Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data

Microbial Genomics, Journal Year: 2024, Volume and Issue: 10(5)

Published: May 24, 2024

Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during SARS-CoV-2 pandemic estimating community infection levels by qPCR. Sequencing pathogen genes genomes from wastewater adds information about genetic diversity, which can be used to identify viral lineages (including variants concern) that are circulating in local population. Capturing diversity sequencing not trivial, as samples often contain diverse mixture with real mutations errors, must deconvoluted computationally short reads. In this study we assess nine different computational tools have recently been developed address challenge. We simulated 100 sequence consisting BA.1, BA.2, Delta lineages, various mixtures, well Delta–Omicron recombinant synthetic ‘novel’ lineage. Most performed identifying true present their relative abundances were generally robust variation depth read length. While many identified down 1 % frequency, results more reliable above 5 threshold. The presence unknown lineage, represents unclassified increases error abundance estimates other but magnitude effect was small most tools. also varied how they labelled novel recombinants. our dataset just one possible use cases these methods, hope it helps users understand potential sources bias analysis appreciate commonalities differences methods.

Language: Английский

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Wastewater surveillance for viral pathogens: A tool for public health

Heliyon, Journal Year: 2024, Volume and Issue: 10(13), P. e33873 - e33873

Published: June 29, 2024

A focus on water quality has intensified globally, considering its critical role in sustaining life and ecosystems. Wastewater, reflecting societal development, profoundly impacts public health. Wastewater-based epidemiology (WBE) emerged as a surveillance tool for detecting outbreaks early, monitoring infectious disease trends, providing real-time insights, particularly vulnerable communities. WBE aids tracking pathogens, including viruses, sewage, offering comprehensive understanding of community health lifestyle habits. With the rise global COVID-19 cases, gained prominence, aiding SARS-CoV-2 levels worldwide. Despite advancements treatment, poorly treated wastewater discharge remains threat, amplifying spread water-, sanitation-, hygiene (WaSH)-related diseases. WBE, serving complementary surveillance, is pivotal community-level viral infections. However, there untapped potential to expand surveillance. This review emphasizes importance link between health, highlighting need further integration into management.

Language: Английский

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Targeted amplicon sequencing of wastewater samples for detecting SARS-CoV-2 variants with high sensitivity and resolution

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 893, P. 164766 - 164766

Published: June 12, 2023

Wastewater-based epidemiology (WBE) is a promising approach for monitoring the spread of SARS-CoV-2 within communities. Although qPCR-based WBE powerful in that it allows quick and highly sensitive detection this virus, can provide limited information about which variants are responsible overall increase or decrease virus sewage, hinders accurate risk assessments. To resolve problem, we developed next generation sequencing (NGS)-based method to determine identity composition individual wastewater samples. Combination optimization targeted amplicon-sequencing nested PCR allowed each variant with sensitivity comparable qPCR. In addition, by targeting receptor binding domain (RBD) S protein, has mutations informative classification, could discriminate most concern (VOC) even sublineages Omicron (BA.1, BA.2, BA.4/5, BA.2.75, BQ.1.1 XBB.1). Focusing on benefit decreasing reads. We applied samples collected from treatment plant Kyoto city throughout 13 months (from January 2021 February 2022) successfully identified lineages wild-type, alpha, delta, omicron BA.1 BA.2 as well their compositions The transition these was good agreement epidemic situation reported during period based clinical testing. These data indicate our NGS-based useful detecting tracking emerging sewage Coupled advantages WBE, potential serve an efficient low cost means community assessment infection.

