High Abundance and Genetic Variability of Atypical Porcine Pestivirus in Pigs from Europe and Asia

Development and application of an indirect ELISA for detection of antibodies against emerging atypical porcine pestivirus

BACKGROUND

Atypical porcine pestivirus (APPV) is a newly discovered swine pestivirus, which can cause congenital tremor and high mortality in newborn piglets and subclinical infection in adult pigs, leading to significant impacts on the pig industry. Currently, there is no approved serological method to assess APPV infection status in pig farms.

METHODS

In this study, the envelope glycoprotein E2 of APPV was highly expressed in suspension HEK293 cells, and further an indirect enzyme-linked immunosorbent assay based on the recombinant E2 protein (E2-iELISA) was developed and evaluated.

RESULTS

The reaction parameters of the E2-iELISA were optimized, and the cutoff value was determined to be 0.2 by analyzing S/P values of 165 negative sera against APPV that were confirmed by virus neutralization test (VNT). Specificity test showed that the method had no cross-reaction with other common swine viruses. The E2-iELISA was evaluated using a panel of swine sera, and showed high sensitivity (113/120, 94.2%) and specificity (65/70, 92.9%), and the agreement rate with VNT was 93.7% (178/190). Subsequently, the E2-iELISA was utilized to investigate the seroprevalence of APPV in pig herds of China. When detecting 1368 pig serum samples collected from nine provinces in China, the overall seroprevalence of APPV was 73.9% (1011/1368).

CONCLUSION

Our findings suggest that the E2-iELISA is specific and sensitive, and could be a valuable tool for serological surveillance of APPV infection in pigs.

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.

Isolation and Molecular Characterization of Atypical Porcine Pestivirus Emerging in China

Atypical porcine pestivirus (APPV) is a recently discovered and very divergent species of the genus Pestivirus within the family Flaviviridae, which causes congenital tremor (CT) in newborn piglets. In this study, an APPV epidemiological investigation was conducted by studying 975 swine samples (562 tissue and 413 serum samples) collected from different parts of China from 2017 to 2021. The results revealed that the overall positive rate of the APPV genome was 7.08% (69/975), among which 50.7% (35/69) of the samples tested positive for one or more other common swine viruses, especially porcine circovirus type 2 (PCV2) with a coinfection rate of 36.2% (25/69). Subsequently, a novel APPV strain, named China/HLJ491/2017, was isolated in porcine kidney (PK)-15 cells for the first time from a weaned piglet that was infected with both APPV and PCV2. The new APPV isolate was confirmed by RT-PCR, sequencing, immunofluorescence assay, and transmission electron microscopy. After clearing PCV2, a pure APPV strain was obtained and further stably propagated in PK-15 cells for more than 30 passages. Full genome sequencing and phylogenetic analysis showed that the China/HLJ491/2017 strain was classified as genotype 2, sharing 80.8 to 97.6% of its nucleotide identity with previously published APPV strains. In conclusion, this study enhanced our knowledge of this new pestivirus and the successful isolation of the APPV strain provides critical material for the investigation of the biological and pathogenic properties of this emerging virus, as well as the development of vaccines and diagnostic reagents.

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.

Development of a Crystal Digital RT-PCR for the Detection of Atypical Porcine Pestivirus

Atypical porcine pestivirus (APPV), a newly discovered virus, is associated with the type A-II congenital tremor (CT) in neonatal piglets. APPV distributes throughout the world and causes certain economic losses to the swine industry. The specific primers and probe were designed targeting the 5' untranslated region (UTR) of APPV to amplify a 90 bp fragment, and the recombinant standard plasmid was constructed. After optimizing the concentrations of primers and probe, annealing temperature, and reaction cycles, a crystal digital RT-PCR (cdRT-PCR) and real-time quantitative RT-PCR (qRT-PCR) were successfully established. The results showed that the standard curves of the qRT-PCR and the cdRT-PCR had R² values of 0.999 and 0.9998, respectively. Both methods could specifically detect APPV, and no amplification signal was obtained from other swine viruses. The limit of detection (LOD) of the cdRT-PCR was 0.1 copies/µL, and that of the qRT-PCR was 10 copies/µL. The intra-assay and inter-assay coefficients of variation of repeatability and reproducibility were less than 0.90% for the qRT-PCR and less than 5.27% for the cdRT-PCR. The 60 clinical tissue samples were analyzed using both methods, and the positivity rates of APPV were 23.33% by the qRT-PCR and 25% by the cdRT-PCR, with a coincidence rate of 98.33%. The results indicated that the cdRT-PCR and the qRT-PCR developed here are highly specific, sensitive methods for the rapid and accurate detection of APPV.

NGS method by library enrichment for rapid pestivirus purity testing in biologics

NGS sequencing was evaluated to understand its added value for animal health vaccine candidates. We have previously established the proof of concept for its application in purity testing on several Master Seeds. Here we evaluate the NGS method after enrichment to detect pestiviruses. To achieve this, we conducted a spiking study using 6 viruses, consisting of 3 pestiviruses and 3 other RNA-viruses at different concentrations into cell suspension. A deep Illumina random sequencing of all nucleic acids (DNA and RNA) was performed. The bioinformatics analysis including both assembly into contigs and annotation were processed using viral public databases for the spiked viruses' identification. Here we present the results of spiking experiments for the simultaneous spike of 6 viruses at 100-10 and 1 TCID₅₀/ml. Using Illumina sequencing, the 3 pestiviruses were all detected at the highest concentration, and even at the lowest one such as 1 TCID₅₀/ml for CSFV. Regarding the other viruses, they were not detected at all. Overall, the study showed consistent results for specific detection of pestiviruses with an increase of sensitivity after enrichment. The sensitivity of NGS evaluated by virus spiking experiments of cells demonstrated that NGS method is a valuable and sensitive tool for specific agent detection required in purity testing during vaccine development. This NGS method should be considered as an alternative tool of current purity testing for the prospective testing of biological products.

