Capsid integrity quantitative PCR to determine virus infectivity in environmental and food applications - A systematic review

Comparison of sample pretreatments used to distinguish between infectious and non-infectious foodborne viruses by RT-qPCR

To detect viruses such as hepatitis A virus (HAV) and human norovirus (HuNoV) in foods, RT-qPCR or other molecular methods are used, which cannot distinguish between infectious and non-infectious virions. Samples can be pretreated to limit detection to intact and presumably infectious virions. We compared propidium monoazide (PMA or PMAxx), platinum (IV) chloride (PtCl4), magnetic silica beads and centrifugal filter using HAV or HuNoV inactivated by heat, pulsed light, or sodium hypochlorite (NaOCl). PMAxx completely or nearly eliminated (3.96 ± 1.24 log gc) the RT-qPCR signal of HAV inactivated at 100°C for 10 min. Pretreatments could not reduce significantly RT-qPCR signal of HAV after pulsed light (0.74 ± 0.36 log gc) and NaOCl (0.24 ± 0.14 log gc) inactivation. Enzymatic treatments did not improve the results obtained with PMAxx. The exudate of raspberry, strawberry or oyster used as food matrices needed dilution by at least tenfold for PMAxx to to yield results comparable to virions without a food matrix. Overall, PMAxx shows good potential to discriminate between infectious and non-infectious despite some remaining limitations.

Advancements in research on the precise eradication of cancer cells through nanophotocatalytic technology

The rapid development of nanotechnology has significantly advanced the application of nanophotocatalysis in the medical field, particularly for cancer therapy. Traditional cancer treatments, such as chemotherapy and radiotherapy, often cause severe side effects, including damage to healthy tissues and the development of drug resistance. In contrast, nanophotocatalytic therapy offers a promising approach by utilizing nanomaterials that generate reactive oxygen species (ROS) under light activation, allowing for precise tumor targeting and minimizing collateral damage to surrounding tissues. This review systematically explores the latest advancements in highly efficient nanophotocatalysts for cancer treatment, focusing on their toxicological profiles, underlying mechanisms for cancer cell eradication, and potential for clinical application. Recent research shows that nanophotocatalysts, such as TiO2, In2O3, and g-C3N4 composites, along with photocatalysts with high conduction band or high valence band positions, generate ROS under light irradiation, which induces oxidative stress and leads to cancer cell apoptosis or necrosis. These ROS cause cellular damage by interacting with key biological molecules such as DNA, proteins, and lipids, triggering a cascade of biochemical reactions that ultimately result in cancer cell death. Furthermore, strategies such as S-scheme heterojunctions and oxygen vacancies (OVs) have been incorporated to enhance charge separation efficiency and light absorption, resulting in increased ROS generation, which improves photocatalytic performance for cancer cell targeting. Notably, these photocatalysts exhibit low toxicity to healthy cells, making them a safe and effective treatment modality. The review also discusses the challenges associated with photocatalytic cancer therapy, including limitations in light penetration and the need for improved biocompatibility. The findings suggest that nanophotocatalytic technology holds significant potential for precision cancer therapy, paving the way for safer and more effective treatment strategies.

Survival of viruses in water microcosms

Human enteric viruses and emerging viruses such as severe acute respiratory syndrome coronavirus 2, influenza virus and monkeypox virus, are frequently detected in wastewater. Human enteric viruses are highly persistent in water, but there is limited information available for non-enteric viruses. The present study evaluated the stability of hepatitis A virus (HAV), murine norovirus (MNV), influenza A virus H3N2 (IAV H3N2), human coronavirus (HCoV) 229E, and vaccinia virus (VACV) in reference water (RW), effluent wastewater (EW) and drinking water (DW) under refrigeration and room temperature conditions. The decay of infectious viruses was analyzed using a monophasic decay model, which largely showed that human enteric viruses exhibit remarkable persistence in water samples. MNV infectivity decreased significantly after 14 days in EW at room temperature compared to 84 days under refrigerated conditions, with decay rates of 0.230 log TCID50/day at room temperature and 0.040 log TCID50/day under refrigeration. A gradual decline in HAV infectivity was observed at room temperature, whereas at refrigerated temperature, infectious viruses were recovered even after 98 days. HCoV-229E, IAV H3N2 and VACV were completely inactivated in DW and EW at room temperature between 7 and 21 days, with longer stability observed under refrigeration. The decay of IAV H3N2, HCoV-229E and VACV in EW and DW was also assessed in parallel using RT-qPCR to determine genome persistence and viability PCR to determine intact viral capsid persistence. Overall, our results suggest that viability PCR is not suitable for tracking virus decay in water under real-world environmental conditions.

Measurement of the Infection and Integrity of Monkeypox Virus: A New Method Using PMAxx-ddPCR

Mpox, caused by the Monkeypox virus (MPV), is a global public health threat. Virus isolation is the gold standard to confirm MPV infection, but this process can face many challenges. As an alternative, a new method was developed in in vitro settings using 50 µM of propidium monoazide (PMAxx, a DNA-binding agent) coupled with digital droplet PCR (ddPCR). Frozen clinical samples analyzed by PMAxx-ddPCR had a median of 0.8 copies/µL, while untreated samples had a median of 29.8 copies/µL. Since a substantial percentage of reduction was observed in these samples (>80%), it was verified whether this reduction could be due to the freezing process. This hypothesis was confirmed both in vitro and using clinical samples. A gradual increase in the mean percentage of reduction was observed after freezing-thawing cycles of MPV-isolate (59.5-81.4%). Moreover, a different percentage of reduction was observed before (68.2%) and after freezing (97.4%) the specimens, suggesting that the freezing process could reduce the number of complete viral particles. Our study shows strong evidence of the usefulness of PMAxx in clinical settings. PMAxx ensures the detection of intact MPV particles, which improves the accuracy of MPV load measurements. This method not only increases the reliability of MPV diagnosis but also overcomes virus isolation limitations.

Evaluation of Three Viral Capsid Integrity qPCR Methods for Wastewater-Based Viral Surveillance

Capsid Integrity qPCR (CI-qPCR) assays offer a promising alternative to cell culture-based infectivity assays for assessing pathogenic human virus viability in wastewater. This study compared three CI-qPCR methods: two novel (Crosslinker, TruTiter) and one established (PMAxx dye). These methods were evaluated on heat-inactivated and non-heat-inactivated 'live' viruses spiked into phosphate-buffered saline (PBS) and wastewater, as well as on viruses naturally present in wastewater samples. The viral panel included Human adenovirus 5 (HAdV), enterovirus A71 (EV), hepatitis-A virus (HAV), influenza-A H3N2 (IAV), respiratory syncytial virus A2 (RSV), norovirus GI, norovirus GII, and SARS-CoV-2. All three methods successfully differentiated between degraded, heat-inactivated, and live viruses in PBS. While all three methods were comparable for HAdV and norovirus GI, PMAxx detected significantly lower gene copies for EV and IAV. In spiked wastewater, PMAxx yielded significantly lower gene copies for all heat-inactivated viruses (HAdV, EV, HAV, IAV, and RSV) compared to the Crosslinker and TruTiter methods. For viruses naturally present in wastewater (un-spiked), no significant difference was observed between PMAxx and TruTiter methods. Intact, potentially infectious viruses were detected using both PMAxx and TruTiter on untreated and treated wastewater samples. A comparative analysis of qPCR data and TEM images revealed that viral flocculation of IAV may interfere with capsid integrity assays using intercalating dyes. In summary, our findings not only advance the development of more effective methods for assessing viral viability in wastewater, but also highlight the potential of CI-qPCR techniques to enhance early warning systems for emerging pathogens, thereby strengthening public health preparedness and response strategies.

