New method using a positively charged microporous filter and ultrafiltration for concentration of viruses from tap water

Electrostatic microfiltration (EM) enriches and recovers viable microorganisms at low-abundance in large-volume samples and enhances downstream detection

Rapid and sensitive detection of pathogens in various samples is crucial for disease diagnosis, environmental surveillance, as well as food and water safety monitoring. However, the low abundance of pathogens (<10 CFU) in large volume (1 mL-1 L) samples containing vast backgrounds critically limits the sensitivity of even the most advanced techniques, such as digital PCR. Therefore, there is a critical need for sample preparation that can enrich low-abundance pathogens from complex and large-volume samples. This study develops an efficient electrostatic microfiltration (EM)-based sample preparation technique capable of processing ultra-large-volume (≥500 mL) samples at high throughput (≥10 mL min-1). This approach achieves a significant enrichment (>8000×) of extremely-low-abundance pathogens (down to level of 0.02 CFU mL-1, i.e., 10 CFU in 500 mL). Furthermore, EM-enabled sample preparation facilitates digital amplification techniques sensitively detecting broad pathogens, including bacteria, fungi, and viruses from various samples, in a rapid (≤3 h) sample-to-result workflow. Notably, the operational ease, portability, and compatibility/integrability with various downstream detection platforms highlight its great potential for widespread applications across diverse settings.

Implementation of a Sensitive Method to Assess High Virus Retention Performance of Low-Pressure Reverse Osmosis Process

Human enteric viruses are important etiological agents of waterborne diseases. Environmental waters are usually contaminated with low virus concentration requiring large concentration factors for effective detection by (RT)-qPCR. Low-pressure reverse osmosis is often used to remove water contaminants, but very few studies focused on the effective virus removal of reverse osmosis treatment with feed concentrations as close as possible to environmental concentrations and principally relied on theoretical virus removal. The very low viral concentrations usually reported in the permeates (i.e. at least 5 log of removal rate) mean that very large volumes of water need to be analysed to have sufficient sensitivity and assess the process efficiency. This study evaluates two methods for the concentration of adenoviruses, enteroviruses and MS2 bacteriophages at different viral concentrations in large (< 200 L) and very large (> 200 L) volumes. The first method is composed of two ultrafiltration membranes with low-molecular weight cut-offs while the second method primarily relies on adsorption and elution phases using electropositive-charged filters. The recovery rates were assessed for both methods. For the ultrafiltration-based protocol, recovery rates were similar for each virus studied: 80% on average at high virus concentrations (106-107 viruses L-1) and 50% at low virus concentrations (103-104 viruses L-1). For the electropositive-charged filter-based method, the average recoveries obtained were about 36% for ADV 41, 57% for CV-B5 and 1.6% for MS2. The ultrafiltration-based method was then used to evaluate the performance of a low-pressure reverse osmosis lab-scale pilot plant. The retentions by reverse osmosis were similar for all studied viruses and the validated recovery rates applied to the system confirmed the reliability of the concentration method. This method was effective in concentrating all three viruses over a wide range of viral concentrations. Moreover, the second concentration method using electropositive-charged filters was studied, allowing the filtration of larger volumes of permeate from a semi-industrial low-pressure reverse osmosis pilot plant. This reference method was used because of the inability of the UF method to filter volumes on the order of one cubic metre.

SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses

As global SARS-CoV-2 burden and testing frequency have decreased, wastewater surveillance has emerged as a key tool to support clinical surveillance efforts. The aims of this study were to identify and characterize SARS-CoV-2 variants in wastewater samples collected from urban centers across South Africa. Here we show that wastewater sequencing analyses are temporally concordant with clinical genomic surveillance and reveal the presence of multiple lineages not detected by clinical surveillance. We show that wastewater genomics can support SARS-CoV-2 epidemiological investigations by reliably recovering the prevalence of local circulating variants, even when clinical samples are not available. Further, we find that analysis of mutations observed in wastewater can provide a signal of upcoming lineage transitions. Our study demonstrates the utility of wastewater genomics to monitor evolution and spread of endemic viruses.

Electropositive Membrane Prepared via a Simple Dipping Process: Exploiting Electrostatic Attraction Using Electrospun SiO2/PVDF Membranes with Electronegative SiO2 Shell

This research aimed to develop a simple and cost-effective method for fabricating electropositive membranes for highly efficient water filtration. Electropositive membranes are novel functional membranes with electropositive properties and can filter electronegative viruses and bacteria using electrostatic attraction. Because electropositive membranes do not rely on physical filtration, they exhibit high flux characteristics compared with conventional membranes. This study presents a simple dipping process for fabricating boehmite/SiO₂/PVDF electropositive membranes by modifying an electrospun SiO₂/PVDF host membrane using electropositive boehmite nanoparticles (NPs). The surface modification enhanced the filtration performance of the membrane, as revealed by electronegatively charged polystyrene (PS) NPs as a bacteria model. The boehmite/SiO₂/PVDF electropositive membrane, with an average pore size of 0.30 μm, could successfully filter out 0.20 μm PS particles. The rejection rate was comparable to that of Millipore GSWP, a commercial filter with a pore size of 0.22 μm, which can filter out 0.20 μm particles via physical sieving. In addition, the water flux of the boehmite/SiO₂/PVDF electropositive membrane was twice that of Millipore GSWP, demonstrating the potential of the electropositive membrane in water purification and disinfection.

Simple Affinity-Based Method for Concentrating Viruses from Wastewater Using Engineered Curli Fibers

Wastewater surveillance is a proven method for tracking community spread and prevalence of some infectious viral diseases. A primary concentration step is often used to enrich viral particles from wastewater prior to subsequent viral quantification and/or sequencing. Here, we present a simple procedure for concentrating viruses from wastewater using bacterial biofilm protein nanofibers known as curli fibers. Through simple genetic engineering, we produced curli fibers functionalized with single-domain antibodies (also known as nanobodies) specific for the coat protein of the model virus bacteriophage MS2. Using these modified fibers in a simple spin-down protocol, we demonstrated efficient concentration of MS2 in both phosphate-buffered saline (PBS) and in the wastewater matrix. Additionally, we produced nanobody-functionalized curli fibers capable of binding the spike protein of SARS-CoV-2, showing the versatility of the system. Our concentration protocol is simple to implement, can be performed quickly under ambient conditions, and requires only components produced through bacterial culture. We believe this technology represents an attractive alternative to existing concentration methods and warrants further research and optimization for field-relevant applications.

CrAssphage as an indicator of human-fecal contamination in water environment and virus reduction in wastewater treatment

Viral indicators of human-fecal contamination in wastewaters and environmental waters have been getting much attention in the past decade. Cross-assembly phage (crAssphage) is the most abundant DNA virus in human feces. Recently, the usefulness of crAssphage as a microbial source tracking and water quality monitoring tool for human-fecal contamination has been highlighted. Here, we conducted a comprehensive review on crAssphage in water, focusing on detection methodology, concentration range in various waters and wastewaters, specificity to human-fecal contamination, and reduction in wastewater treatment systems. This review highlights that crAssphage is globally distributed in wastewaters and various fecal-contaminated water bodies at high concentrations without seasonal fluctuations. CrAssphage is highly specific to human-fecal contamination and is rarely found in animal feces. It also has a good potential as a performance indicator to ensure virus reduction in wastewater treatment systems. Accordingly, crAssphage could be an effective tool for monitoring of human-fecal contamination and potential presence of fecal pathogenic microbes in environmental waters. Bridging the research gaps highlighted in this review would make crAssphage a powerful tool to support the control of water-related health risks.

