Accelerating pandemic response with the emergency Omicron RT‐PCR test: A comprehensive solution for COVID‐19 diagnosis and tracking

Abstract

The Omicron variant of concern (VOC) has surged in many countries and replaced the previously reported VOC. To identify different Omicron strains/sublineages on a rapid, convenient, and precise platform, we report a novel multiplex real‐time reverse transcriptase polymerase chain reaction (RT‐PCR) method in one tube based on the Omicron lineage sequence variants' information. Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) subvariants were used in a PCR‐based assay for rapid identification of Omicron sublineage genotyping in 1000 clinical samples. Several characteristic mutations were analyzed using specific primers and probes for the spike gene, del69–70, and F486V. To distinguish Omicron sublineages (BA.2, BA.4, and BA.5), the NSP1:141–143del in the ORF1a region and D3N mutation in membrane protein occurring outside the spike protein region were analyzed. Results from the real‐time PCR assay for one‐tube accuracy were compared to those of whole genome sequencing. The developed PCR assay was used to analyze 400 SARS‐CoV‐2 positive samples. Ten samples determined as BA.4 were positive for NSP1:141–143del, del69–70, and F486V mutations; 160 BA.5 samples were positive for D3N, del69–70, and F486V mutations, and 230 BA.2 samples were without del69–70. Screening these samples allowed the identification of epidemic trends at different time intervals. Our novel one‐tube multiplex PCR assay was effective in identifying Omicron sublineages.