Torque Teno Sus Virus Research Articles

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.

A molecular epidemiological investigation of PEDV in China: Characterization of co-infection and genetic diversity of S1-based genes.

Porcine epidemic diarrhoea virus (PEDV) is an emerging and re‐emerging epizootic virus of swine that causes substantial economic losses to the pig industry in China and other countries. The variations in the virus, and its co‐infections with other enteric viruses, have contributed to the poor control of PEDV infection. In the current study, a broad epidemiological investigation of PEDV was carried out in 22 provinces or municipalities of China during 2015–2018. The enteric viruses causing co‐infection with PEDV and the genetic diversity of the PEDV S1 gene were also analysed. The results indicated that, of the 543 diarrhoea samples, 66.85% (363/543) were positive for PEDV, and co‐infection rates of PEDV with 13 enteric viruses ranged from 3.58% (13/363) to 81.55% (296/363). Among these enteric viruses, the signs of diarrhoea induced by PEDV were potentially associated with co‐infections with porcine enterovirus 9/10 (PEV) and torque teno sus virus 2 (TTSuV‐2) (p < .05). The 147 PEDV strains identified in our study belong to Chinese pandemic strains and exhibited genetic diversity. The virulence‐determining S1 proteins of PEDV pandemic strains were undergoing amino acid mutations, in which S58_S58insQGVN–N135dup–D158_I159del‐like mutations were common patterns (97.28%, 143/147). When compared with 2011–2014 PEDV strains, the amino acid mutations of PEDV pandemic strains were mainly located in the N‐terminal domain of S1 (S1‐NTD), and 21 novel mutations occurred in 2017 and 2018. Furthermore, protein homology modelling showed that the mutations in pattern of insertion and deletion mutations of the S1 protein of PEDV pandemic strains may have caused structural changes on the surface of the S1 protein. These data provide a better understanding of the co‐infection and genetic evolution of PEDV in China.

Detection of torque teno sus virus infection in Indian pigs.

Background and Aim:Torque teno viruses (TTVs) are circular, single-stranded DNA viruses, which infect a wide range of animals including livestock and companion animals. Swine TTVs (torque teno sus viruses [TTSuVs]) are thought to act as a primary or coinfecting pathogen in pathological conditions such as porcine dermatitis and nephropathy syndrome and post-weaning multisystemic wasting syndrome. So far, the presence of the virus has not been reported in India. Considering that TTSuVs have the potential to cross the species barrier into humans and that pork consumption is common in North-Eastern states of India, the current study aims to investigate the presence of TTSuV in the Indian pig population.Materials and Methods:A total of 416 samples were collected during 2014-2018, from both apparently healthy pigs and also from pigs suspected of having died from classical swine fever and/or porcine reproductive and respiratory syndrome. These samples were screened for TTSuV infection by polymerase chain reaction (PCR) and DNA sequencing techniques.Results:The presence of the virus was confirmed in 110 samples from 12 different states of India. Phylogenetic analysis of the nucleotide sequences obtained from the PCR products indicated the presence of viruses of both Iotatorquevirus and Kappatorquevirus genera in India.Conclusion:The study is the first report on the presence of TTSuVs in India and highlights the circulation of both genera of the virus in the country.

Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus.

The torque teno sus virus (TTSuV) is an emerging virus threating the Suidae species of unclear pathogenicity, although it was previously reported as a worsening factor of other porcine diseases, in particular, porcine circovirus associated disease (PCVAD). Here, a comprehensive codon usage analysis of the open reading frame 1 (ORF1), which encodes the viral capsid protein, was undertaken for the first time to reveal its evolutionary history. We revealed independent phylogenetic processes for the two genera during TTSuV evolution, which was confirmed by principal component analysis (PCA). A low codon usage bias was observed in different genera and different species, with Kappatorquevirus a (TTSuVk2a) displaying the highest, which was mainly driven by mutation pressure and natural selection, especially natural selection. Overall, ATs were more abundant than GCs, along with more A-ended synonymous codons in relative synonymous codon usage (RSCU) analysis. To further confirm the role of natural selection and TTSuV adaptation to the Suidae species, codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses were performed, which showed different adaptations for different TTSuVs. Importantly, we identified a more dominant role of Sus scrofa in the evolution of Iotatorquevirus (TTSuV1), with the highest CAI values and lowest RCDI values compared to Sus scrofa domestica. However, in TTSuVk2, the roles of Sus scrofa and Sus scrofa domestica were the same, regarding codon usage, with similar CAI and RCDI values. Our study provides a new perspective of the evolution of TTSuV and valuable information to develop control measures against TTSuV.