Plate-Based High-Throughput Fluorescence Assay for Assessing Enveloped Virus Integrity

Viruses are a considerable threat to global health and place major burdens on economies worldwide. Manufactured viruses are also being widely used as delivery agents to treat (gene therapies) or prevent diseases (vaccines). Therefore, it is vital to study and fully understand the infectious state of viruses. Current techniques used to study viruses are often slow or nonexistent, making the development of new techniques of paramount importance. Here we present a high-throughput and robust, cell-free plate-based assay (FAIRY: Fluorescence Assay for vIRal IntegritY), capable of differentiating intact from nonintact enveloped viruses, i.e, infectious from noninfectious. Using a thiazole orange-terminated polymer, a 99% increase in fluorescence was observed between treated (heat or virucide) and nontreated. The FAIRY assay allowed for the rapid determination of the infectivity of a range of enveloped viruses, highlighting its potential as a valuable tool for the study of viruses and interventions against them.

Rapid Determination of SARS-CoV-2 Integrity and Infectivity by Using Propidium Monoazide Coupled with Digital Droplet PCR

SARS-CoV-2 is a highly infectious virus responsible for the COVID-19 pandemic. Therefore, it is important to assess the risk of SARS-CoV-2 infection, especially in persistently positive patients. Rapid discrimination between infectious and non-infectious viruses aids in determining whether prevention, control, and treatment measures are necessary. For this purpose, a method was developed and utilized involving a pre-treatment with 50 µM of propidium monoazide (PMAxx, a DNA intercalant) combined with a digital droplet PCR (ddPCR). The ddPCR method was performed on 40 nasopharyngeal swabs (NPSs) both before and after treatment with PMAxx, revealing a reduction in the viral load at a mean of 0.9 Log copies/mL (SD ± 0.6 Log copies/mL). Furthermore, six samples were stratified based on the Ct values of SARS-CoV-2 RNA (Ct < 20, 20 < Ct < 30, Ct > 30) and analyzed to compare the results obtained via a ddPCR with viral isolation and a negative-chain PCR. Of the five samples found positive via a ddPCR after the PMAxx treatment, two of the samples showed the highest post-treatment SARS-CoV-2 loads. The virus was isolated in vitro from both samples and the negative strand chains were detected. In three NPS samples, SARS CoV-2 was present post-treatment at a low level; it was not isolated in vitro, and, when detected, the strand was negative. Our results indicate that the established method is useful for determining whether the SARS-CoV-2 within positive NPS samples is intact and capable of causing infection.

PMAxx-RT-qPCR to Determine Human Norovirus Inactivation Following High-Pressure Processing of Oysters

Norovirus is the leading cause of viral gastroenteritis globally. While person-to-person transmission is most commonly reported route of infection, human norovirus is frequently associated with foodborne transmission, including through consumption of contaminated bivalve molluscan shellfish. Reverse transcription (RT)-qPCR is most commonly used method for detecting human norovirus detection in foods, but does not inform on its infectivity, posing challenges for assessing intervention strategies aimed at risk elimination. In this study, RT-qPCR was used in conjunction with a derivative of the photoreactive DNA binding dye propidium monoazide (PMAxx™) (PMAxx-RT-qPCR) to evaluate the viral capsid integrity of norovirus genogroup I and II (GI and GII) in shellfish following high pressure processing (HPP). Norovirus GI.3 and GII.4 bioaccumulated oysters were subjected to HPP at pressures of 300 and 450 MPa at 15 °C, and 300, 450 and 600 MPa at 20 °C. Samples were analysed using both RT-qPCR and PMAxx-RT-qPCR. For each sample, norovirus concentration (genome copies/g digestive tissue) determined by RT-qPCR was divided by the PMAxx-RT-qPCR concentration, giving the relative non-intact (RNI) ratio. The RNI ratio values relate to the amount of non-intact (non-infectious) viruses compared to fully intact (possible infectious) viruses. Our findings revealed an increasing RNI ratio value, indicating decreasing virus integrity, with increasing pressure and decreasing pressure. At 300 MPa, for norovirus GI, the median [95% confidence interval, CI] RNI ratio values were 2.6 [1.9, 3.0] at 15 °C compared to 1.1 [0.9, 1.8] at 20 °C. At 450 MPa, the RNI ratio values were 5.5 [2.9, 7.0] at 15 °C compared to 1.3 [1.0, 1.6] at 20 °C. At 600 MPa, the RNI ratio value was 5.1 [2.9, 13.4] at 20 °C. For norovirus GII, RT-qPCR and PMAxx-RT-qPCR detections were significantly reduced at 450 and 600 MPa at both 15 °C and 20 °C, with the median [95% CI] RNI ratio value at 300 MPa being 1.1 [0.8, 1.6]. Following HPP treatment, the use of PMAxx-RT-qPCR enables the selective detection of intact and potential infectious norovirus, enhancing our understanding of the inactivation profiles and supporting the development of more effective risk assessment strategies.

Impact of Nanoparticle-Based TiO2 Surfaces on Norovirus Capsids and Genome Integrity

Human noroviruses (HuNoVs) are among the main causes of acute gastroenteritis worldwide. HuNoVs can survive for several days up to weeks at room temperature in the environment, on food, and on food handling and processing surfaces. As a result, this could lead to viral spread through the ingestion of food in contact with contaminated surfaces. The development of stable surface materials with antiviral activity might be useful to reduce viral outbreaks. Metal-based compounds, including photoactivated titanium nanoparticles (TiO2 NPs), are known for their antiviral activity. In this study, we tested the impact of 2000 µg/mL TiO2 NPs, with or without UV activation, on HuNoV GII and murine norovirus. Their recovery rates were reduced by 99.6%. We also evaluated a new TiO2 NP-coating process on a polystyrene surface. This process provided a homogenous coated surface with TiO2 NPs ranging between 5 nm and 15 nm. Without photoactivation, this TiO2 NP-coated polystyrene surface reduced the recovery rates of intact HuNoV GII by more than 94%. When a capsid integrity treatment with PtCl4 or a longer reverse transcription polymerase chain detection approach was used to evaluate virus integrity following contact with the TiO2 NP-coated polystyrene, the HuNoV GII recovery yield reduction varied between 97 and 100%. These results support the hypothesis that TiO2 NP-coated surfaces have the potential to prevent viral transmission associated with contaminated food surfaces.

Evaluation of a new automated viral RNA extraction platform for hepatitis A virus and human norovirus in testing of berries, lettuce, and oysters

Fruits, vegetables, and shellfish are often associated with outbreaks of illness caused particularly by human norovirus (HuNoV) and hepatitis A virus (HAV), the leading causative agents of foodborne illness worldwide. The aim of this study was to evaluate a new automated nucleic acid extraction platform (EGENE-UP EASYPREP) for enteric viruses in several at-risk food matrices and to test its limit of detection in comparison to a semi-automated method (EGENE-UP) using Boom methodology for nucleic acid extraction as suggested in the reference method ISO 15216-2:2019. Fresh and frozen raspberries, frozen blackberries, romaine lettuce and oyster digestive glands were artificially contaminated with HAV, HuNoV GII.4 or HuNoV GI.7 at 102, 103 or 104 genome copies/sample. Virus was then recovered from the food matrix using the ISO method. Viral RNA extracted from frozen berry samples by the automated system was purified on a column for additional removal of RT-qPCR inhibitors. For fresh raspberry, oysters, and romaine lettuce, the two extraction platforms were deemed equivalent. For frozen raspberry, the automated platform appeared to be more efficient for viral recovery, particularly for HAV and HuNoV GI at lower concentrations. With frozen blackberries, the two platforms may be considered equivalent for all targeted viruses. However, the automated method led to less sample-associated inhibition of the PCR, 56.5 % of samples versus 95.0 % for the semi-automated. We thus found that the automated extraction can be performed easily by users while obtaining equivalent or even superior results to the ISO 15216-2:2019 method, and therefore appears to be suitable for routine sanitary monitoring in food processing and for tracing outbreaks of illness.

