SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma.

To investigate the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the immune population, we coincupi bated the authentic virus with a highly neutralizing plasma from a COVID-19 convalescent patient. The plasma fully neutralized the virus for seven passages, but, after 45 d, the deletion of F140 in the spike N-terminal domain (NTD) N3 loop led to partial breakthrough. At day 73, an E484K substitution in the receptor-binding domain (RBD) occurred, followed, at day 80, by an insertion in the NTD N5 loop containing a new glycan sequon, which generated a variant completely resistant to plasma neutralization. Computational modeling predicts that the deletion and insertion in loops N3 and N5 prevent binding of neutralizing antibodies. The recent emergence in the United Kingdom, South Africa, Brazil, and Japan of natural variants with similar changes suggests that SARS-CoV-2 has the potential to escape an effective immune response and that vaccines and antibodies able to control emerging variants should be developed.
Competing Interests: Competing interest statement: R.R. is an employee of the GSK group of companies. E.A., I.P., E.P., N.M., and R.R. are listed as inventors of full-length human monoclonal antibodies described in Italian patent applications 102020000015754 filed on June 30, 2020 and 102020000018955 filed on August 3, 2020.
(Copyright © 2021 the Author(s). Published by PNAS.)