Zheng X, Wang M, Deng Y, Xu X, Lin D, Zhang Y, Li S, Ding J, Shi X, Yau CI. A rapid, high-throughput, and sensitive PEG-precipitation method for SARS-CoV-2 wastewater surveillance. Water Res. 2023;230:119560.

Article  CAS  PubMed  Google Scholar 

Peccia J, Zulli A, Brackney DE, Grubaugh ND, Kaplan EH, Casanovas-Massana A, Ko AI, Malik AA, Wang D, Wang M. Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics. Nat Biotechnol. 2020;38(10):1164–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang T. Wastewater as an information source of COVID-19. Sci Bull. 2022;67(11):1090–2.

Article  CAS  Google Scholar 

Wolfe MK, Archana A, Catoe D, Coffman MM, Dorevich S, Graham KE, Kim S, Grijalva LM, Roldan-Hernandez L, Silverman AI. Scaling of SARS-CoV-2 RNA in settled solids from multiple wastewater treatment plants to compare incidence rates of laboratory-confirmed COVID-19 in their sewersheds. Environ Sci Technol Lett. 2021;8(5):398–404.

Article  CAS  PubMed  Google Scholar 

Ahmed W, Angel N, Edson J, Bibby K, Bivins A, O’Brien JW, Choi PM, Kitajima M, Simpson SL, Li J. First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: a proof of concept for the wastewater surveillance of COVID-19 in the community. Sci Total Environ. 2020;728:138764.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhao L, Zou Y, Li Y, Miyani B, Spooner M, Gentry Z, Jacobi S, David RE, Withington S, McFarlane S, Faust R, Sheets J, Kaye A, Broz J, Gosine A, Mobley P, Busch AWU, Norton J, Xagoraraki I. Five-week warning of COVID-19 peaks prior to the Omicron surge in Detroit, Michigan using wastewater surveillance. Sci Total Environ. 2022;844:157040.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li Y, Miyani B, Zhao L, Spooner M, Gentry Z, Zou Y, Rhodes G, Li H, Kaye A, Norton J, Xagoraraki I. Surveillance of SARS-CoV-2 in nine neighborhood sewersheds in Detroit Tri-County area, United States: Assessing per capita SARS-CoV-2 estimations and COVID-19 incidence. Sci Total Environ. 2022;851:158350.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Miyani B, Fonoll X, Norton J, Mehrotra A, Xagoraraki I. SARS-CoV-2 in Detroit wastewater. J Environ Eng. 2020;146(11):06020004.

Article  CAS  Google Scholar 

Xagoraraki I. Can we predict viral outbreaks using wastewater surveillance? 2020, American Society of Civil Engineers. p. 01820003.

Bibby K, Peccia J. Identification of viral pathogen diversity in sewage sludge by metagenome analysis. Environ Sci Technol. 2013;47(4):1945–51.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Woolhouse M, Scott F, Hudson Z, Howey R, Chase-Topping M. Human viruses: discovery and emergence. Philos Trans R Soc B Biol Sci. 2012;367(1604):2864–71.

Article  Google Scholar 

McCall C, Wu H, Miyani B, Xagoraraki I. Identification of multiple potential viral diseases in a large urban center using wastewater surveillance. Water Res. 2020;184:116160.

Article  CAS  PubMed  PubMed Central  Google Scholar 

O’Brien E, Xagoraraki I. A water-focused one-health approach for early detection and prevention of viral outbreaks. One Health. 2019;7:100094.

Article  PubMed  PubMed Central  Google Scholar 

Levy JI, Andersen KG, Knight R, Karthikeyan S. Wastewater surveillance for public health. Science. 2023;379(6627):26–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Silverman AI, Boehm AB. Systematic review and meta-analysis of the persistence of enveloped viruses in environmental waters and wastewater in the absence of disinfectants. Environ Sci Technol. 2021;55(21):14480–93.

Article  CAS  PubMed  Google Scholar 

Miyani B, McCall C, Xagoraraki I. High abundance of human herpesvirus 8 in wastewater from a large urban area. J Appl Microbiol. 2021;130(5):1402–11.

Article  CAS  PubMed  Google Scholar 

McCall C, Wu H, O’Brien E, Xagoraraki I. Assessment of enteric viruses during a hepatitis outbreak in Detroit MI using wastewater surveillance and metagenomic analysis. J Appl Microbiol. 2021;131(3):1539–54.