Persistence of Infectious Human Norovirus in Estuarine Water

Norovirus is the predominant cause of viral acute gastroenteritis globally. While person-to-person is the most reported transmission route, norovirus is also associated with waterborne and foodborne illness, including from the consumption of contaminated bivalve molluscan shellfish. The main cause of shellfish contamination is via the bioaccumulation of norovirus from growing waters impacted by human wastewater. However, data on the persistence of infectious norovirus in the environment are limited due to a lack of a human norovirus culture method in the past. In this study, we applied the recently established method of norovirus replication in human intestinal enteroids to determine the persistence of norovirus in artificial estuarine water at 25 ppt for up to 21 days at 4 °C and 16 °C in the dark. Infectious norovirus was detected for up to 21 days. The relative infectivity declined from 100 to 3% at day 21, with decay rate constants of 0.07 day-1 at 4 °C and 0.17 day-1 at 16 °C. There was no decrease in norovirus titres as measured by reverse transcription-droplet digital PCR (RT-ddPCR), confirming the lack of the relationship between norovirus infectivity and direct detection by PCR. The results confirm that norovirus can remain infectious for at least 3 weeks in an estuarine water environment, presenting associated health risks.

Guanidinium-Functionalized Polymer Dielectrics for Triboelectric Bacterial Detection

Development of rapid detection strategies that target potentially pathogenic bacteria has gained increasing attention due to the increasing awareness for better health and safety. In this study, we evaluate an intrinsically antimicrobial polymer, 2Gdm, which is a poly(norbornene)-based functional polymer featuring guanidinium groups as side chains, for bacterial detection by the means of triboelectric nanogenerators (TENGs) and triboelectric nanosensors (TENSs). Attachment of bacteria to the sensing layer is anticipated to alter the overall triboelectric properties of the underlying polymer layer. The positively charged guanidinium functional groups can interact with the negatively charged phospholipid bilayer of bacteria and lead to bacterial death, which can then be detected by optical microscopy, X-ray photoelectron microscopy, and more advanced self-powered sensing techniques such as TENGs and TENSs. The double bonds present along the poly(norbornene) backbone allow for thermally induced cross-linking to obtain X-2Gdm and thus rendering materials remain stable in water. By monitoring the change in voltage output after immersion in various concentrations of Gram-negative Escherichia coli (E. coli) and Gram-positive Streptococcus pneumoniae (S. pneumoniae), we have demonstrated the utility of X-2Gdm as a new polymer dielectric for autonomous bacterial detection. As the bacterial concentration increases, the amount of adsorbed bacteria also increases, resulting in a decrease in the surface potential of the X-2Gdm thin film; this reduction in surface potential can cause a decrease in the triboelectric output for both TENGs and TENSs, which serves as a key working mechanism for facile bacterial detection. TENG and TENS systems are capable of detecting E. coli and S. pneumoniae within a range of 4 × 105 to 4 × 108 CFU/mL with a limit of detection of 106 CFU/mL. This report highlights the promising prospects of employing TENGs and TENSs as innovative sensing technologies for rapid bacterial detection by leveraging the electrostatic interactions between bacterial cell membranes and cationic groups present on polymer surfaces.

Use of Capsid Integrity-qPCR for Detecting Viral Capsid Integrity in Wastewater

Quantifying viruses in wastewater via RT-qPCR provides total genomic data but does not indicate the virus capsid integrity or the potential risk for human infection. Assessing virus capsid integrity in sewage is important for wastewater-based surveillance, since discharged effluent may pose a public health hazard. While integrity assays using cell cultures can provide this information, they require specialised laboratories and expertise. One solution to overcome this limitation is the use of photo-reactive monoazide dyes (e.g., propidium monoazide [PMAxx]) in a capsid integrity-RT-qPCR assay (ci-RT-qPCR). In this study, we tested the efficiency of PMAxx dye at 50 μM and 100 μM concentrations on live and heat-inactivated model viruses commonly detected in wastewater, including adenovirus (AdV), hepatitis A (HAV), influenza A virus (IAV), and norovirus GI (NoV GI). The 100 μM PMAxx dye concentration effectively differentiated live from heat-inactivated viruses for all targets in buffer solution. This method was then applied to wastewater samples (n = 19) for the detection of encapsulated AdV, enterovirus (EV), HAV, IAV, influenza B virus (IBV), NoV GI, NoV GII, and SARS-CoV-2. Samples were negative for AdV, HAV, IAV, and IBV but positive for EV, NoV GI, NoV GII, and SARS-CoV-2. In the PMAxx-treated samples, EV, NoV GI, and NoV GII showed -0.52-1.15, 0.9-1.51, and 0.31-1.69 log reductions in capsid integrity, indicating a high degree of potentially infectious virus in wastewater. In contrast, SARS-CoV-2 was only detected using RT-qPCR but not after PMAxx treatment, indicating the absence of encapsulated and potentially infectious virus. In conclusion, this study demonstrates the utility of PMAxx dyes to evaluate capsid integrity across a diverse range of viruses commonly monitored in wastewater.

Detection of Hepatitis A RNA, Hepatitis E RNA, Human Adenovirus F DNA, and Norovirus RNA in Fresh and Frozen Berry Products at Point of Retail in Ireland

Soft fruits are at particular risk of contamination with enteric viruses such as Hepatitis A virus (HAV), Hepatitis E Virus (HEV), Norovirus (NoV), Human Adenovirus (HAdV) and Sapovirus (SaV). The aim of this study was to investigate, for the first time, the presence of these biological agents in ready to eat (RTE) berries at point of retail in Ireland. A sampling strategy was designed in which RTE fresh and frozen strawberries and raspberries were purchased from five retailers between May and October 2018. Reverse Transcriptase Polymerase Chain Reaction (RT-qPCR) assays for HEV RNA, Nov RNA, SaV RNA, and human Adenovirus species F DNA (HAdV-F) were performed on 239 samples (25g portions). Viral nucleic acid was present in 6.7% (n = 16) of samples tested as follows: HAV RNA (n = 5), HAdV-F DNA (n = 5), HEV RNA (n = 3) and NoV GII RNA (n = 3). Sapovirus RNA was not detected in any product. No significant differences were found between berry type, fresh/frozen status, or supermarket source. This study suggests a risk that exists across all retail outlets however only low levels of nucleic acid ranging from 0 to 16 genome copies/g were present. Although these findings may reflect non-viable/non-infectious virus the continued provision of risk mitigation advice to consumers is warranted and further work is required to ensure control measures to reduce contamination are implemented and enforced.

