Current knowledge on epidemiology and evolution of novel porcine circovirus 4.

Porcine circovirus type 4 (PCV4) is a newly emerging virus, with both PCV4 genomic DNA and specific antibodies detected in swine herds in several provinces in China and South Korea. Although the virus was first identified in 2019 in Hunan, China, retrospective research suggests that serum samples collected as early as 2008 were positive for PCV4 antibody. Infections with only PCV4 or co-infections with other pathogens have been associated with several clinical manifestations, but its pathogenesis remains to be determined. The purpose of this review was the following: (1) to characterize PCV4 epidemiology by assessing evolutionary dynamics and genetic diversity of PCV4 strains circulating in swine herds; (2) to reconstruct a computerized 3D model to analyze PCV4 Cap properties; (3) and to summarize the current evidence of PCV4-associated clinical-pathological manifestations. The origin of PCV4 is apparently distinct from other PCV, based on analysis of phylogenetic trees. Of note, PCV4 shares an ancient common ancestor with mink circoviruses. Furthermore, the amino acid residue at position 27 of the PCV4 Cap is a key benchmark to distinguish PCV4a (27S) from PCV4b (27 N), based on PCV4 strains currently available, and variation of this residue may alter Cap antigenicity. In addition, the capsid surface of PCV4 has characteristics of increased polar residues, compared to PCV2, which raises the possibility that PCV4 may target negatively charged host receptors to promote virus infection. Further studies are required, including virus isolation and culture, and more detailed characterization of molecular epidemiology and genetic diversity of PCV4 in swine herds.

Structure, Antigenic Properties, and Highly Efficient Assembly of PCV4 Capsid Protein.

Porcine circovirus type 4 (PCV4), a recently reported circovirus, was first identified in pigs with clinical signs similar to porcine dermatitis nephropathy syndrome (PDNS), in Hunan province, China, in 2019. More knowledge regarding the assembly of capsid protein (Cap) into virus-like particles (VLPs), their structure and antigenic properties, are needed to provide new knowledge for diagnosis and further characterization of PCV4. In this study, high-level expression of PCV4 Cap was achieved in Escherichia coli with purified Cap self-assembling into VLPs (~20 nm) in vitro. Furthermore, these VLPs were internalized in vitro by PK15 and 3D4/21 cell lines. Significant structural differences between PCV4 and PCV2 capsids were demonstrated among loops (loop BC, CD, DE, EF, and GH), based on comparisons of 3D structures. In addition, five potential B cell epitopes identified in silico were mostly located in surface-exposed loops of PCV4 capsid. Cross-reaction between PCV4 and PCV2 or PCV3 conferred by humoral immune responses was deemed unlikely on the basis of ELISA and Western blotting for assessment of VLPs and using PCV4 or PCV2 VLPs. In conclusion, these studies provided new knowledge regarding PCV4 capsid surface patterns. It is noteworthy that the PCV4 VLPs prepared in our study have much potential for development of serological diagnostics for PCV4 and to further characterize this virus.

High Co-infection Status of Novel Porcine Parvovirus 7 With Porcine Circovirus 3 in Sows That Experienced Reproductive Failure.

