ABSTRACT
Omicron, the most heavily mutated SARS-CoV-2 variant so far, is highly resistant to neutralizing antibodies, raising unprecedented concerns about the effectiveness of antibody therapies and vaccines. We examined whether sera from individuals who received two or three doses of inactivated vaccine, could neutralize authentic Omicron. The seroconversion rates of neutralizing antibodies were 3.3% (2/60) and 95% (57/60) for 2- and 3-dose vaccinees, respectively. For three-dose recipients, the geometric mean neutralization antibody titer (GMT) of Omicron was 15, 16.5-fold lower than that of the ancestral virus (254). We isolated 323 human monoclonal antibodies derived from memory B cells in 3-dose vaccinees, half of which recognize the receptor binding domain (RBD) and show that a subset of them (24/163) neutralize all SARS-CoV-2 variants of concern (VOCs), including Omicron, potently. Therapeutic treatments with representative broadly neutralizing mAbs individually or antibody cocktails were highly protective against SARS-CoV-2 Beta infection in mice. Atomic structures of the Omicron S in complex with three types of all five VOC-reactive antibodies defined the binding and neutralizing determinants and revealed a key antibody escape site, G446S, that confers greater resistance to one major class of antibodies bound at the right shoulder of RBD through altering local conformation at the binding interface. Our results rationalize the use of 3-dose immunization regimens and suggest that the fundamental epitopes revealed by these broadly ultrapotent antibodies are a rational target for a universal sarbecovirus vaccine. One sentence summary A sub-set of antibodies derived from memory B cells of volunteers vaccinated with 3 doses of an inactivated SARS-CoV-2 vaccine work individually as well as synergistically to keep variants, including Omicron, at bay.
ABSTRACT
Emergence of variants of concern (VOC) with altered antigenic structures and waning humoral immunity to SARS-CoV-2 are harbingers of a long pandemic. Administration of a third dose of an inactivated virus vaccine can boost the immune response. Here, we have dissected the immunogenic profiles of antibodies from 3-dose vaccinees, 2-dose vaccinees and convalescents. Better neutralization breadth to VOCs, expeditious recall and long-lasting humoral response bolster 3-dose vaccinees in warding off COVID-19. Analysis of 171 complex structures of SARS-CoV-2 neutralizing antibodies identified structure-activity correlates, revealing ultrapotent, VOCs-resistant and broad-spectrum antigenic patches. Construction of immunogenic and mutational heat maps revealed a direct relationship between "hot" immunogenic sites and areas with high mutation frequencies. Ongoing antibody somatic mutation, memory B cell clonal turnover and antibody composition changes in B cell repertoire driven by prolonged and repeated antigen stimulation confer development of monoclonal antibodies with enhanced neutralizing potency and breadth. Our findings rationalize the use of 3-dose immunization regimens for inactivated vaccines. One sentence summaryA third booster dose of inactivated vaccine produces a highly sifted humoral immune response via a sustained evolution of antibodies capable of effectively neutralizing SARS-CoV-2 variants of concern.
Subject(s)
COVID-19ABSTRACT
SARS-CoV-2 has caused the COVID-19 pandemic. Recently, B.1.617 variants have been transmitted rapidly in India. The transmissibility, pathogenicity, and neutralization characteristics of these variants have received considerable interest. In this study, 22 pseudotyped viruses were constructed for B.1.617 variants and their corresponding single amino acid mutations. B.1.617 variants did not exhibit significant enhanced infectivity in human cells, but mutations T478K and E484Q in the receptor binding domain led to enhanced infectivity in mouse ACE2-overexpressing cells. Furin activities were slightly increased against B.1.617 variants and cell–cell fusion after infection of B.1.617 variants was enhanced. Furthermore, B.1.617 variants escaped neutralization by several mAbs, mainly because of mutations L452R, T478K, and E484Q in the receptor binding domain. The neutralization activities of sera from convalescent patients, inactivated vaccine-immunized volunteers, adenovirus vaccine-immunized volunteers, and SARS-CoV-2 immunized animals against pseudotyped B.1.617 variants were reduced by approximately twofold, compared with the D614G variant.
