Four Years of Continuous Weekly Wastewater Analysis Reveals Sequencing as a Robust Alternative to PCR for Respiratory Virome Surveillance.
- 1Baylor College of Medicine
Abstract
Wastewater-based epidemiology uses both targeted and non-targeted bioanalytical approaches to detect and track disease-causing microbes in wastewater. Targeted approaches such as quantitative polymerase chain reaction (qPCR) remain widely used while sequencing-based approaches have slowly gained popularity. However, concordance between established targeted molecular assays and sequencing approaches remains incompletely characterized. To assess the validity of sequencing as an alternative to qPCR, we compared outcomes of both methods targeting five respiratory viruses in wastewater samples collected across 16 Texas cities over 4 years (May 2022-July 2026) of continuous sampling. We found positive correlations between qPCR and sequencing measurements, with both methods independently correlating with statewide clinical emergency department visits. qPCR positivity also increased with genomic sequencing coverage, and sequencing demonstrated greater potential than qPCR as an early respiratory virus outbreak detection method. Our findings support metagenomic sequencing as a sensitive and highly specific alternative to targeted qPCR for wastewater surveillance, and reinforce its utility towards long-term longitudinal monitoring of respiratory viruses.
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BibTeX
@misc{prakash2026four,
title = {{Four Years of Continuous Weekly Wastewater Analysis Reveals Sequencing as a Robust Alternative to PCR for Respiratory Virome Surveillance.}},
author = {H. Prakash and V. Avadhanula and M. J. Tisza and J. Cormier and M. C. Ross and R. K. Perez and J. D. Chang and C. R. Mazurek and J. Deegan and J. F. Petrosino and P. Piedra and J. R. Clark and E. Boerwinkle and A. W. Maresso},
howpublished = {medRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.13.26364774},
url = {https://www.medrxiv.org/content/10.64898/2026.10.13.26364774v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Four Years of Continuous Weekly Wastewater Analysis Reveals Sequencing as a Robust Alternative to PCR for Respiratory Virome Surveillance.
AU - H. Prakash
AU - V. Avadhanula
AU - M. J. Tisza
AU - J. Cormier
AU - M. C. Ross
AU - R. K. Perez
AU - J. D. Chang
AU - C. R. Mazurek
AU - J. Deegan
AU - J. F. Petrosino
AU - P. Piedra
AU - J. R. Clark
AU - E. Boerwinkle
AU - A. W. Maresso
PY - 2026
DA - 2026/10/13
PB - medRxiv
DO - 10.64898/2026.10.13.26364774
UR - https://www.medrxiv.org/content/10.64898/2026.10.13.26364774v1
AB - Wastewater-based epidemiology uses both targeted and non-targeted bioanalytical approaches to detect and track disease-causing microbes in wastewater. Targeted approaches such as quantitative polymerase chain reaction (qPCR) remain widely used while sequencing-based approaches have slowly gained popularity. However, concordance between established targeted molecular assays and sequencing approaches remains incompletely characterized. To assess the validity of sequencing as an alternative to qPCR, we compared outcomes of both methods targeting five respiratory viruses in wastewater samples collected across 16 Texas cities over 4 years (May 2022-July 2026) of continuous sampling. We found positive correlations between qPCR and sequencing measurements, with both methods independently correlating with statewide clinical emergency department visits. qPCR positivity also increased with genomic sequencing coverage, and sequencing demonstrated greater potential than qPCR as an early respiratory virus outbreak detection method. Our findings support metagenomic sequencing as a sensitive and highly specific alternative to targeted qPCR for wastewater surveillance, and reinforce its utility towards long-term longitudinal monitoring of respiratory viruses.
ER -