Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling

https://doi.org/10.1016/j.scitotenv.2021.149691Get rights and content

Highlights

  • SARS-CoV-2 from two wastewater treatment plant influents was sequenced.

  • Wastewater surveillance provides community-level SARS-CoV-2 sequence data.

  • Mutations in Delta, Gamma, and Iota VOCs were detected in South Carolina wastewater.

  • The spike mutation N501Y was detected in July 2020 in South Carolina wastewater.

  • Potential VOCs detected in wastewater in January 2021 were absent from clinical sequences.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for causing the COVID-19 pandemic, can be detected in untreated wastewater. Wastewater surveillance of SARS-CoV-2 complements clinical data by offering earlier community-level detection, removing underlying factors such as access to healthcare, sampling asymptomatic patients, and reaching a greater population. Here, we compare 24-hour composite samples from the influents of two different wastewater treatment plants (WWTPs) in South Carolina, USA: Columbia and Rock Hill. The sampling intervals span the months of July 2020 and January 2021, which cover the first and second waves of elevated SARS-CoV-2 transmission and COVID-19 clinical cases in these regions. We identify four signature mutations in the surface glycoprotein (spike) gene that are associated with the following variants of interest or concern, VOI or VOC (listed in parenthesis): S477N (B.1.526, Iota), T478K (B.1.617.2, Delta), D614G (present in all VOC as of May 2021), and H655Y (P.1, Gamma). The N501Y mutation, which is associated with three variants of concern, was identified in samples from July 2020, but not detected in January 2021 samples. Comparison of mutations identified in viral sequence databases such as NCBI Virus and GISAID indicated that wastewater sampling detected mutations that were present in South Carolina, but not reflected in the clinical data deposited into databases.

Abbreviations

VOC
variant of concern
VOI
variant of interest
WW
wastewater
WWTP
wastewater treatment plant
SNVs
single nucleotide variants
SARS-CoV-2
Severe acute respiratory syndrome coronavirus 2

Keywords

Wastewater-based epidemiology
SARS-CoV-2
Variant detection
Sewage surveillance

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