Fig 1.
Maximum-Likelihood phylogenetic tree of SARS-CoV-2 sequences from Karachi.
The tree was constructed using 21 genomes from this study (AKU) (S2 Table) along with 58 other Pakistani and 449 full-length SARS-CoV-2 reference sequences (S1 File). AKU study sequences are indicated in blue, while other Pakistan sequences are shown in green. AKU sequences clustered with those from India (purple), Saudi Arabia (orange), United States (pink), China (light blue), Australia (turquoise), Bangladesh (yellow), France (light green) and also with other sequences from Pakistan (green). The root of the tree was determined using TreeRate tool by applying generalized midpoint rooting strategy. Nodes with significant (>0.90) aLRT-SH like support values are colored maroon. The tree was visualized and edited in Figtree software.
Fig 2.
Time-resolved phylogenetic distribution of genomic epidemiology of SAR-CoV-2 focused on Asian subsampling (Screenshot of the current Nextstrain display in SVG format are protected by CC-BY license).
Tree option layout is selected as rectangular, branch length is set as time interval while branch labels on the basis of phylogenetic clades (19A, 19B, 20A, 20B, 20C and 20D) showing SARS-CoV-2 genomes from Pakistan highlighted in green.
Fig 3.
Estimation of divergence in Pakistani SARS-CoV-2 strains over time.
Isolates from Pakistan were matched with a sub-sample from Asian over time. The graph shows an estimate of divergence within genomes over the time period.
Fig 4.
Genetic variants found in SARS-CoV-2 genomes.
Clade and time-wise association of genome variants identified in seventy-nine full-length SARS-CoV-2 isolates are identified. Variations of upstream, downstream and non-synonymous SARS-CoV2 genome are presented in the grid format. The isolates represented clades L (n = 7), S (n = 5), V (n = 2), GH (n = 55), GR (n = 9) and O (n = 1). Colors represent clades as, L (orange yellow) S (blue), V (red), G (dark green), GH (light green), GR (grey) and O (yellow).
Fig 5.
Genome-wide site-by-site entropy analysis for SARS-CoV-2 sequences from before and after June, 2020.
The figure shows A) Mean entropy and B) site-by-site entropy for sequences collected before and after June 2020. ‘*’ in 4A indicates statistically significant (p<0.001) difference between the means. Error bars shown standard error of mean.
Fig 6.
Genome-wide site-by-site entropy analysis for prevalent clades L, GR and GH.
The figure shows A) Mean entropy and B) site-by-site entropy for GH, GR and L clade sequences A) The asterisk above the bars show statistically significant (*** = p<0.001; * = p<0.05) difference between the means. Error bars shown standard error of mean.
Fig 7.
Genome-wide site-by-site selection pressure analysis for SARS-CoV-2 sequences from before and after June, 2020.
Selection pressure (relative number of non-synonymous substitutions minus synonymous substitutions (dN–dS)) on each codon is shown for sequences A) before June 2020 and B) after June 2020.