Species-Level Identification of SARS-CoV-2 by <i>E</i> Gene Conservative Locus

Abstract

The appearance of mutations in the genes encoding the surface proteins of the new type of coronavirus SARS-CoV-2, when it circulates in the host population, makes it difficult to use monoclonal antibodies for its species identification. In such cases, the choice of conservative genetic targets allows identification by molecular biological methods. In this work, previously developed primers specific to the E gene fragment were tested to detect a new type of coronavirus on six isolates belonging to different genetic variants (the original Wuhan strain, delta and omicron). The choice of a conservative site of the E gene encoding the small transmembrane protein E as a target for reverse transcription with subsequent amplification (RT-PCR) made it possible to detect coronavirus regardless of its subtypes characterized by antigenic heterogeneity in N- and S‑proteins. The possibility of species-level identification of COVID-19 pathogen circulating in Russia is shown, both in the total reaction volume (in a single test tube) and on biological microarrays.