Detection of Enteric Viruses from Wastewater and River Water in Botswana

Key considerations for pathogen surveillance in wastewater

Wastewater surveillance (WWS) has received significant attention as a rapid, sensitive, and cost-effective tool for monitoring various pathogens in a community. WWS is employed to assess the spatial and temporal trends of diseases and identify their early appearances and reappearances, as well as to detect novel and mutated variants. However, the shedding rates of pathogens vary significantly depending on factors such as disease severity, the physiology of affected individuals, and the characteristics of pathogen. Furthermore, pathogens may exhibit differential fate and decay kinetics in the sewerage system. Variable shedding rates and decay kinetics may affect the detection of pathogens in wastewater. This may influence the interpretation of results and the conclusions of WWS studies. When selecting a pathogen for WWS, it is essential to consider it's specific characteristics. If data are not readily available, factors such as fate, decay, and shedding rates should be assessed before conducting surveillance. Alternatively, these factors can be compared to those of similar pathogens for which such data are available.

A systematic review and meta-analysis indicates a high risk of human noroviruses contamination in vegetable worldwide, with GI being the predominant genogroup

Human noroviruses (HuNoVs) are the most predominant viral agents of acute gastroenteritis. Vegetables are important vehicles of HuNoVs transmission. This study aimed to assess the HuNoVs prevalence in vegetables. We searched the Web of Science, Excerpta Medica Database, PubMed, and Cochrane databases until June 1, 2023. A total of 27 studies were included for the meta-analysis. Statistical analysis was conducted using Stata 14.0 software. This analysis showed that the pooled HuNoVs prevalence in vegetables was 7 % (95 % confidence interval (CI): 3-13) worldwide. The continent with largest number of studies was Europe, and the highest number of samples was lettuce. As revealed by the results of the subgroup meta-analysis, the prevalence of GI genogroup was the highest (3 %, 95 % CI: 1-7). A higher prevalence was seen in vegetables from farms (18 %, 95 % CI: 5-37), while only 4 % (95 % CI: 1-8) in retail. The HuNoVs prevalence of ready-to-eat vegetables and non-ready-to-eat vegetables was 2 % (95 % CI: 0-8) and 9 % (95 % CI: 3-16), respectively. The prevalence by quantitative real time RT-PCR was 8 % (95 % CI: 3-15) compared to 3 % (95 % CI: 0-13) by conventional RT-PCR. Furthermore, the HuNoVs prevalence in vegetables was 6 % (95 % CI: 1-14) in ISO pretreatment method and 8 % (95 % CI: 1-19) in non-ISO method, respectively. This study is helpful in comprehensively understanding the prevalence of HuNoVs contamination in vegetables worldwide.

Detection and quantification of adenovirus, polyomavirus, and papillomavirus in urban sewage

The objective of this study was to assess the occurrence and seasonal frequency of human adenovirus (HAdV), human polyomavirus (HPyV), and human papillomavirus (HPV) in urban sewage. The detection of these viruses was carried out by polymerase chain reaction (PCR), and then the viral concentrations in the positive samples were quantified by quantitative PCR (qPCR). Additionally, HAdV and HPyV genotyping was also performed by PCR. A total of 38/60 (63.3%) positive samples were found. HAdV was the most prevalent virus (26/60; 43.3%), followed by HPyV (21/60; 35%) and HPV (21/60; 35%). The viral concentrations ranged from 3.56 × 102 to 7.55 × 107 genome copies/L. The most common dual viral agents was found between HAdV and HPyV, in eight samples (8/38, 21%). HAdV types 40 and 41 as well as HPyV types JC and BK were identified, with HAdV-40 and HPyV JC being the most prevalent types. Furthermore, the detection rates of HAdV, HPyV, and HPV were higher during the winter season than the other seasons. The high prevalence of HAdV and HPyV supports their suitability as viral indicators of sewage contamination. Furthermore, this study demonstrates the advantages of environmental surveillance as a tool to elucidate the community-circulating viruses.

