Evidence map›Paper›PMID 41931975›Full record

ArticleInternational journal of hygiene and environmental health2026

An integrated framework for early detection and transmissibility assessment of emerging variants in wastewater.

Xingwen Chen, Tin Phan, Wei Lin Lee, Katie Clark, Steven F Rhode, Samantha Brozak, Bruce Pell, Tsultrim Palden, Mats Leifels, Anna Gitter and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in International journal of hygiene and environmental health, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors.

Xingwen ChenDepartment of Environmental and Occupational Health Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
Tin PhanTheoretical Biology and Biophysics, Los Alamos National Laboratory, New Mexico, USA.
Wei Lin LeeAntimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore.
Katie ClarkDepartment of Environmental and Occupational Health Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
Steven F RhodeMassachusetts Water Resources Authority, Boston, MA, USA.
Samantha BrozakSchool of Mathematical and Statistical Sciences, Arizona State University, Arizona, USA.
Bruce PellDepartment of Mathematics and Computer Science, Lawrence Technological University, Michigan, USA.
Tsultrim PaldenDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
Mats LeifelsDivision Water Quality and Health, Department of Pharmacology, Physiology, and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria.
Anna GitterDepartment of Environmental and Occupational Health Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
Yang KuangSchool of Mathematical and Statistical Sciences, Arizona State University, Arizona, USA.
Stefan WuertzCampus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore.
Janelle ThompsonCampus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore.
Kristina D MenaDepartment of Environmental and Occupational Health Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
Eric J AlmAntimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Fuqing WuDepartment of Environmental and Occupational Health Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA. Electronic address: fuqing.wu@uth.tmc.edu.

Funding

A wastewater approach to viral transmission, evolution, and ecologyR01AI192873 · NIAID · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI Fuqing Wu · 2025 to 2026
$1.1M
NIAID NIH HHS R01 AI192873
6 · The paper itself

Abstract

Tracking the emergence of new viral variants is critical for epidemic preparedness, but remains challenging because variants typically circulate at low prevalence during the early phase of outbreaks. Here, we present an integrated framework that combines sensitive variant detection in wastewater with quantitative assessment of transmissibility through dynamic epidemic modeling. Using the SARS-CoV-2 Omicron variant as a proof of concept, we developed a novel nested allele-specific RT-qPCR assay (NAS-PCR) that achieved a thousand-fold increase in sensitivity compared with allele-specific RT-qPCR (limit of detection: 0.5 copies/μl). NAS-PCR detected Omicron in wastewater samples from the Greater Boston area starting in September 2021, more than two months before the first reported clinical case in the U.S. To assess transmissibility, we developed a Susceptible-Infected-Viral load model that estimated Omicron's basic reproduction number (R

Indexed as

COVID-19SARS-CoV-2WastewaterBostonHumansWastewaterBasic reproduction numberEpidemic modelingNested allele-specific PCRSARS-CoV-2 omicronVariant detectionWastewater surveillance

Identifiers

PMID41931975
PMCPMC13188176

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.