Quantitative sars-cov-2 alpha variant b.1.1.7 tracking in wastewater by allele-specific rt-qpcr

Lee, W. L.; Imakaev, M.; Armas, F.; McElroy, K. A.; Gu, X.; Duvallet, C.; Chandra, F.; Chen, H.; Leifels, M.; Mendola, S.; Floyd-O'sullivan, R.; Powell, M. M.; Wilson, S. T.; Berge, K. L. J.; Lim, C. Y. J.; Wu, F.; Xiao, A.; Moniz, K.; Ghaeli, N.; Matus, M.; Thompson, J.; Alm, E. J.

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. © 2021 The Authors. Published by American Chemical Society.