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

Molecular Detection and Genetic Characterization of Vertically Transmitted Viruses in Ducks

To investigate the distribution and genetic variation in four vertically transmitted duck pathogens, including duck hepatitis B virus (DHBV), duck circovirus (DuCV), duck hepatitis A virus 3 (DHAV-3), and avian reoviruses (ARV), we conducted an epidemiology study using PCR and RT-PCR assays on a duck population. We found that DHBV was the most prevalent virus (69.74%), followed by DuCV (39.48%), and then ARV (19.92%) and DHAV-3 (8.49%). Among the 271 duck samples, two, three or four viruses were detected in the same samples, indicating that the coinfection of vertical transmission agents is common in ducks. The genetic analysis results showed that all four identified DuCV strains belonged to genotype 1, the DHAV-3 strain was closely clustered with previously identified strains from China, and the ARV stain was clustered under genotype 1. These indicate that different viral strains are circulating among the ducks. Our findings will improve the knowledge of the evolution of DuCV, DHAV-3, and ARV, and help choose suitable strains for vaccination.

Porcine IGFBP3 promotes porcine circovirus type 2 replication via PERK/eIF2α mediated DNA damage

The infection of porcine circovirus type 2 (PCV2) triggers activation of the protein kinase RNA-like endoplasmic reticulum kinase (PERK) pathway and leads to DNA damage. Insulin-like growth factor-binding protein 3 (IGFBP3) may interact with the endoplasmic reticulum (ER). It remains unclear whether IGFBP3 regulates DNA damage via ER stress to mediate PCV2 replication. In this study, we observed an upregulation of porcine IGFBP3 expression during PCV2 infection, and overexpression of IGFBP3 enhanced the expression of PCV2 Cap protein, PCV2 DNA copy number, and viral titers in PK-15 B6 cells and 3D4/21 cells. Additionally, overexpression of IGFBP3 induced an increase in the DNA damage marker γH2AX by activating the PERK/eIF2α pathway without concomitant activation of ATF4, IRE1α, and ATF6α/GRP78 pathways in PK-15 B6 cells and 3D4/21 cells. Knockdown of IGFBP3 had a reverse effect on PCV2 replication in PK-15 B6 cells and 3D4/21 cells. Furthermore, treatment with etoposide enhanced PCV2 replication while KU57788 decreased it. GSK2606414 and salubrinal limited both DNA damage and viral replication. Therefore, our findings suggest that porcine IGFBP3 promotes PCV2 replication through the PERK/eIF2α pathway-mediated induction of DNA damage in PK-15 B6 cells and 3D4/21 cells. Our study provides a basis for exploring novel antiviral strategies via the extensive understanding of the relationships between host cellular proteins and viral replication.

Emergence of novel porcine circovirus 2d strains in Thailand, 2019-2020

Porcine circovirus 2 (PCV2) has been recognized as a causative agent of porcine circovirus diseases (PCVDs) affecting the global swine industry. In this study, the genetic diversity of PCV2 strains circulating in Thailand between 2019 and 2020 was investigated using 742 swine clinical samples from 145 farms. The results showed PCV2-positive rates of 54.2% (402/742) and 81.4% (118/145) at the sample and farm levels, respectively. Genetic analysis of 51 Thai PCV2 genomic sequences showed that 84.3% (43/51) was PCV2d, 13.7% (7/51) was PCV2b and 1.9% (1/51) was PCV2b/2d recombinant virus. Surprisingly, the majority of the Thai PCV2d sequences from this study (69.77%, 30/43) formed a novel cluster on a phylogenetic tree and contained a unique ¹³³HDAM¹³⁶ on the ORF2 deduced amino acid sequence, which is in one of the previously identified immunoreactive domains strongly involved in virus neutralization. The PCV2b/2d recombinant virus also carried ¹³³HDAM¹³⁶. The emergence of the novel PCV2d strains predominating in Thailand was discussed. This study highlights the need for further investigations on the spreading of these PCV2d strains in other regions and the efficacy of current commercial vaccines.