Monitoring COVID-19 through SARS-CoV-2 quantification in wastewater: progress, challenges and prospects

Wastewater-Based Epidemiology (WBE) is widely used to monitor the progression of the current SARS-CoV-2 pandemic at local levels. In this review, we address the different approaches to the steps needed for this surveillance: sampling wastewaters (WWs), concentrating the virus from the samples and quantifying them by qPCR, focusing on the main limitations of the methodologies used. Factors that can influence SARS-CoV-2 monitoring in WWs include: (i) physical parameters as temperature that can hamper the detection in warm seasons and tropical regions, (ii) sampling methodologies and timetables, being composite samples and Moore swabs the less variable and more sensitive approaches, (iii) virus concentration methodologies that need to be feasible and practicable in simpler laboratories and (iv) detection methodologies that should tend to use faster and cost-effective procedures. The efficiency of WW treatments and the use of WWs for SARS-CoV-2 variants detection are also addressed. Furthermore, we discuss the need for the development of common standardized protocols, although these must be versatile enough to comprise variations among target communities. WBE screening of risk populations will allow for the prediction of future outbreaks, thus alerting authorities to implement early action measurements.

Challenges to detect SARS-CoV-2 on environmental media, the need and strategies to implement the detection methodologies in wastewaters

Understanding risks, putting in place preventative methods to seamlessly continue daily activities are essential tools to fight a pandemic. All social, commercial and leisure activities have an impact on the environmental media. Therefore, to accurately predict the fate and behavior of viruses in the environment, it is necessary to understand and analyze available detection methods, possible transmission pathways and preventative techniques. The aim of this review is to critically analyze and summarize the research done regarding SARS-COV-2 virus detection, focusing on sampling and laboratory detection methods in environmental media. Special attention will be given to wastewater and sewage sludge. This review has summarized the survival of the virus on surfaces to estimate the risk carried by different environmental media (water, wastewater, air and soil) in order to explain which communities are under higher risk. The critical analysis concludes that the detection of SARS-CoV-2 with current technologies and sampling strategies would reveal the presence of the virus. This information could be used to design systematic sampling points throughout the sewage systems when available, taking into account peak flows and more importantly economic factors on when to sample. Such approaches will provide clues for potential future viral outbreak, saving financial resources by reducing testing necessities for viral detection, hence contributing for more appropriate confinement policies by governments and could be further used to define more precisely post-pandemic or additional waves measures if/ when needed.

A Longitudinal Survey for Genome-based Identification of SARS-CoV-2 in Sewage Water in Selected Lockdown Areas of Lahore City, Pakistan: A Potential Approach for Future Smart Lockdown Strategy

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has affected more than 15 million people and, as of 22 July 2019, caused deaths of more than 0.6 million individuals globally. With the excretion of SARS-CoV-2 in the stool of symptomatic and asymptomatic COVID-19 patients, its genome detection in the sewage water can be used as a powerful epidemiological tool to predict the number of positive cases in a population. This study was conducted to detect SARS-CoV-2 genome in sewage water during the lockdown. Sewage samples, from 28 pre-selected sites, were collected on alternate days from 13-25 July, 2020 from two selected areas [Johar Town (n = 05) and Township (n = 23)], where smart lockdown were implemented by the government authorities on 9th July, 2020. Genomic RNA was extracted and the SARS-CoV-2 was detected and quantified using commercially available kit through Real-Time PCR. Out of 28, sixteen samples were positive on day one while 19, 17, 23, 17, 05 and 09 samples were positive on day 3, 5, 7, 9, 11, and 13, respectively. Results revealed a decreased positivity rate and SARS CoV-2 genome copies in sewage towards the end of lockdown however few sampling sites did not follow a clear pattern indicating the complexities in sewage water based surveillance i.e time of sampling etc. Hourly sampling from two sites for 24 hours also revealed the impact of sampling time on detection of SARS-CoV-2 genome in sewage. Results of current study insinuate a possible role of sewage-based COVID-19 surveillance in monitoring and execution of smart lockdowns.

Development and evaluation of DEAE silica gel columns for simultaneous concentration of coliphages and rotavirus from natural water samples

Enteric viruses are commonly present in water bodies in regions with poor sanitation. Although the occurrence of these viruses poses a health risk they are difficult to quantify due to their low concentration and they may remain undetected in the absence of adequate preconcentration. The present study reports the synthesis and utilization of DEAE silica gel (DSiG) as an adsorbent for virus concentration. Two coliphages, MS2 and SUSP2, and an enteric virus, rotavirus A (RVA) were chosen for examining the preconcentration efficiency of DSiG columns. Studies conducted at a low flow rate of 5 mL/min yielded good removal of viruses through adsorption. Studies at a higher flow rate of 50 mL/min followed by elution with optimized eluents yielded a high recovery of MS2 and RVA even when they were present at low concentration (0.01 copy/mL). The eluent Na(1.5 M)-Tw(2%)-G3X (glycine 3X broth, 1.5 M NaCl, 2% Tween, pH 10.2) showed maximum elution of RVA and MS2. Optimal SUSP2 recovery was observed on employing an eluent composed of 1.5 M NaCl, 3% Tween, 0.05 M KH₂PO₄ at pH 9.2. Subsequently, both the eluents were successively applied for elution of the adsorbed viruses. This method was applied for virus preconcentration from lake water in the monsoon and winter seasons. The DSiG column could achieve adequate preconcentration for all the three viruses, i.e., SUSP2, MS2, and RVA, even when they were present at very low concentration and the recovery achieved was comparable to that achieved with ultracentrifugation while the processing time required for handling large volumes of water was considerably lower.

Development of a large volume concentration method for recovery of coronavirus from wastewater

Levels of severe acute respiratory coronavirus type 2 (SARS CoV 2) RNA in wastewater could act as an effective means to monitor coronavirus disease 2019 (COVID-19) within communities. However, current methods used to detect SARS CoV 2 RNA in wastewater are limited in their ability to process sufficient volumes of source material, inhibiting our ability to assess viral load. Typically, viruses are concentrated from large liquid volumes using two stage concentration, primary and secondary. Here, we evaluated a dead-end hollow fiber ultrafilter (D-HFUF) for primary concentration, followed by the CP Select™ for secondary concentration from 2 L volumes of primary treated wastewater. Various amendments to each concentration procedure were investigated to optimally recover seeded OC43 (betacoronavirus) from wastewater. During primary concentration, the D-HFUF recovered 69 ± 18% (n = 29) of spiked OC43 from 2 L of wastewater. For secondary concentration, the CP Select™ system using the Wastewater Application settings was capable of processing 100 mL volumes of primary filter eluates in <25 min. A hand-driven syringe elution proved to be significantly superior (p = 0.0299) to the CP Select™ elution for recovering OC43 from filter eluates, 48 ± 2% compared to 31 ± 3%, respectively. For the complete method (primary and secondary concentration combined), the D-HFUF and CP select/syringe elution achieved overall 22 ± 4% recovery of spiked OC43 through (n = 8) replicate filters. Given the lack of available standardized methodology confounded by the inherent limitations of relying on viral RNA for wastewater surveillance of SARS CoV 2, it is important to acknowledge these challenges when interpreting this data to estimate community infection rates. However, the development of methods that can substantially increase sample volumes will likely allow for reporting of quantifiable viral data for wastewater surveillance, equipping public health officials with information necessary to better estimate community infection rates.

