Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

Nature, Journal Year: 2022, Volume and Issue: 609(7925), P. 101 - 108

Published: July 7, 2022

Abstract As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing infeasible at scale, especially in areas with limited resources, participation, or and/or sequencing capacity, which can also introduce biases 1–3 . RNA concentration wastewater successfully tracks regional infection dynamics provides less biased abundance estimates than 4,5 Tracking virus genomic sequences would improve community detect variants. However, two factors limit wastewater-based surveillance: low-quality sequence data inability estimate relative mixed samples. Here we resolve these issues perform a high-resolution, 295-day effort, the controlled environment of large university campus broader context surrounding county. We developed deployed improved protocols deconvolution software that fully multiple strains from wastewater. detected concern up 14 days earlier samples, identified instances not captured surveillance. Our study scalable solution surveillance allows detection identification cryptic transmission.

Language: Английский

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Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale

Nature Biotechnology, Journal Year: 2022, Volume and Issue: 40(12), P. 1814 - 1822

Published: July 18, 2022

Language: Английский

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Wastewater analysis can be a powerful public health tool—if it’s done sensibly

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(6)

Published: Feb. 3, 2022

The coronavirus disease 2019 (COVID-19) pandemic sparked an explosion of interest in wastewater-based epidemiology (WBE; also known as wastewater monitoring or surveillance). Much has been said, the scientific literature and popular press alike, about public health value tracking severe acute respiratory syndrome 2 (SARS-CoV-2) wastewater. Emergence spread omicron variant recently pushed WBE for COVID-19 management back into headlines. Unfortunately, coverage potential is rarely balanced by a practical discussion limitations tradeoffs, especially when it comes to issues beyond technical challenges encountered lab. Sometimes makes sense way monitor outbreaks other threats, sometimes constraints argue spending scarce resources elsewhere. We grapple with such frequently while managing program Healthy Davis Together (HDT), multi-pronged pandemic-response initiative Davis, CA. Since launching September 2020, grown include in-house analysis collected on weekly, triweekly, daily basis from 70 sites distributed across City University California, (UC Davis) campus sewer systems influent their treatment plants. are glad that our data informing local mitigation efforts. Results UC dorm outflows supporting safe return students campus; results neighborhoods broader city areas helping officials understand spatial changes trends react accordingly. At same time, running campaign requires significant investments money, labor, expertise. Given much information gleaned not directly actionable, and/or duplicates sources, prudent consider these worthwhile. … [↵][1]1To whom correspondence may be addressed. Email: hbischel{at}ucdavis.edu. [1]: #xref-corresp-1-1

Language: Английский

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Early warning of a COVID-19 surge on a university campus based on wastewater surveillance for SARS-CoV-2 at residence halls

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 821, P. 153291 - 153291

Published: Jan. 25, 2022

As COVID-19 continues to spread globally, monitoring the disease at different scales is critical support public health decision making. Surveillance for SARS-CoV-2 RNA in wastewater can supplement surveillance based on diagnostic testing. In this paper, we report results of wastewater-based Emory University campus that included routine sampling sewage from a hospital building, an isolation/quarantine and 21 student residence halls between July 13th, 2020 March 14th, 2021. We examined sensitivity detecting cases building level relation Ct values RT-qPCR samples number patients residing building. Our show weekly using Moore swab was not sensitive enough (6 63 times) reliably detect one or two sporadic The over time same location reflected temporal trend (Pearson's r < −0.8), but there too much uncertainty directly estimate values. After students returned spring 2021 semester, detected most hall sites weeks before surged campus. This finding suggests be used provide early warning outbreaks institutions.

Language: Английский

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Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond

Clinical Microbiology Reviews, Journal Year: 2023, Volume and Issue: 37(1)

Published: Dec. 14, 2023

SUMMARY Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of coronavirus disease 2019 (COVID-19) pandemic. The power and potential this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical within monitored populations but also, fact, functioned as a leading indicator. Teams from across globe innovated novel approaches by which wastewater could be collected diverse sewersheds ranging treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods high-risk buildings such long-term care facilities (LTCF). Efficient processes enabled extraction concentration highly dilute matrix. Molecular genomic tools identify, quantify, characterize its various variants adapted programs applied these mixed environmental systems. Novel data-sharing allowed information mobilized made immediately available public health government decision-makers even public, enabling evidence-informed decision-making based on local dynamics. WBS since been recognized tool transformative potential, providing near-real-time cost-effective, objective, comprehensive, inclusive data changing prevalence measured analytes space time populations. However, consequence rapid innovation hundreds teams simultaneously, tremendous heterogeneity currently exists literature. This manuscript provides state-of-the-art review established details current work underway expanding scope other infectious targets.

