A High-Resolution Approach to Mapping Spike Protein Evolution for Advancing Antibody Therapy Design

The rapid evolution of SARS-CoV-2 continues to undermine the clinical utility of monoclonal antibody (mAb) therapeutics, with successive viral variants escaping neutralization by previously effective treatments. To proactively identify emerging threats to antibody-based interventions, we conducted a comprehensive global analysis of approximately 9.3 million SARS-CoV-2 spike protein sequences collected from 2020 through early 2025. Our study reveals that several spike mutations have achieved near-ubiquitous prevalence worldwide among which most notably V404* (present in 97.4% of sequences), Y436* (93.0%), and T478* (81.4%) yet remain underexplored in functional and structural studies despite their potential to modulate antibody recognition.These high-frequency mutations co-occur with well-documented immune escape substitutions such as E484K, L452R, and N501Y, collectively forming a complex mutational landscape that may impair binding across multiple classes of therapeutic antibodies targeting distinct epitopes. Critically, we also identify lower-frequency mutations including F486*, R346*, and G446* that, while currently circulating below 20% global prevalence, are exhibiting rapid growth trajectories. These variants represent early-warning signals for potential future resistance and warrant urgent experimental validation.By mapping the global distribution and temporal dynamics of spike mutations through a therapeutic lens, our analysis provides a real-time, pharma-focused surveillance framework. This resource enables developers to prioritize conserved, resilient epitopes for next-generation antibody design and to anticipate resistance before it becomes wide spread ultimately supporting more durable and broadly effective counter measures against evolving viral threats.