Quantification and genotyping of torque teno virus at a wastewater treatment plant in Japan

Comparison of de novo assembly using long-read shotgun metagenomic sequencing of viruses in fecal and serum samples from marine mammals

Introduction

Viral diseases of marine mammals are difficult to study, and this has led to a limited knowledge on emerging known and unknown viruses which are ongoing threats to animal health. Viruses are the leading cause of infectious disease-induced mass mortality events among marine mammals.

Methods

In this study, we performed viral metagenomics in stool and serum samples from California sea lions (Zalophus californianus) and bottlenose dolphins (Tursiops truncates) using long-read nanopore sequencing. Two widely used long-read de novo assemblers, Canu and Metaflye, were evaluated to assemble viral metagenomic sequencing reads from marine mammals.

Results

Both Metaflye and Canu assembled similar viral contigs of vertebrates, such as Parvoviridae, and Poxviridae. Metaflye assembled viral contigs that aligned with one viral family that was not reproduced by Canu, while Canu assembled viral contigs that aligned with seven viral families that was not reproduced by Metaflye. Only Canu assembled viral contigs from dolphin and sea lion fecal samples that matched both protein and nucleotide RefSeq viral databases using BLASTx and BLASTn for Anelloviridae, Parvoviridae and Circoviridae families. Viral contigs assembled with Canu aligned with torque teno viruses and anelloviruses from vertebrate hosts. Viruses associated with invertebrate hosts including densoviruses, Ambidensovirus, and various Circoviridae isolates were also aligned. Some of the invertebrate and vertebrate viruses reported here are known to potentially cause mortality events and/or disease in different seals, sea stars, fish, and bivalve species.

Discussion

Canu performed better by producing the most viral contigs as compared to Metaflye with assemblies aligning to both protein and nucleotide databases. This study suggests that marine mammals can be used as important sentinels to surveil marine viruses that can potentially cause diseases in vertebrate and invertebrate hosts.

Phylogenetic analysis of torque teno virus in Romania: possible evidence of distinct geographical distribution

Torque teno virus (TTV) is highly prevalent, but little is known about its circulation in humans. Here, we investigated the geographical distribution and phylogeny of TTV in Romania. A fragment of TTV untranslated region B was sequenced in samples from volunteers across the country. Additional sequences from dialyzed patients were also included in the study. Phylogenetic analysis showed that more than 80% of Romanian sequences clustered with isolates assigned to the species Torque teno virus 1 and Torque teno virus 3 (former genogroup 1), and this analysis discriminated between isolates from the North-East and West regions. Further studies assessing the pathogenic potential of TTV isolates should employ analysis based on genomic regions with phylogenetic resolution below the species level.

Sources, fates and treatment strategies of typical viruses in urban sewage collection/treatment systems: A review

The ongoing coronavirus pandemic (COVID-19) throughout the world has severely threatened the global economy and public health. Due to receiving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a wide variety of sources (e.g., households, hospitals, slaughterhouses), urban sewage treatment systems are regarded as an important path for the transmission of waterborne viruses. This review presents a quantitative profile of the concentration distribution of typical viruses within wastewater collection systems and evaluates the influence of different characteristics of sewer systems on virus species and concentration. Then, the efficiencies and mechanisms of virus removal in the units of wastewater treatment plants (WWTPs) are summarized and compared, among which the inactivation efficiencies of typical viruses by typical disinfection approaches under varied operational conditions are elucidated. Subsequently, the occurrence and removal of viruses in treated effluent reuse and desalination, as well as that in sewage sludge treatment, are discussed. Potential dissemination of viruses is emphasized by occurrence via aerosolization from toilets, the collection system and WWTP aeration, which might have a vital role in the transmission and spread of viruses. Finally, the frequency and concentration of viruses in reclaimed water, the probability of infection are also reviewed for discussing the potential health risks.

