The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity

Thomson, E. C.; Rosen, L. E.; Shepherd, J. G.; Spreafico, R.; da Silva Filipe, A.; Wojcechowskyj, J. A.; Davis, C.; Piccoli, L.; Pascall, D. J.; Dillen, J.; Lytras, S.; Czudnochowski, N.; Shah, R.; Meury, M.; Jesudason, N.; De Marco, A.; Li, K.; Bassi, J.; O'Toole, A.; Pinto, D.; Colquhoun, R. M.; Culap, K.; Jackson, B.; Zatta, F.; Rambaut, A.; Jaconi, S.; Sreenu, V. B.; Nix, J.; Jarrett, R. F.; Beltramello, M.; Nomikou, K.; Pizzuto, M.; Tong, L.; Cameroni, E.; Johnson, N.; Wickenhagen, A.; Ceschi, A.; Mair, D.; Ferrari, P.; Smollett, K.; Sallusto, F.; Carmichael, S.; Garzoni, C.; Nichols, J.

doi:10.1101/2020.11.04.355842

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bioRxiv · 10.1101/2020.11.04.355842

The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity

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Abstract

SARS-CoV-2 can mutate to evade immunity, with consequences for the efficacy of emerging vaccines and antibody therapeutics. Herein we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is the most divergent region of S, and provide epidemiological, clinical, and molecular characterization of a prevalent RBM variant, N439K. We demonstrate that N439K S protein has enhanced binding affinity to the hACE2 receptor, and that N439K virus has similar clinical outcomes and in vitro replication fitness as compared to wild- type. We observed that the N439K mutation resulted in immune escape from a panel of neutralizing monoclonal antibodies, including one in clinical trials, as well as from polyclonal sera from a sizeable fraction of persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.

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Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., Lytras, S., Czudnochowski, N., Shah, R., Meury, M., Jesudason, N., De Marco, A., Li, K., Bassi, J., O'Toole, A., Pinto, D., Colquhoun, R. M., Culap, K., Jackson, B., Zatta, F., Rambaut, A., Jaconi, S., Sreenu, V. B., Nix, J., Jarrett, R. F., Beltramello, M., Nomikou, K., Pizzuto, M., Tong, L., Cameroni, E., Johnson, N., Wickenhagen, A., Ceschi, A., Mair, D., Ferrari, P., Smollett, K., Sallusto, F., Carmichael, S., Garzoni, C., Nichols, J.. 2020-11-05. The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity. https://doi.org/10.1101/2020.11.04.355842

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