Molecular genotypic analysis of porcine circovirus type 2 reveals the predominance of PCV2d in Vietnam (2018-2020) and the association between PCV2h, the recombinant forms, and Vietnamese vaccines

We conducted nucleotide and amino acid sequence alignment and phylogenetic analysis of porcine circovirus ORF2 (Cap protein) from 17 PCV2-positive clinical samples from nine different northern Vietnamese provinces (Mar 2018-Nov 2020), four local vaccines, and 77 reference strains. We identified one PCV2a (1/17 = 5.9%), five PCV2b (5/17 = 29.9%), and 11 PCV2d (11/17 = 64.7%) isolates, while only PCV2d was detected in 2020. Timeline analysis indicated an increasing predominance of PCV2d nationwide (2018-2020). With strong nodal support (98% for nucleotides and 74% for amino acids), the phylogenetic tree topology revealed a distinct PCV2h clade including recombinant/intermediate strains and local vaccines. The Cap protein sequences from 11 PCV2d field strains had the 2d-genotype-typical motif ⁸⁶SNPLSV⁹¹ in loop CD, the motif TGID in loop GH-HI, and the motif ²³⁰PLNPK²³⁴ in loop CT. The PCV2h isolates (and vaccines) had the ⁸⁶SNPLSV⁹¹, SAID, and ²³⁰L(N/H)PK²³⁴ motifs. Selection pressure analysis indicated positive selection at seven sites: A⁶⁸N in immunoreactive region (IRR)-A; ¹¹⁹G and ¹³⁰V in IRR-B; and ¹⁶⁷L, T¹⁹⁰(A/S), ¹⁹⁴D and ²⁰²F in IRR-C. We identified PCV2h as the genotype of the recombinant strains, which resulted from intergenotype recombination of PCV2a, PCV2b, and PCV2d. The current data provide new information about the diversity, distribution, and dominance of the PCV2 genotype in Vietnam.

A Review of Pseudorabies Virus Variants: Genomics, Vaccination, Transmission, and Zoonotic Potential

Pseudorabies virus (PRV), the causative agent of Aujeszky’s disease, has a broad host range including most mammals and avian species. In 2011, a PRV variant emerged in many Bartha K61-vaccinated pig herds in China and has attracted more and more attention due to its serious threat to domestic and wild animals, and even human beings. The PRV variant has been spreading in China for more than 10 years, and considerable research progresses about its molecular biology, pathogenesis, transmission, and host–virus interactions have been made. This review is mainly organized into four sections including outbreak and genomic evolution characteristics of PRV variants, progresses of PRV variant vaccine development, the pathogenicity and transmission of PRV variants among different species of animals, and the zoonotic potential of PRV variants. Considering PRV has caused a huge economic loss of animals and is a potential threat to public health, it is necessary to extensively explore the mechanisms involved in its replication, pathogenesis, and transmission in order to ultimately eradicate it in China.

Molecular detection and phylogenetic analysis of pigeon circovirus from racing pigeons in Northern China

Background

Pigeon circovirus (PiCV) infections in pigeons (Columba livia) have been reported worldwide. Currently, pigeon racing is becoming increasingly popular and considered to be a national sport in China, and even, the greatest competitions of racing pigeons are taking place in China. However, there are still no epidemiologic data regarding PiCV infections among racing pigeons in China. The purpose of our study was to provide information of prevalence, genetic variation and evolution of PiCV from racing pigeons in China.

Results

To trace the prevalence, genetic variation and evolution of PiCV in sick and healthy racing pigeons, 622 samples were collected from 11 provinces or municipalities in China from 2016 to 2019. The results showed that the positive rate of PiCV was 19.3% (120/622) at the sample level and 59.0% (23/39) at the club level, thus suggesting that the virus was prevalent in Chinese racing pigeons. A sequence analysis revealed that the cap genes of the PiCV strains identified in our study displayed a high genetic diversity and shared nucleotide homologies of 71.9%–100% and amino acid homologies of 71.7%–100%. 28 and 36 unique amino acid substitutions were observed in the Cap and Rep proteins derived from our PiCV strains, respectively. A cladogram representation of PiCV strains phylogeny based on 90 cap gene sequences showed that the strains in this study could be further divided into seven clades (A, B, C, E, G, H, and I) and some of them were closely related to worldwide strains from different types of pigeons. A large number of recombination events (31 events) were also detected in the PiCV genomes from Chinese racing pigeons.

