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[Preprint]. 2021 Mar 26:2021.03.18.21253604.

doi: 10.1101/2021.03.18.21253604.

A rapid assessment of wastewater for genomic surveillance of SARS-CoV-2 variants at sewershed scale in Louisville, KY

J L Fuqua^{1

2}, E C Rouchka^{3

4}, S Waigel⁵, K Sokoloski^{2

6}, D Chung^{2

6}, W Zacharias⁵, M Zhang⁷, J Chariker^{3

4}, D Talley⁸, I Santisteban^{1

2}, A Varsani⁹, S Moyer^{10

11}, R H Holm¹², R A Yeager^{12

13}, T Smith¹², A Bhatnagar¹²

Affiliations

¹ Department of Pharmacology and Toxicology, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, United States.
² Center for Predictive Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, United States.
³ Department of Computer Science and Engineering, University of Louisville, 522 East Gray St., Louisville, KY 40202, United States.
⁴ KY-INBRE Bioinformatics Core, University of Louisville, 522 East Gray St., Louisville, KY 40202, United States.
⁵ Department of Medicine, University of Louisville, 530 S. Hancock Jackson St., Louisville, KY 40402, United States.
⁶ Department of Microbiology and Immunology, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, United States.
⁷ Department of Neuroscience Training, University of Louisville, 505 S. Hancock St, Louisville, KY 40202.
⁸ Louisville/Jefferson County Metropolitan Sewer District, Morris Forman Water Quality Treatment Center, 4522 Algonquin Parkway, Louisville KY 40211, United States.
⁹ The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, United States.
¹⁰ Department of Health Management and System Sciences, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray St., Louisville, KY 40202, United States.
¹¹ Department of Public Health and Wellness, Louisville Metro Government, 400 E. Grays St., Louisville, KY 40202, United States.
¹² Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, United States.
¹³ Department of Environmental and Occupational Health Sciences, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray St., Louisville, KY 40202, United States.

PMID: 33791725
PMCID: PMC8010757
DOI: 10.1101/2021.03.18.21253604

A rapid assessment of wastewater for genomic surveillance of SARS-CoV-2 variants at sewershed scale in Louisville, KY

J L Fuqua et al. medRxiv. 2021.

[Preprint]. 2021 Mar 26:2021.03.18.21253604.

doi: 10.1101/2021.03.18.21253604.

Authors

Affiliations

¹ Department of Pharmacology and Toxicology, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, United States.
² Center for Predictive Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, United States.
³ Department of Computer Science and Engineering, University of Louisville, 522 East Gray St., Louisville, KY 40202, United States.
⁴ KY-INBRE Bioinformatics Core, University of Louisville, 522 East Gray St., Louisville, KY 40202, United States.
⁵ Department of Medicine, University of Louisville, 530 S. Hancock Jackson St., Louisville, KY 40402, United States.
⁶ Department of Microbiology and Immunology, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, United States.
⁷ Department of Neuroscience Training, University of Louisville, 505 S. Hancock St, Louisville, KY 40202.
⁸ Louisville/Jefferson County Metropolitan Sewer District, Morris Forman Water Quality Treatment Center, 4522 Algonquin Parkway, Louisville KY 40211, United States.
⁹ The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, United States.
¹⁰ Department of Health Management and System Sciences, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray St., Louisville, KY 40202, United States.
¹¹ Department of Public Health and Wellness, Louisville Metro Government, 400 E. Grays St., Louisville, KY 40202, United States.
¹² Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, United States.
¹³ Department of Environmental and Occupational Health Sciences, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray St., Louisville, KY 40202, United States.

PMID: 33791725
PMCID: PMC8010757
DOI: 10.1101/2021.03.18.21253604

Update in

The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale.
Rouchka EC, Chariker JH, Saurabh K, Waigel S, Zacharias W, Zhang M, Talley D, Santisteban I, Puccio M, Moyer S, Holm RH, Yeager RA, Sokoloski KJ, Fuqua J, Bhatnagar A, Smith T. Rouchka EC, et al. Pathogens. 2021 Oct 1;10(10):1271. doi: 10.3390/pathogens10101271. Pathogens. 2021. PMID: 34684220 Free PMC article.

Abstract

In this communication, we report on the genomic surveillance of SARS-CoV-2 using wastewater samples in Jefferson County, KY. In February 2021, we analyzed seven wastewater samples for SARS-CoV-2 genomic surveillance. Variants observed in smaller catchment areas, such as neighborhood manhole locations, were not necessarily consistent when compared to associated variant results in downstream treatment plants, suggesting catchment size or population could impact the ability to detect diversity.

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Conflict of interest statement

Competing Interests: The authors have no conflicts to report related to the submitted work.

Figures

**Figure 1.. Study sites within Louisville, KY**
Distribution of the sewershed area, treatment plants and community locations, in Jefferson County with corresponding dates, sampled. SARS-CoV-2 was detected at all sites. Samples that contained at least 50% of the single amino acid mutations for a variant with a nucleotide frequency above a 5 % threshold for individual mutations are flagged for review. This relatively low threshold serves the purpose of identifying geographic (sewershed) areas for heightened public health surveillance. With our current metrics we flagged sites 833, 891, and Treatment plant #2 for potential presence of variant B.1.429.

See this image and copyright information in PMC

References

1. Betancourt WW, et al. (2020) Wastewater-based Epidemiology for Averting COVID-19 Outbreaks on The University of Arizona Campus. medRxiv:2020.2011.2013.20231340.
1. Wu F, et al. (2020) SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases. mSystems 5(4). - PMC - PubMed
1. Weidhaas J, et al. (2021) Correlation of SARS-CoV-2 RNA in wastewater with COVID-19 disease burden in sewersheds. Sci Total Environ 775:145790. - PMC - PubMed
1. Yeager RA, et al. (2020) Wastewater sample site selection to estimate geographically-resolved community prevalence of COVID-19: A research protocol. medRxiv:2020.2008.2023.20180224. - PMC - PubMed
1. CDC (Updated March 8, 2021) Variant Cases. (https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html).

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This is a preprint.

A rapid assessment of wastewater for genomic surveillance of SARS-CoV-2 variants at sewershed scale in Louisville, KY

Affiliations

A rapid assessment of wastewater for genomic surveillance of SARS-CoV-2 variants at sewershed scale in Louisville, KY

Authors

Affiliations

Update in

Abstract

Conflict of interest statement

Figures

References

Publication types

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Miscellaneous