Viral communities associated with porcine respiratory disease complex in intensive commercial farms in Sichuan province, China

Porcine respiratory disease complex (PRDC), a common piglet disease, causes substantive economic losses in pig farming. To investigate the viral diversity associated with PRDC, the viral communities in serum and nasal swabs from 26 PRDC-affected piglets were investigated using metagenomics. By deep sequencing and de novo assembly, 17 viruses were identified in two pooled libraries (16 viruses from serum, nine from nasal swabs). Porcine circovirus (PCV)-2, porcine reproductive and respiratory syndrome virus (PRRSV) and pseudorabies virus, all commonly associated with PRDC, were identified in the two pooled samples by metagenomics, but most viruses comprised small linear and circular DNAs (e.g. parvoviruses, bocaviruses and circoviruses). PCR was used to compare the detection rates of each virus in the serum samples from 36 PRDC-affected piglets versus 38 location-matched clinically healthy controls. The average virus category per sample was 6.81 for the PRDC-affected piglets and 4.09 for the controls. Single or co-infections with PCV-2 or PRRSV had very high detection rates in the PRDC-affected piglets. Interestingly, porcine parvovirus (PPV)-2, PPV-3, PPV-6 and torque teno sus virus 1a were significantly associated with PRDC. These results illustrate the complexity of viral communities in the PRDC-affected piglets and highlight the candidate viruses associated with it.

High frequency and extensive genetic heterogeneity of TTSuV1 and TTSuVk2a in PCV2- infected and non-infected domestic pigs and wild boars from Uruguay

Torque teno sus virus (TTSuV) infection is common worldwide in both healthy and diseased swine and a relationship between this virus and a particular disease in pigs has not been established. This work aimed to investigate the presence of TTSuV1 and TTSuVk2a in Porcine Circovirus type 2 (PCV2)-infected and non-infected domestic pigs and free-living wild boars from Uruguay. Our data evidenced a high frequency of detection and a wide circulation of TTSuV among pig herds and wild boar populations. Furthermore, TTSuV1+TTSuVk2a co-infection was more frequent than single infections in domestic pigs. In addition, we thoroughly characterized at the molecular level TTSuV strains by extensive sequence data analysis. Our findings revealed an extremely high genetic heterogeneity among Uruguayan isolates. On the basis of detailed analyses, we proposed a more comprehensive criterion of TTSuV classification which would contribute to shedding light over the genetic diversity of these viruses worldwide. On the other hand, data obtained suggested that neither TTSuV1 nor TTSuVk2a frequency of infection or viral loads have any correlation with PCV2 infection, health status or age. The role of TTSuV during co-infection with other pathogens and the age-related dynamics of TTSuV infection are currently under debate. Therefore, taking into account the controversial epidemiological data regarding these viruses and their ubiquitous infection, a likely role as components of the host microbiota should be brought into discussion.

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.

High detection rates of Torque teno sus virus in co-infection with important viral pathogens in porcine kidneys on St. Kitts Island, Lesser Antilles.

We report here high rates of detection (50.8%, 31/61 pigs) of Torque teno sus virus (TTSuV) in kidneys of slaughter-age, apparently healthy pigs on St. Kitts island, Lesser Antilles. TTSuV1 and TTSuVk2a were detected in 23 (37.7%) and 13 (21.3%) pigs, respectively, including mixed infection in five animals. By nucleotide sequence identities and phylogenetic analysis, significant genetic diversity was observed among both TTSuV1 and TTSuVk2a on St. Kitts, with TTSuVk2a showing higher genetic diversity than TTSuV1. Fourteen (45.2%) and 10 (32.2%) of the TTSuV infected pigs tested positive for porcine circovirus type 2 (PCV2) and porcine parvovirus (PPV), respectively, revealing high rates of co-infection of TTSuV with PCV2 and PPV. This is the first report on detection and genetic diversity of TTSuV from the Lesser Antilles. Also, PCV2 and PPV were detected for the first time in the Lesser Antilles. Considering the impact of pig farming on the regional livestock economy, the increasing demand for local pork and lack of information on emerging and re-emerging porcine viruses in the Lesser Antilles, the present findings have important implications on swine health.