Conclusions

These findings indicate that PiCV strains circulating in China exhibit a high genetic diversity and also contribute to information of prevalence, genetic variation and evolution of PiCV from racing pigeons in China.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08425-8.

Whole-Genome Analysis of Porcine Circovirus Type 2 in Russia

Porcine circovirus type 2 (PCV2) is the causative agent of porcine circovirus-associated diseases (PCVAD) that bring about significant economic losses in the pig industry all over the world. The aim of this study was to investigate the genetic diversity of PCV2 in Russia and characterize the available complete genome sequences. PCV2 DNA was detected at all investigated farms located in different regions of Russia. Whole-genome analysis demonstrated that the majority of PCV2 strains belonged to genotype PCV2d (12 out of 14), while PCV2a and PCV2b were only detected at 2 farms (one at each). Further analysis revealed that all antibody recognition sites in Russian PCV2 strains were different from the corresponding epitopes in a PCV2a vaccine strain, suggesting that PCV2a-based vaccines may only provide limited protection against these strains. PCV2d strains could be grouped into 3 distinct lines which shared 98.7-100% identity within open reading frame 2 (ORF2). It is the first study reporting the genetic diversity of PCV2 strains in Russia. Our data indicated that, similarly to China, Europe, and USA, PCV2a and PCV2b have largely been replaced by PCV2d.

Expression and evaluation of porcine circovirus type 2 capsid protein mediated by recombinant adeno-associated virus 8

Background

Porcine circovirus type 2 (PCV2) is an important infectious pathogen implicated in porcine circovirus-associated diseases (PCVAD), which has caused significant economic losses in the pig industry worldwide.

Objectives

A suitable viral vector-mediated gene transfer platform for the expression of the capsid protein (Cap) is an attractive strategy.

Methods

In the present study, a recombinant adeno-associated virus 8 (rAAV8) vector was constructed to encode Cap (Cap-rAAV) in vitro and in vivo after gene transfer.

Results

The obtained results showed that Cap could be expressed in HEK293T cells and BABL/c mice. The results of lymphocytes proliferative, as well as immunoglobulin G (IgG) 2a and interferon-γ showed strong cellular immune responses induced by Cap-rAAV. The enzyme-linked immunosorbent assay titers obtained and the IgG1 and interleukin-4 levels showed that humoral immune responses were also induced by Cap-rAAV. Altogether, these results demonstrated that the rAAV8 vaccine Cap-rAAV can induce strong cellular and humoral immune responses, indicating a potential rAAV8 vaccine against PCV2.

Conclusions

The injection of rAAV8 encoding PCV2 Cap genes into muscle tissue can ensure long-term, continuous, and systemic expression.

Genetic and phylogenetic analysis of porcine circovirus type 2 on Jeju Island, South Korea, 2019-2020: evidence of a novel intergenotypic recombinant

