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

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.

Multiple genotypes infection and molecular characterization of Torque teno neovison virus: A novel Anelloviridae of mink in China

A novel Torque teno neovison virus (TTVs) was identified in specimens collected from dead mink during an outbreak of the Aleutian mink disease virus. Eighteen complete genomic sequences were obtained, ranging from 2109 to 2158 nucleotides in length and consisting of an untranslated region and three open reading frames. The genomic organization of mink TTVs is similar to previously reported anelloviruses. However, the deduced amino acid sequence of its ORF1 protein shows genetic diversity compared to related anelloviruses, suggesting that it represents a putative new species within the Anelloviridae family. This study provides a detailed molecular characterization of the novel mink anelloviruses, including its codon usage pattern, origin, and evolution. Analysis of the viral genomic sequences reveals the existence of multiple genotypes of co-infection. Principal component analysis and phylogenetic trees confirm the coexistence of multiple genotypes. Furthermore, the codon usage analyses indicate that mink TTVs have a genotype-specific codon usage pattern and show a low codon usage bias. Host-specific adaptation analysis suggests that TTVs are less adapted to mink. The possible origin and evolutionary history of mink TTVs were elucidated. Mink TTVs was genetically closely related to giant panda anellovirus, representing a new species. The observed incongruence between the phylogenetic history of TTVs and that of their hosts suggests that the evolution of anellovirus is largely determined by cross-species transmission. The study provides insights into the co-infection and genetic evolution of anellovirus in China.

The first detection of SARS-CoV-2 RNA in the wastewater of Tehran, Iran

Following the official announcement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide pandemic spread by WHO on March 11, 2020, more than 300,000 COVID-19 cases reported in Iran resulting in approximately 17,000 deaths as of August 2, 2020. In the present survey, we investigated the presence of SARS-CoV-2 RNA in raw and treated wastewater samples in Tehran, Iran. Untreated and treated wastewater samples were gathered from four wastewater treatment plants over a month period from June to July 2020. Firstly, an adsorption-elution concentration method was tested using an avian coronavirus (infectious bronchitis virus, IBV). Then, the method was effectively employed to survey the presence of SARS-CoV-2 genome in influent and effluent wastewater samples. SARS-CoV-2 RNA was found in 8 out of 10 treated wastewater samples utilizing a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) test to detect ORF1ab and N genes. Moreover, the rate of positivity in wastewater samples increased in last sample collection that shows circulation of SARS-CoV-2 was increased among the population. In addition, the high values detected in effluent wastewater from local wastewater treatment plants have several implications in health and ecology that should be further assessed.

Occurrence of various viruses and recent evidence of SARS-CoV-2 in wastewater systems

Viruses are omnipresent and persistent in wastewater, which poses a risk to human health. In this review, we summarise the different qualitative and quantitative methods for virus analysis in wastewater and systematically discuss the spatial distribution and temporal patterns of various viruses (i.e., enteric viruses, Caliciviridae (Noroviruses (NoVs)), Picornaviridae (Enteroviruses (EVs)), Hepatitis A virus (HAV)), and Adenoviridae (Adenoviruses (AdVs))) in wastewater systems. Then we critically review recent SARS-CoV-2 studies to understand the ongoing COVID-19 pandemic through wastewater surveillance. SARS-CoV-2 genetic material has been detected in wastewater from France, the Netherlands, Australia, Italy, Japan, Spain, Turkey, India, Pakistan, China, and the USA. We then discuss the utility of wastewater-based epidemiology (WBE) to estimate the occurrence, distribution, and genetic diversity of these viruses and generate human health risk assessment. Finally, we not only promote the prevention of viral infectious disease transmission through wastewater but also highlight the potential use of WBE as an early warning system for public health assessment.

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.

Monitoring of rotavirus in treated wastewater in Tehran with a monthly interval, in 2017-2018

Rotaviruses are among the major causes of viral acute gastroenteritis in newborns and children younger than 5 years worldwide. The ability of rotaviruses to remain infectious in harsh environments as well as in the wastewater treatment process makes them one of the most prevalent enteric viruses. The current study aimed to determine the presence of rotavirus genomes and to analyze them phylogenetically in secondary treated wastewater (TW) samples. In total, 13 TW samples were collected from September 2017 to August 2018. Viral concentration was carried out using the absorption-elution method, and after RNA extraction and cDNA synthesis, real-time and conventional polymerase chain reaction (PCR) were performed. A phylogenetic tree was drawn using Maximum Likelihood and Tamura 3-parameter using MEGA v.6 software. Rotavirus genomes were detected in 7/13 (53.8%) and 3/13 (23.07%) samples using reverse transcription (RT)-PCR and conventional PCR, respectively. Accordingly, phylogenetic analysis revealed G4P[8], G9P[4], and G9P[8] genotypes among the samples. The presence of rotavirus in secondary TW samples discharged into surface water emphasizes the importance of monitoring and assessing viral contamination in the water sources used for agricultural and recreational purposes.