Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19

SARS-CoV-2 RNA surveillance in large to small centralized wastewater treatment plants preceding the third COVID-19 resurgence in Bangkok, Thailand

Wastewater surveillance for SARS-CoV-2 RNA has been a successful indicator of COVID-19 outbreaks in populations prior to clinical testing. However, this has been mostly conducted in high-income countries, which means there is a dearth of performance investigations in low- and middle-income countries with different socio-economic settings. This study evaluated the applicability of SARS-CoV-2 RNA monitoring in wastewater (n = 132) to inform COVID-19 infection in the city of Bangkok, Thailand using CDC N1 and N2 RT-qPCR assays. Wastewater influents (n = 112) and effluents (n = 20) were collected from 19 centralized wastewater treatment plants (WWTPs) comprising four large, four medium, and 11 small WWTPs during seven sampling events from January to April 2021 prior to the third COVID-19 resurgence that was officially declared in April 2021. The CDC N1 assay showed higher detection rates and mostly lower Ct values than the CDC N2. SARS-CoV-2 RNA was first detected at the first event when new reported cases were low. Increased positive detection rates preceded an increase in the number of newly reported cases and increased over time with the reported infection incidence. Wastewater surveillance (both positive rates and viral loads) showed strongest correlation with daily new COVID-19 cases at 22-24 days lag (Spearman's Rho = 0.85-1.00). Large WWTPs (serving 432,000-580,000 of the population) exhibited similar trends of viral loads and new cases to those from all 19 WWTPs, emphasizing that routine monitoring of the four large WWTPs could provide sufficient information for the city-scale dynamics. Higher sampling frequency at fewer sites, i.e., at the four representative WWTPs, is therefore suggested especially during the subsiding period of the outbreak to indicate the prevalence of COVID-19 infection, acting as an early warning of COVID-19 resurgence.

Understanding and managing uncertainty and variability for wastewater monitoring beyond the pandemic: Lessons learned from the United Kingdom national COVID-19 surveillance programmes

The COVID-19 pandemic has put unprecedented pressure on public health resources around the world. From adversity, opportunities have arisen to measure the state and dynamics of human disease at a scale not seen before. In the United Kingdom, the evidence that wastewater could be used to monitor the SARS-CoV-2 virus prompted the development of National wastewater surveillance programmes. The scale and pace of this work has proven to be unique in monitoring of virus dynamics at a national level, demonstrating the importance of wastewater-based epidemiology (WBE) for public health protection. Beyond COVID-19, it can provide additional value for monitoring and informing on a range of biological and chemical markers of human health. A discussion of measurement uncertainty associated with surveillance of wastewater, focusing on lessons-learned from the UK programmes monitoring COVID-19 is presented, showing that sources of uncertainty impacting measurement quality and interpretation of data for public health decision-making, are varied and complex. While some factors remain poorly understood, we present approaches taken by the UK programmes to manage and mitigate the more tractable sources of uncertainty. This work provides a platform to integrate uncertainty management into WBE activities as part of global One Health initiatives beyond the pandemic.

Review of air disinfection approaches and proposal for thermal inactivation of airborne viruses as a life-style and an instrument to fight pandemics

COVID-19 (Coronavirus Disease 2019) pandemic highlighted the importance of air biosecurity because SARS-CoV-2 is mainly transmitted from person to person via airborne droplets. Preventing infectious droplets from entering the body is one of the best ways to protect against infection. This paper reviews the transmission patterns of airborne pathogens and air disinfection methods. A particular emphasis is put on studies devoted to the thermal inactivation of viruses. These reviews reveal that air heat treatment has not been seriously considered as a possible air disinfection approach. Simple calculations show that the energy input required for thermal disinfection of human's air daily consumption is almost the same as for daily water consumption (by heat treatment from room temperature to 100 °C). Moreover, it is possible to organize a continuous heat recovery from the air already heated during disinfection to the inlet air, thus significantly increasing the energy efficiency. Therefore, I propose a solution for the thermal inactivation of airborne pathogens based on air heating and its subsequent cooling in a heat exchanger with heat recovery. Such a solution could be used to create mobile personal and stationary indoor air disinfectors, as well as heating, ventilation, and air conditioning systems. Thermal disinfection of air to breathe might one day be part of people's daily life like thermal disinfection of drinking water. Aside from limiting infectious disease transmission, thermal inactivation might be the basis for developing inhaled vaccines using thermally inactivated whole pathogens.

Wastewater surveillance of SARS-CoV-2 in Austria: development, implementation, and operation of the Tyrolean wastewater monitoring program

Wastewater-based epidemiology (WBE) is an effective approach for tracking information on spatial distribution and temporal trends of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the community level. Herein, the development, implementation, and operation of the wastewater monitoring program serving Tyrol - a federal province of Austria - are described. The development of this program was initiated by Tyrolean health authorities at the end of the first phase of the Coronavirus disease 2019 (COVID-19) pandemic (May 2020). In close co-operation with the water sector and academic institutions, efficient and effective workflows and processes for wastewater surveillance were established. The monitoring program went into operation in November 2020. By the end of July 2021, a total of 5,270 wastewater influent samples collected at 43 sites were analyzed. The monitoring program provided valuable insights into the development of the pandemic situation in Tyrol and fulfilled several tasks that are of importance in different phases of the pandemic. It represented an early-warning system, provided independent confirmation of temporal trends in COVID-19 prevalence, enabled the assessment of the effectiveness of measures, alerted about bursts of disease activity, and provided evidence for the absence of COVID-19. These findings underline the importance of establishing national wastewater monitoring programs as a complementary source of information for efficient and effective pandemic management.

COVID-19 case prediction via wastewater surveillance in a low-prevalence urban community: a modeling approach

Estimating and predicting the epidemic size from wastewater surveillance results remains challenging for the practical implementation of wastewater-based epidemiology (WBE). In this study, by employing a highly sensitive detection method, we documented the time series of SARS-CoV-2 RNA occurrence in the wastewater influent from an urban community with a 360,000 population in Japan, from August 2020 to February 2021. The detection frequency of the viral RNA increased during the outbreak events of COVID-19 and the highest viral RNA concentration was recorded at the beginning of January 2021, amid the most serious outbreak event during the study period. We found that: (1) direct back-calculation still suffers from great uncertainty dominated by inconsistent detection and the varying gap between the observed wastewater viral load and the estimated patient viral load, and (2) the detection frequency correlated well with reported cases and the prediction of the latter can be carried out via data-driven modeling methods. Our results indicate that wastewater virus occurrence can contribute to epidemic surveillance in ways more than back-calculation, which may spawn future wastewater surveillance implementations.

Longitudinal, virological, and serological assessment of hospitalized COVID-19 patients

Here we described the virological and serological assessment of 23 COVID-19 patients hospitalized and followed up in Milan, Italy, during the first wave of COVID-19 pandemic. Nasopharyngeal (NPS), anal swabs, and blood samples were collected from 23 COVID-19 patients, at hospital admission, and periodically up to discharge, for a median time of 20 days (3-83 days). RNA was isolated and tested for SARS-CoV-2 by qRT-PCR; anti-SARS-CoV-2 IgM and IgG antibody titers were evaluated in serum samples by ELISA. SARS-CoV-2 genome was detected in the NPS swabs of the 23 patients, at the admission, and 8/19 (42.1%) were still positive at the discharge. Anal swabs were positive to SARS-CoV-2 RNA detection in 20/23 (86.9%) patients; 6/19 (31.6%) were still positive at discharge. The mean time of RNA negative conversion was 17 days (4-36 days) and 33 days (4-77 days), for NPS and anal swabs, respectively. SARS-CoV-2-RNA was detected in the blood of 6/23 (26.1%) patients. Thirteen/23 (56.5%) and 17/23 (73.9%) patients were seropositive for IgM and IgG, respectively, at the admission, and the median IgM and IgG levels significantly (p < 0.05) increased after 13 days. Although the limited cohort size, our report provides evidence that SARS-CoV-2 is shed through multiple routes, with important implications in healthcare settings.