Evaluation of three different concentration and extraction methods for recovery efficiency of human adenovirus and human rotavirus virus A

Routine wastewater treatment plants (WWTPs) effluents monitoring is essential because of enteric viruses' low infectious dose beyond molecular detectability. In current study methods for concentration and extraction, inter-method compatibility and recovery efficiency of spiked human adenovirus (HAdV) and human rotavirus A (RVA) were evaluated. For virus concentration, polyethylene glycol precipitation (PEG), charged membrane-based adsorption/elution (CMAE), and glass wool-based concentration (GW) methods were used. Nucleic acid was extracted by PowerViral™ Environmental RNA/DNA Isolation (POW), ZymoBIOMICS™ RNA extraction (ZYMO) and Wizard® Genomic DNA Purification (WGDP) and samples were analyzed by Real-Time PCR. CMAE method yielded significantly higher concentrations for both ARQ (Armored-RNA Quant) and RVA compared to PEG (P =  0.001 and 0.003) and GW (P <  0.0001). Highest HAdV concentration was obtained by PEG (P =  0.001 and < 0.0001) in relation to CMAE and GW. ZYMO yielded a significantly higher ARQ and RVA concentrations (P =  0.03 and 0.0057), whereas significantly higher concentration was obtained by POW for HAdV (P =  0.032). CMAE × ZYMO achieved the highest recovery efficiencies for ARQ (69.77 %) and RVA (64.25, respectively, while PEG × POW present efficiency of 9.7 % for HAdV. These findings provide guidance for understanding of method-related biases for viral recovery efficiency.

Detection and evaluation of rotavirus surveillance methods as viral indicator in the aquatic environments

Group A rotaviruses (RVAs) have been introduced as the most important causative agents of acute gastroenteritis in the young children. One of every 260 children born globally will die due to rotavirus (RV) before 5 years old. The RV is widely known as a viral indicator for health (fecal contamination) because this pathogen has a high treatment resistance nature, which has been listed as a relevant waterborne pathogen by the World Health Organization (WHO). Therefore, monitoring of environmental is important, and RV is one of the best-known indicators for monitoring. It has been proved that common standards for microbiological water quality do not guarantee the absence of viruses. On the other hand, in order to recover and determine RV quantity within water, standard methods are scarce. Therefore, dependable prediction of RV quantities in water sample is crucial to be able to improve supervision efficiency of the treatment procedure, precise quantitative evaluation of the microbial risks as well as microbiological water safety. Hence, this study aimed to introduce approaches to detecting and controlling RV in environmental waters, and discussed the challenges faced to enable a clear perception on the ubiquity of the RV within different types of water across the world.

Coliphages as Indicators for the Microbial Quality of Treated Wastewater Effluents

Wastewater effluents are a reliable water source for non-potable water reuse including unrestricted crop irrigation in arid regions suffering from water scarcity. This study was performed to develop and optimize a procedure to concentrate coliphages from 100 L of treated effluent. Moreover, the reduction of coliphages by filtration and disinfection by either chlorine or UV was compared with that of fecal coliform (FC). The adsorption efficiency of MS2 and Qβ coliphages by the NanoCeram filter was similar and reached 99.8%. Elution efficiency of MS2 coliphage from the NanoCeram filters by a solution of 1% NaPP and 0.05 M glycine, pH 9.5, was 74  ±  9.5%. The highest reconcentration efficiency of MS2 and Qβ coliphages was obtained with polyethylene glycol (PEG) precipitation and reached 76  ±  28% and 90  ±  11%, respectively. In comparison, the reconcentration efficiency of organic flocculation was 0% and 1.3% for Qβ and MS2 coliphages, respectively. The overall recovery efficiency of MS2 coliphages from 100 L tertiary effluent was 57  ±  1.5%. Poor reduction was observed for coliphages compared to FC by filtration and chlorine disinfection although; the reduction of FC, as measured by cultivation, was satisfactory and within the guidelines for unrestricted irrigation. High correlation between the reduction of FC and coliphages was recorded for tertiary effluent disinfected by UV irradiation. Monitoring the microbial quality of tertiary effluent using qPCR for the enumeration of FC was found unsuitable, because DNA levels were unaffected by the treatment processes. The results of this study demonstrated that monitoring the microbial quality of tertiary effluent by FC may not reflect the health risks encountered by the application of these effluents and the addition of coliphages to the monitoring programs may allow for accurate assessment of the health risks introduced by the application of tertiary effluent.

Attachment of human adenovirus onto household paints

Attachment of human adenovirus 40 (HAdV40) onto surfaces coated with three compositionally different household paints was evaluated experimentally and interpreted based on measured physicochemical properties of the paints. Polar, dispersive and electrostatic interactions between HAdV40 and the paints were predicted using the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) model. Quartz crystal microbalance (QCM-D) was used to quantify virus attachment to paints from 1 mM and 150 mM NaCl solutions, with the latter having the ionic strength of a typical respiratory fluid. Acrylic latex water-based, alkyd water-based, and alkyd oil-based paints were all determined to be highly hydrophobic (ΔG_sws < - 48 mJ/m²). XDLVO modeling and preliminary QCM-D tests evaluated virus-paint interactions within and outside pH windows of favorable virus-paint electrostatic interactions. Hydrophobic and electrostatic interactions governed virus attachment while van der Waals interactions played a relatively minor role. In higher ionic strength solutions, the extent of virus attachment correlated with the free energy of virus-paint interfacial interaction, [Formula: see text] : more negative energies corresponded to higher values of the areal mass density of attached viruses. Hydrophobicity was the dominant factor in determining virus adhesion from high ionic strength solutions where electrostatic interactions were screened out. The hydrophobicity of paints, while desirable for minimizing moisture intrusion, also facilitates attachment of colloids such as viruses. The results call for new approaches to the materials design of indoor paints with enhanced resistance to virus adhesion. Paints so formulated should help reduce human exposure to viruses.

Evaluation of two rapid ultrafiltration-based methods for SARS-CoV-2 concentration from wastewater

Quantitative measurements of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in raw wastewater have been implemented worldwide since the beginning of the pandemic. Recent efforts are being made to evaluate different viral concentration methodologies to overcome supplier shortages during lockdowns. A set of 22-wastewater samples seeded with murine hepatitis virus (MHV), a member of the Coronaviridae family, and the bacteriophage MS2, were used to characterize and compare two ultrafiltration-based methods: a centrifugal ultrafiltration device (Centricon® Plus-70) and the automated concentrating pipette CP-Select™. Based on the recovery efficiencies, significant differences were observed for MHV, with Centricon® Plus-70 (24%) being the most efficient method. Nevertheless, concentrations of naturally occurring SARS-CoV-2, Human adenoviruses and JC polyomaviruses in these samples did not result in significant differences between methods suggesting that testing naturally occurring viruses may complement the evaluation of viral concentration methodologies. Based on the virus adsorption to solids and the necessity of a pre-centrifugation step to remove larger particles and avoid clogging when using ultrafiltration methods, we assessed the percentage of viruses not quantified after ultrafiltration. Around 23% of the detected SARS-CoV-2 would be discarded during the debris removal step. The CP-Select™ provided the highest concentration factor (up to 333×) and the lowest LoD (6.19 × 103 GC/l) for MHV and proved to be fast, automatic, highly reproducible and suitable to work under BSL-2 measures.

