Placing Antimicrobial Resistance in the Context of Competing Public Health Priorities in Sub-Saharan Africa, a Perspective from Malawi

Antimicrobial resistance is a major threat to human health that is predicted to impact most heavily on sub-Saharan Africa, however there is a lack of clinical outcome data from drug-resistant infections in this setting. There are reasons to expect the COVID-19 pandemic to have both positive and negative impacts on AMR in Africa. We have recruited a series of prospective longitudinal cohorts from Queen Elizabeth Central Hospital (QECH), Blantyre, Malawi and the surrounding communities in the Southern Region of Malawi. The data from these cohorts has been used to describe the aetiology of febrile illness, the burden of antimicrobial resistance in this setting and the distribution of extended spectrum beta-lactamase producing bacteria in humans, animals and the environment. Amongst a cohort of patients presenting to QECH unwell with febrile illness, 67% were living with human immunodeficiency virus (HIV). We identified a diagnosis in 145 of 225 (64%) participants, most commonly tuberculosis (TB;34%) followed by invasive bacterial infections (17%), arboviral infections (13%), and malaria (9%). In a second cohort with drug resistant infection, resistance to third-generation cephalosporins was associated with an increased probability of in-hospital mortality (hazard ratio [HR] 1.44, 95% CI 1.02-2.04), longer hospital stays (1.5 days, 1.0-2.0) and decreased probability of discharge alive (HR 0.31, 0.22-0.45). In the community cohorts, a paucity of environmental health infrastructure and materials for safe sanitation was identified across all sites and ESBL-Enterobacterales were isolated from 41.8% of human stool, 29.8% of animal stool and 66.2% of river water samples and was associated with the wet season, living in urban areas, advanced age and in household-animal interactions. Life threatening febrile illness is common in Blantyre however, diagnostics are few, however the COVID-19 pandemic has led to rapid expansion of diagnostic capacity. We are, however frequently treating the wrong bugs with ceftriaxone, further there was significant expansion of azithromycin demand and usage during the pandemic. Current management of sepsis has not been optimised and ceftriaxone use is promoting carriage of ESBL bacteria out of the hospital and ESBL E. coli and K. pneumoniae are ubiquitous in the community, where environmental hygiene infrastructure and community antimicrobial stewardship are critically lacking.Copyright © 2023

Metavirome in Sewage and Fecally-Tainted River Waters in the Philippines: Highlighting the Role of Environmental Surveillance in the Covid-19 Pandemic

Intro: The COVID-19 pandemic has triggered global collaborative efforts on response and research to detect SARS-CoV-2 particles not just in the human population but also in wastewater. While the examination of clinical samples from COVID-19 patients links SARS-CoV-2 to specific individuals, the analysis of an amalgam of human feces through environmental surveillance (ES) links SARSCoV-2 to populations and communities served by the wastewater system. Studies on SARS-CoV-2 in the environment were already done in high-resource countries. However, its epidemiology in wastewater bodies in the Philippines is limited. In this study, we used the National ES for Polio and Other Pathogens Network to investigate the molecular epidemiology and transmission dynamics of SARS-CoV-2 at the outset of the pandemic. Method(s): This is a retrospective study of 250 wastewater samples collected from May 2020 to July 2021. Samples were processed using the two-phase concentration technique. Pepper mild mottle virus RNAs were quantified as the internal control. Real-time PCR was used to detect the N-gene of the SARS-CoV-2. Whole genomes were sequenced using the COVID-19 ARTIC v4.0. Phylogenetic and mutation analysis were done and lineage assignments were established using the PANGOLIN software. Finding(s): Forty-two percent (107/250) of the environmental samples detected SARS-CoV-2 particles. Fifty-nine samples with Ct values <=38 were sequenced and the whole genome analysis revealed B.1.1 and B.6. lineages of SARS-CoV-2. When viral load were plotted with the weekly cases in the respective site, we observed that SARS-CoV2 can be detected in wastewater weeks before the spike of cases in the community. Conclusion(s): This is the first report on the detection of B.1.1 and B.6 SARS-CoV-2 particles in waste/surface waters in the Philippines. With the declining incidence of COVID-19 cases, this study provided data regarding the feasibility of establishing environmental surveillance for SARS-CoV-2 as a supplemental tool for human or case monitoring especially in resource-limited settings.Copyright © 2023

