Phylogenetic reconstruction of the initial stages of the spread of the SARS-CoV-2 virus in the Eurasian and American continents
Creators: name: Bukin, Yurij
name: Bondaryuk, Artem
Publisher: name: figshare
Year: 2021
Subjects: subject: 60506 Virology
subject: FOS: Biological sciences

description: The dataset contains a sample of genomes for the SARS-Sov-2 virus, isolated during the first wave of the COVID-19 pandemic (December 2019 - July 2020). Using these datasets, an analysis of the evolutionary history of the virus was carried out using phylogenetic analysis with a molecular clock.<br>SARS-CoV-2_252_genome_coding_part.fas - 252 complete genomes of the SARS-CoV-2 dataset containing the coding portion of the genomes from 21 countries. The names of the sequences indicate the country of origin of the strain, the time of isolation of the strain, the number from the GISAID database (https://gisaid.org) or Genbank (https://www.ncbi.nlm.nih.gov/).<br>SARS-CoV-2_252_genome_coding_part_Bat_coronavirus.fasta - the same dataset with the addition of 4 closely related viruses of the genus Betacoronavirus.<br>SARS-CoV-2_513_genome_coding_part.fas - 513 complete genomes of the SARS-CoV-2 dataset containing the coding portion of the genomes from 21 countries. The names of the sequences indicate the country of origin of the strain, the time of isolation of the strain, the number from the GISAID database (https://gisaid.org) or Genbank (https://www.ncbi.nlm.nih.gov/).<br>SARS-CoV-2_513_genome_coding_part.fas - 513 complete genomes of the SARS-CoV-2 dataset containing the coding portion of the genomes from 21 countries. The names of the sequences indicate the country of origin of the strain, the time of isolation of the strain, the number from the GISAID database (https://gisaid.org) or Genbank (https://www.ncbi.nlm.nih.gov/).<br>SARS-CoV-2_513_genome_coding_part_Bat_coronavirus.fasta - the same dataset with the addition of 4 closely related viruses of the genus Betacoronavirus.<br>SARS-CoV-2_777_genome_coding_part.fas - 513 complete genomes of the SARS-CoV-2 dataset containing the coding portion of the genomes from 21 countries. The names of the sequences indicate the country of origin of the strain, the time of isolation of the strain, the number from the GISAID database (https://gisaid.org) or Genbank (https://www.ncbi.nlm.nih.gov/).<br>SARS-CoV-2_777_genome_coding_part_Bat_coronavirus.fasta - the same dataset with the addition of 4 closely related viruses of the genus Betacoronavirus.<br>252_xml.zip - archive of BEAST 2.6.2 xml files of the coding portion of 252 complete genomes for reconstructions of the evolutionary histories of SARS-CoV-2: Const - reconstruction with a coalescent model of constant population size, Exp - reconstruction with a coalescent model of exponential increase in population size, SC - reconstruction with a strict clock, RC - reconstruction with relaxed clock, no_tips - reconstruction without dating the tree by the time of strain isolation, Bat – files with the addition of 4 closely related viruses of the genus Betacoronavirus. For all reconstructions, division of the dataset into 1 + 2 and 3 codon positions was applied; for each part of the dataset, the HKY + I + G4 nucleotide evolution model was used. To achieve ESS statistics values of more than 200 were used 600000000 generations of Markov chains. During the reconstruction were saved the results of each 30000 generation.<br>513_xml.zip - archive of BEAST 2.6.2 xml files of the coding portion of 513 complete genomes for reconstructions of the evolutionary histories of SARS-CoV-2: Const - reconstruction with a coalescent model of constant population size, Exp - reconstruction with a coalescent model of exponential increase in population size, RC - reconstruction with relaxed clock, Bat – files with the addition of 4 closely related viruses of the genus Betacoronavirus. For all reconstructions, division of the dataset into 1 + 2 and 3 codon positions was applied; for each part of the dataset, the HKY + I + G4 nucleotide evolution model was used. To achieve ESS statistics values of more than 200 were used 1200000000 generations of Markov chains. During the reconstruction were saved the results of each 30000 generation.<br>777_xml.zip - archive of BEAST 2.6.2 xml files of the coding portion of 777 complete genomes for reconstructions of the evolutionary histories of SARS-CoV-2: Const - reconstruction with a coalescent model of constant population size, Exp - reconstruction with a coalescent model of exponential increase in population size, RC - reconstruction with relaxed clock, Bat – files with the addition of 4 closely related viruses of the genus Betacoronavirus. For all reconstructions, division of the dataset into 1 + 2 and 3 codon positions was applied; for each part of the dataset, the HKY + I + G4 nucleotide evolution model was used. To achieve ESS statistics values of more than 200 were used 1900000000 generations of Markov chains. During the reconstruction were saved the results of each 30000 generation.<br>IQ-TREE_252_tree.tree, IQ-TREE_513_tree.tree, IQ-TREE_777_tree.tree - reconstructed, undated maximum likelihood tree with IQTREE program with ultrafast bootstrap and SH-ALRT supports.<br>BEAST_Exp_RC_252_dated_tree.tree, BEAST_Exp_RC_513_dated_tree.tree, BEAST_Exp_RC_777_dated_tree.tree - dated phylogenetic trees, reconstructed using the BEAST 2.6.2 software. The tree was dated by the time of isolation of the virus strains. Coaliscent model - exponential population growth, relaxed molecular clock.<br>BEAST_Exp_RC_dated_252_tree_with_ultrafast_bootstrap_supports.tree, BEAST_Exp_RC_dated_252_tree_with_ultrafast_bootstrap_supports.tree, BEAST_Exp_RC_dated_252_tree_with_ultrafast_bootstrap_supports.tree - dated phylogenetic trees, reconstructed using the BEAST 2.6.2 software. The tree was dated by the time of isolation of the virus strains. Coaliscent model - exponential population growth, relaxed molecular clock with ultrafast bootstrap supports.<br>BEAST_Betacoronavirus_tree_const.pdf - dated phylogenetic trees of SARS-CoV-2 with the addition of 4 closely related viruses of the genus Betacoronavirus, reconstructed using the BEAST 2.6.2 software. The tree was dated by the time of isolation of the virus strains. Coaliscent model - constant population growth, relaxed molecular clock.<br>tree files can be viewed in the FigTree program (http://tree.bio.ed.ac.uk/software/figtree/)