Characterization of two newly emerged torque teno sus virus isolates from a large-scale pig farm in China, in 2018

Torque teno sus virus (TTSuV) infection is common in China's pig herd. Although of uncertain pathogenicity, TTSuVs have been reported as a worsening factor of other porcine diseases, including porcine circovirus associated disease (PCVAD), porcine respiratory diseases complex (PRDC) or porcine dermatitis and nephropathy syndrome (PDNS). To better understand the genetic diversity in TTSuVs, the complete genomes of two newly emerged isolates, referred to as HeN1-A9 and HeN1-A11, collected from pig samples at a large-scale pig farm in China, were analyzed. Phylogenetic relationships of TTSuV sequences separated TTSuV1 and TTSuVk2a groups and divided TTSuV1 into two major subtypes, including TTSuV1a and TTSuV1b; HeN1-A9 and HeN1-A11 strains classified into the TTSuV1a subtype. Recombination analysis demonstrated HeN1-A9 and HeN1-A11 were generated via recombination in the overlapping ORF1/ORF3 region of TTSuV1a genome, which we report for the first time. Furthermore, we found that HeN1-A9 could be replicated in cultured MARC-145 cells for 18 passages. Our findings may be useful for elucidating the characteristics and epidemic status of TTSuVs in China.

Computational genomics of Torque teno sus virus and Porcine circovirus in swine samples from Canada

Emerging viral diseases include pathogens that can threaten the health of the Canadian swineherd. Anelloviruses and Circoviruses comprise of pathogens with veterinary significance. The aim of this study was to determine the genomic organization and phylogenetic relationships of Torque teno sus virus (TTsusV) and Porcine circovirus (PCV) from Canadian pig samples. Fecal and tissue specimens were collected during the winter, spring and summer of 2018. We utilized either virus- or genus-specific PCR assays to characterize the occurrence and genetic diversity of TTsusV and PCV in Canadian pigs. Pairwise comparison of all partial sequences and identity calculation was performed using MAFFT algorithm implemented in Sequence Demarcation Tool (SDT). The obtained full-length sequences were aligned using ClustalW, and phylogeny was inferred using a Maximum likelihood (ML) method by Geneious software. The PCR detection results revealed that the overall positive rate of TTsusV type-1 and type-2 was 45.6% and 32.6%, respectively. The TTsusV isolate MK990454 from Canada clustered in the subtype TTsusV1b, while the TTsusV isolate MK872392 fell in the subtype TTsusV2c, and all showed similarity to known American and Chinese isolates. In addition, our screening PCR showed that 2.7% of stool samples were positive for PCV1. Phylogenetic analysis using the full-length sequence demonstrated that PCV1 (MK872393) isolated from Quebec clustered with other Chinese PCV1 strains. Despite the far geographical distance between Canada and China, the close similarity between Canadian and Chinese TTsusV1 and 2, and PCV1 sequences may be explained by a considerable amount of pig trade between these two nations.

Nationwide prevalence of Torque teno sus virus 1 and k2a in pig populations in Japan

Because broad genetic diversity has recently been detected in Torque teno sus viruses (TTSuV1 and TTSuVk2), the viral genome detection method needs to be improved to understand the prevalence of these viruses. Here, we established single PCR-based detection methods for the TTSuV1 and TTSuVk2a genomes with newly designed primer pairs and applied them to investigate the prevalence of TTSuV1 and TTSuVk2a in Japanese pig populations. The results revealed that 98.2% and 81.7% of the pig farms tested positive for the TTSuV1 and TTSuVk2a genomes, respectively, indicating that both TTSuV1 and TTSuVk2a are widespread in Japan.

Molecular characterization of the ORF2 of Torque teno sus virus 1a and Torque teno sus virus 1b detected in cases of postweaning multisystemic wasting syndrome in Mexico