Prevalence of emerging torque teno virus (TTV) in drinking water, natural waters and wastewater networks (DWNWWS): A systematic review and meta-analysis of the viral pollution marker of faecal and anthropocentric contaminations

The emerging torque teno virus (TTV) has been identified as a biohazard marker of anthropocentric pollution and contamination in drinking water, natural water and wastewater systems (DWNWWS). Therefore, this study aimed at assessing prevalence of TTV in DWNWWS. The study systematically identified and meta-analyzed published studies on TTV prevalence in DWNWWS hosted in Dimensions, Google Scholar, PubMed, Web of Science, and Scopus databases using a random-effects model and mixed-effects meta-regression model for sensitivity analysis. Furthermore, the meta-analysis was stratified to estimate water type-specific TTV prevalence. The study found a total of 58 articles, of which 13 articles subdivided into 31 studies with 374 TTV positive cases and 862 total sample sizes were systematically reviewed and meta-analyzed. The pooled prevalence of TTV in DWNWWS was 37.18% (95%CI: 23.76-55.55%). Prevalence of TTV was significantly different across water types and it was 56.67% (95%CI: 36.94-75.46%) in wastewater, 26.72% (95%CI: 6.87-52.56%) in river water, and 17.17% (95%CI: 0.54-45.39%) in drinking water. TTV incidence in seawater and groundwater was 0% and 25.0% respectively. Funnel plots constructed and associated statistics of rank correlation test and Egger's regression test in this study, show lack of publication bias in the pooled prevalence of TTV in DWNWWS. Although, sample type (QM(df = 1) = 6.9656, p = 0.0083) and concentration methods (QM(df = 1) = 3.8055, p = 0.0511) significantly moderated and accounted for 15.39% and 6.00% of heterogeneity in the prevalence of TTV in DWNWWS respectively. In conclusion, research focus/monitoring activities on TTV is generally inadequate and potential risk of TTV in DWNWWS is underappreciated in most nations; the analyzed studies were from 7 countries (USA, Japan, Italy, Iran, Germany, Egypt, and Brazil). Finally, inefficient concentration method severely influences the prevalence of TTV in DWNWWS and could give rise to underestimation of TTV and mar TTV-based source-tracking of anthropogenic pollutions.

Viral indicators for tracking domestic wastewater contamination in the aquatic environment

Waterborne enteric viruses are an emerging cause of disease outbreaks and represent a major threat to global public health. Enteric viruses may originate from human wastewater and can undergo rapid transport through aquatic environments with minimal decay. Surveillance and source apportionment of enteric viruses in environmental waters is therefore essential for accurate risk management. However, individual monitoring of the >100 enteric viral strains that have been identified as aquatic contaminants is unfeasible. Instead, viral indicators are often used for quantitative assessments of wastewater contamination, viral decay and transport in water. An ideal indicator for tracking wastewater contamination should be (i) easy to detect and quantify, (ii) source-specific, (iii) resistant to wastewater treatment processes, and (iv) persistent in the aquatic environment, with similar behaviour to viral pathogens. Here, we conducted a comprehensive review of 127 peer-reviewed publications, to critically evaluate the effectiveness of several viral indicators of wastewater pollution, including common enteric viruses (mastadenoviruses, polyomaviruses, and Aichi viruses), the pepper mild mottle virus (PMMoV), and gut-associated bacteriophages (Type II/III FRNA phages and phages infecting human Bacteroides species, including crAssphage). Our analysis suggests that overall, human mastadenoviruses have the greatest potential to indicate contamination by domestic wastewater due to their easy detection, culturability, and high prevalence in wastewater and in the polluted environment. Aichi virus, crAssphage and PMMoV are also widely detected in wastewater and in the environment, and may be used as molecular markers for human-derived contamination. We conclude that viral indicators are suitable for the long-term monitoring of viral contamination in freshwater and marine environments and that these should be implemented within monitoring programmes to provide a holistic assessment of microbiological water quality and wastewater-based epidemiology, improve current risk management strategies and protect global human health.

