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Lengthy delays in H5N1 genome submissions to GISAID

Nature Biotechnology volume 43, pages 665–666 (2025)Cite this article

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Real-time surveillance of viral genomes enables the detection of new variants, the assessment of their impact on infectivity and disease severity, the estimation of rates of spread and routes of transmission using new phylogenetic tools, and evidence-based decision making by public health authorities, but it requires access to timely genomic information. Up-to-date genomic information also facilitates rapid, collaborative and interdisciplinary research and evidence-based public health responses (for example, vaccine development and deployment). Viral genetic changes have enabled transmission of the highly pathogenic avian influenza H5N1 to hundreds of species of birds and mammals1,2,3, leading to repeated animal-to-human transmission events, including 72 reported to the World Health Organization in 2024 (ref. 4). Two recent reports describe patients with severe respiratory infections in Canada5 and the United States6 with viruses that were polymorphic for genetic changes previously predicted by deep mutational scanning to improve binding to human cells7. While these changes may have facilitated within-host viral replication, efficient human-to-human transmission of H5N1 has yet to be observed. However, this may change at any time. Real-time reporting of current H5N1 genomes is crucial, yet we find extensive delays of 7.5 months between H5N1 sample collection and submission to the Global Initiative on Sharing All Influenza Data (GISAID) repository for virus data and associated metadata8,9.

Early on in the COVID-19 pandemic, a previous study10 highlighted lengthy delays in SARS-CoV-2 sequence submissions to GISAID, with an average of 48 days between sample collection and submission. This global analysis highlighted countries with rapid data sharing practices and pointed out others that lagged behind. Many countries subsequently improved pipelines for data submission, with collection-to-submission times (CST) now down to 30 days for samples submitted to GISAID in 2024. As an example, Canada had a CST of 88 days early in the pandemic10, but now has a median CST for SARS-CoV-2 sequences of only 16 days. Such dramatic improvements aided global efforts to track variants and to monitor the spread and public health impacts of COVID-19 over the last few years.

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Fig. 1: Collection-to-submission times by country for highly pathogenic avian influenza (H5N1).

Data availability

The findings of this study are based on metadata accessed from GISAID on 26 February 2025 and includes H5N1 sequences up to 31 December 2024 (list of EPI_SET IDs at https://doi.org/10.55876/gis8.250226wp), H1N1 sequences up to 31 December 2013 (EPI_SET IDs at https://doi.org/10.55876/gis8.250226ad) and H1N1 sequences sampled in 2024 (EPI_SET IDs at https://doi.org/10.55876/gis8.250226zt). Summary data for SARS-CoV-2 were obtained from GISAID’s Dates + Location summary file, limited to submissions in 2024 (EPI_SET IDs at https://doi.org/10.55876/gis8.250226hm).

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Acknowledgements

We gratefully acknowledge all data contributors, that is, 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 the GISAID Initiative, on which this study is based. We would like to thank Florence Débarre for comments on an earlier draft. We acknowledge the support of the Natural Sciences and Engineering Research Council of Canada (NSERC RGPIN-2022-03726).

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Authors and Affiliations

  1. Department of Zoology & Biodiversity Research Centre, The University of British Columbia, Vancouver, British Columbia, Canada

    Sarah P. Otto & Sean Vidal Edgerton

Authors
  1. Sarah P. Otto
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  2. Sean Vidal Edgerton
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Contributions

S.P.O. and S.V.E. co-designed the study, planned the manuscript and revised the manuscript; S.P.O. analyzed the data and drafted the manuscript.

Corresponding author

Correspondence to Sarah P. Otto.

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The authors declare no competing interests.

Supplementary information

Supplementary Information

Supplementary Figs. 1 and 2

Supplementary Tables

Summary data on lags by country and by host species for H5N1 and H1N1.

Supplementary Code

Mathematica file to conduct the analyses and generate figures, based on GISAID metadata download files.

Supplementary Code

Mathematica file to conduct the analyses and generate figures, based on GISAID metadata download files (pdf version)

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Otto, S.P., Edgerton, S.V. Lengthy delays in H5N1 genome submissions to GISAID. Nat Biotechnol 43, 665–666 (2025). https://doi.org/10.1038/s41587-025-02636-6

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