The detection of porcine circovirus 3 in Guangxi,China

Porcine circovirus type 3 (PCV 3) is a novel circovirus that was firstly detected in the USA . PCV 3 is associated with porcine dermatitis and nephropathy syndrome (PDNS ), reproductive failure and cardiac and multisystemic inflammation. Latterly, PCV 3 was detected in Guangxi, China. Forty‐one of 108 (37.96%) samples and nine of 47 (19.14%) samples were PCV 3 positive in pig farms and pig slaughter houses, respectively. Three PCV 3 strains were sequenced and designated PCV 3‐China/GX 2016‐1, PCV 3‐China/GX 2016‐2 and PCV 3‐China/GX 2016‐3. The complete genome of PCV 3‐China/GX 2016‐2 and PCV 3‐China/GX 2016‐3 is both 2,000 bp in length, while PCV 3‐China/GX 2016‐1 is of 1,999 bp and has a G deletion at position of 1,155 in its genome. The complete genome and capsid nucleotide of the three PCV 3 strains identified in this study shared 97.5%–99.4% and 96.7%–99.1% identities with that of the other PCV 3 strains available in NCBI , respectively. Phylogenetic analysis based on complete genome and capsid gene of 35 PCV 3 strains showed that the three PCV 3 sequences from Guangxi Province were divided into two clusters. The results of this study contribute to the understanding of PCV 3 molecular epidemiology.     

Genome characterization of a porcine circovirus type 3 in South China

Porcine circovirus type 3 (PCV 3) is a novel circovirus that was associated with porcine dermatitis and nephropathy syndrome, reproductive failure, and multisystemic inflammation. Recently, a PCV 3 strain was identified from pyretic and pneumonic piglets in Guangdong province, China. This virus strain was sequenced and designated PCV 3‐China/GD 2016. The complete genome of PCV 3‐China/GD 2016 is 2,000 bp in length and shared 99.1% and 99.1% nucleotide identities with PCV 3/29160 and PCV 3/2164, respectively. [Corrections added after initial online publication on 13 March 2017: The numbers ‘98.5%’ and ‘97.4%’ has been changed to ‘99.1%’ and ‘99.1%’ in the previous sentence.] Phylogenetic analysis based on the complete genome showed that PCV 3‐China/GD 2016 clustered with the emerging PCV 3 and separated with other virus in genus Circovirus . The results of this study suggest that PCV 3 has existed within the pigs of China. It is urgent to investigate the pathogenicity and epidemiology of this novel circovirus China.     

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.     

First detection of porcine circovirus type 3 on commercial pig farms in Poland

Porcine circovirus type 3 (PCV3) is a novel circovirus species recently discovered in USA and China in cases of porcine dermatitis and nephropathy syndrome, reproductive failure, respiratory disease and multisystemic inflammation. This study reports on the first identification of PCV3 in Europe, in serum from pigs from Polish farms. A total of 1,050 serum samples were collected between 2014 and 2017 from sows and 3–20 weeks old pigs from 14 commercial farms representing different regions of Poland, different size and health status. The samples were pooled by 4–6 and tested with real‐time PCR for PCV3. PCV3 DNA was detected in 12 of 14 farms (85.7%). On the PCV3‐positive farms, the virus was detected in 5.9% to 65% serum pools. PCV3 was most common among weaned pigs and finishers (26.1% and 28.0% of serum pools, respectively). Sequence analysis of 359 nucleotide fragment of ORF2 showed highest identity of 99.7% to PCV3‐US/SD2016 from USA. Our results indicate that PCV3 is a common virus among Polish pigs but no links to unexplained disease conditions were established.     

First detection and genetic analysis of fox‐origin porcine circovirus type 2

Porcine circovirus type 2 (PCV2) is a causative agent of porcine circovirus‐associated disease (PCVAD), which is a serious problem in the swine industry worldwide. In recent years, nonporcine‐origin PCV2 has attracted more and more attention of the researchers. This study reported on the first identification of PCV2 in farmed foxes with reproductive failure. Three fox‐origin PCV2 strains were successfully isolated, sequenced, and designated as FoxHB1, FoxHB2, and FoxHB3 respectively. Pairwise‐sequence comparisons of the complete genomes revealed that three fox‐origin PCV2 strains had nucleotide identities varied from 91.9% to 99.7% with representative strains of PCV2 different genotypes. Meanwhile, phylogenetic analysis based on complete genomes of 44 PCV2 strains indicated that the fox‐origin PCV2 strains belonged to Chinese epidemic genotypes PCV2b and PCV2d. These results provided the first supported evidence that PCV2 could infect foxes, implying that the cross‐species transmission of PCV2 would be a big threat to Chinese fur animal‐bearing industry.     

