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

Munteanu, Viorel
; 
Saldana, Michael A
; 
Dreifuss, David
; 
Ouyang, Wenhao O
; 
Ferdous, Jannatul
; 
Mohebbi, Fatemeh
; 
Roseberry, Jessica Schlueter
; 
Ciorba, Dumitru
; 
Bostan, Viorel
; 
Gordeev, Victor
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Author
Munteanu, Viorel
Saldana, Michael A
Dreifuss, David
Ouyang, Wenhao O
Ferdous, Jannatul
Mohebbi, Fatemeh
Roseberry, Jessica Schlueter
Ciorba, Dumitru
Bostan, Viorel
Gordeev, Victor
Drabcinski, Nicolae
Su, Justin Maine
Kasianchuk, Nadiia
Sharma, Nitesh Kumar
Knyazev, Sergey
Aßmann, Eva
Lobiuc, Andrei
Covasa, Mihai
Crandall, Keith A
Wu, Nicholas C
Mason, Christopher E
Tierney, Braden T
Lucaci, Alexander G
Ophoff, Roel A
Gibas, Cynthia
Rzymski, Piotr
Skums, Pavel
Solo-Gabriele, Helena
Niko, Beerenwinkel
Zelikovsky, Alex
Hölzer, Martin
Smith, Adam
Mangul, Serghei
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Department
Computational Biology
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Journal article
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http://creativecommons.org/licenses/by/4.0/
Language
English
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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.
Citation
V. Munteanu, M.A. Saldana, D. Dreifuss, W.O. Ouyang, J. Ferdous, F. Mohebbi , et al., "SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities," Genome Biology, vol. 27, no. 1, pp. 1-1, 2026, https://doi.org/10.1186/s13059-025-03927-6.
Source
Genome Biology
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Keywords
31 Biological Sciences, 3102 Bioinformatics and Computational Biology, Computational Biology, COVID-19, Genome, Viral, Genomics, Humans, SARS-CoV-2, Wastewater, 3 Good Health and Well Being
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Publisher
Springer Nature
DOI
10.1186/s13059-025-03927-6
Additional links
https://link.springer.com/article/10.1186/s13059-025-03927-6
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