Article  CAS  PubMed  Google Scholar 

Cantalupo PG, Calgua B, Zhao G, Hundesa A, Wier AD, Katz JP, Grabe M, Hendrix RW, Girones R, Wang D. Raw sewage harbors diverse viral populations. MBio. 2011. https://doi.org/10.1128/mbio.00180-11.

Article  PubMed  PubMed Central  Google Scholar 

Child HT, Airey G, Maloney DM, Parker A, Wild J, McGinley S, Evens N, Porter J, Templeton K, Paterson S, Aerle RV, Wade MJ, Jeffries AR, Bassano I. Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater. MBio. 2023;14(6):1–19.

Article  CAS  Google Scholar 

Xagoraraki I, Yin Z, Svambayev Z. Fate of viruses in water systems. J Environ Eng. 2014;140(7):15.

Article  Google Scholar 

Miyani B, Zhao L, Spooner M, Buch S, Gentry Z, Mehrotra A, Norton J, Xagoraraki I. Early warnings of COVID-19 second wave in Detroit. J Environ Eng. 2021;147(8):1–6.

Article  Google Scholar 

Zhao L, Zou Y, David RE, Withington S, McFarlane S, Faust RA, Norton J, Xagoraraki I. Simple methods for early warnings of COVID-19 surges: Lessons learned from 21 months of wastewater and clinical data collection in Detroit, Michigan, United States. Sci Total Environ. 2023;864:161152.

Article  CAS  PubMed  Google Scholar 

GLWA. Our Wastewater System (Great Lakes water Authority). 2023. https://www.glwater.org/our-system/wastewater-system/.

USEPA. Concentration and processing of waterborne viruses bypositive charge 1MDS cartridge filters and organic flocculation. In: Chap.14 in USEPA manual of methods of virology. Washington, DC: USEPA, 2001.

Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci. 2002;99(24):15687–92.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang D, Urisman A, Liu Y-T, Springer M, Ksiazek TG, Erdman DD, Mardis ER, Hickenbotham M, Magrini V, Eldred J. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 2003;1(2):e2.

Article  PubMed  PubMed Central  Google Scholar 

Andrews S. FastQC: a quality control tool for high throughput sequence data. Cambridge: Babraham Bioinformatics, Babraham Institute; 2010.

Google Scholar 

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Menzel P, Ng KL, Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun. 2016;7(1):11257.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ayling M, Clark MD, Leggett RM. New approaches for metagenome assembly with short reads. Brief Bioinform. 2019;21(2):584–94.

Article  PubMed Central  Google Scholar 

Bibby K, Viau E, Peccia J. Viral metagenome analysis to guide human pathogen monitoring in environmental samples. Lett Appl Microbiol. 2011;52(4):386–92.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bağcı C, Patz S, Huson DH. DIAMOND+ MEGAN: fast and easy taxonomic and functional analysis of short and long microbiome sequences. Curr Protoc. 2021;1(3):e59.

Article  PubMed  Google Scholar 

Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, Ruscheweyh H-J, Tappu R. MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput Biol. 2016;12(6):e1004957.

Article  PubMed  PubMed Central  Google Scholar 

Nayfach S, Camargo AP, Schulz F, Eloe-Fadrosh E, Roux S, Kyrpides NC. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat Biotechnol. 2021;39(5):578–85.

Article  CAS  PubMed  Google Scholar 

Nishimura Y, Yoshida T, Kuronishi M, Uehara H, Ogata H, Goto S. ViPTree: the viral proteomic tree server. Bioinformatics. 2017;33(15):2379–80.

Article  CAS  PubMed  Google Scholar 

Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001;29(12):2607–18.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Grant JR, Enns E, Marinier E, Mandal A, Herman EK, Chen C-Y, Graham M, Van Domselaar G, Stothard P. Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic Acids Res. 2023;51(W1):484–92.

Article  Google Scholar 

Li Y, Miyani B, Childs KL, Shiu S-H, Xagoraraki I. Effect of wastewater collection and concentration methods on assessment of viral diversity. Sci Total Environ. 2024;908:168128.

Article  CAS  PubMed  Google Scholar