Bowel ischemia as onset of COVID-19 in otherwise asymptomatic patients with persistently negative swab

BACKGROUND

Asymptomatic patients with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can develop hypercoagulable conditions and acute vascular events. The objective of this study is to determine whether SARS-CoV-2 was present in resected specimens from patients with acute bowel ischemia, but asymptomatic for Coronavirus Disease 2019 (COVID-19) and with persistently real-time polymerase chain reaction negative pharyngeal swab.

METHODS

Three consecutive patients presented severe abdominal symptoms due to extensive ischemia and necrosis of the bowel, with co-existent thrombosis of abdominal blood vessels. None had the usual manifestations of COVID-19, and repeated pharyngeal swabs tested negative. They underwent emergency surgery with intestinal resection. Immunohistochemical testing for SARS-CoV-2 on resected tissue was performed.

RESULTS

All tested samples were strongly positive for SARS-CoV-2.

CONCLUSIONS

This is the first case report in which patients with severe intestinal symptoms presented a marked SARS-CoV-2 positivity in the resected tissues, without any usual clinical manifestations of COVID-19. These results suggest that the patients might be infected with SARS-CoV-2 presenting acute abdominal distress but without respiratory or constitutional symptoms.

Effects of face masks and ventilation on the risk of SARS-CoV-2 respiratory transmission in public toilets: a quantitative microbial risk assessment

Public toilets may increase the risk of COVID-19 infection via airborne transmission; however, related research is limited. We aimed to estimate SARS-CoV-2 infection risk through respiratory transmission using a quantitative microbial risk assessment framework by retrieving SARS-CoV-2 concentrations from the swab tests of 251 Thai patients. Three virus-generating scenarios were investigated: an infector breathing, breathing with a cough, and breathing with a sneeze. The infection risk (95th percentile) was as high as 10^-1 with breathing and increased to 1 with a cough or a sneeze. No significant gender differences for toilet users (receptors) were noted. The highest risk scenario, namely breathing with a sneeze, was further evaluated for risk mitigation measures. Mitigation to a lower risk under 10^-3 succeeded only when the infector and the receptor both wore N95 respirators or surgical masks. Ventilation of up to 20 air changes per hour (ACH) did not decrease the risk. However, an extended waiting time of 10 min between an infector and a receptor resulted in approximately 1.0-log₁₀ further risk reduction when both wore masks with the WHO-recommended 12 ACH. The volume of expelled droplets, virus concentrations, and receptor dwell time were identified as the main contributors to transmission risk.

SARS-CoV-2 loads in urine, sera and stool specimens in association with clinical features of COVID-19 patients

Background

Study design

Results

Conclusion

Transmission risk of SARS-CoV-2 in the watershed triggered by domestic wastewater discharge

The outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has already become an unprecedented global pandemic. However, the transmission of SARS-CoV-2, especially the protected SARS-CoV-2 RNA (pRNA) with infectious particles in waterways, is still largely unexplored. In this study, we developed a model to estimate SARS-CoV-2 transmission from the risk source in the excretion of patients to the final exposure in surface water. The model simulated the spatial and temporal distribution of the viral pRNA concentrations in the surface water of the Elbe watershed from March 2020 to January 2021. The results show that the WWTPs with the maximum capacity of >10,000 population equivalents were responsible for 95% of the viral load discharged into the surface water. We estimated the pRNA concentrations in surface water to be 1.33 × 10-2 copies·L-1 on average in the watershed based on the model simulation on viral transmission. It had considerable variations in spatial and temporal scales, which are dominantly controlled by epidemic situations and virus transport with decay in water, respectively. A quantitative microbial risk assessment was conducted to estimate the viral infection probability from surface water ingestion with consideration of the influence of toilet usage frequency and gender/age population groups. All the infection probabilities in the study period were lower than the reference risk levels of 10-4 and 10-5. The individuals aged 15-34 years had the highest infection probability of 4.86 × 10-9 on average from surface water ingestion during swimming activities. The data provided herein suggest that the low pRNA concentrations and infection probability reflected that the waterways were unlikely to be a significant transmission route for SARS-CoV-2.

Efficacy of Niclosamide vs Placebo in SARS-CoV-2 Respiratory Viral Clearance, Viral Shedding, and Duration of Symptoms Among Patients With Mild to Moderate COVID-19: A Phase 2 Randomized Clinical Trial

IMPORTANCE

Oral anthelmintic niclosamide has potent in vitro antiviral activity against SARS-CoV-2. Repurposed niclosamide could be a safe and efficacious COVID-19 therapy.

OBJECTIVE

To investigate whether niclosamide decreased SARS-CoV-2 shedding and duration of symptoms among patients with mild to moderate COVID-19.

DESIGN, SETTING, AND PARTICIPANTS

This randomized, placebo-controlled clinical trial enrolled individuals testing positive for SARS-CoV-2 by polymerase chain reaction with mild to moderate symptoms of COVID. All trial participants, investigators, staff, and laboratory personnel were kept blind to participant assignments. Enrollment was among individuals reporting at Tufts Medical Center and Wellforce Network in Massachusetts for outpatient COVID-19 testing. The trial opened to accrual on October 1, 2020; the last participant enrolled on April 20, 2021. Trial exclusion criteria included hospitalization at time of enrollment or use of any experimental treatment for COVID-19, including vaccination. Enrollment was stopped before attaining the planned sample size when COVID-19 diagnoses decreased precipitously in Massachusetts. Data were analyzed from July through September 2021.

INTERVENTIONS

In addition to receiving current standard of care, participants were randomly assigned on a 1:1 basis to receive niclosamide 2 g by mouth daily for 7 days or identically labeled placebo at the same dosing schedule.

MAIN OUTCOMES AND MEASURES

Oropharyngeal and fecal samples were self-collected for viral shedding measured by reverse-transcriptase-polymerase-chain-reaction on days 3, 7, 10, and 14, and an additional fecal sample was collected on day 21. A telehealth platform was developed to conduct remote study visits, monitor symptoms, and coordinate sample collection via couriers. The primary end point was the proportion of participants with viral clearance in respiratory samples at day 3 based on the intention-to-treat sample. Mean times to viral clearance and symptom resolution were calculated as restricted mean survival times and accounted for censored observations.

RESULTS

Among 73 participants, 36 individuals were enrolled and randomized to niclosamide and 37 individuals to placebo. Participant characteristics were similar across treatment groups; among 34 patients receiving placebo and 33 patients receiving niclosamide in the intention-to-treat sample, mean (SD) age was 36.0 (13.3) years vs 36.8 (12.9) years and there were 21 (61.8%) men vs 20 (60.6%) men. The overall mean (SD) age was 36.4 (13.0) years. For the primary end point, 66.67% (95% CI, 50.74% to 81.81%) of participants receiving niclosamide and 55.88% (95% CI, 40.27% to 72.73%) of participants receiving placebo had oropharyngeal SARS-CoV-2 clearance at day 3 (P = .37). Among 63 participants with symptoms, niclosamide did not significantly shorten symptom duration, which was 12.01 (95% CI, 8.82 to 15.2) days in the niclosamide group vs 14.61 (95% CI, 11.25 to 17.96) days in the placebo group (mean difference, -2.6 [95% CI, -7.23 to 2.03] days). Niclosamide was well-tolerated; the most commonly reported adverse events in the placebo and niclosamide groups were headaches (11 patients [32.4%] vs 7 patients [21.2%]; P = .31) and cough (8 patients [23.5%] vs 7 patients [21.2%]; P = .82).

CONCLUSIONS AND RELEVANCE

In this randomized clinical trial, there was no significant difference in oropharyngeal clearance of SARS-CoV-2 at day 3 between placebo and niclosamide groups. Confirmation in larger studies is warranted.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT04399356.

