting temperatures (melting peaks at 87°C for CSFV and 81.5 °C for PCV3), and no specific fluorescence signals were detected for other non-targeted porcine pathogens. The assay had a high degree of linearity (R2 > 0.998) with the detection limits of 23 copies/μL for CSFV and 36 copies/μL for PCV3, and exhibited high repeatability and reproducibility with a low coefficient of variation below 2.0% in both intra- and inter-assay. In this study, 130 clinical samples collected from sick pigs in the field were tested by this assay with the positive rates of 9.23% (12/130) for CSFV and 21.54% (28/130) for PCV3 respectively, and the positive rate of CSFV and PCV3 co-infection was 6.92% (9/130). Our results showed that the developed method was a reliable diagnostic tool to monitor and survey CSFV, PCV3 and CSFV/PCV3 co-infection in the field.

Co-infection status of porcine circoviruses (PCV2 and PCV3) and porcine epidemic diarrhea virus (PEDV) in pigs with watery diarrhea in Henan province, central China

Porcine circoviruses (PCV2 and PCV3) and porcine epidemic diarrhea virus (PEDV) are important swine viruses that threaten the swine industry worldwide. Here, we evaluated the co-infection status of PCV2, PCV3 and PEDV in 76 enteric samples from piglets with severe diarrhea disease in Henan, China. All samples were tested by PCR/RT-PCR. Our results showed that the infection rate of PCV2, PCV3 and PEDV was 82.89%, 76.32% and 68.42%, respectively. Interestingly, most of these samples exhibited mixed infections. The co-infection rates of PCV2 and PCV3, PCV2 and PEDV, PCV3 and PEDV were 69.74%, 57.89% and 53.95%, respectively. And the triple infection rate was 48.68%. Furthermore, the genetic characteristics of PCV2 and PCV3 were analyzed based on the cap genes. Two PCV2 genotypes, PCV2b and PCV2d, were circulating in the fields. The cap gene of PCV2b and PCV2d isolates only shared 94.6%-95.0% nucleotide identities. The PCV3 isolates together with the reference strains could be divided into four clades (clade1-4), and the cap genes of these isolates have 98.6%-100% nucleotide identities to each other. Distinctive amino acid substitutions were also characterized on the cap protein of PCV2 and PCV3 isolates. Our studies provide the new knowledge on the co-infectious status of PCV2, PCV3 and PEDV in China. The results also provide insight into the genetic diversity and molecular epidemiology of PCV2 and PCV3.

Full-genome sequences of porcine circovirus 3 (PCV3) and high prevalence in mummified fetuses from commercial farms in Brazil

The clinical implications of recently discovered porcine circovirus 3 (PCV3) infections are still unknown. The potential role of this emerging virus in reproductive loss in swine has been described. Herein, we report a high prevalence of PCV3 in mummified fetuses from sows maintained in modern farms in Rio Grande do Sul, Santa Catarina, Paraná, Goiás, and Mato Grosso do Sul states, Brazil. For this analysis, 276 mummified fetuses from 11 commercial swine farms were included. The presence of PCV3 DNA was confirmed using PCR, and the complete sequence of five different viral strains was obtained. Sequences of PCV3 genomes available on GenBank were then used for phylogenetic tree construction. Of the 276 mummified fetuses examined, 270 (nearly 97%) were positive for PCV3. In 93.1% of the fetuses, co-infections with at least one of the following agents were identified: porcine parvovirus (PPV), porcine circovirus 2 (PCV2) and Leptospira spp. Twelve fetuses were positive for PCV3 alone. The amino acid sequence of the capsid gene for the five viral strains shared 98-100% homology among them. Analysis of the DNA sequence indicates that the viruses identified in this study belong to the PCV3a1 subgroup. In summary, PCV3 DNA was detected in mummified fetuses at a surprisingly high rate. The role of PCV3 in porcine circovirus-associated disease (PCVAD) is still uncertain. However, considering that PCV3 has been detected in a variety of conditions, even in healthy animals, the present results confirm the need to investigate PCV3 as a causative agent of fetal mummification in swine.