Development and Evaluation of Antigen-Specific Dual Matrix Pestivirus K ELISAs Using Longitudinal Known Infectious Status Samples

Pestivirus K, commonly known as atypical porcine pestivirus (APPV), is the most common cause of congenital tremor (CT) in pigs. Currently, there is limited information on the infection dynamics of and immune response against APPV and no robust serologic assay to assess the effectiveness of preventative measures. To that end, known infection status samples were generated using experimental inoculation of cesarean-derived, colostrum-deprived pigs. Pigs (2 per pen) were inoculated with minimum essential medium (n = 6; negative control) or APPV (n = 16). Serum, pen-based oral fluid samples, and nasal swabs were collected through 70 days postinoculation (dpi). The immune response to recombinant APPV Erns, E2, or NS3 antigens was evaluated using both serum and oral fluids via indirect enzyme-linked immunosorbent assays (ELISAs). APPV was detected by real-time reverse transcription-PCR (RT-qPCR) in all oral fluid and serum samples from APPV-inoculated animals by 24 and 35 dpi, respectively. All samples remained genome positive until 70 dpi. Detection of nasal shedding was less consistent, with APPV being detected by RT-qPCR in all inoculated animals at 42, 49, and 56 dpi. Antibodies were first detected in oral fluids at 14 dpi, 10 days before serum detection, and concurrently with the first oral fluids RT-qPCR detection. Across sample types and time points, the Erns ELISA outperformed the other targets. In conclusion, both oral fluid and serum APPV Erns ELISAs can be used to economically evaluate the individual and herd status prior to and following intervention strategies.

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.

Congenital tremor and splay leg in piglets – insights into the virome, local cytokine response, and histology

Background

Atypical porcine pestivirus (APPV) is a neurotropic virus associated with congenital tremor type A-II. A few experimental studies also indicate an association between APPV and splay leg. The overarching aim of the present study was to provide insights into the virome, local cytokine response, and histology of the CNS in piglets with signs of congenital tremor or splay leg.

Results

Characterization of the cytokine profile and virome of the brain in piglets with signs of congenital tremor revealed an APPV-associated upregulation of Stimulator of interferon genes (STING). The upregulation of STING was associated with an increased expression of the gene encoding IFN-α but no differential expression was recorded for the genes encoding CXCL8, IFN-β, IFN-γ, IL-1β, IL-6, or IL-10. No viral agents or cytokine upregulation could be detected in the spinal cord of piglets with signs of splay leg or in the brain of piglets without an APPV-infection. The histopathological examination showed no lesions in the CNS that could be attributed to the APPV-infection, as no difference between sick and healthy piglets could be seen.

Conclusion

The results from this study provide evidence of an APPV-induced antiviral cytokine response but found no lesions related to the infection nor any support for a common causative agent.

DNAJC14-Independent Replication of the Atypical Porcine Pestivirus

Atypical porcine pestiviruses (APPV; Pestivirus K) are a recently discovered, very divergent species of the genus Pestivirus within the family Flaviviridae. The presence of APPV in piglet-producing farms is associated with the occurrence of so-called “shaking piglets,” suffering from mild to severe congenital tremor type A-II. Previous studies showed that the cellular protein DNAJC14 is an essential cofactor of the NS2 autoprotease of all classical pestiviruses. Consequently, genetically engineered DNAJC14 knockout cell lines were resistant to all tested noncytopathogenic (non-cp) pestiviruses. Surprisingly, we found that the non-cp APPV can replicate in these cells in the absence of DNAJC14, suggesting a divergent mechanism of polyprotein processing. A complete laboratory system for the study of APPV was established to learn more about the replication of this unusual virus. The inactivation of the APPV NS2 autoprotease using reverse genetics resulted in nonreplicative genomes. To further investigate whether a regulation of the NS2-3 cleavage is also existing in APPV, we constructed synthetic viral genomes with deletions and duplications leading to the NS2 independent release of mature NS3. As observed with other pestiviruses, the increase of mature NS3 resulted in elevated viral RNA replication levels and increased protein expression. Our data suggest that APPV exhibit a divergent mechanism for the regulation of the NS2 autoprotease activity most likely utilizing a different cellular protein for the adjustment of replication levels.

IMPORTANCE DNAJC14 is an essential cofactor of the pestiviral NS2 autoprotease, limiting replication to tolerable levels as a prerequisite for the noncytopathogenic biotype of pestiviruses. Surprisingly, we found that the atypical porcine pestivirus (APPV) is able to replicate in the absence of DNAJC14. We further investigated the NS2-3 processing of APPV using a molecular clone, monoclonal antibodies, and DNAJC14 knockout cells. We identified two potential active site residues of the NS2 autoprotease and could demonstrate that the release of NS3 by the NS2 autoprotease is essential for APPV replication. Defective interfering genomes and viral genomes with duplicated NS3 sequences that produce mature NS3 independent of the NS2 autoprotease activity showed increased replication and antigen expression. It seems likely that an alternative cellular cofactor controls NS2-3 cleavage and thus replication of APPV. The replication-optimized synthetic APPV genomes might be suitable live vaccine candidates, whose establishment and testing warrant further research.

The Diversity and Spatiotemporally Evolutionary Dynamic of Atypical Porcine Pestivirus in China

The presence of congenital tremor (CT) type A-II in newborn piglets, caused by atypical porcine pestivirus (APPV), has been a focus since 2016. However, the source, evolutionary history, and transmission pattern of APPV in China remain poorly understood. In this study, we undertook phylogenetic analyses based on available complete E2 gene sequences along with 98 newly sequenced E2 genes between 2016 and 2020 in China within the context of global genetic diversity. The phylogenies revealed four distinct lineages of APPV, and interestingly, all lineages could be detected in China with the greatest diversity. Bayesian phylogenetic analyses showed that the E2 gene evolves at a mean rate of 1.22 × 10⁻³ (8.54 × 10⁻⁴-1.60 × 10⁻³) substitutions/site/year. The most recent common ancestor for APPVs is dated to 1886 (1837–1924) CE, somewhat earlier than the documented emergence of CT (1922 CE). Our phylogeographic analyses suggested that the APPV population possibly originated in the Netherlands, a country with developed livestock husbandry, and was introduced into China during the period 1837–2010. Guangdong, as a primary seeding population together with Central and Southwest China as epidemic linkers, was responsible for the dispersal of APPVs in China. The transmission pattern of “China lineages” (lineage 3 and lineage 4) presented a “south to north” movement tendency, which was likely associated with the implementation of strict environmental policy in China since 2000. Reconstruction of demographic history showed that APPV population size experienced multiple changes, which correlated well with the dynamic of the number of pigs in the past decades in China. Besides, positively selected pressure and geography-driven adaptation were supposed to be key factors for the diversification of APPV lineages. Our findings provide comprehensive insights into the diversity and spatiotemporal dynamic of APPV in China.

