An emerging novel virus: Atypical porcine pestivirus (APPV)

Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China

BACKGROUND

Atypical porcine pestivirus (APPV) is a novel, highly variable porcine pestivirus. Previous reports have suggested that the virus is associated with congenital tremor (CT) type A-II in piglets, and little information is available about the correlation between the virus and sow abortion, or on coinfection with other viruses. In China, reported APPV strains were mainly isolated from South China and Central China, and data about the APPV genome from northern China are relatively scarce.

METHODS

Eleven umbilical cords, one placenta, and one aborted piglet, were collected from aborted sows of the same farm in Shandong Province of northern China. Nucleic acids were extracted from the above samples, and subsequently pooled for viral metagenomics sequencing and bioinformatics analysis. The viral coexistence status and complete genome characteristics of APPV in Shandong Province were determined.

RESULTS

In abortion cases, APPV was present with Getah virus, porcine picobirnavirus, porcine kobuvirus, porcine sapovirus, Po-Circo-like virus, porcine serum-associated circular virus, porcine bocavirus 1, porcine parvovirus 1, porcine parvovirus 3 and porcine circovirus 3, etc. The first complete genome sequence(11,556 nt) of APPV in Shandong Province of northern China, was obtained using viral metagenomics and designated APPV-SDHY-2022. Comparison with Chinese reference strains revealed that the polyprotein of APPV-SDHY-2022 shared 82.6-84.2%, 93.2-93.6%, and 80.7-85% nucleotide identity and 91.4-92.4%, 96.4-97.7%, and 90.6-92.2% amino acid identity with those of the Clade I, Clade II and Clade III strains, respectively. Phylogenetic analysis based on the complete polyprotein CDS and NS5A sequences concluded that APPV-SDHY-2022 belongs to Clade II. Analysis of the NS5A nucleotide sequences revealed homology of greater than 94.6% for the same isoform, 84.7-94.5% for different isoforms of the same clade and 76.8-81.1% for different clades. Therefore, Clade II was further divided into three subclades, and APPV-SDHY-2022 belonged to subclade 2.3. Members of Clade II have 20 unique amino acids in individual proteins, distinguishing them from Clade I and Clade III members. The E2 protein showed the greatest diversity of putative N-glycosylation sites with 9 patterns, and APPV-SDHY-2022 along with other Chinese APPV strains shared the conserved B-cell conformational epitope residues 39E, 70R, 173R, 190K and 191N of the E2 protein.

CONCLUSIONS

We reported viral coexistence and the first complete genome sequence of APPV from abortion cases and from Shandong Province. The new APPV isolate belongs to an independent branch of Clade II. Our results increase the molecular and epidemiological understanding of APPV in China.

Screening for atypical porcine pestivirus in Swedish boar semen used for artificial insemination and a characterisation of the seminal RNA microbiome including the virome

BACKGROUND

This study aimed to characterise the RNA microbiome, including the virome of extended semen from Swedish breeding boars, with particular focus on Atypical porcine pestivirus (APPV). This neurotropic virus, associated with congenital tremor type A-II in piglets, was recently demonstrated to induce the disease through insemination with semen from infected boars.

RESULTS

From 124 Artificial Insemination (AI) doses from Swedish breeding boars, APPV was detected in one dose in addition to a sparse seminal RNA virome, characterised by retroviruses, phages, and some fecal-associated contaminants. The detected seminal microbiome was large and characterized by Gram-negative bacteria from the phylum Proteobacteria, mainly consisting of apathogenic or opportunistic bacteria. The proportion of bacteria with a pathogenic potential was low, and no antimicrobial resistance genes (ARGs) were detected in the datasets.

CONCLUSION

Overall, the results indicate a good health status among Swedish breeding boars. The detection of APPV in semen raises the question of whether routine screening for APPV in breeding boars should be instigated.

