Molecular detection of Torque teno sus virus from domestic pigs in North Central, Nigeria, 2022-2023.

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.

BackgroundTorque teno sus virus 1 (TTSuV1), a member of the Anelloviridae family, is highly prevalent in swine populations and exhibits substantial genetic diversity. Despite its ubiquity, TTSuV1 remains understudied, particularly regarding its genetic diversity, host-specific differentiation, and intra-host variation. These characteristics are critical for understanding its evolution, transmission dynamics, and potential applications in biosecurity monitoring.MethodsField and laboratory protocols included capturing wild pigs, collecting whole blood samples, and screening for TTSuV1-positive samples through PCR. TOPO TA cloning was used to amplify individual viral variants within hosts, and whole genome sequencing (WGS) was performed on selected clones. A dated phylogenetic tree was reconstructed using TTSuV1 whole genome sequences obtained from wild pig samples in this study and all available sequences from NCBI. To evaluate genetic differentiation between wild and domestic pigs, partial viral sequences (~700 bp) were analyzed using phylogenetic D statistic and analysis of molecular variance (AMOVA). Intra-host variation was assessed by calculating pairwise identity percentages among viral clones from individual hosts and constructing haplotype networks.ResultsPhylogenetic analysis of whole genome sequences grouped TTSuV1 into four clades, with sequences from wild pigs distributed across all clades. Known subtypes 1a, 1b, and 1c were localized within Clades 3 and 4, leaving sequences in Clades 1 and 2 with unidentified subtypes. Partial sequence analysis revealed significant host-specific genetic differentiation: the D statistic confirmed a non-random association between host type (wild vs. domestic) and phylogeny, and AMOVA further showed contributions of both host type and geography to overall variation. Intra-host variation analysis provided evidence for multiple sources of genetic diversity within individual hosts. Pairwise identity percentages among viral clones ranged from 63.6% to 100%, with lower identity values indicating co-infection with distinct viral variants. Haplotype network analysis revealed mutational steps between haplotypes from the same host, suggesting that intra-host evolution also contributes to within-host genetic variation.ConclusionsThis study highlights the significant genetic diversity and host-specific differentiation of TTSuV1, with wild pigs playing a key role in its evolution. Both intra-host evolution and co-infection contribute to its diversity, underscoring its potential as a tool for monitoring biosecurity risks and cross-transmission between wild and domestic pigs.

Torque teno virus (TTV) is ubiquitous and species-specific, and two different TTV species, Torque teno sus virus 1 (TTSuV1) and Torque teno sus virus 2 (TTSuV2), have been described in...

Torque teno sus virus (TTSuV) is a member of the recently created family Anelloviridae. Two distinct species of TTSuVs, 1 (TTSuV1) and 2 (TTSuV2) have been reported so far in domestic pigs and wild boars. Although TTSuVs have not been clearly linked to any specific disease of pigs, a relation between TTSuV infections and postweaning multisystemic wasting syndrome (PMWS) has been suggested. To examine further this possibility, the present study was conducted in search for TTSuV1 and TTSuV2 genomes in tissues of PMWS and non-PMWS-affected animals. PMWS diagnosis was established by clinical signs, characteristic macroscopic and histopathologic lesions and the presence of porcine circovirus type 2 DNA. Samples of five different tissues (lungs, kidneys, livers, spleens, and lymph nodes) from PMWS-affected and non-PMWS-affected pigs were examined with two specific PCR assays developed to amplify TTSuV1 and TTSuV2 genome segments. TTSuV1 DNA was detected in tissues of non-diseased animals to significantly higher levels than in tissues of PMWS-affected pigs (p≤0.001). Regarding TTSuV2, viral genomes were detected in nearly all samples from both PMWS-affected (94.7%) and non-affected pigs (100%), with no significant differences in the frequencies of detection of TTSuV2 genomes in both groups. No significant differences were detected on the distribution of TTSuV1 and TTSuV2 in the different tissues examined (p=0.970).

Torque teno sus virus (TTSuV) is a non-enveloped circular ssDNA virus which frequently infects swine and has been associated with hepatic, respiratory, and autoimmune disorders. TTSuV’s pathogenic role is still uncertain, and clear data in the literature on virus reservoirs are lacking. The aims of this study were to investigate the presence of potentially zoonotic TTSuV in wild animals in Northern Italy and to evaluate their role as reservoirs. Liver samples were collected between 2016 and 2020 during four hunting seasons from wild boars (Sus scrofa), red deer (Cervus elaphus), roe deer (Capreolus capreolus), and chamois (Rupicapra rupicapra). Samples originated from areas in Northern Italy characterized by different traits, i.e., mountains and flatland with, respectively low and high farm density and anthropization. Viral identification was carried out by end-point PCR with specific primers for TTSuV1a and TTSuVk2a species. TTSuV prevalence in wild boars was higher in the mountains than in the flatland (prevalence of 6.2% and 2.3%, respectively). In wild ruminants only TTSuVk2a was detected (with a prevalence of 9.4%). Our findings shed light on the occurrence and distribution of TTSuV in some wild animal species, investigating their possible role as reservoirs.

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 1 (TTSuV1) is a ubiquitous, non-pathogenic virus in both wild and domestic pigs and has potential value as a molecular marker for monitoring cross-population viral transmission and biosecurity breaches. In this study, we integrated genetic data with Bayesian transmission inference to examine the dynamics of TTSuV1 transmission within and between wild and farmed pigs in Arkansas. Transmission steps, defined as the number of transmission events linking two hosts, were used to identify barriers to transmission, such as biosecurity measures or geographic separation. TTSuV1 was highly prevalent in farmed pigs (96.59%) and invasive wild pigs (47.76%), with sequences from both groups distributed across four major subtypes. Transmission step analyses revealed that wild–farmed pig pairs were consistently separated by numerous transmission steps (>10 steps), indicating strong isolation and little evidence of recent spillover. In contrast, few transmission steps (≤5 steps) were common within populations, reflecting localized circulation. Our findings support the use of TTSuV1 as a molecular marker to characterize cross-population viral movement and spillover, as well as to delineate population structure in swine systems. Practically, this approach offers a novel framework for using viral genomics to detect cross-population spillover events and monitor biosecurity breaches in swine production systems.

