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

Nature Biotechnology, Год журнала: 2022, Номер 40(12), С. 1814 - 1822

Опубликована: Июль 18, 2022

Язык: Английский

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Wastewater monitoring can anchor global disease surveillance systems

The Lancet Global Health, Год журнала: 2023, Номер 11(6), С. e976 - e981

Опубликована: Май 17, 2023

To inform the development of global wastewater monitoring systems, we surveyed programmes in 43 countries. Most monitored predominantly urban populations. In high-income countries (HICs), composite sampling at centralised treatment plants was most common, whereas grab from surface waters, open drains, and pit latrines more typical low-income middle-income (LMICs). Almost all analysed samples in-country, with an average processing time 2·3 days HICs 4·5 LMICs. Whereas 59% regularly for SARS-CoV-2 variants, only 13% LMICs did so. share their data internally, partnering organisations, but not publicly. Our findings show richness existing ecosystem. With additional leadership, funding, implementation frameworks, thousands individual initiatives can coalesce into integrated, sustainable network disease surveillance-one that minimises risk overlooking future health threats.

Язык: Английский

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

Water Research, Год журнала: 2022, Номер 219, С. 118535 - 118535

Опубликована: Май 3, 2022

Язык: Английский

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Passive sampling to scale wastewater surveillance of infectious disease: Lessons learned from COVID-19

The Science of The Total Environment, Год журнала: 2022, Номер 835, С. 155347 - 155347

Опубликована: Апрель 21, 2022

Much of what is known and theorized concerning passive sampling techniques has been developed considering chemical analytes. Yet, historically, biological analytes, such as Salmonella typhi, have collected from wastewater via with Moore swabs. In response to the COVID-19 pandemic, re-emerging a promising technique monitor SARS-CoV-2 RNA in wastewater. Method comparisons disease surveillance using composite, grab, for detection found variety materials routinely produced qualitative results superior grab samples useful sub-sewershed COVID-19. Among individual studies, concentrations derived samplers demonstrated heterogeneous correlation paired composite ranging weak (R2 = 0.27, 0.31) moderate 0.59) strong 0.76). sampler materials, electronegative membranes shown great promise linear uptake observed exposure durations 24 48 h several cases positivity on par samples. Continuing development methods infectious diseases diverse forms fecal waste should focus optimizing efficient recovery kit-free extraction, resource-efficient testing capable rapidly producing or quantitative data. With refinements could prove be fundamental tool scaling disease, especially among 1.8 billion persons living low-resource settings served by non-traditional collection infrastructure.

Язык: Английский

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Comparative Assessment of Filtration- and Precipitation-Based Methods for the Concentration of SARS-CoV-2 and Other Viruses from Wastewater

Microbiology Spectrum, Год журнала: 2022, Номер 10(4)

Опубликована: Авг. 11, 2022

Wastewater-based epidemiology (WBE) has been widely used to track levels of SARS-CoV-2 infection in the community during COVID-19 pandemic. Due rapid expansion WBE, many methods have and developed for virus concentration detection wastewater. However, very little information is available on relative performance these approaches. In this study, we compared five commonly wastewater quantification pathogenic viruses (SARS-CoV-2, norovirus, rotavirus, influenza, measles viruses), fecal indicator (crAssphage, adenovirus, pepper mild mottle virus), process control (murine norovirus bacteriophage Phi6) laboratory spiking experiments. The evaluated included those based either ultrafiltration (Amicon centrifugation units InnovaPrep device) or precipitation (using polyethylene glycol [PEG], beef extract-enhanced PEG, ammonium sulfate). two best were further tested 115 unspiked samples. We found that volume composition characteristics target greatly affected recovery, regardless method concentration. All are suitable routine concentration; however, Amicon PEG yielded recoveries. recommend use ultrafiltration-based low sample volumes with high titers precipitation-based rare pathogen high-volume IMPORTANCE As wastewater-based utilized surveillance at level countries, it crucial develop validate reliable sewage. most important step viral efficient particles and/or their genome subsequent analysis. different dead-end also discovered physico-chemical properties a great effect recovery. Hence, start should be carefully selected ongoing future national programs beyond.

Язык: Английский

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SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs

Nature Genetics, Год журнала: 2023, Номер 55(1), С. 26 - 33

Опубликована: Янв. 1, 2023

The first step in SARS-CoV-2 genomic surveillance is testing to identify people who are infected. However, global rates falling as we emerge from the acute health emergency and remain low many low- middle-income countries (mean = 27 tests per 100,000 day). We simulated COVID-19 epidemics a prototypical country investigate how rates, sampling strategies sequencing proportions jointly impact outcomes, showed that spatiotemporal biases delay time detection of new variants by weeks months can lead unreliable estimates variant prevalence, even when proportion samples sequenced increased. Accordingly, investments wider access diagnostics support approximately 100 day could enable more timely reliable prevalence. performance programs fundamentally limited diagnostic testing.

