COVID-19 mRNA third dose induces a unique hybrid immunity-like antibody response

Abstract

The continuous evolution of SARS-CoV-2 generated highly mutated variants, like omicron BA.1 and BA.2, able to escape natural and vaccine-induced primary immunity1,2. The administration of a third dose of mRNA vaccines induces a secondary response with increased protection. We investigated, at single-cell level, the longitudinal evolution of the neutralizing antibody response in four donors after three mRNA doses3. A total of 4,100 spike protein specific memory B cells were single cell sorted and 350 neutralizing antibodies were identified. The third dose increased the antibody neutralization potency and breadth against all SARS-CoV-2 variants of concern as previously observed with hybrid immunity3. However, the B cell repertoire that stands behind the response is dramatically different. The increased neutralizing response was largely due to the expansion of B cell germlines poorly represented after two doses, and the reduction of germlines predominant after primary immunization such as IGHV3-53;IGHJ6-1 and IGHV3-66;IGHJ4-1. Divergently to hybrid immunity, cross-protection after a third dose was mainly guided by Class 1/2 antibodies encoded by IGHV1-58;IGHJ3-1 and IGHV1-69;IGHJ4-1 germlines. The IGHV2-5;IGHJ3-1 germline, which induced broadly cross-reactive Class 3 antibodies after infection or viral vector vaccination, was not induced by a third mRNA dose. Our data show that while neutralizing breadth and potency can be improved by different immunization regimens, each of them has a unique molecular signature which should be considered while designing novel vaccines and immunization strategies.

mRNA vaccines and hybrid immunity use different B cell germlines to neutralize Omicron BA.4 and BA.5

“…Human samples from COVID-19 infected and vaccinated donors, who received two or three vaccine doses, of both sexes, who gave their written consent, were previously collected through a collaboration with the Azienda Ospedaliera Universitaria Senese, Siena (IT) 16,17 . Subjects in the seropositive 2 nd dose cohort resulted positive to SARS-CoV-2 infection between October and November 2020 16 .…”

“…In addition to the functional characterization and epitope mapping analyses, we investigated the B cell germline and V-J gene rearrangements (IGHV;IGHJ) used by highly cross-reactive nAbs against omicron variants. Of the 482 nAbs assessed in this study we previously recovered 430 heavy chain sequences: 46 from SN2, 176 from SN3 and 208 from SP2 16,17 . In SN2 subjects, predominant B cell germlines neutralizing the Wuhan strain include IGHV1-69;IGHJ4-1, IGHV3-30;IGHJ6-1, IGHV3-53;IGHJ6-1, IGHV3-66;IGHJ4-1 B cell germlines 16,[22][23][24][25] .…”

“…A collection of 482 neutralizing human monoclonal antibodies (nAbs) against the SARS-CoV-2 virus originally isolated in Wuhan, were used in this study. They derived from three different cohorts: SARS-CoV-2 seronegative subjects vaccinated with two (SN2) or three (SN3) doses of COVID-19 mRNA vaccines, and subjects exposed to SARS-CoV-2 infection and subsequently vaccinated with two doses of the same mRNA vaccines (seropositive 2 nd dose; SP2) 16,17 . All subjects, with the exception of VAC-010 in the SN3 cohort which was immunized with mRNA-1273, received the BNT162b2 mRNA vaccine 16,17 .…”

“…2). RBD-targeting nAbs were previously classified based on their ability to compete with the Class 1/2 antibody J08 18 , the Class 3 antibody S309 19 , and the Class 4 antibody CR3022 20 , or for their lack of competition with the three tested antibodies (Not-competing) 17,21 . The SN2 group (n = 46) showed mainly nAbs targeting the RBD-Class 1/2 epitope region against Wuhan (n = 26; 56.5%), BA.1 (n = 1; 100%) and BA.2 (n = 2; 50%), while no neutralization activity was observed against the BA.4 and BA.5 omicron variants (Fig.…”

Analysis of anti-Omicron neutralizing antibody titers in different vaccinated and unvaccinated convalescent plasma sources

“…As the immune system processes the same antigen in different forms there are numerous opportunities for processing the protein in different manners that can diversity the specificity of the immune response and thus increase the likelihood of eliciting antibodies that react with variant proteins. Stucturally, it has been shown that mRNA third dose vaccination induces mostly mainly class 1/2 antibodies encoded by IGHV1-58;IGHJ3-1 and IGHV1-69;IGHJ4-1 germlines, but not the IGHV2-5;IGHJ3-1 germline, broadly cross-reactive Class 3 antibodies seen after infection 39 .…”