Molecular detection and phylogenetic analysis of porcine circovirus type 3 in 21 Provinces of China during 2015–2017

The emerging Porcine circovirus type 3 (PCV3) is associated with porcine dermatitis and nephropathy syndrome, reproductive failure and cardiac and multisystemic inflammation. To trace the prevalence and evolution of PCV3 in pigs with respiratory diseases or digestive diseases in China, 616 samples were collected from 21 provinces or municipalities of China from 2015 to 2017. All samples were analysed with PCR and a cap‐gene‐based phylogeny. The results indicated that the positive rate of PCV3 was 12.2% (75/616) at the sample level; 24.1% (42/174) at the farm level; 10.4% (50/480) in the digestive‐disease‐affected samples; 26.6% (25/94) in the respiratory‐disease‐affected samples; all 42 healthy samples were negative for PCV3. A statistical analysis showed that PCV3 infection was closely associated with both digestive diseases (p < 0.05) and respiratory diseases (p < 0.01). A sequence analysis revealed that the cap genes of the 51 PCV3 strains identified in our study shared nucleotide homologies of 97.2%–100% and amino acid homologies of 96.3%–100%. A total of 17 amino acid mutations were observed among the Cap proteins of the 51 PCV3 strains, of which R¹⁰/K, A²⁴/V, R²⁷/K, T⁷⁷/S, F¹⁰⁴/Y, I¹⁵⁰/L are mutations among worldwide strains. A phylogenetic analysis demonstrated that the 51 PCV3 strains formed three clades, including PCV3a (15/51, 29.4%), PCV3b (21/51, 41.2%) and PCV3c (15/51, 29.4%). These data provide evidence that PCV3 exhibits high prevalence and genetic diversity and is associated with digestive diseases and respiratory diseases in pig.     

Identification and genetic characterization of porcine circovirus type 3 in China

A novel circovirus called porcine circovirus type 3 (PCV3) was recently reported to exist in the USA. This circovirus is associated with porcine dermatitis, nephropathy syndrome and reproductive failure. This study reports on the first identification, widely epidemic, different phylogenetic clusters, potential role in sow reproductive failure and possible origins of PCV3 in China.     

Detection of porcine circovirus‐like virus P1 in Hebei,China

Porcine circovirus‐like virus P1 is a novel unclassified circovirus that was first detected in China and may be associated with post‐weaning multisystemic wasting syndrome (PMWS ) and congenital tremor. In this study, we detected P1 infection in pigs in Hebei Province, China, in 2017. One hundred and forty of 500 (28.0%) serum samples from 25 pig farms with different PMWS status in seven cities were P1 positive on PCR . Twelve P1 strains were sequenced, and the complete genomes of 11 P1 strains were 648 nucleotides (nt) in length, whereas that of strain ZJK 02 was 647 nt, with a G deletion at position of 183 in its genome. The complete genomic and capsid protein sequences of the 12 P1 strains analysed in this study shared 98.8%–100.0% and 86.5%–100.0% identity, respectively. A phylogenetic analysis based on the complete genomic and capsid sequences of 26 P1 strains showed that the 12 P1 sequences from Hebei Province clustered on two small branches. Further studies of the evolution and pathogenesis of P1 are required.     

Insights into the epidemic characteristics and evolutionary history of the novel porcine circovirus type 3 in southern China

Porcine circovirus type 3 (PCV 3) is a newly identified circovirus from swine in the USA , China and Poland. This novel circovirus has been associated with porcine dermatitis and nephropathy syndrome (PDNS ), reproductive failure and multisystemic inflammation; moreover, PCV 3 poses a potential threat to the swine industry. In this retrospective study, a phylogenetic analysis was conducted to address the epidemiology and evolutionary dynamics of this novel circovirus. The total positive sample rate of PCV 3 was 26.7% (76/285) and has increased gradually over the past 3 years. Of these PCV 3‐positive samples, 22.3% (17/76) were coinfected with PCV 2. PCV 3 can be detected in multiple sample types with different positive rates, and the positive rate is highest among stillborn. We also divide PCV 3 into three clades (PCV 3a, PCV 3b and PCV 3c) based on two amino acid mutations (A24V and R27K) on the cap protein in this study. In addition, the origin of PCV 3 was approximately 1966 and may have originated from a bat‐associated circovirus. Our results suggested that PCV 3 is widely distributed in southern China and has been circulating in swine herds for nearly half a century. PCV 3 has evolved into different clades caused by mutations in cap proteins; thus, further research on PCV 3 epidemiology should be conducted.     

