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

Prevalence estimation of Pestivirus scrofae (atypical porcine pestivirus) among Hungarian pig herds and the effects of different sample types on detection rates

BACKGROUND

Atypical porcine pestivirus (APPeV), also known as Pestivirus scrofae, is a member of the Pestivirus genus within the Flaviviridae family. Experimental infections have directly linked APPeV to congenital tremor (CT) type A-II in congenitally infected piglets born to challenged sows. Here, we report the assessment of the prevalence of APPeV in Hungarian pig herds and the influence of different sample types on detection rates.

RESULTS

Altogether, 2650 blood serum, 198 oral fluid and 163 processing fluid samples were obtained via a systemic approach from 26 Hungarian farms and one Slovakian farm. The samples originated from different age groups and were analyzed via reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The estimated prevalence of APPeV was determined to be 66.67% in the sampled farms, indicating the widespread distribution of the virus within Hungary. Within the positive farms, APPeV genetic material was detected in the serum (21%), processing fluid (57%), and oral fluid (72%) samples. Notably, in some farms, the presence of APPeV was confirmed in only specific sample types, and five farms had APPeV in all three sample types. Age group analysis revealed that 10-week-old animals had the highest positivity rate in their blood serum (27%), whereas 20-week-old animals presented the highest rate in their oral fluid samples (59%). Processing fluid and oral fluid samples proved to be valuable for noninvasive diagnostic matrices, allowing for efficient population-level virus detection. We determined the partial NS2-3 coding region of 15 Hungarian strains and a Slovakian strain, and our phylogenetic analysis revealed that very similar strains can be found on different farms.

CONCLUSION

In conclusion, our study provides insights into APPeV prevalence in Hungarian pig herds, emphasizing the importance of different sample types for accurate diagnostics. These findings contribute to our understanding of the virus's distribution across different age groups.

Isolation and Phylogenetic Analysis of Atypical Porcine Pestivirus Isolates Identified in Russian Swine Herds

Atypical porcine pestivirus (APPV) was first identified in 2015 in North America by high-throughput sequencing. APPV is associated with congenital tremor A-II and is widely distributed worldwide. In this study, a total of 2630 samples of domestic pigs obtained from 14 regions of Russia from 2020 to 2024 were screened for APPV presence by qRT-PCR. APPV was detected in 12 farms located in eight regions. The overall positive rate was 8.8%. It has been established that APPV has been circulating in Russian swine herds since at least 2020. The phylogenetic analysis demonstrated that the Russian isolates are variable and assigned into three clusters. The isolates from the Krasnoyarsk Krai, Belgorod, Tomsk, and Kursk regions and the Republic of Buryatia share a high nucleotide identity (94.3-98.8%) with the Hungarian strains, while the isolates from the Moscow and Pskov regions share a nucleotide identity (89.2-94.3%) with strains from the USA. The isolate from the Republic of Mordovia has a high nucleotide identity (97.1%) with the South Korean strain. In vitro studies of the Russian isolates revealed the replication of the Belgorod 151 strain in SPEV cells. Thus, this is the first large-scale study that confirms the circulation of APPV in swine herds in Russia and describes its isolation in cell culture.

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.

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.

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.

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.