Possible risks posed by single-stranded DNA viruses of pigs associated with xenotransplantation.

Routine large‐scale xenotransplantation from pigs to humans is getting closer to clinical reality owing to several state‐of‐the‐art technologies, especially the ability to rapidly engineer genetically defined pigs. However, using pig organs in humans poses risks including unwanted cross‐species transfer of viruses and adaption of these pig viruses to the human organ recipient. Recent developments in the field of virology, including the advent of metagenomic techniques to characterize entire viromes, have led to the identification of a plethora of viruses in many niches. Single‐stranded DNA (ssDNA) viruses are the largest group prevalent in virome studies in mammals. Specifically, the ssDNA viral genomes are characterized by a high rate of nucleotide substitution, which confers a proclivity to adapt to new hosts and cross‐species barriers. Pig‐associated ssDNA viruses include torque teno sus viruses (TTSuV) in the Anelloviridae family, porcine parvoviruses (PPV), and porcine bocaviruses (PBoV) both in the family of Parvoviridae, and porcine circoviruses (PCV) in the Circoviridae family, some of which have been confirmed to be pathogenic to pigs. The risks of these viruses for the human recipient during xenotransplantation procedures are relatively unknown. Based on the scant knowledge available on the prevalence, predilection, and pathogenicity of pig‐associated ssDNA viruses, careful screening and monitoring are required. In the case of positive identification, risk assessments and strategies to eliminate these viruses in xenotransplantation pig stock may be needed.

Presence of Torque teno sus virus 1 and 2 in porcine circovirus 3-positive pigs.

In this study, the co-infection of Torque teno sus virus (TTSuV) and porcine circovirus type 3 (PCV3) was reported. One hundred and ten of 132 (83.3%) PCV3-positive samples were co-infected with Torque teno sus virus 1 (TTSuV1). Ninety-four of 132 (71.2%) PCV3-positive samples were co-infected with Torque teno sus virus 2 (TTSuV2). Sixty-six of 132 (50.0%) of PCV3-positive samples were co-infected with both TTSuV1 and TTSuV2. There were no clinical signs of infection in pigs that were both PCV3-positive and PCV2-negative, in either multiparous sows or live-born infants. The high co-infection rate provides valuable information for the further study of the pathological correlation between PCV3 and TTSuVs.

Complete Genome Sequence of Torque teno indri virus 1, a Novel Anellovirus in Blood from a Free-Living Lemur.

ABSTRACTWe identified Torque teno indri virus 1 (TTIV1), the first anellovirus in a free-living lemur (Indri indri). The complete circular 2,572-nucleotide (nt) TTIV1 genome is distantly related to torque teno sus virus. Phylogenetic and sequence analyses support TTIV1 as a putative member of a new genus within the Anelloviridae family.

Prevalence of the Novel Torque Teno Sus Virus Species k2b from Pigs in the United States and Lack of Association with Post-Weaning Multisystemic Wasting Syndrome or Mulberry Heart Disease.

The family Anelloviridae includes a number of viruses infecting humans (Torque teno viruses, TTV) and other animals including swine (Torque teno sus viruses, TTSuV). Two genetically distinct TTSuV species have been identified from swine thus far (TTSuV1 and TTSuVk2), although their definitive association with disease remains debatable. In 2012, a novel TTSuV species was identified from commercial swine serum and classified in the genus Kappatorquevirus as TTSuVk2b. The other Kappatorquevirus species, TTSuVk2a, has been associated with post-weaning multisystemic wasting syndrome (PMWS) when coinfected with porcine circovirus type 2 (PCV2). Therefore, in this study, we initially amplified a portion of TTSuVk2b ORF1 and, subsequently, assessed the molecular prevalence of the virus in pigs in the United States. A total of 127 serum and 115 tissue samples were obtained from pigs with PMWS or mulberry heart disease (MHD) in six states and tested by PCR for the presence of TTSuVk2b DNA. Approximately 27.6% of the serum and 21.7% of tissue samples tested positive for TTSuVk2b DNA, and the positive products were confirmed by sequencing. However, we did not detect a correlation between TTSuVk2b infection and PMWS or MHD. The near full-length genomic sequence of US TTSuVk2b was determined, and sequence analysis revealed that the US TTSuVk2b isolates were 95% identical to the TTSuVk2b isolate from Spain, with most of the variations clustering in ORF1. We conclude that the novel TTSuVk2b species is present in pigs in the United States and its potential association with a disease warrants further investigation.

