Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR

Figures & data

Figure 1. Differential melting temperatures of PCR products with non-Delta SARS-CoV-2 and the Delta variant. (A) With the 6-FAM probe designed to match the area incorporating the C22995A mutation exactly, dilutions of a control SARS-CoV-2 Delta variant (positive control from Kansas State Veterinary Diagnostic Laboratory) used in the Delta RT-FRET-PCR had a T_m of around 56.1°C. With the SARS-CoV-2 strains that did not have the mutation (2019-nCOV/USA-WA1/2020), the A to C mismatch with the probe resulted in a lower T_m of around 52.5°C. The T_m values did not vary significantly with the copy number. The negative control was RNA from a human nasal swab negative for SARS-CoV-2 by routine diagnostic PCR. (B) T_m analysis of representative Delta RT FRET-PCR products from controls and human nasal swab samples with non-Delta variant SARS-CoV-2 (blue lines) and Delta variants (red lines), all confirmed by DNA sequencing. The T_m values for the non-Delta strains were around 52.5°C, while those of the Delta variant were clearly different at around 56.1°C.