Effective intravenous delivery of adenovirus armed with TNFα and IL-2 improves anti-PD-1 checkpoint blockade in non-small cell lung cancer

Lung cancer remains among the most difficult-to-treat malignancies and is the leading cause of cancer-related deaths worldwide. The introduction of targeted therapies and checkpoint inhibitors has improved treatment outcomes; however, most patients with advanced-stage non-small cell lung cancer (NSCLC) eventually fail these therapies. Therefore, there is a major unmet clinical need for checkpoint refractory/resistant NSCLC. Here, we tested the combination of aPD-1 and adenovirus armed with TNFα and IL-2 (Ad5-CMV-mTNFα/mIL-2) in an immunocompetent murine NSCLC model. Moreover, although local delivery has been standard for virotherapy, treatment was administered intravenously to facilitate clinical translation and putative routine use. We showed that treatment of tumor-bearing animals with aPD-1 in combination with intravenously injected armed adenovirus significantly decreased cancer growth, even in the presence of neutralizing antibodies. We observed an increased frequency of cytotoxic tumor-infiltrating lymphocytes, including tumor-specific cells. Combination treatment led to a decreased percentage of immunosuppressive tumor-associated macrophages and an improvement in dendritic cell maturation. Moreover, we observed expansion of the tumor-specific memory T cell compartment in secondary lymphoid organs in the group that received aPD-1 with the virus. However, although the non-replicative Ad5-CMV-mTNFα/mIL-2 virus allows high transgene expression in the murine model, it does not fully reflect the clinical outcome in humans. Thus, we complemented our findings using NSCLC ex vivo models fully permissive for the TNFα and IL-2- armed oncolytic adenovirus TILT-123. Overall, our data demonstrate the ability of systemically administered adenovirus armed with TNFα and IL-2 to potentiate the anti-tumor efficacy of aPD-1 and warrant further investigation in clinical trials.

SARS-CoV-2 in the environment: Contamination routes, detection methods, persistence and removal in wastewater treatment plants

The present study reviewed the occurrence of SARS-CoV-2 RNA and the evaluation of virus infectivity in feces and environmental matrices. The detection of SARS-CoV-2 RNA in feces and wastewater samples, reported in several studies, has generated interest and concern regarding the possible fecal-oral route of SARS-CoV-2 transmission. To date, the presence of viable SARS-CoV-2 in feces of COVID-19 infected people is not clearly confirmed although its isolation from feces of six different patients. Further, there is no documented evidence on the infectivity of SARS-CoV-2 in wastewater, sludge and environmental water samples, although the viral genome has been detected in these matrices. Decay data revealed that SARS-CoV-2 RNA persisted longer than infectious particle in all aquatic environment, indicating that genome quantification of SARS-CoV-2 does not imply the presence of infective viral particles. In addition, this review also outlined the fate of SARS-CoV-2 RNA during the different steps in the wastewater treatment plant and focusing on the virus elimination along the sludge treatment line. Studies showed complete removal of SARS-CoV-2 during the tertiary treatment. Moreover, thermophilic sludge treatments present high efficiency in SARS-CoV-2 inactivation. Further studies are required to provide more evidence with respect to the inactivation behavior of infectious SARS-CoV-2 in different environmental matrices and to examine factors affecting SARS-CoV-2 persistence.

Quantification and molecular characterization of intact rotavirus species A (RVA) in municipal solid waste leachate

AIMS

Leachate comprises a solid waste decomposition product found fresh in collection trucks or as an effluent in landfills. This study aimed to assess the occurrence, concentrations, and genetic diversity of intact rotavirus species A (RVA) in solid waste leachate.

METHODS AND RESULTS

Leachate samples were concentrated by ultracentrifugation, treated with propidium monoazide (PMA), and exposed to LED photolysis. Treated and untread samples were extracted using the QIAamp Fast DNA Stool mini kit, and nucleic acids were screened for RVA employing a Taqman® Real-time PCR. The PMA RT-qPCR method detected RVA in eight out of nine truck samples and in 15.40% (2/13) of the landfill leachate samples. The RVA concentrations in the PMA-treated samples ranged from 4.57 × 103 to 2.15 × 107 genomic copies (GC) 100 mL-1 in truck leachate and from 7.83 × 103 to 1.42 × 104 GC 100 mL-1 in landfill samples. Six truck leachate samples were characterized as RVA VP6 genogroup I2 by partial nucleotide sequencing.

CONCLUSIONS

The high intact RVA detection rates and concentrations in truck leachate samples indicate potential infectivity and comprise a warning for solid waste collectors concerning hand-to-mouth contact and the splash route.

Environmental assessment of sewage contamination in the surroundings of a marine outfall combining human mastadenovirus and fecal indicator bacteria

This study assessed the microbiological contamination of the marine area of a metropolitan region, where a marine outfall is used as a sanitary solution for domestic sewage. For human mastadenovirus (HAdV) quantification 134 water samples were concentrated by skimmed milk flocculation method and analyzed with qPCR and PMAxx-qPCR, being the latter to assess the capsid integrity viral. HAdV with intact capsids were detected in 10 % (16/102) of samples classified as suitable for bathing using at least one fecal bacterial indicator. Spatial analysis of the results showed that the drainage channels of the basin that flow into the sea are the main sources of microbiological contamination in the foreshore zone, where intact HAdV reached a concentration of up to 3 log genomic copies/L. HAdV serotypes A12, D, F40 and F41 were characterized. Our results suggest the use of intact HAdV as a complementary parameter to assess the quality of recreational waters.

Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis

Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial and aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to the detection of aged eDNA that has long since been released from the individual and is more likely to be detected at a site further away from its source. In order to address the issue, this manuscript focuses on the state of eDNA, proposing new methodologies to estimate the age of eDNA: (1) DNA damage rate, (2) eDNA particle size distribution, and (3) viable cell-derived eDNA. In addition, the manuscript also focuses on the shorter persistence of environmental RNA (eRNA) compared with eDNA, highlighting the application of eRNA and environmental nucleic acid ratio for assessing the age of the genetic materials in water. Although substantial further research is essential to support the feasibility of these methodologies, incorporating time-scale information into eDNA analysis would update current eDNA analysis, improve the accuracy and reliability of eDNA-based monitoring, and further refine eDNA analysis as a useful monitoring tool in ecology, fisheries and various environmental sciences.

Impact of Capsid and Genomic Integrity Tests on Norovirus Extraction Recovery Rates

Human norovirus (HuNoV) is the leading pathogen responsible for food-borne illnesses. However, both infectious and non-infectious HuNoV can be detected by RT-qPCR. This study evaluated the efficiency of different capsid integrity treatments coupled with RT-qPCR or a long-range viral RNA (long RT-qPCR) detection to reduce the recovery rates of heat inactivated noroviruses and fragmented RNA. The three capsid treatments evaluated (RNase, the intercalating agent PMAxx and PtCl₄) reduced the recovery of heat inactivated HuNoV and murine norovirus (MNV) spiked on lettuce, when combined with the ISO 15216-1:2017 extraction protocols. However, PtCl₄ also reduced non-heat-treated noroviruses recovery as estimated by RT-qPCR. The PMAxx and RNase treatments had a similar effect on MNV only. The most efficient approaches, the RNase and PMAxx treatments, reduced the heat-inactivated HuNoV recovery rates estimated using RT-qPCR by 2 and >3 log, respectively. The long RT-qPCR detection approach also reduced the recovery rates of heat inactivated HuNoV and MNV by 1.0 and 0.5 log, respectively. Since the long-range viral RNA amplification could be applied to verify or confirm RT-qPCR results, it also provides some advantages by reducing the risk of false positive HuNoV results.

Continuous inactivation of human adenoviruses in water by a novel g-C3N4/WO3/biochar memory photocatalyst under light-dark cycles

Viruses transmitted by water have raised considerable concerns for public health. A novel memory photocatalyst of g-C₃N₄/WO₃/biochar was successfully developed for effective inactivation of human adenoviruses (HAdVs) in water, in which WO₃ as an electron-storage reservoir and biochar as an electron shuttle is employed to synergistically improve photocatalytic activity of g-C₃N₄. The tertiary composite exhibited continuous photocatalytic performance for HAdVs inactivation without regrowth in water under light-dark cycles, i.e., ∼3.9-log inactivation under 6-h visible light irradiation and an additional ∼1.1-log inactivation under the following 6-h dark. The enhanced virucidal mechanism was attributed to the heterojunction formation and especially the electron-transfer pathway switching via biochar incorporation, contributing to electron transfer and storage in the light phase and then electron release in the dark phase, along with obviously increased generation of the virus-killing •OH radicals under light-dark cycles.

