Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2
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 rapidl...
| Main Authors: | , , , , , , , , , , , , , , , |
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Elsevier
2023-06-01
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| Series: | Heliyon |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844023041245 |
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| author | G.A. Shipulin YuA. Savochkina A.K. Shuryaeva E.E. Glushchenko A.R. Luparev V.A. Polyakova D.I. Danilov E.E. Davydova K.S. Vinogradov I.F. Stetsenko A.A. Aiginin A.D. Matsvay K.B. Kolbutova S.A. Bogdan M.A. Vashukova S.M. Yudin |
| author_facet | G.A. Shipulin YuA. Savochkina A.K. Shuryaeva E.E. Glushchenko A.R. Luparev V.A. Polyakova D.I. Danilov E.E. Davydova K.S. Vinogradov I.F. Stetsenko A.A. Aiginin A.D. Matsvay K.B. Kolbutova S.A. Bogdan M.A. Vashukova S.M. Yudin |
| author_sort | G.A. Shipulin |
| collection | DOAJ |
| description | 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 (1х103 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. |
| first_indexed | 2024-03-13T06:48:00Z |
| format | Article |
| id | doaj.art-062b94f55c0443e6867317ce2400df33 |
| institution | Directory Open Access Journal |
| issn | 2405-8440 |
| language | English |
| last_indexed | 2024-03-13T06:48:00Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
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| series | Heliyon |
| spelling | doaj.art-062b94f55c0443e6867317ce2400df332023-06-08T04:19:36ZengElsevierHeliyon2405-84402023-06-0196e16917Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2G.A. Shipulin0YuA. Savochkina1A.K. Shuryaeva2E.E. Glushchenko3A.R. Luparev4V.A. Polyakova5D.I. Danilov6E.E. Davydova7K.S. Vinogradov8I.F. Stetsenko9A.A. Aiginin10A.D. Matsvay11K.B. Kolbutova12S.A. Bogdan13M.A. Vashukova14S.M. Yudin15Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, RussiaFederal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, RussiaFederal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia; Corresponding author.Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, RussiaFederal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, RussiaFederal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, RussiaFederal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, RussiaFederal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, RussiaFederal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, RussiaFederal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, RussiaFederal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, RussiaFederal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, RussiaChief Federal State Budgetary Healthcare Institution “Centre of Hygiene and Epidemiology” of the Federal Medical Biological Agency, Moscow, RussiaChief Federal State Budgetary Healthcare Institution “Centre of Hygiene and Epidemiology” of the Federal Medical Biological Agency, Moscow, RussiaClinical Infectious Diseases Hospital Named After S.P. Botkin, St. Petersburg, RussiaFederal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, RussiaThe 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 (1х103 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.http://www.sciencedirect.com/science/article/pii/S2405844023041245CoronavirusSARS-COV-2RT-PCRVariant of concernDeltaOmicron |
| spellingShingle | G.A. Shipulin YuA. Savochkina A.K. Shuryaeva E.E. Glushchenko A.R. Luparev V.A. Polyakova D.I. Danilov E.E. Davydova K.S. Vinogradov I.F. Stetsenko A.A. Aiginin A.D. Matsvay K.B. Kolbutova S.A. Bogdan M.A. Vashukova S.M. Yudin Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2 Heliyon Coronavirus SARS-COV-2 RT-PCR Variant of concern Delta Omicron |
| title | Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2 |
| title_full | Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2 |
| title_fullStr | Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2 |
| title_full_unstemmed | Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2 |
| title_short | Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2 |
| title_sort | development and application of an rt pcr assay for the identification of the delta and omicron variants of sars cov 2 |
| topic | Coronavirus SARS-COV-2 RT-PCR Variant of concern Delta Omicron |
| url | http://www.sciencedirect.com/science/article/pii/S2405844023041245 |
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