Detection and genome sequencing of porcine circovirus 3 in neonatal pigs with congenital tremors in South China

Porcine circovirus 3 (PCV3) is a novel circovirus first discovered in the United States in piglets and sows with porcine dermatitis and nephropathy syndrome, reproductive failure, cardiac and multisystemic inflammation. Here, seven PCV3 strains were identified for the first time from neonatal pigs with clinical signs of congenital tremors (CT) in South China. The tissue tropism of PCV3 in CT‐affected piglets was analysed by the real‐time quantitative PCR, and the result showed that high loads of viral genomes were detected in the brains and hearts. The complete genomes of seven new PCV3 revealed 96.8%–99.6% nucleotide identities with eleven other PCV3 strains previously reported from the United States and China. Phylogenetic analysis based on the complete genome sequences showed that all PCV3 strains clustered together and were clearly separated from other circovirus species. This study reports on the first identification of PCV3 in CT‐affected newborn piglets and provides the epidemiological information of neonatal piglets with CT in Guangdong and Guangxi Provinces of China.     

Detection and genetic characterization of porcine circovirus 3 (PCV3) in pigs in India

Porcine circovirus type 3 (PCV3), a novel circovirus, has been reported recently from major swine growing countries globally, and the virus is associated with diseases like porcine dermatitis, nephropathy syndrome and reproductive failure. This report describes the identification of PCV3 associated with reproductive failure in sows and piglet mortality and circulation of the virus in healthy pigs in India. The pathological changes in various tissues from stillborn piglet and characterization of the virus genomes were reported. The genome sequences of Indian PCV3 strains showed 91.4%–99.8% nucleotide identity with other sequences of PCV3 strains circulating worldwide. The phylogenetic analysis showed clustering of Indian strains into a separate group with the isolate from USA (MN/2016) under PCV3a genotype. The results confirmed the circulation of PCV3 in Indian pigs and its association with clinical cases. This study speculates emergence of PCV3 as an important pig pathogen in the country, which warrants the thorough investigation on PCV3 epidemiology, pathogenesis and to implement the control measures.     

Epidemiological investigation and phylogenetic analysis of caprine parainfluenza virus type 3 in sheep of China

Caprine parainfluenza virus type 3 (CPIV3) is a new member of the Respirovirus genus in the Paramyxivirudae family, mainly causing respiratory disease. Up to now, accumulating evidence has focused on CPIV3 infection in goats, with little understood about its epidemiology in sheep. To that end, we collected 1,163 sheep sera samples from nine provinces/autonomous regions in 2012 and 1,863 samples from six provinces/autonomous regions during 2016–2017, with serological prevalence of 50.3% (95% CI: 47.5, 53.3) and 64.9% (95% CI: 62.9, 67.2), respectively. Pathogenic detection by qRT‐PCR was also performed on serum samples collected in 2016–2017, and the percentage of CPIV3 positive samples was 21.5% (95% CI: 19.7, 23.5). Sequence alignment and phylogenetic analyses revealed 11 novel CPIV3 strains based on the M gene sequences. The M gene and full‐length sequences of CPIV3 strains derived from sheep shared high nucleotide similarity with goat‐origin strains, indicating conserved genome characteristics between the viruses. Furthermore, sequence evolution and epidemiological analysis show that CPIV3 is widespread throughout China. This is the first report describing CPIV3 infection in sheep in China, showing a high sero‐prevalence and contributes to the assessment of the epidemiology of CPIV3 in China.     

