VirPool: Model-Based Estimation of SARS-CoV-2 Variant Proportions in Wastewater Samples

Gafurov, Askar; Baláž, Andrej; Amman, Fabian; Boršová, Kristína; Čabanová, Viktória; Klempa, Boris; Bergthaler, Andréas; Vinař, Tomáš; Brejová, Broňa

doi:10.1101/2022.06.21.22276717

Cited by 2 publications

(1 citation statement)

References 37 publications

(55 reference statements)

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“…On the other hand, as a result of the proliferation of SARS-CoV-2 variants, specific mutations have been monitored to study the evolution of variants (Bar-Or et al 2021) and the total SARS-CoV-2 concentration (Radu et al 2022). Recently, statistical methods have been proposed that make it possible to analyze the readings of mutation frequencies in the virus genome in order to obtain precise estimates of the proportions of variants (Barbeito et al 2022, Gafurov et al 2022, Karthikeyan et al 2022, Radu et al 2022, Valieris et al 2022). In this paper, the joint mutation distribution is estimated using GISAID data and the variant proportions are estimated using maximum likelihood.…”

Section: Motivation and Backgroundmentioning

confidence: 99%

SARS-CoV-2 VARIANT PREVALENCE ESTIMATION USING WASTEWATER SAMPLES

López-de-Ullibarri¹,

Tomás

Trigo-Tasende³

et al. 2023

Preprint

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The present work describes a statistical model to account for sequencing information of SARS-CoV-2 variants in wastewater samples. The model expresses the joint probability distribution of the number of genomic reads corresponding to mutations and non-mutations in every locus in terms of the variant proportions and the joint mutation distribution within every variant. Since the variant joint mutation distribution can be estimated using GISAID data, the only unknown parameters in the model are the variant proportions. These are estimated using maximum likelihood. The method is applied to monitor the evolution of variant proportions using genomic data coming from wastewater samples collected in A Coruna (NW Spain) in the period May 2021 - March 2022. Although the procedure is applied assuming independence among the number of reads along the genome, it is also extended to account for Markovian dependence of counts along loci in the aggregated information coming from wastewater samples.

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Section: Motivation and Backgroundmentioning

confidence: 99%

SARS-CoV-2 VARIANT PREVALENCE ESTIMATION USING WASTEWATER SAMPLES

López-de-Ullibarri¹,

Tomás

Trigo-Tasende³

et al. 2023

Preprint

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Wastewater early warning system for SARS-CoV-2 outbreaks and variants in a Coruña, Spain

Trigo-Tasende

Vallejo

Rumbo‐Feal

et al. 2023

Environ Sci Pollut Res

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Wastewater-based epidemiology has been widely used as a cost-effective method for tracking the COVID-19 pandemic at the community level. Here we describe COVIDBENS, a wastewater surveillance program running from June 2020 to March 2022 in the wastewater treatment plant of Bens in A Coruña (Spain). The main goal of this work was to provide an effective early warning tool based in wastewater epidemiology to help in decision-making at both the social and public health levels. RT-qPCR procedures and Illumina sequencing were used to weekly monitor the viral load and to detect SARS-CoV-2 mutations in wastewater, respectively. In addition, own statistical models were applied to estimate the real number of infected people and the frequency of each emerging variant circulating in the community, which considerable improved the surveillance strategy. Our analysis detected 6 viral load waves in A Coruña with concentrations between 103 and 106 SARS-CoV-2 RNA copies/L. Our system was able to anticipate community outbreaks during the pandemic with 8–36 days in advance with respect to clinical reports and, to detect the emergence of new SARS-CoV-2 variants in A Coruña such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529 and BA.2) in wastewater with 42, 30, and 27 days, respectively, before the health system did. Data generated here helped local authorities and health managers to give a faster and more efficient response to the pandemic situation, and also allowed important industrial companies to adapt their production to each situation. The wastewater-based epidemiology program developed in our metropolitan area of A Coruña (Spain) during the SARS-CoV-2 pandemic served as a powerful early warning system combining statistical models with mutations and viral load monitoring in wastewater over time.

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VirPool: Model-Based Estimation of SARS-CoV-2 Variant Proportions in Wastewater Samples

Cited by 2 publications

References 37 publications

SARS-CoV-2 VARIANT PREVALENCE ESTIMATION USING WASTEWATER SAMPLES

SARS-CoV-2 VARIANT PREVALENCE ESTIMATION USING WASTEWATER SAMPLES

Wastewater early warning system for SARS-CoV-2 outbreaks and variants in a Coruña, Spain

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