Supplementary Data for: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches

Pascal Mutz; Nash D. Rochman; Yuri I. Wolf; Guilhem Faure; Feng Zhang; Eugene V Koonin

doi:10.5281/zenodo.6323447

Abstract

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&lt;p&gt;&lt;strong&gt;Supplementary Data&lt;/strong&gt;&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Tables&lt;/strong&gt;&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Table S1:&lt;/strong&gt; Virus characteristics including abbreviation, family, order, tax id, sequence length threshold (for nearly complete genomes), vaccination status, mode of transmission, circulation (human or human/zoonotic), available treatment, and disease progression (acute or chronic).&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Table S2:&lt;/strong&gt; Sequence IDs of outgroup constituents.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Table S3:&lt;/strong&gt; GISAID acknowledgements for the SARS-CoV-2 sequences used in this study.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Table S4:&lt;/strong&gt; Summary of manual sequence curation indicating lab- or vaccine-related keywords used to prune sequences.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Table S5:&lt;/strong&gt; Sequence IDs for EVA and H3N2 e10, e100, d10, and d100 subtrees.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Table S6:&lt;/strong&gt; Sequence IDs for ML and GL lineages.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Table S7:&lt;/strong&gt; Sequence IDs for the H3N2 &ldquo;new&rdquo; and &ldquo;old&rdquo; subtrees.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Table S8:&lt;/strong&gt; Mutation rates (in units of nucleotide substitutions per site per year) and estimated dates for the last common ancestor of all tree/subtrees. Negative dates represent years prior to 0 CE.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Table S9:&lt;/strong&gt; Mean dN/dS values.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Table S10:&lt;/strong&gt; Yearly viral cases and generation time estimations (with references).&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Table S11:&lt;/strong&gt; Metadata including the sequence ID, host, date of isolation, location of isolation, and subtype.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Table S12:&lt;/strong&gt;&nbsp;Overview of key parameters including number of GLs N, Ne, and MRCA for each virus species as well as the mean over all species.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Directories&lt;/strong&gt;&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Alignments&lt;/strong&gt; ORFeome alignments (excluding stop codons) with the exception of SARS-CoV-2.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Correlated Subtrees&lt;/strong&gt; Subtrees representing all correlated-clades (genealogical lineages; GL) in Newick format.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Diversity TMRCA and Skyline Plots&lt;/strong&gt; .png files.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;e/d/n/o Subtrees&lt;/strong&gt; EVA and H3N2 subtrees, evenly and diversely sampled as well as &ldquo;early&rdquo; and &ldquo;late&rdquo; subtrees for H3N2.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Genealogical Trees&lt;/strong&gt; Including global topologies (.main), subtrees, and grafted trees (.grafted).&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Maximally Diverse Subtrees:&lt;/strong&gt; Genealogical trees sampled to contain the same number of leaves as each respective tree in the Simulated Trees directory.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;ORF References&lt;/strong&gt; The first and last nucleotide of each ORF in the reference sequence.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Redundancy Tables&lt;/strong&gt; List of all redundant isolates and the corresponding representative in the ORFeome-unique alignment.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Reference Sequences&lt;/strong&gt; Genbank page for all reference sequences.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Rooted Trees&lt;/strong&gt; Global topologies for each virus.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Simulated Trees:&lt;/strong&gt; Neutral models, based on Yule-Harding, for each virus.&lt;br&gt;\nUltrametric Trees For each global topology.&lt;/p&gt;\n\n&lt;p&gt;&lt;strong&gt;Ultrametric Trees &lt;/strong&gt;For each global topology.&lt;/p&gt;

Supplementary Data for: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches

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