Porcine circovirus type 2 (PCV2) is the most ubiquitous viral pathogen of pigs and has persistently affected the global swine industry. Since first being identified in South Korea in 1999, the virus has undergone considerable genetic change and genotype shifts during the past two decades. These events have contributed to the coexistence of genotypes PCV2a, PCV2b, and PCV2d in Korean pig populations, which may promote viral recombination. The genotypic and phylogenetic characteristics of PCV2 strains circulating in pig herds on Jeju Island from 2019 to 2020 were the focus of this study. Genotype-specific PCR indicated that PCV2d is the dominant viral genotype and that coinfections with PCV2d and PCV2a (75%) or PCV2a and PCV2b (25%) are common in provincial pig herds. The complete genome sequences of 11 PCV2 strains, including three PCV2a, two PCV2b, and six PCV2d strains, were determined. A genomic comparison showed that all of the viruses had the highest nucleotide sequence identity to their corresponding genotypic reference strain. Notably, genetic and phylogenetic analysis revealed that one PCV2d strain, KNU-1931, exhibited nucleotide sequence variation in the ORF1 gene when compared to other PCV2d strains but showed a high degree of similarity to the PCV2b strains. Comprehensive recombination analysis suggested that KNU-1931 originated from natural recombination within ORF1 between PCV2b (the minor parent) and PCV2d (the major parent) strains. Our findings provide information about the frequency of genetic recombination between two different PCV2 genotypes circulating in the field domestically, illustrating the importance of continual intergenotypic recombination for viral fitness when multiple genotypes are present.

Evidence of porcine circovirus type 2 and co-infection with ungulate protoparvovirus 1 (porcine parvovirus) in mummies and stillborn piglets in subclinically infected farm

Porcine circovirus type 2 (PCV2) and protoparvovirus 1 (PPV) were detected as single infection (6/131) and (11/131) respectively, or co-infection (6/131) in fetuses and stillborn piglets from normal deliveries in a farm without reproductive problems. Twenty in twenty-three positive samples were over 70 days of gestation, which is when the fetus becomes immunocompetent, and the presence of a NADL-2 PPV strain suggests fetal immune system impairment. Phylogenetic analysis of sequences obtained showed that 8/9 sequences are related to cluster 13 and the remaining is grouped into cluster 11 sequences. An increase in variability in ORF2 sequences in Argentina was observed. It is not clear whether the detection of fetuses positive to PPV and PCV2 is of epidemiological importance in a subclinically affected farm. However, the results of this study showed that currently used vaccines and vaccine protocols do not fully protect against PPV or PCV2 fetus infection.

Molecular characteristics of a novel duck circovirus subtype 1d emerging in Anhui, China

The frequency of infection of duck circovirus (DuCV) in Anhui province, China is not well-characterized. Therefore, in this study, we collected 69 samples from sick ducks and tested them for the presence of DuCV by conventional polymerase chain reaction (PCR) analysis. The complete viral genomes of five DuCV strains from five different cities were randomly selected, amplified via PCR, sequenced, and subjected to recombination analysis. The five DuCV genomes were named as AHAU9, AHAU25, AHAU28, AHAU37, and AHAUHQ. We found that 36.2 % of the ducks were infected with DuCV. The five DuCV strains had genome lengths ranging from 1987 to 1995 nucleotides, with a sequence similarity of 81.8-98.2 %. Among them, AHAU28, AHAU37, and AHAUHQ were closely related to the reference strain YF180403, GX1105 strain, and wd2015028 of DuCV, respectively. AHAU9 and AHAU25 were found to belong to a new DuCV subtype, DuCV-1d. Moreover, recombination analysis showed that the DuCV-1d subtype strains had the same recombination pattern. These results improve the understanding of the frequency of DuCV infection in Anhui province. Our findings may be useful for preventing and controlling the spread of DuCV.

Emergence of a novel pathogenic recombinant virus from Bartha vaccine and variant pseudorabies virus in China