Development and use of a droplet digital PCR (ddPCR) assay to achieve sensitive and fast atypical porcine pestivirus detection

Atypical porcine pestivirus (APPV) is a recently discovered RNA virus, which mainly caused congenital tremor in piglets. Droplet digital PCR (ddPCR) is an absolute quantitative method that does not rely on the standard curve but has high sensitivity and accuracy. The present study aimed to develop a ddPCR detection assay for APPV. Furthermore, we evaluated the limit of detection, sensitivity, specificity and reproducibility of the ddPCR and real-time quantitative PCR (qPCR) and tested 135 clinical samples to calculate the detection rate of the two methods. The results showed that both methods had a strong linear relationship and quantitative correlation. The ddPCR assay had a minimum detection limit of 0.15 copies/μL for APPV, with a sensitivity 100 times that of qPCR. We tested clinical samples and found that the APPV ddPCR had a 27.4% positive detection rate, noticeably higher than that of the qPCR (14.8%). Additionally, the APPV ddPCR method had excellent repeatability and specificity. In brief, our study provided a novel, feasible and sensitive diagnostic technique to identify and monitor APPV.

New Emergence of the Novel Pestivirus Linda Virus in a Pig Farm in Carinthia, Austria

Linda virus (LindaV) was first identified in a pig farm in Styria, Austria in 2015 and associated with congenital tremor (CT) type A-II in newborn piglets. Since then, only one more LindaV affected farm was retrospectively discovered 10 km away from the initially affected farm. Here, we report the recent outbreak of a novel LindaV strain in a farrow-to-finish farm in the federal state Carinthia, Austria. No connection between this farm and the previously affected farms could be discovered. The outbreak was characterized by severe CT cases in several litters and high preweaning mortality. A herd visit two months after the onset of clinical symptoms followed by a diagnostic workup revealed the presence of several viremic six-week-old nursery pigs. These animals shed large amounts of virus via feces and saliva, implying an important epidemiological role for within- and between-herd virus transmission. The novel LindaV strain was isolated and genetically characterized. The findings underline a low prevalence of LindaV in the Austrian pig population and highlight the threat when introduced into a pig herd. Furthermore, the results urge the need to better understand the routes of persistence and transmission of this enigmatic pestivirus in the pig population.

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.

Detection and localization of atypical porcine pestivirus in the testicles of naturally infected, congenital tremor affected piglets

Atypical porcine pestivirus (APPV) belongs to the genus Pestivirus within the family Flaviviridae. Recently, APPV has been identified as the causative agent of congenital tremor (CT) type AII. The disease is a neurological disorder that affects newborn piglets and is characterized by generalized trembling of the animals and often splay legs. CT is well known worldwide, and the virus seems to be highly prevalent in major swine producing areas. However, little is known about the epidemiology of the infection, transmission and spread of the virus between herds. Here, we show the high prevalence of APPV in processing fluid samples collected from Hungarian pig herds which led us to investigate the cellular targets of the virus in the testicles of newborn piglets affected by CT. By the development of an RNA in situ hybridization assay and the use of immunohistochemistry on consecutive slides, we identified the target cells of APPV in the testicle: interstitial Leydig cells, peritubular myoid cells and smooth muscle cells of medium-sized arteries. Previous studies have shown that APPV can be found in the semen of sexually mature boars suggesting the role of infected boars and their semen in the transmission of the virus similar to many other members of the Flaviviridae family. As in our case, the virus has not been identified in cells beyond the Sertoli cell barrier, further studies on infected adult boars' testicles and other reproductive glands are needed to analyze the possible changes in the cell tropism of APPV that might contribute to its prolonged extraction by the semen beyond the period of viraemia.

Proposed Update to the Taxonomy of Pestiviruses: Eight Additional Species within the Genus Pestivirus, Family Flaviviridae

Pestiviruses are plus-stranded RNA viruses belonging to the family Flaviviridae. They comprise several important pathogens like classical swine fever virus and bovine viral diarrhea virus that induce economically important animal diseases. In 2017, the last update of pestivirus taxonomy resulted in demarcation of 11 species designated Pestivirus A through Pestivirus K. Since then, multiple new pestiviruses have been reported including pathogens associated with disease in pigs or small ruminants. In addition, pestivirus sequences have been found during metagenomics analysis of different non-ungulate hosts (bats, rodents, whale, and pangolin), but the consequences of this pestivirus diversity for animal health still need to be established. To provide a systematic classification of the newly discovered viruses, we analyzed the genetic relationship based on complete coding sequences (cds) and deduced polyprotein sequences and calculated pairwise distances that allow species demarcation. In addition, phylogenetic analysis was performed based on a highly conserved region within the non-structural protein NS5B. Taking into account the genetic relationships observed together with available information about antigenic properties, host origin, and characteristics of disease, we propose to expand the number of pestivirus species to 19 by adding eight additional species designated Pestivirus L through Pestivirus S.

Comparative Analysis of Tunisian Sheep-like Virus, Bungowannah Virus and Border Disease Virus Infection in the Porcine Host

Apart from the established pestivirus species Pestivirus A to Pestivirus K novel species emerged. Pigs represent not only hosts for porcine pestiviruses, but are also susceptible to bovine viral diarrhea virus, border disease virus (BDV) and other ruminant pestiviruses. The present study focused on the characterization of the ovine Tunisian sheep-like virus (TSV) as well as Bungowannah virus (BuPV) and BDV strain Frijters, which were isolated from pigs. For this purpose, we performed genetic characterization based on complete coding sequences, studies on virus replication in cell culture and in domestic pigs, and cross-neutralization assays using experimentally derived sera. TSV forms a distinct phylogenetic group more closely related to Pestivirus C (classical swine fever virus, CSFV) than to Pestivirus D (BDV). In contrast to BDV and BuPV, TSV replicates by far more efficiently on ovine than on porcine cells. Nevertheless, pigs were susceptible to TSV. As a consequence of close antigenic relatedness of TSV to CSFV, cross-reactivity was detected in CSFV-specific antibody assays. In conclusion, TSV is genetically closely related to CSFV and can replicate in domestic pigs. Due to close antigenic relatedness, field infections of pigs with TSV and other ruminant pestiviruses can interfere with serological diagnosis of classical swine fever.