Simulation Studies Provide Evidence of Aerosol Transmission of SARS-CoV-2 in a Multi-Story Building via Air Supply, Exhaust and Sanitary Pipelines

A cross-layer non-vertical transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurred in a quarantine hotel in Guangzhou, Guangdong Province, China in June 2021. To explore the cross-layer transmission path and influencing factors of viral aerosol, we set up different scenarios to carry out simulation experiments. The results showed that the air in the polluted room can enter the corridor by opening the door to take food and move out the garbage, then mix with the fresh air taken from the outside as part of the air supply of the central air conditioning system and re-enter into different rooms on the same floor leading to the same-layer transmission. In addition, flushing the toilet after defecation and urination will produce viral aerosol that pollutes rooms on different floors through the exhaust system and the vertical drainage pipe in the bathroom, resulting in cross-layer vertical transmission, also aggravating the transmission in different rooms on the same floor after mixing with the air of the room and entering the corridor to become part of the air supply, and meanwhile, continuing to increase the cross-layer transmission through the vertical drainage pipe. Therefore, the air conditioning and ventilation system of the quarantine hotel should be operated in full fresh air mode and close the return air; the exhaust volume of the bathroom should be greater than the fresh air volume. The exhaust pipe of the bathroom should be independently set and cannot be interconnected or connected in series. The riser of the sewage and drainage pipeline of the bathroom should maintain vertical to exhaust independently and cannot be arbitrarily changed to horizontal pipe assembly.

Validation of Two Commercial Multiplex Real-Time PCR Assays for Detection of SARS-CoV-2 in Stool Donors for Fecal Microbiota Transplantation

Recurrent infection by Clostridioides difficile has recently been treated by fecal microbiota transplantation (FMT). As viable SARS-CoV-2 was recovered from stool of asymptomatic individuals, the FMT procedure could be a potential risk of SARS-CoV-2 transmission, thus underlying the need to reliably detect SARS-CoV-2 in stool. Here, we performed a multicentric study to explore performances of two commercially available assays for detection of SARS-CoV-2 RNA in stool of potential FMT donors. In three hospitals, 180 stool samples were spiked with serial 10-fold dilutions of a SARS-CoV-2 inactivated lysate to evaluate the Seegene Allplex™ SARS-CoV-2 (SC2) and SARS-CoV-2/FluA/FluB/RSV (SC2FABR) Assays for the detection of viral RNA in stool of FMT donors. The results revealed that both assays detected down to 2 TCID50/mL with comparable limit of detection values, SC2 showing more consistent target positivity rate than SC2FABR. Beyond high amplification efficiency, correlation between CT values and log concentrations of inactivated viral lysates showed R2 values ranging from 0.88 to 0.90 and from 0.87 to 0.91 for the SC2 and SC2FABR assay, respectively. The present results demonstrate that both methods are highly reproducible, sensitive, and accurate for SARS-CoV-2 RNA detection in stool, suggesting a potential use in FMT-donor screening.

SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases

Current estimates of COVID-19 prevalence are largely based on symptomatic, clinically diagnosed cases. The existence of a large number of undiagnosed infections hampers population-wide investigation of viral circulation. Here, we quantify the SARS-CoV-2 concentration and track its dynamics in wastewater at a major urban wastewater treatment facility in Massachusetts, between early January and May 2020. SARS-CoV-2 was first detected in wastewater on March 3. SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 4-10 days earlier in wastewater than in clinical data. We inferred viral shedding dynamics by modeling wastewater viral load as a convolution of back-dated new clinical cases with the average population-level viral shedding function. The inferred viral shedding function showed an early peak, likely before symptom onset and clinical diagnosis, consistent with emerging clinical and experimental evidence. This finding suggests that SARS-CoV-2 concentrations in wastewater may be primarily driven by viral shedding early in infection. This work shows that longitudinal wastewater analysis can be used to identify trends in disease transmission in advance of clinical case reporting, and infer early viral shedding dynamics for newly infected individuals, which are difficult to capture in clinical investigations.

Wastewater surveillance to infer COVID-19 transmission: A systematic review

Successful detection of SARS-COV-2 in wastewater suggests the potential utility of wastewater-based epidemiology (WBE) for COVID-19 community surveillance. This systematic review aims to assess the performance of wastewater surveillance as early warning system of COVID-19 community transmission. A systematic search was conducted in PubMed, Medline, Embase and the WBE Consortium Registry according to PRISMA guidelines for relevant articles published until 31st July 2021. Relevant data were extracted and summarized. Quality of each paper was assessed using an assessment tool adapted from Bilotta et al.'s tool for environmental science. Of 763 studies identified, 92 studies distributed across 34 countries were shortlisted for qualitative synthesis. A total of 26,197 samples were collected between January 2020 and May 2021 from various locations serving population ranging from 321 to 11,400,000 inhabitants. Overall sample positivity was moderate at 29.2% in all examined settings with the spike (S) gene having maximum rate of positive detections and nucleocapsid (N) gene being the most targeted. Wastewater signals preceded confirmed cases by up to 63 days, with 13 studies reporting sample positivity before the first cases were detected in the community. At least 50 studies reported an association of viral load with community cases. While wastewater surveillance cannot replace large-scale diagnostic testing, it can complement clinical surveillance by providing early signs of potential transmission for more active public health responses. However, more studies using standardized and validated methods are required along with risk analysis and modelling to understand the dynamics of viral outbreaks.

Detection of SARS-CoV-2 RNA in Bivalve Mollusks by Droplet Digital RT-PCR (dd RT-PCR)

Bivalve shellfish are readily contaminated by human pathogens present in waters impacted by municipal sewage, and the detection of SARS-CoV-2 in feces of infected patients and in wastewater has drawn attention to the possible presence of the virus in bivalves. The aim of this study was to collect data on SARS-CoV-2 prevalence in bivalve mollusks from harvesting areas of Campania region. A total of 179 samples were collected between September 2019 and April 2021 and were tested using droplet digital RT-PCR (dd RT-PCR) and real-time RT-PCR. Combining results obtained with different assays, SARS-CoV-2 presence was detected in 27/179 (15.1%) of samples. A median viral concentration of 1.1 × 102 and 1.4 × 102 g.c./g was obtained using either Orf1b nsp14 or RdRp/gene E, respectively. Positive results were unevenly distributed among harvesting areas and over time, positive samples being more frequent after January 2021. Partial sequencing of the spike region was achieved for five samples, one of which displaying mutations characteristic of the Alpha variant (lineage B.1.1.7). This study confirms that bivalve mollusks may bioaccumulate SARS-CoV-2 to detectable levels and that they may represent a valuable approach to track SARS-CoV-2 in water bodies and to monitor outbreak trends and viral diversity.

Consensus Statement on Urinary Stone Treatment During A Pandemic: A Delphi Process from the Endourological Society TOWER Research Initiative

INTRODUCTION

The COVID-19 pandemic has had a significant impact on the care of patients with urolithiasis. Recommendations and prioritization of endourologic surgical procedures vary among regions and a comprehensive overall international directive is needed. We used the Delphi method to obtain international consensus on managing urolithiasis patients during the pandemic.

METHODS

A three-round Delphi process was used to elicit expert consensus (53 global key opinion leaders within the Endourological Society from 36 countries) on an extensive survey on management of endourologic patients in a pandemic. Questions addressed general management, inpatient and outpatient procedures, clinic visits, follow-up care and best practices for suspension and resumption of routine care.

RESULTS

Consensus was achieved in 64/84 (76%) questions. Key consensus findings included: consultations should be delivered remotely when possible. Invasive surgical procedures for urolithiasis patients should be reserved for high-risk situations (infection, renal failure, etc.). To prevent aerosolization, spinal anesthesia is preferred over general, whenever feasible. Treatment of asymptomatic renal stones should be deferred. Primary definitive treatment of obstructing or symptomatic stones (both renal and ureteral) is preferred over temporizing drainage. Extracorporeal shock wave lithotripsy should be continued for obstructive ureteral stones. There was consensus on treatment modalities and drainage strategies depending on location and size of the stone.

CONCLUSION

International endourologist members of the Endourological Society participated in this Delphi initiative to provide expert consensus on management of urolithiasis during a pandemic. These results can be applied currently and during a future pandemic.

