Equity and efficiency in global respiratory virus genomic surveillance

Summary Public health interventions for respiratory virus outbreaks increasingly rely on genomic sequencing for the rapid identification of new (variant) viruses 1–5 . However, global sequencing efforts are unevenly distributed 6–9 , with some high-income countries sequencing at >100,000 times the rate of many low-income countries. Given the importance of virus genomic sequencing and substantial global disparities in sequencing capacities, there is a need for meaningful minimum sequencing targets and functional upper bounds that maximise resource efficiency 1,2,8,10,11 . Here, using mathematical models and analyses of data on global SARS-CoV-2 sequencing output in 2022, we show that increases in sequencing rates typical of low-income countries are >100-fold more effective at reducing time to detection of new variants than increases from rates typical of high-income countries. We find that relative to 2022 sequencing rates, establishing a minimum respiratory virus sequencing capacity of two sequences per million people per week (S/M/wk) with a two-week time from sample collection to sequence deposition in all countries, while simultaneously capping sequencing rates at 30 S/M/wk in all countries, could reduce mean time to first variant detection globally by weeks-to-months while also reducing global sequencing output by >60%. Our results show that investing in a minimum global respiratory virus sequencing capacity is far more effective at improving variant surveillance than expanding local sequencing efforts in countries with existing high-intensity respiratory virus surveillance programs and can guide rightsizing of global respiratory virus genomic surveillance infrastructure.