Quantitative SARS-CoV-2 Alpha Variant B.1.1.7 Tracking in Wastewater by Allele-Specific RT-qPCR

The critical need for surveillance of SARS-CoV-2 variants concern has prompted the development methods that can track in wastewater. Here, we develop and present an open-source method based on allele-specific RT-qPCR (AS RT-qPCR) detects quantifies B.1.1.7 variant, targeting spike protein mutations at three independent genomic loci are highly predictive (HV69/70del, Y144del, A570D). Our assays reliably detect quantify low levels with cross-reactivity, variant proportions down to 1% a background mixed SARS-CoV-2. Applying our wastewater samples from United States, occurrence over time 19 communities. AS results align clinical trends, summation wild-type sequences quantified by matches indicated U.S. CDC N1 N2 assays. This work paves way as rapid inexpensive