Replication Data for: SARS-CoV-2 Omicron Variant of Concern in Seychelles: Introduction and Spread

This is a replication dataset for the manuscript titled: "SARS-CoV-2 Omicron Variant of Concern in Seychelles: Introduction and Spread." The 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 package includes R and python scripts used to analyze data: Figure1.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. Figure2.R - This r code plots the Omicron lineages phylogenetic tree of BA.1-like, BA.1-like, BA.1-like, BA.1-like lineages. Figure3.R Figure4.R - This r code plots the number of transition events between Seychelles and the rest of world. SuppFig1.R - This r code plots the number of daily COVID-19 cases from March 2020 to September 2022 and highlights the period when Omicron VOC was circulating. SuppFig2.R - This r code plots the number of transition events between discrete locations i.e within Seychelles AncestralChanges.py