Genomic epidemiology of SARS-CoV-2 from Uttar Pradesh, India

Abstract

The various strains and mutations of SARS-CoV-2 have been tracked using several forms of genomic classification systems. The present study reports high-throughput sequencing and analysis of 99 SARS-CoV-2 specimens from Western Uttar Pradesh using sequences obtained from the GISAID database, followed by phylogeny and clade classification. Phylogenetic analysis revealed that Omicron lineages BA-2-like (55.55%) followed by Delta lineage-B.1.617.2 (45.5%) were predominantly circulating in this area Signature substitution at positions S: N501Y, S: D614G, S: T478K, S: K417N, S: E484A, S: P681H, and S: S477N were commonly detected in the Omicron variant-BA-2-like, however S: D614G, S: L452R, S: P681R and S: D950N were confined to Delta variant-B.1.617.2. We have also identified three escape variants in the S gene at codon position 19 (T19I/R), 484 (E484A/Q), and 681 (P681R/H) during the fourth and fifth waves in India. Based on the phylogenetic diversification studies and similar changes in other lineages, our analysis revealed indications of convergent evolution as the virus adjusts to the shifting immunological profile of its human host. To the best of our knowledge, this study is an approach to comprehensively map the circulating SARS-CoV-2 strains from Western Uttar Pradesh using an integrated approach of whole genome sequencing and phylogenetic analysis. These findings will be extremely valuable in developing a structured approach toward pandemic preparedness and evidence-based intervention plans in the future.

Figure 1

Highlighted regions of the map of Uttar Pradesh displaying the sample collection points.

Figure 2

Next Clade classification among 99 genomic sequences of Delta and Omicron Variants.

Figure 3

Pangolin classification among 99 genomic sequences of Delta and Omicron Variants.

Figure 4

Representation of mutations observed within 75 samples of the Omicron Variants with different colors corresponding to different genes. Mutation common (G142D, T478K, and D614G) in Omicron and Delta variants are highlighted with blue color.

Figure 5

Representation of mutations observed within 23 samples of Delta Variant with different colors corresponding to different genes. Specific Mutations (L452R, P681R, and D950N) in the Spike protein of the Delta variants are highlighted with yellow color.

Figure 6

Heatmap of presence, and absence of spike protein mutation among 99 genome sequences. Red color represents the presence and blue represents the absence.

Figure 7

Maximum likelihood tree of the SARS-CoV-2 sequences. The maximum likelihood phylogenetic tree was inferred from the sequences retrieved from Western Uttar Pradesh (Red diamond) along with other GISAID sequences from Eastern Uttar Pradesh (light blue diamond), Maharashtra (green diamond), and Kerala (yellow diamond). The reference sequence of Wuhan is represented by (blue diamond).