Replication Data for: Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021

This is a replication dataset for the submitted manuscript: "Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021." The data package contains data and analysis scripts for generating figures included in the manuscript. Whole genome sequences are available from GISAID database accession number EPI_ISL_4880527 - EPI_ISL_4880796, EPI_ISL_4880796 - EPI_ISL_5943661 and EPI_ISL_6705004 - EPI_ISL_6705093.

The related study is part of a regional collaborative COVID-19 public health rapid response initiative overseen by WHO-AFRO and Africa-CDC do decribe the SARS-CoV-2 genomic epidemiology in Africa.

Data analysis R code and python script is as provided below;

1. Figure_1&2_17Feb2022.R - This r code plots the Seychelles government intervention levels, number of daily COVID-19 cases, the temporal patterns of SARS CoV-2 Lineages in Seychelles.
2. Figure3_12March2022.R - This r code plots the lineages-specific phylogenetic tree of Omicron, Alpha, Beta, Delta VOC, and Non-VOC.
3. Figure4_12March2022.R - This r code plots the global time resolved tree and the number of transition events between discrete locations.
4. Supplimentary Figure1_12March2022 - This r code plots the monthly COVID-19 cases and number of samples received at KWTRP for whole genome sequencing.
5. SupplemenataryFigure3a_b_12March2022.R -This r code plots the frequency of amino acid and deletion mutation in Seychelles sequences.
6. AncestralChanges.py

Data Access: Open License: Creative Commons Attribution 4.0 International