Clinical aspects and weight gain reduction in swine infected with porcine circovirus type 2 and torque teno sus virus in Brazil

Simultaneous Porcine circovirus type 2 (PCV-2) and Torque teno sus virus (TTSuV) infections have been reported around the world, generally linked to severe infections. In the present study, 257 swine plasma samples from 31 swine herds located in Brazil, were PCR screened for PCV-2 and TTSuV-1/2 and correlated with clinical data. PCV-2 was detected in 25%, followed by 38.1% and 42.4% of TTSuV-1 and TTSuV-2, respectively. Co-infections of two or three viruses were found in 32.3% of samples. PCV-2 was more frequently detected in the growing (p=0.030) and finishing phases (p=0.0005) while TTSuV-2 in the nursery (p=0.009). Only TTSuV-1 was statistically associated to clinical disease (multiple signs), in combination or not with PCV-2 or TTSuV-2 (p=0.015). PCV-2/TTSuV co-infections were more frequently related to weight gain reduction in comparison to mono-infections (p=0.049) and no-infections (p=0.027), and also in animals with (p=0.011) or without (p=0.037) clinical signs, being the nursery the most affected phase (p=0.025). Our results uphold the pathogenic potential of TTSuV in naturally infected pigs and the clinical/economical impact of this agent, especially in co-infections. Studies addressing the physiopathological mechanisms of simultaneous infections are needed.

Retrospective Analysis of Bacterial and Viral Co-Infections in Pneumocystis spp. Positive Lung Samples of Austrian Pigs with Pneumonia.

Aim of this study was the retrospective investigation of viral (porcine circovirus type 2 (PCV2), porcine reproductive and respiratory syndrome virus (PRRSV), torque teno sus virus type 1 and 2 (TTSuV1, TTSuV2)) and bacterial (Bordetella bronchiseptica (B. b.), Mycoplasma hyopneumoniae (M. h.), and Pasteurella multocida (P. m.)) co-infections in 110 Pneumocystis spp. positive lung samples of Austrian pigs with pneumonia. Fifty-one % were positive for PCV2, 7% for PRRSV, 22% for TTSuV1, 48% for TTSuV2, 6% for B. b., 29% for M. h., and 21% for P. m. In 38.2% only viral, in 3.6% only bacterial and in 40.0% both, viral and bacterial pathogens were detected. In 29.1% of the cases a co-infection with 1 pathogen, in 28.2% with 2, in 17.3% with 3, and in 7.3% with 4 different infectious agents were observed. The exposure to Pneumocystis significantly decreased the risk of a co-infection with PRRSV in weaning piglets; all other odds ratios were not significant. Four categories of results were compared: I = P. spp. + only viral co-infectants, II = P. spp. + both viral and bacterial co-infectants, III = P. spp. + only bacterial co-infectants, and IV = P. spp. single infection. The evaluation of all samples and the age class of the weaning piglets resulted in a predomination of the categories I and II. In contrast, the suckling piglets showed more samples of category I and IV. In the group of fattening pigs, category II predominated. Suckling piglets can be infected with P. spp. early in life. With increasing age this single infections can be complicated by co-infections with other respiratory diseases.

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 5.6×104GE/µl for bile and 7.16×103GE/g for sausages. TTSuV nucleotide sequence analysis confirmed a wide heterogeneity among the circulating TTSuV strains, which included both TTSuV1 and TTSuV2.

Lack of strong anti-viral immune gene stimulation in Torque Teno Sus Virus1 infected macrophage cells

While recent findings suggest that swine TTVs (TTSuVs) can act as primary or co-infecting pathogens, very little is known about viral immunity. To determine whether TTSuVs downregulate key host immune responses to facilitate their own survival, a swine macrophage cell line, 3D4/31, was used to over-express recombinant TTSuV1 viral particles or the ORF3 protein. Immune gene expression profiles were assessed by a quantitative PCR panel consisting of 22 immune genes, in cell samples collected at 6, 12, 24 and 48h post-transfection. Despite the upregulation of IFN-β and TLR9, interferon stimulated innate genes and pro-inflammatory genes were not upregulated in virally infected cells. The adaptive immune genes, IL-4 and IL-13, were significantly downregulated at 6h post-transfection. The ORF3 protein did not appear do not have a major immuno-suppressive effect, nor did it stimulate anti-viral immunity. Data from this study warrants further investigation into the mechanisms of TTV related immuno-pathogenesis.