Language: Английский

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Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet

Microbiology and Molecular Biology Reviews, Journal Year: 2023, Volume and Issue: 87(3)

Published: June 27, 2023

Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, water filtration. are also intimately associated with complex multicellular organisms such as humans, other animals, plants, insects perform crucial the health of their hosts. Although we starting to understand microbiomes in different systems interconnected, there is still a poor understanding microbiome transfer connectivity. In this review show how connected within transferred between habitats discuss functional consequences these connections. Microbiome occurs abiotic (e.g., air, soil, water) biotic environments, can either be mediated through vectors or food) direct interactions. Such processes may include transmission pathogens antibiotic resistance genes. However, here, highlight fact positive effects on human where transmitted microorganisms potentially providing novel adaptation ecosystems.

Language: Английский

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Making waves: Wastewater surveillance of SARS-CoV-2 in an endemic future

Water Research, Journal Year: 2022, Volume and Issue: 219, P. 118535 - 118535

Published: May 3, 2022

Language: Английский

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Citywide wastewater SARS-CoV-2 levels strongly correlated with multiple disease surveillance indicators and outcomes over three COVID-19 waves

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 855, P. 158967 - 158967

Published: Sept. 24, 2022

Language: Английский

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Wastewater surveillance of SARS-CoV-2 and chemical markers in campus dormitories in an evolving COVID − 19 pandemic

Journal of Hazardous Materials, Journal Year: 2022, Volume and Issue: 446, P. 130690 - 130690

Published: Dec. 28, 2022

In this study, we report the implementation of a comprehensive wastewater surveillance testing program at university campus in Singapore to identify Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infected individuals and usage pharmaceuticals personal care products (PPCPs) as well other emerging contaminants (ECs). This unique co-monitoring simultaneously measured SARS-CoV-2 with chemical markers/contaminants COVID-19 situation evolved from pandemic endemic stages, following nationwide mass vaccination drive. RNA concentrations dormitories were using real-time reverse transcription-polymerase chain reaction (RT-qPCR) corroborated number symptomatic cases confirmed antigen rapid test (ART). Consistent results observed where detected increased proportionately residing on campus. Similarly, wide range ECs, including disinfectants antibiotics, through sensitive liquid chromatography tandem spectrometry (LC-MS/MS) techniques establish PPCPs consumption patterns during various stages Singapore. Statistical correlation was few ECs belonging disinfectants, PCPs antibiotics. A high concentration subsequent positive reported indicates that could serve marker such unprecedented times.

Language: Английский

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Wastewater-based monitoring of SARS-CoV-2 at UK airports and its potential role in international public health surveillance

PLOS Global Public Health, Journal Year: 2023, Volume and Issue: 3(1), P. e0001346 - e0001346

Published: Jan. 19, 2023

It is well established that air travel plays a key role in the global spread of many enteric and respiratory diseases, including COVID-19. Even with restrictions (e.g. mask wearing, negative COVID-19 test prior to departure), SARS-CoV-2 may be transmitted by asymptomatic or pre-symptomatic individuals carrying virus. Due limitation current clinical surveillance approaches, complementary methods need developed allow estimation frequency entry across international borders. Wastewater-based epidemiology (WBE) represents one such approach, allowing unbiased sampling carriage passenger cohorts entering via airports. In this study, we monitored sewage samples from terminals (n = 150) aircraft 32) at three major airports UK for 1–3 weeks March 2022. As raw were more turbid than typical municipal wastewater, used beef extract treatment followed polyethylene glycol (PEG) precipitation concentrate viruses, reverse transcription quantitative PCR (RT-qPCR) detection faecal indicator virus, crAssphage. All taken sewers arrival Heathrow Bristol airports, 85% sites Edinburgh airport, positive SARS-CoV-2. This suggests high prevalence among passengers and/or airport staff members. Samples derived also showed 93% positivity. No difference viral was found before after lifted. Our results suggest WBE useful tool monitoring transfer rate human pathogens other disease-causing agents borders should form part wider efforts monitor contain future disease outbreaks.

Language: Английский

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