Role of Probiotics in the Management of COVID-19: A Computational Perspective

Coronavirus disease 2019 (COVID-19) was declared a pandemic at the beginning of 2020, causing millions of deaths worldwide. Millions of vaccine doses have been administered worldwide; however, outbreaks continue. Probiotics are known to restore a stable gut microbiota by regulating innate and adaptive immunity within the gut, demonstrating the possibility that they may be used to combat COVID-19 because of several pieces of evidence suggesting that COVID-19 has an adverse impact on gut microbiota dysbiosis. Thus, probiotics and their metabolites with known antiviral properties may be used as an adjunctive treatment to combat COVID-19. Several clinical trials have revealed the efficacy of probiotics and their metabolites in treating patients with SARS-CoV-2. However, its molecular mechanism has not been unraveled. The availability of abundant data resources and computational methods has significantly changed research finding molecular insights between probiotics and COVID-19. This review highlights computational approaches involving microbiome-based approaches and ensemble-driven docking approaches, as well as a case study proving the effects of probiotic metabolites on SARS-CoV-2.

Monitoring the Viral Transmission of SARS-CoV-2 in Still Waterbodies Using a Lanthanide-Doped Carbon Nanoparticle-Based Sensor Array

The latest epidemic of extremely infectious coronavirus disease 2019 (COVID-19) has created a significant public health concern. Despite substantial efforts to contain severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within a specific location, shortcomings in the surveillance of predominantly asymptomatic infections constrain attempts to identify the epidemiological spread of the virus. Continuous surveillance of wastewater streams, including sewage, offers opportunities to track the spread of SARS-CoV-2, which is believed to be found in fecal waste. To demonstrate the feasibility of SARS-CoV-2 detection in wastewater systems, we herein present a novel facilely constructed fluorescence sensing array based on a panel of three different lanthanide-doped carbon nanoparticles (LnCNPs). The differential fluorescence response pattern due to the counterion-ligand interactions allowed us to employ powerful pattern recognition to effectively detect SARS-CoV-2 and differentiate it from other viruses or bacteria. The sensor results were benchmarked to the gold standard RT-qPCR, and the sensor showed excellent sensitivity (1.5 copies/μL) and a short sample-to-results time of 15 min. This differential response of the sensor array was also explained from the differential mode of binding of the LnCNPs with the surface proteins of the studied bacteria and viruses. Therefore, the developed sensor array provides a cost-effective, community diagnostic tool that could be potentially used as a novel epidemiologic surveillance approach to mitigate the spread of COVID-19.

Transmission of Respiratory Viral Diseases to Health Care Workers: COVID-19 as an Example

Health care workers (HCWs) can acquire infectious diseases, including coronavirus disease 2019 (COVID-19), from patients. Herein, COVID-19 is used with the source–pathway–receptor framework as an example to assess evidence for the role of aerosol transmission and indirect contact transmission of viral respiratory infectious diseases. Evidence for both routes is strong for COVID-19 and other respiratory viruses, but aerosol transmission is likely dominant for COVID-19. Key knowledge gaps about transmission processes and control strategies include the distribution of viable virus among respiratory aerosols of different sizes, the mechanisms and efficiency by which virus deposited on the facial mucous membrane moves to infection sites inside the body, and the performance of source controls such as face coverings and aerosol containment devices. To ensure that HCWs are adequately protected from infection, guidelines and regulations must be updated to reflect the evidence that respiratory viruses are transmitted via aerosols.

Expected final online publication date for the Annual Review of Public Health, Volume 43 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

[Polio Environmental Surveillance and Its Application to SARS-CoV-2 Detection]

The polio eradication program, launched in 1988, has successfully decreased the number of poliomyelitis patients worldwide. However, in areas with immunization gaps where oral polio vaccine coverage has dropped, outbreaks of more virulent vaccine-derived polioviruses (VDPVs) have become a threat to public health. In Japan, inactivated polio vaccine replaced oral polio vaccine as the routine immunization in 2012. Polio environmental surveillance (ES) has been conducted nationwide since 2013 to efficiently monitor the wild type poliovirus or VDPV, which may be imported from overseas. ES may also be utilized to detect other viruses in stool samples. We propose a method of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection based on the polio ES network, and establish a procedure to detect fragments of SARS-CoV-2 genome in wastewater solids. Our findings suggest that polio ES can be used to simultaneously monitor SARS-CoV-2 RNA fragments in sewage waters.

Urinary Tract Infections: Virus

Although viruses are common in the urinary tract in healthy people, viral infections can become a major concern in immunocompromised individuals. Patients undergoing hematopoietic stem cell or solid organ transplantation may be particularly susceptible to BK and other viruses, and experience a high risk of mortality. The most common presentation in this setting is hemorrhagic cystitis. The treatment is mostly supportive, including the reduction of immunosuppression; a variety of experimental agents has also been proposed. A different context is offered by chronic (HBV, HCV, HIV) or acute/subacute (Dengue, Hantavirus, etc.) infections, where the kidneys can be secondarily involved and suffer from several glomerular syndromes. Many protocols based on different oral direct-acting antivirals and combined antiretrovirals are available, according to the systemic infection. Viral infections can be classified according to the organ involved, i.e. lower (bladder) or upper urinary tract (kidneys, ureters), and to the mechanism of injury. A section is dedicated to the current breakout of SARS-CoV-2, which does not spare the urinary tract, sometimes with serious implications. Even if this topic is mostly the discipline of ultra-dedicated physicians, this overview has a practical approach and could be useful to a wider medical audience, especially in times of viral pandemics.

Monitoring occurrence of SARS-CoV-2 in school populations: A wastewater-based approach

Clinical testing of children in schools is challenging, with economic implications limiting its frequent use as a monitoring tool of the risks assumed by children and staff during the COVID-19 pandemic. Here, a wastewater-based epidemiology approach has been used to monitor 16 schools (10 primary, 5 secondary and 1 post-16 and further education) in England. A total of 296 samples over 9 weeks have been analysed for N1 and E genes using qPCR methods. Of the samples returned, 47.3% were positive for one or both genes with a detection frequency in line with the respective local community. WBE offers a low cost, non-invasive approach for supplementing clinical testing and can provide longitudinal insights that are impractical with traditional clinical testing.

Absence of virological and epidemiological evidence that SARS-CoV-2 poses COVID-19 risks from environmental fecal waste, wastewater and water exposures

This review considers evidence for infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presence and COVID-19 infection and illness resulting from exposure to environmental fecal wastes and waters. There is no documented evidence that (1) infectious, replication-capable SARS-CoV-2 is present in environmental fecal wastes, wastewater or water, and (2) well-documented epidemiological evidence of COVID-19 infection, illness or death has never been reported for these exposure media. COVID-19 is transmitted mainly by direct personal contact and respiratory secretions as airborne droplets and aerosols, and less so by respiratory-secreted fomites via contact (touch) exposures. While SARS-CoV-2 often infects the gastrointestinal tract of infected people, its presence as infectious, replication-capable virus in environmental fecal wastes and waters has never been documented. There is only rare and unquantified evidence of infectious, replication-capable SARS-CoV-2 in recently shed feces of COVID-19 hospital patients. The human infectivity dose-response relationship of SARS-CoV-2 is unknown, thereby making it impossible to estimate evidence-based quantitative health effects assessments by quantitative microbial risk assessment methods requiring both known exposure assessment and health effects assessment data. The World Health Organization, Water Environment Federation, US Centers for Disease Control and Prevention and others do not consider environmental fecal wastes and waters as sources of exposure to infectious SARS-CoV-2 causing COVID-19 infection and illness.