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.

Atypical porcine pestivirus-A widespread virus in the Swedish wild boar population

The recently identified causative agent of congenital tremor in domestic piglets, atypical porcine pestivirus (APPV), was detected in serum from Swedish wild boar. A previous study from Sweden described APPV in domestic piglets suffering from congenital tremor, but the APPV situation in the wild boar population was unknown. In this study, 595 serum samples from wild boar originating from 13 counties in the south and central parts of Sweden, collected between 2000 and 2018, were analysed for the presence of the APPV-genome and for antibodies against the APPV-glycoprotein E^rns . The results revealed that APPV is highly abundant in the Swedish wild boar population; 12% (73/595) were APPV-genome positive in serum and 72% (433/595) of the tested wild boars displayed APPV-specific antibodies. The present study also shows that APPV has been present in the Swedish wild boar population since at least the year 2000. The viral sequences obtained from the wild boars were highly similar to those obtained from Swedish domestic pigs positive for APPV and suffering from congenital tremor, suggesting a viral exchange between wild boars and domestic pigs. The high proportion of viraemic and seropositive wild boar is indicative of wild boar being an important reservoir for APPV.

Vaccination with virus-like particles of atypical porcine pestivirus inhibits virus replication in tissues of BALB/c mice

Congenital tremor (CT) type A-II in piglets is a worldwide disease caused by an emerging atypical porcine pestivirus (APPV). Preparation and evaluation of vaccines in laboratory animals is an important preliminary step toward prevention and control of the disease. Here, virus-like particles (VLPs) of APPV were prepared and VLPs vaccine was evaluated in BALB/c mice. Purified E^rns and E2 proteins expressed in E. coli were allowed to self-assemble into VLPs, which had the appearance of hollow spherical particles with a diameter of about 100 nm by transmission electron microscopy (TEM). The VLPs induced strong antibody responses and reduced the viral load in tissues of BALB/c mice. The data from animal challenge experiments, RT-PCR, and immunohistochemical analysis demonstrated that BALB/c mice are an appropriate laboratory model for APPV. These results suggest the feasibility of using VLPs as a vaccine for the prevention and control of APPV and provide useful information for further study of APPV in laboratory animals.

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.

Prevalence of Linda Virus Neutralizing Antibodies in the Austrian Pig Population

A novel pestivirus species, termed Lateral-shaking Inducing Neuro-Degenerative Agent virus (LindaV), was discovered in a piglet-producing farm in Austria in 2015 related to severe congenital tremor cases. Since the initial outbreak LindaV has not been found anywhere else. In this study, we determined the seroprevalence of LindaV infections in the domestic pig population of Austria. A fluorophore labeled infectious cDNA clone of LindaV (mCherry-LindaV) was generated and used in serum virus neutralization (SVN) assays for the detection of LindaV specific neutralizing antibodies in porcine serum samples. In total, 637 sera from sows and gilts from five federal states of Austria, collected between the years 2015 and 2020, were analyzed. We identified a single serum showing a high neutralizing antibody titer, that originated from a farm (Farm S2) in the proximity of the initially affected farm. The analysis of 57 additional sera from Farm S2 revealed a wider spread of LindaV in this pig herd. Furthermore, a second LindaV strain originating from this farm could be isolated in cell culture and was further characterized at the genetic level. Possible transmission routes and virus reservoir hosts of this emerging porcine virus need to be addressed in future studies.

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.

Atypical Porcine Pestiviruses: Relationships and Conserved Structural Features

For two decades, the genus pestivirus has been expanding and the host range now extends to rodents, bats and marine mammals. In this review, we focus on one of the most diverse pestiviruses, atypical porcine pestivirus or pestivirus K, comparing its special traits to what is already known at the structural and functional level from other pestiviruses.

Detection of Atypical Porcine Pestivirus in Piglets from Danish Sow Herds

Atypical porcine pestivirus (APPV) was first discovered in North America in 2015 and was later shown to be associated with congenital tremor (CT) in piglets. CT is an occasional challenge in some Danish sow herds. Therefore, we initiated an observational case control study to clarify a possible relationship between CT and APPV in Danish pig production. Blood samples were collected from piglets affected by CT (n = 55) in ten different sow herds and from healthy piglets in five sow herds without a history of CT piglets (n = 25), as well as one sow herd with a sporadic occurrence of CT (n = 5). APPV was detected by RT-qPCR in all samples from piglets affected by CT and in three out of five samples from piglets in the herd with a sporadic occurrence of CT. In the herds without a history of CT, only one out of 25 piglets were positive for APPV. In addition, farmers or veterinarians in CT-affected herds were asked about their experience of the issue. CT is most often seen in gilt litters, and a substantial increase in pre-weaning mortality is only observed in severe cases. According to our investigations, APPV is a common finding in piglets suffering from CT in Denmark.

Porcine Complement Regulatory Protein CD46 Is a Major Receptor for Atypical Porcine Pestivirus but Not for Classical Swine Fever Virus

Pestiviruses comprise animal pathogens such as classical swine fever virus (CSFV) and bovine viral diarrhea virus (BVDV) that cause notifiable diseases with great economic impact. Several additional pestivirus species affecting animal health were recently identified, including atypical porcine pestivirus (APPV).