Phylogenetic and genetic variation analyses of porcine circovirus type 2 isolated from China

Porcine circovirus type 2 (PCV 2) is a causative agent of PCV 2‐associated disease, which is a growing problem in the swine industry worldwide. High nucleotide substitution occurs in the capsid (Cap) gene of PCV 2, which allows the continuous evolution and the emergence of novel PCV 2 strains. In this study, we sequenced 24 Chinese PCV 2 strains collected from healthy and diseased pigs between 2013 and 2015. Analyses of the genome, Cap and phylogeny classified the 24 Chinese PCV 2 strains as PCV ‐2a (four of 24), PCV ‐2b (five of 24) and PCV ‐2d (15 of 24). All strains shared 89.5%–100% and 87.2%–100% identities with the nucleotide and amino acid (aa) sequences of Cap, respectively. Selection pressure analysis showed that five sites at the epitope regions in Cap were under positive selection. Further analysis by Jameson–Wolf antigenic index indicated that aa substitutions occurring at the epitope regions contributed to the antigenic alterations of the different PCV 2 strains. High genetic variation and genotype shift to PCV 2d occurred in recent years, and different genotypes coexisted in Chinese pig herds. The data provide evidence for the increased genetic diversity and insights into the molecular epidemiology of PCV 2.     

Detection and genetic characterization of Porcine circovirus type 3 in Italy

Porcine circovirus type 3 (PCV3) was recently proposed as a new porcine circovirus. It has been described by researchers in the USA and China and associated with porcine dermatitis and nephropathy syndrome, reproductive failure and systemic inflammation disease. The study reports the occurrence of the new virus in Italy. PCV3 was detected in the tissues of foetuses and stillborn piglets coming from two farms located in the Po Valley. The genome sequences of the two Italian strains share 99.7% to 97.8% of nucleotide identity with those available in GenBank. Results strengthen the hypothesis of PCV3 as a new emerging porcine circovirus, widespread all over the world. It follows the urgency of investigating in depth epidemiology and pathogenicity associated with this new virus.     

Detection and phylogenetic analysis of porcine bocaviruses carried by murine rodents and house shrews in China

Bocaparvovirus infections of humans and both wild and domestic animals have been widely reported around the world. In this study, we detected and genetically characterized porcine bocavirus (PBoV) carried by murine rodents (Rattus norvegicus, Rattus tanezumi, and Rattus losea) and house shrews (Suncus murinus) in China. Between May 2015 and May 2017, 496 murine rodents and 23 house shrews were captured in four Chinese provinces. Nested polymerase chain reaction was used to investigate the prevalence of PBoV in throat swab, faecal and serum samples. A total of 7.5% (39/519) throat swab samples, 60.5% (309/511) faecal samples, and 22.9% (52/227) serum samples were PBoV‐positive. The prevalence among R. norvegicus and R. tanezumi was higher than that among R. losea and house shrews. PBoV‐positive samples were found in all four provinces. Phylogenetic analysis based on partial viral capsid protein 1/2 (VP1/VP2) showed that sequences obtained in this study formed a novel group (PBoV G4). In addition, five near full‐length PBoV genomes (4,715–4,798 nt) were acquired. These genomes encoded two non‐structural proteins, NS1 (1,908 nt in four genomes and 1,923 nt in the remaining genome) and NP1 (600 nt), and the structural proteins, VP1/VP2 (1,851 nt). Phylogenetic analysis showed that PBoV G4 is distinct from rodent, human, and other bocaviruses. In conclusion, PBoV G4 prevalence was high among two common murine rodents in China, and the pathogenecity of PBoV G4 need to be further clarified.     

Retrospective study of porcine circovirus 3 infection in China

PCV 3 is an emerging swine virus associated with porcine dermatitis and nephropathy syndrome (PDNS ), reproductive failure, respiratory diseases and systematic inflammation. Although first identified in 2015, the earliest case has been traced back to 2009 in the United States. In China, PCV 3 infection was first detected in 2015, but little information has been available about its occurrence and prevalence there before 2015. In this study, 200 porcine clinical samples collected from 20 provinces, five autonomous regions and four municipalities between 1990 and 1999 were analysed for PCV 3 infection by PCR . Results showed that 6.5% of the porcine samples collected from eight provinces and one autonomous region were PCV 3 positive, with the earliest cases occurring in 1996. Nucleotide sequence analysis showed that PCV 3 strains obtained in this study shared 96.6%–99.7% and 97.1%–99.4% sequence identity at the ORF 2 gene and genome levels with all available reference strains from China and other countries, indicating the high genetic stability of PCV 3 over the past 20 years.     