Self-assembly into virus-like particles of the recombinant capsid protein of porcine circovirus type 3 and its application on antibodies detection

PCV3 capsid protein (Cap) is an important antigen for diagnosis and vaccine development. To achieve high-level expression of recombinant PCV3 Cap in Escherichia coli (E. coli), the gene of wild-type entire Cap (wt-eCap) was amplified from clinical samples, and three optimized entire Cap (opti-eCap) and one optimized Cap deleted nuclear location signal (NLS) (opti-dCap) gene fragments encoding the same amino acid sequence with wt-eCap were synthesized based on the codon bias of E. coli. Those gene fragments were inserted into the pET30a expression vector. One recombinant strain with the highest expressed soluble eCap from four entire Cap (one wt-eCap and three opti-eCap) and one recombinant strain expressed opti-dCap were selected for further purification. The purified eCap and dCap were identified by transmission electron microscopy (TEM), a large number of round hollow particles with a diameter of 10 nm virus-like particles (VLPs) were observed in eCap, whereas irregular aggregation of proteins observed in dCap. After formation the VLPs were applied as a coating antigen to establish an indirect ELISA (I-ELISA) for detection of PCV3-specific antibody in swine serum. 373 clinical swine serum samples from China collected in 2019 were tested utilizing the VLP-based I-ELISA method under optimized conditions. To the best of our knowledge, this is the first report of self-assembly into VLPs of PCV3 recombinant Cap. Our results demonstrated that the VLP-based I-ELISA will be a valuable tool for detecting the presence of PCV3 antibodies in serum samples and will facilitate screening of large numbers of swine serum for clinical purposes.

Molecular Detection and Genetic Diversity of porcine Circovirus Type 3 in Commercial Pig Farms in Xinjiang Province, China

Introduction

Porcine circovirus type 3 (PCV3) is a newly discovered porcine circovirus. The molecular characteristics and genetic evolution of PCV3 in Xinjiang province, China still being unclear, the aim of the study was their elucidation.

Material and Methods

A total of 393 clinical samples were collected from pigs on commercial farms in nine different regions of Xinjiang and phylogenetic analysis based on full-length Cap genes was performed.

Results

The prevalence at farm level was 100%, while in all the tested samples it was 22.39%. Nine PCV3 strains were detected in Xinjiang province and they shared 98.9–99.3% nucleotide and 97.5–100.0% Cap gene amino acid sequence identities with other epidemic strains from China and abroad. Compared with other epidemic strains of PCV3, there were 26 base mutation sites in the Cap gene in the nine Xinjiang strains, resulting in the mutation of amino acids at positions 20, 24, 75, 77, 108, 111 and 206. Phylogenetic analysis showed that these strains can be divided into two different genetic groups, to the first of which five strains affiliated and divided between subgroups 1.1 and 1.2, and to the second of which the other four strains affiliated and similarly divided between subgroups 2.1 and 2.2.

Conclusion

PCV3 circulates widely among commercial pig farms in Xinjiang province, China, and displays obvious genetic diversity. The results provide epidemiological information useful for the prevention and control of PCV3 infection in the pig industry.

Genotyping based on complete coding sequences of porcine circovirus type 3 is stable and reliable

Porcine circovirus type 3 (PCV3) is a newly identified virus, which is associated with PDNS-like clinical signs, reproductive failure, cardiac and multiorgan inflammation. However, the genotype of PCV3 is still controversial. Here, we reconstructed the phylogenies of 194 complete coding sequences of PCV3 using five different phylogenetic methods. The results showed five trees reconstructed using different methods displayed similar phylogenies, indicating genotyping based on complete coding sequences of PCV3 is stable and accurate.

A Shift in Porcine Circovirus 3 (PCV-3) History Paradigm: Phylodynamic Analyses Reveal an Ancient Origin and Prolonged Undetected Circulation in the Worldwide Swine Population

The identification of a new circovirus (Porcine circovirus 3, PCV-3) has raised a remarkable concern because of some analogies with Porcine circovirus 2 (PCV-2). Preliminary results suggest an extremely recent PCV-3 emergence and high mutation rate. Retrospective studies prove its circulation at least since the early 1990s, revealing that PCV-3 could have been infecting pigs for an even longer period. Therefore, a new evaluation, based on an updated collection of PCV-3 sequences spanning more than 20 years, is performed using a phylodynamic approach. The obtained results overrule the previous PCV-3 history concept, indicating an ancient origin. These evidences are associated with an evolutionary rate far lower (10-5-10-6 substitution/site/year) than the PCV-2 one. Accordingly, the action of selective pressures on PCV-3 open reading frames (ORFs) seems to be remarkably lower compared to those acting on PCV-2, suggesting either a reduced PCV-3 plasticity or a less efficient host-induced natural selection. A complex and not-directional viral flow network is evidenced through phylogeographic analysis, indicating a long lasting circulation rather than a recent emergence followed by spreading. Being recent emergence has been ruled out, efforts should be devoted to understand whether its recent discovery is simply due to improved detection capabilities or to the breaking of a previous equilibrium.