Pestiviruses such as bovine viral diarrhea virus (BVDV) and classical swine fever virus (CSFV) belong to the family Flaviviridae and represent pathogens of outstanding veterinary relevance. Pestiviruses enter cells via receptor-mediated endocytosis. For entry in bovine cells, complement regulatory protein CD46_bov serves as a cellular receptor for BVDV. In this study, the role of porcine CD46_pig in cellular entry was investigated for the recently discovered atypical porcine pestivirus (APPV), CSFV, and Bungowannah virus (BuPV) in order to elucidate the observed differences in host cell tropism. A cell culture-adapted APPV variant, which shows enhanced viral replication in vitro, was generated and demonstrated a strict tropism of APPV for porcine cells. One of the porcine cell lines displayed areas of CD46_pig-expressing cells and areas of nonexpressing cells, and one single cell line revealed not to express any CD46_pig. The CD46_pig-deficient porcine lymphoma cell line, known to facilitate CSFV replication, was the only porcine cell line nonpermissive to APPV, indicating a significant difference in the entry mechanism of APPV and CSFV. Infection experiments with a set of genetically engineered CD46_pig knockout cells confirmed that CD46_pig is a major receptor of APPV as CD46_bov is for BVDV. In contrast, it is apparently not an essential determinant in host cell entry of other porcine pestiviruses such as CSFV and BuPV. Existence of a CD46_pig-independent entry mechanism illustrates that the pestiviral entry process is more diverse than previously recognized.

IMPORTANCE Pestiviruses comprise animal pathogens such as classical swine fever virus (CSFV) and bovine viral diarrhea virus (BVDV) that cause notifiable diseases with great economic impact. Several additional pestivirus species affecting animal health were recently identified, including atypical porcine pestivirus (APPV). APPV is associated with health problems in piglets and is highly abundant in pig populations worldwide. Complement control protein CD46 serves as a receptor for diverse bacterial and viral pathogens, including particular adenoviruses, herpesviruses, measles virus (MeV), and BVDV. Porcine CD46 (CD46_pig) was suggested to be a major receptor for CSFV. Here, we identified remarkable differences in relevance of CD46_pig during entry of porcine pestiviruses. Resembling BVDV, efficient APPV infection in cell culture depends on CD46_pig, while other porcine pestiviruses can efficiently enter and infect cells in the absence of CD46_pig. Thus, the study provides insights into the entry process of these pathogens and may help to understand differences in their biology.

Genetic diversity and prevalence of Atypical Porcine Pestivirus in the Midwest of US swine herds during 2016-2018

Atypical porcine pestivirus (APPV), a highly divergent pestivirus, has a wide geographical distribution around the world. APPV is known to cause type A-II congenital tremors in newborn piglets. The main objective of this study is to access APPV prevalence in the US swine herds utilizing a newly developed quantitative real-time RT-PCR assay. Retrospective analysis of 1,785 samples revealed a 19.0% prevalence in Midwest swine herds over a period of three years (2016-2018). Among all clinical and field samples that were APPV positive, 82 samples (24.19%) were also positive for one or more swine viral pathogens. Two APPV US strains identified in this study demonstrated significant sequence diversity (~12% in full genome) compared to the first reported APPV strain from the United States in 2014. Of the two strains identified in this study, USA/023005/2016 is closer to two strains identified in Germany, and USA/047310/2017 shares more similarities with two US strains including Minnesota-1 and ISDVDL2014016573. Partial NS5B sequences (9127-9836 nt of the polyprotein gene) obtained from 54 APPV-positive samples revealed considerable sequence diversity, ranging from 85.8% to 100% nucleotide identity, within the US strains in samples from different geographic regions. Analysis of all US samples indicates high prevalence of APPV in Minnesota (37.35%), followed by Illinois (32.86%), Iowa (30.60%) and Kansas (21.89%). APPV was detected in 15.48% of samples assayed from 2017, slightly higher than that in 2016 (13.08%), but much lower than 2018 (28.77%). Among the various sample types tested, oral fluid samples had the highest prevalence and lowest average Ct value suggesting their suitability as a reliable diagnostic specimen for APPV detection. Overall, sequence variation among APPV strains and prevalence of the pathogen within the United States provides a basis for understanding the genetic diversity and molecular epidemiology of APPV in the US swine herds.

Comprehensive Analysis of Synonymous Codon Usage Bias for Complete Genomes and E2 Gene of Atypical Porcine Pestivirus

Atypical porcine pestivirus (APPV) is an emerging novel pestivirus causing the congenital tremor (CT) in piglets. The worldwide distribution characteristic of APPV make it a threat to global swine health. E2 is the major envelope glycoprotein of APPV and the crucial target for vaccine development. Considering the genetic variability of APPV complete genomes and its E2 gene as well as gaps for codon analysis, a comprehensive analysis of codon usage patterns was performed. Relative synonymous codon usage (RSCU) and effective number of codon (ENC) analyses showed that a relatively instable change existed and a slight low codon usage bias (CUB) were displayed in APPV genomes. ENC-plot analysis and correlation analyses of nucleotide compositions and ENC showed that mutation pressure and natural selection both affected the codon usage bias of the APPV and natural selection had a more obvious influence for E2 gene compared with complete genomes. Principal component analysis (PCA) and correlation analyses confirmed the above results. Correlation analyses between Gravy and Aromaticity values and the codon bias showed that natural selection played an important role in shaping the synonymous codon bias. Furthermore, neutrality plot analysis showed that natural selection was the main force while mutation pressure was a minor force influencing the codon usage pattern of the APPV E2 gene and complete genomes. The results could illustrate the codon usage patterns of APPV genomes and provided valuable basic data for further fundamental research of evolution of APPV.

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.

Atypical Porcine Pestivirus Circulation and Molecular Evolution within an Affected Swine Herd

Atypical porcine pestivirus (APPV) is a single-stranded RNA virus from the family Flaviviridae, which is linked to congenital tremor (CT) type A-II in newborn piglets. Here, we retrospectively investigated the molecular evolution of APPV on an affected herd between 2013 and 2019. Monitoring was done at regular intervals, and the same genotype of APPV was found during the entire study period, suggesting no introductions from outside the farm. The nucleotide substitutions over time did not show substantial amino acid variation in the structural glycoproteins. Furthermore, the evolution of the virus showed mainly purifying selection, and no positive selection. The limited pressure on the virus to change at immune-dominant regions suggested that the immune pressure at the farm might be low. In conclusion, farms can have circulation of APPV for years, and massive testing and removal of infected animals are not sufficient to clear the virus from affected farms.