Dynamics of Infection of Atypical Porcine Pestivirus in Commercial Pigs from Birth to Market: A Longitudinal Study

Atypical porcine pestivirus (APPV) was found to be associated with pigs demonstrating congenital tremors (CT), and clinical signs in pigs have been reproduced after experimental challenge. Subsequently, APPV has been identified in both symptomatic and asymptomatic swine of all ages globally. The objective of this research was to perform a longitudinal study following two cohorts of pigs, those born in litters with pigs exhibiting CT and those born in litters without CT, to analyze the virus and antibody dynamics of APPV infection in serum from birth to market. There was a wide range in the percentage of affected pigs (8-75%) within CT-positive litters. After co-mingling with CT-positive litters at weaning, pigs from CT-negative litters developed viremia that was cleared after approximately 2 months, with the majority seroconverting by the end of the study. In contrast, a greater percentage of pigs exhibiting CT remained PCR positive throughout the growing phase, with less than one-third of these animals seroconverting. APPV RNA was present in multiple tissues from pigs in both groups at the time of marketing. This study improved our understanding of the infection dynamics of APPV in swine and the impact that the immune status and timing of infection have on the persistence of APPV in serum and tissues.

Coding-Complete Genome Sequences of Two Atypical Porcine Pestivirus Strains from Anhui Province, China

In 2021, two atypical porcine pestivirus (APPV) strains, AH06/2021 and AH22/2021, were identified from suckling piglets showing congenital tremor in Anhui Province, China. Genome sequence analysis indicated that the two strains shared 81.19% to 93.98% nucleotide identities with other APPV strains.

Development of a quadruple PCR-based gene microarray for detection of vaccine and wild-type classical swine fever virus, African swine fever virus and atypical porcine pestivirus

BACKGROUND

Classical swine fever (CSF), African swine fever (ASF), and atypical porcine pestivirus (APPV) are acute, virulent, and contagious viral diseases currently hampering the pig industry in China, which result in mummification or stillbirths in piglets and mortality in pigs. Diagnostic assays for the differentiation of infection and vaccination of CSFV, in addition to the detection of ASFV and APPV, are urgently required for better prevention, control, and elimination of these viral diseases in China.

METHODS

A quadruple PCR-based gene microarray assay was developed in this study to simultaneously detect wild-type and vaccine CSFV strains, ASFV and APPV according to their conserved regions. Forty-two laboratory-confirmed samples, including positive samples of 10 other swine viral diseases, were tested using this assay to confirm its high specificity.

RESULTS

This assay's limit of detections (LODs) for the wild-type and vaccine CSFV were 6.98 and 6.92 copies/µL. LODs for ASFV and APPV were 2.56 × 10 and 1.80 × 10 copies/µL, respectively. When compared with standard RT-PCR or qPCR for CSFV (GB/T 26875-2018), ASFV (MARR issue No.172), or APPV (CN108611442A) using 219 clinical samples, the coincidence was 100%. The results showed that this assay with high sensitivity could specifically distinguish ASFV, APPV, and CSFV, including CSFV infection and immunization.

CONCLUSION

This assay provides a practical, simple, economic, and reliable test for the rapid detection and accurate diagnosis of the three viruses and may have good prospects for application in an epidemiological investigation, prevention, and control and elimination of these three diseases.

Detection and investigation of atypical porcine pestivirus in a swine production system

