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Want to track pandemic variants faster? Fix the bioinformatics bottleneck

Tools, rules and incentives are buckling under the flood of coronavirus genome sequences — to help control the pandemic, researchers need new approaches.
  1. Emma B. Hodcroft

    1. Emma B. Hodcroft is a postdoctoral researcher at Nextstrain and the University of Bern, Bern, Switzerland.

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  2. Nicola De Maio

    1. Nicola De Maio is a scientist in molecular evolution at EMBL–European Bioinformatics Institute, Cambridge, UK.

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  3. Rob Lanfear

    1. Rob Lanfear is associate professor in molecular evolution at the Australian National University, Canberra, Australia, and a paid consultant for GISAID.

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  4. Duncan R. MacCannell

    1. Duncan R. MacCannell is chief science officer for the Office of Advanced Molecular Detection at the Centers for Disease Control and Prevention, Georgia, Atlanta, USA.

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  5. Bui Quang Minh

    1. Bui Quang Minh is senior lecturer in computational phylogenomics at the Australian National University, Canberra, Australia.

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  6. Heiko A. Schmidt

    1. Heiko A. Schmidt is a senior postdoctoral researcher at CIBIV, Max Perutz Labs, Medical University of Vienna and University of Vienna, Austria.

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  7. Alexandros Stamatakis

    1. Alexandros Stamatakis is a permanent research group leader at the Heidelberg Institute for Theoretical Studies, Heidelberg, Germany, and a professor of computer science at the Karlsruhe Institute of Technology, Karlsruhe, Germany.

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  8. Nick Goldman

    1. Nick Goldman is group leader and head of research at the EMBL–European Bioinformatics Institute, Cambridge, UK.

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  9. Christophe Dessimoz

    1. Christophe Dessimoz is professor of bioinformatics at the University of Lausanne, Switzerland, and at University College London, and group leader at the Swiss Institute of Bioinformatics.

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The prospect of reduced vaccine potency from fast-spreading SARS-CoV-2 variants has spurred a global rush to increase genomic surveillance for the coronavirus. This is crucial for quickly identifying and tracking emergent strains. It can also pin down how transmission occurs between individuals more definitively than typical contact tracing can. As this article went to press, laboratories around the world had sequenced more than 610,000 SARS-CoV-2 samples; that number could well exceed one million by the end of the pandemic. In theory, these genomes could help us to understand the spread of the virus through communities and across the globe, allowing us to stall infections. In practice, such analyses reveal much less than they might do.

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Nature 591, 30-33 (2021)

doi: https://doi.org/10.1038/d41586-021-00525-x

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Competing Interests

R.L. is a paid consultant to GISAID, an organization that shares genomic data on SARS-CoV-2 and other viruses.

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