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

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Oct. 10, 2023

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

Language: Английский

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Wastewater based epidemiology as a public health resource in low- and middle-income settings.

Environmental Pollution, Journal Year: 2024, Volume and Issue: 351, P. 124045 - 124045

Published: April 25, 2024

In the face of emerging and re-emerging diseases, novel innovative approaches to population scale surveillance are necessary for early detection quantification pathogens. The last decade has seen rapid development wastewater environmental (WES) address public health challenges, which led establishment wastewater-based epidemiology (WBE) being deployed monitor a range hazards. WBE exploits fact that excretions secretions from urine, gut discharged in wastewater, particularly sewage, such sampling sewage systems provides an warning system disease outbreaks by providing indication pathogen circulation. While been mainly used locations with networked systems, here we consider its value less connected populations typical lower-income settings, assess opportunity afforded pit latrines sample communities localities. We propose where struggle access diagnostic facilities, despite several additional unconnected remains important means large relatively cost-effective manner.

Language: Английский

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Environmental surveillance and wastewater-based epidemiology for infectious diseases in Low and Middle Income Countries: A scoping review of mathematical modelling and analytical studies

Published: Feb. 7, 2025

Language: Английский

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Wastewater surveillance overcomes socio-economic limitations of laboratory-based surveillance when monitoring disease transmission: The South African experience during the COVID-19 pandemic

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(2), P. e0311332 - e0311332

Published: Feb. 25, 2025

Wastewater and environmental surveillance has been promoted as a communicable disease tool because it overcomes inherent biases in laboratory-based surveillance. Yet, little empirical evidence exists to support this notion, remains largely an intuitive, though highly plausible hypothesis. Our interdisciplinary study uses WES data show for underreporting of SARS-CoV-2 the context measurable statistically significant associations between economic conditions incidence testing rates. We obtained geolocated, anonymised, laboratory-confirmed cases, wastewater viral load socio-demographic Gauteng Province, South Africa. spatially located all create single dataset sewershed catchments served by two large treatment plants. conducted epidemiological, persons infected principal component analysis explore relationships variables. Overall, we demonstrate co-contributory influences socio-economic indicators on access cumulative incidence, thus reflecting that apparent rates mirror socioeconomic considerations rather than true epidemiology. These analyses how provides valuable information contextualise interpret epidemiological data. Whilst is useful have these established SARS-CoV-2, implications beyond are legion reasons, namely clinical broadly applicable across pathogens infecting humans will find their way into albeit varying quantities. should be implemented strengthen systems, especially where inequalities limit interpretability conventional

Language: Английский

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Analysis Insights to Support the Use of Wastewater and Environmental Surveillance Data for Infectious Diseases and Pandemic Preparedness

Epidemics, Journal Year: 2025, Volume and Issue: unknown, P. 100825 - 100825

Published: March 1, 2025

Wastewater-based epidemiology is the detection of pathogens from sewage systems and interpretation these data to improve public health. Its use has increased in scope since 2020, when it was demonstrated that SARS-CoV-2 RNA could be successfully extracted wastewater affected populations. In this Perspective we provide an overview recent advances pathogen within wastewater, propose a framework for identifying utility sampling suggest areas where analytics require development. Ensuring both collection analysis are tailored towards key questions at different stages epidemic will inference made. For analyses useful methods determine absence infection, early reliably estimate trajectories prevalence, detect novel variants without reliance on consensus sequences. This research area included many innovations have improved collected optimistic innovation continue future.

Language: Английский

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Recent Technologies for the Determination of SARS‐CoV‐2 in Wastewater

ChemistrySelect, Journal Year: 2025, Volume and Issue: 10(13)

Published: April 1, 2025

Abstract The COVID‐19 pandemic outbreak raised major concerns in public health globally, raising the crucial need for development of methods to monitor spread communities worldwide. Wastewater‐based epidemiology (WBE) surveillance has been used as a novel tool outbreaks because its affordability and efficiency tracking infectious contaminants. Unlike other means tracking, wastewater is independent individuals having accessibility healthcare, doctor visits, or infection testing availability. Consequently, considerable awareness complete infections, including at community level. In WBE studies, polymerase chain reaction‐based (PCR) techniques are referred “gold‐standard” method detecting SARS‐CoV‐2 many countries. Nevertheless, despite extensive sensitive selective PCR‐based methods, these have shown some limitations that hinder their application, such requirement repeated heating cooling cycles analysis time 3–4 h. alternative do not rely on same consumables conventionally employed electrochemical biosensing, environmental water samples offers favorable advantages improved turnaround times portability. However, currently highly focused clinical applications than wastewater. This review focuses disadvantages associated with conventional alternative: electrochemical‐bioreceptor‐based technique SARS‐CoV‐2. addition, highlights broad use WBE, binding affinity various bioreceptors toward viral proteins, enhancing analytical properties biosensors integration techniques. integrated systems, especially, electrochemical‐CRISPR based, high sensitivities (down concentrations atto‐molar), potential application low‐resource areas.