Язык: Английский

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Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing

PLoS ONE, Год журнала: 2023, Номер 18(4), С. e0284483 - e0284483

Опубликована: Апрель 21, 2023

SARS-CoV-2 surveillance of viral populations in wastewater samples is recognized as a useful tool for monitoring epidemic waves and boosting health preparedness. Next generation sequencing RNA isolated from convenient cost-effective strategy to understand the molecular epidemiology provide insights on population dynamics variants at community level. However, low- middle-income countries, groups have performed data has not been extensively shared scientific community. Here we report results co-circulation abundance concern (VOCs) Uruguay, small country Latin America, between November 2020—July 2021 using surveillance. was characterized by targeted Receptor Binding Domain region within spike gene. Two computational approaches were used track variants. The analysis showed transition overall predominance No-VOCs successive VOCs, agreement with clinical nasal swabs. mutations K417T, E484K N501Y, that characterize Gamma VOC, detected early December 2020, several weeks before first case reported. Interestingly, non-synonymous mutation described Delta L452R, very low frequency since April when recently sequence (SAM Refiner). Wastewater NGS-based reliable complementary introduction prevalence VOCs level allowing public decisions. This approach allows tracking symptomatic asymptomatic individuals, who are generally under-reported countries limited testing capacity. Our suggests wastewater-based can contribute improving responses countries.

Язык: Английский

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A narrative review of wastewater surveillance: pathogens of concern, applications, detection methods, and challenges

Frontiers in Public Health, Год журнала: 2024, Номер 12

Опубликована: Июль 30, 2024

The emergence and resurgence of pathogens have led to significant global health challenges. Wastewater surveillance has historically been used track water-borne or fecal-orally transmitted pathogens, providing a sensitive means monitoring within community. This technique offers comprehensive, real-time, cost-effective approach disease surveillance, especially for diseases that are difficult monitor through individual clinical screenings.

Язык: Английский

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Critical Needs for Integrated Surveillance: Wastewater-Based and Clinical Epidemiology in Evolving Scenarios with Lessons Learned from SARS-CoV-2

Food and Environmental Virology, Год журнала: 2024, Номер 16(1), С. 38 - 49

Опубликована: Янв. 2, 2024

Abstract During the COVID-19 pandemic, wastewater-based epidemiology (WBE) and clinical surveillance have been used as tools for analyzing circulation of SARS-CoV-2 in community, but both approaches can be strongly influenced by some sources variability. From challenging perspective integrating environmental data, we performed a correlation analysis between concentrations raw sewage incident cases areas served medium-size wastewater treatment plants (WWTPs) from 2021 to 2023. To this aim, datasets were adjusted several variability: WBE data factors including analytical protocol, flow, population size, while adjustments considered demographic composition population. Then, addressed impact on differences among sewerage networks variations frequency type swab tests due changes political regulatory scenarios. Wastewater significantly correlated when restrictive containment measures limited movements effect ( ρ = 0.50) confirmed exclusively through molecular testing 0.49). Moreover, positive (although weak) arose WWTPs located densely populated 0.37) with shorter lengths 0.28). This study provides methodological interpreting which could also useful other infections. Data evaluation possible bias need carefully integrated

Язык: Английский

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Wastewater Genomic Surveillance Captures Early Detection of Omicron in Utah

Microbiology Spectrum, Год журнала: 2023, Номер 11(3)

Опубликована: Май 8, 2023

Wastewater-based epidemiology has emerged as a powerful public health tool to trace new outbreaks, detect trends in infection, and provide an early warning of COVID-19 community spread. Here, we investigated the spread SARS-CoV-2 infections across Utah by characterizing lineages mutations detected wastewater samples. We sequenced over 1,200 samples from 32 sewersheds collected between November 2021 March 2022. Wastewater sequencing confirmed presence Omicron (B.1.1.529) on 19, 2021, up 10 days before its corresponding detection via clinical sequencing. Analysis diversity revealed Delta most frequently lineage during (67.71%), but it started declining December with onset (B.1.1529) sublineage BA.1 (6.79%). The proportion increased ~58% January 4, 2022, completely displaced February 7, genomic surveillance BA.3, that was not identified Utah's surveillance. Interestingly, several Omicron-defining began appear prevalence January, aligning surge cases. Our study highlights importance tracking epidemiologically relevant detecting emerging stages outbreak. provides unbiased representation community-wide infection dynamics is excellent complementary surveillance, potential guiding action policy decisions. IMPORTANCE SARS-CoV-2, virus responsible for pandemic, had significant impact health. Global emergence novel variants, shift at-home tests, reduction tests demonstrate need reliable effective strategy contain Monitoring viruses way establish baseline levels complement efforts. particular, can valuable insights into evolution variants. characterized using whole-genome introduction B.1.1.519 (Omicron) Utah. data showed appeared prior patient samples, indicating signal. findings are important perspective timely identification communities high transmission could help guide interventions.

Язык: Английский

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