A commercial farrow-to-finish farm was suspicious of atypical porcine pestivirus (APPV) after observing clinical signs of congenital tremors (CT) and splay leg (SL) of newborn pigs. If introduced onto the farrow-to-finish, the two potential routes of introduction could be through replacement gilts or incoming semen doses. Therefore, this study aimed to determine the prevalence of clinical APPV within the sampled population, identify the route of APPV introduction to this system, and determine prevalence of detectable APPV RNA within a population of gilt multiplication farm offspring through an isolation nursery and finisher barn. Farrowing records were analyzed for the presence of CT or SL and corresponding parity of the dam. Overall, prevalence of clinically affected litters within batch farrowing groups ranged from 0 to 31%. Phylogenetic analysis was conducted on a serum sample from a gilt at the isolation nursery, semen dose for the farrow-to-finish farm, and serum of a CT piglet. Results indicated that the virus circulating in clinically affected piglets was most similar to an incoming semen dose (98.9% nucleotide identity). Blood samples were collected at four time points and revealed APPV clinical prevalence was 37.5–77.5% during the nursery phase and 0–26% during the finisher phase. Oral fluids were also collected during the finisher phase and APPV clinical prevalence was 100% for all sampling time points. In summary, introduction of APPV into naïve herds is associated with increased clinical CT and SL cases and is detectable in asymptomatic pigs during the nursery and finisher production phases. This study found that potential screening tests for APPV could include oral fluids or qRT-PCR analysis of semen doses especially when trying to identify prevalence levels on naïve farm.

Genetic characterization of atypical porcine pestivirus from neonatal piglets with congenital tremor in Hubei province, China

Background

Atypical porcine pestivirus (APPV) is a single-stranded RNA virus with high genetic variation that causes congenital tremor (CT) in newborn piglets, belonging to the genus Pestivirus of the family Flaviviridae. Increasing cases of APPV infection in China in the past few years would pose severe challenges to the development of pig production. In view of the high genetic variability of APPV, the genetic characteristics of APPV in Hubei province was determined.

Methods

52 tissue samples from 8 CT-affected newborn piglets were collected at two different periods in the same pig farm in Hubei province. Viral nucleic acid was extracted to detect pathogens that can cause CT in piglets or other common clinical pathogens by RT-PCR. Haematoxylin and eosin (HE) staining, immunohistochemical (IHC) analysis, and qRT-PCR were performed to observe histopathological changes and histological distribution, and detect the viral load of APPV in CT-affected piglets. The full-length genome of APPV was obtained and sequence analysis was conducted to determine the phylogenetic relationship.

Results

Histopathological observation and histological distribution analysis showed that the histological lesions and distribution of APPV were mainly in central nervous system (CNS) tissues and immune tissues. Viral load analysis revealed that the viral copy number was higher in the cerebellum, submaxillary lymph nodes, tonsil, and serum than in other tissues. Phylogenetic analysis showed that CH-HB2020 and CH-HB2021 belonged to Clade I.3, and is most closely related to APPV_CH-GX2016. Sequence alignment based on APPV encoding sequences (CDS) showed that the nucleotide identities of CH-HB2020 or CH-HB2021 with Clade I, Clade II, and Clade III strains were 83.5–98.6%, 83.1–83.5%, and 81.1–81.4%, respectively, while the amino acid identities were 91.9–99.2%, 91.2–95.3%, and 90.77–91.4%, respectively. No recombination event was observed in CH-HB2020 or CH-HB2021 strains.

Conclusions

These findings enhance our understanding of the pathogenesis of APPV and may provide potential molecular evidence for its prevalence and transmission.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-022-01780-8.

Development of a one-step multiplex qRT–PCR assay for the detection of African swine fever virus, classical swine fever virus and atypical porcine pestivirus

Background

African swine fever virus (ASFV), classical swine fever virus (CSFV) and atypical porcine pestivirus (APPV) have caused great economic losses to the swine industry in China. Since coinfections of ASFV, CSFV and APPV occur in certain pig herds, it is necessary to accurately and differentially detect these pathogens in field-collected samples. In this study, a one-step multiplex real-time quantitative reverse transcription-polymerase chain reaction (multiplex qRT–PCR) was developed for the simultaneous and differential detection of ASFV, CSFV and APPV.