Impact of sewer overflow on public health: A comprehensive scientometric analysis and systematic review

Sewer overflow (SO), which has attracted global attention, poses serious threat to public health and ecosystem. SO impacts public health via consumption of contaminated drinking water, aerosolization of pathogens, food-chain transmission, and direct contact with fecally-polluted rivers and beach sediments during recreation. However, no study has attempted to map the linkage between SO and public health including Covid-19 using scientometric analysis and systematic review of literature. Results showed that only few countries were actively involved in SO research in relation to public health. Furthermore, there are renewed calls to scale up environmental surveillance to safeguard public health. To safeguard public health, it is important for public health authorities to optimize water and wastewater treatment plants and improve building ventilation and plumbing systems to minimize pathogen transmission within buildings and transportation systems. In addition, health authorities should formulate appropriate policies that can enhance environmental surveillance and facilitate real-time monitoring of sewer overflow. Increased public awareness on strict personal hygiene and point-of-use-water-treatment such as boiling drinking water will go a long way to safeguard public health. Ecotoxicological studies and health risk assessment of exposure to pathogens via different transmission routes is also required to appropriately inform the use of lockdowns, minimize their socio-economic impact and guide evidence-based welfare/social policy interventions. Soft infrastructures, optimized sewer maintenance and prescreening of sewer overflow are recommended to reduce stormwater burden on wastewater treatment plant, curtail pathogen transmission and marine plastic pollution. Comprehensive, integrated surveillance and global collaborative efforts are important to curtail on-going Covid-19 pandemic and improve resilience against future pandemics.

Risk of pediatric inflammatory multi-system syndrome (PIMS or MIS-C) in pediatric patients with COVID-19 presenting with gastrointestinal symptoms

INTRODUCTION AND OBJECTIVES

Pediatric inflammatory multisystem syndrome (PIMS) is a life-threatening complication in pediatric patients with SARS-CoV-2 infection. An increase in the association of gastrointestinal symptoms and the presence of PIMS has been observed. The objective of this study was to analyze whether pediatric patients with COVID-19, who debut with gastrointestinal symptoms, have a higher risk of developing PIMS.

MATERIAL AND METHODS

An observational, analytical and retrolective study was carried out with a review of the records of patients diagnosed with COVID-19. Demographic, clinical and laboratory variables were recorded.

RESULTS

A total of 248 patients who met the selection criteria were included. Of Those 40% were female, with a mean age of 7 +/- 5.8 years. Gastrointestinal symptoms were the initial presentation in 103 patients, with vomiting being the most frequent symptom, followed by abdominal pain and diarrhea. In total 52 patients developed PIMS, 30 of whom presented with gastrointestinal symptoms. A RR of 1.57 (97% CI of 1.17-2.11) was found for the presentation of PIMS in patients positive for SARS-CoV-2 who present with gastrointestinal symptoms.

CONCLUSIONS

There is an increased risk of developing pediatric multisystem inflammatory syndrome when there are gastrointestinal symptoms in pediatric patients with COVID-19.

The devil is in the details: emerging insights on the relevance of wastewater surveillance for SARS-CoV-2 to public health

The severe health consequences and global spread of the COVID-19 pandemic have necessitated the rapid development of surveillance programs to inform public health responses. Efforts to support surveillance capacity have included an unprecedented global research response into the use of genetic signals of SARS-CoV-2 in wastewater following the initial demonstration of the virus' detectability in wastewater in early 2020. The confirmation of fecal shedding of SARS-CoV-2 from asymptomatic, infected and recovering individuals further supports the potential for wastewater analysis to augment public health conventional surveillance techniques based on clinical testing of symptomatic individuals. We have reviewed possible capabilities projected for wastewater surveillance to support pandemic management, including independent, objective and cost-effective data generation that complements and addresses attendant limitations of clinical surveillance, early detection (i.e., prior to clinical reporting) of infection, estimation of disease prevalence, tracking of trends as possible indicators of success or failure of public health measures (mask mandates, lockdowns, vaccination, etc.), informing and engaging the public about pandemic trends, an application within sewer networks to identify infection hotspots, monitoring for presence or changes in infections from institutions (e.g., long-term care facilities, prisons, educational institutions and vulnerable industrial plants) and tracking of appearance/progression of viral variants of concern.

Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater

Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for methods that enable specific and timely detection and quantification of the occurrence of these variants in the community. In this study, we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. This assay enabled simultaneous enumeration of lineage B.1.351 (containing the 501Y mutation) and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Detection of N501Y was possible in samples with mixtures of WT with low proportions of B.1.351 (0.5%) and could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. The application to raw sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method can be applied to wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, K417T, E484K, L452R) or future mutations present in SARS-CoV-2 variants of concern. Monitoring these mutations can be used to obtain insight in the introduction and spread of VOC and support public health decision-making regarding measures to limit viral spread or allocation of testing or vaccination.

Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater

Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for methods that enable specific and timely detection and quantification of the occurrence of these variants in the community. In this study, we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. This assay enabled simultaneous enumeration of lineage B.1.351 (containing the 501Y mutation) and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Detection of N501Y was possible in samples with mixtures of WT with low proportions of B.1.351 (0.5%) and could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. The application to raw sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method can be applied to wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, K417T, E484K, L452R) or future mutations present in SARS-CoV-2 variants of concern. Monitoring these mutations can be used to obtain insight in the introduction and spread of VOC and support public health decision-making regarding measures to limit viral spread or allocation of testing or vaccination.

Lessons learned from SARS-CoV-2 measurements in wastewater

Standardized protocols for wastewater-based surveillance (WBS) for the RNA of SARS-CoV-2, the virus responsible for the current COVID-19 pandemic, are being developed and refined worldwide for early detection of disease outbreaks. We report here on lessons learned from establishing a WBS program for SARS-CoV-2 integrated with a human surveillance program for COVID-19. We have established WBS at three campuses of a university, including student residential dormitories and a hospital that treats COVID-19 patients. Lessons learned from this WBS program address the variability of water quality, new detection technologies, the range of detectable viral loads in wastewater, and the predictive value of integrating environmental and human surveillance data. Data from our WBS program indicated that water quality was statistically different between sewer sampling sites, with more variability observed in wastewater coming from individual buildings compared to clusters of buildings. A new detection technology was developed based upon the use of a novel polymerase called V2G. Detectable levels of SARS-CoV-2 in wastewater varied from 102 to 106 genomic copies (gc) per liter of raw wastewater (L). Integration of environmental and human surveillance data indicate that WBS detection of 100 gc/L of SARS-CoV-2 RNA in wastewater was associated with a positivity rate of 4% as detected by human surveillance in the wastewater catchment area, though confidence intervals were wide (β ~ 8.99 ∗ ln(100); 95% CI = 0.90-17.08; p < 0.05). Our data also suggest that early detection of COVID-19 surges based on correlations between viral load in wastewater and human disease incidence could benefit by increasing the wastewater sample collection frequency from weekly to daily. Coupling simpler and faster detection technology with more frequent sampling has the potential to improve the predictive potential of using WBS of SARS-CoV-2 for early detection of the onset of COVID-19.

On the Critical Role of Human Feces and Public Toilets in the Transmission of COVID-19: Evidence from China

The surprising spread speed of the COVID-19 pandemic creates an urgent need for investigating the transmission chain or transmission pattern of COVID-19 beyond the traditional respiratory channels. This study therefore examines whether human feces and public toilets play a critical role in the transmission of COVID-19. First, it develops a theoretical model that simulates the transmission chain of COVID-19 through public restrooms. Second, it uses stabilized epidemic data from China to empirically examine this theory, conducting an empirical estimation using a two-stage least squares (2SLS) model with appropriate instrumental variables (IVs). This study confirms that the wastewater directly promotes the transmission of COVID-19 within a city. However, the role of garbage in this transmission chain is more indirect in the sense that garbage has a complex relationship with public toilets, and it promotes the transmission of COVID-19 within a city through interaction with public toilets and, hence, human feces. These findings have very strong policy implications in the sense that if we can somehow use the ratio of public toilets as a policy instrument, then we can find a way to minimize the total number of infections in a region. As shown in this study, pushing the ratio of public toilets (against open defecation) to the local population in a city to its optimal level would help to reduce the total infection in a region.

