Fig 1. Detection and classification of mutations from GISAID SARS-CoV-2 genome sequences. Illustration of the distribution of synonymous and nonsynonymous variants for each gene in the raw dataset, MAF ≥ 0.5%, and MAF ≥ 1% thresholds are shown. A set of 72 variants in total was observed with MAF ≥ 0.5% threshold and utilized in subsequent analysis. MAF- Minor Allele Frequency.

Fig 2. Principal Component Analysis using 2352 GISAID sequences. Principal Component Analysis of 2352 SARS-CoV-2 sequences shows three distinct clusters of color-coded samples (see the legend for their continent of origin). All three clusters diverge from a single point (red circle). The North American cluster (black oval) shows least variance among the three. The European cluster (orange oval) is well-defined with few interspersed Asian samples, an indication of its origin. The third cluster (Blue oval) shows the most variance and includes samples from Oceania, Asia, and others.

Fig 3. Identification of SARS-CoV-2 genetic clusters in different continents. Illustration of the seven (C1 to C7, color-coded) genetic subdivisions of SARS-CoV-2 sequences across continents using variants with MAF ≥ 0.5%. Differential proportions of strong LD (C), weak LD (D), haplotype block (E), nonsynonymous (F), and synonymous (G) variants across continental datasets are shown.

Fig 4. Estimation of haplotype blocks in continental samples. Haplotype block estimation and extent of linkage disequilibrium observed between variants in Asia, Europe, and North America, identified a single block with different lengths in Asia and Europe, while in North America two blocks were identified.

Fig 5. Correlation between LD and physical distance across continental SARS-CoV-2 genomes. (A) Upward peaks show strong LD and downward peaks show weak LD. North America and Oceania showed strong LD in the region overlapping the S protein. Strong LD among variants suggested that these de novo mutations were not broken by recombination events, (B) Smooth lines showed clear differences in LD over physical distance across continental datasets, (C) The genomic structure of SARS-CoV-2 is depicted.

Fig 6. 3D modelling of SARS-CoV-2 Spike protein. (A) Trimeric structure of SARS-CoV-S spike like protein (PBD:6VSB). (B) Overlay of the SARS-CoV-S spike like protein (PBD ID: 6VSB, blue) with the modelled SARS-CoV-2 S protein (PDB ID: 6M71, magenta). (C) The surface of the modelled S protein with the RRAR furin cleavage site (blue).