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Development of a Test System to Detect the Omicron Variant of SARS-CoV-2 and the Frequency of Its Detection in Patients

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 Dece...

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Detalles Bibliográficos
Autores principales: Filipenko, M. L., Oskorbin, I. P., Shamovskaya, D. V., Kharpov, E. A., Stepanov, A. A., Romanov, V. V., Kuznetsov, V. V., Boyarskikh, U. A., Kechin, A. A., Pechkovsky, E. V., Krivoruchko, A. B., Ivanov, A. M., Kushlinskii, N. E., Vlasov, V. V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9218049/
https://www.ncbi.nlm.nih.gov/pubmed/35737161
http://dx.doi.org/10.1007/s10517-022-05524-0
Descripción
Sumario: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.