Dataset Information

Development and Application of Real-Time PCR-Based Screening for Identification of Omicron SARS-CoV-2 Variant Sublineages.

ABSTRACT: The Omicron strain is currently the main dominant variant of SARS-CoV-2, with a large number of sublineages. In this article, we present our experience in tracing it in Russia using molecular diagnostic methods. For this purpose, different approaches were used; for example, we developed multiprimer panels for RT-PCR and Sanger and NGS sequencing methods. For the centralized collection and analysis of samples, the VGARus database was developed, which currently includes more than 300,000 viral sequences.

SUBMITTER: Esman A

PROVIDER: S-EPMC10298075 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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Development and Application of Real-Time PCR-Based Screening for Identification of Omicron SARS-CoV-2 Variant Sublineages.

Esman Anna A Dubodelov Dmitry D Khafizov Kamil K Kotov Ivan I Roev German G Golubeva Anna A Gasanov Gasan G Korabelnikova Marina M Turashev Askar A Cherkashin Evgeniy E Mironov Konstantin K Cherkashina Anna A Akimkin Vasily V

Genes 20230602 6

The Omicron strain is currently the main dominant variant of SARS-CoV-2, with a large number of sublineages. In this article, we present our experience in tracing it in Russia using molecular diagnostic methods. For this purpose, different approaches were used; for example, we developed multiprimer panels for RT-PCR and Sanger and NGS sequencing methods. For the centralized collection and analysis of samples, the VGARus database was developed, which currently includes more than 300,000 viral seq ...[more]

PMID: 37372398

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Project description:BackgroundThe SARS-CoV-2 Omicron variant, with the main subtypes BA.5.2 and BF.7 in China, led to off-target effects on the S and N genes from December 1, 2022, to January 31, 2023. The kits used for studying and developing these agents were not adequately and independently evaluated. It is important to verify the performance of commercial Real-Time quantitative PCR (RT-qPCR) tests.ObjectiveWe conducted a clinical evaluation of two Real Time SARS-CoV-2 Omicron assays to verify their performance using various detection reagents and clinical specimens.MethodsWe performed clinical evaluations of two existing Chinese SARS-CoV-2 Omicron RT-qPCR kits 2019-nCoV nucleic acid diagnostic kits (Fosun Biotechnology, National instrument registration 20203400299, Shanghai, China) and COVID-19 nucleic acid detection kits (eDiagnosis Biomedicine, National instrument registration 20203400212, Wuhan, China) and using BSD (Bondson) (Guangzhou Bondson Biotechnology Co. Ltd, batch number 2022101), quality controls provided by the inspection center and a large number of clinically confirmed specimens.ResultsThe concordance rates for the Fosun and eDiagnosis kits were 95% and 100%, respectively. The detection limit for the Fosun and eDiagnosis kits was verified to be 300 copies/mL and 500 copies/mL. The Fosun assay exhibited the largest coefficient of variation (CV) for ORF1ab and N gene at the detection limit concentration (4.80%, 3.49%), whereas eDiagnosis showed a smaller CV (0.93%, 1.10%). In the reference product from the Hangzhou Clinical Laboratory Center test, it was found that Fosun had the lowest sensitivity of 93.47% and a specificity of 100%, while eDiagnosis exhibited 100% for both sensitivity and specificity. The lowest single target gene detection rate of Fosun reagents was 68.7% for the ORF1ab gene and 87.5% for the N gene, while eDiagnosis detection rate was 100%. Among the clinical group S specimens, the missed detection rate of the Fosun reagent was 10.9%, which was higher than the 3.9% of eDiagnosis. However, there was no significant difference in the clinical diagnostic efficiency of the two reagents.ConclusionsThe ORF1ab and N assays of SARS-CoV-2 Omicron on the eDiagnosis platform yielded higher values compared to those on the Fosun platform. Consequently, the eDiagnosis kit has also been used as standard detection reagents. Considering that the Fosun reagent has a relatively low detection limit and targets three single genes, it is more advantageous as a confirmatory reagent for the new museum.

Dataset Information

Development and Application of Real-Time PCR-Based Screening for Identification of Omicron SARS-CoV-2 Variant Sublineages.

Publications

Development and Application of Real-Time PCR-Based Screening for Identification of Omicron SARS-CoV-2 Variant Sublineages.

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