Study on the possibility of raw seawater into beverage - using ethanol as a renewable resource

In COVID-19 pandemic in the world, alcohol (ethanol) can be listed as a sterilizing disinfectant. It absolutely played a Messianic function on the sterilization effect. And it is said that it has one more function called "salinity reduction" but that function is not widely known. The two functions (Sterilization & Salinity Reduction) mentioned above are extremely important regarding the theme of "raw seawater into beverage" in this study. It is thought that if the two functions are achieved other water quality items such as NO-2 and other items can be cleared with comparative ease. To put briefly the feature of modern waterworks in a word, it can be said that "source of water is river water and its sterilization is chlorine". In this study, we set up it with a completely new sanitization method (great reset), that is, "source of water is mixtures (seawater and rainwater) and its sterilization is ethanol". And it can be also expected that the capture and storage of ethanol as a renewable resource is basically possible by utilizing sunlight as a natural power. Therefore, we think that this resolves itself into a question of the choice (sense of value/culture) of the users. It means that how users finally balance out with three factors, i.e., cost, risk (safety) and benefit. Based on the viewpoint mentioned above, we examined the possibility of raw seawater into beverage using ethanol as a renewable resource to create humankind's wisdom to the settlement (breakthrough) of the water scarcity in the world including Asia and Africa. As a result, we have obtained the new findings that suggest the possibility of raw seawater into beverage using ethanol as a renewable resource.

Impact of COVID-19 Nationwide Lockdowns and Unlock Phases in India on River Water Quality of Upper Part of the Ganga River

The river water quality index (RWQI) of the upper Ganga canal has been computed to assess the effect of lockdown and unlock phases lead down by COVID-19 in India. Geospatial distribution of RWQI from January 2019 to December 2021 in the study area revealed significant impacts of lockdown on water quality. However, unlock phases (post lockdown) have deteriorated water quality since August 2020 and reached to actual conditions of the river by August 2021. To evaluate the lockdown as a management strategy to clean the river, other factors were reviewed including rainfall data, migration, and other activities. The results revealed that all the monitoring stations have improved water quality index ranging from 3 to 45 between March to June 2020. The River Ganga at Haridwar showed a two-fold improvement in the water quality index making it the highest positive impact of the lockdown, and at Rishikesh, the water quality index showed the least changes. The average decrease in RWQI has been observed to be 13 units in the year 2020 as compared to 2019 between March to June. In October 2020, RWQI has been observed to be higher as compared to the years 2019 and 2021. This is possibly due to a shift in rainfall patterns and other factors such as evapotranspiration, precipitation, and atmospheric temperature involved in river water quality control. Up to 60% reduction in average total coliforms and fecal coliforms has been observed due to the nationwide lockdown and a shift in human behavior towards cleaner and sustainable approaches. © 2023, Chulalongkorn University - Environmental Research Institute. All rights reserved.

From city to sea: Spatiotemporal dynamics of floating macrolitter in the Tiber River

