Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic
By Y. Turakhia, Bryan Thornlow, A. Hinrichs, N. de Maio, Landen Gozashti, Robert Lanfear, David Haussler, Russell B. Corbett-Detig. Nature Genetics, 2021
364 citations recorded by the source corpus.
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. Ultrafast Sample placement on Existing tRees (UShER) is an efficient method that facilitates the addition of new SARS-CoV-2 genome sequences onto the existing phylogeny, aiding in real-time analysis of viral evolution during the COVID-19 pandemic.
Subfields: Ecology, Epidemiology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/6d9f593f2b6a77a95ca1f245ae48dbfe3bf33d23
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- Tom Gibbs
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Citations in the corpus
- Nextclade: clade assignment, mutation calling and quality control for viral genomes (2021, methodology): “While Nextclade has some similarities to UShER (Turakhia et al., 2021), these two tools address different use cases.”
- GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics (2022, methodology): “…language models (PLMs), using amino acid alphabets, are the most heavily investigated biological LLMs (Elnaggar et al., 2022, Rives et al., 2021), with demonstrated success in many downstream tasks (e.g., protein function prediction (Unsal et al., 2022)) and engineering (Ferruz et al., 2022).”
- The UCSC Genome Browser database: 2023 update (2022, neutral): “The full tree including GISAID sequences cannot be redistributed due to GISAID restrictions (www.gisaid.org), but we offer download files for a public sequence tree with over 6 million sequences (https://hgdownload.gi.ucsc.edu/goldenPath/ wuhCor1/UShER SARS-CoV-2/) (31).”