Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates

Abstract

SARS-CoV-2 is mutating and creating divergent variants by altering the composition of essential constituent proteins. Pharmacologically, it is crucial to understand the diverse mechanism of mutations for stable vaccine or anti-viral drug design. Our current study concentrates on all the constituent proteins of 469 SARS-CoV-2 genome samples, derived from Indian patients. However, the study may easily be extended to the samples across the globe. We perform clustering analysis towards identifying unique variants in each of the SARS-CoV-2 proteins. A total of 536 mutated positions within the coding regions of SARS-CoV-2 proteins are detected among the identified variants from Indian isolates. We quantify mutations by focusing on the unique variants of each SARS-CoV-2 protein. We report the average number of mutation per variant, percentage of mutated positions, synonymous and non-synonymous mutations, mutations occurring in three codon positions and so on. Our study reveals the most susceptible six (06) proteins, which are ORF1ab, Spike (S), Nucleocapsid (N), ORF3a, ORF7a, and ORF8. Several non-synonymous substitutions are observed to be unique in different SARS-CoV-2 proteins. A total of 57 possible deleterious amino acid substitutions are predicted, which may impact on the protein functions. Several mutations show a large decrease in protein stability and are observed in putative functional domains of the proteins that might have some role in disease pathogenesis. We observe a good number of physicochemical property change during above deleterious substitutions.

Keywords: AA, amino acid; COVID-19; CP, codon position; CTD, C-terminal domain; CoV, coronaviruses; Codon position; Deleterious substitutions; Functional domain; HR, heptapeptide repeat; Mut, mutation; NS, non-synonymous; NTD, N-terminal domain; Non-synonymous mutations; Protein stability; SARS, severe acute respiratory syndrome; Syn, synonymous; TM, transmembrane domain.

Fig. 1

Comparison of unique variant among ten different countries. (A) Percentage of unique variant in each SARS-CoV-2 protein. The number at the top of the bar indicates the number of noise-free collected samples; (B) number of common unique variant between India and other country.

Fig. 2

Distribution of observed number of mutations (x-axis) and relative frequency of number of variants (y-axis) for each SARS-CoV-2 protein. The five proteins ORF1ab, ORF3a, S, N, M are observed multiple mutations in different variants, whereas in six proteins, ORF6, ORF7a, ORF7b, ORF8, ORF10 and E are found exactly a single mutation in each variant.

Fig. 3

Average number of mutation per variant. Proteins are ranked by avg. mutation, highest (left) to lowest (right).

Fig. 4

Quantification of synonymous and non-synonymous mutation. (A) Percentage of synonymous vs. non-synonymous mutation type in three codon positions taking all proteins together; (B) percentage of non-synonymous and synonymous mutation type in all SARS-CoV-2 protein.

Fig. 5

Percentage of mutation in SARS-CoV-2 proteins in each codon position (1st, 2nd and 3rd). (A) Protein-wise in each codon position, and (B) aggregate by all proteins in three different codon positions; (C) overall percentage of synonymous vs. non-synonymous mutation taking all codon positions and proteins.

Fig. 6

(A) Number of distinct mutation type count shown for non-synonymous category in each protein and each codon position; (B) number of distinct mutation type count shown for non-synonymous category by aggregate all codon positions.

Fig. 7

The quantification of nucleotide mutation type in non-synonymous category. (A) Percentage of each type of nucleotide mutation; (B) mutation type by associate number of SARS-CoV-2 protein count.

Fig. 8

(A) The amino acid substitution type observed with more than two mutated positions in SARS-CoV-2 genome. (B) The amino acid substitution type associated with more than two SARS-CoV-2 proteins.

Fig. 9

The non-synonymous amino acid substitution type count in each of the SARS-CoV-2 protein.

Fig. 10

The non-synonymous amino acid substitution categorization by percentage of deleterious and neutral mutation type predicted by PROVEAN score. (A) Percentage is shown for SARS-CoV-2 proteins taking all codon positions together; (B) percentage is shown for three codon positions in each of SARS-CoV-2 proteins.