Full-genome sequences of the first two SARS-CoV-2 viruses from India

Abstract

Background & objectives: Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally affected 195 countries. In India, suspected cases were screened for SARS-CoV-2 as per the advisory of the Ministry of Health and Family Welfare. The objective of this study was to characterize SARS-CoV-2 sequences from three identified positive cases as on February 29, 2020.

Methods: Throat swab/nasal swab specimens for a total of 881 suspected cases were screened by E gene and confirmed by RdRp (1), RdRp (2) and N gene real-time reverse transcription-polymerase chain reactions and next-generation sequencing. Phylogenetic analysis, molecular characterization and prediction of B- and T-cell epitopes for Indian SARS-CoV-2 sequences were undertaken.

Results: Three cases with a travel history from Wuhan, China, were confirmed positive for SARS-CoV-2. Almost complete (29,851 nucleotides) genomes of case 1, case 3 and a fragmented genome for case 2 were obtained. The sequences of Indian SARS-CoV-2 though not identical showed high (~99.98%) identity with Wuhan seafood market pneumonia virus (accession number: NC 045512). Phylogenetic analysis showed that the Indian sequences belonged to different clusters. Predicted linear B-cell epitopes were found to be concentrated in the S1 domain of spike protein, and a conformational epitope was identified in the receptor-binding domain. The predicted T-cell epitopes showed broad human leucocyte antigen allele coverage of A and B supertypes predominant in the Indian population.

Interpretation & conclusions: The two SARS-CoV-2 sequences obtained from India represent two different introductions into the country. The genetic heterogeneity is as noted globally. The identified B- and T-cell epitopes may be considered suitable for future experiments towards the design of vaccines and diagnostics. Continuous monitoring and analysis of the sequences of new cases from India and the other affected countries would be vital to understand the genetic evolution and rates of substitution of the SARS-CoV-2.

Keywords: India; Kerala; genomes; next-generation sequencing; phylogeny; real-time reverse transcription-polymerase chain reaction; severe acute respiratory syndrome coronavirus 2; Epitope.

Fig. 1

Phylogenetic tree of the complete genomes of severe acute respiratory syndrome coronavirus 2 viruses. Indian viruses are shown in magenta font colour.

Fig. 2

Predicted conformational B-cell epitopes mapped on the pre-fusion structure of the modelled Indian severe acute respiratory syndrome coronavirus 2 spike protein using the pre-fusion structure of severe acute respiratory syndrome-coronavirus-2 (6VSB.PDB) (colour key: blue - epitopes 67-261; green - epitopes 341-507 based on the predicted epitopes as shown in Supplementary Table II). (A) Top view (B) Side view.