Equity and efficiency in global respiratory virus genomic surveillance

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.