Lengthy delays in H5N1 genome submissions to GISAID

Abstract

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 mammals^1,2,3, 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 metadata^8,9.

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.