Rivers are undoubtedly the main pathway of waste dispersed in the environment that from land reaches oceans and seas increasing the amount of marine litter. Major cities are a great source of riverine litter as large urbanization can originate pressure on the integrated waste management resulting in litter entering the rivers. Within this study, we aim to investigate the dynamic of floating riverine macrolitter (items >2.5 cm) in the city of Rome before it reaches the sea by assessing the composition, amount, and seasonal trends of litter transported from the urban centre to the main river mouth of Tiber River. Visual surveys for a whole year (March 2021–February 2022) were conducted from two bridges, Scienza Bridge (in the city) and Scafa Bridge (at the main river mouth) and followed JRC/RIMMEL protocol for riverine litter monitoring. Overall, similar litter composition was observed from the city centre to the mouth with a prevalence of plastic material, mainly related to fragmentation process (i.e. plastic pieces) and single use items, mainly in food and beverage sectors. An extrapolated annual loading of 4 × 105 items/year was estimated at the main mouth of Tiber River. The litter flux seems to be influenced by the seasonal variability and hydrometeorological parameters. The frequency of size classes decreases with increasing size in both sites, and more than half of the recorded items were below 10 cm. Specific categories belonging to "other plastics” have been reported related to anti-Covid-19 behaviour such as face masks and beverage sector, e.g. bottle lids and rings. The main colour of plastics was white, suggesting weathering process of floating riverine litter. This study contributes to increasing knowledge of the origin, composition and spatiotemporal dynamics of riverine floating litter from the city and entering the sea. © 2022 Elsevier B.V.

Cholera

Cholera, a diarrheal infection caused by the gram-negative bacillus Vibrio cholerae, belongs to the Vibrionaceae family. According to the who in 2017, 34 countries reported a total of 1 227 391 cases of cholera and 5 654 deaths, with a fatality rate of 0.5%. The Asian continent is responsible for 84% and Africa for 14% of all cholera cases worldwide, and in America, Haiti reported 13 681 cases (1%). Practically, most of the cases correspond to developing countries, which translates to us a health problem and/or infrastructure (access to safe water), conditions for outbreaks and epidemics. In Mexico, in 2018 a case was reported in an adult, being the human intestine is not the only reservoir of V. cholerae 01, since it survives and multiplies in estuaries, swamps, rivers and in the sea. Some fish and various shellfish, especially bivalve molluscs from contaminated waters, are a potential source of transmission if eaten raw or undercooked. It can also be spread through other types of food such as rice, coconut water, undercooked pork, and vegetables irrigated with black water. The route of transmission is fecal-oral. Outbreaks associated with the ingestion of contaminated water appear explosively and are generally related to a common source. Cholera occurs mainly in low socioeconomic environments with poor sanitation conditions, it is frequent in people who are exposed to consumption of river water and/or street foods and in food handlers. Given all these aspects, we must always think about this pathology, given the sanitary conditions that are currently distracting from the current coronavirus pandemic, coupled with many regions with floods and the consumption of contaminated water.

The dynamics of the first wave of COVID-19 on environment and wildlife– a boon or a bane?

Even though COVID-19 has drastically weighed upon the humankind, still there is a "silver lining" to see in this dark time. Amidst of this pandemic, most of the human activities were restricted to break the chain of infection which resulted the remarkable change in nature. It has been reported that due to halt in air travel, reduction in the use of fossil fuels, way less functioning of vehicles, shutdown of industries has complied the change in air pollution levels and also change in river water quality. Reports also showed the reduction in particulate matter (PM 2.5 and PM 10), greenhouse gases emissions, massive improvement in the Air quality index (AQI), reduction in the NOX and SOX's levelhas clearly stipulated that nature has got it's time to "revive". Even the global carbon emission has reported to reduced reluctantly which is expected to be the biggest such drop since World War II. Despite conducting water-cleansing projects and spending a lot of money, the situation of the water bodies were far better now during first lockdown. Moreover, migration and breeding of the birds and animals have been reported to be restored to normal pattern due to depletion in man-animal conflict. Apart from the positive, negative impacts on the nature are also being experienced. Our review work is highlighting such impacts witnessed during the first wave of COVID-19, like, the significant improvement in air and water quality, reduction in environmental noise, therefore an in turn cleaner and quieter habitat for the wildlife to mate and also to quench their curiosities by their surprising excursions;but there are also some negative aspects as well, like reduction in recycling and the increase in waste, increased poaching and even lone shuttering of zoo animals.