Monitoring of SARS-CoV-2 RNA in wastewater as an epidemiological surveillance tool in Mendoza, Argentina

Wastewater-based epidemiology (WBE) is an emerging tool that gives temporal and spatial information on a population's health status. Here, we report the epidemiological dynamics of a population of ~1.2 million residents in the metropolitan region of Mendoza province, Argentina, within the period July 2020 to January 2021. We combined the use of WBE of two wastewater treatment plants with epidemiological surveillance of the corresponding populations. We applied two viral concentration methods (polyethylene glycol precipitation and aluminum-based adsorption-flocculation) and RNA isolation methods in each wastewater sample to increase the possibility of detection and quantification of nucleocapsid markers (N1 and N2) of SARS-CoV-2 by RT-qPCR. Overall, our results allowed us to trace the rise, exponential growth, plateau, and fall of SARS-CoV-2 infections for 26 weeks. Individual analysis for each wastewater treatment plant showed a positive correlation between the viral load of SARS-CoV-2 genetic markers and COVID-19 cases that were diagnosed per week. Our findings indicate that WBE is a useful epidemiological indicator to anticipate the increase in COVID-19 cases and monitor the advance of the pandemic and different waves of infections.

Urinary Tract Virome as an Urgent Target for Metagenomics

Virome—a part of a microbiome—is a term used to describe all viruses found in the specific organism or system. Recently, as new technologies emerged, it has been confirmed that kidneys and the lower urinary tract are colonized not only by the previously described viruses, but also completely novel species. Viruses can be both pathogenic and protective, as they often carry important virulence factors, while at the same time represent anti-inflammatory functions. This paper aims to show and compare the viral species detected in various, specific clinical conditions. Because of the unique characteristics of viruses, new sequencing techniques and databases had to be developed to conduct research on the urinary virome. The dynamic development of research on the human microbiome suggests that the detailed studies on the urinary system virome will provide answers to many questions about the risk factors for civilization, cancer, and autoimmune diseases.

Bidet Toilet Use May Cause Anal Symptoms and Nosocomial Infection

Electric bidet toilets are widely used in Japan and are sanitary devices, that are integral to daily life. Approximately, half of the population washed the anus before or after defecation. Cleaning the anus after defecation using the bidets contributes to hand hygiene and local comfort, and it may be effective against constipation. However, excessive bidet use potentially causes anal pruritus and anal incontinence (AI). Physicians are advised to instruct patients with anal pruritus to avoid excessive cleaning of the anus and those with AI to discontinue bidet use. For the estimation of the inherent severity of AI, physicians should instruct a bidet user with AI to discontinue bidet use and assess the severity of AI later. Additionally, the nozzle surface and splay water of bidet toilets may be contaminated with fecal indicator bacteria, such as Escherichia coli and Pseudomonas aeruginosa, as well as antimicrobial-resistant bacteria, rendering them a potential vehicle for cross-infection. In the hospital setting, compromised patients must be cautious regarding the shared use of bidet toilets to prevent infection by antimicrobial-resistant bacteria. Specifically, they should be provided with bidet toilets exclusive for them or may need to be instructed to not use a bidet.

Averting an Outbreak of SARS-CoV-2 in a University Residence Hall through Wastewater Surveillance

A wastewater surveillance program targeting a university residence hall was implemented during the spring semester 2021 as a proactive measure to avoid an outbreak of COVID-19 on campus. Over a period of 7 weeks from early February through late March 2021, wastewater originating from the residence hall was collected as grab samples 3 times per week. During this time, there was no detection of SARS-CoV-2 by reverse transcriptase quantitative PCR (RT-qPCR) in the residence hall wastewater stream. Aiming to obtain a sample more representative of the residence hall community, a decision was made to use passive samplers beginning in late March onwards. Adopting a Moore swab approach, SARS-CoV-2 was detected in wastewater samples just 2 days after passive samplers were deployed. These samples also tested positive for the B.1.1.7 (Alpha) variant of concern (VOC) using RT-qPCR. The positive result triggered a public health case-finding response, including a mobile testing unit deployed to the residence hall the following day, with testing of nearly 200 students and staff, which identified two laboratory-confirmed cases of Alpha variant COVID-19. These individuals were relocated to a separate quarantine facility, averting an outbreak on campus. Aggregating wastewater and clinical data, the campus wastewater surveillance program has yielded the first estimates of fecal shedding rates of the Alpha VOC of SARS-CoV-2 in individuals from a nonclinical setting. IMPORTANCE Among early adopters of wastewater monitoring for SARS-CoV-2 have been colleges and universities throughout North America, many of whom are using this approach to monitor congregate living facilities for early evidence of COVID-19 infection as an integral component of campus screening programs. Yet, while there have been numerous examples where wastewater monitoring on a university campus has detected evidence for infection among community members, there are few examples where this monitoring triggered a public health response that may have averted an actual outbreak. This report details a wastewater-testing program targeting a residence hall on a university campus during spring 2021, when there was mounting concern globally over the emergence of SARS-CoV-2 variants of concern, reported to be more transmissible than the wild-type Wuhan strain. In this communication, we present a clear example of how wastewater monitoring resulted in actionable responses by university administration and public health, which averted an outbreak of COVID-19 on a university campus.

Averting an Outbreak of SARS-CoV-2 in a University Residence Hall through Wastewater Surveillance

A wastewater surveillance program targeting a university residence hall was implemented during the spring semester 2021 as a proactive measure to avoid an outbreak of COVID-19 on campus. Over a period of 7 weeks from early February through late March 2021, wastewater originating from the residence hall was collected as grab samples 3 times per week. During this time, there was no detection of SARS-CoV-2 by reverse transcriptase quantitative PCR (RT-qPCR) in the residence hall wastewater stream. Aiming to obtain a sample more representative of the residence hall community, a decision was made to use passive samplers beginning in late March onwards. Adopting a Moore swab approach, SARS-CoV-2 was detected in wastewater samples just 2 days after passive samplers were deployed. These samples also tested positive for the B.1.1.7 (Alpha) variant of concern (VOC) using RT-qPCR. The positive result triggered a public health case-finding response, including a mobile testing unit deployed to the residence hall the following day, with testing of nearly 200 students and staff, which identified two laboratory-confirmed cases of Alpha variant COVID-19. These individuals were relocated to a separate quarantine facility, averting an outbreak on campus. Aggregating wastewater and clinical data, the campus wastewater surveillance program has yielded the first estimates of fecal shedding rates of the Alpha VOC of SARS-CoV-2 in individuals from a nonclinical setting. IMPORTANCE Among early adopters of wastewater monitoring for SARS-CoV-2 have been colleges and universities throughout North America, many of whom are using this approach to monitor congregate living facilities for early evidence of COVID-19 infection as an integral component of campus screening programs. Yet, while there have been numerous examples where wastewater monitoring on a university campus has detected evidence for infection among community members, there are few examples where this monitoring triggered a public health response that may have averted an actual outbreak. This report details a wastewater-testing program targeting a residence hall on a university campus during spring 2021, when there was mounting concern globally over the emergence of SARS-CoV-2 variants of concern, reported to be more transmissible than the wild-type Wuhan strain. In this communication, we present a clear example of how wastewater monitoring resulted in actionable responses by university administration and public health, which averted an outbreak of COVID-19 on a university campus.

What is the risk of acquiring SARS-CoV-2 from the use of public toilets?

Public toilets and bathrooms may act as a contact hub point where community transmission of SARS-CoV-2 occurs between users. The mechanism of spread would arise through three mechanisms: inhalation of faecal and/or urinary aerosol from an individual shedding SARS-CoV-2; airborne transmission of respiratory aerosols between users face-to-face or during short periods after use; or from fomite transmission via frequent touch sites such as door handles, sink taps, lota or toilet roll dispenser. In this respect toilets could present a risk comparable with other high throughput enclosed spaces such as public transport and food retail outlets. They are often compact, inadequately ventilated, heavily used and subject to maintenance and cleaning issues. Factors such as these would compound the risks generated by toilet users incubating or symptomatic with SARS-CoV-2. Furthermore, toilets are important public infrastructure since they are vital for the maintenance of accessible, sustainable and comfortable urban spaces. Given the lack of studies on transmission through use of public toilets, comprehensive risk assessment relies upon the compilation of evidence gathered from parallel studies, including work performed in hospitals and prior work on related viruses. This narrative review examines the evidence suggestive of transmission risk through use of public toilets and concludes that such a risk cannot be lightly disregarded. A range of mitigating actions are suggested for both users of public toilets and those that are responsible for their design, maintenance and management.

