This repo contains Nextstrain builds for SARS-CoV-2 that are focused on the spread and evolution of the virus in Sierra Leone. Builds present in the repository will be visible at the Nextstrain website. An initial analysis of the first 11 SARS-CoV-2 genomes from Sierra Leone can be found here.
The SARS-CoV-2 genomes included in this build are those shared in GISAID EpiCoV database. Specific sequences from Sierra Leone were generate by Kenema Government Hospital and are publicly available on GenBank in BioProject PRJNA655973.
The builds hosted here are produced using an Augur-based pipeline heavily based on the Bedford lab's hCoV-19 pipeline. If you would like to run a similar analysis, we suggest taking a look at the information provided in their repository.
Disclaimer. Please note that this data is still based on work in progress and should be considered preliminary. If you intend to include any of these data in publications, please let us know – otherwise please feel free to download and use without restrictions. We have shared this data with the hope that people will download and use it, as well as scrutinize it so we can improve our methods and analyses. Please contact us if you have any questions or comments.