The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera

Abstract

One year in the coronavirus disease 2019 (COVID-19) pandemic, the first vaccines are being rolled out under emergency use authorizations. It is of great concern that newly emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can escape antibody-mediated protection induced by previous infection or vaccination through mutations in the spike protein. The glutamate (E) to Lysine (K) substitution at position 484 (E484K) in the receptor binding domain (RBD) of the spike protein is present in the rapidly spreading variants of concern belonging to the B.1.351 and P.1 lineages. We performed in vitro microneutralization assays with both the USA-WA1/2020 virus and a recombinant (r)SARS-CoV-2 virus that is identical to USA-WA1/2020 except for the E484K mutation introduced in the spike RBD. We selected 34 sera from study participants based on their SARS-CoV-2 spike ELISA antibody titer (negative [N=4] versus weak [N=8], moderate [N=11] or strong positive [N=11]). In addition, we included sera from five individuals who received two doses of the Pfizer SARS-CoV-2 vaccine BNT162b2. Serum neutralization efficiency was lower against the E484K rSARS-CoV-2 (vaccination samples: 3.4 fold; convalescent low IgG: 2.4 fold, moderate IgG: 4.2 fold and high IgG: 2.6 fold) compared to USA-WA1/2020. For some of the convalescent donor sera with low or moderate IgG against the SARS-CoV-2 spike, the drop in neutralization efficiency resulted in neutralization ID50 values similar to negative control samples, with low or even absence of neutralization of the E484K rSARS-CoV-2. However, human sera with high neutralization titers against the USA-WA1/2020 strain were still able to neutralize the E484K rSARS-CoV-2. Therefore, it is important to aim for the highest titers possible induced by vaccination to enhance protection against newly emerging SARS-CoV-2 variants. Two vaccine doses may be needed for induction of high antibody titers against SARS-CoV-2. Postponing the second vaccination is suggested by some public health authorities in order to provide more individuals with a primer vaccination. Our data suggests that this may leave vaccinees less protected against newly emerging variants.

Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies

“…Moreover, they are consistent with studies showing loss of neutralization potency of human convalescent serum against VSV-SARS-CoV-2 chimeric virus variants containing the E484K mutation 34 and selection of escape E484K mutants under serial passage of convalescent COVID-19 plasma 35 . Indeed, similar findings with authentic SARS-CoV-2 viruses encoding E484K mutations were recently reported 36 . One unique trend we noticed was that convalescent and vaccine-induced immune sera neutralized infection of the chimeric SARS-CoV-2 strains encoding the Brazilian spike (B.1.1.248) better than the South African spike (B.1.351) even though both viruses encoded E484 and N501 mutations.…”

Molecular Epidemiology of SARS-CoV-2 in Cyprus

“…In Brazil, the P.1 (20J/501Y.V3, VOC-202101/02) lineage emerged in December 2020 [26]. The P.1 lineage contains ten mutations in the spike protein that may affect its ability to be recognized by antibodies [27,28].…”

Genes of SARS-CoV-2 and emerging variants

“…Importantly the S protein is also the major viral protein eliciting both humoral and cell-mediated immune responses, making it an excellent vaccine candidate 6 . However, mutations in the S protein pose a significant threat by possible generation of mutant strains with the potential to escape antibody neutralisation, thus rendering the current vaccine strategy less effective [7][8][9][10] .…”