Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • COMMENT

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.

    View author publications

    You can also search for this author in PubMed  Google Scholar

  2. Nicola De Maio

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

    View author publications

    You can also search for this author in PubMed  Google Scholar

  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.

    View author publications

    You can also search for this author in PubMed  Google Scholar

  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.

    View author publications

    You can also search for this author in PubMed  Google Scholar

  5. Bui Quang Minh

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

    View author publications

    You can also search for this author in PubMed  Google Scholar

  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.

    View author publications

    You can also search for this author in PubMed  Google Scholar

  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.

    View author publications

    You can also search for this author in PubMed  Google Scholar

  8. Nick Goldman

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

    View author publications

    You can also search for this author in PubMed  Google Scholar

  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.

    View author publications

    You can also search for this author in PubMed  Google Scholar

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.

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Nature 591, 30-33 (2021)

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

References

  1. Hadfield, J. et al. Bioinformatics 34, 4121–4123 (2018).

    Article  PubMed  Google Scholar 

  2. Swadi, T. et al. Emerg. Infect. Dis. 27, 687–693 (2021).

    Article  PubMed  Google Scholar 

  3. Lemieux, J. E. Science 371, eabe3261 (2021).

    Article  PubMed  Google Scholar 

  4. van Dorp, L. et al. Nature Commun. 11, 5986 (2020).

    Article  PubMed  Google Scholar 

  5. Starr, T. N. et al. Cell 182, 1295–1310 (2020).

    Article  PubMed  Google Scholar 

  6. Geoghegan, J. L. et al. Nature Commun. 11, 6351 (2020).

    Article  PubMed  Google Scholar 

  7. Turakhia, Y. et al. Preprint at bioRxiv https://doi.org/10.1101/2020.09.26.314971 (2020).

  8. du Plessis, L. et al. Science 371, 708–712 (2021).

    Article  PubMed  Google Scholar 

  9. Turakhia, Y. et al. PLoS Genet. 16, e1009175 (2020).

    Article  PubMed  Google Scholar 

  10. Nature 590, 195–196 (2021).

    Article  PubMed  Google Scholar 

  11. Yozwiak, N. L., Schaffner, S. F. & Sabeti, P. C. Nature 518, 477–479 (2015).

    Article  PubMed  Google Scholar 

  12. Haussler, D. et al. Nature (in the press).

Download references

Competing Interests

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

Subjects

Latest on:

Nature Careers

Jobs

  • PhD position (all genders) in AI for biomedical data analysis

    PhD position (all genders) in AI for biomedical data analysis Part time  | Temporary | Arbeitsort: Hamburg-Eppendorf UKE_Zentrum für Molekulare Neu...

    Hamburg (DE)

    Universitätsklinikum Hamburg-Eppendorf

  • Assistant Professor Position

    The Lewis-Sigler Institute at Princeton University invites applications for a tenure-track faculty position at the Assistant Professor level.

    Princeton University, Princeton, New Jersey, US

    The Lewis-Sigler Institute for Integrative Genomics at Princeton University

  • Systems Biology Faculty Position

    We seek tenure-track faculty candidates at the level of Assistant Professor with interests in microbial genetics, microbial physiology

    Dallas, Texas

    Lyda Hill Department of Bioinformatics

  • [DGIST] 2024-2025 Tenure-Track Faculty Public Invitation

    South Korea (KR)

    DGIST

  • Locum Editor, BMC Infectious Diseases

    As an Editor with a background in biomedical sciences, you will handle editorial content for BMC Infectious Diseases.

    London or Heidelberg– Hybrid Working Model

    Springer Nature Ltd

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing

Search

Advanced search

Quick links