Phylogeny and evolution of porcine teschovirus 8 isolated from pigs in China with reproductive failure

Analysis on the genome of a teschovirus type 1 isolates with swine diarrhea

Porcine Teschoviruses (PTVs) are associated with polioencephalomyelitis and various diseases, including reproductive and gastrointestinal disorders of pigs and wild boars, but rarely detected in the feces of pigs. In this study, a sample of swine diarrhea that tested positive for PTVs is subjected to high-throughput sequencing. The viral genome was 7221 nucleotides (nt) in length, which was consisted of twelve genes. Phylogenetic analysis showed and it was closely related to the PTV-HNMY(MG755212.1). The nucleotide homology of VP1 gene of PTVs JS2021 with PTV-1AF 296102.1 reached 82.97%, belonging to a branch of PTV-1 serotype. The nucleotide homology of VP1 protein with other serotypes of PTV is quite different from that of other serotypes of PTV. Bioinformatics analysis showed that PTVs have four capsid proteins, namely VP1, VP2, VP3 and VP4. The VP1 encodes a 29 kDa protein, which is the main protective antigen, a theoretical isoelectric point of 6.73, no transmembrane domain, no signal peptide and potential phosphorylation site. The VP1 protein is an unstable hydrophilic intracellular protein, which contains four secondary structures: irregular curl (c), extended chain (e), α-helix (h) and β-folded (t). The tertiary structure is heart-shaped and has multiple B cell epitopes. By analyzing the tertiary structure, we found that the amino acid at position 129 of VP1 mutated and reduction a larger alpha helix. This may lead to the main cause of piglet diarrhea. These findings enriched our knowledge of the viruses in the role of swine diarrhea, and help to develop an effective strategy for disease prevention and control.

Detection of porcine enteric picornaviruses from faecal samples of Indian pigs

Porcine enteric picornaviruses often consequence diarrhoea and nervous complications in pig and pose enormous loss to pig farming. The present study expands the limited Indian data of porcine enteric picornaviruses which is needed for the early implementation of control measures and to check further outbreaks. A total of 398 porcine faecal samples from Uttar Pradesh, Madhya Pradesh, Chhattisgarh and Jharkhand state of India were screened for porcine teschovirus (PTV), porcine sapelovirus (PSV) and enterovirus G (EV-G) by reverse transcriptase-polymerase chain reaction (RT-PCR) using 5'UTR-specific primers. The prevalence of PTV, PSV and EV-G was found to be 12.81% (51/398), 5.77% (23/398) and 24.37% (97/398), respectively. EV-G was relatively higher in circulation in Indian pigs among all the included enteric picornaviruses. Conversely, the concurrent infection of more than one enteric picornavirus was also frequent.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-022-00756-0.

Porcine teschovirus, sapelovirus, and enterovirus in Swiss pigs: multiplex RT-PCR investigation of viral frequencies and disease association

Porcine teschovirus (PTV), sapelovirus (PSV-A), and enterovirus (EV-G) are enteric viruses that can infect pigs and wild boars worldwide. The viruses have been associated with several diseases, primarily gastrointestinal, neurologic, reproductive, and respiratory disorders, but also with subclinical infections. However, for most serotypes, proof of a causal relationship between viral infection and clinical signs is still lacking. In Switzerland, there has been limited investigation of the occurrence of the 3 viruses. We used a modified multiplex reverse-transcription PCR protocol to study the distribution of the viruses in Swiss pigs by testing 363 fecal, brain, and placental or abortion samples from 282 healthy and diseased animals. We did not detect the 3 viruses in 94 placental or abortion samples or in 31 brain samples from healthy pigs. In brain tissue of 81 diseased pigs, we detected 5 PSV-A and 4 EV-G positive samples. In contrast, all 3 viruses were detected at high frequencies in fecal samples of both healthy and diseased pigs. In healthy animals, PTV was detected in 47%, PSV-A in 51%, and EV-G in 70% of the 76 samples; in diseased animals, frequencies in the 81 samples were 54%, 64%, and 68%, respectively. The viruses were detected more frequently in fecal samples from weaned and fattening pigs compared to suckling piglets and sows. Co-detections of all 3 viruses were the most common finding. Based on clinical and pathology data, statistical analysis yielded no evidence for an association of virus detection and disease. Further research is required to determine if pathogenicity is linked to specific serotypes of these viruses.