Molecular Detection of Torque Teno Sus Virus and Coinfection with African Swine Fever Virus in Blood Samples of Pigs from Some Slaughterhouses in Nigeria.

Torque teno sus virus 1 (TTSuV1a/TTSuV1b) infection is present in pig herds worldwide. This study investigated the prevalence of TTSuV1a/TTSuV1b infections in domestic pigs from some slaughterhouses in Nigeria as well as coinfection with African swine fever virus (ASFV) and described the phylogeny in relation to global strains. One hundred and eighty-one (181) blood samples from four slaughterhouses were used for the study and viral nucleic acid detection was carried out by PCR. Comparative sequence analysis was carried out to infer phylogeny. The overall prevalence of TTSuV1a/b was 17.7%. Prevalence of individual genotypes was 10.5% and 7.2% for TTSuV1a and TTSuV1b, respectively. Coinfection of ASFV/TTSuV1a/b was 7.7% while that of TTSuV1a and TTSuV1b was 1.7%. ASFV alone was detected in 11.91% of the total samples. The Nigerian TTSuV1a and TTSuV1b shared a sequence identity of 91–100% and 95–100%, respectively, among each other. The ASFV sequences were 100% identical to members of genotype 1. This is the first report on the presence of TTSuV1a/b in domestic pigs in Nigeria and coinfection with ASFV. Although the prevalence of TTSuV1a/b in Nigeria was low, we recommend further studies to establish the trend and possible role in the pathogenesis of ASFV.

Porcine Viruses Not Previously Reported in Feral Swine in Florida

Although national surveillance is conducted throughout the United States for multiple pathogens associated with feral swine, many pathogens that persist in wild pigs globally have not been the subject of investigations within the U.S. We surveyed feral swine in Florida for two viruses that are ubiquitous in domestic and wild pigs in Europe: torque teno sus virus type 1 and porcine lymphotropic herpesvirus. We found these viruses to be prevalent in feral swine in Florida. We detected viral DNA in nasal and genital swabs or whole blood collected from animals at multiple locations throughout the state. Our results suggest that not only are animals infected with these viruses, but that they are actively shedding virus and capable of transmitting them at multiple, geographically disparate locations. These viruses have the potential to be pathogenic when an animal is coinfected with other porcine viruses, and these viruses pose a potential threat to other wildlife, livestock, and people.

Functional characterization of a new promoter isolated from torque teno sus virus 1.

Torque teno sus virus 1 (TTSuV1) has a non-enveloped, single-stranded, negative-sense circular DNA genome, and it is widely distributed in pigs. Open reading frame 1 (ORF1) of TTSuV1 can be transcribed into mRNA and then translated into protein; however, its promoter has not yet been identified. We used a dual-luciferase reporter system, involving pGL3-Basic and pRL-TK, to identify the promoter of TTSuV1 ORF1. Our results revealed that the sequence between nucleotides 196 and 525 promoted the transcription of the firefly luciferase gene. The core sequence of the promoter was between nucleotides 250 and 400. A comparison of the identified TTSuV1 ORF1 promoter with that from cytomegalovirus (CMV) suggested that the two promoters were similar in strength. Our findings provide new information regarding the molecular biology of TTSuV1 and have revealed a new promoter that can be used in plasmids for numerous applications.

Full genome sequences of torque teno sus virus strains that coinfected a pig with postweaning multisystemic wasting syndrome in Japan: implications for genetic diversity.

We determined the complete genome sequences of torque teno sus viruses (TTSuVs) detected in pigs with postweaning multisystemic wasting syndrome (PMWS) and in healthy pigs in Japan. Unexpectedly, we found coinfection of a PMWS-affected pig in Japan with one strain of TTSuV1, five strains of TTSuV2, and one strain of PCV2. Full-genome sequencing of each of these strains, followed by phylogenetic analysis, revealed broad genetic diversity in the TTSuV2 strains infecting the PMWS-affected pig. These results suggest that the geographical bias in the available genetic information about TTSuVs has a limited impact on the evaluation of their genetic diversity.