Pathogens, Vol. 11, Pages 1461: Genomic Variability of SARS-CoV-2 Omicron Variant Circulating in the Russian Federation during Early December 2021 and Late January 2022

Figure 1. The schedule of SARS-CoV-2 Omicron samples collection in Russia, representing two datasets: GISAID (blue) and Moscow (orange).

Figure 1. The schedule of SARS-CoV-2 Omicron samples collection in Russia, representing two datasets: GISAID (blue) and Moscow (orange).

Pathogens 11 01461 g001 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 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). Pathogens 11 01461 g002

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 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.

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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 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).

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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 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.

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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 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.

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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 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.

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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 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.

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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.

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.

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Table 1. SARS-CoV-2 genomes used in this study for the comparative analysis.

Table 1. SARS-CoV-2 genomes used in this study for the comparative analysis.

SourceNumber of SamplesFMBA542GISAID global756GISAID Russian397UShER1702Wuhan genomes4Bat coronavirus RaTG131

Table 2. Phylogenetic groups identified by phylogenetic analysis.

Table 2. Phylogenetic groups identified by phylogenetic analysis.

Group of StrainsNumber of BA.1 StrainsNumber of BA.2 StrainsNumber of Non-Clustered StrainsRussian Moscow483554Russian GISAID370270Global sample GISAID683730Total15361554

Table 3. Delta-specific substitutions identified in Omicron strains in Russian and global subsampled GISAID dataset.

Table 3. Delta-specific substitutions identified in Omicron strains in Russian and global subsampled GISAID dataset.

SubstitutionNumber of GenomesPangolin ClassificationM:I82T18BA.1, BA.1.1., BA.1.1.13, BA.1.1.15, BA.2S:L452R12BA.1, BA.1.1, BA.1.17S:L452R, M:I82T12BA.1, BA.1.1, BA.1.17,N:R203M1BA.1.1S:L452R, M:I82T, ORF1a:P2046L1BA.1.1

Table 4. Neutralizing epitope analysis based on BA.1 and BA.2 SARS-CoV-2 lineages genome sequences.

Table 4. Neutralizing epitope analysis based on BA.1 and BA.2 SARS-CoV-2 lineages genome sequences.

Type of EpitopeBA.1 MutationsBA.2 MutationsNeutralizing Epitopes in BA.1 and BA.2TotalDiscontinuous Epitopes Number22819682311Linear Epitopes Number3358

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