Prevalence of torque viruses in HIV-infected and non-HIV-infected Nigerian subjects: analysis of near-full-length genome sequences

Torque teno virus (TTV), torque teno mini virus (TTMV) and torque teno midi virus (TTMDV) are members of the family Anelloviridae that are known to infect humans. Although no pathogenic roles have been associated with anelloviruses, their high prevalence and perceived ubiquitousness have provoked scientific interest in understanding their molecular and biological characteristics. We used nested PCR to determine the prevalence of anelloviruses among 130 human immunodeficiency virus (HIV)-infected patients and 130 healthy blood donors, and analyzed three near-full-length genome sequences of TTV isolates from HIV-infected and non-HIV infected Nigerians. Statistical analysis showed that the rate of TTV infection was significantly higher in the HIV-infected group (65%) than in the blood donor group (26%) (p < 0.05, χ² = 40.3). TTMV and TTMDV infections were very high in both groups, ranging between 88 and 95%. No significant association was found between TTV infection and age, sex, CD4⁺ cell count, HIV viral load or alanine aminotransferase (ALT) level. Near-full-length genome sequences of TTV isolates FL100, FL08 and BD67 determined by next-generation sequencing were 3.6 kb, 3.2 kb and 2.9 kb, respectively, in size. Their GenBank accession numbers are MK820644, MK820645, MK820646, respectively. These isolates shared 59% sequence identity across the whole genome and clustered in two different phylogenetic groups. Our study established for the first time the circulation of TTV, TTMV and TTMDV in the Nigerian population, with a disproportionately higher prevalence of TTV in HIV-infected patients. The near-complete TTV genome sequences from Nigeria are similar to the sequences KT163879 and KT163916 (3748 and 3190 respectively), obtained from the plasma of HIV-infected subjects from the United States, and EU305675 (2919), identified in human plasma samples from France.

Occurrence and molecular characterization of Torque teno virus (TTV) in a wastewater treatment plant in Tehran

Torque teno virus (TTV) is a single-stranded DNA virus which is predominantly transmitted by the fecal-oral route and may be excreted in the absence of the clinical symptoms. TTV was previously considered a probable cause of hepatitis, but further studies could not strongly connect TTV to any serious health problem. TTV is highly resistant to water and wastewater treatment processes and can be a useful indicator for determining the fecal contamination of water. The purpose of the present study was to assess the prevalence and molecular characterization of TTV in treated wastewater in Tehran. Thirteen effluent samples were collected monthly from the biggest wastewater treatment plant in Tehran, Iran (from September 2017 to August 2018). The presence of the TTV was monitored in the samples by the nested polymerase chain reaction (PCR) method. The TTV genome was found in 76.9% of the samples, and TTV of groups 1 and 3 were determined using phylogenetic analysis. Therefore, treated wastewater can play a key role in the transmission of TTV and the usage of treated wastewater as a source of potable water needs to be carefully controlled.

Comparative enteric viruses and coliphage removal during wastewater treatment processes in a sub-tropical environment

Microbiological safety of reclaimed water is one of the most important issues in managing potential health risks related to wastewater recycling. Presence and removal of human adenovirus (HAdV), human polyomavirus (HPyV), human torque teno virus (HTtV) and somatic coliphage family Microviridae in three wastewater treatment plants (WWTP) in sub-tropical Brisbane, Australia was investigated. All three WWTPs employ activated sludge process with added on Bardenpho process for nutrient removal. HPyV, HAdV, HTtV and Microviridae were consistently detected in the influent (10⁵ to 10⁶ Genomic copies (GC) L^-1) and secondary treated effluent (10² to 10³GCL^-1). The results of this study suggest that, under appropriate conditions, WWTPs with activated sludge process in sub-tropical climate could be an effective treatment barrier with >3 log₁₀ removal of enteric virus. The geometric mean of pooled data for each virus from all sites showed the highest removal for HPyV (3.65 log₁₀) and lowest for HAdV (2.79 log₁₀) which was statistically significant (p=0.00001). Whereas, the removal rate of HTtV and Microviridae was identical (2.81 log₁₀). A poor correlation between the presence of enteric virus in influent or effluent with routinely monitored physicochemical parameters suggests limited use of physicochemical parameters as predictors of enteric virus presence. High prevalence of HAdV in influent and effluent combined with comparatively low removal suggest that it could be used as a model microorganism for determining enteric virus removal efficacy. Additional tertiary treatment may be required prior to effluent reuse for non-potable purposes or discharge into the recreational waters to prevent exposure of people to health hazards.