Baseline assessment of heavy metal pollution during COVID-19 near river mouth of Kerian River, Malaysia

River water quality is a serious concern among scientist and government agencies due to increasing anthropogenic activities and uncontrolled industrial discharge to rivers. The present study was conducted near the river mouth of the Kerian River to assess heavy metal pollution during COVID-19 pandemic-lockdown conditions and post-COVID-19 pandemic-unlock conditions. Twelve samples of shallow, middle, and bottom depths were collected at four locations along a 9.6 km reach. A concentration of eight heavy metals including Cadmium, Chromium, Copper, Iron, Manganese, Nickel, Lead, and Zinc were extracted through atomic absorption spectrometry. Total suspended solid was measured during laboratory experimentation. The results showed that, during the pandemic, concentrations of Nickel, Zinc, and Iron were high at shallow, middle, and bottom depths, respectively. Decreasing orders of heavy metal concentration are variable at different depths due to either their high sinking tendency with other existing components of water matrix or the anthropogenic source. However, almost all values of heavy metals are under the permissible limit of National Water Quality Standards of Malaysia and Food and Drug Administration. A possible reason for the lack of heavy metal pollution may be the restriction of anthropogenic activities during the COVID-19 pandemic. Additionally, no significant differences were observed in total suspended solid.

Impact of Nationwide Lockdown During Covid-19 on Water Quality of Yamuna River in District Mathura (U. P.)

COVID-19 is a pandemic that affected the majority of countries of the world. After the COVID-19 outburst, the Indian Government declared the complete lockdown starting on the night of 24 March 2020. The lockdown period is in its 4th phase. In the recent year it has been very fascinating to remind that the behaviour in the environment is vastly optimistic and all layers of the earth are under the repairing mode during the lockdown. With these healing environments, the conditions of the Yamuna River water in Mathura (polluted river) have also been found to be upgrading. In this present concern, we work on the concentration of BOD, COD, pH, and other physicochemical parameters for the study, i.e. TDS, Chlorides, Alkalinity, Magnesium, Calcium, Fluoride, Sulphate, Nitrate, Hardness and Total Coliform of Yamuna River (Mathura), respectively, which was found to be reduced as compared to pre-lockdown concentration, i.e. 57, 57, 3.6, 11.7, 5.1, 7.4, 9.5, 4.2, 62.5, 14.8, 33.3, and 4.5%. In the present work, the water of Yamuna River was analysed during the lockdown phase in ITL Labs Pvt. Ltd., Delhi (India). Yamuna River showed a better quality of water during the lockdown. As per results and trend analysis, the value was reducing in this lockdown phase, which is a matter of concern. Major locations of Yamuna water sample collection are Mathura region, i.e. adjacent to the road 50 m from Adda village in Naujheel of Mathura district in Uttar Pradesh. © 2022, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

Direct Sunlight Driven In2S3 Thin Film Based Water Treatment Proto-Type

A multi-faceted energy intensive technology that can be used for water disinfection and synthesis of electrolysed water (EW) is the need of the hour to achieve a sustainable post COVID 19 water management strategy. Direct sunlight driven processes are legislatively green technologies and hold the key in environmental sustenance. The development of a laboratory proto type reactor powered by a photovoltaic module for the treatment open source river water is described in this paper. This paper reports on the efficacy of the developed proto type technology for multipurpose application namely: (1) the production of Electrolysed water (EW) in a cost efficient manner using direct sunlight and (2) the removal of organic impurity from water using direct sunlight without the use of any photo catalyst or membrane. The prototype reactor utilizes chemical spray pyrolysis deposited highly photo-conducting indium sulphide thin films grown on fluorine doped tin oxide (F:SnO2) substrate (coated using chemical spray pyrolysis technique in-house) as the photo electrode. Dissolved organic matter arising in river water has distinctive fluorescence properties, and this research has utilized it to identify dissolved organic substances in both random samples and treated water. The work proves that photovoltaic module powered electrolytic reactors consisting of In2S3 electrodes can be used for treatment of river water. A diaphragm free, energy intensive route for the production of electrolysed water with the use of non-hazardous NaCl as the electrolyte has been demonstrated here. We conclude that In2S3 electrodes can be used for non-photo catalytic reduction of humic-derived impurities in river water. These results are also encouraging on the prospects of treating Nitrates present in the river water. The likes of techniques as described in this report that do not use photo catalyst or membranes may pave way for real time photovoltaic module powered floating reactors that can decontaminate water bodies on a large scale. The technique used by us demonstrates that a chlorine free route can be optimized for the synthesis of EW eliminating the production of large amounts of wastewater with high levels of biological oxygen demand (BOD).