Results

The one-step multiplex qRT–PCR presented here was able to simultaneously detect ASFV, CSFV and APPV but could not amplify other viruses, including porcine circovirus type 2 (PCV2), pseudorabies virus (PRV), porcine reproductive and respiratory syndrome virus (PRRSV), foot-and-mouth disease virus (FMDV), porcine parvovirus (PPV), porcine epidemic diarrhoea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine rotavirus (PRoV), porcine deltacoronavirus (PDCoV), border disease virus (BDV), bovine viral diarrhoea virus type 1 (BVDV-1), BVDV-2, etc. The limit of detection (LOD) of the assay was 2.52 × 10¹ copies/μL for ASFV, CSFV and APPV. A repeatability test using standard recombinant plasmids showed that the intra- and interassay coefficients of variation (CVs) were less than 2%. An assay of 509 clinical samples collected in Guangxi Province, southern China, from October 2018 to December 2020 showed that the positive rates of ASFV, CSFV and APPV were 45.58, 12.57 and 3.54%, respectively, while the coinfection rates of ASFV and CSFV, ASFV and APPV, CSFV and APPV were 4.91, 1.38, 0.98%, respectively. Phylogenetic analysis based on the nucleotide sequences of the partial ASFV p72 gene showed that all ASFV strains from Guangxi Province belonged to genotypes I and II.

Conclusion

A one-step multiplex qRT–PCR with high specificity, sensitivity and repeatability was successfully developed for the simultaneous and differential detection of ASFV, CSFV and APPV.

Fc-Mediated E2-Dimer Subunit Vaccines of Atypical Porcine Pestivirus Induce Efficient Humoral and Cellular Immune Responses in Piglets

Congenital tremor (CT) type A-II in piglets is caused by an emerging atypical porcine pestivirus (APPV), which is prevalent in swine herds and a serious threat to the pig production industry. This study aimed to construct APPV E2 subunit vaccines fused with Fc fragments and evaluate their immunogenicity in piglets. Here, APPV E2Fc and E2ΔFc fusion proteins expressed in Drosophila Schneider 2 (S2) cells were demonstrated to form stable dimers in SDS-PAGE and western blotting assays. Functional analysis revealed that aE2Fc and aE2ΔFc fusion proteins could bind to FcγRI on antigen-presenting cells (APCs), with the affinity of aE2Fc to FcγRI being higher than that of aE2ΔFc. Moreover, subunit vaccines based on aE2, aE2Fc, and aE2ΔFc fusion proteins were prepared, and their immunogenicity was evaluated in piglets. The results showed that the Fc fusion proteins emulsified with the ISA 201VG adjuvant elicited stronger humoral and cellular immune responses than the IMS 1313VG adjuvant. These findings suggest that APPV E2 subunit vaccines fused with Fc fragments may be a promising vaccine candidate against APPV.

Genetic characterization of atypical porcine pestivirus (APPV) in China and the successful isolation of a novel APPV strain within genotype 2

Atypical porcine pestivirus (APPV) is one major causative agent of congenital tremor (CT) type A-II. In this study, the geographical distribution and genetic characteristics of APPV strains in China were established. To date, APPV has been detected in at least ten provinces/regions of China. Genetic variability analysis showed that NS3 genes were highly conserved among Chinese APPV strains, while NS5A-, N^pro-, and E^rns-encoding genes were highly variable. Phylogenetic analysis revealed that all of the reference strains could be classified into 3 genotypes (1-3) and 7 subgenotypes (1.1-1.7). The Chinese APPV strains were assigned to all 3 genotypes and to 5 subgenotypes (1.2 and 1.4-1.7) of genotype 1. Amino acid insertions/deletions in nonstructural proteins, including NS3, NS5A, and NS5B, could only be found in Chinese APPV strains. Among the three envelope glycosylation proteins (E^rns, E1, and E2), E^rns was the most heavily glycosylated protein, and the N-glycosylation sites of E2 in different APPV strains showed apparent correlations with genetic types. Furthermore, a novel APPV strain named China/HeN01/2018 belonging to genotype 2 was identified in Henan Province. It was then isolated and successfully propagated in embryonic porcine kidney epithelial cells (SPEV cells). This study provides updated information to better understand the divergence of APPV strains in China. This first successful isolation of a Chinese APPV strain provides a research foundation for future studies.

