Inequities and global declines in SARS-CoV-2 genomic data availability hinder response to emerging variants

Genomic epidemiology has transformed the way public health scientists detect, monitor, and respond to infectious disease threats such as SARS-CoV-2 on a global scale. Early in the COVID-19 pandemic, vast inequities in whole-genome sequence data availability between high- and low-income countries were highlighted, but the persistence of these disparities five years into a global pandemic has not been quantified. Also, while it is generally known that genomic surveillance of SARS-CoV-2 largely declined following the end of the COVID-19 public health emergency, this has not been formally measured, and how it impacts our ability to detect and characterize new variants, remains unknown. Therefore, we performed an analysis of SARS-CoV-2 sequence submissions on the Global Initiative for Sharing All Influenza Data (GISAID) platform from 2020 to 2025, by country and World Bank income classification. There were large differences in SARS-CoV-2 sequence submissions by income classification, indicating a disparity in our ability to monitor SARS-CoV-2 evolution worldwide, which has important consequences for preventative measures such as vaccine strain selection. Nevertheless, there are important barriers to sustainable sharing of SARS-CoV-2 sequence data, which we discuss in detail, along with their relevance to other pathogens of public health importance. Also, the decrease in sequence submissions in high income countries from 577 million at the peak of the pandemic, to under 50 million in 2024, represents a loss of capacity to monitor SARS-CoV-2 evolution in countries with known capabilities. Ultimately, data drive the impact of genomic epidemiology, and long-term investments in genomic surveillance programs, as well as incentives for timely data sharing, are urgently needed to detect and characterize new viral variants worldwide.