Virome Metagenomics
Virome metagenomic sequencing is a laboratory technology that screens for all known human and animal viruses in a single test. Applied to wastewater, it reveals which viral pathogens are circulating in a community.
A proven approach, scaled for a global event
The assay employed in this program has successfully monitored viruses throughout the state of Texas over the last four years (see the TexWEB dashboard). It has identified changes in seasonal pathogen abundances, surfaced public-health-relevant outbreaks, and proven itself as an early warning system for newly emerged (Avian Flu) and remerged viruses (measles). This assay represents the next leap forward in wastewater epidemiology.
How it works
Weekly Collection
Samples are collected from wastewater treatment plants Each sample represents approximately the past 24 hours of community wastewater.
Nucleic Acid Extraction & Viral Capture
In the lab we extract nucleic acids and capture the viruses present using nanoparticle baits that are mixed into the sample and selectively bind viral particles — enriching the signal far above what untargeted sequencing can recover.
Metagenomic Sequencing
Captured viruses are sequenced. Because each virus has its own specific code, sequencing enables precise identification and lets us track viral abundance in near real time.
RPKMF Quantification
We compute RPKMF (reads per kilobase of transcript per million filtered reads), normalizing for sequencing depth and genome size. RPKMF produces quantitative trends that mirror seasonal viral patterns.
For full methodology details, see Tisza et al., Nature Communications (2023).
Key Publications
Detection, persistence, and rising prevalence of oncogenic viruses revealed by wastewater metagenomics.
Prakash H, Perez RK, Ross M, Tisza M, et al.
Landmark study showing cancer-causing viruses can be tracked in wastewater. Three years across 16 Texas cities detected six known and three suspected oncogenic viruses, with rising HPV and Epstein-Barr signal after 2024.
Read paperSequencing-Based Detection of Measles in Wastewater: Texas, January 2025.
Javornik Cregeen S, Tisza MJ, Hanson B, Cook M, et al.
Landmark prospective detection of measles in two Houston plants in January 2025 with no detections in the prior ~3 years. A linked investigation identified two unvaccinated infected travelers in the same sewershed.
Read paperSequencing-Based Detection of Avian Influenza A(H5N1) Virus in Wastewater in Ten Cities.
Tisza MJ, Hanson BM, Clark JR, Wang L, et al.
Pioneering sequencing-based detection of H5N1 across ten cities during the 2024 dairy-cattle outbreak — flagging the zoonotic virus at the community level well before detection by other means.
Read paperWastewater sequencing reveals community and variant dynamics of the collective human virome.
Tisza M, Javornik Cregeen S, Avadhanula V, Zhang P, et al.
Landmark study analyzing 363 longitudinal wastewater samples with a viral probe-capture panel — detected over 450 pathogenic viruses from 28 families, most never previously found in such samples. Signals tracked SARS-CoV-2, influenza, and mpox clinical data.
Read paperPublication History
These publications describe foundational studies critical to the establishment of pathogen-based wastewater epidemiology, particularly in the field of wastewater metagenomics.
SeqBoard: a genomics-based data dashboard for comprehensive wastewater virome monitoring.
Bauer C, Reger N, Rustem HAL, Tisza M, et al.
Describes SeqBoard, the first public-facing dashboard that turns wastewater viral sequencing data into accessible trend information for the public, public health officials, and genomics experts.
DOI: 10.1093/jamia/ocag088Wastewater Surveillance to Inform Cancer Epidemiology and Evidence-Based Interventions.
Healy HG, Hoar C, Ahmed W, Bibby K, et al.
Multidisciplinary review arguing wastewater surveillance could complement cancer surveillance by tracking oncoviruses, bacterial carcinogens, and chemical carcinogens.
DOI: 10.1021/acs.est.6c01391Detection, persistence, and rising prevalence of oncogenic viruses revealed by wastewater metagenomics.
Prakash H, Perez RK, Ross M, Tisza M, et al.
Landmark study showing cancer-causing viruses can be tracked in wastewater. Three years across 16 Texas cities detected six known and three suspected oncogenic viruses, with rising HPV and Epstein-Barr signal after 2024.
DOI: 10.1128/aem.00547-26Tracking HIV Through Wastewater: Ethical Considerations in Public Health Surveillance.
Fletcher FE, Pertuit OR, Troisi C, Kerr J, et al.
Examines the public-health ethics of using wastewater surveillance to identify areas with undiagnosed or untreated HIV — stigma prevention, privacy, and limits on data use.
DOI: 10.1093/cid/ciag241ASewers to Solutions: A Guide to Wastewater Pathogen Monitoring.