Advances in virus detection methods for wastewater-based epidemiological applications

Wastewater-based epidemiology (WBE) is a powerful tool that has the potential to reveal the extent of an ongoing disease outbreak or to predict an emerging one. Recent studies have shown that SARS-CoV-2 concentration in wastewater may be correlated with the number of COVID-19 cases in the corresponding population. Most of the recent studies and applications of wastewater-based surveillance of SARS-CoV-2 applied the "gold standard" real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR) detection method. However, this method also has its limitations. The paper aimed to present recent improvements and applications of the PCR-based methods for SARS-CoV-2 monitoring in wastewater. Furthermore, it aimed to review alternative methods utilized and/or proposed for the detection of the virus in wastewater matrices. From the review, it was found that several studies have investigated the use of reverse-transcription digital polymerase reaction (RT-dPCR), which was generally shown to have a lower limit of detection (LOD) over the RT-qPCR. Aside from this, non-PCR-based and non-RNA based methods have also been explored for the detection of SARS-CoV-2 in wastewater, with detailed attention given to the detection of SARS-CoV-2 proteins. The potential methods for protein detection include mass spectrometry, the use of immunosensors, and nanotechnological applications. In addition, the review of recent studies also revealed two types of emerging methods related to the detection of SARS-CoV-2 in wastewater: i) capsid-integrity assays to infer about the infectivity of SARS-CoV-2 present in wastewater, and ii) alternative methods for detection of SARS-CoV-2 variants of concern (VOCs) in wastewater. The recent studies on proposed methods of SARS-CoV-2 detection in wastewater have considered improving this approach in one or more of the following aspects: rapidity, simplicity, cost, sensitivity, and specificity. However, further studies are needed in order to realize the full application of these methods for WBE in the field.

Recent Methods for the Viability Assessment of Bacterial Pathogens: Advances, Challenges, and Future Perspectives

Viability assessment is a critical step in evaluating bacterial pathogens to determine infectious risks to public health. Based on three accepted viable criteria (culturability, metabolic activity, and membrane integrity), current viability assessments are categorized into three main strategies. The first strategy relies on the culturability of bacteria. The major limitation of this strategy is that it cannot detect viable but nonculturable (VBNC) bacteria. As the second strategy, based on the metabolic activity of bacteria, VBNC bacteria can be detected. However, VBNC bacteria sometimes can enter a dormant state that allows them to silence reproduction and metabolism; therefore, they cannot be detected based on culturability and metabolic activity. In order to overcome this drawback, viability assessments based on membrane integrity (third strategy) have been developed. However, these techniques generally require multiple steps, bulky machines, and laboratory technicians to conduct the tests, making them less attractive and popular applications. With significant advances in microfluidic technology, these limitations of current technologies for viability assessment can be improved. This review summarized and discussed the advances, challenges, and future perspectives of current methods for the viability assessment of bacterial pathogens.

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.

Capsid integrity detection of pathogenic viruses in waters: Recent progress and potential future applications

Waterborne diseases caused by pathogenic human viruses are a major public health concern. To control the potential risk of viral infection through contaminated waters, a rapid, reliable tool to assess the infectivity of pathogenic viruses is required. Recently, an advanced approach (i.e., capsid integrity (RT-)qPCR) was developed to discriminate intact viruses (potentially infectious) from inactivated viruses. In this approach, samples were pretreated with capsid integrity reagents (e.g., monoazide dyes or metal compounds) before (RT -)qPCR. These reagents can only penetrate inactivated viruses with compromised capsids to bind to viral genomes and prevent their amplification, but they cannot enter viruses with intact capsids. Therefore, only viral genomes of intact viruses were amplified or detected by (RT-)qPCR after capsid integrity treatment. In this study, we reviewed recent progress in the development and application of capsid integrity (RT-)qPCR to assess the potential infectivity of viruses (including non-enveloped and enveloped viruses with different genome structures [RNA and DNA]) in water. The efficiency of capsid integrity (RT-)qPCR has been shown to depend on various factors, such as conditions of integrity reagent treatment, types of viruses, environmental matrices, and the capsid structure of viruses after disinfection treatments (e.g., UV, heat, and chlorine). For the application of capsid integrity (RT-)qPCR in real-world samples, the use of suitable virus concentration methods and process controls is important to control the efficiency of capsid integrity (RT-)qPCR. In addition, potential future applications of capsid integrity (RT-)qPCR for determining the mechanism of disinfection treatment on viral structure (e.g., capsid or genome) and a combination of capsid integrity treatment and next-generation sequencing (NGS) (capsid integrity NGS) for monitoring the community of intact pathogenic viruses in water are also discussed. This review provides essential information on the application of capsid integrity (RT-)qPCR as an efficient tool for monitoring the presence of pathogenic viruses with intact capsids in water.

Quantification of infectious Human mastadenovirus in environmental matrices using PMAxx-qPCR

Molecular methodologies providing data on viral concentration and infectivity have been successfully used in environmental virology, supporting quantitative risk assessment studies. The present study aimed to assess human mastadenovirus (HAdV) intact particles using a derivative of propidium monoazide associated with qPCR (PMAxx-qPCR) in aquatic matrices. Initially, different concentrations of PMAxx were evaluated to establish an optimal protocol for treating different naturally contaminated matrices, using 10 min incubation in the dark at 200 rpm at room temperature and 15 min of photoactivation in the PMA-Lite™ LED photolysis device. There was no significant reduction in the quantification of infectious HAdV with increasing concentration of PMAxx used (20 μM, 50 μM, and 100 μM), except for sewage samples. In this matrix, a reduction of 5.01 log of genomic copies (GC)/L was observed from the concentration of 50 μM and revealed 100% HAdV particles with damaged capsids. On the other hand, the mean reduction of 0.51 log in stool samples using the same concentration mentioned above demonstrated 83% of damaged particles eliminated in the stool. Following, 50 μM PMAxx-qPCR protocol revealed a log reduction of 0.91, 0.67, and 1.05 in other samples of raw sewage, brackish, and seawater where HAdV concentration reached 1.47 × 10⁴, 6.81 × 10², and 2.33 × 10² GC/L, respectively. Fifty micrometers of PMAxx protocol helped screen intact viruses from different matrices, including sea and brackish water.