The novel SARS-CoV-2 pandemic: Possible environmental transmission, detection, persistence and fate during wastewater and water treatment

The contagious SARS-CoV-2 virus, responsible for COVID-19 disease, has infected over 27 million people across the globe within a few months. While literature on SARS-CoV-2 indicates that its transmission may occur predominantly via aerosolization of virus-laden droplets, the possibility of alternate routes of transmission and/or reinfection via the environment requires considerable scientific attention. This review aims to collate information on possible transmission routes of this virus, to ascertain its fate in the environment. Concomitant with the presence of SARS-CoV-2 viral RNA in faeces and saliva of infected patients, studies also indicated its occurrence in raw wastewater, primary sludge and river water. Therefore sewerage system could be a possible route of virus outbreak, a possible tool to assess viral community spread and future surveillance technique. Hence, this review looked into detection, occurrence and fate of SARS-CoV-2 during primary, secondary, and tertiary wastewater and water treatment processes based on published literature on SARS-CoV and other enveloped viruses. The review also highlights the need for focused research on occurrence and fate of SARS-CoV-2 in various environmental matrices. Utilization of this information in environmental transmission models developed for other enveloped and enteric viruses can facilitate risk assessment studies. Preliminary research efforts with SARS-CoV-2 and established scientific reports on other coronaviruses indicate that the threat of virus transmission from the aquatic environment may be currently non-existent. However, the presence of viral RNA in wastewater provides an early warning that highlights the need for effective sewage treatment to prevent a future outbreak of SARS-CoV-2.

Approaches applied to detect SARS-CoV-2 in wastewater and perspectives post-COVID-19

Currently, SARS-CoV-2 has been detected in the influent of wastewater treatment plants (WWTP), pumping stations, manholes, sewer networks and sludge of WWTP and facilities of countries as France, Spain, Italy, Netherlands, United States, Australia, Ecuador, Brazil and Japan. Although this virus has been detected in the wastewater streams, there is no robust method for its detection and quantification in wastewater. This review compiled and analyzed the virus concentration approaches applied to detect the SARS-CoV-2, besides to provide insights about the methodology for viral concentration, limit of detection, occurrence, persistence, and perspectives post-COVID-19 related with the implications of the virus presence in wastewater. The SARS-COV-2 detection in wastewater has been related to virus concentration methods, which present different recovery rates of the virus. The most used viral concentration methods have been the polyethylene glycol (PEG) for precipitation of viral material and the ultrafiltration at molecular weight level. After viral concentration, the detection and quantification of SARS-COV-2 in wastewater are mainly via quantitative reverse transcription polymerase chain reaction (RT-qPCR), which is the clinical assay adapted for environmental purposes. Although in some experiments the positive control during RT-qPCR is running a surrogated virus (e.g., Mengovirus or Dengue virus), RT-qPCR or reverse transcription droplet digital PCR (RT-ddPCR) targeting the gene encoding nucleocapsid (N1, N2 and N3) of SARS-COV-2 are highly recommended to calculate the limit of detection in wastewater samples. Current results suggest that a rigorous methodology to elucidate the positive cases in a region from genomic copies in wastewater is needed.

Quantitative detection of human adenovirus from river water by monolithic adsorption filtration and quantitative PCR

Water contaminated with fecally derived viruses, also known as enteric viruses, represents a particularly high risk for human health. However, they have not been included in water quality regulations yet. The detection of these viruses is often more expensive and time-consuming compared to the analysis of conventional fecal indicator organisms. In addition, most methods are not sensitive enough to detect small viral loads that may already cause serious health issues if present in water. In this study, we established a workflow for the successful and direct enrichment of human adenovirus (HAdV) from artificially contaminated river water based on monolithic adsorption filtration (MAF) and quantitative polymerase reaction (qPCR). With a clear focus on efficiency, we used targeted synthetic DNA fragments as standard for the quantification of HAdV by qPCR, leading to accurate and robust results with a qPCR efficiency of 95 %, a broad working range over 6 orders of magnitude and an LOD of 1 GU/μL. We carried out a cascade of spiking experiments, enhancing the complexity of the spiking matrix with each step to progressively evaluate MAF for the direct concentration of HAdV. We found that negatively charged MAF using monoliths with hydroxyl groups (MAF-OH) showed a better reproducibility and a significantly faster turnaround time than skimmed milk flocculation (SMF) when concentrating HAdV35 from artificially contaminated, acidified mineral water. We then validated positively charged MAF using monoliths with diethyl aminoethyl groups (MAF-DEAE) for the direct concentration of HAdV5 without pre-conditioning of water samples using tap water as spiking matrix with a less defined and controlled water chemistry. Finally, we evaluated MAF-DEAE for the direct concentration of HAdV5 from surface water using river water as representative matrix with an undefined water chemistry. We found, that MAF-DEAE achieved reproducible recoveries of HAdV5, independently of the spiked concentration level or sample volume. Furthermore, we showed, that MAF-DEAE drastically reduced the limit of detection (LOD) of HAdV5 by a factor of 115 from 6.0 ∙ 10³ GU/mL before to 5.2 ∙ 10¹ GU/mL after MAF-DEAE. We identified that recoveries increased for smaller processing volumes with a peak at 0.5 L of 84.0 % and showed that recovery efficiency depends on sample volume and matrix type. The here presented workflow based on MAF-DEAE and qPCR offers an easy-to-implement and highly efficient alternative to existing approaches and allows for a fast detection of HAdV in water.

Food Safety in Post-COVID-19 Pandemic: Challenges and Countermeasures

Understanding food safety hazard risks is essential to avoid potential negative heath impacts in the food supply chain in a post-COVID-19 pandemic era. Development of strategies for virus direction in foods plays an important role in food safety and verification. Early warning, tracing, and detection should be implemented as an integrated system in order to mitigate thecoronavirus disease 2019 (COVID-19) outbreak, in which the detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is critical as it not only concerns screening of populations but also monitoring of possible contaminated sources such as the food supply chain. In this review, we point out the consequences in different aspects of our daily life in the post-COVID-19 pandemic from the perspective of the food supply chain and the food industry. We summarize the possible transmission routes of COVID-19 in the food supply chain before exploring the development of corresponding detection tools of SARS-CoV-2. Accordingly, we compare different detection methods for the virus in foods, including different pretreatments of food matrices in the virus detection. Finally, the future perspectives are proposed.

Inactivation and Elimination of SARS-CoV-2 in Biosamples Using Simple Fixatives and Ultrafiltration

The Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) causes Coronavirus disease-2019 (COVID-19), which is an ongoing pandemic that has significantly affected the health, economy, and socio-economic status of individuals worldwide. Laboratory research using in vitro, ex vivo and in vivo models has been accelerated to understand the pathogenesis of SARS-CoV-2 infection. However, such experimental research involving SARS-CoV-2 is restricted to biocontainment/safety level-3 (BSL-3) settings, due to the high pathogenicity of this virus. Since many of the downstream analyses of SARS-CoV-2-infected biological samples need to be conducted in a non-BSL3 setting, it is important to ensure that the samples are fully decontaminated and safe for subsequent analysis. Here, we report the effectiveness of standard procedures used to fix cells and tissues for pathological analysis, including 2% or 4% paraformaldehyde, 50%–70% ethanol, 10% neutral buffered formalin and ultrafiltration using membranes with a molecular weight cut-off (MWCO) ranging from 3 to 30 kDa, for inactivating or eliminating SARS-CoV-2. We validated these methods in experimental laboratory samples, such as viral inoculum in cell culture media, SARS-CoV-2 infected host cells and animal tissue lysates. We found that 15 minutes’ treatment of viral inoculum (10⁵ plaque-forming units; PFU) or SARS-CoV-2 infected cells with paraformaldehyde or 70% ethanol resulted in complete inactivation of the virus. The treatment of infected hamster lung tissues with 10% neutral buffered formalin also fully inactivated the virus. However, only 3 kDa ultracentrifuge filter was effective in eliminating the virus to an undetectable limit in the filtrate. Our validated methods are useful for decontaminating biological samples to reduce infection risk and safe handling in BSL2 facilities.