Classical swine fever virus: the past, present and future

Classical swine fever (CSF) is among the most relevant viral epizootic diseases of swine. Due to its severe economic impact, CSF is notifiable to the world organisation for animal health. Strict control policies, including systematic stamping out of infected herds with and without vaccination, have permitted regional virus eradication. Nevertheless, CSF virus (CSFV) persists in certain areas of the world and has re-emerged regularly. This review summarizes the basic established knowledge in the field and provides a comprehensive and updated overview of the recent advances in fundamental CSFV research, diagnostics and vaccine development. It covers the latest discoveries on the genetic diversity of pestiviruses, with implications for taxonomy, the progress in understanding disease pathogenesis, immunity against acute and persistent infections, and the recent findings in virus-host interactions and virulence determinants. We also review the progress and pitfalls in the improvement of diagnostic tools and the challenges in the development of modern and efficacious marker vaccines compatible with serological tests for disease surveillance. Finally, we highlight the gaps that require research efforts in the future.

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.

Detection of atypical porcine pestivirus in Swedish piglets with congenital tremor type A-II

Background

Congenital tremor (CT) type A-II is a neurological disorder characterized by tremor of the head and body of newborn piglets. The suggested causative agent of the disease is the recently found atypical porcine pestivirus (APPV). The virus has been detected in piglets suffering from congenital tremor in central Europe, South and North America and in China but no studies has so far been performed in the Nordic countries. The overarching goal of this study was to investigate if APPV is present in the brain tissue of Swedish piglets suffering from congenital tremor.

From June 2017 – June 2018, 15 piglets from four Swedish farms with ongoing outbreaks of congenital tremor and 13 piglets with splay leg originating from four different farms, were investigated for presence of APPV RNA in brain tissue. Matched healthy control piglets (n = 8) were also investigated. Two APPV-specific RT-qPCR methods targeting the NS3 and NS5B region, respectively, were used. A retrospective study was performed on material from Swedish piglets with congenital tremor sampled in 2004 (n = 11) and 2011/2012 (n = 3) using the described APPV-specific RT-qPCR methods. The total number of piglets with signs of CT in this study was 29.

Results

Atypical porcine pestivirus-RNA was detected in 93% (27/29) of the piglets suffering from congenital tremor. All piglets with congenital tremor from 2004 (n = 11) and 2012 (n = 3) were PCR-positive with respect to APPV, whereas, all of the healthy controls (n = 11) were negative. The piglets with congenital tremor sampled 2017–2018 had an odds ratio of 91.8 (95% CI 3.9128 to 2153.7842, z = 2.807, P = 0.0050) to test positive for APPV by qRT-PCR compared to the healthy piglets (Fishers exact test p < 0.0001). These findings make it interesting to continue investigating APPV in the Swedish pig-population.

Conclusion

This is the first description of atypical porcine pestivirus in piglets suffering from congenital tremor type A-II in Sweden and the Nordic countries. The virus has been present in the Swedish pig population since at least 2004.

Genetic characterization and recombination analysis of atypical porcine pestivirus

Atypical porcine pestivirus (APPV) is recognised as the etiology of congenital tremor (CT) Type A-II and poses a challenge to pig production. Here, we described a CT case in piglets caused by APPV infection in central China in 2017. Interestingly, different from a previous report, more CT litters were observed in the second and third parity sows compared to the first and fourth parity. Evolutionary analysis and recombination evaluation were conducted for the isolate and 61 APPV genomes were available in GenBank. Phylogenetic analysis revealed a high level of genetic variation of APPV and the coexistence of three clades (Clades I-III) in China. The isolate was clustered into Clade I, which seemed to be prevalent worldwide and displayed higher genetic variability (Subgroups 1-4) compared with Clade II and Clade III, both of which were only reported in China. Notably, three putative recombinants were identified and characterized in APPV. The recombination events occurred in inter-clades (Clade II and III) or intra-clades (Clade I). To the best of our knowledge, this study presents the first evidence of homologous recombination within Pestivirus K. These results provide new clinical presentations of APPV infection and may be helpful in better understanding the large amount of genetic variations in this genus.

Prevalence and Genetic Diversity of Atypical Porcine Pestivirus (APPV) Detected in South Korean Wild Boars

Atypical porcine pestivirus (APPV), currently classified as pestivirus K, causes congenital tremor (CT) type A-II in piglets. Eighteen APPV strains were identified from 2297 South Korean wild boars captured in 2019. Phylogenetic analysis of the structural protein E2 and nonstructural proteins NS3 and Npro classified the APPV viruses, including reference strains, into Clades I, II and III. Clade I was divided into four subclades; however, the strains belonging to the four subclades differed slightly, depending on the tree analysis, the NS3, E2, and Npro genes. The maximum-likelihood method was assigned to South Korean wild boar APPV strains to various subclades within the three trees: subclades I.1 and I.2 in the E2 tree, subclade I.1 in the Npro tree, and subclades I.1 and I.4 in the NS3 ML tree. In conclusion, APPV among South Korean wild boars belonging to Clade I may be circulating at a higher level than among the South Korean domestic pig populations.

Seroprevalence of atypical porcine pestivirus in a closed pig herd with subclinical infection

Atypical porcine pestivirus (APPV) has recently been reported to be associated with congenital tremor in newborn piglets. Only limited information is available about the prevalence at herd level in endemically infected herds. Therefore, the aim of this study was to determine the within-herd prevalence of APPV in a sub-clinically infected sow herd in Switzerland and to analyse associations between the serological status as well as the age and sex of the pigs, litter number and days after the last insemination. In a census sampling, blood was collected from 125 sows, aged 180 days or older, and six boars. Sera were examined applying an indirect APPV-specific ELISA to individual sera and an APPV RT-PCR targeting the NS3 encoding regions of APPV to pools of five. The APPV antibody status was classified into low (S/P value ≤ 0.5), intermediate (S/P value = 0.5-1) and high reactivity (S/P value > 1.0). None of the pooled serum samples was positive for specific genome fragments of APPV. Of the 131 samples, 53.4% were highly reactive, 39.7% showed an intermediate reactivity, and 6.9% showed a low reactivity in the indirect ELISA, that is, were serologically negative. Significant associations between the S/P values and the age of the pigs (p < .001), the litter number (p < .001) and the numbers of days after the last insemination (p = .0188) were observed. The results indicate that this sow herd was previously infected with APPV, while viremia was not detected in any of the adult pigs. This might explain the absence of clinical signs in the suckling pigs. Potential reinfection and circulation of APPV in this sow herd might be due to semen from commercial boar studs or APPV-positive animals in the absence of specific clinical signs.

