Detecting SARS-CoV-2 Variants in Wastewater and Their Correlation With Circulating Variants in the Communities

Li, Lin; Uppal, Timsy; Hartley, Philip; Gorzalski, Andrew; Pandori, Mark; Picker, Michael A.; Verma, Subhash C.; Pagilla, Krishna

doi:10.21203/rs.3.rs-1435729/v1

Cited by 2 publications

(1 citation statement)

References 17 publications

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“…Although the PCR-based methods can provide timely and cost-effective estimation of disease prevalence, it is incapable of targeting emerging variants and providing genetic information to track virus evolution. 12,15,[34][35][36] In contrast, the ATOPlex sequencing method not only enables accurate quantification of the RNA concentration in wastewater but is also capable of identifying the co-occurrence of different VOCs, thus demonstrating wastewater as a valuable tool to monitor disease trends and variant dynamics in the community. This study found a stronger Pearson's correlation between ATOPlex sequencing and number of daily new cases compared to the PCR-based method, particularly in the LG region (The correlation coefficients (|r|) for ATOPlex, N1, and N2 in relation to the daily new cases were found to be 0.66, 0.38, and 0.23, respectively.…”

Section: Discussionmentioning

confidence: 99%

Wastewater Tiling Amplicon Sequencing Reveals Longitudinal Dynamics of SARS-CoV-2 Variants Prevalence in the Community

Wang,

Ni,

Tian

et al. 2023

Preprint

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SARS-CoV-2 continues to evolve, while the decline in clinical sequencing efforts hampers public health sectors to prepare for the menace of ongoing variant emergence and future COVID-19 surges.1Wastewater-based epidemiology (WBE) has been proposed to provide complementary insights on the variants being transmitted in communities.2However, limited research has been dedicated to the use sequencing methods for tracking disease prevalence and variant dynamics in wastewater, particularly on a large scale. Here, we employed a tiling amplicon sequencing to track the dynamics of variant of concern (VOC) in wastewater collected from Queensland, Australia from 2020 to 2022. RNA concentrations in wastewater measured by ATOPlex showed a stronger correlation and greater consistency with the number of daily new cases than a PCR-based method. The VOC dynamics observed in wastewater were largely in line with clinical reports. These findings support that WBE and sensitive sequencing methods can serve as a long-term approach for disease surveillance, thus aiding in disease outbreak prevention, control, and management.

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Section: Discussionmentioning

confidence: 99%

Wastewater Tiling Amplicon Sequencing Reveals Longitudinal Dynamics of SARS-CoV-2 Variants Prevalence in the Community

Wang,

Ni,

Tian

et al. 2023

Preprint

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Combining individual and wastewater whole genome sequencing improves SARS-CoV-2 surveillance

Troendle,

Lee,

Reyne

et al. 2024

Preprint

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Background: Robust methods to track pathogens support public health surveillance. Both wastewater (WW) and individual whole genome sequencing (WGS) are used to assess viral variant diversity and spread. However, their relative performance and the information provided by each approach have not been sufficiently quantified. Therefore, we conducted a comparative evaluation using extensive individual and wastewater longitudinal SARS-CoV-2 WGS datasets in Northern Ireland (NI). Methods: WGS of SARS-CoV-2 was performed on >4k WW samples and >23k individuals across NI from 14th November 2021 to 11th March 2023. SARS-CoV-2 RNA was amplified using the ARTIC nCov-2019 protocol and sequenced on an Illumina MiSeq. Wastewater data were analysed using Freyja to determine variant compositions, which were compared to individual data through time series and correlation analyses. Inter-programme agreements were evaluated by mean absolute error (MAE) calculations. WW treatment plant (WWTP) performances were ranked by mean MAE. Volatile periods were identified using numerical derivative analyses. Geospatial spreading patterns were determined by horizontal curve shifting. Findings: Strong concordance was observed between wastewater and individual variant compositions and distributions, influenced by sequencing rate and variant diversity. Overall variant compositions derived from individual sequences and each WWTP were regionally clustered rather than dominated by local population size. Both individual and WW sequencing detected common nucleotide substitutions across many variants and complementary additional substitutions. Conserved spreading patterns were identified using both approaches. Interpretation: Both individual and wastewater WGS effectively monitor SARS-CoV-2 variant dynamics. Combining these approaches enhances confidence in predicting the composition and spread of major variants, particularly with higher sequencing rates. Each method detects unique mutations, and their integration improves overall genome surveillance.

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Detecting SARS-CoV-2 Variants in Wastewater and Their Correlation With Circulating Variants in the Communities

Cited by 2 publications

References 17 publications

Wastewater Tiling Amplicon Sequencing Reveals Longitudinal Dynamics of SARS-CoV-2 Variants Prevalence in the Community

Wastewater Tiling Amplicon Sequencing Reveals Longitudinal Dynamics of SARS-CoV-2 Variants Prevalence in the Community

Combining individual and wastewater whole genome sequencing improves SARS-CoV-2 surveillance

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