Primary concentration - The critical step in implementing the wastewater based epidemiology for the COVID-19 pandemic: A mini-review

The recent outbreak of a novel coronavirus SARS-CoV-2 has posed a significant global public health threat and caused dramatic social and economic disruptions. A new research direction is attracting a significant amount of attention in the academic community of environmental sciences and engineering, in which rapid community-level monitoring could be achieved by applying the methodology of wastewater based epidemiology (WBE). Given the fact that the development of a mass balance on the total number of viral RNA copies in wastewater samples and the infected stool specimens is the heart of WBE, the result of the quantitative RNA detection in wastewater has to be highly sensitive, accurate, and reliable. Thus, applying effective concentration methods before the subsequent RNA extraction and RT-qPCR detection is a must-have procedure for the WBE. This review provides new insights into the primary concentration methods that have been adopted by the eighteen recently reported COVID-19 wastewater detection studies, along with a brief discussion of the mechanisms of the most commonly used virus concentration methods, including the PEG-based separation, electrostatically charged membrane filtration, and ultrafiltration. In the end, two easy and well-proven concentration strategies are recommended as below, aiming to maximize the practical significance and operational effectiveness of the SARS-CoV-2 virus concentration from wastewater samples.

Extracellular DNA (eDNA): Neglected and Potential Sources of Antibiotic Resistant Genes (ARGs) in the Aquatic Environments

Over the past decades, the rising antibiotic resistance bacteria (ARB) are continuing to emerge as a global threat due to potential public health risk. Rapidly evolving antibiotic resistance and its persistence in the environment, have underpinned the need for more studies to identify the possible sources and limit the spread. In this context, not commonly studied and a neglected genetic material called extracellular DNA (eDNA) is gaining increased attention as it can be one of the significant drivers for transmission of extracellular ARGS (eARGs) via horizontal gene transfer (HGT) to competent environmental bacteria and diverse sources of antibiotic-resistance genes (ARGs) in the environment. Consequently, this review highlights the studies that address the environmental occurrence of eDNA and encoding eARGs and its impact on the environmental resistome. In this review, we also brief the recent dedicated technological advancements that are accelerating extraction of eDNA and the efficiency of treatment technologies in reducing eDNA that focuses on environmental antibiotic resistance and potential ecological health risk.

Comparison of virus concentration methods for the RT-qPCR-based recovery of murine hepatitis virus, a surrogate for SARS-CoV-2 from untreated wastewater

There is currently a clear benefit for many countries to utilize wastewater-based epidemiology (WBE) as part of ongoing measures to manage the coronavirus disease 2019 (COVID-19) global pandemic. Since most wastewater virus concentration methods were developed and validated for nonenveloped viruses, it is imperative to determine the efficiency of the most commonly used methods for the enveloped severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Municipal wastewater seeded with a human coronavirus (CoV) surrogate, murine hepatitis virus (MHV), was used to test the efficiency of seven wastewater virus concentration methods: (A-C) adsorption-extraction with three different pre-treatment options, (D-E) centrifugal filter device methods with two different devices, (F) polyethylene glycol (PEG 8000) precipitation, and (G) ultracentrifugation. MHV was quantified by reverse-transcription quantitative polymerase chain reaction and the recovery efficiency was calculated for each method. The mean MHV recoveries ranged from 26.7 to 65.7%. The most efficient methods were adsorption-extraction methods with MgCl2 pre-treatment (Method C), and without pre-treatment (Method B). The third most efficient method used the Amicon® Ultra-15 centrifugal filter device (Method D) and its recovery efficiency was not statistically different from the most efficient methods. The methods with the worst recovery efficiency included the adsorption-extraction method with acidification (A), followed by PEG precipitation (F). Our results suggest that absorption-extraction methods with minimal or without pre-treatment can provide suitably rapid, cost-effective and relatively straightforward recovery of enveloped viruses in wastewater. The MHV is a promising process control for SARS-CoV-2 surveillance and can be used as a quality control measure to support community-level epidemic mitigation and risk assessment.

Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travellers

BACKGROUND

Wastewater-based epidemiology (WBE) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be an important source of information for coronavirus disease 2019 (COVID-19) management during and after the pandemic. Currently, governments and transportation industries around the world are developing strategies to minimize SARS-CoV-2 transmission associated with resuming activity. This study investigated the possible use of SARS-CoV-2 RNA wastewater surveillance from airline and cruise ship sanitation systems and its potential use as a COVID-19 public health management tool.

METHODS

Aircraft and cruise ship wastewater samples (n = 21) were tested for SARS-CoV-2 using two virus concentration methods, adsorption-extraction by electronegative membrane (n = 13) and ultrafiltration by Amicon (n = 8), and five assays using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) and RT-droplet digital PCR (RT-ddPCR). Representative qPCR amplicons from positive samples were sequenced to confirm assay specificity.

RESULTS

SARS-CoV-2 RNA was detected in samples from both aircraft and cruise ship wastewater; however concentrations were near the assay limit of detection. The analysis of multiple replicate samples and use of multiple RT-qPCR and/or RT-ddPCR assays increased detection sensitivity and minimized false-negative results. Representative qPCR amplicons were confirmed for the correct PCR product by sequencing. However, differences in sensitivity were observed among molecular assays and concentration methods.

CONCLUSIONS

The study indicates that surveillance of wastewater from large transport vessels with their own sanitation systems has potential as a complementary data source to prioritize clinical testing and contact tracing among disembarking passengers. Importantly, sampling methods and molecular assays must be further optimized to maximize detection sensitivity. The potential for false negatives by both wastewater testing and clinical swab testing suggests that the two strategies could be employed together to maximize the probability of detecting SARS-CoV-2 infections amongst passengers.

Credibility of polymeric and ceramic membrane filtration in the removal of bacteria and virus from water: A review

The prevalence of many waterborne diseases and the increased mortality rate starting from children to adult persons rises the need to purify water before consumption. Owing to the number of advantages associated with membrane filtration technologies, they are widely being implemented across the world for the production of pathogen free water. This article hence focuses on numerous such examples of using membrane technology in the production of drinking water. Membranes are even being coated with various materials to enhance their surface properties such as electrostatic and hydrophobic attraction capacity to aid for such separation. Various metal oxide coatings are seen to be gaining importance now-a-days and also, articles citing the use of silver coating are very large in number, owing to the excellent antipathogenic property shown by various silver compounds. It needs mention that examples have also been cited in this article where virus concentration was carried out with a purpose of producing different vaccines, virus adsorption in membrane and its subsequent elution (VIRADEL) being the most discussed one. In addition to these, description about the virus and bacteria quantification techniques are also mentioned in this article. The elaborated study of all these processes and the derived future prospects regarding the production of pathogen free water will certainly be helpful for the researchers working in this field, irrespective of the beginners or the experienced ones, to direct their research more innovatively.

First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community

Infection with SARS-CoV-2, the etiologic agent of the ongoing COVID-19 pandemic, is accompanied by the shedding of the virus in stool. Therefore, the quantification of SARS-CoV-2 in wastewater affords the ability to monitor the prevalence of infections among the population via wastewater-based epidemiology (WBE). In the current work, SARS-CoV-2 RNA was concentrated from wastewater in a catchment in Australia and viral RNA copies were enumerated using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) resulting in two positive detections within a six day period from the same wastewater treatment plant (WWTP). The estimated viral RNA copy numbers observed in the wastewater were then used to estimate the number of infected individuals in the catchment via Monte Carlo simulation. Given the uncertainty and variation in the input parameters, the model estimated a median range of 171 to 1,090 infected persons in the catchment, which is in reasonable agreement with clinical observations. This work highlights the viability of WBE for monitoring infectious diseases, such as COVID-19, in communities. The work also draws attention to the need for further methodological and molecular assay validation for enveloped viruses in wastewater.

