Porcine circovirus-like virus P1 in cattle, goats and rabbits in China

Vertical transmission of porcine circovirus-like virus P1 in BALB/c mice

BACKGROUND

Porcine circovirus-like virus P1 is the animal virus with the smallest genome discovered so far, and it has become widely distributed in the Chinese mainland in recent years.

RESULTS

In this study, a BALB/c mouse model was used to reveal P1 infection in female reproductive systems and the vertical transmission of the virus. The female reproductive system, including the ovary and uterus, was harvested on day 14 postinfection and examined for pathological lesions. One-day-old mice without colostrum born from infected or uninfected mothers were collected, and P1 virus distribution in the different organs was investigated. During the trials, all the mice showed no clinical symptoms or gross lesions. However, stillbirth did occur in groups infected with the P1 virus. P1 nucleic acid was detected in the heart, liver, spleen, lung, kidney, and brain tissues of 1-day-old mice born from infected mice. Microscopic lesions in P1-infected female mice were characterized by necrosis of the ovarian follicular granulosa cells and abscission, follicular atresia, necrosis of the endometrial epithelial and uterine glandular epithelial cells, and hyperplasia of the squamous endometrial epithelium. The spermatocytes in the seminiferous tubules of the infected male mice were disorderly arranged, and the germ and Sertoli cells were shed, necrotic, and decreased in number. Immunohistochemical results identified P1-positive particles in the nucleus and cytoplasm of cells from the ovary and uterus of female mice.

CONCLUSIONS

This study shows that the P1 virus could cause pathological damage to the reproductive system of female mice and could be transmitted vertically.

First detection and complete genome analysis of porcine circovirus-like virus P1 and porcine circovirus-2 in yak in China

Porcine circovirus-like virus P1, like porcine circovirus type 2 (PCV2), is a potential pathogen of post-weaning multisystemic wasting syndrome in swine. Yaks are a valuable species and an iconic symbol of the Tibet Plateau which is the highest and largest plateau in the world. In this study, a total of 105 yak diarrheal samples, collected from 13 farms in Linzhi in the Tibet Plateau from January 2019 to December 2021, that were screened for P1 and PCV2 by polymerase chain reaction, 10.48% (n = 11) were positive for P1, 4.76% (n = 5) for PCV2, and 5.71% (n = 6) were positive for coinfection of P1 and PCV2. In addition, the whole genomes of eight P1 strains and eight PCV2 strains were sequenced. Alignment of deduced amino acid sequences of P1 ORF1 and PCV2 ORF2 gene revealed that ON012566 had one unique amino acid mutation at residues 137 (T to P). This mutation has important implication for the study of virus virulence, tissue tropism, and immune response. Phylogenetic analysis shows that the yak-origin P1 strains in this study with cattle-origin P1 reference strains were grouped into one cluster. The yak-origin PCV2 (ON012566) and a buffalo-origin PCV2 (KM116514) reference strain clustered in the same branch in the PCV2b regions. Meanwhile, the remaining PCV2 strains and buffalo-origin PCV2 reference strain (ON012565) clustered in the PCV2d regions. To summarize, to our knowledge, this is the first report on the molecular prevalence and genome characteristics of P1 and PCV2 in yaks in the world and will contribute to further study of the molecular epidemiology, source, and evolution of P1 and PCV2 strains.

Nearly 20 Years of Genetic Diversity and Evolution of Porcine Circovirus-like Virus P1 from China

Porcine circovirus-like virus P1 can infect many kinds of animals and mainly causes postweaning multisystemic wasting syndrome. In China, the genetic diversity, variation, and evolutionary processes of this virus have not been described yet. To improve our knowledge of its genetic diversity, evolution, and gene flow, we performed a bioinformatics analysis using the available nucleotide sequences of the P1 virus; among them, 12 nucleotide sequences were from ten pig farms in Jiangsu Province in this epidemiological survey, and 84 sequences were downloaded from GenBank. The P1 sequences showed a rich composition of AT nucleotides. Analyses of the complete genomic sequences were polymorphic and revealed high haplotype (gene) diversity and nucleotide diversity. A phylogenetic analysis based on the NJ method showed that all P1 virus sequences formed two distinct groups: A and B. High genetic differentiation was observed between strains from groups A and B. The codon usage pattern of P1 was affected by dinucleotide compositions. Dinucleotide UU/CC was overrepresented, and dinucleotide CG was underrepresented. The mean evolutionary rate of the P1 virus was estimated to be 3.64 × 10−4 nucleotide substitutions per site per year (subs/site/year). The neutrality tests showed negative values. The purifying selection and recombination events may play a major driving role in generating the genetic diversity of the P1 population. The information from this research may be helpful to obtain new insights into the evolution of P1.

