Robust Performance of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method

Segelhurst, Emily; Bard, Jonathan; Pillsbury, Annemarie N; Alam, Md Mahbubul; Lamb, Natalie A; Zhu, Chonglin; Pohlman, Alyssa; Boccolucci, Amanda; Emerson, Jamaal; Marzullo, Brandon; Yergeau, Donald; Nowak, Norma J.; Bradley, Ian; Surtees, Jennifer A.; Ye, Yinyin

doi:10.1021/acsestwater.2c00456

Cited by 3 publications

(3 citation statements)

References 51 publications

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“…The number of vertebrate viral families detected for the targeted/SV-DE method was 4 for WWTP M and 5 for WWTP O (Figure S4). Segelhurst et al, 2022 used a tangential-flow filtration method to recover 53% more complete or near complete SARS-CoV-2 genomes from wastewater samples as compared to concentration using precipitation . Still, a previous study by Hjelmsø et al, 2017 evaluated the impact of polyethylene glycol precipitation (PEG), skimmed milk flocculation, glass wool filtration, and monolithic adsorption filtration on the sequencing of viruses in wastewater.…”

Section: Resultsmentioning

confidence: 99%

Targeted Metagenomic Sequencing for Detection of Vertebrate Viruses in Wastewater for Public Health Surveillance

McCall,

Leo Elworth,

Wylie

et al. 2023

ACS EST Water

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Viruses of concern for quantitative wastewater monitoring are usually selected as a result of an outbreak and subsequent detection in wastewater. In addition, targeted metagenomics could proactively be used for widespread identification and sequencing of viruses of concern when used as an initial screening tool. To evaluate the utility of targeted metagenomics for wastewater screening, we used ViroCap, a panel of probes designed to target all known vertebrate viruses. Untreated wastewater was collected from wastewater treatment plants (WWTPs) and building-level manholes associated with vulnerable populations in Houston, TX. We evaluated differences in vertebrate virus detection between WWTP and building-level samples, classified human viruses in wastewater, and performed phylogenetic analysis on astrovirus sequencing reads to evaluate targeted metagenomics for subspecies-level classification. Vertebrate viruses varied widely across building-level samples. Rarely detected and abundant viruses were identified in WWTP and building-level samples including enteric, respiratory, and bloodborne viruses. Furthermore, full-length genomes were assembled from astrovirus reads, and two human astrovirus serotypes were classified in wastewater samples. This study demonstrates the utility of targeted metagenomics as an initial screening step for public health surveillance.

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Section: Resultsmentioning

confidence: 99%

Targeted Metagenomic Sequencing for Detection of Vertebrate Viruses in Wastewater for Public Health Surveillance

McCall,

Leo Elworth,

Wylie

et al. 2023

ACS EST Water

View full text Add to dashboard Cite

show abstract

“…The wide-spread availability of at-home diagnostic tools has reduced collection rates. Furthermore, many pandemic monitoring groups have adopted wastewater-based approaches(22, 23, 24). While wastewater serves as viable tools for measuring overall infection rates, and deconvolution techniques gives an indication of relative proportions of lineages, broad monitoring through wastewater introduces a gap in data for localities without municipal treatment facilities, though recent analysis suggests the feasibility of the method for rural communities (25).…”

Section: Discussionmentioning

confidence: 99%

“…Excluding commercial vehicles, we can detect distinct commuter corridors linking different EDRs. For example, the Capital District Region (Exits [23][24][25][26] show increased frequency of travel with the Mid-Hudson (Exits 16-21).…”

Section: Establishing Broad Travel Patterns Using Transit Datasetmentioning

confidence: 99%

Genomic Profiling and Spatial SEIR Modeling of COVID-19 Transmission in Western New York

Bard,

Jiang,

Emerson

et al. 2023

Preprint

Self Cite

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The COVID-19 pandemic has prompted an unprecedented global effort to understand and mitigate the spread of the SARS-CoV-2 virus. In this study, we present a comprehensive analysis of COVID-19 in Western New York, integrating individual patient-level genomic sequencing data with a spatially informed agent-based disease Susceptible-Exposed-Infectious-Removed (SEIR) computational model. The integration of genomic and spatial data enables a multi-faceted exploration of the factors influencing the transmission patterns of COVID-19, including population density, movement dynamics, and genetic variations in the viral genomes replicating in New York State (NYS). Our findings shed light on local dynamics of the pandemic, revealing potential hotspots of transmission. Additionally, the genomic analysis provides insights into the genetic heterogeneity of SARS-CoV-2 within a single lineage at a region-specific level. This interdisciplinary approach, bridging genomics and spatial modeling, contributes to a more holistic understanding of COVID-19 dynamics. The results of this study have implications for future public health strategies, guiding targeted interventions and resource allocation to effectively control the spread of similar viruses in the Western New York region.

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Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond

Parkins,

Lee,

Acosta

et al. 2024

Clin Microbiol Rev

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SUMMARY Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.

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Robust Performance of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method

Cited by 3 publications

References 51 publications

Targeted Metagenomic Sequencing for Detection of Vertebrate Viruses in Wastewater for Public Health Surveillance

Targeted Metagenomic Sequencing for Detection of Vertebrate Viruses in Wastewater for Public Health Surveillance

Genomic Profiling and Spatial SEIR Modeling of COVID-19 Transmission in Western New York

Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond

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