Simultaneous detection of porcine reproductive and respiratory syndrome virus and porcine circovirus 3 by SYBR Green І-based duplex real-time PCR

The SYBR Green І-based duplex real-time PCR assay was developed for simultaneous detection of porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus 3 (PCV-3) genomes. PRRSV and PCV-3 were distinguished in the same sample by their distinctive melting temperature (Tm) which was 84 °C for PRRSV and 81.5 °C for PCV-3, and other non-targeted swine viruses showed no specific melting peaks. The detection limits of this assay were 46.1copies/μL for PRRSV and 49.3copies/μL for PCV-3, respectively. Thirty-three lung samples of porcine with respiratory and reproductive failure symptoms were collected and confirmed by the SYBR Green І-based real-time PCR assay and conventional PCR assay. The real-time PCR detection results showed that the PRRSV positive rate was 45.45%, the PCV-3 positive rate was 63.63%, the PRRSV and PCV-3 co-infection positive rate was 36.36%, which were more sensitive than conventional PCR detection. This duplex real-time PCR assay could be a rapid, sensitive and reliable method for the detection of PRRSV and PCV-3 co-infection.

Commercial E2 subunit vaccine provides full protection to pigs against lethal challenge with 4 strains of classical swine fever virus genotype 2

Classical swine fever (CSF) still threatens the swine industry in China, with genotype 2 isolates of CSFV dominating the epizootics. In 2018 the first E2 subunit marker vaccine against CSFV (Tian Wen Jing, TWJ-E2®), containing a baculovirus-expressed E2 glycoprotein of a genotype 1.1 vaccine strain, was officially licensed in China and commercialized. To evaluate the cross-protective efficacy of TWJ-E2 against different virulent genotype 2 Chinese field isolates (2.1b, 2.1c, 2.1 h, and 2.2), 4-week-old pigs were immunized with the TWJ-E2 vaccine according to the manufacturer's instructions and then challenged with genotype 2 strains. A group vaccinated with the conventional C-strain vaccine was included for comparison. TWJ-E2 vaccinated pigs developed higher levels of E2 and neutralizing antibodies than those receiving the commercial C-strain vaccine. All TWJ-E2 and C-strain vaccinated pigs survived challenge without development of fever, clinical signs or pathological lesions. In contrast, all unvaccinated control pigs displayed severe CSF disease with 40-100% mortalities by 24 days post challenge. None of the TWJ-E2 and C-strain vaccinated pigs developed viremia, viral shedding from tonsils, E^rns protein in the sera, or viral RNA loads in different tissues after challenge, all of which were detected in the challenged unvaccinated controls. We conclude that vaccination of young pigs with TWJ-E2 provides complete immune protection against genotypically heterologous CSFVs and prevents viral shedding after challenge, with an efficacy at least comparable to that elicited by the conventional C-strain vaccine.

Evolution and Genetic Diversity of Porcine Circovirus 3 in China

The identification of a new circovirus (Porcine Circovirus 3, PCV3) has raised concern because its impact on swine health is not fully known. In Fujian Province in eastern China, even its circulating status and genetic characteristics are unclear. Here, we tested 127 tissue samples from swine from Fujian Province that presented respiratory symptoms. All of the PCV3 positive samples were negative for many other pathogens involved in respiratory diseases like PCV2, PRRSV, and CSFV, suggesting that PCV3 is potentially pathogenic. From phylogenetic analysis, PCV3 strains are divided into two main clades and five sub-clades; PCV3a-1, PCV3a-2, PCV3a-3, PCV3b-1, and PCV3b-2. Our identified strains belong to genotypes PCV3a-1, PCV3a-2, PCV3a-3, and PCV3b-2, indicating a high degree of genetic diversity of PCV3 in Fujian province until 2019. Interestingly, we found the time of the most recent common ancestor (tMRCA) of PCV3 was dated to the 1950s, and PCV3 has a similar evolutionary rate as PCV2 (the main epidemic genotypes PCV2b and PCV2d). In addition, positive selection sites N56D/S and S77T/N on the capsid gene are located on the PCV3 antigen epitope, indicating that PCV3 is gradually adaptive in swine. In summary, our results provide important insights into the epidemiology of PCV3.