Genotyping atypical porcine pestivirus using NS5a

Atypical porcine pestivirus (APPV) is an emerging virus discovered in 2014 and it can cause congenital tremors in pigs. Molecular epidemiology serves as an essential tool in monitoring and controlling the disease. Virus epidemiology mainly relies on genome sequencing and phylogenetic characterization. Previous molecular epidemiology studies have been using different genes/regions for phylogeny, namely whole genome, Npro, and E2 coding sequences. However, with increasing number of APPV sequences available in GenBank, no systemic studies have been performed for detailed classification of APPV strains around the globe. The goal of this study is to propose a classification strategy or taxonomy of APPV strains at genotype, subgenotype, and isolate levels. A total of 76 whole genomes and 16 partial polyprotein coding sequences were analyzed for genetic variability and suitability of all individual genes for viral phylogenies. Our results revealed that, among all the viral genes, NS5a coding sequences were proved to be the most suitable alternative for tracing APPV strains supported by its capability of reproducing the same phylogenetic and evolutionary information as the whole viral genome did. Also, a reliable cutoff to accurately classify APPV at different levels is established. We propose a genotyping scheme with three well-defined genotypes (1-3) and 7 subgenotypes for genotype 1 (1.1-1.7). For whole genome analysis, a threshold value of 84%-91% pairwise identity allows separation of all APPV subgenotypes, whereas 80% identity clearly segregate the three major APPV genotypes. For NS5a gene analysis, 82%-91% identity allows subgenotype separation and 76% identity segregate APPV genotypes. Additionally, genetic distance of whole genome exhibits ≤8% in isolate level, 9%-14% in subgenotype level, and 17%-22% in genotype level, while for NS5a encoding sequences the genetic distance displays ≤9% in isolate level, 9.9%-19.1% in subgenotype level, and 21.6%-29.7% in genotype level. These allow a clear segregation among APPV genotypes, subgenotypes, and isolates. Therefore, the proposed strategy in this study provides a solid and improved basis for molecular phylogenetics to understand APPV genetic diversity, trace the origins and control the spread of new disease outbreaks.

Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)

Atypical porcine pestivirus (APPV) has been identified as the main causative agent for congenital tremor (CT) type A-II in piglets, which is threatening the health of the global swine herd. However, the evolution of APPV remains largely unknown. In this study, phylogenetic analysis showed that APPV could be divided into three phylogroups (I, II, and III). Phylogroups I and II included viral strains from China, while phylogroup III contained strains from Europe, North America, and Asia. Phylogroups I and II are tentatively thought to be of Chinese origin. Next, compositional property analysis revealed that a high frequency of nucleotide A and A-end codons was used in the APPV genome. Intriguingly, the analysis of preferred codons revealed that the AGA[Arg] and AGG[Arg] were overrepresented. Dinucleotide CC was found to be overrepresented, and dinucleotide CG was underrepresented. Furthermore, it was found that the weak codon usage bias of APPV was mainly dominated by selection pressures versus mutational forces. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses showed that the codon usage patterns of phylogroup II and III were more similar to the one of a pig than phylogroup I, suggesting that phylogroup II and III may be more adaptive to pigs. Overall, this study provides insights into APPV evolution through phylogeny and codon usage pattern analysis.

Development of a quantitative real time RT-PCR assay for sensitive and rapid detection of emerging Atypical Porcine Pestivirus associated with congenital tremor in pigs