Waterborne Viruses and F-Specific Coliphages in Mixed-Use Watersheds: Microbial Associations, Host Specificities, and Affinities with Environmental/Land Use Factors

From the years 2008 to 2014, a total of 1,155 water samples were collected (spring to fall) from 24 surface water sampling sites located in a mixed-used but predominantly agricultural (i.e., dairy livestock production) river basin in eastern Ontario, Canada. Water was analyzed for viable F-specific DNA (F-DNA) and F-specific RNA (F-RNA) (genogroup I [GI] to GIV) coliphage and a suite of molecularly detected viruses (norovirus [GI to GIV], torque teno virus [TTV], rotavirus, kobuvirus, adenovirus, astrovirus, hepatitis A, and hepatitis E). F-DNA and F-RNA coliphage were detected in 33 and 28% of the samples at maximum concentrations of 2,000 and 16,300 PFU · 100 ml^-1, respectively. Animal TTV, human TTV, kobuvirus, astrovirus, and norovirus GIII were the most prevalent viruses, found in 23, 20, 13, 12, and 11% of samples, respectively. Viable F-DNA coliphage was found to be a modest positive indicator of molecularly detected TTV. F-RNA coliphage, unlike F-DNA coliphage, was a modest positive predictor of norovirus and rotavirus. There were, however, a number of significant negative associations among F-specific coliphage and viruses. F-DNA coliphage densities of >142 PFU · 100 ml^-1 delineated conditions when ∼95% of water samples contained some type of virus. Kobuvirus was the virus most strongly related to detection of any other virus. Land use had some associations with virus/F-specific coliphage detection, but season and surface water flow were the variables that were most important for broadly delineating detection. Higher relative levels of detection of human viruses and human F-RNA coliphage were associated with higher relative degrees of upstream human land development in a catchment.

IMPORTANCE

This study is one of the first, to our knowledge, to evaluate relationships among F-specific coliphages and a large suite of enteric viruses in mixed-use but agriculturally dominated surface waters in Canada. This study suggested that relationships between viable F-specific coliphages and molecularly detected viruses do exist, but they are not always positive. Caution should be employed if viable F-specific coliphages are to be used as indicators of virus presence in surface waters. This study elucidates relative effects of agriculture, wildlife, and human activity on virus and F-specific coliphage detection. Seasonal and meteorological attributes play a strong role in the detection of most virus and F-specific coliphage targets.

Torquetenovirus: the human virome from bench to bedside

Torquetenovirus (TTV) is the most abundant component of human virome. Virologists have long ignored this orphan and highly divergent virus, in part because TTV cannot be cultured and because it lacks serology reagents and animal models. Nevertheless, it is almost endemic worldwide and is insensitive to current antiviral drugs, so its monitoring is useful in various conditions. To date, TTV as a marker has proved useful in at least two circumstances: to identify anthropogenic pollution and to assess functional immune competence in immunosuppressed individuals. This review summarizes recent findings about TTV and discusses the main hurdles in translating them into clinical diagnostics.

Global occurrence of Torque teno virus in water systems

Bacterial indicator organisms are used globally to assess the microbiological safety of waters. However, waterborne viral outbreaks have occurred in drinking water systems despite negative bacterial results. Using viral markers may therefore provide more accurate health risk assessment data. In this study, fecal, wastewater, stormwater, surface water (fresh and salt), groundwater, and drinking water samples were analyzed for the presence or concentration of traditional indicators, innovative indicators and viral markers. Samples were obtained in the United States, Italy, and Australia and results compared to those reported for studies conducted in Asia and South America as well. Indicators included total coliforms, Escherichia coli, enterococci, male-specific coliphages, somatic coliphages and microviradae. Viral markers included adenovirus, polyomavirus, and a potential new surrogate, Torque teno virus (TTV). TTV was more frequently found in wastewaters (38-100%) and waters influenced by waste discharges (25%) than in surface waters used as drinking water sources (5%). TTV was also specific to human rather than animal feces. While TTV numbers were strongly correlated to other viral markers in wastewaters, suggesting its utility as a fecal contamination marker, data limitations and TTV presence in treated drinking waters demonstrates that additional research is needed on this potential viral indicator.

