Wastewater sequencing reveals community and variant dynamics of the collective human virome

Michael Tisza, Sara Javornik Cregeen, Vasanthi Avadhanula, Ping Zhang, Tulin Ayvaz, Karen Feliz, Kristi L. Hoffman, Justin R. Clark, Austen Terwilliger, Matthew C. Ross, Juwan Cormier, Hannah Moreno, Li Wang, Katelyn Payne, David Henke, Catherine Troisi, Fuqing Wu, Janelle Rios, Jennifer Deegan, Blake Hansen, John Balliew, Anna Gitter, Kehe Zhang, Runze Li, Cici X. Bauer, Kristina D. Mena, Pedro A. Piedra, Joseph F. Petrosino (), Eric Boerwinkle () and Anthony W. Maresso ()
Additional contact information
Michael Tisza: Baylor College of Medicine
Sara Javornik Cregeen: Baylor College of Medicine
Vasanthi Avadhanula: Baylor College of Medicine
Ping Zhang: Baylor College of Medicine
Tulin Ayvaz: Baylor College of Medicine
Karen Feliz: Baylor College of Medicine
Kristi L. Hoffman: Baylor College of Medicine
Justin R. Clark: Baylor College of Medicine
Austen Terwilliger: Baylor College of Medicine
Matthew C. Ross: Baylor College of Medicine
Juwan Cormier: Baylor College of Medicine
Hannah Moreno: Baylor College of Medicine
Li Wang: Baylor College of Medicine
Katelyn Payne: Baylor College of Medicine
David Henke: Baylor College of Medicine
Catherine Troisi: University of Texas Health Science Center at Houston
Fuqing Wu: University of Texas Health Science Center at Houston
Janelle Rios: University of Texas Health Science Center at Houston
Jennifer Deegan: University of Texas Health Science Center at Houston
Blake Hansen: University of Texas Health Science Center at Houston
John Balliew: El Paso Water Utility
Anna Gitter: University of Texas Health Science Center at Houston
Kehe Zhang: University of Texas Health Science Center at Houston
Runze Li: University of Texas Health Science Center at Houston
Cici X. Bauer: University of Texas Health Science Center at Houston
Kristina D. Mena: University of Texas Health Science Center at Houston
Pedro A. Piedra: Baylor College of Medicine
Joseph F. Petrosino: Baylor College of Medicine
Eric Boerwinkle: University of Texas Health Science Center at Houston
Anthony W. Maresso: Baylor College of Medicine

Nature Communications, 2023, vol. 14, issue 1, 1-10

Abstract: Abstract Wastewater is a discarded human by-product, but its analysis may help us understand the health of populations. Epidemiologists first analyzed wastewater to track outbreaks of poliovirus decades ago, but so-called wastewater-based epidemiology was reinvigorated to monitor SARS-CoV-2 levels while bypassing the difficulties and pit falls of individual testing. Current approaches overlook the activity of most human viruses and preclude a deeper understanding of human virome community dynamics. Here, we conduct a comprehensive sequencing-based analysis of 363 longitudinal wastewater samples from ten distinct sites in two major cities. Critical to detection is the use of a viral probe capture set targeting thousands of viral species or variants. Over 450 distinct pathogenic viruses from 28 viral families are observed, most of which have never been detected in such samples. Sequencing reads of established pathogens and emerging viruses correlate to clinical data sets of SARS-CoV-2, influenza virus, and monkeypox viruses, outlining the public health utility of this approach. Viral communities are tightly organized by space and time. Finally, the most abundant human viruses yield sequence variant information consistent with regional spread and evolution. We reveal the viral landscape of human wastewater and its potential to improve our understanding of outbreaks, transmission, and its effects on overall population health.

Date: 2023
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DOI: 10.1038/s41467-023-42064-1

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