Language: Английский

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Environmental Dissemination of SARS-CoV-2: An Analysis Employing Crassphage and Next-Generation Sequencing Protocols

Food and Environmental Virology, Journal Year: 2025, Volume and Issue: 17(1)

Published: Jan. 7, 2025

Language: Английский

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Targeted Enrichment Sequencing Utilizing a Respiratory Pathogen Panel for Genomic Wastewater-Based Viral Epidemiology in Uruguay

Food and Environmental Virology, Journal Year: 2025, Volume and Issue: 17(1)

Published: Jan. 9, 2025

Language: Английский

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Hyperplex PCR enables highly multiplexed analysis of point mutations in wastewater: long-term SARS-CoV-2 variant surveillance in Sweden as a case study

Water Research, Journal Year: 2025, Volume and Issue: 274, P. 123154 - 123154

Published: Jan. 16, 2025

Language: Английский

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Cryptic transmission of a SARS-CoV-2 variant detected by wastewater surveillance in Panama

Frontiers in Cellular and Infection Microbiology, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 29, 2025

The COVID-19 pandemic highlighted the critical role of viral genomic surveillance, prompting numerous countries to enhance their monitoring systems for acute respiratory infections (ARIs), especially influenza-like illnesses (ILIs). Given significance asymptomatic cases in severe syndrome coronavirus 2 (SARS-CoV-2) transmission, often undetected by ILI a more comprehensive approach was essential track circulation SARS-CoV-2 variants population. In response, many swiftly adopted wastewater which allowed early detection before they were identified through molecular characterization from confirmed clinical cases. this report, we detail implementation surveillance Panama during first half 2024. Wastewater samples collected monthly duplicate at two collection points three districts city metropolitan area testing RT-qPCR, and positive analyzed next-generation sequencing identify sublineages. A total 36 822 obtained sequencing. Sublineages detected compared those same period time. identification Omicron sublineage JN.1.16.1 capital its surroundings, not country, despite global circulation. This highlights need sustain both programs beyond like that serve as pivotal exchange hubs.

Language: Английский

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Epidemiology Update of Hepatitis E Virus (HEV) in Uruguay: Subtyping, Environmental Surveillance and Zoonotic Transmission

Viruses, Journal Year: 2023, Volume and Issue: 15(10), P. 2006 - 2006

Published: Sept. 27, 2023

Hepatitis E Virus (HEV) infection is an emergent zoonotic disease of increasing concern in developed regions. HEV genotype 3 (HEV-3) mainly transmitted through consumption contaminated food high-income countries and classified into at least 13 subtypes (3a–3n), based on p-distance values from complete genomes. In Latin America, epidemiology studies are very scant. Our group has previously detected HEV3 clinical cases, swine, wild boars, captive white-collared peccaries, spotted deer Uruguay. Herein, we aimed to provide novel insights updated overview the molecular Uruguay, including data wastewater-based surveillance studies. A thorough analysis whole genomes partial ORF2 sequences Uruguayan human domestic pig strains showed that they formed a separate monophyletic cluster with high nucleotide identity exhibited over established cut-off (0.093) compared reference subtypes’ sequences. Furthermore, found overall prevalence 10.87% (10/92) wastewater, where two samples revealed close relationship humans, animal reservoirs/hosts isolates conclusion, single, new HEV-3 subtype currently circulates different epidemiological settings propose its designation as 3o along sequence.

Language: Английский

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RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 12, 2024

Abstract Rapid evolution of SARS-CoV-2 has resulted in the emergence numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, limitations capturing full epidemiological dynamics circulating variants general population. This study utilized receptor-binding domain (RBD) amplicon sequencing wastewater samples monitor community and El Paso, TX. Over 17 months, we identified 91 observed waves dominant transitioning from BA.2 BA.2.12.1, BA.4&5, BQ.1, XBB.1.5. Our findings demonstrated early detection identification unreported outbreaks, showing strong consistency with clinical data at local, state, national levels. Alpha diversity analyses revealed periodical variations, highest winter outbreak lag phases, likely due lower competition among before growth phase. The underscores importance low transmission periods for rapid mutation variant evolution. highlights effectiveness integrating RBD surveillance tracking viral evolution, understanding emergence, enhancing preparedness.

Language: Английский

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Incursion of SARS-CoV-2 BA.2.86.1 variant into Israel: National-scale wastewater surveillance using a novel quantitative real-time PCR assay

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 933, P. 173164 - 173164

Published: May 11, 2024

Language: Английский

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