A case study of enteric virus removal and insights into the associated risk of water reuse for two wastewater treatment pond systems in Bolivia

Wastewater treatment ponds (WTP) are one of the most widespread treatment technologies in the world; however, the mechanisms and extent of enteric virus removal in these systems are poorly understood. Two WTP systems in Bolivia, with similar overall hydraulic retention times but different first stages of treatment, were analyzed for enteric virus removal. One system consisted of a facultative pond followed by two maturation ponds (three-pond system) and the other consisted of an upflow anaerobic sludge blanket (UASB) reactor followed by two maturation (polishing) ponds (UASB-pond system). Quantitative polymerase chain reaction with reverse transcription (RT-qPCR) was used to measure concentrations of norovirus, rotavirus, and pepper mild mottle virus, while cell culture methods were used to measure concentrations of culturable enteroviruses (EV). Limited virus removal was observed with RT-qPCR in either system; however, the three-pond system removed culturable EV with greater efficiency than the UASB-pond system. The majority of viruses were not associated with particles and only a small proportion was associated with particles larger than 180 μm; thus, it is unlikely that sedimentation is a major mechanism of virus removal. High concentrations of viruses were associated with particles between 0.45 and 180 μm in the UASB reactor effluent, but not in the facultative pond effluent. The association of viruses with this size class of particles may explain why only minimal virus removal was observed in the UASB-pond system. Quantitative microbial risk assessment of the treated effluent for reuse for restricted irrigation indicated that the three-pond system effluent requires an additional 1- to 2-log10 reduction of viruses to achieve the WHO health target of <10(-4) disability-adjusted life years (DALYs) lost per person per year; however, the UASB-pond system effluent may require an additional 2.5- to 4.5-log10 reduction of viruses.

Effects of rainfall events on the occurrence and detection efficiency of viruses in river water impacted by combined sewer overflows

Rainfall events can introduce large amount of microbial contaminants including human enteric viruses into surface water by intermittent discharges from combined sewer overflows (CSOs). The present study aimed to investigate the effect of rainfall events on viral loads in surface waters impacted by CSO and the reliability of molecular methods for detection of enteric viruses. The reliability of virus detection in the samples was assessed by using process controls for virus concentration, nucleic acid extraction and reverse transcription (RT)-quantitative PCR (qPCR) steps, which allowed accurate estimation of virus detection efficiencies. Recovery efficiencies of poliovirus in river water samples collected during rainfall events (<10%) were lower than those during dry weather conditions (>10%). The log10-transformed virus concentration efficiency was negatively correlated with suspended solid concentration (r(2)=0.86) that increased significantly during rainfall events. Efficiencies of DNA extraction and qPCR steps determined with adenovirus type 5 and a primer sharing control, respectively, were lower in dry weather. However, no clear relationship was observed between organic water quality parameters and efficiencies of these two steps. Observed concentrations of indigenous enteric adenoviruses, GII-noroviruses, enteroviruses, and Aichi viruses increased during rainfall events even though the virus concentration efficiency was presumed to be lower than in dry weather. The present study highlights the importance of using appropriate process controls to evaluate accurately the concentration of water borne enteric viruses in natural waters impacted by wastewater discharge, stormwater, and CSOs.

Presence of Torque teno virus (TTV) in tap water in public schools from Southern Brazil

Torque teno virus (TTV) was surveyed in tap water collected in schools from three municipalities located in the south of Brazil. TTV genomes were found in 11.7 % (4/34) of the samples. TTV DNA was detected in 10.5 % (2/19) of the samples collected at the city of Caxias do Sul and in 25 % (2/8) of the samples from Pelotas. Those cities have a low rate of sewage treatment. All samples from Santa Cruz do Sul, which has nearly 92 % of its sewage treated, were negative. These results suggest that the amount of sewage treated may have an effect on the detection rates of TTV DNA in drinking water in a given urban area, showing a mild negative correlation (r = -0.76), when comparing the percentage of sewage treatment to the detection of TTV genomes. The detection rate of TTV was also compared with Escherichia coli, showing a strong correlation (r = 0.97), indicating that TTV may be a suitable marker of fecal contamination.