Isolation and genetic characteristics of a neurotropic teschovirus variant belonging to genotype 1 in northeast China

Porcine teschovirus (PTV) is a causative agent of reproductive disorders, encephalomyelitis, respiratory diseases, and diarrhea in swine, with a worldwide distribution. In this work, we identified PTV-associated nonsuppurative encephalitis as a potential cause of posterior paralysis in neonatal pigs in northeast China. Using indirect immunofluorescence assay, western blot, electron microscopy, and genome sequencing, we identified a neurotropic PTV strain, named CHN-NP1-2016, in the supernatants of pooled cerebrum and cerebellum samples from an affected piglet. Nucleotide sequence alignment revealed that the whole genome of CHN-NP1-2016 shared the highest sequence similarity (86.76% identity) with PTV 1 strain Talfan. A combination of phylogenetic and genetic divergence analysis was applied based on the deduced amino acid sequence of the P1 gene with a cutoff value of the genetic distance (0.102 ± 0.008) for defining PTV genotypes, and this showed that CHN-NP1-2016 is a variant of genotype 1. In total, 16 unique mutations and five mutant clusters were detected in the capsid proteins VP1 and VP2 of CHN-NP1-2016 when compared to other PTV1 isolates. Importantly, we detected three mutant clusters located in the exposed surface loops of the capsid protein, potentially indicating significant differences in major neutralization epitopes. Moreover, a potential recombination event in the P1 region of PTV CHN-NP1-2016 was detected. These findings provide valuable insights into the role of recombination in the evolution of teschoviruses. To our knowledge, this is the first case report of PTV-1-associated encephalitis in northeast China. Future investigations will narrow on the serology and pathogenicity of this novel isolate.

Identification of novel genotypes belonging to the species Teschovirus A from indigenous pigs in western Jiangxi, China

Teschovirus A is currently the sole species in the genus Teschovirus, whose members are divided into 13 subtypes: porcine teschovirus (PTV) 1-13. However, recent discoveries of novel PTV genotypes have suggested that a new species, "Teschovirus B", should be established. Here, we have identified six of the 19 known genotypes and two novel genotypes (PTV 17-18), revealing the high genetic diversity of the PTV subpopulation in indigenous pigs of western Jiangxi, China. Moreover, we determined the nearly complete genome sequences of PTV 17-SG9 and PTV 18-SG10. Together with PTV 1-13, these novel genotypes were confirmed to be members of the species Teschovirus A based on phylogenetic and genetic divergence analysis. Consequently, the species Teschovirus A now includes at least 15 PTV genotypes.

Identification and genotypic characterization of porcine teschovirus from selected pig populations in India

Porcine teschovirus (PTV) previously classified as porcine enteroviruses in the family Picornaviridae are associated with a wide range of illnesses in swine ranging from asymptomatic infection to acute fatal encephalomyelitis, diarrhea, and pneumonia. This study was planned to investigate whether porcine teschovirus is prevalent among pigs in India and to characterize the PTV identified in the study population. The study conducted in certain farms of North India revealed that 13 of 190 (6.84%) fecal samples were PTV positive by RT-PCR. Three viruses were successfully isolated from fecal samples using IB-RS-2 cell lines which were confirmed by RT-PCR and sequencing. Molecular characterization based on the VP1 region of the viral genome identified the isolated viruses as serotype 5 and serotype 8 of PTV. A new variant of teschovirus was also identified which showed significant nucleotide diversity from the known serotypes of the teschoviruses. This is the first report of isolation, identification, and characterization of porcine teschoviruses in India.

