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Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic.
Turakhia, Yatish; Thornlow, Bryan; Hinrichs, Angie S; De Maio, Nicola; Gozashti, Landen; Lanfear, Robert; Haussler, David; Corbett-Detig, Russell.
  • Turakhia Y; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA. yturakhi@ucsc.edu.
  • Thornlow B; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA. yturakhi@ucsc.edu.
  • Hinrichs AS; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
  • De Maio N; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
  • Gozashti L; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
  • Lanfear R; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
  • Haussler D; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
  • Corbett-Detig R; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
Nat Genet ; 53(6): 809-816, 2021 06.
Article in English | MEDLINE | ID: covidwho-1223103
ABSTRACT
As the SARS-CoV-2 virus spreads through human populations, the unprecedented accumulation of viral genome sequences is ushering in a new era of 'genomic contact tracing'-that is, using viral genomes to trace local transmission dynamics. However, because the viral phylogeny is already so large-and will undoubtedly grow many fold-placing new sequences onto the tree has emerged as a barrier to real-time genomic contact tracing. Here, we resolve this challenge by building an efficient tree-based data structure encoding the inferred evolutionary history of the virus. We demonstrate that our approach greatly improves the speed of phylogenetic placement of new samples and data visualization, making it possible to complete the placements under the constraints of real-time contact tracing. Thus, our method addresses an important need for maintaining a fully updated reference phylogeny. We make these tools available to the research community through the University of California Santa Cruz SARS-CoV-2 Genome Browser to enable rapid cross-referencing of information in new virus sequences with an ever-expanding array of molecular and structural biology data. The methods described here will empower research and genomic contact tracing for SARS-CoV-2 specifically for laboratories worldwide.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Software / Computational Biology / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Limits: Humans Language: English Journal: Nat Genet Journal subject: Genetics, Medical Year: 2021 Document Type: Article Affiliation country: S41588-021-00862-7

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Software / Computational Biology / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Limits: Humans Language: English Journal: Nat Genet Journal subject: Genetics, Medical Year: 2021 Document Type: Article Affiliation country: S41588-021-00862-7