Monitoring Human Viral Pathogens Reveals Potential Hazard for Treated Wastewater Discharge or Reuse

Wastewater discharge to the environment or its reuse after sanitization poses a concern for public health given the risk of transmission of human viral diseases. However, estimating the viral infectivity along the wastewater cycle presents technical challenges and still remains underexplored. Recently, human-associated crAssphage has been investigated to serve as viral pathogen indicator to monitor fecal impacted water bodies, even though its assessment as biomarker for infectious enteric viruses has not been explored yet. To this end, the occurrence of potentially infectious norovirus genogroup I (GI), norovirus GII, hepatitis A virus (HAV), rotavirus A (RV), and human astrovirus (HAstV) along with crAssphage was investigated in influent and effluent water sampled in four wastewater treatment plants (WWTPs) over 1 year by a PMAxx-based capsid integrity RT-qPCR assay. Moreover, influent and effluent samples of a selected WWTP were additionally assayed by an in situ capture RT-qPCR assay (ISC-RT-qPCR) as estimate for viral infectivity in alternative to PMAxx-RT-qPCR. Overall, our results showed lower viral occurrence and concentration assessed by ISC-RT-qPCR than PMAxx-RT-qPCR. Occurrence of potentially infectious enteric virus was estimated by PMAxx-RT-qPCR as 88–94% in influent and 46–67% in effluent wastewaters with mean titers ranging from 4.77 to 5.89, and from 3.86 to 4.97 log₁₀ GC/L, with the exception of HAV that was sporadically detected. All samples tested positive for crAssphage at concentration ranging from 7.41 to 9.99 log₁₀ GC/L in influent and from 4.56 to 6.96 log₁₀ GC/L in effluent wastewater, showing higher mean concentration than targeted enteric viruses. Data obtained by PMAxx-RT-qPCR showed that crAssphage strongly correlated with norovirus GII (ρ = 0.67, p < 0.05) and weakly with HAstV and RV (ρ = 0.25–0.30, p < 0.05) in influent samples. In effluent wastewater, weak (ρ = 0.27–0.38, p < 0.05) to moderate (ρ = 0.47–0.48, p < 0.05) correlations between crAssphage and targeted viruses were observed. Overall, these results corroborate crAssphage as an indicator for fecal contamination in wastewater but a poor marker for either viral occurrence and viral integrity/infectivity. Despite the viral load reductions detected in effluent compared to influent wastewaters, the estimates of viral infectivity based on viability molecular methods might pose a concern for (re)-using of treated water.

Discrimination and surveillance of infectious severe acute respiratory syndrome Coronavirus 2 in wastewater using cell culture and RT-qPCR

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA has been extensively detected in raw wastewater in studies exploring wastewater-based epidemiology (WBE) for early warning purposes. Nonetheless, only a few limited studies investigated the presence of SARS-CoV-2 in treated wastewaters to determine the potential health risks across the water cycle. The detection of SARS-CoV-2 has been done mostly by RT-qPCR and ddPCR, which only provides information on the presence of nucleic acids rather than information on potential infectivity. In this study, we set to develop and evaluate the use of viability RT-qPCR for the selective discrimination and surveillance of infectious SARS-CoV-2 in secondary-treated wastewater. Enzymatic (nuclease) and viability dye (Reagent D) pretreatments were applied to infer infectivity through RT-qPCR using porcine epidemic diarrhea virus (PEDV) as a CoV surrogate. Infectivity tests were first performed on PEDV purified RNA, then on infectious and heat-inactivated PEDV, and finally on heat inactivated PEDV spiked in concentrated secondary-treated wastewater. The two viability RT-qPCR methods were then applied to 27 secondary-treated wastewater samples positive for SARS-CoV-2 RNA at the outlet of five large urban wastewater treatment plants in Portugal. Reagent D pretreatment showed similar behavior to cell culture for heat-inactivated PEDV and both viability RT-qPCR methods performed comparably to VERO E6 cell culture for SARS-CoV-2 present in secondary-treated wastewater, eliminating completely the RT-qPCR signal. Our study demonstrated the lack of infectious SARS-CoV-2 viral particles on secondary-treated wastewater through the application of two pretreatment methods for the rapid inference of infectivity through RT-qPCR, showing their potential application in environmental screening. This study addressed a knowledge gap on the public health risks of SARS-CoV-2 across the water cycle.

Detection and identification of potentially infectious gastrointestinal and respiratory viruses at workplaces of wastewater treatment plants with viability qPCR/RT-qPCR

This study aimed to qualitatively and quantitatively assess the prevalence of the most common respiratory and gastrointestinal viruses in the air, surface swab, and influent/effluent samples collected in wastewater treatment plants (WWTPs). Application of qPCR/RT-qPCR (quantitative polymerase chain reaction/reverse-transcription quantitative polymerase chain reaction) assays combined with PMA (propidium monoazide) dye pretreatment allowed detecting the potentially infectious and disintegrated viral particles in collected samples. In the air at workplaces in WWTPs, the most frequent isolation with the highest concentrations (reaching up to 10³ gc/m³ of potentially infectious intact viral particles) were observed in case of adenoviruses (AdVs) and rotaviruses (RoVs), followed by noroviruses (NoVs). Viruses were significantly more often detected in the air samples collected with Coriolis μ impinger, than with MAS-100NT impactor. The temperature negatively (Spearman correlation: –1 < R < 0; p < 0.05), while RH (relative humidity) positively (0 < R < 1; p < 0.05) affected airborne concentrations of potentially infectious viral particles. In turn, the predominant viruses on studied surfaces were RoVs and noroviruses GII (NoV GII) with concentrations of potentially infectious virions up to 10⁴ gc/100 cm². In the cases of SARS-CoV-2 and presumptive SARS-CoV-2 or other coronaviruses, their concentrations reached up to 10³ gc/100 cm². The contamination level of steel surfaces in WWTPs was similar to this on plastic ones. This study revealed that the qualitative and quantitative characteristics of respiratory and gastrointestinal viruses at workplaces in WWTPs is important for proper exposure assessment and needs to be included in risk management in occupational environment with high abundance of microbial pollutants derived from wastewater.

Porous surfaces: stability and recovery of coronaviruses

The role of indirect contact in the transmission of SARS-CoV-2 is not clear. SARS-CoV-2 persists on dry surfaces for hours to days; published studies have largely focused on hard surfaces with less research being conducted on different porous surfaces, such as textiles. Understanding the potential risks of indirect transmission of COVID-19 is useful for settings where there is close contact with textiles, including healthcare, manufacturing and retail environments. This article aims to review current research on porous surfaces in relation to their potential as fomites of coronaviruses compared to non-porous surfaces. Current methodologies for assessing the stability and recovery of coronaviruses from surfaces are also explored. Coronaviruses are often less stable on porous surfaces than non-porous surfaces, for example, SARS-CoV-2 persists for 0.5 h-5 days on paper and 3-21 days on plastic; however, stability is dependent on the type of surface. In particular, the surface properties of textiles differ widely depending on their construction, leading to variation in the stability of coronaviruses, with longer persistence on more hydrophobic materials such as polyester (1-3 days) compared to highly absorbent cotton (2 h-4 days). These findings should be considered where there is close contact with potentially contaminated textiles.

Human adenovirus in municipal solid waste leachate and quantitative risk assessment of gastrointestinal illness to waste collectors

Leachate is a variable effluent from waste management systems generated during waste collection and on landfills. Twenty-two leachate samples from waste collection trucks and a landfill were collected from March to December 2019 in the municipality of Rio de Janeiro (Brazil) and were analyzed for Human Adenovirus (HAdV), bacterial indicators and physico-chemical parameters. For viral analysis, samples were concentrated by ultracentrifugation and processed for molecular analysis using QIAamp Fast DNA Stool mini kit® for DNA extraction followed by nested-PCR and qPCR/PMA-qPCR TaqMan® system. HAdV was detected by nested-PCR in 100% (9/9) and 83.33% (12/13) of the truck and landfill leachate samples, respectively. Viral concentrations ranged from 8.31 × 10¹ to 6.68 × 10⁷ genomic copies per 100 ml by qPCR and PMA-qPCR. HAdV species A, B, C, and F were characterized using nucleotide sequencing. HAdV were isolated in A549 culture cells in 100% (9/9) and 46.2% (6/13) from truck and landfill leachate samples, respectively. Regardless of the detection methods, HAdV concentration was predicted by the quantity of total suspended solids. A quantitative microbial risk assessment was performed to measure the probability of gastrointestinal (GI) illness attributable to inadvertent oral ingestion of truck leachate, revealing the higher probability of disease for the direct splashing into the oral cavity (58%) than for the gloved hand-to-mouth (33%). In a scenario where waste collectors do not wear gloves as protective personal equipment, the risk increases to 67%. This is the first study revealing infectious HAdV in solid waste leachate and indicates a potential health risk for waste collectors.