A review of congenital tremor type A-II in piglets

Congenital tremor (CT) is a neurological disease that affects new-born piglets. It was described in 1922 and six different forms, designated type AI-V and type B, are described based on the causative agents, as well as specific histological findings in the central nervous system (CNS). The various forms present with identical clinical signs consisting of mild to severe tremor of the head and body, sometimes complicated with ataxia. By definition, all A-forms have hypomyelination of the CNS, whereas there are no histopathological lesions with the B-form. The cause of the A-II form was long unknown, however, at present several different viruses have been proposed as the causative agent: porcine circovirus-II (PCV-II), astrovirus, PCV-like virus P1, and atypical porcine pestivirus (APPV). Currently, APPV is the only virus that has been proven to fulfill Mokili's Metagenomic Koch's Postulates. Following infection of the pregnant sow, the virus passes the placental barrier and infects the fetus. Interestingly, no clinical signs of disease have been associated with APPV in adult pigs. Furthermore, other viruses cannot be ruled out as additional potential causes of CT. Given the increased interest and research in CT type A-II, the aim of this review is to summarize current knowledge.

Detection of atypical porcine pestivirus genome in newborn piglets affected by congenital tremor and high preweaning mortality1

Recently, piglets from a high-health status farm began exhibiting congenital tremors, high preweaning mortality and incidence of splayed legs. Postmortem histological examination identified a small number of scattered white matter vacuoles in the cerebellum and underlying brainstem of affected piglets. Presence of potential viral sources associated with this neurologic condition was initially infirmed using quantitative PCR for atypical porcine pestivirus (APPV), porcine teschovirus, and porcine sapelovirus. Using metagenomic analysis, APPV was identified as the main microbial species in serum obtained from piglets affected by congenital tremor. These piglets had higher preweaning mortality rates (46.4% vs. 15.3%) and incidence of splayed legs (33.0% vs. 0.8 %) compared to unaffected piglets. Piglets affected by congenital tremor had higher viral titer (P < 0.15) and larger birth weights (P < 0.05) compared to normal litter mates. Whole-genome sequencing and genome assembly of the novel APPV strain (MK728876) was carried out using Oxford Nanopore and related bioinformatics pipelines. Phylogenic analysis demonstrated that this strain along with other completely sequenced APPV strains were grouped into 2 clades, both including strains-inducing congenital tremor. Strains appear to cluster based on region but there were still significant differences within regions. Future research needs to address potential underdiagnosis due to genetic diversity but also to understand mode of transmission, variation in virulence, and the role of host genetics in APPV susceptibility.

Molecular Survey and Phylogenetic Analysis of Atypical Porcine Pestivirus (APPV) Identified in Swine and Wild Boar from Northern Italy

Atypical porcine pestivirus (APPV) is a newly recognized member of the Flaviviridae family. This novel porcine pestivirus was first described in 2015 in the USA, where it has been associated with congenital tremor type A-II in new-born piglets. APPV is widely distributed in domestic pigs in Europe and Asia. In this study, a virological survey was performed in Northern Italy to investigate the presence of APPV using molecular methods. Testing of 360 abortion samples from pig herds revealed two APPV strains from distinct provinces in the Lombardy region and testing of 430 wild boar blood samples revealed three strains, one from Lombardy and two from Emilia Romagna. The nucleotide sequencing of a fragment of the nonstructural protein 3-coding region revealed a high similarity to the previously detected European strains (Spanish, German, and Italian) of APPV.

Seroprevalences of Newly Discovered Porcine Pestiviruses in German Pig Farms

Several novel porcine pestiviruses that are linked to disease outbreaks in commercial pig farms were discovered during recent years. Bungowannah pestivirus (BuPV; new species Pestivirus F) causes sudden death in young pigs, but has only ever been isolated in the Australian region Bungowannah. Atypical porcine pestivirus (APPV; new species Pestivirus K) on the other hand has been found in multiple countries worldwide and is potentially linked to congenital tremor, a disease that causes considerable production problems in pig farms. To assess the seroprevalences of both viruses in German commercial farms during the years 2009/10 and 2018, two approaches were selected. Antibodies against Pestivirus F were detected by a traditional in-house indirect immunofluorescence test against the culture-grown virus isolate, while for the detection of Pestivirus K-specific antibodies, a newly developed test system utilizing a chimeric construct of bovine viral diarrhea virus 1 (BVDV-1; species Pestivirus A) containing the E1 and E2 encoding sequences of APPV was established. A total of 1115 samples originating from 122 farms located in seven German federal states were investigated. Antibodies against Bungowannah virus could not be detected, confirming the absence of this virus in other regions than the initially affected Australian pig farm complex. In contrast, antibodies against APPV were highly prevalent throughout Germany at both investigated time points. The seroprevalence at the state level fluctuated to some degree, but the overall percentage remained stable, as is to be expected for an endemic pestivirus lacking any form of control measures.

Characterization of the Humoral Immune Response Induced after Infection with Atypical Porcine Pestivirus (APPV)

Atypical porcine pestivirus (APPV) is a widely distributed pathogen causing congenital tremor (CT) in piglets. So far, no data are available regarding the humoral immune response against APPV. In this study, piglets and their sows from an affected herd were tested longitudinally for viral genome and antibodies. APPV genome was detected in the majority of the piglets (14/15) from CT affected litters. Transient infection of gilts was observed. Kinetics of E^rns- and E2-specific antibodies and their neutralizing capacity were determined by recently (E^rns) and newly (E2) developed antibody ELISAs and virus neutralization assays. Putative maternally derived antibodies (MDA) were detected in most piglets, but displayed only low to moderate neutralizing capacity (ND₅₀ ≤ 112). Horizontal APPV transmission occurred when uninfected and infected piglets were mingled on the flat deck. Horizontally infected piglets were clinically inapparent and showed only transient viremia with subsequently consistently high E2 antibody levels. For piglets from CT affected litters, significantly lower neutralizing antibody titers were observed. Results indicate that E2 represents the main target of neutralizing antibodies. Characterization of the humoral immune response against APPV will help to provide valuable serological diagnosis, to understand the epidemiology of this novel pathogen, and to implement tailored prevention strategies.