Performance of two swine manure treatment systems on chemical composition and on the reduction of pathogens

Swine effluents must be correctly handled to avoid negative environmental impacts. In this study, the profiles of two swine manure treatment systems were evaluated: a solid-liquid separation step, followed by an anaerobic reactor, and an aerobic step (System 1); and a biodigester followed by serial lagoons (System 2). Both systems were described by the assessment of chemical, bacterial and viral parameters. The results showed that in System 1, there was reduction of chemicals (COD, phosphorus, total Kjeldhal nitrogen - TKN - and NH(3)), total coliforms and Escherichia coli; however, the same reduction was not observed for Salmonella sp. Viral particles were significantly reduced but not totally eliminated from the effluent. In System 2, there was a reduction of chemicals, bacteria and viruses with no detection of Salmonella sp., circovirus, parvovirus, and torque teno virus in the effluent. The chemical results indicate that the treated effluent can be reused for cleaning swine facilities. However, the microbiological results show a need of additional treatment to achieve a complete inactivation for cases when direct contact with animals is required.

Human anelloviruses and the central nervous system

Torque teno virus and related anelloviruses are a recent addition to the list of agents that cause chronic productive infections and high levels of plasma viraemia in humans. Many aspects of the natural history and pathogenesis of these under many respects surprising viruses are still poorly understood. In this review, we briefly outline the general properties of anelloviruses, examine what is currently known about the interactions they establish with the central nervous system (CNS), and discuss the possible pathological consequences.

Evaluation of pepper mild mottle virus, human picobirnavirus and Torque teno virus as indicators of fecal contamination in river water

A reliable indicator is needed to predict and reduce the risk of infection associated with fecal contamination of surface water. Since Pepper mild mottle virus (PMMoV), human picobirnaviruses (hPBV) and Torque teno virus (TTV) have been detected at substantial levels in human feces, we explored whether detection of nucleic acids of these viruses is a suitable indicator of fecal contamination in river water. From September 2008 to December 2009, water samples (n = 111) were collected from the Ruhr and Rhine rivers and from the influents and effluents of a wastewater plant (n = 12). Quantitative real time (RT-) PCR was used to determine the abundance of PMMoV, hPBV, and TTV in comparison to human adenoviruses (HAdV) and human polyomaviruses (HPyV) that are frequently detected in surface water and were previously proposed as indicators. While PMMoV was detected in all river water samples, the other viruses were detected less frequently. The concentration of the studied viruses in positive river water ranged from 5 × 10(1) to 1.07 × 10(6) genome equivalents per liter (gen.equ./l). All wastewater samples were positive for PMMoV, HAdV and HPyV, while TTV and hPBV were detected in 6/12 and 3/12 of samples, respectively. To determine if PMMoV is specific to human-derived fecal waste, fecal samples from human (n = 20) and animal (n = 53) were also tested. In contrast to the ubiquity of PMMoV in human feces (19/20) the virus was only detected at low concentration in a minority of the animal fecal samples tested (7/15 from chicken, 1/10 from Geese and 1/6 from cows). Therefore, in this setting TTV and hPBV do not seem to be suitable indicators of fecal contamination in water. Whereas, the high excretion level and dissemination of PMMoV in human sewage and river water suggest that PMMoV could be a promising indicator of fecal pollution in surface water.

Prevalence of swine Torque teno virus genogroups 1 and 2 in Japanese swine with suspected post-weaning multisystemic wasting syndrome and porcine respiratory disease complex

Torque teno virus (TTV) was first isolated from a human hepatitis patient in 1997. TTV was also identified in several animals, including pigs, cattle, sheep, cats and dogs. In this study, we analysed the prevalence of swine TTV genogroups 1 (TTV1) and 2 (TTV2) in Japanese swine populations with suspected post-weaning multisystemic wasting syndrome and porcine respiratory disease by using a nested polymerase chain reaction method. Of 153 serum samples from 16 different herds in Japan, TTV1 was detected in 46 samples (30%), TTV2 in 47 samples (31%) and both in 15 samples (10%). There was no significant difference in the detection rate among geographical regions. The overall prevalence rate of TTV genogroups was significantly lower in < or = 30-day-old pigs (11%) compared to that in older age groups (54-82%). These results suggest that swine TTV may be widespread in post-weaning pigs and could play aetiological roles in pig diseases in Japan. This is the first report on the prevalence of swine TTV in Japan.