First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community

Infection with SARS-CoV-2, the etiologic agent of the ongoing COVID-19 pandemic, is accompanied by the shedding of the virus in stool. Therefore, the quantification of SARS-CoV-2 in wastewater affords the ability to monitor the prevalence of infections among the population via wastewater-based epidemiology (WBE). In the current work, SARS-CoV-2 RNA was concentrated from wastewater in a catchment in Australia and viral RNA copies were enumerated using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) resulting in two positive detections within a six day period from the same wastewater treatment plant (WWTP). The estimated viral RNA copy numbers observed in the wastewater were then used to estimate the number of infected individuals in the catchment via Monte Carlo simulation. Given the uncertainty and variation in the input parameters, the model estimated a median range of 171 to 1,090 infected persons in the catchment, which is in reasonable agreement with clinical observations. This work highlights the viability of WBE for monitoring infectious diseases, such as COVID-19, in communities. The work also draws attention to the need for further methodological and molecular assay validation for enveloped viruses in wastewater.

First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community

Infection with SARS-CoV-2, the etiologic agent of the ongoing COVID-19 pandemic, is accompanied by the shedding of the virus in stool. Therefore, the quantification of SARS-CoV-2 in wastewater affords the ability to monitor the prevalence of infections among the population via wastewater-based epidemiology (WBE). In the current work, SARS-CoV-2 RNA was concentrated from wastewater in a catchment in Australia and viral RNA copies were enumerated using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) resulting in two positive detections within a six day period from the same wastewater treatment plant (WWTP). The estimated viral RNA copy numbers observed in the wastewater were then used to estimate the number of infected individuals in the catchment via Monte Carlo simulation. Given the uncertainty and variation in the input parameters, the model estimated a median range of 171 to 1,090 infected persons in the catchment, which is in reasonable agreement with clinical observations. This work highlights the viability of WBE for monitoring infectious diseases, such as COVID-19, in communities. The work also draws attention to the need for further methodological and molecular assay validation for enveloped viruses in wastewater.

First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community

Infection with SARS-CoV-2, the etiologic agent of the ongoing COVID-19 pandemic, is accompanied by the shedding of the virus in stool. Therefore, the quantification of SARS-CoV-2 in wastewater affords the ability to monitor the prevalence of infections among the population via wastewater-based epidemiology (WBE). In the current work, SARS-CoV-2 RNA was concentrated from wastewater in a catchment in Australia and viral RNA copies were enumerated using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) resulting in two positive detections within a six day period from the same wastewater treatment plant (WWTP). The estimated viral RNA copy numbers observed in the wastewater were then used to estimate the number of infected individuals in the catchment via Monte Carlo simulation. Given the uncertainty and variation in the input parameters, the model estimated a median range of 171 to 1,090 infected persons in the catchment, which is in reasonable agreement with clinical observations. This work highlights the viability of WBE for monitoring infectious diseases, such as COVID-19, in communities. The work also draws attention to the need for further methodological and molecular assay validation for enveloped viruses in wastewater.

Evaluation of three different filters and two methods for recovering viruses from drinking water

Among the enteric viruses implicated in waterborne outbreaks, human norovirus and hepatitis A virus (HAV) are a serious public health issue. Most foodborne viruses are difficult or currently unlikely to cultivate. Because of the lack of a cell culture method, real-time reverse transcriptase PCR is commonly used for the detection of norovirus in foodstuffs and environmental samples. Due to low infectious doses in humans and low virus concentration in water sample, filter adsorption methods were used for concentrating viruses from water. The ISO (Anonymous, ISO 15216-1, 2017) describes standardized molecular methods for detecting HAV and norovirus in bottled water. This method includes a two-step procedure: concentrating the virus using a microporous electropositive filter (47 mm diameter, 0.45 μm pore size) then molecular detection. The Zetapor filter, which had a charged membrane with a pore size of 0.45 μm, was commonly used in the past to concentrate viruses from water or from salad leaves following virus elution. But, unfortunately, the Zetapor filter is no longer marketed and it is therefore necessary to assess an alternative filter. The aim of this study was to compare the ability of two electropositive filters with a pore size of 0.45 μm or 0.22 μm and one uncharged filter (0.45 μm) to recover norovirus and HAV from two different types of drinking water (bottled water and tap water) with the adsorption-elution method proposed by ISO (Anonymous, ISO 15216-1, 2017) (method A) and with direct viral extraction using filters (method B). The mean extraction yields for norovirus and HAV calculated with RNA extracts ranged from 0.2 % - 4.81 % with method A and from 5.05 % - 53.58 % with method B, and did not differ significantly between the two types of drinking water tested. For method B, the mean extraction yields for HAV and norovirus were evaluated according to results from the three filters used. The recovery rate of HAV and norovirus ranged between 3.47 % and 62.41 % with the 0.45 μm electropositive filter and were higher than the other filters. The 0.45 μm electropositive filter could be used to concentrate viruses for routine viral monitoring of drinking water for researchers who want to adopt the method in their lab routine.

Potential indicators of virus transport and removal during soil aquifer treatment of treated wastewater effluent

Increased water demands have led to a notable interest in the use of treated wastewater for reuse. Typically, this results from the implementation of advanced treatment of final effluent from wastewater treatment plants prior to reuse for potable or non-potable purposes. Soil aquifer treatment (SAT) is a natural treatment process in which water from sources of varying quality is infiltrated into the soil to further improve its quality. The goal of this study was to determine the log₁₀ reduction values (LRVs) of viruses naturally present in treated effluent and evaluate two potential indicators of virus removal and transport, pepper mild mottle virus (PMMoV) and crAssphage, during SAT of treated effluent. Groundwater was sampled at three wells with different attributes within the Sweetwater Recharge Facility (SWRF) in Tucson, AZ. These sites vary greatly in operational parameters such as effluent infiltration rates and wetting/drying cycles, which may influence virus removal efficiency. Detection of adenovirus, enterovirus, PMMoV, and crAssphage were determined by qPCR/RT-qPCR and log₁₀ reduction values (LRVs) were determined. PMMoV and crAssphage were detected in groundwater associated with a set of recharge basins that exhibited shorter wetting/drying cycles and faster infiltration rates. LRVs for crAssphage and PMMoV at this site ranged from 3.9 to 5.8, respectively. Moreover, PMMoV was detected downflow of the SAT sites, indicating the potential degradation of microbial groundwater quality in the region surrounding managed aquifer recharge facilities. Overall, PMMoV and crAssphage showed potential as conservative process indicators of virus removal during SAT, particularly for attribution of LRV credits. Moreover, the detection of these viruses indicated the potential influence of wetting/drying cycles on virus removal by SAT, a parameter that has not yet been studied with respect to biological contaminants.

