Quantitative SARS-CoV-2 Alpha variant B.1.1.7 tracking in wastewater by allele-specific RT-qPCR
Reference: Environmental Science & Technology Letters (2021) 8: 675-682

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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Published By
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., Janelle THOMPSON, Alm E.J.