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The ongoing evolution of UShER during the SARS-CoV-2 pandemic

Nature Genetics volume 56, pages 4–7 (2024)Cite this article

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While the number of SARS-CoV-2 genome sequences grew to over 15 million, the Ultrafast Sample placement on Existing tRees (UShER) tool suite maintained a comprehensive phylogenetic tree in near real time. This experience, and critical performance improvements throughout the pandemic, provide valuable lessons for rapidly scaling analyses.

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Fig. 1: The evolution of UShER algorithms in use during the pandemic.

Data Availability

SARS-CoV-2 genome sequences and metadata used to build the tree were aggregated from multiple sources. Sequences in member databases of the International Nucleotide Sequence Database Collaboration (INSDC; GenBank, European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ)) are freely available and were retrieved using National Center for Biotechnology Information (NCBI) datasets (https://www.ncbi.nlm.nih.gov/datasets/taxonomy/2697049/). COVID-19 Genomics UK Consortium (COG-UK) sequences may be freely downloaded from https://cog-uk.s3.climb.ac.uk/phylogenetics/latest/ and most have been submitted to ENA and are available from INSDC. China National Center for Bioinformation (CNCB) makes additional sequences available in GenBase (https://ngdc.cncb.ac.cn/genbase/). Global Initiative on Sharing All Influenza Data (GISAID) data are available after registration and acceptance of the GISAID user agreement (https://gisaid.org/terms-of-use/). Sequence accessions from all sources for 15,831,377 genomes used in the 2023-08-01 tree are available from https://doi.org/10.5281/zenodo.10076358.

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Acknowledgements

We gratefully acknowledge the authors and their originating laboratories responsible for obtaining the specimens, and their submitting laboratories for generating the genetic sequence and metadata and sharing via public repositories and/or the GISAID Initiative, on which this research is based. This work was funded by the Centers for Disease Control and Prevention (CDC) grant BAA 200-2021-11554.

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Authors and Affiliations

  1. Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA

    Angie Hinrichs & Russell Corbett-Detig

  2. Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, USA

    Cheng Ye & Yatish Turakhia

  3. Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA

    Russell Corbett-Detig

Authors
  1. Angie Hinrichs
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  2. Cheng Ye
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  4. Russell Corbett-Detig
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Correspondence to Russell Corbett-Detig.

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Nature Genetics thanks Art Poon and the other, anonymous, reviewer(s) for their contribution to the peer review of the work.

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Hinrichs, A., Ye, C., Turakhia, Y. et al. The ongoing evolution of UShER during the SARS-CoV-2 pandemic. Nat Genet 56, 4–7 (2024). https://doi.org/10.1038/s41588-023-01622-5

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