Novel species of Teschovirus B comprises at least three distinct evolutionary genotypes

Conventionally, Porcine teschovirus (PTV) consists of 13 genotypes (PTV 1-13, which belong to Teschovirus A); however, several novel members including PTV 14-22 have been discovered recently. PTV 21 was identified as a novel Teschovirus species named Teschovirus B. In this study, almost all 22 reported PTV genotypes except PTV 6, 7, 12 and 20 were identified in the pig populations of western Jiangxi, China, which reflects the high genotype diversity. Moreover, to the best of our knowledge, the nearly complete genome of PTV 22-JiangX1 was first sequenced in the present study. The homology comparison of the polyprotein genes showed that PTV 22-JiangX1 shared a relatively high nucleotide and deduced amino acid sequence identities ranging from 78.3% to 82.0% and 84.6% to 89.3%, respectively, with PTV 19 and 21. Additionally, the PTV strain of JiangX1 represents genotype 22 with the PTV 19, and 21 strains proved to be members of Teschovirus B based on the phylogenetic and evolutionary divergence analyses. Finally, we determined that the novel Teschovirus B species comprises at least three PTV genotypes.

Longitudinal survey of Teschovirus A, Sapelovirus A, and Enterovirus G fecal excretion in suckling and weaned pigs

Fecal samples from 27 pigs were longitudinally analyzed for Teschovirus A (TV-A), Sapelovirus A (SV-A), and Enterovirus G (EV-G) RNA presence. Suckling piglet fecal samples were negative for the three enteric picornaviruses. However, these picornaviruses were detected in 22/27 weaned pig fecal samples. This study provides new data on TV-A, SV-A, and EV-G infection dynamics.

Metagenomic identification and sequence analysis of a Teschovirus A-related virus in porcine feces in Japan, 2014-2016

Porcine Teschoviruses (PTVs) are associated with polioencephalomyelitis and various diseases, including reproductive and gastrointestinal disorders, of pigs and wild boars, and are also detected in the feces of healthy pigs. The genus Teschovirus contains a single species Teschovirus A that currently includes 13 serotypes. In the present study, we identified novel PTVs that are distantly related to Teschovirus A and were found in fecal samples of pigs with or without diarrhea in Japan. Phylogenetic analysis of amino acid (aa) sequences of the complete coding region revealed that these newly identified viruses did not cluster with any strains of PTVs or other strains within the picornavirus supergroup 1, suggesting that the viruses may not belong to Teschovirus A or any genus of the family Picornaviridae. These novel PTVs share a type IV internal ribosomal entry site and conserved characteristic motifs in the coding region, yet exhibit 62.2-79.0%, 86.6-92.8%, 77.1-81.0%, and 84.3-86.7% aa identities to PTV strains in P1, 2C, 3C, and 3D regions, respectively. In contrast, PTV 1-13 strains of the Teschovirus A share 76.5-92.1%, 88.1-99.7%, 93.2-100%, and 95.8-100% aa identities in the P1, 2C, 3C, and 3D, respectively, within the species. These data imply that the newly identified viruses belong to teschoviruses, and may represent a novel species in the genus Teschovirus.

Genetic diversity and recombination of enterovirus G strains in Japanese pigs: High prevalence of strains carrying a papain-like cysteine protease sequence in the enterovirus G population

To study the genetic diversity of enterovirus G (EV-G) among Japanese pigs, metagenomics sequencing was performed on fecal samples from pigs with or without diarrhea, collected between 2014 and 2016. Fifty-nine EV-G sequences, which were >5,000 nucleotides long, were obtained. By complete VP1 sequence analysis, Japanese EV-G isolates were classified into G1 (17 strains), G2 (four strains), G3 (22 strains), G4 (two strains), G6 (two strains), G9 (six strains), G10 (five strains), and a new genotype (one strain). Remarkably, 16 G1 and one G2 strain identified in diarrheic (23.5%; four strains) or normal (76.5%; 13 strains) fecal samples possessed a papain-like cysteine protease (PL-CP) sequence, which was recently found in the USA and Belgium in the EV-G genome, at the 2C–3A junction site. This paper presents the first report of the high prevalence of viruses carrying PL-CP in the EV-G population. Furthermore, possible inter- and intragenotype recombination events were found among EV-G strains, including G1-PL-CP strains. Our findings may advance the understanding of the molecular epidemiology and genetic evolution of EV-Gs.

