DOI: 10.5061/dryad.1c59zw42d
title: Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations

description: 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, Kenya,
 and Nigeria as key sources of viral transmissions between Sub-Saharan
 African nations. These findings provide insight into the viral strains
 that are circulating in Africa and their evolutionary patterns.
description: 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
 multicore software version v1.6.12 and NextClade, phylogeny reconstruction
 on the dataset was performed numerous times. Lineage
 classification PANGOLin, a web application was used to
 classify sequences into their lineages. The objective was to determine the
 SARS-CoV-2 lineages that are circulating in Africa that are most important
 from an epidemiological perspective, as well as the lineage dynamics
 within and across the African continent, due to the fact that this naming
 system integrates genetic and geographic data concerning SARS-CoV-2
 dynamics. Phylogeographic reconstruction
 VOC, (VOI) and VUM were designated based on the WHO framework as
 of 20 January 2022. We included one lineage, namely A.23.1 and labelled it
 as VOI for the purposes of this analysis. This lineage was included
 because it demonstrated the continued evolution of African lineages into
 potentially more transmissible variants. VOI, VOC, and VUM that emerged on
 the African continent were marked. These were A.23.1 (VOI), B.1.351 and
 B.1.1.529 (VOC), B.1.640, and B.1.525 (VUM). Genome sequences of these
 five lineages were extracted from NCBI database for phylogeographic
 reconstruction. A similar approach to that described above (including
 alignment using online MAFFT) was employed. Phylogeographic reconstruction
 for all variants circulating in Africa and all VOI, VOC, and VUM was
 conducted using PASTML.
description: # 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 saitou and nei * DedupA.23.1.fasta.ckp.gz – is a checkpoint file of the entire run gzip compressed to save space * DedupA.23.1.fasta.iqtree – shows the main report file that is self-readable with computational results. It also contains a textual representation of the final tree * DedupA.23.1.fasta.log – shows the log file of the entire run * DedupA.23.1.fasta.mldist – shows pairwise distance matrix of final tree given by IQTREE * DedupA.23.1.fasta.treefile – is the ML tree in NEWICK format, which can be visualized by any supported tree viewer programs like FigTree iTOL **B.1.1.529** - folder with information of Omicron (B.1.1.529) lineage * B.1.1.529dates.csv – information on sequence ID, where they were collected (State) and when they were collected (Date) in csv file format separated by a comma * B.1.1.529dates.txt - information on sequence ID, where they were collected (State) and when they were collected (Date) in csv file format separated by tab * B.1.1.529dates.xlsx – information on sequence ID, where they were collected (State) and when they were collected (Date) in xlsx file format * DedupB.1.1.529.fasta – a fasta file with A.23.1 sequences cleaned of duplicates * DedupB.1.1.529.fasta.bionj – contains neighbor-joining algorithm of saitou and nei * DedupB.1.1.529.fasta.ckp.gz – is a checkpoint file of the entire run gzip compressed to save space * DedupB.1.1.529.fasta.iqtree – shows the main report file that is self-readable with computational results. It also contains a textual representation of the final tree * DedupB.1.1.529.fasta.log – shows the log file of the entire run * DedupB.1.1.529.fasta.mldist – shows pairwise distance matrix of final tree given by IQTREE * DedupB.1.1.529.fasta.treefile – is the ML tree in NEWICK format, which can be visualized by any supported tree viewer programs like FigTree iTOL **B.1.351** - folder with information of Beta (B.1.351) lineage * B.1.351dates.csv – information on sequence ID, where they were collected (State) and when they were collected (Date) in csv file format separated by a comma * B.1.351dates.txt - information on sequence ID, where they were collected (State) and when they were collected (Date) in csv file format separated by tab * B.1.351dates.xlsx – information on sequence ID, where they were collected (State) and when they were collected (Date) in xlsx file format * DedupB.1.351.fasta – a fasta file with A.23.1 sequences cleaned of duplicates * DedupB.1.351.fasta.bionj – contains neighbor-joining algorithm of saitou and nei * DedupB.1.351.fasta.ckp.gz – is a checkpoint file of the entire run gzip compressed to save space * DedupB.1.351.fasta.iqtree – shows the main report file that is self-readable with computational results. It also contains a textual representation of the final tree * DedupB.1.351.fasta.log – shows the log file of the entire run * DedupB.1.351.fasta.mldist – shows pairwise distance matrix of final tree given by IQTREE * DedupB.1.351.fasta.treefile – is the ML tree in NEWICK format, which can be visualized by any supported