Importance of E484K and N501Y mutations in SARS-CoV-2 for genomic surveillance: rapid detection by restriction enzyme analysis

ABSTRACT

IntroductionVariants of Concern of SARS-CoV-2 (VOCs), the new coronavirus responsible for COVID-19, have emerged in several countries. Two mutations in the gene coding for the Spike protein of the viral genome are particularly important and associated with some of these variants E484K and N501Y. Restriction enzyme analysis is proposed as a rapid method to detect these two mutations. MethodologyA search on GISAID was performed in April 2021 to detect the frequency of these two mutations in the sequence available and their association with other lineages. A small amplicon from the Spike gene was digested with two enzymes HpyAV, which allows detecting E484K mutation, and MseI, for detecting the N501Y one. ResultsThe mutations E484K and N501Y, associated with VOCs, have emerged in several other lineages, particularly E484K. A 100% correlation was observed with sequencing results. ConclusionsThe proposed methodology, which allows screening a great number of samples, will probably help to provide more information on the prevalence and epidemiology of these mutations worldwide, to select the candidates for whole-genome sequencing.