Worldwide Torque teno sus virus (TTSuV, genus Iotatorquevirus) species have been regarded as possible agents associated with porcine circovirus-associated disease. Iotatorquevirus species possess high genomic variability, suggesting that diverse genotypes are widely geographically distributed. In this study, we validated the genomic variability of Iotaroquevirus species in pigs with postweaned multisystemic wasting syndrome. Genomic DNA from nine TTSuV1a-positive tissues and 15 TTSuV1b-positive tissues was used to amplify the complete ORF2 of each species by nested PCR to perform a molecular characterization. It was found that Mexican TTSuV1a sequences belong to genotype B, sharing phylogenetic origin, high nucleic acid and amino acid sequence similarity and dominant epitope conformation with commercially linked countries, such as the United States, Canada and China, whereas the Mexican TTSuV1b sequences belong to genotype A, being more divergent among each other and displaying low nucleotide identity with worldwide genotype A sequences. In both Iotatorquevirus species, a PTPase-like signature motif was identified in the predicted amino acid sequence, being more conserved for Mexican TTSuV1b sequences than for Mexican TTSuV1a sequences, in which several substitutions were observed. These changes may influence the conformation of dominant epitopes as different arrays were determined among TTSuV1a genotypes. ORF2 variability may account for pathogenic differences by modifying viral replication and immune response, as depicted for human TTV.

Detection of Torque Teno Sus Virus in Pork Bile and Liver Sausages

Torque teno viruses (TTV) are small DNA viruses widespread among humans and pigs. The clinical significance of TTV infections in either humans or pigs is uncertain. In fact, TTV viremia is highly prevalent in patients with different pathologies, but it can also be frequently observed in healthy subjects. Virus infection in pigs is considered a putative cofactor in several diseases; despite being detected frequently in healthy animals, its role still remains unknown. The present study aimed to investigate the presence of Torque teno sus virus (TTSuV) in 62 bile samples collected from pigs at slaughterhouse and in 36 fresh pork liver sausages bought at point of sale. Quantitative Real-Time PCR, confirmed that 19.4 and 58.3 % of bile and sausage samples tested positive for TTSuV, respectively. The mean viral load was established as 5.6 × 10⁴ GE/µl for bile and 7.16 × 10³ GE/g for sausages. TTSuV nucleotide sequence analysis confirmed a wide heterogeneity among the circulating TTSuV strains, which included both TTSuV1 and TTSuV2.

Development of an indirect ELISA assay for the detection of IgG antibodies against the ORF1 of Torque teno sus viruses 1 and 2 in conventional pigs

Torque teno sus viruses (TTSuV, family Anelloviridae) cause long lasting and persistent infection in pigs under subclinical scenarios, and are potentially linked to several economically important swine diseases. Currently, little is known about swine immune response against TTSuV infections. In this study, an ELISA assay was developed based on the ORF1-A recombinant protein of two known TTSuVs, namely TTSuV1 (genus Iotatorquevirus) and TTSuV2 (genus Kappatorquevirus). The assay was used to study the development of the humoral immune response against TTSuV1 and TTSuV2 in longitudinally sampled clinically healthy pigs and their dams. Anti ORF1-A IgG was found in serum of pigs and sows for both TTSuVs. From 15 sows, 15 (100%) and 13 (83%) had anti ORF1-A IgG against TTSuV1 and TTSuV2, respectively. Pig sero-prevalences at the first sampling (4 weeks of age) were 65% (24/37) and 5% (2/37) for TTSuV1 and TTSuV2, respectively. For TTSuV1, the highest anti ORF1-A IgG prevalence was observed at weeks 21 and 25, with 68% (25/37) sero-positive pigs. Quantitative PCR (qPCR) results at week 21 revealed that 26 out of 32 (81%) pigs were positive for TTSuV1. In the case of TTSuV2, the highest anti ORF1-A IgG prevalence was observed at week 21, with 84% (31/37) pigs being sero-positive. At the same week, 92% (34/37) of pigs were qPCR positive. In summary, anti ORF1-A IgGs were detected in both sows and piglets at different ages, indicating that these animals could mount a humoral immune response against both TTSuVs. However, the high percentage of viremic pigs in presence of anti ORF1-A IgG suggests that these antibodies are not able to remove TTSuVs from circulation.

Development and validation of a 4-plex antibody assay for simultaneous detection of IgG antibodies against Torque teno sus virus 1 (TTSuV1), TTSuV2, and porcine reproductive and respiratory syndrome virus types 1 and 2

A fluorescent microbead-based immunoassay (FMIA) for simultaneous detection of IgG antibodies against Torque teno sus virus 1 (TTSuV1), TTSuV2, porcine reproductive and respiratory syndrome virus type 1 (PRRSV-1) and PRRSV-2 was developed. Serum samples were obtained over time from 20 pigs. Twelve of 20 were exposed to TTSuV2 on day 0, 20/20 were vaccinated with a PRRSV-2 vaccine on day 35, and 20/20 were exposed to PRRSV-2 on day 63. Anti-TTSuV antibodies were detected in 30% of the pigs on day 0, and 90% by day 35. All PRRSV-2 vaccinated pigs had detectable anti-PRRSV-2 IgG 21 days after vaccination. Field samples from 17 farms were also tested. The seroprevalence of both PRRSV and TTSuV increased with age. Comparison of the PRRSV-2 FMIA to an ELISA revealed good correlation in young pigs but a high rate of false positives in older pigs. Cross-reaction between PRRSV types was a problem.