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.

Detection and Genetic Characterization of Atypical Porcine Pestivirus in Piglets With Congenital Tremors in Southern China

Atypical porcine pestivirus (APPV) is an RNA virus newly discovered from swine in Asia, Europe, and the Americas. This novel virus has been confirmed as the cause of congenital tremor (CT) in piglets, which causes extensive economic losses to the swine industry. To investigate the genetic diversity and evolutionary relationship of APPV in China, 83 piglet samples with severe CT clinical signs were obtained from 12 commercial swine farms in 3 provinces of Southern China. RT-PCR revealed that the positive rates of APPV were as high as 100% (12/12) for the swine farms and 90.4% (75/83) for the samples. Subsequently, 21 positive samples and 3 positive samples were selected for partial E2 gene and complete polyprotein gene sequencing, respectively. Phylogenetic analysis showed that 62.5% of the sequences belonged to a novel APPV clade provisionally named genotype 3, which showed 81.0–82.1% sequence identity to genotypes 1 and 2. Amino acid sequence alignment showed that E2 protein of genotype 3 has three specific mutation sites, namely I19V, Y82F, and N107G. The results of the present study demonstrate that a novel APPV subgenotype, which is widely distributed in severe CT clinical samples in Southern China, was genetically diverse. We advocate for the inclusion of genotype 3 during revision of the APPV typing method.

Genetic variability of porcine pegivirus in pigs from Europe and China and insights into tissue tropism

Pegiviruses belong to the family Flaviviridae and have been found in humans and other mammalian species. To date eleven different pegivirus species (Pegivirus A-K) have been described. However, little is known about the tissue tropism and replication of pegiviruses. In 2016, a so far unknown porcine pegivirus (PPgV, Pegivirus K) was described and persistent infection in the host, similar to human pegivirus, was reported. In this study, qRT-PCR, phylogenetic analyses and fluorescence in situ hybridization (FISH) were implemented to detect and quantify PPgV genome content in serum samples from domestic pigs from Europe and Asia, in tissue and peripheral blood mononuclear cell (PBMC) samples and wild boar serum samples from Germany. PPgV was detectable in 2.7% of investigated domestic pigs from Europe and China (viral genome load 2.4 × 10² to 2.0 × 10⁶ PPgV copies/ml), while all wild boar samples were tested negative. Phylogenetic analyses revealed pairwise nucleotide identities >90% among PPgVs. Finally, PPgV was detected in liver, thymus and PBMCs by qRT-PCR and FISH, suggesting liver- and lymphotropism. Taken together, this study provides first insights into the tissue tropism of PPgV and shows its distribution and genetic variability in Europe and China.

12 novel atypical porcine pestivirus genomes from neonatal piglets with congenital tremors: A newly emerging branch and high prevalence in China

Atypical porcine pestivirus (APPV), a newly discovered member of the genus Pestivirus, is considered to be associated with congenital tremors (CT) in piglets. From June 2016 to January 2018, 440 serum and tissue samples from CT-affected piglets in Anhui, Guangdong and Guangxi provinces were collected to detect APPV. The results showed a high level of 63.4% preference for APPV in 27 swine farms and complicated co-infection cases between APPV and other 12 swine viruses. Meanwhile, 12 novel APPV genomes were screened and identified. Results showed that complete genomes, N^pro and NS5A genes of these novel 12 APPV sequences revealed 80.5%-99.8%, 78%-100% and 76.9%-99.8% nucleotide identities, respectively. Phylogenetic analyses based on sequences of full-length genomes, N^pro and NS5A genes of APPV indicated three well-defined clades including a newly emerging branch in China. This study provides novel epidemiological information of APPV in China.

Atypical Porcine Pestivirus (APPV) as a New Species of Pestivirus in Pig Production

The genus Pestivirus, which belongs to the family Flaviviridae, includes ssRNA+ viruses responsible for infectious diseases in swine, cattle, sheep, goats, and other domestic and wild animals. Recently, several putative pestiviruses species have been discovered and characterized in mammalian species (giraffe pestivirus, antelope pestivirus, HoBi virus, Bungowannah virus, and Linda virus); one of these is a genetically distinct pestivirus, named atypical porcine pestivirus (APPV), discovered using the next-generation sequencing technology. APPV has been detected in piglets with congenital tremor (CT) from four different continents, including North America, South America, Europe, and Asia. There is strong evidence that experimental inoculation and in field outbreaks involving APPV induce CT in piglets. Additionally, splay leg (SL) syndrome has been observed concurrently with CT, and it was induced by APPV in experimental studies and some field cases. Animals with a persistent and/or chronic infection condition can shed the virus over time. Viral-RNA is frequently detected in different tissues from CT-piglets; however, high loads of APPV are detected most consistently in central nervous tissue. Moreover, the APPV genome has been recently detected in semen and preputial swabs from boar studs, as well as in serum and tissue samples from wild boars and domestic adult pigs, all known to be clinically healthy. Phylogenetic analysis revealed that the APPV sequence (complete or partial polyprotein) exhibits high genetic diversity between viral strains detected in different countries and formed independent clusters according to geographic location. Additional studies are needed to evaluate the molecular detection and sero-prevalence of APPV around the world. Lastly, more research is needed to understand clinical presentations associated with APPV infection, as well as the economic losses related to the virus in pig production worldwide.

Prevalence and genome characteristics of atypical porcine pestivirus in southwest China

Atypical porcine pestivirus (APPV) causes congenital tremor (CT) in piglets and has a wide geographical distribution. In this study, we evaluated APPV prevalence using 165 piglet sera from southwest China. Viral RNA was detectable by qRT-PCR in 43.6 % (17/39, 95 % CI 27.8-60.4 %) of piglets with CT, while viral RNA was not detected in the sera of any healthy piglets. The seven complete APPV genomes were obtained from distinct farms and were 11 269-11 459 nucleotides in length. The genomes of the seven strains shared 82.8-98 % identity with the APPV reference strains. Phylogenetic analysis of the complete genomes as well as E2 and Nrpo sequences revealed that the seven APPVs clustered into two groups: four strains belonged to genogroups A and D and three strains belonged to a novel APPV genotype, tentatively called genogroup E. This study provides important insights into the epidemiological features and genetic diversity of APPV.