Porcine parvoviruses (PPVs) and porcine circoviruses (PCVs) infect pigs worldwide, with PPV1-7 and PCV2 infections common in pigs. Although PPV7 was only identified in 2016, co-infection of PPV7 and PCV2 is already common, and PPV7 may stimulate PCV2 replication. PCV3, a novel type of circovirus, is prevalent in pig populations worldwide and considered to cause reproductive disorders and dermatitis nephrotic syndrome. In recent studies, pigs were commonly infected with both PCV3 and PPV7. Our objective was to investigate the co-infections between PPV7 and PCV3 in samples from swine on farms in Hunan, China, and assess the potential impacts of PPV7 on PCV3 viremia. A total of 209 samples, known to be positive (105) or negative (104) for PCV3, were randomly selected from serum samples that were collected from commercial swine herds in seven regions from 2016 to 2018 in our previous studies; these samples were subjected to real-time PCR to detect PPV7. Of these samples, 23% (48/209) were positive for PPV7. Furthermore, the PPV7 positive rate was significantly higher in PCV3 positive serum (31.4%, 33/105) than in PCV3 negative serum (14.4%, 15/104). Another 62 PCV3 positive sow serum samples and 20 PCV3 positive aborted fetuses were selected from 2015 to 2016 in our other previous study. These samples were designated as being from farms with or without long-standing histories of reproductive failure (RF or non-RF), respectively, and they were also subjected to real-time PCR to detect PPV7 and to determine whether PPV7 affected PCV3 viremia. Among the 62 serum samples (39 PCV3 positive RF-serum and 23 PCV3 positive non-RF-serum), 45.1% (28/62) were positive for PPV7 and PCV3, and the PPV7 positive rate was significantly higher in PCV3 positive RF-serum (51.2%, 20/39) than in PCV3 positive non-RF-serum (34.8%, 8/23). In addition, there was a higher positive rate of PPV7 (55%, 11/20) in PCV3 positive aborted fetus samples. In addition, the copy number of PCV3 in PPV7 positive samples was significantly higher than that in PPV7 negative serum samples. Based on these findings, we concluded that PPV7 may stimulate PCV3 replication.

Porcine Parvovirus 7: Evolutionary Dynamics and Identification of Epitopes toward Vaccine Design.

Porcine parvovirus 7 (PPV7) belonging to the genus Chapparvovirus in the family Parvoviridae, has been identified in the USA, Sweden, Poland, China, South Korea and Brazil. Our objective was to determine the phylogeny, estimate the time of origin and evolutionary dynamics of PPV7, and use computer-based immune-informatics to assess potential epitopes of its Cap, the main antigenic viral protein, for vaccines or serology. Regarding evolutionary dynamics, PPV7 had 2 major clades, both of which possibly had a common ancestor in 2004. Furthermore, PPV7 strains from China were the most likely ancestral strains. The nucleotide substitution rates of NS1 and Cap genes were 8.01 × 10-4 and 2.19 × 10-3 per site per year, respectively, which were higher than those reported for PPV1-4. The antigenic profiles of PPV7 Cap were revealed and there were indications that PPV7 used antigenic shift to escape from the host's immune surveillance. Linear B cell epitopes and CD8 T cell epitopes of Cap with good antigenic potential were identified in silico; these conserved B cell epitopes may be candidates for the PPV7 vaccine or for the development of serological diagnostic methods.

Immunoinformatic Analysis of T- and B-Cell Epitopes for SARS-CoV-2 Vaccine Design.

Currently, there is limited knowledge about the immunological profiles of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). We used computer-based immunoinformatic analysis and the newly resolved 3-dimensional (3D) structures of the SARS-CoV-2 S trimeric protein, together with analyses of the immunogenic profiles of SARS-CoV, to anticipate potential B-cell and T-cell epitopes of the SARS-CoV-2 S protein for vaccine design, particularly for peptide-driven vaccine design and serological diagnosis. Nine conserved linear B-cell epitopes and multiple discontinuous B-cell epitopes composed of 69 residues on the surface of the SARS-CoV-2 trimeric S protein were predicted to be highly antigenic. We found that the SARS-CoV-2 S protein has a different antigenic profile than that of the SARS-CoV S protein due to the variations in their primary and 3D structures. Importantly, SARS-CoV-2 may exploit an immune evasion mechanism through two point mutations in the critical and conserved linear neutralization epitope (overlap with fusion peptide) around a sparsely glycosylated area. These mutations lead to a significant decrease in the antigenicity of this epitope in the SARS-CoV-2 S protein. In addition, 62 T-cell epitopes in the SARS-CoV-2 S protein were predicted in our study. The structure-based immunoinformatic analysis for the SARS-CoV-2 S protein in this study may improve vaccine design, diagnosis, and immunotherapy against the pandemic of COVID-19.