Sequential treatment using a hydrophobic resin and gel filtration to improve viral gene quantification from highly complex environmental concentrates

Assays based on the polymerase chain reaction (PCR) are widely applied to quantify enteric viruses in aquatic environments to study their fates and potential infection risks. However, inhibitory substances enriched by virus concentration processes can result in inaccurate quantification. This study aimed to find a method for improving virus quantification by mitigating the effects of inhibitory environmental concentrates, using previous knowledge of the properties of the inhibitory substances. Performances of anion exchange resins, gel filtration, and a hydrophobic resin (DAX-8) were comparatively evaluated using poliovirus and its extracted RNA spiked into humic acid solutions. These solutions served as good representatives of the inhibitory environmental concentrates. A sequential treatment using DAX-8 resin and gel filtration produced the most favorable results, i.e., low virus losses that were stable and a reduced inhibitory effect. Furthermore, the sequential treatment was applied to another set of 15 environmental concentrates. Without the sequential treatment, serious underestimation (>4.0 log₁₀ to 1.1 log₁₀) of a molecular process control (murine norovirus) was measured for eight samples. With the treatment, the control was detected with <1.0 log₁₀ underestimation for all samples. The treatment improved the quantification of seven types of indigenous viruses. In summary, the sequential treatment is effective in improving the viral quantification in various of environmental concentrates.

Consecutive ultrafiltration and silica adsorption for recovery of extracellular antibiotic resistance genes from an urban river

The dissemination of antibiotic resistance (AR) has attracted global attention because of the increasing antibiotic treatment failure it has caused. Through natural transformation, a live bacterium takes up extracellular DNA (exDNA), which facilitates AR dissemination. However, recovery of exDNA from water samples is challenging. In this study, we validated a consecutive ultrafiltration-based protocol to simultaneously recover intracellular DNA (inDNA), dissolved exDNA (Dis_exDNA, dissolved in the bulk water), and adsorbed exDNA (Ads_exDNA, adsorbed to the surfaces of suspended particles). Using hollow fiber ultrafiltration (HFUF), all DNA fractions were concentrated from environmental water samples, after which Dis_exDNA (supernatant) was separated from inDNA and Ads_exDNA (pellets) using centrifugation. Ads_exDNA was washed off from the pellets with proteinase K and sodium phosphate buffer. Dis_exDNA and Ads_exDNA were further concentrated using centrifugal ultrafiltration, from which silica binding was performed. inDNA was extracted from washed pellets with a commercial kit. For inDNA, HFUF showed recovery efficiencies of 96.5 ± 18.5% and 88.0 ± 2.0% for total cells and cultured Escherichia coli, respectively (n = 3). To represent all possible DNA fragments in water environment, exDNA with different lengths (10.0, 4.0, 1.0, and 0.5 kbp) were spiked to test the recovery efficiencies for Dis_exDNA. The whole process achieved 62.2%-62.9% recovery for 10 and 4 kbp exDNA, and 38.8%-44.5% recovery for 1.0 and 0.5 kbp exDNA. Proteinase K treatment enhanced the recovery of Ads_exDNA by 4.0-10.7 times. The protocol was applied to water samples from an urban river in Tokyo, Japan. The abundance of AR genes (ARGs) in inDNA, Dis_exDNA, and Ads_exDNA increased downstream of wastewater treatment plants. ARGs in Ads_exDNA and Dis_exDNA accounted for 1.8%-26.7% and 0.03%-20.9%, respectively, of the total DNA, implying that Ads_exDNA and Dis_exDNA are nonnegligible potential pools for the horizontal transfer of ARGs.

Interlaboratory Comparative Study to Detect Potentially Infectious Human Enteric Viruses in Influent and Effluent Waters

Wastewater represents the main reusable water source after being adequately sanitized by wastewater treatment plants (WWTPs). In this sense, only bacterial quality indicators are usually checked to this end, and human pathogenic viruses usually escape from both sanitization procedures and controls, posing a health risk on the use of effluent waters. In this study, we evaluated a protocol based on aluminum adsorption-precipitation to concentrate several human enteric viruses, including norovirus genogroup I (NoV GI), NoV GII, hepatitis A virus (HAV), astrovirus (HAstV), and rotavirus (RV), with limits of detection of 4.08, 4.64, 5.46 log genomic copies (gc)/L, 3.31, and 5.41 log PCR units (PCRU)/L, respectively. Furthermore, the method was applied in two independent laboratories to monitor the presence of NoV GI, NoV GII, and HAV in effluent and influent waters collected from five WWTPs at two different sampling dates. Concomitantly, a viability PMAxx-RT-qPCR was applied to all the samples to get information on the potential infectivity of both influent and effluent waters. The ranges of the titers in influent waters for NoV GI, NoV GII, RV, and HAstV were 4.80-7.56, 5.19-7.31 log gc/L, 5.41-6.52, and 4.59-7.33 log PCRU/L, respectively. In effluent waters, the titers ranged between 4.08 and 6.27, 4.64 and 6.08 log gc/L, < 5.51, and between 3.31 and 5.58 log PCRU/L. Moreover, the viral titers detected by viability RT-qPCR showed statistical differences with RT-qPCR alone, suggesting the potential viral infectivity of the samples despite some observed reductions. The proposed method could be applied in ill-equipped laboratories, due to the lack of a requirement for a specific apparatus (i.e., ultracentrifuge).

Recovery and Detection of Enteric Viruses from Non-Traditional Irrigation Water Sources

The variability of environmental water samples impacts the allowance of one method to be universally ideal for all water types and volumes. Surface and reclaimed waters can be used for crop irrigation and may be referred to as non-traditional irrigation waters as these water types may be associated with a higher risk of microbial contamination compared to groundwater. These waters are typically more microbially and chemically complex than groundwater and have a higher risk of viral contamination. To detect viruses in these water types, an infinite number of variations can be made to traditional recovery methods. This protocol was developed based on a commonly used virus adsorption and elution (VIRADEL) method. Additional steps were included to simplify and efficiently reduce particulates in the viral concentrate and remove DNA from eluted nucleic acids prior to detection. Method alterations allow for volumes up to 40 liters to be processed with consistent recovery of enteric viruses including Aichi virus, hepatitis A virus, and noroviruses belonging to genogroups GI and GII. No inhibition was observed among either surface or reclaimed water samples. This protocol could be utilized in the monitoring of a wide array of irrigation water sources throughout irrigation processes.

Evaluation of Secondary Concentration Methods for Poliovirus Detection in Wastewater

Effective surveillance of human enteric viruses is critical to estimate disease prevalence within a community and can be a vital supplement to clinical surveillance. This study sought to evaluate simple, effective, and inexpensive secondary concentration methods for use with ViroCap™ filter eluate for environmental surveillance of poliovirus. Wastewater was primary concentrated using cartridge ViroCap filters, seeded with poliovirus type 1 (PV1), and then concentrated using five secondary concentration methods (beef extract-Celite, ViroCap flat disc filter, InnovaPrep® Concentrating Pipette, polyethylene glycol [PEG]/sodium chloride [NaCl] precipitation, and skimmed-milk flocculation). PV1 was enumerated in secondary concentrates by plaque assay on BGMK cells. Of the five tested methods, PEG/NaCl precipitation and skimmed-milk flocculation resulted in the highest PV1 recoveries. Optimization of the skimmed-milk flocculation method resulted in a greater PV1 recovery (106 ± 24.8%) when compared to PEG/NaCl precipitation (59.5 ± 19.4%) (p = 0.004, t-test). The high PV1 recovery, short processing time, low reagent cost, no required refrigeration, and requirement for only standard laboratory equipment suggest that the skimmed-milk flocculation method would be a good candidate to be field-validated for secondary concentration of environmental ViroCap filter samples containing poliovirus.