Language: Английский

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Harnessing methods, data analysis, and near-real-time wastewater monitoring for enhanced public health response using high throughput sequencing.

Environmental Research, Journal Year: 2025, Volume and Issue: unknown, P. 121633 - 121633

Published: April 1, 2025

Language: Английский

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Wastewater-integrated pathogen surveillance dashboards enable real-time, transparent, and interpretable public health risk assessment and dissemination

PLOS Global Public Health, Journal Year: 2025, Volume and Issue: 5(5), P. e0004443 - e0004443

Published: May 5, 2025

Timely pathogen surveillance and reporting is essential for effective public health guidance. Web dashboards have become a key tool communicating information to stakeholders, care workers, the broader community. Over SARS-CoV-2 pandemic, wastewater has increasingly been incorporated into workflows outbreak monitoring response, enabling community-representative low-cost supplement clinical surveillance. However, methods used visualization dissemination of data differ across programs, best practices are yet be defined. In this work, we demonstrate perform wastewater-based in tandem with local national scales, leveraging custom-built, reproducible, open-source software. Using centralized aggregation analysis hub approach, establish multiple pipelines storage, wrangling, standardized analyses, deploy custom-built web that allow immediate release. We find our approach computing architectures, strategies, provides an adaptable model incorporate additional pathogens epidemiological data.

Language: Английский

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Molecular epidemiology of SARS-CoV-2 in Northern South Africa: wastewater surveillance from January 2021 to May 2022

Frontiers in Public Health, Journal Year: 2023, Volume and Issue: 11

Published: Dec. 19, 2023

Introduction Wastewater-based genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) provides a comprehensive approach to characterize evolutionary patterns and distribution viral types in population. This study documents the molecular epidemiology SARS-CoV-2, Northern South Africa, from January 2021 May 2022. Methodology A total 487 wastewater samples were collected influent eight treatment facilities tested for SARS-CoV-2 RNA using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). positive with genome copies/mL ≥1,500 subjected allele-specific genotyping (ASG) targeting Spike protein; 75 whole sequencing (WGS) on ATOPlex platform. Variants concern (VoC) lineages assigned Nextclade PangoLIN Software. Concordance VoC between ASG WGS analyses was determined. Sequence relationship determined by phylogenetic analysis. Results Seventy-five percent (365/487) RNA. Delta Omicron more predominant at prevalence 45 32%, respectively, they detected as early February 2021, while Beta least 5%. 11/60 (18%) sequences clades only, but not specific name. Phylogenetic analysis used investigate these other sequences, further them. variant assignment seen 51.2% sequences. There intra-variant diversity among sequences; mutation E484K absent. Three previously undescribed mutations (A361S, V327I, D427Y) VoC. Discussion Conclusion The detection VoCs sites earlier outbreak than has been reported regions Africa highlights importance population-based approaches over individual sample-based surveillance. Inclusion non-Spike protein targets could improve specificity ASG, since all share similar mutations. Finally, continuous application sensitive technologies such next generation (NGS) is necessary documentation whose implications when investigated enhance diagnostics, vaccine development efforts.

Language: Английский

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Leveraging wastewater-based epidemiology to monitor the spread of neglected tropical diseases in African communities

Infectious Diseases, Journal Year: 2024, Volume and Issue: 56(9), P. 697 - 711

Published: June 26, 2024

Neglected tropical diseases continue to cause a significant burden worldwide, with Africa accounting for more than one-third of the global burden. Over past decade, progress has been made in eliminating, controlling, and eradicating these Africa. By December 2022, 47 out 54 African countries had eliminated at least one neglected disease, were close achieving this milestone. Between 2020 2021, there was an 80 million reduction people requiring intervention. However, continued efforts are needed manage address their social economic burden, as they deepen marginalisation stigmatisation. Wastewater-based epidemiology involves analyzing wastewater detect quantify biomarkers disease-causing pathogens. This approach can complement current disease surveillance systems provide additional layer information monitoring spread detecting outbreaks. is particularly important due limited traditional methods. also provides tsunami-like warning system outbreaks facilitate timely intervention optimised resource allocation, providing unbiased reflection community's health compared systems. In review, we highlight potential wastewater-based innovative transmission within communities improving existing Our analysis shows that enhance Africa, early detection management Buruli ulcers, hookworm infections, ascariasis, schistosomiasis, dengue, chikungunya, echinococcosis, rabies, cysticercosis better control.

Language: Английский

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