Monitoring the spread of the SARS-CoV-2 (Coronaviridae: Coronavirinae: Betacoronavirus; Sarbecovirus) variants in the Moscow region using targeted high-throughput sequencing

Abstract

Introduction. Since the outbreak of the COVID-19 pandemic caused by SARS-CoV-2 novel coronavirus, the international community has been concerned about the emergence of mutations altering some biological properties of the pathogen like increasing its infectivity or virulence. Particularly, since the end of 2020, several variants of concern have been identified around the world, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2). However, the existing mechanism of detecting important mutations are not always effective enough, since only a relatively small part of all pathogen samples can be examined by whole genome sequencing due to its high cost.Material and methods. In this study, we have designed special primer panel and used it for targeted highthroughput sequencing of several significant S-gene (spike) regions of SARS-CoV-2. The Illumina platform averaged approximately 50,000 paired-end reads with a length of ≥150 bp per sample. This method was used to examine 579 random samples obtained from COVID-19 patients in Moscow and the Moscow region from February to June 2021.Results. This study demonstrated the dynamics of distribution of several SARS-CoV-2 strains and its some single mutations. It was found that the Delta strain appeared in the region in May 2021, and became prevalent in June, partially displacing other strains.Discussion. The obtained results provide an opportunity to assign the viral samples to one of the strains, including the previously mentioned in time- and cost-effective manner. The approach can be used for standardization of the procedure of searching for mutations in individual regions of the SARS-CoV-2 genome. It allows to get a more detailed data about the epidemiological situation in a region.

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

“…The use of this kit in practice has made it possible to drastically reduce the number of samples submitted for whole-genome sequencing in order to identify and monitor strains containing the S:N501Y mutation [ 15 ]. However, the further emergence of strains characterized by the appearance of additional mutations in the S-protein gene showed that genomic substitutions at the sites of LAMP primers can reduce the effectiveness of this technique [ 16 ].…”

The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia

“…The fast spread of Delta may be associated with its reduced sensitivity to neutralization by antibodies [ 10 ] as well as increased efficiency of fusion with human cells [ 11 ]. Delta has spread rapidly in Russia, increasing in frequency from 1% in April to over 90% in June [ 12 , 13 ].…”

The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia

“…2021b ). Delta has spread rapidly in Russia, increasing in frequency from 1 per cent in April to over 90 per cent in June ( Borisova et al. 2021 ; Knorre et al 2021 ).…”