Discrimination of non-infectious SARS-CoV-2 particles from fomites by viability RT-qPCR

The ongoing coronavirus 2019 (COVID-19) pandemic constitutes a concerning global threat to public health and economy. In the midst of this pandemic scenario, the role of environment-to-human COVID-19 spread is still a matter of debate because mixed results have been reported concerning SARS-CoV-2 stability on high-touch surfaces in real-life scenarios. Up to now, no alternative and accessible procedures for cell culture have been applied to evaluate SARS-CoV-2 infectivity on fomites. Several strategies based on viral capsid integrity have latterly been developed using viability markers to selectively remove false-positive qPCR signals resulting from free nucleic acids and damaged viruses. These have finally allowed an estimation of viral infectivity. The present study aims to provide a rapid molecular-based protocol for detection and quantification of viable SARS-CoV-2 from fomites based on the discrimination of non-infectious SARS-CoV-2 particles by platinum chloride (IV) (PtCl4) viability RT-qPCR. An initial assessment compared two different swabbing procedures to recover inactivated SARS-CoV-2 particles from fomites coupled with two RNA extraction methods. Procedures were validated with human (E229) and porcine (PEDV) coronavirus surrogates, and compared with inactivated SARS-CoV-2 suspensions on glass, steel and plastic surfaces. The viability RT-qPCR efficiently removed the PCR amplification signals from heat and gamma-irradiated inactivated SARS-CoV-2 suspensions that had been collected from specified surfaces. This study proposes a rapid viability RT-qPCR that discriminates non-infectious SARS-CoV-2 particles on surfaces thus helping researchers to better understand the risk of contracting COVID-19 through contact with fomites and to develop more efficient epidemiological measures.

Capsid integrity RT-qPCR for the selective detection of intact SARS-CoV-2 in wastewater

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes have been detected in wastewater worldwide. However, the assessment of SARS-CoV-2 infectivity in wastewater has been limited due to the stringent requirements of biosafety level 3. The main objective of this study is to investigate the applicability of capsid integrity RT-qPCR for the selective detection of intact SARS-CoV-2 in wastewater. Three capsid integrity reagents, namely ethidium monoazide (EMA, 0.1-100 μM), propidium monoazide (PMA, 0.1-100 μM), and cis-dichlorodiammineplatinum (CDDP, 0.1-1000 μM), were tested for their effects on different forms (including free genomes, intact and heat-inactivated) of murine hepatitis virus (MHV), which was used as a surrogate for SARS-CoV-2. CDDP at a concentration of 100 μM was identified as the most efficient reagent for the selective detection of infectious MHV by RT-qPCR (CDDP-RT-qPCR). Next, two common virus concentration methods including ultrafiltration (UF) and polyethylene glycol (PEG) precipitation were investigated for their compatibility with capsid integrity RT-qPCR. The UF method was more suitable than the PEG method since it recovered intact MHV (mean ± SD, 38% ± 29%) in wastewater much better than the PEG method did (0.013% ± 0.015%). Finally, CDDP-RT-qPCR was compared with RT-qPCR alone for the detection of SARS-CoV-2 in 16 raw wastewater samples collected in the Greater Tokyo Area. Five samples were positive for SARS-CoV-2 when evaluated by RT-qPCR alone. However, intact SARS-CoV-2 was detected in only three positive samples when determined by CDDP-RT-qPCR. Although CDDP-RT-qPCR was unable to determine the infectivity of SARS-CoV-2 in wastewater, this method could improve the interpretation of positive results of SARS-CoV-2 obtained by RT-qPCR.

Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples

Isolation, contact tracing and restrictions on social movement are being globally implemented to prevent and control onward spread of SARS-CoV-2, even though the infection risk modelled on RNA detection by RT-qPCR remains biased as viral shedding and infectivity are not discerned. Thus, we aimed to develop a rapid viability RT-qPCR procedure to infer SARS-CoV-2 infectivity in clinical specimens and environmental samples. We screened monoazide dyes and platinum compounds as viability molecular markers on five SARS-CoV-2 RNA targets. A platinum chloride-based viability RT-qPCR was then optimized using genomic RNA, and inactivated SARS-CoV-2 particles inoculated in buffer, stool, and urine. Our results were finally validated in nasopharyngeal swabs from persons who tested positive for COVID-19 and in wastewater samples positive for SARS-CoV-2 RNA. We established a rapid viability RT-qPCR that selectively detects potentially infectious SARS-CoV-2 particles in complex matrices. In particular, the confirmed positivity of nasopharyngeal swabs following the viability procedure suggests their potential infectivity, while the complete prevention of amplification in wastewater indicated either non-infectious particles or free RNA. The viability RT-qPCR approach provides a more accurate ascertainment of the infectious viruses detection and it may complement analyses to foster risk-based investigations for the prevention and control of new or re-occurring outbreaks with a broad application spectrum.

Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples

Isolation, contact tracing and restrictions on social movement are being globally implemented to prevent and control onward spread of SARS-CoV-2, even though the infection risk modelled on RNA detection by RT-qPCR remains biased as viral shedding and infectivity are not discerned. Thus, we aimed to develop a rapid viability RT-qPCR procedure to infer SARS-CoV-2 infectivity in clinical specimens and environmental samples. We screened monoazide dyes and platinum compounds as viability molecular markers on five SARS-CoV-2 RNA targets. A platinum chloride-based viability RT-qPCR was then optimized using genomic RNA, and inactivated SARS-CoV-2 particles inoculated in buffer, stool, and urine. Our results were finally validated in nasopharyngeal swabs from persons who tested positive for COVID-19 and in wastewater samples positive for SARS-CoV-2 RNA. We established a rapid viability RT-qPCR that selectively detects potentially infectious SARS-CoV-2 particles in complex matrices. In particular, the confirmed positivity of nasopharyngeal swabs following the viability procedure suggests their potential infectivity, while the complete prevention of amplification in wastewater indicated either non-infectious particles or free RNA. The viability RT-qPCR approach provides a more accurate ascertainment of the infectious viruses detection and it may complement analyses to foster risk-based investigations for the prevention and control of new or re-occurring outbreaks with a broad application spectrum.

Monitoring the presence and persistence of SARS-CoV-2 in water-food-environmental compartments: State of the knowledge and research needs

The recent spread of severe acute respiratory syndrome coronavirus (SAR-CoV-2) and the accompanied coronavirus disease 2019 (COVID-19) has continued ceaselessly despite the implementations of popular measures, which include social distancing and outdoor face masking as recommended by the World Health Organization. Due to the unstable nature of the virus, leading to the emergence of new variants that are claimed to be more and rapidly transmissible, there is a need for further consideration of the alternative potential pathways of the virus transmissions to provide the needed and effective control measures. This review aims to address this important issue by examining the transmission pathways of SARS-CoV-2 via indirect contacts such as fomites and aerosols, extending to water, food, and other environmental compartments. This is essentially required to shed more light regarding the speculation of the virus spread through these media as the available information regarding this is fragmented in the literature. The existing state of the information on the presence and persistence of SARS-CoV-2 in water-food-environmental compartments is essential for cause-and-effect relationships of human interactions and environmental samples to safeguard the possible transmission and associated risks through these media. Furthermore, the integration of effective remedial measures previously used to tackle the viral outbreaks and pandemics, and the development of new sustainable measures targeting at monitoring and curbing the spread of SARS-CoV-2 were emphasized. This study concluded that alternative transmission pathways via human interactions with environmental samples should not be ignored due to the evolving of more infectious and transmissible SARS-CoV-2 variants.

