SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities

Viorel Munteanu, Department of Computers, Informatics and Microelectronics, Technical University of Moldova, Chisinau, 2045, Moldova. viorel.munteanu@lt.utm.md.
Michael A. Saldana, Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA, 90089, USA.
David Dreifuss, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
Wenhao O. Ouyang, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Jannatul Ferdous, Department of Bioinformatics and Genomics, University of North Carolina Charlotte, Charlotte, USA.
Fatemeh Mohebbi, Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA, 90033, USA.
Jessica Schlueter Roseberry, Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, USA.
Dumitru Ciorba, Department of Computers, Informatics and Microelectronics, Technical University of Moldova, Chisinau, 2045, Moldova.
Viorel Bostan, Department of Computers, Informatics and Microelectronics, Technical University of Moldova, Chisinau, 2045, Moldova.
Victor Gordeev, Department of Electrical Engineering and Computer Science, "Ştefan Cel Mare" University of Suceava, Suceava, 720229, Romania.
Nicolae Drabcinski, Department of Computers, Informatics and Microelectronics, Technical University of Moldova, Chisinau, 2045, Moldova.
Justin Maine Su, Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
Nadiia Kasianchuk, Department of Computer Science, Kyiv School of Economics, Kiev, 03113, Ukraine.
Nitesh Kumar Sharma, Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, Los Angeles, CA, 90033, USA.
Sergey Knyazev, Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, Los Angeles, CA, 90033, USA.
Eva Aßmann, Genome Competence Center (MF 1), Method Development and Research Infrastructure, Robert Koch Institute, Berlin, 13353, Germany.
Andrei Lobiuc, College of Medicine and Biological Sciences, "Ştefan Cel Mare" University of Suceava, Suceava, 720229, Romania.
Mihai Covasa, College of Medicine and Biological Sciences, "Ştefan Cel Mare" University of Suceava, Suceava, 720229, Romania.
Keith A. Crandall, Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA.
Nicholas C. Wu, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Christopher E. Mason, Department of Systems and Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA.
Braden T. Tierney, Department of Systems and Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA.
Alexander G. Lucaci, Department of Systems and Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA.
Roel A. Ophoff, Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.
Cynthia Gibas, Department of Bioinformatics and Genomics, University of North Carolina Charlotte, Charlotte, USA.
Piotr Rzymski, Department of Environmental Medicine, Poznan University of Medical Sciences, Poznan, Poland.
Pavel Skums, School of Computing, University of Connecticut, Storrs, CT, USA.
Helena Solo-Gabriele, Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL, USA.
Beerenwinkel Niko, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
Alex Zelikovsky, College of Medicine and Biological Sciences, "Ştefan Cel Mare" University of Suceava, Suceava, 720229, Romania.
Martin Hölzer, Genome Competence Center (MF 1), Method Development and Research Infrastructure, Robert Koch Institute, Berlin, 13353, Germany.
Adam Smith, Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA, 90089, USA.

Document Type

Journal Article

Publication Date

1-12-2026

Journal

Genome biology

Volume

27

Issue

1

DOI

10.1186/s13059-025-03927-6

Abstract

Wastewater-based genomic surveillance (WWGS) has proven effective for monitoring SARS-CoV-2 and other viruses within communities. It enables rapid detection of known and emerging mutations and provides insights into circulating lineages. Despite its advantages, WWGS faces challenges in sample processing and computational analysis, particularly in distinguishing similar lineages and identifying novel ones. Recent methods for wastewater sequencing (WWS) analysis remain largely untested amid declining clinical surveillance and ongoing viral evolution. This review examines opportunities and limitations of WWGS, focusing on sample preparation, sequencing technologies, and bioinformatics approaches, and highlights its potential to strengthen public health monitoring systems.

Department

Biostatistics and Bioinformatics

Link to Full Text

Share

COinS