Abstract
Infection-enhancing antibodies may limit the efficiency of Covid-19 vaccines. We analyzed the evolution ofneutralizing and facilitating epitopes in 1,860,489 SARS-CoV-2 genomes stored in the Los Alamos databasefrom June to November 2021. The structural dynamics of these epitopes was determined by molecular modelingof the spike protein on a representative panel of SARS-CoV-2 variants. D614, which belongs to an antibody-dependent-enhancement (ADE) epitope common to SARS-CoV-1 and SARS-CoV-2, has mutated to D614G in2020, which could explain why ADE has not been detected following mass vaccination. A second epitopelocated in the N-terminal domain (NTD), specific of SARS-CoV-2, is highly conserved among most variants. Incontrast, the neutralizing epitope of the NTD showed extensive variations in SARS-CoV-2 variants. The balancebetween facilitating and neutralizing antibodies is in favor of neutralization for the Wuhan strain, alpha and betavariants, but not for gamma, delta, lambda, and mu. The recently emerging omicron variant is atypic as itsmutational profiles affects both neutralization and ADE epitopes. Overall, our data reveal that the evolution ofSARS-CoV-2 has dramatically affected the ADE/neutralization balance. Future vaccines should consider thesefindings to design new formulations adapted to SARS-CoV-2 variants and lacking ADE epitopes in the spikeprotein.