Tracking SARS-CoV-2 genomic variants in wastewater sequencing data with LolliPop Author summary Wastewater-based epidemiology has become a valuable tool for tracking viruses like SARS-CoV-2 across entire communities. Sequencing wastewater can reveal which viral variants are circulating, offering early insights into variant dynamics while avoiding the biases of clinical testing. A central challenge is to infer the relative abundances of these variants from observed mutation data. This task is complicated by the fact that variant profiles can be highly similar, and the data is often noisy with many missing read count values from genomic positions with no coverage, especially when the incidence of the pathogen is low. We developed LolliPop, a statistical method that leverages the time series structure of wastewater data to robustly deconvolve variant abundances and compute fast confidence intervals. Using both simulated data and real data from the Swiss national variant monitoring, we show that LolliPop is accurate and robust to high levels of missing data.

LolliPop enables accurate deconvolution of SARS-CoV-2 variants from wastewater sequencing, strengthening genomic surveillance and early outbreak detection. 🧬🚰 #WastewaterEpidemiology #COVID19 #Bioinformatics
📄 https://doi.org/10.1371/journal.pcbi.1014003
👤 EVBC member: Niko Beerenwinkel

The Unseen Oracle: How Wastewater Epidemiology Is Revolutionizing Public Health and the Perils That Lie Ahead "Wastewater epidemiology offers an early warning for disease outbreaks but faces critical funding and ethical challenges that threaten its future."

From Sewers to Sentinels: The CDC's Disease Tracking System Covers 151 Million Americans, But Its Future Is Uncertain
#WastewaterEpidemiology #PublicHealth #DiseaseSurveillance #CDC #NWSS #HealthTech #Science #FactRage #FactRageNews

tglm.us/E690W

Optimizing RT-qPCR multiplex assays for simultaneous detection of enteric and respiratory viruses in wastewater | Journal of Water and Health | IWA Publishing HIGHLIGHTS. Triplex assays to detect enteric viruses in wastewater.Monitored levels of Coxsackievirus A6, Enterovirus D68, Norovirus GII, and Enterovirus i

NEW PAPER: Optimizing RT-qPCR multiplex assays for simultaneous detection of enteric and respiratory viruses in wastewater #OA #WastewaterEpidemiology

iwaponline.com/jwh/article/...

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#EnvironmentalScienc #OneHealth #WaterQuality #CWBE #CommunityScience #WasteWaterEpidemiology #Ecotoxicology #EarlyWarningSystems #WaterInnovation #ClimateChange #Sustainability

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Benchmarking sequencing technologies for #wastewater-based #SARSCoV2 #surveillance reveals trade-offs between cost, timeliness, and accuracy.
#VirusBioinformatics #WastewaterEpidemiology #SARSCoV2Surveillance #NGS

📄 doi.org/10.1016/j.wa...
EVBC👤: Niko Beerenwinkel