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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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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
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author 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.
author_facet 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.
author_sort Filipenko, M. L.
collection PubMed
description 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.
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spelling pubmed-92180492022-06-23 Development of a Test System to Detect the Omicron Variant of SARS-CoV-2 and the Frequency of Its Detection in Patients 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. Bull Exp Biol Med Article 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. Springer US 2022-06-23 2022 /pmc/articles/PMC9218049/ /pubmed/35737161 http://dx.doi.org/10.1007/s10517-022-05524-0 Text en © Springer Science+Business Media, LLC, part of Springer Nature 2022 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Article
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.
Development of a Test System to Detect the Omicron Variant of SARS-CoV-2 and the Frequency of Its Detection in Patients
title Development of a Test System to Detect the Omicron Variant of SARS-CoV-2 and the Frequency of Its Detection in Patients
title_full Development of a Test System to Detect the Omicron Variant of SARS-CoV-2 and the Frequency of Its Detection in Patients
title_fullStr Development of a Test System to Detect the Omicron Variant of SARS-CoV-2 and the Frequency of Its Detection in Patients
title_full_unstemmed Development of a Test System to Detect the Omicron Variant of SARS-CoV-2 and the Frequency of Its Detection in Patients
title_short Development of a Test System to Detect the Omicron Variant of SARS-CoV-2 and the Frequency of Its Detection in Patients
title_sort development of a test system to detect the omicron variant of sars-cov-2 and the frequency of its detection in patients
topic Article
url 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
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