Coronavirus in water media: Analysis, fate, disinfection and epidemiological applications

Considerable attention has been recently given to possible transmission of SARS-CoV-2 via water media. This review addresses this issue and examines the fate of coronaviruses (CoVs) in water systems, with particular attention to the recently available information on the novel SARS-CoV-2. The methods for the determination of viable virus particles and quantification of CoVs and, in particular, of SARS-CoV-2 in water and wastewater are discussed with particular regard to the methods of concentration and to the emerging methods of detection. The analysis of the environmental stability of CoVs, with particular regard of SARS-CoV-2, and the efficacy of the disinfection methods are extensively reviewed as well. This information provides a broad view of the state-of-the-art for researchers involved in the investigation of CoVs in aquatic systems, and poses the basis for further analyses and discussions on the risk associated to the presence of SARS-CoV-2 in water media. The examined data indicates that detection of the virus in wastewater and natural water bodies provides a potentially powerful tool for quantitative microbiological risk assessment (QMRA) and for wastewater-based epidemiology (WBE) for the evaluation of the level of circulation of the virus in a population. Assays of the viable virions in water media provide information on the integrity, capability of replication (in suitable host species) and on the potential infectivity. Challenges and critical issues relevant to the detection of coronaviruses in different water matrixes with both direct and surrogate methods as well as in the implementation of epidemiological tools are presented and critically discussed.

Microbiological survey and occurrence of bacterial foodborne pathogens in raw and ready-to-eat green leafy vegetables marketed in Tehran, Iran

Fresh leafy (FL) and ready-to-eat (RTE) vegetables are recognized as an important source of foodborne disease outbreaks worldwide. Currently, there are no data available for the prevalnce of bacterial foodborne pathogens (FBPs) in raw vegetables consumed in Iran. Here, we evalated the presence of common bacterial FBPs among 366 samples of raw vegetables including 274 FL and 92 RTE collected from 21 districts of Tehran. The presence of FBPs were screened using conventional microbiological culture methods and real-time PCR assays. Overall, a higher rate of bacterial contamination was detected in FL compared to RTE samples using both detection methods. The results obtained by microbiological methods showed that Staphylococcus aureus (134/366, 36.6%), followed by Escherichia coli (85/366, 23.2%) and Clostridium perfringens (66/366, 18%) were detetcted as the most prevalent pathogens in this study. Vibrio cholerae was not detected in any of the samples either by microbiological methods or by the real-time PCR assays. There was a noticeable reduction in the proportion of Campylobacter positive samples using conventional microbiological methods (3.5%) compared to the real-time PCR assay (20.7%). The proportion of FL and RTE positive samples obtained by conventional microbiological methods was significantly different (P < 0.05) for C. perfringens, Campylobacter spp. and S. aureus. The proportion of positive samples in FL and RTE vegetables obtained by the real-time PCR assays was significantly different (P < 0.05) for C. perfringens, S. aureus, Helicobacter pylori and STEC/EHEC, the last one was found more frequently in RTE than in FL samples. Our findings indicated a contamination of FL and RTE vegetables in Iran with a range of well-known and emerging FBPs. Positivity and the distribution of bacterial species from the current data indicated different contamination sources, and overall a lack of effective decontamination steps during the production chain. Moreover, further information about the quality of the water, the hygiene measures implemented during the processing, storage and marketing are required to better identify the critical points and define the proper measures.

Bacteriophages as Fecal Pollution Indicators

Bacteriophages are promising tools for the detection of fecal pollution in different environments, and particularly for viral pathogen risk assessment. Having similar morphological and biological characteristics, bacteriophages mimic the fate and transport of enteric viruses. Enteric bacteriophages, especially phages infecting Escherichia coli (coliphages), have been proposed as alternatives or complements to fecal indicator bacteria. Here, we provide a general overview of the potential use of enteric bacteriophages as fecal and viral indicators in different environments, as well as the available methods for their detection and enumeration, and the regulations for their application.

T4-like Phages Reveal the Potential Role of Viruses in Soil Organic Matter Mineralization

Viruses are the most abundant biological entities in the world, but their ecological functions in soil are virtually unknown. We hypothesized that greater abundance of T4-like phages will increase bacterial death and thereby suppress soil organic carbon (SOC) mineralization. A range of phage and bacterial abundances were established in sterilized soil by reinoculation with 10^-3 and 10^-6 dilutions of suspensions of unsterilized soil. The total and viable 16S rRNA gene abundance (a universal marker for bacteria) was measured by qPCR to determine bacterial abundance, with propidium monoazide (PMA) preapplication to eliminate DNA from non-viable cells. Abundance of the g23 marker gene was used to quantify T4-like phages. A close negative correlation between g23 abundance and viable 16S rRNA gene abundance was observed. High abundance of g23 led to lower viable ratios for bacteria, which suggested that phages drove microbial necromass production. The CO₂ efflux from soil increased with bacterial abundance but decreased with higher abundance of T4-like phages. Elimination of extracellular DNA by PMA strengthened the relationship between CO₂ efflux and bacterial abundance, suggesting that SOC mineralization by bacteria is strongly reduced by the T4-like phages. A random forest model revealed that abundance of T4-like phages and the abundance ratio of T4-like phages to bacteria are better predictors of SOC mineralization (measured as CO₂ efflux) than bacterial abundance. Our study provides experimental evidence of phages' role in organic matter turnover in soil: they can retard SOC decomposition but accelerate bacterial turnover.

Human Fecal Pollution Monitoring and Microbial Risk Assessment for Water Reuse Potential in a Coastal Industrial-Residential Mixed-Use Watershed

Rapid economic development has caused industrial expansion into residential communities, leading to higher fecal pollution loads that could be discharged into aquatic environments. However, little is known regarding the potential microbial impact on human health. This study investigated microbial contamination from coastal industrial–residential community areas in nine sampling sites in waterways during three dry events. A general microbial source tracking (MST) marker, GenBac3, was detected in all samples from all three events, indicating continuing fecal pollution in the area, mostly from human sewage contamination. This was shown by the human-specific genetic marker crAssphage (88.9%) and human polyomavirus (HPyVs; 92.6%) detection. Enteric human adenovirus (HAdV40/41) showed three positive results only from residential sites in the first event. No spatial difference was observed for MST markers and traditional fecal indicators (total coliforms and Escherichia coli) in each event. Still, a significantly lower abundance of GenBac3, HPyVs, and total coliforms in the first sampling event was detected. Spearman’s rho analysis indicated a strong correlation among certain pairs of microbial parameters. Multivariate analysis revealed two clusters of samples separated by land use type (industrial vs. residential). According to factor analysis of mixed data, the land use parameter was more associated with physicochemical parameters (i.e., salinity, conductivity, water temperature, and dissolved oxygen). A Quantitative Microbial Risk Assessment (QMRA) was then conducted to estimate the annual infection risks of HAdV40/41 for non-potable water reuse purposes using predicted concentrations from crAssphage and HPyVs. The highest risks (95th percentiles) were ranked by food crop irrigation, aquaculture, and toilet flushing, at 10^–1, 10^–2, and 10^–3 per person per year (pppy). Required treatment levels to achieve a 10^–4 pppy annual infection risk were estimated. QMRA-based water treatment scenarios were suggested, including chlorination for toilet flushing reuse and depth filtration prior to chlorination for aquaculture and food crop irrigation. Microbial monitoring combined with a QMRA could provide better insights into fecal pollution patterns and the associated risks, facilitating effective water quality management and appropriate prior treatments for water reuse.