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

<p>This is a replication dataset for the manuscript titled: "<a href="">SARS-CoV-2 Omicron Variant of Concern in Seychelles: Introduction and Spread</a>."</p>

<p>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.</p>

<p>Data package includes R and python scripts used to analyze data:
<ol>
<li>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.</li>
<li>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.</li>
<li>Figure3.R </li>
<li>Figure4.R - This r code plots the number of transition events between Seychelles and the rest of world.</li>
<li>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.</li>
<li>SuppFig2.R - This r code plots the number of transition events between discrete locations i.e within Seychelles</li>
<li>AncestralChanges.py</li>
</ol>