Nonstructural proteins of Torque teno sus virus 2 from O2AUG: prediction to experimental validation

The expression profiles of nonstructural proteins (NSPs) in Torque teno sus virus 2 (TTSuV2) have not yet been characterized. Here, we determined the coding sequences of the TTSuV2 NSPs ORF2, ORF2/2, and ORF2/2/3 by overlapping polymerase chain reaction (PCR) and subsequent expression in bacterial and mammalian cells. We generated two monoclonal antibodies (mAbs), 2E5 and 6F8, from mice immunized with mixed Escherichia coli expressing His-tagged ORF2 and ORF2/2. Enzyme-linked immunosorbent assay (ELISA) and western blot analysis revealed that, 2E5 mAbs bound to the consensus sequences of ORF2, ORF2/2, and ORF2/2/3, while 6F8 recognized the common sequences of ORF2/2 and ORF2/2/3. Immunofluorescence assay (IFA) revealed that ORF2 was localized in the cytoplasm, ORF2/2, in the nucleus but not the nucleolus, and ORF2/2/3, in the peri-nuclear region. To identify the expression profiles of TTSuV NSPs, a circular TTSuV2_ZJ (GenBank: KF660540) genomic DNA clone was constructed and transfected into HEK293T and HeLa cells. Splicing mRNAs and the expression and localization of ORF2/2 and ORF2/2/3 were identified by RT-PCR, western blot analysis, and IFA, respectively. However, ORF2 was not detected either at the RNA or protein level. Our study is the first to provide experimental evidence of the existence of ORF2/2 and ORF2/2/3 at the protein level. Moreover, the mAbs have potential applications in future research on TTSuV2 viral protein function and diagnosis of related diseases.

Torque teno sus virus in pigs: an emerging pathogen?

The newly established family Anelloviridae includes a number of viruses infecting humans (Torque teno viruses) and other animal species. The ones infecting domestic swine and wild boar are nowadays named Torque teno sus viruses (TTSuV), which are small circular single-stranded DNA viruses highly prevalent in the pig population. So far, two genetically distinct TTSuV species are infecting swine. Both TTSuVs appear to efficiently spread by vertical and horizontal transmission routes; in fact, foetuses may be infected and the prevalence and viral loads increase by age of the animals. Detailed immunological studies on TTSuVs are still lacking, but it seems that there are no efficient immunological responses limiting viraemia. These viruses are currently receiving more attention due to the latest results on disease association. Torque teno sus viruses have been circulating unnoticed in pigs for a long time, and even considered non-pathogenic by themselves; there is increasing evidence that points to influence the development of some diseases or even affect their outcome. Such link has been mainly established with porcine circovirus diseases.

Emerging and re-emerging swine viruses

In the past two decades or so, a number of viruses have emerged in the global swine population. Some, such as porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2), cause economically important diseases in pigs, whereas others such as porcine torque teno virus (TTV), now known as Torque teno sus virus (TTSuV), porcine bocavirus (PBoV) and related novel parvoviruses, porcine kobuvirus, porcine toroviruses (PToV) and porcine lymphotropic herpesviruses (PLHV), are mostly subclinical in swine herds. Although some emerging swine viruses such as swine hepatitis E virus (swine HEV), porcine endogenous retrovirus (PERV) and porcine sapovirus (porcine SaV) may have a limited clinical implication in swine health, they do pose a potential public health concern in humans due to zoonotic (swine HEV) or potential zoonotic (porcine SaV) and xenozoonotic (PERV, PLHV) risks. Other emerging viruses such as Nipah virus, Bungowannah virus and Menangle virus not only cause diseases in pigs but some also pose important zoonotic threat to humans. This article focuses on emerging and re-emerging swine viruses that have a limited or uncertain clinical and economic impact on pig health. The transmission, epidemiology and pathogenic potential of these viruses are discussed. In addition, the two economically important emerging viruses, PRRSV and PCV2, are also briefly discussed to identify important knowledge gaps.