SARS-CoV-2 in a stream running through an underprivileged, underserved, urban settlement in São Paulo, Brazil: A 7-month follow-up

Analysis of chlorhexidine, antibiotics and bacterial community composition in water environments from Brazil, Cameroon and Madagascar during the COVID-19 pandemic

The widespread of chlorhexidine and antibiotics in the water bodies, which grew during the global COVID-19 pandemic, can increase the dispersion of antibiotic resistance. We assessed the occurrence of these pharmaceutical compounds as well as SARS-CoV-2 and analysed the bacterial community structure of hospital and urban wastewaters from Brazil, Cameroon, and Madagascar. Water and wastewater samples (n = 59) were collected between January-June 2022. Chlorhexidine, azithromycin, levofloxacin, ceftriaxone, gentamicin and meropenem were screened by Ultra-High-Performance Liquid Chromatography coupled with mass spectrometer. SARS-CoV-2 was detected based on the nucleocapsid gene (in Cameroon and Madagascar), and envelope and spike protein-encoding genes (in Brazil). The total community-DNA was extracted and used for bacterial community analysis based on the 16S rRNA gene. To unravel likely interaction between pharmaceutical compounds and/or SARS-CoV-2 with the water bacterial community, multivariate statistics were performed. Chlorhexidine was found in hospital wastewater effluent from Brazil with a maximum concentration value of 89.28 μg/L. Additionally, antibiotic residues such as azithromycin and levofloxacin were also present at concentrations between 0.32-7.37 μg/L and 0.11-118.91 μg/L, respectively. In Cameroon, azithromycin was the most found antibiotic present at concentrations from 1.14 to 1.21 μg/L. In Madagascar instead, ceftriaxone (0.68-11.53 μg/L) and levofloxacin (0.15-0.30 μg/L) were commonly found. The bacterial phyla statistically significant different (P < 0,05) among participating countries were Proteobacteria, Patescibacteria and Dependentiae which were mainly abundant in waters sampled in Africa and, other phyla such as Firmicutes, Campylobacterota and Fusobacteriota were more abundant in Brazil. The phylum Caldisericota was only found in raw hospital wastewater samples from Madagascar. The canonical correspondence analysis results suggest significant correlation of azithromycin, meropenem and levofloxacin with bacteria families such as Enterococcaceae, Flavobacteriaceae, Deinococcaceae, Thermacetogeniaceae and Desulfomonilaceae, Spirochaetaceae, Methanosaetaceae, Synergistaceae, respectively. Water samples were also positive for SARS-CoV-2 with the lowest number of hospitalized COVID-19 patients in Madagascar (n = 7) and Brazil (n = 30). Our work provides new data about the bacterial community profile and the presence of pharmaceutical compounds in the hospital effluents from Brazil, Cameroon, and Madagascar, whose limited information is available. These compounds can exacerbate the spreading of antibiotic resistance and therefore pose a risk to public health.

Cross-continental comparative experiences of wastewater surveillance and a vision for the 21st century

The COVID-19 pandemic has brought the epidemiological value of monitoring wastewater into sharp focus. The challenges of implementing and optimising wastewater monitoring vary significantly from one region to another, often due to the array of different wastewater systems around the globe, as well as the availability of resources to undertake the required analyses (e.g. laboratory infrastructure and expertise). Here we reflect on the local and shared challenges of implementing a SARS-CoV-2 monitoring programme in two geographically and socio-economically distinct regions, São Paulo state (Brazil) and Wales (UK), focusing on design, laboratory methods and data analysis, and identifying potential guiding principles for wastewater surveillance fit for the 21st century. Our results highlight the historical nature of region-specific challenges to the implementation of wastewater surveillance, including previous experience of using wastewater surveillance, stakeholders involved, and nature of wastewater infrastructure. Building on those challenges, we then highlight what an ideal programme would look like if restrictions such as resource were not a constraint. Finally, we demonstrate the value of bringing multidisciplinary skills and international networks together for effective wastewater surveillance.