Epidemiology and molecular characterization of Porcine teschovirus in Hunan, China

Porcine teschoviruses (PTVs) have been shown to be widely distributed in pig populations. In this study, 261 faecal and 91 intestinal content samples collected from pigs at 29 farms in Hunan, China, were tested for the presence of PTV by reverse transcription-polymerase chain reaction (RT-PCR). An overall PTV-positivity rate of 19.03% was detected by RT-PCR, and a high PTV infection rate was circulating in asymptomatic fattening and nursery pigs. In total, 40 PTV isolates (PTV-HuNs) were obtained. Alignment of their coding sequences with those of other known PTVs revealed that the genomic sequence of the polyprotein contains 6,606-6,621 nucleotides, encoding a 2,202-2,207-amino acid sequence. Phylogenetic analyses based on the VP1 gene and capsid protein gene exhibited 13 main lineages corresponding to PTV serotypes 1-13, and seven PTV serotypes (PTV 2-6, 9, and 11) were identified in the isolates obtained in our study; this is the first report of PTV 5, 9 and 11 in China. Recombination analysis among the PTV-HuNs indicated that nine recombination events have occurred, including both inter- and intraserotype events. In addition, results demonstrated that only limited positive selection is acting on the global population of PTV isolates, and purifying selection is predominant. In conclusion, this study revealed a high infection rate of PTVs circulating in asymptomatic fattening and nursery pigs. The 40 PTV-HuNs showed high genetic diversity, and genetic analysis of all available PTV sequences revealed that strong purifying selection and recombination play important roles in the genetic diversity and evolution of the virus.

Molecular survey of porcine teschovirus, porcine sapelovirus, and enterovirus G in captive wild boars (Sus scrofa scrofa) of Paraná state, Brazil

AbstractPorcine teschovirus (PTV), porcine sapelovirus (PSV), and enterovirus G (EV-G) are infectious agents specific to pig host species that are endemically spread worldwide. This study aimed to investigate the natural infection by these porcine enteric picornaviruses in wild boars (Sus scrofa scrofa) of Paraná state, Brazil, and to evaluate peccaries (Pecari tajacu and Tayassu pecari) as alternative host species for these viruses. Fecal samples (n=36) from asymptomatic wild boars (n=22) with ages ranging from 2 to 7 months old (young, n=14) and 2 to 4 years old (adult, n=8) and from peccaries (6 to 8 months old, n=14) were collected from a farm and a zoo, respectively, both located in Paraná state. Reverse transcription-polymerase chain reaction (RT-PCR) and nested-PCR (n-PCR) assays targeting the 5'non-translated region of the virus genome were used for screening the viruses. Porcine enteric picornaviruses were detected in 12 out of the 22 wild boar fecal samples. According to each of the viruses, EV-G was most frequently (11/22, 50%) detected, followed by PTV (10/22, 45.5%) and PSV (4/22, 18.2%). Regarding the age groups, young wild boars were more frequently (9/14, 64.3%) infected with PTV, PSV, and EV-G than adult animals (3/8, 37.4%). One n-PCR amplified product for each of the viruses was submitted to sequencing analysis and the nucleotide sequences were compared with the related viruses, which showed similarities varying from 97.7% to 100% for PTV, 92.4% to 96.2% for PSV, and 87.1% to 100% for EV-G. Peccaries tested negative for the viruses and in this study they did not represent infection reservoirs. This study is the first to report the molecular detection of PTV, PSV, and EV-G from captive wild boars in a South American country and the first to screen peccaries as alternative host species for porcine enteric picornavirus.