The prevalence of novel porcine circovirus type 3 isolates in pig farms in China

The emerging porcine circovirus type 3 (PCV3) has been reported in Chinese swine herds since 2017. We performed a nationwide investigation on the prevalence of PCV3 in pig breeding farms and slaughterhouses in China. A total of 4,040 tonsil samples were collected from 89 farms in 25 provinces, and 1,419 lymph node samples were collected from 50 slaughterhouses in 27 provinces. The PCR results showed that in pig breeding farms, the positive rate was 41.6% (37/89) at the farm level and 5.0% (201/4040) at the individual level. In the slaughterhouses, the positive rate was 62.0% (31/50) at the farm level and 8.0% (114/1419) at the individual level. The PCR-positive samples were further sequenced, and 19 new PCV3 isolates were identified. The complete genomes of the 19 virus isolates showed 97.4%-99.7% nucleotide identity with other PCV3 isolates. The phylogenetic analysis revealed that the 19 isolates were divided into PCV3a and PCV3b genotype clusters based on the PCV3 complete genome sequences. This study indicated that PCV3 has spread extensively in both pig breeding farms and slaughterhouses. The positive rate of PCV3 was higher in eastern China compared to other regions in China. Furthermore, this study will help us understand the prevalence and genetic variation of PCV3 in Chinese swine herds.

Prevalence of porcine circovirus type 3 in pigs in the southeastern Chinese province of Zhejiang

Background

Porcine circovirus type 3 (PCV3) was first reported in US in 2016. The virus was also identified later in China. Prevalence of PCV3 in Zhejiang province in southeastern China is not clear though it has been reported in many parts of China.

Results

PCV3 infection and its co-infection with other swine viral pathogens in pig herds of Zhejiang province were retrospectively investigated by quantitative PCR (qPCR) and its sero-prevalence by indirect ELISA. PCV3 was found positive in 67.1% of the 283 clinical samples taken from 2014 to 2017 as shown by qPCR. Single infection with PCV3 accounted for only one-third of the samples, and majority were of co-infections, predominantly with PEDV (41.6%) but generally low with other swine viruses. Indirect ELISA using the PCV3 capsid protein as the coating antigen revealed an average sero-positive rate of 52.6% (40.8 to 60.8%) in 2345 serum samples from 2011 to 2017, with earliest yet high positive findings in samples taken in 2012. Of 203 serum samples, the qPCR method showed more positive findings than ELISA (81.3% vs 56.2%). With 89 serum samples negative by ELISA, vast majority (n = 81) were found positive by qPCR. There was negative correlation in levels of PCV3 DNA and anti-capsid antibody response. ORF2-based phylogenetic analysis revealed three major groups (PCV3a, PCV3b and PCV3c) of the 200 strains, 38 from this study and 162 reference strains from GenBank. Most of the strains from this study were clustered into PCV3c. Of the putative signature residues of the capsid protein (aa 24, 27, 77 and 150) relative to the three groups, only the PCV3a group strains showed a distinct pattern of residues VKSI (95% of the strains), while the other two groups did not have such a ‘signature’ pattern.

Conclusions

Results from this study provided further evidence that the novel virus PCV3 was widely distributed in China and might have emerged in Zhejiang province before 2014, most probably back in 2012 when there was high PCV3 sero-prevalence. PCV3 might be viremic in pigs and could spread by fecal shedding.

Electronic supplementary material

The online version of this article (10.1186/s12917-019-1977-7) contains supplementary material, which is available to authorized users.

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

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This study was the first seroprevalence and genetic investigation of PCV3 in dogs in the Guangxi province, China.

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This work is the first in the world to obtain the complete genome of dog PCV3.

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These PCV3 strains from the Guangxi province help to determine that PCV3 from dog origin and pig origin are from different branches.

Porcine circovirus type 3 (PCV3) is an emerging circovirus species associated with several diseases. The study aimed to investigate the frequency of porcine circovirus 3 (PCV3) and its coinfection with canine parvovirus type 2 (CPV-2) in dogs in the Guangxi province from 2015 to 2017, China, and to examine the genome diversity of PCV3. Using polymerase chain reaction (PCR) amplification and sequencing, 96 of 406 (23.6%)samples were positive for PCV3, 38 out of 406 (9.4%) samples were coinfected with both PCV3 and CPV-2. The CPV-positive rate was significantly higher in the PCV3-positive samples than in the non-PCV3 samples, and the difference was extremely significant (P < 0.01). The complete genome (n=4) and ten capsid genes (n=10) of PCV3 were sequenced. Multiple sequence alignment results showed that these sequences shared 98.5–100% nucleotide similarity with the reference genome sequence and 97.5–100% nucleotide similarity with the reference capsid gene sequence. PCV3 was classified into two different genotypes, according to phylogenetic analysis based on the whole genome. These strains were clustered in PCV3a, showing a close relationship with PCV3-US/SD2016. Surprisingly, we separately analyzed these PCV3 strains from the Guangxi province and found that the dog and pig PCV3 are from different branches. In summary, this was the first seroprevalence and genetic investigation of PCV3 in dogs in the Guangxi province, China, and the first complete genome PCV3 from dogs obtained in the world. The results provide insights into the epidemiology and pathogenesis of this important virus.