Stability of SARS-CoV-2 phylogenies


Autoři: Yatish Turakhia aff001;  Nicola De Maio aff003;  Bryan Thornlow aff001;  Landen Gozashti aff001;  Robert Lanfear aff005;  Conor R. Walker aff003;  Angie S. Hinrichs aff002;  Jason D. Fernandes aff001;  Rui Borges aff008;  Greg Slodkowicz aff009;  Lukas Weilguny aff003;  David Haussler aff001;  Nick Goldman aff003;  Russell Corbett-Detig aff001
Působiště autorů: Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America aff001;  Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America aff002;  European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom aff003;  Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America aff004;  Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia aff005;  Department of Genetics, University of Cambridge, Cambridge, United Kingdom aff006;  Howard Hughes Medical Institute, University of California, Santa Cruz, CA, United States of America aff007;  Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria aff008;  MRC Laboratory of Molecular Biology, Cambridge, United Kingdom aff009
Vyšlo v časopise: Stability of SARS-CoV-2 phylogenies. PLoS Genet 16(11): e1009175. doi:10.1371/journal.pgen.1009175
Kategorie: Research Article
doi: 10.1371/journal.pgen.1009175

Souhrn

The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately leveraged these data to infer the evolutionary relationships among viral samples and to study key biological questions, including whether host viral genome editing and recombination are features of SARS-CoV-2 evolution. This global sequencing effort is inherently decentralized and must rely on data collected by many labs using a wide variety of molecular and bioinformatic techniques. There is thus a strong possibility that systematic errors associated with lab—or protocol—specific practices affect some sequences in the repositories. We find that some recurrent mutations in reported SARS-CoV-2 genome sequences have been observed predominantly or exclusively by single labs, co-localize with commonly used primer binding sites and are more likely to affect the protein-coding sequences than other similarly recurrent mutations. We show that their inclusion can affect phylogenetic inference on scales relevant to local lineage tracing, and make it appear as though there has been an excess of recurrent mutation or recombination among viral lineages. We suggest how samples can be screened and problematic variants removed, and we plan to regularly inform the scientific community with our updated results as more SARS-CoV-2 genome sequences are shared (https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473 and https://virological.org/t/masking-strategies-for-sars-cov-2-alignments/480). We also develop tools for comparing and visualizing differences among very large phylogenies and we show that consistent clade- and tree-based comparisons can be made between phylogenies produced by different groups. These will facilitate evolutionary inferences and comparisons among phylogenies produced for a wide array of purposes. Building on the SARS-CoV-2 Genome Browser at UCSC, we present a toolkit to compare, analyze and combine SARS-CoV-2 phylogenies, find and remove potential sequencing errors and establish a widely shared, stable clade structure for a more accurate scientific inference and discourse.

Klíčová slova:

Alleles – Genomics – Microbial mutation – Phylogenetic analysis – Phylogenetics – SARS CoV 2 – Trees – Viral evolution


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