Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data DOI Open Access
Steven G. Sutcliffe, Susanne A. Kraemer, Isaac Ellmen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 21, 2023

Abstract 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 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 noise bias data appreciate commonalities differences methods.

Language: Английский

Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission DOI Creative Commons
Smruthi Karthikeyan, Joshua I. Levy,

Peter De Hoff

et al.

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

Citations

366
Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples DOI Creative Commons
Orsolya Pipek, Anna Medgyes‐Horváth, József Stéger

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 15, 2024

Abstract Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis more than 2 million raw read datasets submitted to European COVID-19 Data Portal identify recombination. Co-infection was observed in 0.35% investigated cases. Two independent procedures were implemented detect We show that sensitivity is predominantly determined by density lineage-defining mutations along genome, thus used an expanded list mutually exclusive defining specific variant combinations increase statistical power. call attention multiple challenges rendering detection difficult provide guidelines reduction false positives arising from chimeric sequences produced during PCR amplification. Additionally, three recombination hotspots Delta – Omicron BA.1 recombinants.

Language: Английский

Citations

15
Wastewater surveillance of open drains for mapping the trajectory and succession of SARS-CoV-2 lineages in 23 cities of Maharashtra State (India) during June 2022 to May 2023 DOI Creative Commons

Sejal Matra,

Harshada Ghode,

Vinay Rajput

et al.

Heliyon, Journal Year: 2025, Volume and Issue: 11(4), P. e42534 - e42534

Published: Feb. 1, 2025

The timely detection of SARS-CoV-2 is crucial for controlling its spread, especially in areas vulnerable to outbreaks. However, due a lack sustainable and low cost methods, early such outbreaks impacting middle-income countries (LMICs). Leveraging Wastewater-Based Epidemiology (WBE), we examined the dissemination evolution SARS CoV2 virus open drains across urban, suburban densely populated cities selected regions state Maharashtra, third largest India. In period from June 2022 May 2023, 44.89 % RNA were positive RT-qPCR wastewater samples collected regions. Whole genome sequencing revealed 22 distinct lineages, with Omicron variant, followed by XBB dominating, alongside other variants as BF, BQ, CH, BA.2.86, albeit lower frequencies. Wastewater surveillance provided insights into viral transmission, complementing clinical surveillance. Notably, our study detected emerging prior reporting, highlighting potential WBE detection. Findings underscore correlation between population density trend load. This also highlighted significance using low-cost, tool, LMICs, where adequate methods are lacking or difficult deploy accessibility.

Language: Английский

Citations

1
Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples DOI Creative Commons

Tunc Kayikcioglu,

Jasmine Amirzadegan,

Hugh Rand

et al.

PeerJ, Journal Year: 2023, Volume and Issue: 11, P. e14596 - e14596

Published: Jan. 26, 2023

The accurate identification of SARS-CoV-2 (SC2) variants and estimation their abundance in mixed population samples (

Language: Английский

Citations

20
Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data DOI Creative Commons
Steven G. Sutcliffe, Susanne A. Kraemer, Isaac Ellmen

et al.

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

Citations

8
Genomic surveillance reveals early detection and transition of delta to omicron lineages of SARS-CoV-2 variants in wastewater treatment plants of Pune, India DOI
Vinay Rajput, Rinka Pramanik,

Vinita Malik

et al.

Environmental Science and Pollution Research, Journal Year: 2023, Volume and Issue: 30(56), P. 118976 - 118988

Published: Nov. 3, 2023

Language: Английский

Citations

11
Systematic SARS-CoV-2 S-gene sequencing in wastewater samples enables early lineage detection and uncovers rare mutations in Portugal DOI Creative Commons
Ana C. Reis, Daniela Pinto, Sílvia Monteiro

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 921, P. 170961 - 170961

Published: Feb. 15, 2024

As the COVID-19 pandemic reached its peak, many countries implemented genomic surveillance systems to track evolution and transmission of SARS-CoV-2. Transition from endemic phase prioritized alternative testing strategies maintain effective epidemic at population level, with less intensive sequencing efforts. One such promising approach was Wastewater-Based Surveillance (WBS), which offers non-invasive, cost-effective means for analysing virus trends sewershed level. From 2020 onwards, wastewater has been recognized as an instrumental source information public health, national international authorities exploring options implement increasingly relying on WBS early warning potential pathogen outbreaks. In Portugal, several pioneer projects joined academia, water utilities Public Administration around WBS. To validate strategy, it is crucial collect long term performance data. this work, we present one year systematic SARS-CoV-2 in representing 35 % mainland population. We employed two complementary methods lineage determination - allelic discrimination by RT-PCR S-gene sequencing. This combination allowed us monitor variant near-real-time identify low-frequency mutations. Over course year-long study, spanning May 2022 April 2023, successfully tracked dominant Omicron sub-lineages, their progression evolution, aligned concurrent clinical Our results underscore effectiveness a tracking system variants, ability unveil mutations undetected via massive samples demonstrating uncover new detect rare genetic variants. findings emphasize that knowledge diversity level can be extended far beyond routine genotyping.