Clark JR, Maresso AW.
Review of the current state of wastewater-based epidemiology — molecular detection, data analysis, programs, and interventions — from 1940s origins through the COVID-19-driven resurgence.
DOI: 10.1146/annurev-med-062024-125121Wastewater Parvovirus B19 Signal Amid Rising Maternal Cases.
Clark JR, Tisza MJ, Hammerquist AL, Prakash H, et al.
Widespread detection of parvovirus B19 across 43 Texas sites using hybrid-capture virome sequencing. The wastewater signal rose roughly a month before case surges, enabling real-time mutation tracking.
DOI: 10.1101/2025.07.07.25331044Turning analysis into action: opportunities and challenges in implementing wastewater science for public health decision-making.
Gitter A, Ruvalcaba V, Clark K, Tran Carapucci T, et al.
Addresses the practical gap between generating wastewater surveillance data and using it to guide public health action — interpretation, communication, ethics, and decision-making.
DOI: 10.3389/fpubh.2025.1562659Sequencing-Based Detection of Measles in Wastewater: Texas, January 2025.
Javornik Cregeen S, Tisza MJ, Hanson B, Cook M, et al.
Landmark prospective detection of measles in two Houston plants in January 2025 with no detections in the prior ~3 years. A linked investigation identified two unvaccinated infected travelers in the same sewershed.
DOI: 10.2105/AJPH.2025.308146Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater.
Chen X, Balliew J, Bauer CX, Deegan J, et al.
RBD amplicon sequencing on 17 months of El Paso wastewater tracked 91 SARS-CoV-2 variants — detecting them earlier than clinical sequencing, with highest diversity during low-transmission periods.
DOI: 10.1016/j.jinf.2024.106284Sequencing-Based Detection of Avian Influenza A(H5N1) Virus in Wastewater in Ten Cities.
Tisza MJ, Hanson BM, Clark JR, Wang L, et al.
Pioneering sequencing-based detection of H5N1 across ten cities during the 2024 dairy-cattle outbreak — flagging the zoonotic virus at the community level well before detection by other means.
DOI: 10.1056/NEJMc2405937Wastewater analysis of Mpox virus in a city with low prevalence of Mpox disease: an environmental surveillance study.
Oghuan J, Chavarria C, Vanderwal SR, Gitter A, et al.
Detected mpox DNA in all four El Paso sewersheds during early 2023 despite only one reported clinical case — viral signal rose one to two weeks before that case was reported.
DOI: 10.1016/j.lana.2023.100639Wastewater sequencing reveals community and variant dynamics of the collective human virome.
Tisza M, Javornik Cregeen S, Avadhanula V, Zhang P, et al.
Landmark study analyzing 363 longitudinal wastewater samples with a viral probe-capture panel — detected over 450 pathogenic viruses from 28 families, most never previously found in such samples. Signals tracked SARS-CoV-2, influenza, and mpox clinical data.
DOI: 10.1038/s41467-023-42064-1Wastewater pandemic preparedness: Toward an end-to-end pathogen monitoring program.
Clark JR, Terwilliger A, Avadhanula V, Tisza M, et al.
First framework for an integrated, statewide wastewater program to track pathogens of pandemic potential using exclusively metagenomic sequencing — coordinating engineering, molecular science, geospatial analytics, epidemiology, and messaging.
DOI: 10.3389/fpubh.2023.1137881Assessment of a SARS-CoV-2 wastewater monitoring program in El Paso, Texas, from November 2020 to June 2022.
Gitter A, Bauer C, Wu F, Ramphul R, et al.
Evaluated a 19-month SARS-CoV-2 program across four El Paso facilities serving a largely binational, minority population. Wastewater concentrations led reported cases by 4–24 days.
DOI: 10.1080/09603123.2022.2159017Evaluating recovery, cost, and throughput of different concentration methods for SARS-CoV-2 wastewater-based epidemiology.
LaTurner ZW, Zong DM, Kalvapalle P, Reyes Gamas K, et al.
Compared five concentration methods for SARS-CoV-2 RNA on recovery, cost, and throughput. HA filtration with bead beating performed best for sensitivity and cost.
DOI: 10.1016/j.watres.2021.117043Wastewater Analysis of SARS-CoV-2 as a Predictive Metric of Positivity Rate for a Major Metropolis.
Stadler LB, Ensor KB, Clark JR, Kalvapalle P, et al.
The first major systemized effort to track SARS-CoV-2 in wastewater at scale — 39 sites across Houston (3.6M+ people) over 22 weeks. Marked Texas's early entry (April 2020) into WBE.
DOI: 10.1101/2020.11.04.20226191