Pseudorabies virus (PRV), the causative agent of Aujeszky's disease, has resulted in substantial economic losses in the swine industry worldwide. Previous reports have shown that the PRV variant is responsible for the Pseudorabies outbreaks in Bartha-K61-vaccinated farms in China. However, there is limited information about the evolution of recombination of the PRV variant. Here, we isolated two PRV variants from a Bartha-K61-vaccinated swine farm, named them the JSY7 and JYS13 strains, analysed their complete genomic sequences and evaluated pathogenicity. As results, the JSY7 and JSY13 strains showed different cytopathic effects and plaque sizes. The JSY7 and JSY13 strains had the same Aspartate insertions in the gE protein as other PRV variants. The JSY7 and JSY13 strains were clustered into the same clade based on a genomic phylogenetic analysis. However, the JSY7 strain was relatively close to recent PRV isolates in China, while the JSY13 strain was more closely related to earlier PRV isolates. Interestingly, the gC gene phylogenetic tree showed that the JSY7 strain belonged to genotype II lineage 3, while the JSY13 strain belonged to genotype I and is the same branch with the Bartha strain. Furthermore, the PRV variants were relatively distant from the Bartha strain in the phylogenetic analysis of the gB, gC and gD genes. Importantly, a recombination analysis showed that the JSY13 strain might be a natural recombinant between the minor parental genotype I Bartha strain and the major parental genotype II JSY7 strain. Finally, we also found that the JSY13 strain showed a moderate virulence compared to the JSY7 strain in mice. Taken together, our data provide direct evidence for genomic recombination of PRV in nature, which may play an important role in the evolution and virulence of PRV. This discovery suggests that live PRV vaccine can act as genetic donors for genomic recombination.

Genetic analysis of porcine circovirus type 2 (PCV2) in Queensland, Australia

OBJECTIVE

To determine the current porcine circovirus type 2 (PCV2) genotypes circulating in pigs in Queensland (QLD).

METHODS

The PCV2 infection status of pigs was determined by real-time PCR testing of 210 lymph nodes and 30 serum samples derived from 45 QLD farms. PCV2-positive samples from 22 pigs from 15 farms were subjected to conventional polymerase chain reaction (PCR) and sequencing of the full PCV2 genome. Phylogenetic analysis of 17 of these sequences in relation to published PCV2 sequences was then performed, and the genotypes were compared.

RESULTS

PCV2 DNA was detected in 95 lymph nodes and 15 serum samples. Phylogenetic analysis of 17 PCV2 sequences demonstrated that seven belonged to genotype PCV2b, two to PCV2d, one to PCV2f and seven to an "intermediate group" that clustered with PCV2d on the full genome analysis.

CONCLUSION

This work confirms earlier studies reporting the presence of PCV2b in Australia. It is the first study to report that PCV2d and PCV2f are also present in this country. PCV2d is currently a fast-spreading genotype globally, with reported high virulence. The potential implications of these findings with respect to pathogenicity and vaccine efficacy require further investigation.

High rates of detection and complete genomic analysis of porcine circovirus 2 (PCV2) in the Lesser Antilles island of St. Kitts: Identification of PCV2b-PCV2d recombinants

Although porcine circovirus 2 (PCV2) is an economically important pathogen of swine, there is a lack of information on PCV2 from the Lesser Antilles. In this retrospective study, we report high rates of detection of PCV2 DNA in porcine faecal (41.3%, 26/63) and kidney (32.8%, 20/61) samples from the Lesser Antilles island of St. Kitts. Most of the PCV2-positive faecal samples were from diarrhoeic piglets (23/26), with 15 animals exhibiting stunted growth and/or weight loss. Although the PCV2-positive kidneys were from slaughter age, clinically healthy pigs, microscopically, various degrees of inflammation (mild, moderate or severe) were observed in 18 kidneys. Rotavirus-A, porcine parvovirus and torque teno sus virus were detected in 2, 4 and 14 PCV2-positive samples, respectively. The complete genomes of 18 St. Kitts PCV2 strains were amplified using three overlapping nested PCR assays designed in the present study. By phylogenetic analysis of PCV2 open reading frame 2 (ORF2) and complete genomes, 15 St. Kitts strains were assigned to genotype PCV2b. The remaining three PCV2 strains were identified as PCV2b-PCV2d recombinants, with the involvement of ORF2 in two of the strains. To our knowledge, this is the first report on detection and genotyping of PCV2 strains from the Lesser Antilles. Considering the significant contributions of pig farming to the regional livestock economy and increasing demand for local pork in the Lesser Antilles, our findings emphasize the importance of future studies on surveillance and genotyping of PCV2 in other Caribbean islands of the region.