Leveraging wastewater sequencing to strengthen global public health surveillance

BMC Global and Public Health, Journal Year: 2025, Volume and Issue: 3(1)

Published: March 21, 2025

Language: Английский

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Evaluation of sampling methods for genomic surveillance of SARS-CoV-2 variants in aircraft wastewater samples

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: March 25, 2025

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing threat to global health. Wastewater-based surveillance (WBS) has proven be important tool for tracking the dissemination of SARS-CoV-2 variants concern (VOCs) in community. In Canada, metagenomic analysis aircraft wastewater was adopted at early stage pandemic track importation emerging into country. However, need determine presence sublineages meant that sampling methods utilized were not adequately validated. Here, we compared two different genomic VOCs sewage samples. Methods Eighty-eight composite samples collected over nine weeks using both autosampler and passive torpedo samplers same location. nucleic acid quantified RT-qPCR. RNA extracted sequenced with MiniSeq system tiled-amplicon sequencing approach ARTIC V4.1 primer sets. Raw reads preprocessed mutations, lineages, other sequence metrics from compared. Results The yielded comparable viral load by RT-qPCR, but produced higher genome coverage relative samplers. Omicron lineages identified differed method. BQ.1* BA.5.2*, which predominant clinical time, as dominant sampler, respectively. Additionally, captured diversity abundance VOCs, including (XBB* CH.1* lineages), well more clinically relevant mutations (S:K444T, T22942A, S:R346T) sampler. Overall, the passive concordant results measuring RT-qPCR wastewater. Conclusions Taken together, our suggest underestimation These data can used optimize approaches

Language: Английский

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Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data

GigaScience, Journal Year: 2024, Volume and Issue: 13

Published: Jan. 1, 2024

Abstract Background Sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from wastewater samples has emerged as a valuable tool for detecting the presence and relative abundances SARS-CoV-2 variants in community. By analyzing viral genetic material present wastewater, researchers public health authorities can gain early insights into spread virus lineages emerging mutations. Constructing reference datasets known their mutation profiles become state-of-the-art assigning sequencing data. However, selecting sequences or mutations directly affects predictive power. Results Here, we show impact mutation- sequence-based reconstruction abundance estimation. We benchmark 3 datasets: (i) synthetic “spike-in”’ mixtures; (ii) German 2021, mainly comprising Alpha; (iii) obtained at an international airport Germany end including first signals Omicron. The approaches differ sublineage detection, with marker mutation-based method, particular, being challenged by increasing number lineages. estimations both depend on representative references optimized parameter settings. performing escalation experiments, demonstrate effects size alternative allele frequency cutoffs how different settings lead to results our test illustrate lineage composition references. Conclusions Our study highlights current computational challenges, focusing general design, which impacts allocations. advantages disadvantages that may be relevant further developments community context defining robust quality metrics.

Language: Английский

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Reconstructing SARS-CoV-2 lineages from mixed wastewater sequencing data

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Aug. 31, 2024

Abstract Wastewater surveillance of SARS-CoV-2 has emerged as a critical tool for tracking the spread COVID-19. In addition to estimating relative case numbers using quantitative PCR, genomic RNA can be extracted from wastewater and sequenced. There are many existing techniques sequenced determine abundance known lineages in sample. However, it is very challenging predict novel data due its mixed composition unreliable coverage. this work, we present technique based on non-negative matrix factorization which able reconstruct lineage definitions by analyzing across different samples. We test method both synthetic real sequencing data. show that major such Omicron Delta well sub-lineages BA.5.2.1. provide determining emerging without need clinical This could used routine monitoring other viral pathogens wastewater. Additionally, may more full-genome sequences viruses with fewer available genomes.

Language: Английский

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Synthetic data: how could it be used in infectious disease research?

Future Microbiology, Journal Year: 2024, Volume and Issue: 19(17), P. 1439 - 1444

Published: Sept. 30, 2024

Language: Английский

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Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes

BMC Bioinformatics, Journal Year: 2024, Volume and Issue: 25(1)

Published: March 23, 2024

Abstract Background Metagenomic profiling algorithms commonly rely on genomic differences between lineages, strains, or species to infer the relative abundances of sequences present in a sample. This observation plays an important role analysis diverse microbial communities, where targeted sequencing 16S and 18S rRNA, both well-known hypervariable regions, have led insights into diversity discovery novel organisms. However, variable nature discriminatory regions can also act as double-edged sword, sought-after variability make it difficult design primers for their amplification through PCR. Moreover, most are not necessarily informative purpose differentiation; one should focus that maximize number lineages be distinguished. Results Here we AmpliDiff, computational tool simultaneously finds highly viral genomes single species, well allowing these regions. We show found by AmpliDiff used accurately estimate SARS-CoV-2 example wastewater data. obtain errors comparable with using whole genome information abundances. Furthermore, our results is robust against incomplete input data designed bind sampled months after were selected. Conclusions With provide effective, cost-efficient alternative estimating lineage metagenomes.

Language: Английский

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Real-Time Monitoring of SARS-CoV-2 Variants in Oklahoma Wastewater through Allele-Specific RT-qPCR

Microorganisms, Journal Year: 2024, Volume and Issue: 12(10), P. 2001 - 2001

Published: Sept. 30, 2024

During the COVID-19 pandemic, wastewater surveillance was used to monitor community transmission of SARS-CoV-2. As new genetic variants emerged, need for timely identification these in became an important focus. In response increased reports Omicron across United States, Oklahoma Wastewater Surveillance team utilized allele-specific RT-qPCR assays detect and differentiate variants, such as Omicron, from other found Oklahoma. The PCR showed presence variant on average two weeks before official reports, which confirmed through genomic sequencing selected samples. Through continued November 2021 January 2022, we also demonstrated transition prevalence Delta local communities. We further assessed how this correlated with certain demographic factors characterizing each community. Our results highlight a rapid, simple, cost-effective method monitoring spread SARS-CoV-2 wastewater. Additionally, they demonstrate that specific ethnic composition household income can correlate timing introduction spread.

Language: Английский

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Genomic surveillance of Canadian airport wastewater samples allows early detection of emerging SARS-CoV-2 lineages

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Nov. 3, 2024

Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has shown wastewater (WW) surveillance to be an effective means of tracking the emergence viral lineages which arrive by many routes transmission including via transportation hubs. In Canadian province Ontario, numerous municipal treatment plants (WWTPs) participate in WW infectious disease targets such as SARS-CoV-2 qPCR and whole genome sequencing (WGS). Greater Toronto Airports Authority (GTAA), operator Pearson International Airport (Toronto Pearson), been participating since January 2022. As a major international airport Canada largest national hub, this is ideal location for globally emerging variants concern (VOCs). study, collected from Pearson’s two terminals pooled aircraft sewage was processed WGS using tiled-amplicon approach targeting virus genome. Data generated analyzed monitor trends lineage frequencies. Initial detections were compared between samples, samples surrounding regions, Ontario clinical data published Public Health Ontario. Results enabled early detection VOCs individual mutations On average, novel at preceded 1–4 weeks, up 16 weeks one case. This project illustrates efficacy transitory hubs sets example that could applied other viruses part preparedness strategy provide monitoring on mass scale.

Language: Английский

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