SARS-CoV-2 surveillance in untreated wastewater: detection of viral RNA in a low-resource community in Buenos Aires, Argentina

OBJECTIVE

To measure SARS-CoV-2 RNA in sewage in a low-resource community in order to determine if it can be considered as an estimator of changes in the prevalence of COVID-19 in the population.

METHODS

In this descriptive observational study we collected samples of surface waters contaminated with sewage and optimized a method of purification of viral RNA using PEG concentration. We determined the amount of genetic material by quantitative real-time PCR using the CDC method for SARS-CoV-2 detection.

RESULTS

We quantified viral RNA in surface waters contaminated with sewage of a low resource community and determined that temporal trends of SARS-CoV-2 in wastewater samples mirrored trends in COVID-19 active cases.

CONCLUSIONS

Measuring of SARS-CoV-2 RNA in sewage can be applied in low-resource communities without connection to sewers as an estimator of changes in the prevalence of COVID-19.

High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) likely emerged from a zoonotic spill-over event and has led to a global pandemic. The public health response has been predominantly informed by surveillance of symptomatic individuals and contact tracing, with quarantine, and other preventive measures have then been applied to mitigate further spread. Non-traditional methods of surveillance such as genomic epidemiology and wastewater-based epidemiology (WBE) have also been leveraged during this pandemic. Genomic epidemiology uses high-throughput sequencing of SARS-CoV-2 genomes to inform local and international transmission events, as well as the diversity of circulating variants. WBE uses wastewater to analyse community spread, as it is known that SARS-CoV-2 is shed through bodily excretions. Since both symptomatic and asymptomatic individuals contribute to wastewater inputs, we hypothesized that the resultant pooled sample of population-wide excreta can provide a more comprehensive picture of SARS-CoV-2 genomic diversity circulating in a community than clinical testing and sequencing alone. In this study, we analysed 91 wastewater samples from 11 states in the USA, where the majority of samples represent Maricopa County, Arizona (USA). With the objective of assessing the viral diversity at a population scale, we undertook a single-nucleotide variant (SNV) analysis on data from 52 samples with >90% SARS-CoV-2 genome coverage of sequence reads, and compared these SNVs with those detected in genomes sequenced from clinical patients. We identified 7973 SNVs, of which 548 were "novel" SNVs that had not yet been identified in the global clinical-derived data as of 17^th June 2020 (the day after our last wastewater sampling date). However, between 17^th of June 2020 and 20^th November 2020, almost half of the novel SNVs have since been detected in clinical-derived data. Using the combination of SNVs present in each sample, we identified the more probable lineages present in that sample and compared them to lineages observed in North America prior to our sampling dates. The wastewater-derived SARS-CoV-2 sequence data indicates there were more lineages circulating across the sampled communities than represented in the clinical-derived data. Principal coordinate analyses identified patterns in population structure based on genetic variation within the sequenced samples, with clear trends associated with increased diversity likely due to a higher number of infected individuals relative to the sampling dates. We demonstrate that genetic correlation analysis combined with SNVs analysis using wastewater sampling can provide a comprehensive snapshot of the SARS-CoV-2 genetic population structure circulating within a community, which might not be observed if relying solely on clinical cases.

High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) likely emerged from a zoonotic spill-over event and has led to a global pandemic. The public health response has been predominantly informed by surveillance of symptomatic individuals and contact tracing, with quarantine, and other preventive measures have then been applied to mitigate further spread. Non-traditional methods of surveillance such as genomic epidemiology and wastewater-based epidemiology (WBE) have also been leveraged during this pandemic. Genomic epidemiology uses high-throughput sequencing of SARS-CoV-2 genomes to inform local and international transmission events, as well as the diversity of circulating variants. WBE uses wastewater to analyse community spread, as it is known that SARS-CoV-2 is shed through bodily excretions. Since both symptomatic and asymptomatic individuals contribute to wastewater inputs, we hypothesized that the resultant pooled sample of population-wide excreta can provide a more comprehensive picture of SARS-CoV-2 genomic diversity circulating in a community than clinical testing and sequencing alone. In this study, we analysed 91 wastewater samples from 11 states in the USA, where the majority of samples represent Maricopa County, Arizona (USA). With the objective of assessing the viral diversity at a population scale, we undertook a single-nucleotide variant (SNV) analysis on data from 52 samples with >90% SARS-CoV-2 genome coverage of sequence reads, and compared these SNVs with those detected in genomes sequenced from clinical patients. We identified 7973 SNVs, of which 548 were "novel" SNVs that had not yet been identified in the global clinical-derived data as of 17th June 2020 (the day after our last wastewater sampling date). However, between 17th of June 2020 and 20th November 2020, almost half of the novel SNVs have since been detected in clinical-derived data. Using the combination of SNVs present in each sample, we identified the more probable lineages present in that sample and compared them to lineages observed in North America prior to our sampling dates. The wastewater-derived SARS-CoV-2 sequence data indicates there were more lineages circulating across the sampled communities than represented in the clinical-derived data. Principal coordinate analyses identified patterns in population structure based on genetic variation within the sequenced samples, with clear trends associated with increased diversity likely due to a higher number of infected individuals relative to the sampling dates. We demonstrate that genetic correlation analysis combined with SNVs analysis using wastewater sampling can provide a comprehensive snapshot of the SARS-CoV-2 genetic population structure circulating within a community, which might not be observed if relying solely on clinical cases.

Toxicological insights of Spike fragments SARS-CoV-2 by exposure environment: A threat to aquatic health?

The Spike protein (S protein) is a critical component in the infection of the new coronavirus (SARS-CoV-2). The objective of this work was to evaluate whether peptides from S protein could cause negative impact in the aquatic animals. The aquatic toxicity of SARS-CoV-2 Spike protein peptides derivatives has been evaluated in tadpoles (n = 50 tadpoles/5 replicates of 10 animals) from species Physalaemus cuvieri (Leptodactylidae). After synthesis, purification, and characterization of peptides (PSDP2001, PSDP2002, PSDP2003) an aquatic contamination has been simulated with these peptides during 24 h of exposure in two concentrations (100 and 500 ng/mL). The control group ("C") was composed of tadpoles kept in polyethylene containers containing de-chlorinated water. Oxidative stress, antioxidant biomarkers and AChE activity were assessed. In both concentrations, PSPD2002 and PSPD2003 increased catalase and superoxide dismutase antioxidants enzymes activities, as well as oxidative stress (nitrite levels, hydrogen peroxide and reactive oxygen species). All three peptides also increased acetylcholinesterase activity in the highest concentration. These peptides showed molecular interactions in silico with acetylcholinesterase and antioxidant enzymes. Aquatic particle contamination of SARS-CoV-2 has cholinesterasic effect in P. cuvieri tadpoles. These findings indicate that the COVID-19 can constitute environmental impact or biological damage potential.

