{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Hunt M"],"funding":["NHGRI NIH HHS","Wellcome Trust","NIGMS NIH HHS"],"pubmed_abstract":["The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved wit"],"journal":["bioRxiv : the preprint server for biology"],"pagination":["2024.04.29.591666"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11092452"],"repository":["biostudies-literature"],"pubmed_title":["Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny."],"pmcid":["PMC11092452"],"funding_grant_id":["U24 HG002371","210918/Z/18/Z","R35 GM128932","P20 GM103443","CC2112","T32 HG012344"],"pubmed_authors":["Ranasinghe D","Sironen T","Tegally H","Amuzu DSY","Huska M","Russo M","Barkham T","Houwaart T","Street T","Gyamfi J","Smura T","Carr RAA","Mvula B","Jarva H","Chen YYC","Iranzadeh A","Screaton G","Hinrichs AS","Ngoi JM","Lataretu M","Groc S","Kotzen B","Knaggs J","da Paixao JP","Gnimpieba EZ","Lemieux J","Bashton M","Kurkela S","Sessions OM","Ruis C","Boers SA","de Maio N","Constantinides B","Dejnirattisai W","Nagarajan N","Rodger G","Wilkinson RJ","Endler L","Mongkolsapaya J","Francisco NM","Holzer M","IMSSC2 Laboratory Network Consortium","Benedetti E","Lappalainen M","Scaria V","Hsiao NY","Kant R","Bediako Y","Heemskerk D","Vapalahti O","Karim L","Jeewandara C","de Oliveira T","Tegomoh B","Swann J","Avaro M","Jolly B","Montes B","Supasa P","Suphavilai C","Batty EM","Ki KKK","Nelson A","Engelmann I","Webster H","Peto TE","Hunt M","Campos J","Sanderson T","Dattero ME","San JE","Iqbal Z","Malavige GN","Mora JAM","Quashie PK","Corbett-Detig R","Sisay A","Dearlove BL","Amenga-Etego LN","Cuba F","Poklepovich T","Joseph R","Panning M","Williamson C","Walker A","Crook D","Lumley S","Ayivor-Djanie R","Smith D","Duedu KO","Sanderson ND","Awandare GA","De Belder D","Fowler PW","Zair X","Dilthey A","Fuchs J","Morang'a CM","Bergthaler A","Anderson D","Liu C","Mashe T"],"additional_accession":[]},"is_claimable":false,"name":"Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.","description":"The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved wit","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Nov","modification":"2026-07-08T03:12:38.244Z","creation":"2025-08-30T03:05:56.773Z"},"accession":"S-EPMC11092452","cross_references":{"pubmed":["38746185"],"doi":["10.1101/2024.04.29.591666"]}}