Time-lapse sentinel surveillance of SARS-CoV-2 spread in India
Fig 2
(a) Mismatch distribution curve of pairwise differences among SARS-CoV-2 genomes. (b) Demographic history of SARS-CoV-2 genomes estimated using Coalescent Bayesian Skyline plot. We applied a strict molecular clock and a substitution rate at 8×10−4/site/year to the MCMC run for 2.5×107 generations, sampled at every 1000 generations and discarded the first 2500 samples as burn-in. Other parameters were set as default values and results are visualized using TRACER v. 1.6. Bayesian skyline plot shows an overall increasing population size. The solid line represents the median estimates of Neμ (Ne = effective population size; μ = generation time) and the blue lines around median estimates indicate the 95% highest posterior density (HPD) estimate of the historic effective population size. The lines with nodes overlaid on BSP represented case histories of COVID-19 with data retrieved from MoHFW. The data was available in absolute number before transforming it to the log form to best fit with the axis also represented BSP results. The red line depicted number of deaths, green- number of recoveries, pink- number of active cases and blue represented total number of confirmed cases.