The evolution of SARS-CoV-2

Nature Reviews Microbiology, Год журнала: 2023, Номер 21(6), С. 361 - 379

Опубликована: Апрель 5, 2023

Язык: Английский

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

Nature, Год журнала: 2022, Номер 609(7925), С. 101 - 108

Опубликована: Июль 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.

Язык: Английский

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Real-world COVID-19 vaccine effectiveness against the Omicron BA.2 variant in a SARS-CoV-2 infection-naive population

Nature Medicine, Год журнала: 2023, Номер 29(2), С. 348 - 357

Опубликована: Янв. 18, 2023

The SARS-CoV-2 Omicron variant has demonstrated enhanced transmissibility and escape of vaccine-derived immunity. Although first-generation vaccines remain effective against severe disease death, robust evidence on vaccine effectiveness (VE) all infections, irrespective symptoms, remains sparse. We used a community-wide serosurvey with 5,310 subjects to estimate how vaccination histories modulated risk infection in infection-naive Hong Kong during large wave BA.2 epidemic January-July 2022. estimated that infected 45% (41-48%) the local population. Three four doses BNT162b2 or CoronaVac were 7 days after (VE 48% (95% credible interval 34-64%) 69% (46-98%) for three BNT162b2, respectively; VE 30% (1-66%) 56% (6-97%) CoronaVac, respectively). At 100 immunization, waned 26% (7-41%) 35% (10-71%) 6% (0-29%) 11% (0-54%) CoronaVac. rapid waning conferred by an increasingly complex viral evolutionary landscape highlight necessity rapidly deploying updated followed vigilant monitoring VE.

Язык: Английский

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Wastewater surveillance of pathogens can inform public health responses

Nature Medicine, Год журнала: 2022, Номер 28(10), С. 1992 - 1995

Опубликована: Сен. 8, 2022

Язык: Английский

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

Clinical Microbiology Reviews, Год журнала: 2023, Номер 37(1)

Опубликована: Дек. 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.

Язык: Английский

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Impact of the COVID-19 pandemic on the prevalence of influenza A and respiratory syncytial viruses elucidated by wastewater-based epidemiology

The Science of The Total Environment, Год журнала: 2023, Номер 880, С. 162694 - 162694

Опубликована: Март 8, 2023

Since the COVID-19 pandemic, a decrease in prevalence of Influenza A virus (IAV) and respiratory syncytial (RSV) has been suggested by clinical surveillance. However, there may be potential biases obtaining an accurate overview infectious diseases community. To elucidate impact on IAV RSV, we quantified RSV RNA wastewater collected from three treatment plants (WWTPs) Sapporo, Japan, between October 2018 January 2023, using highly sensitive EPISENS™ method. From to April 2020, M gene concentrations were positively correlated with confirmed cases corresponding area (Spearman's r = 0.61). Subtype-specific HA genes also detected, their showed trends that consistent clinically reported cases. B serotypes detected wastewater, 0.36-0.52). The detection ratios decreased 66.7 % (22/33) 42.4 (14/33) 4.56 (12/263) 32.7 (86/263), respectively city after prevalence. present study demonstrates usefulness wastewater-based epidemiology combined preservation (wastewater banking) as tool for better management viral diseases.

Язык: Английский

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Wastewater-based surveillance is an efficient monitoring tool for tracking influenza A in the community

Water Research, Год журнала: 2024, Номер 257, С. 121650 - 121650

Опубликована: Апрель 21, 2024

Around the world, influenza A virus has caused severe pandemics, and risk of future pandemics remains high. Currently, surveillance is based on clinical diagnosis reporting disease cases. In this study, we apply wastewater-based to monitor amount RNA at population level. We report levels in 10 wastewater treatment plant catchment areas covering 40% Finnish population. Altogether, 251 monthly composite influent samples (collected between February 2021 2023) were analysed from supernatant fraction using specific RT-qPCR method. During study period, an epidemic occurred three waves Finland. This shows that can be detected 24 h samples. The gene copy number correlated with confirmed cases National Infectious Diseases Register. median Kendall's τ correlation strength was 0.636 (min= 0.486 max=0.804) it statistically significant all WTTPs. Wastewater-based independent individual testing method cost-efficiently reflects circulation entire Thus, monitoring complements available, but often too sparse, information improves health care public preparedness for pandemics.

Язык: Английский

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Timely Monitoring of SARS-CoV-2 RNA Fragments in Wastewater Shows the Emergence of JN.1 (BA.2.86.1.1, Clade 23I) in Berlin, Germany

Viruses, Год журнала: 2024, Номер 16(1), С. 102 - 102

Опубликована: Янв. 10, 2024

The importance of COVID-19 surveillance from wastewater continues to grow since case-based in the general population has been scaled back world-wide. In Berlin, Germany, quantitative and genomic monitoring for SARS-CoV-2 is performed three treatment plants (WWTP) covering 84% December 2021. Omicron sublineage JN.1 (B.2.86.1.1), was first identified on 22 October 2023 rapidly became dominant sublineage. This change accompanied by a parallel still ongoing increase notification-based 7-day-hospitalization incidence ICU utilization, indicating increasing activity (hospital-prone) higher strain healthcare system. retrospect, unique mutations could be as early September but were unknown relevance at time. timely detection new sublineages therefore depends availability sequences GISAID updates Pango lineage definitions Nextclade. We show that provides public health evidence regional level, complementing existing indicators.

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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Tracing COVID-19 Trails in Wastewater: A Systematic Review of SARS-CoV-2 Surveillance with Viral Variants

Water, Год журнала: 2023, Номер 15(6), С. 1018 - 1018

Опубликована: Март 7, 2023

The emergence of new variants SARS-CoV-2 associated with varying infectivity, pathogenicity, diagnosis, and effectiveness against treatments challenged the overall management COVID-19 pandemic. Wastewater surveillance (WWS), i.e., monitoring infections in communities through detecting viruses wastewater, was applied to track spread globally. However, there is a lack comprehensive understanding use WWS for variants. Here we systematically reviewed published articles reporting different wastewater by following PRISMA guidelines provided current state art this study area. A total 80 studies were found that reported until November 2022. Most these (66 out 80, 82.5%) conducted Europe North America, resource-rich countries. There high variation sampling strategy around world, composite (50/66 studies, 76%) as primary method In contrast, grab more common (8/14 57%) resource-limited Among detection methods, reverse transcriptase polymerase chain reaction (RT-PCR)-based sequencing quantitative RT-PCR commonly used wastewater. variants, B1.1.7 (Alpha) variant appeared earlier pandemic most (48/80 studies), followed B.1.617.2 (Delta), B.1.351 (Beta), P.1 (Gamma), others All same pattern clinical within timeline, demonstrating tracked all timely way when emerged. Thus, may be utilized identify presence or absence follow development transmission existing emerging Routine powerful infectious disease tool implemented

Язык: Английский

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