Quantitative SARS-CoV-2 Alpha Variant B.1.1.7 Tracking in Wastewater by Allele-Specific RT-qPCR
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acs.estlett.1c00375.pdf
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Author(s)
Lee, Wei Lin
Imakaev, Maxim
Armas, Federica
McElroy, Kyle A.
Gu, Xiaoqiong
Duvallet, Claire
Chandra, Franciscus
Chen, Hongjie
Leifels, Mats
Mendola, Samuel
Date Issued
July 2021
Journal
Environmental Science & Technology Letters
Publisher
American Chemical Society (ACS)
Citation
Lee, Wei Lin et al. "Quantitative SARS-CoV-2 Alpha Variant B.1.1.7 Tracking in Wastewater by Allele-Specific RT-qPCR." Environmental Science & Technology Letters (July 2021): dx.doi.org/10.1021/acs.estlett.1c00375. © 2021 The Authors
Version
Final published version
Abstract
The critical need for surveillance of SARS-CoV-2 variants of concern has prompted the development of methods that can track variants in wastewater. Here, we develop and present an open-source method based on allele-specific RT-qPCR (AS RT-qPCR) that detects and quantifies the B.1.1.7 variant, targeting spike protein mutations at three independent genomic loci that are highly predictive of B.1.1.7 (HV69/70del, Y144del, and A570D). Our assays can reliably detect and quantify low levels of B.1.1.7 with low cross-reactivity, and at variant proportions down to 1% in a background of mixed SARS-CoV-2. Applying our method to wastewater samples from the United States, we track the occurrence of B.1.1.7 over time in 19 communities. AS RT-qPCR results align with clinical trends, and summation of B.1.1.7 and wild-type sequences quantified by our assays matches SARS-CoV-2 levels indicated by the U.S. CDC N1 and N2 assays. This work paves the way for AS RT-qPCR as a method for rapid inexpensive surveillance of SARS-CoV-2 variants in wastewater.
MIT Department
Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics
Massachusetts Institute of Technology. Department of Biological Engineering
Singapore-MIT Alliance in Research and Technology (SMART)
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Creative Commons Attribution-NonCommercial-NoDerivs License
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DOI of Published Version
https://doi.org/10.1021/acs.estlett.1c00375