The occurrence of porcine circovirus 3 without clinical infection signs in Shandong Province

Porcine circovirus type 3 (PCV3) was detected in Shandong, China. One hundred and thirty‐two of 222 (59.46%) samples were PCV3 positive, while 52 of 132 (39.39%) samples were co‐infected with PCV2. There were no clinical signs of infection in either multiparous sows or live‐born infants. Two strains of PCV3 were indentified from natural stillborn foetuses. Phylogenetic analysis showed the two strains of PCV3 are 96% identical to the known PCV3/Pig/USA (KX778720.1, KX966193.1 and KX898030.1) and closely related to Barbel Circovirus. Further studies of the epidemiology of PCV3 and the co‐infection with PCV2 are needed.     

Presence of Torque teno sus virus 1 and 2 in porcine circovirus 3‐positive pigs

In this study, the co‐infection of Torque teno sus virus (TTS uV) and porcine circovirus type 3 (PCV 3) was reported. One hundred and ten of 132 (83.3%) PCV 3‐positive samples were co‐infected with Torque teno sus virus 1 (TTS uV1). Ninety‐four of 132 (71.2%) PCV 3‐positive samples were co‐infected with Torque teno sus virus 2 (TTS uV2). Sixty‐six of 132 (50.0%) of PCV 3‐positive samples were co‐infected with both TTS uV1 and TTS uV2. There were no clinical signs of infection in pigs that were both PCV 3‐positive and PCV 2‐negative, in either multiparous sows or live‐born infants. The high co‐infection rate provides valuable information for the further study of the pathological correlation between PCV 3 and TTS uVs.     

Similar frequency of Porcine circovirus 3 (PCV‐3) detection in serum samples of pigs affected by digestive or respiratory disorders and age‐matched clinically healthy pigs

Porcine circovirus 3 (PCV‐3) has been identified in pigs affected by different disease conditions, although its pathogenicity remains unclear. The objective of the present study was to assess the frequency of PCV‐3 infection in serum samples from animals suffering from post‐weaning respiratory or digestive disorders as well as in healthy animals. A total of 315 swine serum samples were analysed for PCV‐3 DNA detection by conventional PCR; positive samples were further assayed with a quantitative PCR and partially sequenced. Sera were obtained from 4 week‐ to 4 month‐old pigs clinically diagnosed with respiratory (n = 129) or digestive (n = 126) disorders. Serum samples of age‐matched healthy animals (n = 60) served as negative control. Pigs with clinical respiratory signs had a wide variety of pulmonary lesions including suppurative bronchopneumonia, interstitial pneumonia, fibrinous‐necrotizing pneumonia and/or pleuritis. Animals with enteric signs displayed histopathological findings like villus atrophy and fusion, catarrhal enteritis and/or catarrhal colitis. Overall, PCV‐3 DNA was detected in 19 out of 315 analysed samples (6.0%). Among the diseased animals, PCV‐3 was found in 6.2% (8 out of 129) and 5.6% (7 out of 126) of pigs with respiratory and digestive disorders, respectively. The frequency of PCV‐3 PCR positive samples among healthy pigs was 6.7% (4 out of 60). No apparent association was observed between PCR positive cases and any type of histopathological lesion. The phylogenetic analysis of the partial genome sequences obtained showed high identity among viruses from the three groups of animals studied. In conclusion, PCV‐3 was present in the serum of diseased and healthy pigs to similar percentages, suggesting that this virus does not seem to be causally associated with respiratory or enteric disorders.     

Emergence of a novel recombinant porcine circovirus type 2 in China: PCV2c and PCV2d recombinant

Porcine circovirus type 2 (PCV2) has been causing huge economic losses in Chinese swine herds since it was first identified in China in 1999. Genotypes of PCV2 except for PCV2c coexist in swine herds in China, which may facilitate virus recombination. In the current study, six novel PCV2 strains were detected in China, and these strains shared high nucleotide similarity of the Rep gene with the PCV2c strain DK1987PMWSfree and high homology of the Cap gene with PCV2d. Genome sequence analysis revealed that the complete genomes of these strains were 1767 nucleotides (nt) in length and shared 99.8%–99.9% nucleotide identity with each other and 91.7%–98.7% with representative strains. Phylogenetic analysis, sequencing analysis, base‐by‐base comparisons and comprehensive recombination analysis demonstrated that these six strains originated from recombination within the Rep gene between PCV2c and PCV2d strains. Surprisingly, further investigation through theoretical recombination analysis of Chinese PCV2 GenBank sequences showed that these novel patterns of recombinant PCV2 strains have been generated since 2010. Collectively, our findings provide additional evidence of inter‐genotypic recombination of PCV2.