Abstract
We developed a new test system to detect the omicron variant of SARS-CoV-2 using allele-specific reverse transcription PCR and estimated the frequency of its detection in patients living in the Novosibirsk Region. Clinical samples were divided into 3 groups: samples collected from December 1 to December 30, 2021 (group 1; n=66), from December 30, 2021 to January 10, 2022 (group 2; n=20), and from January 11 to January 22, 2022 (group 3; n=101). Based on the identification of 5 mutations specific to SARS-CoV-2 (B.1.1.529), two systems of oligonucleotide primers and probes were developed for detecting this coronavirus genotype in clinical samples. Limit of detection (LOD 95 ) was 4×10 3 genome equivalents per 1 ml of clinical sample for the first test system and 2×10 3 for the for the second test system. The omicron variant of SARS-CoV-2 was absent in group 1 of studied samples, but was detected in 20% (4/20) of group 2 samples and 88% of group 2 samples collected within less than 2 weeks of January 2022. Using developed test system, we showed that in less than 2 weeks the omicron variant has become dominant in patients, which confirms previously published data on its exceptional contagiousness.
Keywords: SARS-CoV 2; allele-specific reverse transcription PCR (AS-RT-PCR); coronavirus; mutations; omicron variant.
【저자키워드】 coronavirus, mutations, Omicron variant, SARS-CoV 2, allele-specific reverse transcription PCR (AS-RT-PCR), 【초록키워드】 SARS-CoV-2, Mutation, SARS-CoV, Genome, RT-PCR, clinical samples, Region, clinical, Patient, Genotype, Omicron variant, B.1.1.529, reverse transcription PCR, patients, Frequency, allele, probes, primer, contagiousness, first test, probe, dominant, detect, collected, less, exceptional, 【제목키워드】 SARS-CoV-2, Test, detection, omicron, development, System,