Modeling the population effects of escape mutations in SARS-CoV-2 to guide vaccination strategies

SARS-Cov-2 escape mutations (EM) have been detected and are spreading. Vaccines may need adjustment to respond these or future mutations. We designed a population level model integrating both waning immunity EM. also set of criteria for elaborating fitting this cross-neutralization other data with goal minimizing vaccine decision errors. formulated four related models. These differ regarding which strains can drift in the host when that was elicited by different strains. Across changing mutation parameter values, variations led patterns where: 1) EM rare first epidemic, 2) rebound outbreaks after outbreak accelerated increasing drifting, 3) long term endemic infection is determined mostly rates small effects drifting parameter, 4) caused loss effectiveness, under some conditions: vaccines induced higher levels than without them. The differences similarities across models suggest paths developing specifying epitopes where act. This provides base on construct epitope specific evolutionary using new high-throughput assay from samples guide decisions.