SARS-CoV-2 Variants Monitoring Using Real-Time PCR.

Area of Science:

• Virology
• Molecular Biology
• Epidemiology

Background:

• The 2021 World Health Organization (WHO) temporary recommendations allow targeted RT-PCR assays for SARS-CoV-2 mutation screening alongside whole-genome sequencing.
• The emergence of the Omicron variant in 2021-2022 led to a significant increase in morbidity, necessitating rapid variant identification.

Purpose of the Study:

• To develop a laboratory technique for differentiating major circulating SARS-CoV-2 variants during the 2021-2022 period.
• To implement a widely accessible real-time PCR methodology for national SARS-CoV-2 variant monitoring across Russia.

Main Methods:

• Development of a targeted RT-PCR-based mutation detection assay.
• Application of real-time PCR methodology in diagnostic institutions across 85 regions of Russia.
• Typing of over 6000 biological samples using the developed methodology.

Main Results:

• The developed methodology successfully differentiated between SARS-CoV-2 variants, including Delta and Omicron.
• As of August 25, 2022, 7% of typed samples were identified as the Delta variant and 92% as the Omicron variant.
• Reagents for 140,000 tests have been distributed to regional organizations, supporting widespread surveillance.

Conclusions:

• The CRIE-developed real-time PCR technique is effective for differentiating key SARS-CoV-2 variants.
• The methodology enhances the capacity for nationwide variant monitoring, crucial for epidemiological decision-making.
• The widespread availability of this technique supports robust public health surveillance efforts.