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

Microbial Genomics, Год журнала: 2024, Номер 10(5)

Опубликована: Май 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.

Язык: Английский

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Detection of SARS-COV-2 variants and their proportions in wastewater samples using next-generation sequencing in Finland

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Апрель 2, 2024

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants may have different characteristics, e.g., in transmission, mortality, and the effectiveness of vaccines, indicating importance variant detection at population level. Wastewater-based surveillance SARS-CoV-2 RNA fragments has been shown to be an effective way monitor COVID-19 pandemic Wastewater is a complex sample matrix affected by environmental factors PCR inhibitors, causing insufficient coverage sequencing, for example. Subsequently, results where part genome does not sufficient are uncommon. To identify their proportions wastewater over time, we utilized next-generation sequencing with ARTIC Network's primer set bioinformatics pipeline evaluate presence partial data. Based on data from November 2021 February 2022, Delta was dominant until mid-December Helsinki, Finland’s capital, thereafter late December 2022 Omicron became most common variant. At same outcompeted previous Finland new cases. The findings agreement information obtained patient samples when visually comparing trends sewerage network area. This indicates that temporal spatial

Язык: Английский

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Correspondence of SARS-CoV-2 genomic sequences obtained from wastewater samples and COVID-19 patient at long-term care facilities

The Science of The Total Environment, Год журнала: 2024, Номер 916, С. 170103 - 170103

Опубликована: Янв. 17, 2024

Wastewater-based epidemiology (WBE) has been in the spotlight because of applicability early detection virus outbreak and new variants at catchment area. However, there a notable absence research directly confirming association between SARS-CoV-2 wastewater patient specimens. In this study, we performed quantitative qualitative investigation with genetic-level comparison COVID-19 patients positive samples long-term care facilities. Wastewater were collected via passive sampling from manholes, load was determined by qPCR. We correlation analysis case number, which suggested that detected earlier than ascertainment case. Six six RNA cases wastewater, respectively, two facilities then applied for amplicon sequencing analysis. Mutation revealed high sequence similarity (>99 %). To best our knowledge, is first study demonstrating WBE also effective predicting predominant variant facility-level, helpful to develop early-warning system occurrence variant.

Язык: Английский

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Pentagon Found Daily, Metagenomic Detection of Novel Bioaerosol Threats to Be Cost-Prohibitive: Can Virtualization and AI Make It Cost-Effective?

Health Security, Год журнала: 2024, Номер 22(2), С. 108 - 129

Опубликована: Апрель 1, 2024

In 2022, the Pentagon Force Protection Agency found threat agnostic detection of novel bioaerosol threats to be "not feasible for daily operations" due cost reagents used metagenomics, sequencing instruments, and labor subject matter experts analyze bioinformatics. Similar operational difficulties might extend many 280,000 buildings (totaling 2.3 billion square feet) at 5,000 secure US Department Defense military sites, 250 Navy ships, as well civilian buildings. These economic barriers can still addressed in a manner by dynamically pooling samples from dry filter units, called spike-triggered virtualization, whereby depth are automatically modulated based on biothreats output. By running high average factor, annual per unit reduced 10 100 times depending chosen trigger thresholds. Artificial intelligence further enhance sensitivity virtualization. The risk infection during 12- 24-hour window between incident its remains, but some cases it 80% or more with high-speed indoor air cleaning exceeding 12 changes hour, which is similar rate passenger airplanes flight. That level hour higher likely cost-prohibitive using central heating ventilation conditioning systems, achieved economically portable filtration rooms typical ceiling heights (less than approximately $0.50 $1 foot do-it-yourself units $2 $5 high-efficiency particulate filters.

Язык: Английский

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Nested PCR effective to detect low viral loads of SARS-CoV-2 in animal samples

Preventive Veterinary Medicine, Год журнала: 2024, Номер 231, С. 106303 - 106303

Опубликована: Авг. 3, 2024

Язык: 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, Год журнала: 2025, Номер 274, С. 123154 - 123154

Опубликована: Янв. 16, 2025

Язык: Английский

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Dissemination of local sub-variants of SARS-CoV-2 detected by detailed mutation analysis in wastewater-based epidemiology

PLoS ONE, Год журнала: 2025, Номер 20(5), С. e0317076 - e0317076

Опубликована: Май 28, 2025

Wastewater-based epidemiology (WBE) is effective for identifying the predominant SARS-CoV-2 variants within specific populations as well early warning of disease outbreaks. The variant analysis in WBE has been limited to quantifying proportion variants, and it unable trace their origins dissemination pathways. This study aims elucidate emergence transmission locally sub-variants through detailed mutation wastewater genomic surveillance. Genome mutations at each nucleotide position S region were examined identify unique geographically distinct cities Komatsu Hamamatsu. Notably, XBT variant, which had never reported clinical samples from Japan, was detected Komatsu. Moreover, a sub-variant BA.5 duration 17 weeks whereas absent Mutation also revealed significant differences common BA.2.75 sub-variant’s prevalence 35 weeks, contrast only one week These findings underscore efficacy wastewater-based timing entry duration, enhancing our understanding origins, pathways, evolutionary trajectories epidemically important variants.

Язык: Английский

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Combining analysis of individual and wastewater whole genome sequencing improves SARS-CoV-2 surveillance

Water Research, Год журнала: 2025, Номер unknown, С. 123953 - 123953

Опубликована: Июнь 1, 2025

Язык: Английский

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Simultaneous extraction and detection of DNA and RNA from viruses, prokaryotes, and eukaryotes in wastewater using a modified COPMAN

The Science of The Total Environment, Год журнала: 2023, Номер 907, С. 167866 - 167866

Опубликована: Окт. 19, 2023

Wastewater surveillance can offer a comprehensive grasp of infectious disease prevalence and human health because wastewater contains various human-derived microbial pathogens, including viruses, bacteria, fungi. However, methods capable simultaneous detection multiple groups targets in the automated systems large-scale are still under development. Here, we demonstrated modification, involving addition bead-beating, to existing COPMAN (COagulation Proteolysis method using MAgnetic beads for Nucleic acids wastewater) enabled enhanced microorganisms, SARS-CoV-2. The modified method, termed bead-beating (BB-COPMAN), was evaluated through spike-and-recovery experiments comparative analysis against three previously reported DNA/RNA detection. Our study targeted range enveloped non-enveloped RNA viruses (SARS-CoV-2, PMMoV), DNA virus (crAssphage), archaea, gram-negative gram-positive bacteria (E. coli, Lachnospiraceae), antibiotic resistance gene (ampC), fungi (Candida albicans). recovery rates BB-COPMAN were 17 2.1-fold higher, respectively, compared Additionally, exhibited highest extraction efficiency among tested methods, achieving 1.2–5.7 times more 1.1–69 yield on average. allowed SARS-CoV-2 from all nine samples PMMoV at concentrations 39–97 higher than other methods. Moreover, detected larger amounts four out six method. These results that enables single flow nucleic acid extraction, making well-suited systems. In conclusion, is promising assessing wide pathogenic microorganisms.

Язык: Английский

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

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 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.

Язык: Английский

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