High-resolution melting analysis to discriminate between the SARS-CoV-2 Omicron variants BA.1 and BA.2

Takuro Koshikawa; Hiroshi Miyoshi

doi:10.1016/j.bbrep.2022.101306

High-resolution melting analysis to discriminate between the SARS-CoV-2 Omicron variants BA.1 and BA.2

Biochem Biophys Rep. 2022 Sep:31:101306. doi: 10.1016/j.bbrep.2022.101306. Epub 2022 Jul 1.

Authors

Takuro Koshikawa¹, Hiroshi Miyoshi¹

Affiliation

¹ Department of Microbiology, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae, Kawasaki, 216-8511, Japan.

Abstract

High-resolution melting (HRM) analysis was conducted to discriminate between SARS-CoV-2 Omicron variant BA.1 (B.1.1.529.1) and subvariant BA.2 (B.1.1.529.2). We performed two-step PCR consisting of the first PCR and the second nested PCR to prepare the amplicon for HRM analysis, which detected G339D, N440K, G446S and D796Y variations in the SARS-CoV-2 spike protein. The melting temperatures (Tms) of the amplicons from the cDNA of the Omicron variant BA.1 and subvariant BA.2 receptor binding domain (RBD) in spike protein were the same: 75.2 °C (G339D variation) and 73.4 °C (D796Y variation). These Tms were distinct from those of SARS-CoV-2 isolate Wuhan-Hu-1, and were specific to the Omicron variant. In HRM analyses that detected the N440K and G446S variations, the Tms of amplicons from the cDNA of the Omicron variant BA.1 and subvariant BA.2 RBDs were 73.0 °C (N440K and G446S variations) and 73.5 °C (G446S variation). This difference indicates that the SARS-CoV-2 Omicron variants BA.1 and BA.2 can be clearly discriminated. Our study demonstrates the usefulness of HRM analysis after two-step PCR for the discrimination of SARS-CoV-2 variants.

Keywords: HRM analysis; Omicron; RBD; SARS-CoV-2; Subvariant; high-resolution melting, HRM; melting temperature, Tm; nucleotide, nt; receptor binding domain, RBD; severe acute respiratory syndrome coronavirus 2, SARS-CoV-2; wild type, wt.