Nontargeted Screening of Contaminants of Emerging Concern in the Glen Valley Wastewater Treatment Plant, Botswana

There is growing concern about the prevalence and impact of contaminants of emerging concern (CECs). The environmental monitoring of CECs has, however, been limited in low- and middle-income countries due to the lack of advanced analytical instrumentation locally. In the present study we employed a nontargeted and suspect screening workflow via liquid chromatography coupled with high-resolution mass spectrometry (HRMS) to identify known and unknown pollutants in the Glen Valley wastewater treatment plant, Botswana, complemented by analysis of groundwater samples. The present study represents the first HRMS analysis of CECs in water samples obtained in Botswana. Suspect screening of 5942 compounds qualitatively identified 28 compounds, including 26 pharmaceuticals and two illicit drugs (2-ethylmethcathinone and 11-nor-9-carboxy-Δ9-tetrahydrocannabinol). Nontargeted analysis tentatively identified the presence of 34 more compounds including (5ξ)-12,13-dihydroxypodocarpa-8,11,13-trien-7-one, 12-aminododecanoic acid, atenolol acid, brilliant blue, cyclo leucylprolyl, decanophenone, DL-carnitine, N,N'-dicyclohexylurea, N4-acetylsulfamethoxazole, NP-003672, and 24 polyethylene glycol polymers. The highest number of detections were in influent wastewater (26 CECs) followed by effluent wastewater (10 CECs) and, lastly, groundwater (4 CECs). Seventeen CECs detected in the influent water were not detected in the effluent waters, suggesting reduced emissions due to wastewater treatment. Two antiretroviral compounds (abacavir and tenofovir) were detected in the influent and effluent sources. This suggests that wastewater treatment plants are a major pathway of chemical pollution to the environment in Botswana and will help inform prioritization efforts for monitoring and remediation that is protective of these key ecosystems. Environ Toxicol Chem 2024;43:52-61. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Investigation of SARS-CoV-2 RNA contamination in water supply resources of Tabriz metropolitan during a peak of COVID-19 pandemic

It is crucial to have access to clean water resources during the COVID-19 pandemic for hygiene, since virus infection through wastewater leaks in metropolitan areas can be a threat. Accurate monitoring of urban water resources during the pandemic seems to be the only way to confirm safe and infected resources. Here, in this study, the amount of Severe Acute Respiratory Syndrome Coronavirus 2's Ribonucleic Acid (SARS-CoV-2 RNA) in the Tabriz urban water network located in the northwest of Iran was investigated by an extensive sampling of the city's water sources at a severe peak of the COVID-19 pandemic. The sampling process comprised a range of water sources, including wells, qanats, water treatment facilities, dams, and reservoirs. For each sample, a combination of polyethylene glycol (PEG) and sodium chloride (NaCl) was used for concentration and a laboratory RNA-based method was conducted for quantification. Before applying the extraction and quantification procedure to real samples, the proposed concentration method was verified with synthetic serum samples for the first time. After the concentration, RNA extraction was done by the BehPrep extraction column method, and Reverse Transcription Polymerase Chain Reaction (RT-PCR) detection of the virus was done by Covitech COVID-19 RT-PCR kit. In none of the water supply resources, SARS-COV-2 RNA has been detected except in a sample grabbed from a well adjacent to an urban wastewater discharge point downstream. The results of molecular analysis for the positive sample showed that the CT value and concentration of the virus genome were equal to 32.57 and 5720 copies/L, respectively. Quantitative analysis of real samples shows that the city's water network was safe at the time of the study. However, given that the positive sample was exposed to wastewater leakage, periodic sampling from wells and qanats is suggested during the pandemic until it can be proven that the leakage to these water sources is impossible.

Multiple Novel Human Norovirus Recombinants Identified in Wastewater in Pretoria, South Africa by Next-Generation Sequencing

The genogroup II genotype 4 (GII.4) noroviruses are a major cause of viral gastroenteritis. Since the emergence of the Sydney_2012 variant, no novel norovirus GII.4 variants have been reported. The high diversity of noroviruses and periodic emergence of novel strains necessitates continuous global surveillance. The aim of this study was to assess the diversity of noroviruses in selected wastewater samples from Pretoria, South Africa (SA) using amplicon-based next-generation sequencing (NGS). Between June 2018 and August 2020, 200 raw sewage and final effluent samples were collected fortnightly from two wastewater treatment plants in Pretoria. Viruses were recovered using skimmed milk flocculation and glass wool adsorption-elution virus recovery methods and screened for noroviruses using a one-step real-time reverse-transcription PCR (RT-PCR). The norovirus BC genotyping region (570-579 bp) was amplified from detected norovirus strains and subjected to Illumina MiSeq NGS. Noroviruses were detected in 81% (162/200) of samples. The majority (89%, 89/100) of raw sewage samples were positive for at least one norovirus, compared with 73% (73/100) of final effluent samples. Overall, a total of 89 different GI and GII RdRp-capsid combinations were identified, including 51 putative novel recombinants, 34 previously reported RdRp-capsid combinations, one emerging novel recombinant and three Sanger-sequencing confirmed novel recombinants.