Genomic Rearrangement and Recombination of Porcine Circovirus Type 2 and Porcine Circovirus-Like Virus P1 in China

Porcine circovirus type 2 (PCV2) belongs to the genus Circovirus of the family Circoviridae, and it has been associated with porcine circovirus (associated) disease (PCVD or PCVAD) in pigs. PCVAD is the generic term for a series of disease syndromes that have caused economic losses to the pig industry worldwide. Since the discovery of PCV2 in the late 1990s, the virus has continued to evolve, and novel genotypes have continued to appear. Moreover, there has been recombination between different genotypes of PCV2. This review attempts to illustrate some progress concerning PCV2 in genome rearrangement and genomic recombination with non-PCV2-related nucleic acids, particularly focusing on the porcine circovirus-like virus P1 formed by the recombination of PCV2. The presence of rearranged PCV2 genomes can be demonstrated both in vivo and in vitro, and these subviral molecules ranged from 358 to 1,136 bp. Depending on whether it has the ability to encode a protein, the agents formed by PCV2 recombination can be divided into two categories: porcine circovirus-like viruses and porcine circovirus-like mini agents. We mainly discuss the porcine circovirus-like virus P1 regarding genomic characterization, etiology, epidemiology, and pathogenesis. Further research needs to be conducted on the pathogenicity of other porcine circovirus-like viruses and porcine circovirus-like mini agents and the effects of their interactions with PCV2, especially for the porcine circovirus-like mini agents that do not have protein-coding functions in the genome.

Identification of a novel statovirus in a faecal sample from a calf with enteric disease

A novel clade of RNA viruses was identified in the mammalian gastrointestinal tract by next-generation sequencing. Phylogenetically, these viruses are related to the genera Tombusviridae (plant viruses) and Flaviviridae, which includes mammalian, avian and insect hosts. Named in line with their characterization as stool-associated Tombus-like viruses, it is unclear if statoviruses infect mammals or are dietary in origin. Here, metagenomic sequencing of faecal material collected from a 10-week-old calf with enteric disease found that 20 % of the reads mapped to a de novo-assembled 4 kb contig with homology to statoviruses. Phylogenetic analysis of the statovirus genome found a clear evolutionary relationship with statovirus A, but, with only 47 % similarity, we propose that the statovirus sequence presents a novel species, statovirus F. A TaqMan PCR targeting statovirus F performed on faecal material found a cycle threshold of 11, suggesting a high titre of virus shed from the calf with enteric disease. A collection of 48 samples from bovine enteric disease diagnostic submissions were assayed by PCR to investigate statovirus F prevalence and 6 of 48 (12.5 %) were positive. An ELISA to detect antibodies to the coat protein found that antibodies to statovirus F were almost ubiquitous in bovine serum. Combined, the PCR and ELISA results suggest that statovirus F commonly infects cattle. Further research is needed to elucidate the aetiological significance of statovirus infection.

Interaction of porcine circovirus-like virus P1 capsid protein with host proteins

Background

Porcine circovirus-like virus P1 is a relatively new kind of virus that is closely related to the post-weaning multisystemic wasting syndrome, congenital tremors, and abortions in swine. The molecular mechanisms of P1 virus infection and pathogenesis are fully unknown. To analyze P1 and its host interactions, we used a yeast two-hybrid (Y2H) assay to identify cellular proteins interacting with the Cap of the P1 virus. In this study, the Cap of the P1 virus exhibited no self-activation and toxicity to yeast cells and was used as bait to screen the Y2H library prepared from the pancreas tissue.

Results

Five cellular proteins (EEP, Ral GDS, Bcl-2-L-12, CPS1, and one not identified) were found to interact with P1 Cap. The interaction between Cap and Ral GDS was confirmed by co-immunoprecipitation.

Conclusions

Our data are likely to support the future investigation of the underlying mechanism of P1 infection and pathogenesis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-02926-6.

