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

Abstract

According to the temporary recommendations of the 2021 World Health Organization (WHO), in addition to whole-genome sequencing, laboratories in various countries can also screen for known mutations utilizing targeted RT-PCR-based mutation detection assays. The aim of this work was to generate a laboratory technique to differentiate the main circulating SARS-CoV-2 variants in 2021–2022, when a sharp increase in morbidity was observed with the appearance of the Omicron variant. Real-time PCR methodology is available for use in the majority of scientific and diagnostic institutions in Russia, which makes it possible to increase the coverage of monitoring of variants in the territories of all 85 regions in order to accumulate information for the Central Services and make epidemiological decisions. With the methodology developed by the Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (FSSCRP Human Wellbeing) (CRIE), more than 6000 biological samples have been typed, and 7% of samples with the Delta variant and 92% of samples with the Omicron variant have been identified as of 25 August 2022. Reagents for 140,000 definitions have been supplied to regional organizations.

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

“…For Mix E484A+ P681R, the diagnostic specificity of the assay was 93.8–100% and the diagnostic sensitivity was 97.7–100.0% (the criteria for single-target P681R were confirmed experimentally in previous work [ 30 ]).…”

“… * Wilson score interval; ** For the P681R mutation, sensitivity and specificity were calculated earlier (during Delta variant circulation [ 30 ]). CI–confidence interval.…”

To Analyze the Sensitivity of RT-PCR Assays Employing S Gene Target Failure with Whole Genome Sequencing Data during Third Wave by SARS-CoV-2 Omicron Variant

“…At the beginning of the pandemic, detection of the virus using a PCR-based technique and clinical correlation was the only relevant and optimal method for diagnosing a coronavirus infection. Such diagnostic techniques can be cost and time-saving to monitor the emergence of new variants compared to sequencing technology [2]. However, their sensitivity is not always sufficient to detect viruses in low viral load biological samples.…”