Genomic Variability of SARS-CoV-2 Omicron Variant Circulating in the Russian Federation during Early December 2021 and Late January 2022

Abstract

Analysis of genomic variability of pathogens associated with heightened public health concerns is an opportunity to track transmission routes of the disease and helps to develop more effective vaccines and specific diagnostic tests. We present the findings of a detailed genomic analysis of the genomic variability of the SARS-CoV-2 Omicron variant that spread in Russia between 8 December 2021 and 30 January 2022. We performed phylogenetic analysis of Omicron viral isolates collected in Moscow (n = 589) and downloaded from GISAID (n = 397), and identified that the BA.1 lineage was predominant in Russia during this period. The BA.2 lineage was also identified early in December 2021. We identified three cases of BA.1/BA.2 coinfections and one case of Delta/Omicron coinfection. A comparative genomic analysis of SARS-CoV-2 viral variants that spread in other countries allowed us to identify possible cases of transmission. We also found that some mutations that are quite rare in the Global Omicron dataset have a higher incidence rate, and identified genetic markers that could be associated with ways of Omicron transmission in Russia. We give the genomic variability of single nucleotide variations across the genome and give a characteristic of haplotype variability of Omicron strains in both Russia and around the world, and we also identify them.

Keywords: COVID-19; Omicron; SARS-CoV-2; molecular epidemiology; whole genome sequencing.

Figure 1

The schedule of SARS-CoV-2 Omicron samples collection in Russia, representing two datasets: GISAID (blue) and Moscow (orange).

Figure 2

Phylogenetic tree built using the maximum likelihood method, including the Russian Moscow and GISAID datasets, and a global subsampled GISAID dataset. BA.1 cluster branches are marked with green, BA.2 branches with orange. The identifiers of the Russian strains from the GISAID dataset are marked with green; Russian Moscow, pink, Great Britain, blue; and USA, orange. More detailed information is available in the supplementary materials (Supplementary Figure S1).

Figure 3

Proportion of reads across the genome corresponding to Delta (orange) and Omicron (blue) variants identified in the sample LQ-22654. Each bar is a position in the genome, marked by a corresponding gene and amino acid substitution.

Figure 4

Proportion of reads in S gene corresponding BA.1 (blue) and BA.2 (orange) variants identified in t samples LQ-23066 (A), LQ-21013 (B), and LQ-21871 (C).

Figure 5

The structure of genomic transmission of BA.1 strains, including genomes of the Russian isolates from Moscow, Russian isolate from GISAID, and closely related genomes from the global dataset identified with UShER.

Figure 6

The structure of genomic transmission of BA.2 strains, including genomes of the Russian isolates from Moscow, Russian isolates from GISAID, and closely related genomes from the global dataset identified with UShER.

Figure 7

BA.2 cluster showing the relatedness of the Russian SARS-CoV-2 Omicron strains with the most closely related isolates from the GISAID dataset. BA2 cluster is marked with orange branches, strains from coinfected patients are associated with light blue branches. Russian Moscow strains are marked with the pink color font, Russian GISAID Omicron strains are marked with a green color, global isolates from other countries are marked with a black. Bootstrap for each inner node is marked with a circle coloured according to the values.

Figure 8

Frequency of nucleotide substitutions across the SARS-CoV-2 genome identified in different datasets of BA.1 and BA.2 lineages. (A) Omicron BA.1. (B) Omicron BA.2.

Figure 9

Heatmap visualization of coexisting amino acid substitutions identified in different lineages. The frequency of substitution coexistence is described in two datasets of SARS-CoV-2 strais: global and Russian. (A) Amino acid substitutions in BA.1 lineage in the Russian and global population. (B) Amino acid substitutions in BA.2. lineage in the Russian and global population.