Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
Authors: Hunt Martin , Hinrichs Angie S. , Anderson Daniel , Karim Lily , Dearlove Bethany L , Knaggs Jeff , Constantinides Bede , Fowler Philip W. , Rodger Gillian , Street Teresa , Lumley Sheila , Webster Hermione , Sanderson Theo , Ruis Christopher , Kotzen Benjamin , de Maio Nicola , Amenga-Etego Lucas N. , Amuzu Dominic S. Y. , Avaro Martin , Awandare Gordon A. , Ayivor-Djanie Reuben , Barkham Timothy , Bashton Matthew , Batty Elizabeth M , Bediako Yaw , Belder Denise De , Benedetti Estefania , Bergthaler Andreas , Boers Stefan A. , Campos Josefina , Carr Rosina Afua Ampomah , Chen Yuan Yi Constance , Cuba Facundo , Dattero Maria Elena , Dejnirattisai Wanwisa , Dilthey Alexander , Duedu Kwabena Obeng , Endler Lukas , Engelmann Ilka , Francisco Ngiambudulu M. , Fuchs Jonas , Gnimpieba Etienne Z. , Groc Soraya , Gyamfi Jones , Heemskerk Dennis , Houwaart Torsten , Hsiao Nei-yuan , Huska Matthew , Hölzer Martin , Iranzadeh Arash , Jarva Hanna , Jeewandara Chandima , Jolly Bani , Joseph Rageema , Kant Ravi , Ki Karrie Ko Kwan , Kurkela Satu , Lappalainen Maija , Lataretu Marie , Lemieux Jacob , Liu Chang , Malavige Gathsaurie Neelika , Mashe Tapfumanei , Mongkolsapaya Juthathip , Montes Brigitte , Mora Jose Arturo Molina , Morang’a Collins M. , Mvula Bernard , Nagarajan Niranjan , Nelson Andrew , Ngoi Joyce M. , da Paixão Joana Paula , Panning Marcus , Poklepovich Tomas , Quashie Peter K. , Ranasinghe Diyanath , Russo Mara , San James Emmanuel , Sanderson Nicholas D. , Scaria Vinod , Screaton Gavin , Sessions October Michael , Sironen Tarja , Sisay Abay , Smith Darren , Smura Teemu , Supasa Piyada , Suphavilai Chayaporn , Swann Jeremy , Tegally Houriiyah , Tegomoh Bryan , Vapalahti Olli , Walker Andreas , Wilkinson Robert J , Williamson Carolyn , Zair Xavier ,   IMSSC2 Laboratory Network Consortium, de Oliveira Tulio , Peto Timothy EA , Crook Derrick , Corbett-Detig Russell , Iqbal Zamin 
Published: May 2024

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 with the virus and amplicon schemes. These errors have significant impacts on the phylogeny, and therefore over the last few years, many thousands of hours of researchers time has been spent in “eyeballing” trees, looking for artefacts, and then patching the tree.

Given the huge value of this dataset, we therefore set out to reprocess the complete set of public raw sequence data in a rigorous amplicon-aware manner, and build a cleaner phylogeny. Here we provide a global tree of 4,471,579 samples, built from a consistently assembled set of high quality consensus sequences from all available public data as of June 2024, viewable athttps://viridian.taxonium.org. Each genome was constructed using a novel assembly tool called Viridian (https://github.com/iqbal-lab-org/viridian), developed specifically to process amplicon sequence data, eliminating artefactual errors and mask the genome at low quality positions. We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny. We hope the tree, consensus sequences and Viridian will be a valuable resource for researchers.