Incomplete sanitation in the Metropolitan Region of São Paulo results in detection of SARS-CoV-2 in headwater streams

Among the largest metropolitan regions in the world, the Metropolitan Region of São Paulo (MRSP) represents an important case study for the COVID-19 respiratory disease pandemic because it is home to >20 million people, making it one of the largest metropolitan regions in the global south. Besides the high population density, the MRSP has several problems related to social and economic aspects, which may reflect in the dynamics of SARS-CoV-2 virus, such as low income, lack of sanitation and social vulnerability in the peripheral regions of MRSP. In these regions, the input of untreated sewage on the streams and rivers can be frequently observed, which may represent an indicator of poor sewer system. Therefore, this study aimed to identify if streams draining urbanized regions without appropriate sanitation are prone to receive higher loads of detectable SARS-CoV-2 in its waters. For this, we collected water samples from 45 headwater streams distributed across an urbanization gradient (0-100 % of urbanization) in the MRSP, with three replicates in each stream and analyzed the concentrations of SARS-CoV-2 RNA targeting the nucleocapsid N1 and N2 genomic regions. In addition, we analyzed the relationship between the concentrations of SARS-CoV-2 RNA and sanitation and social variables. Our results showed that the concentrations of SARS-CoV-2 RNA were higher in the streams draining medium to high urbanized catchments, especially because of the lack of sanitation and the higher probabilities to detect SARS-CoV-2 RNA in the stream water was associated with households without a septic tank or sewage system within the catchment, followed by per capita household income. These results reflect the lack of urbanization planning and the lack of sanitation, especially in the poor regions from the MRSP, adding another risk for the already vulnerable population in a metropolitan region from the global south during a pandemic disease.

Environmental monitoring of SARS-CoV-2 in the metropolitan area of Porto Alegre, Rio Grande do Sul (RS), Brazil

Since starts the coronavirus disease 2019 (COVID-19) pandemic identified the presence of genomic fragments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in various environmental matrices: domestic sewage, surface waters, and contaminated freshwater. Environmental monitoring of SARS-CoV-2 is a tool for evaluating trend curves over the months, compared to several clinical cases of the disease. The objective of this study was to monitor the SARS-CoV-2 in environmental samples collected in different sites in a metropolitan area of Porto Alegre, Southern Brazil. During 10 months from 2020 to 2021, 300 samples were collected weekly and biweekly from nine points located in 3 cities: one point from a wastewater treatment plant (WWTP) in São Leopoldo (fortnightly collection), two points in Dilúvio Stream in Porto Alegre (fortnightly collection), two points in Pampa and Luiz Rau Streams (weekly collection), and two points in public fountains (fortnightly collection) in Novo Hamburgo. After collection, samples were concentrated by ultracentrifugation, and viral nucleic acids were extracted using MagMax® Core Nucleic Acid Purifications kits and submitted to RT-qPCR, using E, N1, and N2 gene targets of SARS-CoV-2. Only 7% (3/41) samples from public fountains were positive, with a mean viral load (VL) of SARS-CoV-2 RNA of 5.02 × 101 gc/l (2.41~8.59 × 101 gc/l), while the streams had average VL of 7.43 × 105 gc/l (Pampa), 7.06 × 105 gc/l (Luiz Rau), 2.01 × 105 gc/l (Dilúvio), and 4.46 × 105 cg/l (WWTP). The results showed varying levels of viral presence in different sample types, with a demonstrated correlation between environmental viral load and clinical COVID-19 cases. These findings contribute to understanding virus persistence and transmission pathways in the environment. Continuous monitoring, especially in less developed regions, is crucial for early detection of vaccine resistance, new variants, and potential COVID-19 resurgence.