Monitoring SARS-CoV-2 in the Wastewater and Rivers of Tapachula, a Migratory Hub in Southern Mexico.

The COVID-19 pandemic has been monitored by applying different strategies, including SARS-CoV-2 detection with clinical testing or through wastewater-based epidemiology (WBE). We used the latter approach to follow SARS-CoV-2 dispersion in Tapachula city, located in Mexico's tropical southern border region. Tapachula is a dynamic entry point for people seeking asylum in Mexico or traveling to the USA. Clinical testing facilities for SARS-CoV-2 monitoring are limited in the city. A total of eighty water samples were collected from urban and suburban rivers and sewage and a wastewater treatment plant over 4 months in Tapachula. We concentrated viral particles with a PEG-8000-based method, performed RNA extraction, and detected SARS-CoV-2 particles through RT-PCR. We considered the pepper mild mottle virus as a fecal water pollution biomarker and analytical control. SARS-CoV-2 viral loads (N1 and N2 markers) were quantified and correlated with official regional statistics of COVID-19 bed occupancy and confirmed cases (r > 91%). Our results concluded that WBE proved a valuable tool for tracing and tracking the COVID-19 pandemic in tropical countries with similar water temperatures (21-29 °C). Monitoring SARS-CoV-2 through urban and suburban river water sampling would be helpful in places lacking a wastewater treatment plant or water bodies with sewage discharges.

Use of Passive and Grab Sampling and High-Resolution Mass Spectrometry for Non-Targeted Analysis of Emerging Contaminants and Their Semi-Quantification in Water

Different groups of organic micropollutants including pharmaceuticals and pesticides have emerged in the environment in the last years, resulting in a rise in environmental and human health risks. In order to face up and evaluate these risks, there is an increasing need to assess their occurrence in the environment. Therefore, many studies in the past couple of decades were focused on the improvements in organic micropollutants’ extraction efficiency from the different environmental matrices, as well as their mass spectrometry detection parameters and acquisition modes. This paper presents different sampling methodologies and high-resolution mass spectrometry-based non-target screening workflows for the identification of pharmaceuticals, pesticides, and their transformation products in different kinds of water (domestic wastewater and river water). Identification confidence was increased including retention time prediction in the workflow. The applied methodology, using a passive sampling technique, allowed for the identification of 85 and 47 contaminants in the wastewater effluent and river water, respectively. Finally, contaminants’ prioritization was performed through semi-quantification in grab samples as a fundamental step for monitoring schemes.

COVID-19 Lockdowns-Effect on Concentration of Pharmaceuticals and Illicit Drugs in Two Major Croatian Rivers.

In order to prevent the spread of COVID-19, contingency measures in the form of lockdowns were implemented all over the world, including in Croatia. The aim of this study was to detect if those severe, imposed restrictions of social interactions reflected on the water quality of rivers receiving wastewaters from urban areas. A total of 18 different pharmaceuticals (PhACs) and illicit drugs (IDrgs), as well as their metabolites, were measured for 16 months (January 2020-April 2021) in 12 different locations at in the Sava and Drava Rivers, Croatia, using UHPLC coupled to LCMS. This period encompassed two major Covid lockdowns (March-May 2020 and October 2020-March 2021). Several PhACs more than halved in river water mass flow during the lockdowns. The results of this study confirm that Covid lockdowns caused lower cumulative concentrations and mass flow of measured PhACs/IDrgs in the Sava and Drava Rivers. This was not influenced by the increased use of drugs for the treatment of the COVID-19, like antibiotics and steroidal anti-inflammatory drugs. The decreases in measured PhACs/IDrgs concentrations and mass flows were more pronounced during the first lockdown, which was stricter than the second.

