Optimizing Global Genomic Surveillance for Early Detection of Emerging SARS-CoV-2 Variants

Abstract

Background: Global viral threats underscore the need for effective genomic surveillance, but high costs and uneven resource distribution hamper its implementation. Targeting surveillance to international travelers in major travel hubs may offer a more efficient strategy for the early detection of SARS-CoV-2 variants. Methods: We developed and calibrated a multiple-strain metapopulation model of global SARS-CoV-2 transmission using extensive epidemiological, phylogenetic, and high-resolution air travel data. We then compared baseline surveillance with various resource-allocation approaches that prioritize travelers, focusing on Omicron BA.1/BA.2 retrospectively and on hypothetical future variants under different emergence, transmission and vaccine effectiveness scenarios. Findings: Focusing existing surveillance resources on travelers at key global hubs significantly shortened detection delays without increasing total surveillance efforts. In retrospective analyses of Omicron BA.1/BA.2, traveler-targeted approaches consistently outperformed baseline strategies, even when overall resources were reduced. Simulations indicate that focusing surveillance on key travel hubs outperform baseline practices in detecting future variants, across different possible origins, even with reduced resources. This approach also remains effective in future pandemic scenarios with varying reproductive numbers and vaccine effectiveness. Interpretation: These findings provide a quantitative, cost-effective framework for strengthening global genomic surveillance. By reallocating resources toward international travelers in select travel hubs, early detection of emerging variants can be enhanced, informing rapid public health interventions and bolstering preparedness for future pandemics.