Circular Rep-Encoding Single-Stranded DNA Sequences in Milk from Water Buffaloes (Bubalus arnee f. bubalis)

Isolation and characterization of circular replicase-encoding single-stranded (ss) DNA from animal, plant and environmental samples are rapidly evolving in virology. We detected 21 circular DNA elements, including one genomoviral sequence, in individual milk samples from domesticated Asian water buffaloes (Bubalus arnee f. bubalis). Most of the obtained genomes are related to Sphinx 1.76 and Sphinx 2.36 sequences and share a high degree of similarity to recently published circular DNAs—named BMMF (bovine meat and milk factors)—that have been isolated from commercial milk, as well as from bovine serum. Characteristic features such as rep genes, tandem repeats and inverted repeats were detected. These BMMF have recently been found to be present in taurine-type dairy cattle breeds descending from the aurochs (Bos primigenius). Importantly, the occurrence of BMMF has been linked to the higher incidence of colorectal and breast cancer in North America and Western Europe compared with Asia. This is the first report of circular ssDNA detected in milk from the domesticated form of the wild Asian water buffalo (B. arnee) belonging to the subfamily Bovinae. This novelty should be taken into account in view of the above-mentioned cancer hypothesis.

Characterization of porcine circovirus-like virus P1 replication and lesions in BALB/c mice

Five-week-old male BALB/c mice were inoculated intraperitoneally with a single (sP1) or multiple doses (mP1) of porcine circovirus-like virus P1 or cell culture medium. None of the mice exhibited clinical signs or gross lesions throughout the study. However, the body weights of the mP1 mice were significantly decreased, and the mice inoculated with P1 exhibited viral replication, seroconversion, and microscopic lesions. P1 nucleic acid was detected in the heart, liver, spleen, lung, bladder, testis, brain, thymus, and pancreatic tissues. Special P1 antibody was found in the P1-inoculated mice. Microscopic lesions in the sP1 and mP1 mice were characterized by interstitial pneumonia, including edema in the connective tissue around the pulmonary vessels, mild inflammatory cell infiltrate, thickened alveolar walls, myocardial necrosis, and dissolution of Purkinje cell nuclei. The results showed that the P1 virus could infect BALB/c mice. Thus, BALB/c mice may serve as models for P1 research.

First molecular identification of porcine circovirus-like agents in dogs and cats in China

Porcine circovirus-like agents comprise two types of viruses: porcine circovirus-like viruses (P1, P2, P3, and P4) and porcine circovirus-like mini agents (PCVL258, PCVL264, PCVL201, and PCVL347). Of these, P1 has been identified in pigs, cattle, goats, and rabbits in China; P2, P3, P4, PCVL258, and PCVL264 have been identified in pigs; and PCVL201 and PCVL347 have been identified in cattle. The purpose of this study was to determine whether dogs and cats have been exposed to porcine circovirus-like agents. We screened 158 serum samples from diseased dogs and 41 from cats in China by PCR and nucleotide sequencing. In dogs, approximately 18% (n = 28) were positive for P1, 17% (n = 26) for PCVL258, and 9% (n = 14) for PCVL264; in cats, 17.1% (n = 7) were positive for P1, 9.8% (n = 4) for P4, and 14.6% (n = 6) for PCVL258. The P1 genomes in this study consisted of 648 nucleotides (nt) and shared 96.8 to 100% nt identity with other P1 genomes in GenBank. The P4 genome shared 98.3 to 100% nt identity with other reported P4 genomes, and PCVL258 and PCVL264 showed 100% nt identity with previously reported genomes. To our knowledge, this is the first report on molecular characterization of porcine circovirus-like agents in dogs and cats. Further studies are needed to clarify the epidemiology, evolution, and pathogenesis of porcine circovirus-like agents in dogs and cats.

Complete genome sequences of porcine circovirus-like virus P1 mutants with 163 amino acids in the capsid protein

Porcine circovirus-like virus P1 is a novel circovirus that was originally detected in China in 2005. Here, we report the genome sequences of P1 isolates JS02, JS03, and HuN06, each with 163 amino acids in its capsid protein. The complete genome of each of these isolates contains 649 nucleotides and has a T insertion at position 207. Phylogenetic analysis based on complete genome sequences of 18 P1 reference strains grouped 16 P1 sequences from this study into one cluster, with the JS02, JS03, and HuN06 isolates forming an independent clade. However, phylogenetic analysis based on amino acid sequences of the capsid protein showed that the JS02, JS03, and HuN06 strains were on the same large branch with PCV2, distinct from other P1 isolates. These results help us to understand the origin and evolution of P1.

Complete genome sequences of porcine-circovirus-like mini agents in pigs and cattle

Porcine circovirus (PCV) genomes are single-stranded circular DNAs of about 1770 nucleotides (nt). Here, we present for the first time two small PCV-like agents with circular DNA genomes (258 and 264 nt) in pigs and two (201 and 347 nt) in cattle, with no obvious protein-coding capacity. Sequences of the four PCV-like mini agents differed by 1.5%-18.7% from each other and by 4.5%-56.7% from other reference PCV strains and PCV-like viruses.