دورية أكاديمية
Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2.
| العنوان: | Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2. |
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| المؤلفون: | Shipulin GA; Federal State Budgetary Institution 'Centre for Strategic Planning and Management of Biomedical Health Risks' of the Federal Medical Biological Agency, Moscow, Russia., Savochkina Y; Federal State Budgetary Institution 'Centre for Strategic Planning and Management of Biomedical Health Risks' of the Federal Medical Biological Agency, Moscow, Russia., Shuryaeva AK; Federal State Budgetary Institution 'Centre for Strategic Planning and Management of Biomedical Health Risks' of the Federal Medical Biological Agency, Moscow, Russia., Glushchenko EE; Federal State Budgetary Institution 'Centre for Strategic Planning and Management of Biomedical Health Risks' of the Federal Medical Biological Agency, Moscow, Russia., Luparev AR; Federal State Budgetary Institution 'Centre for Strategic Planning and Management of Biomedical Health Risks' of the Federal Medical Biological Agency, Moscow, Russia., Polyakova VA; Federal State Budgetary Institution 'Centre for Strategic Planning and Management of Biomedical Health Risks' of the Federal Medical Biological Agency, Moscow, Russia., Danilov DI; Federal State Budgetary Institution 'Centre for Strategic Planning and Management of Biomedical Health Risks' of the Federal Medical Biological Agency, Moscow, Russia., Davydova EE; Federal State Budgetary Institution 'Centre for Strategic Planning and Management of Biomedical Health Risks' of the Federal Medical Biological Agency, Moscow, Russia., Vinogradov KS; Federal State Budgetary Institution 'Centre for Strategic Planning and Management of Biomedical Health Risks' of the Federal Medical Biological Agency, Moscow, Russia., Stetsenko IF; Federal State Budgetary Institution 'Centre for Strategic Planning and Management of Biomedical Health Risks' of the Federal Medical Biological Agency, Moscow, Russia., Aiginin AA; Federal State Budgetary Institution 'Centre for Strategic Planning and Management of Biomedical Health Risks' of the Federal Medical Biological Agency, Moscow, Russia., Matsvay AD; Federal State Budgetary Institution 'Centre for Strategic Planning and Management of Biomedical Health Risks' of the Federal Medical Biological Agency, Moscow, Russia., Kolbutova KB; Chief Federal State Budgetary Healthcare Institution 'Centre of Hygiene and Epidemiology' of the Federal Medical Biological Agency, Moscow, Russia., Bogdan SA; Chief Federal State Budgetary Healthcare Institution 'Centre of Hygiene and Epidemiology' of the Federal Medical Biological Agency, Moscow, Russia., Vashukova MA; Clinical Infectious Diseases Hospital Named After S.P. Botkin, St. Petersburg, Russia., Yudin SM; Federal State Budgetary Institution 'Centre for Strategic Planning and Management of Biomedical Health Risks' of the Federal Medical Biological Agency, Moscow, Russia. |
| المصدر: | Heliyon [Heliyon] 2023 Jun; Vol. 9 (6), pp. e16917. Date of Electronic Publication: 2023 Jun 01. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Elsevier Ltd Country of Publication: England NLM ID: 101672560 Publication Model: Print-Electronic Cited Medium: Print ISSN: 2405-8440 (Print) Linking ISSN: 24058440 NLM ISO Abbreviation: Heliyon Subsets: PubMed not MEDLINE |
| أسماء مطبوعة: | Original Publication: London : Elsevier Ltd, [2015]- |
| مستخلص: | The emergence of mutations in the coronavirus genome provides opportunities for occurrence new strains with higher transmissibility, severity and duration of the disease poses. In 2020, a new variant of the coronavirus SARS-COV-2 - Delta was identified in India. This genetic variant has spread rapidly and became dominant in many countries, including Russia. In November 2021, a new outbreak of COVID-19 occurred in Africa driven by a variant SARS-COV-2 named later Omicron. Both variants had increased transmissibility compared to previously encountered variants and quickly, replacing its around the world. To promptly monitor the epidemiological situation in the country, to assess the spread of dominant genetic variants of the virus and to take appropriate measures, we have developed an RT‒PCR reagent kit for the identification of Delta and Omicron by detecting a corresponding combination of major mutations. The minimum set of mutations was chosen which allows to differentiate Delta and Omicron variants, in order to increase the analysis productivity and reduce costs. Primers and LNA-modified probes were selected to detect mutations in the S gene, typical for the Delta and Omicron. Similar approach can be implemented for the rapid development of assays for differentiating important SARS-COV-2 variants or for other viruses genotyping for epidemiological surveillance or for diagnostic use in order to assist in making clinical decisions. It was demonstrated that the results of VOC Delta and Omicron detection and their typical mutations were concordant with genotyping based on WGS results for all 847 samples of SARS-CoV-2 RNA. The kit has high analytical sensitivity (1х10 3 copies/mL of SARS-CoV-2 RNA) for each of the detected genetic variants and possesses 100% analytic specificity for microorganism panel testing. The diagnostic sensitivity (95% confidence interval) obtained during pivotal trials was 91.1-100% for Omicron and 91.3-100% for Delta, while the diagnostic specificity with a 95% confidence interval was 92.2-100%. The use of a set of reagents in combination with sequencing of SARS-CoV-2 RNA as part of epidemiological monitoring made it possible to quickly track the dynamics of changes in Delta and Omicron prevalence in the Moscow region in the period from December 2021 to July 2022. Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. (© 2023 The Authors.) |
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| فهرسة مساهمة: | Keywords: COVID-19; Coronavirus; Delta; Omicron; RT-PCR; SARS-COV-2; Variant of concern |
| تواريخ الأحداث: | Date Created: 20230608 Latest Revision: 20230619 |
| رمز التحديث: | 20230620 |
| مُعرف محوري في PubMed: | PMC10234363 |
| DOI: | 10.1016/j.heliyon.2023.e16917 |
| PMID: | 37287602 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 2405-8440 |
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| DOI: | 10.1016/j.heliyon.2023.e16917 |