Language: Английский

Citations

3
Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2 DOI Creative Commons
Marie Lataretu, Oliver Drechsel,

René Kmiecinski

et al.

F1000Research, Journal Year: 2024, Volume and Issue: 12, P. 1091 - 1091

Published: April 16, 2024

Background Accurate genome sequences form the basis for genomic surveillance programs, added value of which was impressively demonstrated during COVID-19 pandemic by tracing transmission chains, discovering new viral lineages and mutations, assessing them infectiousness resistance to available treatments. Amplicon strategies employing Illumina sequencing have become widely established variant detection reference-based reconstruction SARS-CoV-2 genomes, are routine bioinformatics tasks. Yet, specific challenges arise when analyzing amplicon data, example, crucial even lineage-determining mutations occur near primer sites. Methods We present CoVpipe2, a workflow developed at Public Health Institute Germany reconstruct genomes based on short-read data accurately. The decisive factor here is reliable, accurate, rapid considering specifics used protocol. Besides fundamental tasks like quality control, mapping, calling, consensus generation, we also implemented additional features ease mixed samples recombinants. Results highlight common pitfalls in clipping, detecting heterozygote variants, dealing with low-coverage regions deletions. introduce CoVpipe2 address above compared successfully validated pipeline against selected publicly benchmark datasets. high usability, reproducibility, modular design that specifically addresses characteristics protocols but can be whole-genome data. Conclusions has seen multiple improvement cycles continuously maintained alongside frequently updated schemes developments scientific community. Our easy set up use serve as blueprint other pathogens future due its flexibility modularity, providing long-term perspective continuous support. written Nextflow freely accessible from \href{https://github.com/rki-mf1/CoVpipe2}{github.com/rki-mf1/CoVpipe2} under GPL3 license.

Language: Английский

Citations

3
Wastewater early warning system for SARS-CoV-2 outbreaks and variants in a Coruña, Spain DOI Creative Commons
Noelia Trigo‐Tasende, Juán A. Vallejo, Soraya Rumbo‐Feal

et al.

Environmental Science and Pollution Research, Journal Year: 2023, Volume and Issue: 30(32), P. 79315 - 79334

Published: June 7, 2023

Abstract Wastewater-based epidemiology has been widely used as a cost-effective method for tracking the COVID-19 pandemic at community level. Here we describe COVIDBENS, wastewater surveillance program running from June 2020 to March 2022 in treatment plant of Bens A Coruña (Spain). The main goal this work was provide an effective early warning tool based help decision-making both social and public health levels. RT-qPCR procedures Illumina sequencing were weekly monitor viral load detect SARS-CoV-2 mutations wastewater, respectively. In addition, own statistical models applied estimate real number infected people frequency each emerging variant circulating community, which considerable improved strategy. Our analysis detected 6 waves with concentrations between 10 3 RNA copies/L. system able anticipate outbreaks during 8–36 days advance respect clinical reports and, emergence new variants such Alpha (B.1.1.7), Delta (B.1.617.2), Omicron (B.1.1.529 BA.2) 42, 30, 27 days, respectively, before did. Data generated here helped local authorities managers give faster more efficient response situation, also allowed important industrial companies adapt their production situation. wastewater-based developed our metropolitan area (Spain) served powerful combining monitoring over time.

Language: Английский

Citations

9
Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission DOI Creative Commons
Smruthi Karthikeyan, Joshua I. Levy,

Peter De Hoff

et al.

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: Dec. 27, 2021

Summary 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 testing/sequencing capacity, which can also introduce biases. RNA concentration wastewater successfully tracks regional infection dynamics provides less biased abundance estimates than testing. 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 sequencing effort, the controlled environment of large university campus broader context surrounding county. We develop deploy improved protocols deconvolution software that fully multiple strains from wastewater. concern up 14 days earlier samples, identify instances not captured surveillance. Our study scalable solution surveillance allows detection identification cryptic transmission.

Language: Английский

Citations

20