Detection of the SARS-CoV-2 Omicron Variant in COVID-19 Patients from South Tangerang Using SNP-Probes S371L and K417N

The COVID-19 pandemic caused by the SARS-CoV-2 virus has posed a global challenge. Experts from various branches of science have endeavoured to find solutions to control its spread, one of which has been the quick and precise detection of the virus and its variants in patients. This study aimed to detect the presence of SARS-CoV-2, notably the rapidly spreading Omicron variant, using the spike (S)-gene target failure (SGTF) and S-gene target positive (SGTP) with the principle of the single nucleotide polymorphism (SNP)-probe test. Our descriptive experimental approach detected Omicron variants with the SNP-probe technique using samples of SARS-CoV-2 patients and controls. The probes were designed to recognize the nucleotide code of the amino acids in positions 371 and 417 of SARS-CoV-2. The existence of variants was monitored by the presence or absence of a fluorescence signal, which was translated into a sigmoidal graph using a real-time (RT)-PCR machine. One hundred and twelve samples that had tested positive for SARS-CoV-2 and the Omicron variant using a registered commercial kit showed a similar result to our in-house-developed SNP-probe 371 and 417 assays. The results of this study indicate that the SNP-probe we designed can be used in the detection of the SARS-CoV-2 Omicron variant