Members of the family Anelloviridae are emerging circular DNA viruses infecting many species of vertebrates including pigs. To date, members of two distinct genera, Iotatorquevirus, including torque teno sus virus 1a and torque teno sus virus 1b (TTSuV1a and TTSuV1b), and Kappatorquevirus, including torque teno sus virus k2a and torque teno sus virus k2b (TTSuVk2a and TTSuVk2b), have been identified in domestic pigs and wild boars. The goal of this study was to evaluate the prevalence and genetic diversity of these viruses based on 5' non-coding genes in Chinese swine herds experiencing clinical symptoms. One hundred eighty-five clinical samples from 11 different regions, collected during 2008-2009, were analyzed using a PCR method, and the results revealed a high TTSuV-positive rate of 78.9% (146/185) in pigs. Moreover, we detected co-infection with multiple TTSuV strains in the same pig. Nucleotide sequencing results revealed greater genetic diversity within the genus Kappatorquevirus than within the genus Iotatorquevirus. In addition, TTSuVk2b, a novel virus discovered in New Zealand in 2012, was also identified in this study. In summary, the present work helps us obtain more knowledge about the epidemiology and genetic diversity of TTSuVs.

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.

Age-related tissue distribution of swine Torque teno sus virus 1 and 2

In the present study, Torque teno sus viruses (TTSuVs) were detected in tissue and blood samples obtained from domestic pigs in central China, and complete genomes of TTSuVs were characterized. A total of three tissue samples (3/20, 15 %) from post-weaning multisystemic wasting syndrome-affected pigs and 30 blood samples (30/40, 75 %) from healthy pigs were positive for Torque teno sus virus 1 (TTSuV1) and/or 2 (TTSuV2). Two TTSuV strains (TTV1Hn54 and TTV2Hn93) comprising 2,794 and 2,875 nucleotides, respectively, each had four open reading frames (ORFs) and the untranslated region with TATA box and GC-rich region. Genomic sequence of TTV2Hn93 strain was unique in length compared with other TTSuV2 genomic sequences. Interestingly, three rolling-circle replication (RCR) motif-IIIs (YXXK) which were located at amino acid (aa) position 166-169, 328-331, and 379-382, respectively, were found in the ORF1 of TTV1Hn54. Two RCR motif-IIIs (YXXK) at the aa position 105-108 and 480-483 respectively, were also identified in the ORF1 of TTV2Hn93. Phylogenetic tree based on complete genomes showed that TTV1Hn54 strain was designated into type TTSuV1b and had a slight high sequence identity of 91 % with the Canada strain (JQ120664). TTV2Hn93 strain was classified into subtype TTSuV2d and shared the highest identity (97 %) with the Spain strain (GU570207).

Simple SummaryWorldwide demand for food is expected to increase due to population growth and swine accounts for more than one-third of meat produced worldwide. Several factors affect the success of livestock production systems, including animal disease control. Despite the importance of infectious diseases to animal health and the productivity of the global swine industry, pathogens of swine, in particular emerging viruses, such as Senecavirus A, Torque teno sus virus, and Linda virus, have gained limited interest. We performed a systematic analysis of the literature, with a focus on the main macroscopical and histological findings related to those viruses to fill the gap and highpoint these potentially hazardous pathogens.Swine production represents a significant component in agricultural economies as it occupies over 30% of global meat demand. Infectious diseases could constrain the swine health and productivity of the global swine industry. In particular, emerging swine viral diseases are omnipresent in swine populations, but the limited knowledge of the pathogenesis and the scarce information related to associated lesions restrict the development of data-based control strategies aimed to reduce the potentially great impact on the swine industry. In this paper, we reviewed and summarized the main pathological findings related to emerging viruses, such as Senecavirus A, Torque teno sus virus, and Linda virus, suggesting a call for further multidisciplinary studies aimed to fill this lack of knowledge and better clarify the potential role of those viral diseases in swine pathology.

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.

Understanding the epidemiology and transmission dynamics of transboundary animal diseases (TADs) among wild pigs (Sus scrofa) will aid in preventing the introduction or containment of TADs among wild populations. Given the challenges associated with studying TADs in free-ranging populations, a surrogate pathogen system may predict how pathogens may circulate and be maintained within wild free-ranging swine populations, how they may spill over into domestic populations, and how management actions may impact transmission. We assessed the suitability of Torque teno sus virus 1 (TTSuV1) to serve as a surrogate pathogen for molecular epidemiological studies in wild pigs by investigating the prevalence, persistence, correlation with host health status and genetic variability at two study areas: Archbold’s Buck Island Ranch in Florida and Savannah River Site in South Carolina. We then conducted a molecular epidemiological case study within Archbold’s Buck Island Ranch site to determine how analysis of this pathogen could inform transmission dynamics of a directly transmitted virus. Prevalence was high in both study areas (40%, n = 190), and phylogenetic analyses revealed high levels of genetic variability within and between study areas. Our case study showed that pairwise host relatedness and geographic distance were highly correlated to pairwise viral genetic similarity. Molecular epidemiological analyses revealed a distinct pattern of direct transmission from pig to pig occurring within and between family groups. Our results suggest that TTSuV1 is highly suitable for molecular epidemiological analyses and will be useful for future studies of transmission dynamics in wild free-ranging pigs.

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