Wastewater aerosols produced during flushing toilets, WWTPs, and irrigation with reclaimed municipal wastewater as indirect exposure to SARS-CoV-2

The detection of SARS-CoV-2 RNA in raw and treated wastewater can open up a fresh perspective to waterborne and aerosolized wastewater as a new transmission route of SARS-CoV-2 RNA during the current pandemic. The aim of this paper is to discuss the potential transmission of SARS-CoV-2 RNA from wastewater aerosols formed during toilet flushing, plumbing failure, wastewater treatment plants, and municipal wastewater reuse for irrigation. Moreover, how these aerosols might increase the risk of exposure to this novel coronavirus (SARS-CoV-2 RNA). This article supplies a review of the literature on the presence of SARS-CoV-2 RNA in untreated wastewater, as well as the fate and stability of SARS-CoV-2 RNA in wastewater. We also reviewed the existing literatures on generation and transmission of aerosolized wastewater through flush a toilet, house's plumbing networks, WWTPs, wastewater reuse for irrigation of agricultural areas. Finally, the article briefly studies the potential risk of infection with exposure to the fecal bioaerosols of SARS-CoV-2 RNA for the people who might be exposed through flushing toilets or faulty building plumbing systems, operators/workers in wastewater treatment plants, and workers of fields irrigated with treated wastewater - based on current knowledge. Although this review highlights the indirect transmission of SARS-CoV-2 RNA through wastewater aerosols, no research has yet clearly demonstrated the role of aerosolized wastewater in disease transmission regarding the continuation of this pandemic. Therefore, there is a need for additional studies on wastewater aerosols in transmission of COVID-19.

An optimised protocol for detection of SARS-CoV-2 in stool

BACKGROUND

SARS-CoV-2 has been detected in stool samples of COVID-19 patients, with potential implications for faecal-oral transmission. Compared to nasopharyngeal swab samples, the complexity of the stool matrix poses a challenge in the detection of the virus that has not yet been solved. However, robust and reliable methods are needed to estimate the prevalence and persistence of SARS-CoV-2 in the gut and to ensure the safety of microbiome-based procedures such as faecal microbiota transplant (FMT). The aim of this study was to establish a sensitive and reliable method for detecting SARS-CoV-2 in stool samples.

RESULTS

Stool samples from individuals free of SARS-CoV-2 were homogenised in saline buffer and spiked with a known titre of inactivated virus ranging from 50 to 750 viral particles per 100 mg stool. Viral particles were concentrated by ultrafiltration, RNA was extracted, and SARS-CoV-2 was detected via real-time reverse-transcription polymerase chain reaction (RT-qPCR) using the CDC primers and probes. The RNA extraction procedure we used allowed for the detection of SARS-CoV-2 via RT-qPCR in most of the stool samples tested. We could detect as few as 50 viral particles per 100 mg of stool. However, high variability was observed across samples at low viral titres. The primer set targeting the N1 region provided more reliable and precise results and for this primer set our method had a limit of detection of 1 viral particle per mg of stool.

CONCLUSIONS

Here we describe a sensitive method for detecting SARS-CoV-2 in stool samples. This method can be used to establish the persistence of SARS-CoV-2 in stool and ensure the safety of clinical practices such as FMT.

Emerging contaminants, SARS-COV-2 and wastewater treatment plants, new challenges to confront: A short review

The current pandemic caused by SARS-CoV-2 has put public health at risk, being wastewater-based epidemiology (WBE) a potential tool in the detection, prevention, and treatment of present and possible future outbreaks, since this virus enters wastewater through various sources such as feces, vomit, and sputum. Thus, advanced technologies such as advanced oxidation processes (AOP), membrane technology (MT) are identified through a systematic literature review as an alternative option for the destruction and removal of emerging contaminants (drugs and personal care products) released mainly by infected patients. The objectives of this review are to know the implications that the new COVID-19 outbreak is generating and will generate in water compartments, as well as the new challenges faced by wastewater treatment plants due to the change in a load of contaminants and the solutions proposed based on the aforementioned technologies to be applied to preserve public health and the environment.

The role of airborne particles and environmental considerations in the transmission of SARS-CoV-2

Corona Virus Disease 2019 (COVID-19) caused by the novel coronavirus, results in an acute respiratory condition coronavirus 2 (SARS-CoV-2) and is highly infectious. The recent spread of this virus has caused a global pandemic. Currently, the transmission routes of SARS-CoV-2 are being established, especially the role of environmental transmission. Here we review the environmental transmission routes and persistence of SARS-CoV-2. Recent studies have established that the transmission of this virus may occur, amongst others, in the air, water, soil, cold-chain, biota, and surface contact. It has also been found that the survival potential of the SARS-CoV-2 virus is dependent on different environmental conditions and pollution. Potentially important pathways include aerosol and fecal matter. Particulate matter may also be a carrier for SARS-CoV-2. Since microscopic particles can be easily absorbed by humans, more attention must be focused on the dissemination of these particles. These considerations are required to evolve a theoretical platform for epidemic control and to minimize the global threat from future epidemics.

Wastewater monitoring as a supplementary surveillance tool for capturing SARS-COV-2 community spread. A case study in two Greek municipalities

A pilot study was conducted from late October 2020 until mid-April 2021, aiming to examine the association between SARS-CoV-2 RNA concentrations in untreated wastewater and recorded COVID-19 cases in two Greek municipalities. A population of Random Forest and Linear Regression Machine Learning models was trained and evaluated incorporating the concentrations of SARS-CoV-2 RNA in 111 wastewater samples collected from the inlets of two Wastewater Treatment Plants, along with physicochemical parameters of the wastewater influent. The model's predictions were adequately associated with the 7-day cumulative cases with the correlation coefficients (after 5-fold cross validation) ranging from 0.754 to 0.960 while the mean relative errors ranged from 30.42% to 59.46%. Our results provide indications that wastewater-based predictions can be applied in diverse settings and in prolonged time periods, although the accuracy of these predictions may be mitigated. Wastewater-based epidemiology can support and strengthen epidemiological surveillance.

Making waves: Defining the lead time of wastewater-based epidemiology for COVID-19

Individuals infected with SARS-CoV-2, the virus that causes COVID-19, may shed the virus in stool before developing symptoms, suggesting that measurements of SARS-CoV-2 concentrations in wastewater could be a "leading indicator" of COVID-19 prevalence. Multiple studies have corroborated the leading indicator concept by showing that the correlation between wastewater measurements and COVID-19 case counts is maximized when case counts are lagged. However, the meaning of "leading indicator" will depend on the specific application of wastewater-based epidemiology, and the correlation analysis is not relevant for all applications. In fact, the quantification of a leading indicator will depend on epidemiological, biological, and health systems factors. Thus, there is no single "lead time" for wastewater-based COVID-19 monitoring. To illustrate this complexity, we enumerate three different applications of wastewater-based epidemiology for COVID-19: a qualitative "early warning" system; an independent, quantitative estimate of disease prevalence; and a quantitative alert of bursts of disease incidence. The leading indicator concept has different definitions and utility in each application.

Elimination of SARS-CoV-2 along wastewater and sludge treatment processes

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is shed in the feces of infected people. As a consequence, genomic RNA of the virus can be detected in wastewater. Although the presence of viral RNA does not inform on the infectivity of the virus, this presence of genetic material raised the question of the effectiveness of treatment processes in reducing the virus in wastewater and sludge. In this work, treatment lines of 16 wastewater treatment plants were monitored to evaluate the removal of SARS-CoV-2 RNA in raw, processed waters and sludge, from March to May 2020. Viral RNA copies were enumerated using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) in 5 different laboratories. These laboratories participated in proficiency testing scheme and their results demonstrated the reliability and comparability of the results obtained for each one. SARS-CoV-2 RNA was found in 50.5% of the 101 influent wastewater samples characterized. Positive results were detected more frequently in those regions with a COVID-19 incidence higher than 100 cases per 100,000 inhabitants. Wastewater treatment plants (WWTPs) significantly reduced the occurrence of virus RNA along the water treatment lines. Secondary treatment effluents showed an occurrence of SARS-CoV-2 RNA in 23.3% of the samples and no positive results were found after MBR and chlorination. Non-treated sludge (from primary and secondary treatments) presented a higher occurrence of SARS-CoV-2 RNA than the corresponding water samples, demonstrating the affinity of virus particles for solids. Furthermore, SARS-CoV-2 RNA was detected in treated sludge after thickening and anaerobic digestion, whereas viral RNA was completely eliminated from sludge only when thermal hydrolysis was applied. Finally, co-analysis of SARS-CoV-2 and F-specific RNA bacteriophages was done in the same water and sludge samples in order to investigate the potential use of these bacteriophages as indicators of SARS-CoV-2 fate and reduction along the wastewater treatment.

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.