tree viewer programs like FigTree iTOL **B.1.525** - folder with information of Eta (B.1.525) lineage * B.1.525dates.csv – information on sequence ID, where they were collected (State) and when they were collected (Date) in csv file format separated by a comma * B.1.525dates.txt - information on sequence ID, where they were collected (State) and when they were collected (Date) in csv file format separated by tab * B.1.525dates.xlsx – information on sequence ID, where they were collected (State) and when they were collected (Date) in xlsx file format * DedupB.1.525.fasta – a fasta file with A.23.1 sequences cleaned of duplicates * DedupB.1.525.fasta.bionj – contains neighbor-joining algorithm of saitou and nei * DedupB.1.525.fasta.ckp.gz – is a checkpoint file of the entire run gzip compressed to save space * DedupB.1.525.fasta.iqtree – shows the main report file that is self-readable with computational results. It also contains a textual representation of the final tree * DedupB.1.525.fasta.log – shows the log file of the entire run * DedupB.1.525.fasta.mldist – shows pairwise distance matrix of final tree given by IQTREE * DedupB.1.525.fasta.treefile – is the ML tree in NEWICK format, which can be visualized by any supported tree viewer programs like FigTree iTOL **B.1.640** - folder with information of IHU Variant (B.1.640) lineage * B.1.640dates.csv – information on sequence ID, where they were collected (State) and when they were collected (Date) in csv file format separated by a comma * B.1.640dates.txt - information on sequence ID, where they were collected (State) and when they were collected (Date) in csv file format separated by tab * B.1.640dates.xlsx – information on sequence ID, where they were collected (State) and when they were collected (Date) in xlsx file format * DedupB.1.640.fasta – a fasta file with A.23.1 sequences cleaned of duplicates * DedupB.1.525.fasta.bionj – contains neighbor-joining algorithm of saitou and nei * DedupB.1.640.fasta.ckp.gz – is a checkpoint file of the entire run gzip compressed to save space * DedupB.1.640.fasta.iqtree – shows the main report file that is self-readable with computational results. It also contains a textual representation of the final tree * DedupB.1.640.fasta.log – shows the log file of the entire run * DedupB.1.640.fasta.mldist – shows pairwise distance matrix of final tree given by IQTREE * DedupB.1.640.fasta.treefile – is the ML tree in NEWICK format, which can be visualized by any supported tree viewer programs like FigTree iTOL **Variants** – contains PASTML information on all variants * PASTMLallDates.csv – information on Accession, Release Date, Pangolin, Length, Geo Location, and Collection Date of all sequences used in this study * Sequences_gisaid.fasta – all sequences from GISAID database used in this study * Sequences_ncbi.fasta – all sequences fron NCBI database used in this study * Sequence_ref.fasta – reference sequence from NCBI database **Pastml_A.23.1.zip** – all information generated with PASTML * Colours.character_states.tab – it shows states and the corresponding colour * Combined_ancestral_states.tab it shows nodes and corresponding states * iTOL_colorstrip-state.txt – it shows node ids with their corresponding color, labels, shapes and title of state * iTOL_popup_info.txt – shows ancestral character reconstruction (ACR) results * iTOL_style-state.txt – shows node id with corresponding type, node, color size factor and label * iTOL_tree_id.txt – contains the tree id number * iTOL_url.txt – contain the url address where you can view the tree online * marginal_probabilities.character_state.model_F81.tab – contains the tree in txt format * named.tree_dedupA.23.1.fasta_I5UVQqr.nexus – contains the tree in nexus format * named.tree_dedupA.23.1.fasta_I5UVQqr.nwk – contains the tree in nwk format * params.character_state.method_MPPA.model_F81.tab – contains parameters of the tree * pastml_compressed_visualisation.html – contains the visualization of the compressed tree * pastml_full_tree_visualisation.html – contains the visualization of the full tree **pastml_all.zip** * Colours.character_Geo_location.tab – it shows states and the corresponding colour * Combined_ancestral_states.tab it shows nodes and corresponding states * iTOL_colorstrip-Geo_location.txt – it shows node ids with their corresponding color, labels, shapes and title of state * iTOL_popup_info.txt – shows ancestral character reconstruction (ACR) results * iTOL_style-Geo_location.txt – shows node id with corresponding type, node, color size factor and label * iTOL_tree_id.txt – contains the tree id number * iTOL_url.txt – contain the url address where you can view the tree online * marginal_probabilities.character_Geo_location.model_F81.tab – contains the tree in txt format * named.tree_newick_format_tree_O932IMJ.nexus – contains the tree in nexus format * named.tree_newick_format_tree_O932IMJ.nwk – contains the tree in nwk format * params.character_Geo_location.method_MPPA.model_F81.tab – contains parameters of the tree * pastml_compressed_visualisation.html – contains the visualization of the compressed tree **pastml_B.1.1.529.zip** * Colours.character_states.tab – it shows states and the corresponding colour * Combined_ancestral_states.tab it shows nodes and corresponding states * iTOL_colorstrip-state.txt – it shows node ids with their corresponding color, labels, shapes and title of state * iTOL_popup_info.txt – shows ancestral character reconstruction (ACR) results * iTOL_style-state.txt – shows node id with corresponding type, node, color size factor and label * iTOL_tree_id.txt – contains the tree id number * iTOL_url.txt – contain the url address where you can view the tree online * marginal_probabilities.character_state.model_F81.tab – contains the tree in txt format * named.tree_dedupB.1.1.529.fasta_ps1F5W0.nexus – contains the tree in nexus format * named.tree_dedupB.1.1.529.fasta_ps1F5W0.nwk – contains the tree in nwk format * params.character_state.method_MPPA.model_F81.tab – contains parameters of the tree * pastml_compressed_visualisation.html – contains the visualization of the compressed tree * pastml_full_tree_visualisation.html – contains the visualization of the full tree **pastml_B.1.640.zip** * Colours.character_states.tab – it shows states and the corresponding colour * Combined_ancestral_states.tab it shows nodes and corresponding states * iTOL_colorstrip-state.txt – it shows node ids with their corresponding color, labels, shapes and title of state * iTOL_popup_info.txt – shows ancestral character reconstruction (ACR) results * iTOL_style-state.txt – shows node id with corresponding type, node, color size factor and label * iTOL_tree_id.txt – contains the tree id number * iTOL_url.txt – contain the url address where you can view the tree online * marginal_probabilities.character_state.model_F81.tab – contains the tree in txt format * named.tree_dedupB.1.640mafft.fasta_xuZ6Isj.nexus – contains the tree in nexus format * named.tree_dedupB.1.640mafft.fasta_xuZ6Isj.nwk – contains the tree in nwk format * params.character_state.method_MPPA.model_F81.tab – contains parameters of the tree * pastml_compressed_visualisation.html – contains the visualization of the compressed tree * pastml_full_tree_visualisation.html – contains the visualization of the full tree **pastml_B.1351.2.zip** * Colours.character_states.tab – it shows states and the corresponding colour * Combined_ancestral_states.tab it shows nodes and corresponding states * iTOL_colorstrip-state.txt – it shows node ids with their corresponding color, labels, shapes and title of state * iTOL_popup_info.txt – shows ancestral character reconstruction (ACR) results * iTOL_style-state.txt – shows node id with corresponding type, node, color size factor and label * iTOL_tree_id.txt – contains the tree id number * iTOL_url.txt – contain the url address where you can view the tree online * marginal_probabilities.character_state.model_F81.tab – contains the tree in txt format * named.tree_dedupB.1.351mafft.fasta_FaWRLNq.nexus – contains the tree in nexus format * named.tree_dedupB.1.351mafft.fasta_FaWRLNq.nwk – contains the tree in nwk format * params.character_state.method_MPPA.model_F81.tab – contains parameters of the tree * pastml_compressed_visualisation.html – contains the visualization of the compressed tree * pastml_full_tree_visualisation.html – contains the visualization of the full tree **pastml_B.1525.zip** * Colours.character_Geo_location.tab – it shows states and the corresponding colour * Combined_ancestral_states.tab it shows nodes and corresponding states * iTOL_colorstrip-Geo_location.txt – it shows node ids with their corresponding color, labels, shapes and title of state * iTOL_popup_info.txt – shows ancestral character reconstruction (ACR) results * iTOL_style-Geo_location.txt – shows node id with corresponding type, node, color size factor and label * iTOL_tree_id.txt – contains the tree id number * iTOL_url.txt – contain the url address where you can view the tree online * marginal_probabilities.character_Geo_location.model_F81.tab – contains the tree in txt format * named.tree_mafftVOCs.fasta.nexus – contains the tree in nexus format * named.tree_mafftVOCs.fasta.nwk – contains the tree in nwk format * params.character_Geo_location.method_MPPA.model_F81.tab – contains parameters of the tree * pastml_compressed_visualisation.html – contains the visualization of the compressed tree * pastml_full_tree_visualisation.html – contains the visualization of the full tree ## Sharing/Access information Data was derived from the following sources: * [https://www.ncbi.nlm.nih.gov/](https://www.ncbi.nlm.nih.gov/) * [https://gisaid.org/](https://gisaid.org/) ## Code/Software GOALIGN DEDUP (to remove duplicates) goalign dedup -i 'name of fasta file' &gt; 'name of output fasta file without duplicates' IQ-TREE v1.6.12 iqtree -s NameOfFastaFile -m GTR+G