20-Month monitoring of SARS-CoV-2 in wastewater of Curitiba, in Southern Brazil

The COVID-19 pandemic resulted in the collapse of healthcare systems and led to the development and application of several approaches of wastewater-based epidemiology to monitor infected populations. The main objective of this study was to carry out a SARS-CoV-2 wastewater based surveillance in Curitiba, Southern Brazil Sewage samples were collected weekly for 20 months at the entrance of five treatment plants representing the entire city and quantified by qPCR using the N1 marker. The viral loads were correlated with epidemiological data. The correlation by sampling points showed that the relationship between the viral loads and the number of reported cases was best described by a cross-correlation function, indicating a lag between 7 and 14 days amidst the variables, whereas the data for the entire city presented a higher correlation (0.84) with the number of positive tests at lag 0 (sampling day). The results also suggest that the Omicron VOC resulted in higher titers than the Delta VOC. Overall, our results showed that the approach used was robust as an early warning system, even with the use of different epidemiological indicators or changes in the virus variants in circulation. Therefore, it can contribute to public decision-makers and health interventions, especially in vulnerable and low-income regions with limited clinical testing capacity. Looking toward the future, this approach will contribute to a new look at environmental sanitation and should even induce an increase in sewage coverage rates in emerging countries.

Contribution of wastewater-based epidemiology to SARS-CoV-2 screening in Brazil and the United States

Wastewater-based epidemiology (WBE) is a valuable tool for investigating the existence, prevalence, and spread of pathogens, such as SARS-CoV-2, in a given population. WBE, proposed as part of the SARS-CoV-2 surveillance strategy for monitoring virus circulation, may complement clinical data and contribute to reducing the spread of the disease through early detection. In developing countries such as Brazil, where clinical data are scarce, information obtained from wastewater monitoring can be crucial for designing public health interventions. In the United States, the country with the largest number of confirmed SARS-CoV-2 cases worldwide, WBE programs have begun to be carried out to investigate correlations with coronavirus disease 2019 (COVID-19) clinical data and support health agencies in decision-making to prevent the spread of the disease. This systematic review aimed to assess the contribution of WBE to SARS-CoV-2 screening in Brazil and the United States and compare studies conducted in a developed and developing country. Studies in Brazil and the United States showed WBE to be an important epidemiological surveillance strategy in the context of the COVID-19 pandemic. WBE approaches are useful for early detection of COVID-19 outbreaks, estimation of clinical cases, and assessment of the effectiveness of vaccination program.

One-year surveillance of SARS-CoV-2 in wastewater from vulnerable urban communities in metropolitan São Paulo, Brazil

The current COVID-19 pandemic has emphasized the vulnerability of communities living in the urban outskirts and informal settlements. The lack of reliable COVID-19 case data highlights the importance and application of wastewater-based epidemiology. This study aimed to monitor the COVID-19 trends in four vulnerable urban communities (slums and low-income neighborhoods) in metropolitan São Paulo by assessing the SARS-CoV-2 RNA viral load in wastewater. We analyzed 160 samples from May 2020 to June 2021 with weekly or fortnightly samplings. The samples were ultracentrifuged with glycine elution and quantified by N1/N2 SARS-CoV-2 RT-qPCR. The results of positivity were 100% (Paraisópolis, Heliópolis and Cidade Tiradentes) and 76.9% (Vila Brasilândia). The new case numbers of COVID-19, counted from the onset of symptoms, positively correlated with SARS-CoV-2 N1 viral loads from the two largest communities (p<0.001). SARS-CoV-2 infectivity was tested in Vero E6 cells after concentration with the two techniques, ultrafiltration (Centricon^® Plus-70 10 kDa) and sucrose cushion ultracentrifugation, but none of the evaluated samples presented positive results. Next-generation sequencing (NGS) analysis from samples collected in March and August 2021 revealed the presence of the clade 20 J (lineage P.1) belonging to the most prevalent circulating variant in the country. Our results showed that wastewater surveillance data can be used as complementary indicators to monitor the dynamics and temporal trends of COVID-19. The infectivity test results strengthened the evidence of low risk of infection associated with SARS-CoV-2 in wastewater.