A Mobile Laboratory Enables Fecal Pollution Source Tracking in Catchments Using Onsite qPCR Assays

Onsite molecular diagnostics can revolutionize fecal pollution source tracking. We aimed to validate a method for onsite qPCR assays with a miniature speaker-sized Q qPCR instrument and other portable equipment items. We showed that marker genes for total bacteria (16S) and E. coli (rodA) in 100 mL of river water measured with this method agreed within ±0.3 log10 units with results obtained when using conventional laboratory equipment items. We then deployed the portable method in a mobile laboratory (‘lab in a van’) and quantified HF183 marker genes for human host associated Bacteroides in river water within 3 h of sampling. We also used the mobile laboratory to investigate urban river water and effluents from two storm drains and a retention pond and collected comprehensive microbial and physicochemical water quality data. We found significantly higher HF183 gene levels in the older storm drain compared to the river water (6.03 ± 0.04 vs. 4.23 ± 0.03 log10 gene copies per 100 mL), and a principal component analysis revealed that storm drain effluent retention in a pond beneficially altered water characteristics, making them more like those of the receiving river. In conclusion, onsite qPCR assays can be performed with portable equipment items to quickly test water.

Detection of Eight Cannabinoids and One Tracer in Wastewater and River Water by SPE-UPLC–ESI-MS/MS

The consumption of illicit drugs represents a global social and economic problem. Using suitable analytical methods, monitoring, and detection of different illegal drugs residues and their metabolites in wastewater samples can help combat this problem. Our article defines a method to develop, validate, and practically applicate a rapid and robust analytical process for the evaluation of six naturally occurring cannabinoids (CBG, CBD, CBDV, CBN, THC, THCV), two cannabinoids in acidic form (CBDA, THCA-A), and the major cannabis-related human metabolite (THC-COOH). After SPE offline enrichment, we used a UPLC–ESI-MS/MS system, which permitted the determination of several by-products. Studied matrices were samples of different origins: (i) effluent water from a wastewater treatment plant in the Porto urban area;(ii) environmental water from Febros River, the last left-bank tributary of the Douro River. The multi-residue approach was substantiated and successfully employed to analyze the water samples collected in the above locations. The rapid and precise quantification of nine different cannabinoids in different water samples occurred within nine minutes at the ng L−1 level. The appearance of dozens of ng L−1 of some cannabis secondary metabolites, such as CBD, CBDA, CBN, THCA-A, indicates this plant species’ widespread usage among the general population in the considered area.

Effects of COVID-19 pandemic lockdown on microbial and metals contaminations in a part of Thirumanimuthar River, South India: A comparative health hazard perspective.

Twenty-two water samples from the Thirumanimuthar River course in southern India were collected before COVID-19 lockdown and during COVID-19 lockdown periods and were analyzed for microbiological parameters (fecal coliform bacteria, total coliform bacteria, Escherichia coli, and fecal streptococci) and heavy metals (Fe, Mn, Zn, Cu, Cd, Ni, Pb and Cr). The lockdown has decreased microbial populations and heavy metals. Fe, Cu, Cd, Ni, Pb and Cr exceeded the drinking water limits, respectively, in 77%, 45%, 27%, 18%, 9% and 91% of the pre-lockdown samples. During the lockdown period, Fe, Cu and Cd concentrations in 23% and Cr in 50% of the samples exceeded the limits. Heavy Metal Pollution Index (PI) expressed that 27%, 64% and 9% of the pre-lockdown samples represented 'low', 'medium' and 'high' pollution categories, respectively, but 68% and 32% of the lockdown period samples represented 'low' and 'medium' categories, respectively. The Metal Index (MI) exposed that all samples of pre-lockdown were under the seriously affected category, whereas 54% and 46% of lockdown samples were under strongly and seriously affected categories, respectively. Health risk evaluation predicted that 95%, 91% and 86% of pre-lockdown samples and 45%, 36% and 33% of lockdown period samples were at risk among children, teenagers and adults, respectively. As there is no integrated study on river water quality of COVID-19 lockdown this work is uniquely carried out by combining heavy metal pollution, microbial contamination and human health risk evaluation.

