Journal
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
Volume 8, Issue 8, Pages 675-682Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.estlett.1c00375
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Funding
- National Research Foundation, Prime Minister's Office, Singapore, under its Campus for Research Excellence and Technological Enterprise (CREATE) program, Intra-CREATE Thematic Grant (Cities) Grant [NRF2019-THE001-0003a]
- Singapore Ministry of Education
- National Research Foundation through an RCE award
- Massachusetts Consortium on Pathogen Readiness
- China Evergrande Group
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This study developed a detection method for tracking the B.1.1.7 variant in wastewater, which can reliably detect low levels of B.1.1.7 and provide rapid and inexpensive surveillance of SARS-CoV-2 variants.
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.
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