Assessment of two volumetrically different concentration approaches to improve sensitivities for SARS-CoV-2 detection during wastewater monitoring

McMinn, Brian R.; Korajkic, Asja; Pemberton, Adin; Kelleher, Julie; Ahmed, Warish; Villegas, Eric N.; Oshima, Kevin H.

doi:10.1016/j.jviromet.2022.114645

Cited by 11 publications

(4 citation statements)

References 58 publications

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“…However, in such cases large volumes of wastewater are required to reliably detect protein targets such as antibodies in the liquid fractions. Further innovation in process engineering is needed; possibly borrowing from the knowledge gained with concentrating low-copy SARS-CoV-2 RNA from large volumes (53).…”

Section: Discussionmentioning

confidence: 99%

Urban wastewater contains a functional human antibody repertoire of mucosal origin

Stephenson,

Eid,

Wong

et al. 2024

Preprint

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Wastewater-based surveillance of human disease offers timely insights to public health, helping to mitigate infectious disease outbreaks and decrease downstream morbidity and mortality. These systems rely on nucleic acid amplification tests for monitoring disease trends, while antibody-based seroprevalence surveys gauge community immunity. However, serological surveys are resource-intensive and subject to potentially long lead times and sampling bias. We identified and characterized a human antibody repertoire, predominantly secretory IgA, isolated from a central wastewater treatment plant and building-scale wastewater collection points. These antibodies partition to the solids fraction and retain immunoaffinity for SARS-CoV-2 and Influenza A virus antigens. This stable pool could enable real-time tracking of correlates of vaccination, infection, and immunity, aiding in establishing population-level thresholds for immune protection and assessing the efficacy of future vaccine campaigns, particularly those that are designed to induce humoral mucosal immunity.

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Section: Discussionmentioning

confidence: 99%

Urban wastewater contains a functional human antibody repertoire of mucosal origin

Stephenson,

Eid,

Wong

et al. 2024

Preprint

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“…Mutations with prevalence of >=90 % for each VOC investigated here (Alpha, B.1.351, Gamma, Delta, Lambda, Mu, BA.1, BA.2, BA.3) based on the GISAID msa from 27-03-2022. This included 300 mutations associated with lineages including Alpha (28), B.1.351 (19), Gamma (32), Delta (25), Lambda (25), Mu (26), BA.1 (42), BA.2 (62), and BA.3 (41). Of these, 253 were unique mutations with 40,56,18 associated with BA.1, BA.2 and Delta, respectively.…”

Section: Basicmentioning

confidence: 99%

“…However, challenges persist both upstream and downstream of sequencing. Upstream, the quality of results may vary according to the population size contributing to the wastewater catchment area [ 8 ], variability in viral shedding [ 17 18 ] virus enrichment methods [ 19 ], and in-sewer degradation of viral-particles (e.g. pH, temperature, travel-time) [ 20 21 ].…”

Section: Introductionmentioning

confidence: 99%

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

Sutcliffe,

Kraemer,

Ellmen

et al. 2024

Microbial Genomics

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

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“…Mutations with prevalence of >=90% for each VOC investigated here (Alpha, B.1.351, Gamma, Delta, Lambda, Mu, BA.1, BA.2, BA.3) based on the GISAID msa from 27-03-2022. This included 300 mutations associated with lineages including Alpha (28), B.1.351 (19), Gamma (32), Delta (25), Lambda (25), Mu (26), BA.1 (42), BA.2 (62), and BA.3 (41). Of these, 253 were unique mutations with 40,56,18 associated with BA.1, BA.2 and Delta respectively.…”

Section: Basicmentioning

confidence: 99%

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

Sutcliffe,

Kraemer,

Ellmen

et al. 2023

Preprint

View full text Add to dashboard Cite

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

show abstract

Assessment of two volumetrically different concentration approaches to improve sensitivities for SARS-CoV-2 detection during wastewater monitoring

Cited by 11 publications

References 58 publications

Urban wastewater contains a functional human antibody repertoire of mucosal origin

Urban wastewater contains a functional human antibody repertoire of mucosal origin

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

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

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