Decay of infectious SARS-CoV-2 and surrogates in aquatic environments.

The introduction of SARS-CoV-2 containing human stool and sewage into water bodies may raise public health concerns. However, assessment of public health risks by faecally contaminated water is limited by a lack of knowledge regarding the persistence of infectious SARS-CoV-2 in water. In the present study the decay rates of viable infectious SARS-CoV-2 and SARS-CoV-2 RNA were determined in river and seawater at 4 and 20°C. These decay rates were compared to S. typhimurium bacteriophage MS2 and pepper mild mottle virus (PMMoV). Persistence of viable SARS-CoV-2 was temperature dependent, remaining infectious for significantly longer periods of time in both freshwater and seawater at 4°C than at 20°C. T90 for infectious SARS-CoV-2 in river water was 2.3 days and 3.8 days at 20°C and 4°C, respectively. The T90 values were 1.1 days and 2.2 days in seawater at 20°C and 4°C, respectively. In contrast to the rapid inactivation of infectious SARS-CoV-2 in river and sea water, viral RNA was relatively stable. The RNA decay rates were increased in non-sterilised river and seawater, presumably due to the presence of microbiota. The decay rates of infectious MS2, MS2 RNA and PMMoV RNA differed significantly from the decay rate of SARS-CoV-2 RNA, suggesting that their use as surrogate markers for the persistence of SARS-CoV-2 in the environment is limited.

First environmental surveillance for the presence of SARS-CoV-2 RNA in wastewater and river water in Japan.

Wastewater-based epidemiology is a powerful tool to understand the actual incidence of coronavirus disease 2019 (COVID-19) in a community because severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, can be shed in the feces of infected individuals regardless of their symptoms. The present study aimed to assess the presence of SARS-CoV-2 RNA in wastewater and river water in Yamanashi Prefecture, Japan, using four quantitative and two nested PCR assays. Influent and secondary-treated (before chlorination) wastewater samples and river water samples were collected five times from a wastewater treatment plant and three times from a river, respectively, between March 17 and May 7, 2020. The wastewater and river water samples (200-5000 mL) were processed by using two different methods: the electronegative membrane-vortex (EMV) method and the membrane adsorption-direct RNA extraction method. Based on the observed concentrations of indigenous pepper mild mottle virus RNA, the EMV method was found superior to the membrane adsorption-direct RNA extraction method. SARS-CoV-2 RNA was successfully detected in one of five secondary-treated wastewater samples with a concentration of 2.4 × 103 copies/L by N_Sarbeco qPCR assay following the EMV method, with sequence confirmation of the qPCR product, whereas all the influent samples were tested negative for SARS-CoV-2 RNA. This result could be attributed to higher limit of detection for influent (4.0 × 103-8.2 × 104 copies/L) with a lower filtration volume (200 mL) compared to that for secondary-treated wastewater (1.4 × 102-2.5 × 103 copies/L) with a higher filtration volume of 5000 mL. None of the river water samples tested positive for SARS-CoV-2 RNA. Comparison with the reported COVID-19 cases in Yamanashi Prefecture showed that SARS-CoV-2 RNA was detected in the secondary-treated wastewater sample when the cases peaked in the community. This is the first study reporting the detection of SARS-CoV-2 RNA in wastewater in Japan.