Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations

The dynamics of coronavirus disease-19 (COVID-19) have been extensively researched in many settings around the world, but little is known about these patterns in Africa. 7540 complete nucleotide genomes from 51 African nations were obtained and analysed from the National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing Influenza Data (GISAID) databases to examine genetic diversity and spread dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) lineages circulating in Africa. Utilising a variety of clade and lineage nomenclature schemes, we looked at their diversity, and used maximum parsimony inference methods to recreate their evolutionary divergence and history. According to this study, only 465 of the 2610 Pango lineages found to have existed in the world circulated in Africa after three years of the COVID-19 pandemic outbreak, with five different lineages dominating at various points during the outbreak. We identified South Africa, Ken..., Dataset mining and workflow
SARS-CoV-2 genome sequences collected from Africa were obtained from NCBI database and GISAID database on February 26, 2023. 24415 African sequences were retrieved from both databases so as to examine the number of lineages circulating within Africa. The two databases had only 8044 complete genome sequences combined from Africa, and these sequences excluding those with low coverage using NextClade were retrieved to determine spread dynamics. 5908 sequences from 23 African countries were available in the NCBI and 2137 sequences from 41 African countries from GISAID database. The sequences were aligned using the online version of the MAFFT multiple sequence alignment tool, with the Wuhan-Hu-1 (MN 908947.3) as the reference sequence, and sequences with more than 5.0% ambiguous letters were removed. Duplicates were removed using goalign dedup software and only high quality African complete sequences remained (n=7540). 
Phylogenetic reconstruction
Using IQ-TREE mu..., , # Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations

[https://doi.org/10.5061/dryad.1c59zw42d](https://doi.org/10.5061/dryad.1c59zw42d)

## Description of the data

**A.23.1** – folder with information of Variant A (A.23.1) lineage

*  \_out.220209031522640G0LQd4KgcYqlpNnB3CSHJlsfnormal.txt – all A.23.1 sequences used in this study
* A.23.1dates.csv – information on sequence ID, where they were collected (State) and when they were collected (Date) in csv file format            separated by a comma
* A.23.1dates.xlsx – information on sequence ID, where they were collected (State) and when they were collected (Date) in xlsx file format
* A.23.1dates2.txt - information on sequence ID, where they were collected (State) and when they were collected (Date) in csv file format separated by tab
* DedupA.23.1.fasta – a fasta file with A.23.1 sequences cleaned of duplicates
* DedupA.23.1.fasta.bionj – contains neighbor-joining algorithm of sait...