Atypical Porcine Pestivirus (APPV) is reported as the etiologic agent for type AII congenital tremors in newborn piglets. Initial PCR-based diagnostic tests to detect APPV were designed based on the limited sequence information and are not capable of detecting the majority of APPV strains. A sensitive and reliable PCR-based diagnostic test is critical for accurate detection of APPV. In this study, a quantitative reverse transcription PCR (RT-qPCR) assay was developed for reliable detection of all currently known APPV strains. The assay design also included swine 18S rRNA gene as an internal control to monitor RNA extraction efficiency. Two APPV gene fragments, one each from NS5b and NS3, were cloned and used to determine the dynamic range of detection, linearity and analytical sensitivity/limit of detection (LOD). Both individual and multiplex assays (duplex and triplex) had correlation coefficients of >0.99 and PCR amplification efficiencies of >90 %. Comparison of detection limit and analytical sensitivity between individual, and multiplex assays indicated no inhibition of PCR sensitivity upon multiplexing. The detection limit for APPV target, based on analytical sensitivity, is 7.75 copies (NS5b) and 5.2 copies (NS3) per reaction. Assay specificity was verified by testing nucleic acids of other closely related pestiviruses and clinical samples that are positive for other common swine pathogens. Assay sensitivity was also assessed on synthesized gene fragments of the most divergent China strains. Testing 339 known APPV-positive and 202 negative clinical samples demonstrated a good diagnostic sensitivity and specificity. Data from six independent runs, including 5 replicates of three clinical samples with three Ct ranges, were utilized to assess inter-assay repeatability and intra-assay reproducibility. This analysis demonstrated intra-assay/inter-assay coefficients of variation of 0.71 % and 0.01 %, respectively, with a PCR efficiency of 92.71 % for the triplex assay. Testing of 1785 clinical samples revealed ∼19 % prevalence of APPV in the US swine herds and oral fluids demonstrates to be a reliable specimen for viral detection. This multiplex RT-qPCR assay offers a rapid and reliable detection of APPV in swine herds and serves as useful tool in APPV surveillance and epidemiological investigations.

Detection and genetic analysis of a novel atypical porcine pestivirus from piglets with congenital tremor in Japan

Atypical porcine pestivirus (APPV), which has been confirmed to be associated with congenital tremor (CT) in pigs, is a newly discovered porcine virus that has been found in the Americas, Europe and Asia; however, no report of APPV in Japan has been published. We identified an APPV in the central nervous system of Japanese piglets with CT and firstly determined and analysed the complete genome sequence. Phylogenetic analysis using the complete genome nucleotide sequence of the Japanese APPV, named Anna/2020, and those of APPVs from the NCBI database showed that APPVs were divided into three genotypes (genotypes 1 to 3), and that Anna/2020 clustered with the genotype 3 APPV strains, but distantly branched from these strains. Pairwise complete coding region nucleotide sequence comparisons revealed that there was 94.0%- 99.7% sequence identity among the genotype 3 strains, while Anna/2020 showed 87.0%-89.3% identity to those genotype 3 strains, suggesting that Anna/2020 represents a novel APPV lineage within genotype 3. Retrospective examinations using RT-PCR revealed one genotype 1 and two novel genotype 3 APPVs from pigs without CT, and that novel genotype 3 APPVs have been prevalent in Japan since at least 2007.

Disruption of interferon-β production by the Npro of atypical porcine pestivirus

Atypical porcine pestivirus (APPV) is an emerging porcine virus that threatens global swine production. Pestiviruses can prevent interferon (IFN) production to avoid the host innate immune response, and the N^pro viral protein can play a critical role. Knowledge of the host immune response to APPV infection is limited. Here, we showed that the IFN-β production was suppressed by APPV-N^pro and the IFN regulatory factor 3 (IRF3) promoter activity stimulated by adaptor molecules of the IFN-β signaling pathway was also inhibited in the APPV-N^pro-expressed cells. The APPV-N^pro was able to interact with IRF3 and interfere the phosphorylation of IRF3, indicated that the IFN-β antagonism of APPV-N^pro mainly depended on blocking IRF3 activity. To identify the functional region of APPV-N^pro, a panel of truncated APPV-N^pro was constructed, and its influence on the IRF3 activation was investigated. The results showed that the N-terminal 31–51 amino acids of APPV-N^pro were mainly associated with inhibition of the IFN-β response. Taken together, this is the first study focusing on elucidating the function of APPV protein by revealing a novel mechanism of N^pro in disruption of host IFN-β production, which will enlighten future study in addressing APPV pathogenesis and immune evasion.