Evaluation of Secondary Concentration Methods for Poliovirus Detection in Wastewater

Effective surveillance of human enteric viruses is critical to estimate disease prevalence within a community and can be a vital supplement to clinical surveillance. This study sought to evaluate simple, effective, and inexpensive secondary concentration methods for use with ViroCap™ filter eluate for environmental surveillance of poliovirus. Wastewater was primary concentrated using cartridge ViroCap filters, seeded with poliovirus type 1 (PV1), and then concentrated using five secondary concentration methods (beef extract-Celite, ViroCap flat disc filter, InnovaPrep® Concentrating Pipette, polyethylene glycol [PEG]/sodium chloride [NaCl] precipitation, and skimmed-milk flocculation). PV1 was enumerated in secondary concentrates by plaque assay on BGMK cells. Of the five tested methods, PEG/NaCl precipitation and skimmed-milk flocculation resulted in the highest PV1 recoveries. Optimization of the skimmed-milk flocculation method resulted in a greater PV1 recovery (106 ± 24.8%) when compared to PEG/NaCl precipitation (59.5 ± 19.4%) (p = 0.004, t-test). The high PV1 recovery, short processing time, low reagent cost, no required refrigeration, and requirement for only standard laboratory equipment suggest that the skimmed-milk flocculation method would be a good candidate to be field-validated for secondary concentration of environmental ViroCap filter samples containing poliovirus.

Critical issues in application of molecular methods to environmental virology

Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.

A Review of the Most Commonly Used Methods for Sample Collection in Environmental Surveillance of Poliovirus

We performed a review of the environmental surveillance methods commonly used to collect and concentrate poliovirus (PV) from water samples. We compared the sampling approaches (trap vs grab), the process methods (precipitation vs filtration), and the various tools and chemical reagents used to separate PV from other viruses and pathogens in water samples (microporous glass, pads, polyethylene glycol [PEG]/dextran, PEG/sodium chloride, NanoCeram/ViroCap, and ester membranes). The advantages and disadvantages of each method are considered, and the geographical areas where they are currently used are discussed. Several methods have demonstrated the ability to concentrate and recover PVs from environmental samples. The details of the particular sampling conditions and locations should be considered carefully in method selection.

Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes

There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.

Shifts in dissolved organic matter and microbial community composition are associated with enhanced removal of fecal pollutants in urban stormwater wetlands

Constructed stormwater wetlands provide a host of ecosystem services, including potentially pathogen removal. We present results from a multi-wetland study that integrates across weather, chemical, microbiological and engineering design variables in order to identify patterns of microbial contaminant removal from inlet to outlet within wetlands and key drivers of those patterns. One or more microbial contaminants were detected at the inlet of each stormwater wetland (Escherichia coli and Enterococcus > Bacteroides HF183 > adenovirus). Bacteroides HF183 and adenovirus concentrations declined from inlet to outlet at all wetlands. However, co-removal of pathogens and fecal indicator bacteria only occurred at wetlands where microbial assemblages at the inlet (dominated by Proteobacteria and Bacteriodetes) were largely displaced by indigenous autotrophic microbial communities at the outlet (dominated by Cyanobacteria). Microbial community transitions (characterized using pyrosequencing) were well approximated by a combination of two rapid indicators: (1) fluorescent dissolved organic matter, and (2) chlorophyll a or phaeophytin a fluorescence. Within-wetland treatment of fecal markers and indicators was not strongly correlated with the catchment-to-wetland area ratio, but was diminished in older wetlands, which may point to a need for more frequent maintenance.

Efficiency of Reovirus Concentration from Water with Positively Charged Filters

This study examined the efficacy of reovirus concentration from large volumes of water using two positively charged filters: Zeta Plus 1MDS and NanoCeram. The results indicated that an average of 61 and 81% of input reoviruses were effectively recovered, respectively, from recycled water and tap water using NanoCeram filtration.

A review on recent progress in the detection methods and prevalence of human enteric viruses in water

Waterborne human enteric viruses, such as noroviruses and adenoviruses, are excreted in the feces of infected individuals and transmitted via the fecal-oral route including contaminated food and water. Since viruses are normally present at low concentrations in aquatic environments, they should be concentrated into smaller volumes prior to downstream molecular biological applications, such as quantitative polymerase chain reaction (qPCR). This review describes recent progress made in the development of concentration and detection methods of human enteric viruses in water, and discusses their applications for providing a better understanding of the prevalence of the viruses in various types of water worldwide. Maximum concentrations of human enteric viruses in water that have been reported in previous studies are summarized to assess viral abundances in aquatic environments. Some descriptions are also available on recent applications of sequencing analyses used to determine the genetic diversity of viral genomes in water samples, including those of novel viruses. Furthermore, the importance and significance of utilizing appropriate process controls during viral analyses are discussed, and three types of process controls are considered: whole process controls, molecular process controls, and (reverse transcription (RT)-)qPCR controls. Although no standards have been established for acceptable values of virus recovery and/or extraction-(RT-)qPCR efficiency, use of at least one of these appropriate control types is highly recommended for more accurate interpretation of observed data.

Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments

Sewage contains a mixed ecosystem of diverse sets of microorganisms, including human pathogenic viruses. Little is known about how conventional as well as advanced treatments of sewage, such as ozonation, reduce the environmental spread of viruses. Analyses for viruses were therefore conducted for three weeks in influent, after conventional treatment, after additional ozonation, and after passing an open dam system at a full-scale treatment plant in Knivsta, Sweden. Viruses were concentrated by adsorption to a positively charged filter, from which they were eluted and pelleted by ultracentrifugation, with a recovery of about 10%. Ion Torrent sequencing was used to analyze influent, leading to the identification of at least 327 viral species, most of which belonged to 25 families with some having unclear classification. Real-time PCR was used to test for 21 human-related viruses in inlet, conventionally treated, and ozone-treated sewage and outlet waters. The viruses identified in influent and further analyzed were adenovirus, norovirus, sapovirus, parechovirus, hepatitis E virus, astrovirus, pecovirus, picobirnavirus, parvovirus, and gokushovirus. Conventional treatment reduced viral concentrations by one to four log10, with the exception of adenovirus and parvovirus, for which the removal was less efficient. Ozone treatment led to a further reduction by one to two log10, but less for adenovirus. This study showed that the amount of all viruses was reduced by conventional sewage treatment. Further ozonation reduced the amounts of several viruses to undetectable levels, indicating that this is a promising technique for reducing the transmission of many pathogenic human viruses.

Characterization of Natural Organic Substances Potentially Hindering RT-PCR-Based Virus Detection in Large Volumes of Environmental Water

Quantitative detection of pathogenic viruses in the environmental water is essential for the assessment of water safety. It is known that some of natural organic substances interfere with virus detection processes, i.e., nucleic acid extraction and reverse transcription-PCR. Such substances are carried over into a sample after virus concentration. In this study, inhibitory substances in coastal water samples were characterized in view of their effects on efficiency of virus detection and property as organic matters. Among 81 samples tested, 77 (95%) showed low recoveries (<10%) of spiked murine norovirus. These recovery rates were correlated with the levels of organic matter present in virus concentrates as measured by ultraviolet absorbance at 254 nm (r = -0.70 - -0.71, p < 0.01). High-performance gel chromatography and fluorescence excitation-emission matrix spectroscopy revealed that organic fractions in the 10-100 kDa size range, which were not dominant in the original samples, and those possessing humic acid-like fluorescence properties were dominant in virus concentrates. The inhibitory effect was more pronounced during summer. Substances originating from seawater seemed to cause a more pronounced effect than those originating from wastewater. Our data highlight the previously unknown characteristics of natural inhibitory substances and are helpful in establishing an effective sample purification technique.