Haogao Gu | Searcharxiv

arXiv2025

A novel approach to profile global circulation pathway of SARS-CoV-2 variants by site-based mutation dynamics

The genetic evolution of SARS-CoV-2 has caused recurring epidemic waves, understanding its global dispersal patterns is critical for effective surveillance. We developed the Site-based mutation dynamics - Equal Power Sampling (S-EPS) framework, a phylogenetic-free, bias-correcting framework for profiling viral source-sink dynamics. Applying S-EPS to 6.6 million SARS-CoV-2 genomes (March 2020 - June 2024) from 13 regions worldwide, we identified Africa and the Indian subcontinent as the predominant sources of key mutations. Southeast Asia serves as an early transmission hub, while Russia and South America mainly acted as sinks. Key mutations took longer to establish fitness in source regions than externally. Once an amino acid substitution on the receptor-binding domain reached 1% prevalence in major sources, there is an 80% probability it would spread elsewhere, with a 2-month median lead time (IQR: 1-4). Our findings underscore the importance of genetic surveillance, with S-EPS offering enhanced capability for monitoring emerging viral threats.

q-bio.PE↗

arXiv2025

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

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.

q-bio.PE↗