Evolution and genetic diversity of atypical porcine pestivirus (APPV) from piglets with congenital tremor in Guangxi Province, Southern China

Atypical porcine pestivirus (APPV) was identified and associated with congenital tremor (CT) type A‐II in new born piglets and has been reported in many countries. In China, the first APPV identification in swine herds was reported in Guangdong province in 2016. To investigate the genetic characteristics of APPV in Guangxi province, 53 tissue samples from neonatal piglets with CT were collected and detected from October 2017 to May 2019. Five APPV strains which were named as GX04/2017, GX01‐2018, GX02‐2018, GX01‐2019 and GX02‐2019 were obtained. Sequence analysis revealed that all six APPV strains from Guangxi province, including five strains from this study and one from a previous report, shared 83.3%‐97.5% nucleotide identity of complete genome and 91.7%‐99.1% amino acid identity of the open reading frame (ORF), and shared 77.7%‐97.7% nucleotide identity of complete genome and 90.6%‐99.3% amino acid identity of ORF with reference strains. Phylogenetic analysis indicated that all APPV strains could be divided into three clades based on the complete genome, N^pro, E^rns and E2 gene sequences, respectively; and the APPV strains from Guangxi province distributed in two clades (clades I and II). No sign of recombination was observed from Guangxi strains. Evolution analysis performed on the complete genome of 58 APPV strains showed that America, Europe and Asia strains during 2006–2019 evolved at a mean rate of 1.37 × 10^–4 substitutions/site/year, and the most recent common ancestor (tMRCA) of them was estimated as 1,700.5 years ago. The findings of this study indicated that there existed a high degree of genetic diversity of APPV from Guangxi province, Southern China, which provided important information on the epidemiological features and evolutionary relationships of APPV.

Development a multiplex RT-PCR assay for simultaneous detection of African swine fever virus, classical swine fever virus and atypical porcine pestivirus

African swine fever virus (ASFV), classical swine fever virus (CSFV) and atypical porcine pestivirus (APPV) have caused considerable financial losses to the pig industry worldwide, and it is critical to achieve early and accurate diagnosis of these viruses to control the diseases induced by them. In this study, three pairs of specific primers were designed based on the highly conserved genome regions of these viruses, and a multiplex reverse transcription-polymerase chain reaction (mRT-PCR) assay for ASFV, CSFV and APPV was established after various reaction conditions were optimized. The mRT-PCR assay consisted of two steps, that is, reverse transcription (RT) and mPCR. The assay was highly specific, sensitive, and reproducible for ASFV, CSFV and APPV without cross-reaction with other swine pathogens. The sensitivity of this assay, which used purified plasmid constructs containing specific viral target fragments as templates, was 6.34 × 10² copies/μL for ASFV and 6.34 × 10¹ copies/μL for both CSFV and APPV. A total of 384 clinical samples from piglets suspected to be infected in Guangxi Province, Southern China, during 2018-2019 were analyzed by the established mRT-PCR method. The results showed that the positive rates of ASFV, CSFV and APPV were 43.75 %, 13.28 % and 4.17 %, respectively, and the coinfection rates of ASFV/CSFV, ASFV/APPV and CSFV/APPV were 5.47 %, 1.83 % and 1.30 %, respectively. To understand the epidemiological characteristics of APPV, the newly discovered virus, in Guangxi Province, the clinical samples from APPV-positive animals were selected randomly for amplification and sequencing, and the complete genomic sequences of four APPV strains were obtained. Phylogenetic analysis demonstrated that APPV strains from Guangxi Province had a high degree of genetic diversity. This study provides an important tool for rapid detection and accurate diagnosis of ASFV, CSFV and APPV.