Subject(s)
COVID-19ABSTRACT
COVID-19 has spread worldwide. However, SARS-CoV-2 serological markers, which usually important indicators of disease progression, remains to be studied. To determine serological patterns during infection and their corresponding influencing factors, we conducted a cohort study including 115 patients with COVID-19 from 41 hospitals. The study included measuring IgM, IgG, and neutralizing antibodies (NAb) in serum, conducting epidemiological survey of the subjects, and retrieving clinical indicators from electronic medical records. We found NAb had the highest seroconversion rate (79.61%), followed by IgG (60.42%), and IgM (26.56%). Seroconversion rate peaked 20–40 d post-infection with NAb reaching 100%. The Geometric mean of NAb ID50 is 201 (30 to 6271). The NAb titer was positively correlated with duration of infection (p = 0), IgM (p = 0.016), and IgG (p = 0). Compared with IgM or IgG, NAb has better diagnostic sensitivity and serological patterns are valuable for clinical diagnosis and disease monitoring.
Subject(s)
COVID-19ABSTRACT
Ten emerging SARS-CoV-2 variants—B.1.1.298, B.1.1.7, B.1.351, P.1, P.2, B.1.429, B.1.525, B.1.526-1, B.1.526-2, B.1.1.318—and seven corresponding single amino acid mutations in the receptor-binding domain were examined using SARS-CoV-2 pseudovirus. The results indicate that the current SARS-CoV-2 variants do not increase infectivity among humans. The K417N/T, N501Y, or E484K-carrying variants exhibited increased abilities to infect to mouse ACE2-overexpressing cells. The activities of Furin, TMPRSS2, and cathepsin L were increased against most of the variants. RBD amino acid mutations comprising K417T/N, L452R, Y453F, S477N, E484K, and N501Y caused significant immune escape from 11 of 13 monoclonal antibodies. However, the resistance to neutralization by convalescent serum or vaccines was mainly caused by the E484K mutation, while the neutralization of E484K-carrying variants was decreased by 1.1–6.2-fold. The convalescent serum from B.1.1.7- and B.1.351-infected patients neutralized the variants themselves better than other SARS-CoV-2 variants.
ABSTRACT
The SARS-CoV-2 variant VUI/202012/01 has been reported to spread unexpectedly fast in the United Kingdom. It is estimated that its transmissibility may increase by 70%. In this study, the top five variants circulating in the UK including D614G+L18F+A222V, D614G+A222V, D614G+S477N, VUI/202012/01 and D614G+69-70del+439K were analyzed for their infective and neutralizing characteristics. The pseudotyped viruses were constructed for the five variants and 12 single mutants composed those variants. We found that the VUI/202012/01 variant does enhance its infectivity due to the cumulative effect of multiple mutations including 69-70del and 144/145del mutations in NTD, A570D in RBD, and S982A in S2. Meanwhile, mutations N501Y, N439K and S477N in RBD can cause a significant decrease in the neutralization activity for some mAbs. Although VUI/202012/01 did not affect the neutralization effect of convalescent sera, it affected the neutralization activity of animal immunized sera by RBD protein or recombinant spike DNA to some extent.
ABSTRACT
The spike protein of SARS-Cov-2 has been undergoing mutations and is highly glycosylated. It is critically important to investigate the biological significance of these mutations. Here we investigated 80 natural mutants and 26 glycosylation mutants for the infectivity and reactivity to a panel of neutralizing antibodies and sera from convalescent patients. D614G, along with several double mutations with D614G and another mutation in the same strains, were significantly more infectious, so was N149H, a glycosylation mutant. Most natural mutants within receptor binding domain were less infectious but some became more resistant to neutralizing antibodies. Moreover, the majority of glycosylation mutations were less infectious, revealing the importance of glycosylation for viral infectivity. Interestingly, N234Q was markedly resistant to neutralizing antibodies, whereas N165Q became more sensitive. These findings could be of value in informing our strategy for the development of vaccine and therapeutic antibodies.Funding: This work was supported by National Science and Technology Major Projects of Drug Discovery [grant number 2018ZX09101001] and National Science and Technology Major Projects of Infectious Disease [grant number 2017ZX10304402].Conflict of Interest: All authors declare no competing interest.
Subject(s)
Communicable DiseasesABSTRACT
Jianhui Nie, Qianqian Li, and Jiajing Wu contributed equally to this work.Pseudotyped viruses are useful virological tools due to their safety and versatility. Based on a VSV pseudotyped virus production system, we developed a pseudotyped virus-based neutralization assay against SARS-CoV-2 in biosafety level 2 facilities. This protocol includes production, titration of the SARS-CoV-2 S pseudotyped virus and neutralization assay based on it. Various types of samples targeting virus attachment and entry could be evaluated for their potency, including serum samples derived from animals and humans, monoclonal antibodies, fusion inhibitors (peptides or small molecules). If the pseudotyped virus stock has been prepared in advance, it will take 2 days to get the potency data for the candidate samples. Experience of handling cells is needed before implementing this protocol.