Pestivirus K (Atypical Porcine Pestivirus): Update on the Virus, Viral Infection, and the Association with Congenital Tremor in Newborn Piglets

The atypical porcine pestivirus (APPV) belongs to the species Pestivirus K of the genus Pestivirus and the family Flaviviridae, and it has been associated with congenital tremor (CT) type A-II in newborn piglets. Although APPV was discovered in 2015, evidence shows that APPV has circulated in pig herds for many years, at least since 1986. Due to the frequently reported outbreaks of CT on different continents, the importance of this virus for global pig production is notable. Since 2015, several studies have been conducted to clarify the association between APPV and CT. However, some findings regarding APPV infection and the measures taken to control and prevent the spread of this virus need to be contextualized to understand the infection better. This review attempts to highlight advances in the understanding of APPV associated with type A-II CT, such as etiology, epidemiology, diagnosis, and control and prevention measures, and also describes the pathophysiology of the infection and its consequences for pig production. Further research still needs to be conducted to elucidate the host's immune response to APPV infection, the control and prevention of this infection, and the possible development of vaccines.

Development of the reverse genetics system for emerging atypical porcine pestivirus using in vitro and intracellular transcription systems

Atypical porcine pestivirus (APPV) is a novel pestivirus causing congenital tremor (CT) type AII in piglets and exhibiting a broad geographical distribution. Lack of an operating system for the viral genome is one of bottlenecks which restrict further research on pathogenesis and gene functions of APPV. Reverse genetics system (RGS) is a feasible solution to this bottleneck problem, but, to-date, no RGSs have been developed for APPV. Here, for the first time, recombinant APPV CH-GD2017 were rescued using in vitro and intracellular transcription systems and the virons were observed via transmission electron microscopy. As the process of in vitro transcription is time-consuming and inefficient, a full-length cDNA clone in an intracellular transcription was further constructed using an RNA polymerase II system. Then, the rescued virus was identified via RT-PCR detection, indirect immunofluorescent assay, and transmission electron microscopy. Development of the RGS for APPV will provide an important tool for further research on this newly emerging pathogen.

Long-Term Circulation of Atypical Porcine Pestivirus (APPV) within Switzerland

In 2015, a new pestivirus was described in pig sera in the United States. This new "atypical porcine pestivirus" (APPV) was later associated with congenital tremor (CT) in newborn piglets. The virus appears to be distributed worldwide, but the limited knowledge of virus diversity and the use of various diagnostic tests prevent direct comparisons. Therefore, we developed an APPV-specific real-time RT-PCR assay in the 5'UTR of the viral genome to investigate both retro- and prospectively the strains present in Switzerland and their prevalence in domestic pigs. Overall, 1080 sera obtained between 1986 and 2018 were analyzed, revealing a virus prevalence of approximately 13% in pigs for slaughter, whereas it was less than 1% in breeding pigs. In the prospective study, APPV was also detected in piglets displaying CT. None of the samples could detect the Linda virus, which is another new pestivirus recently reported in Austria. Sequencing and phylogenetic analysis revealed a broad diversity of APP viruses in Switzerland that are considerably distinct from sequences reported from other isolates in Europe and overseas. This study indicates that APPV has already been widely circulating in Switzerland for many years, mainly in young animals, with 1986 being the earliest report of APPV worldwide.

Viral load and histological distribution of atypical porcine pestivirus in different tissues of naturally infected piglets

A newly identified atypical porcine pestivirus (APPV) associated with congenital tremors in newborn piglets has been shown to have a worldwide geographic distribution. In view of the function of E^rns in pestivirus infection and replication, the viral load and histological distribution of APPV in different tissues of naturally infected piglets were analyzed by quantitative RT-PCR and immunohistochemical detection using E^rns as the target. The results showed that the viral copy number was higher in the cerebellum, submandibular lymph nodes, and thymus than in other tissues, indicating that these are important target organs of APPV. The histological distribution of APPV was mainly in the matrix and nerve fiber in nervous tissues, endothelial cells in lymphoid tissues, and epithelial cells in other tissues, suggesting that these cells were target cells of APPV. The results will provide basic data for elucidating the pathogenesis and deepening the understanding of this newly discovered pathogen.