Exposure histories to SARS-CoV-2 variants and vaccinations will shape the specificity of antibody responses. To understand the specificity of Delta-elicited antibody immunity, we characterize the ...polyclonal antibody response elicited by primary or mRNA vaccine-breakthrough Delta infections. Both types of infection elicit a neutralizing antibody response focused heavily on the receptor-binding domain (RBD). We use deep mutational scanning to show that mutations to the RBD's class 1 and class 2 epitopes, including sites 417, 478, and 484-486 often reduce binding of these Delta-elicited antibodies. The anti-Delta antibody response is more similar to that elicited by early 2020 viruses than the Beta variant, with mutations to the class 1 and 2, but not class 3 epitopes, having the largest effects on polyclonal antibody binding. In addition, mutations to the class 1 epitope (e.g., K417N) tend to have larger effects on antibody binding and neutralization in the Delta spike than in the D614G spike, both for vaccine- and Delta-infection-elicited antibodies. These results help elucidate how the antigenic impacts of SARS-CoV-2 mutations depend on exposure history.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The Omicron BA.1 variant of SARS-CoV-2 escapes convalescent sera and monoclonal antibodies that are effective against earlier strains of the virus. This immune evasion is largely a consequence of ...mutations in the BA.1 receptor binding domain (RBD), the major antigenic target of SARS-CoV-2. Previous studies have identified several key RBD mutations leading to escape from most antibodies. However, little is known about how these escape mutations interact with each other and with other mutations in the RBD. Here, we systematically map these interactions by measuring the binding affinity of all possible combinations of these 15 RBD mutations (2
=32,768 genotypes) to 4 monoclonal antibodies (LY-CoV016, LY-CoV555, REGN10987, and S309) with distinct epitopes. We find that BA.1 can lose affinity to diverse antibodies by acquiring a few large-effect mutations and can reduce affinity to others through several small-effect mutations. However, our results also reveal alternative pathways to antibody escape that does not include every large-effect mutation. Moreover, epistatic interactions are shown to constrain affinity decline in S309 but only modestly shape the affinity landscapes of other antibodies. Together with previous work on the ACE2 affinity landscape, our results suggest that the escape of each antibody is mediated by distinct groups of mutations, whose deleterious effects on ACE2 affinity are compensated by another distinct group of mutations (most notably Q498R and N501Y).
To combat future severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and spillovers of SARS-like betacoronaviruses (sarbecoviruses) threatening global health, we designed mosaic ...nanoparticles that present randomly arranged sarbecovirus spike receptor-binding domains (RBDs) to elicit antibodies against epitopes that are conserved and relatively occluded rather than variable, immunodominant, and exposed. We compared immune responses elicited by mosaic-8 (SARS-CoV-2 and seven animal sarbecoviruses) and homotypic (only SARS-CoV-2) RBD nanoparticles in mice and macaques and observed stronger responses elicited by mosaic-8 to mismatched (not on nanoparticles) strains, including SARS-CoV and animal sarbecoviruses. Mosaic-8 immunization showed equivalent neutralization of SARS-CoV-2 variants, including Omicrons, and protected from SARS-CoV-2 and SARS-CoV challenges, whereas homotypic SARS-CoV-2 immunization protected only from SARS-CoV-2 challenge. Epitope mapping demonstrated increased targeting of conserved epitopes after mosaic-8 immunization. Together, these results suggest that mosaic-8 RBD nanoparticles could protect against SARS-CoV-2 variants and future sarbecovirus spillovers.
Abstract
Among the 30 nonsynonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three ...functionally important regions of the S-gene at sites that will likely impact (1) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (2) interactions of Spike with ACE2 receptors, and (3) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any virus within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and, in combination with other mutations, adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron overall previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.
The use of molybdenum as a quantitative paleo-atmosphere redox sensor is predicated on the assumption that Mo is hosted in sulfides in the upper continental crust (UCC). This assumption is tested ...here by determining the mineralogical hosts of Mo in typical Archean, Proterozoic, and Phanerozoic upper crustal igneous rocks, spanning a compositional range from basalt to granite. Common igneous sulfides such as pyrite and chalcopyrite contain very little Mo (commonly below detection limits of around 10 ng/g) and are not a significant crustal Mo host. By contrast, volcanic glass and Ti-bearing phases such as titanite, ilmenite, magnetite, and rutile contain significantly higher Mo concentrations (e.g., up to 40 µg/g in titanite), and can account for the whole-rock Mo budget in most rocks. However, mass balance between whole-rock and mineral data is not achieved in 4 out of 10 granites analyzed with in-situ methods, where Mo may be hosted in undetected trace molybdenite. Significant Mo depletion (i.e., UCC-normalized Mo/Ce < 1) occurs in nearly every granitic rock analyzed here, but not in oceanic basalts or their differentiates (Greaney et al., 2017; Jenner and O’Neill, 2012). On average, granites are missing ∼60% of their expected Mo contents. There are two possible reasons for this: (1) Mo partitions into an aqueous magmatic vapor/fluid phase that is expelled from cooling plutons, and/or (2) Mo is partitioned into titaniferous phases during partial melting and fractional crystallization of an evolving magma. The first scenario is likely given the high solubility of oxidized Mo. However, correlations between Mo/Ce and Nb/La in several plutonic suites suggest fractionating phases such as rutile or Fe-Ti oxides may sequester Mo in lower crustal rocks or in subducting slabs in arc settings.
Understanding the molecular basis for immune recognition of SARS-CoV-2 spike glycoprotein antigenic sites will inform the development of improved therapeutics. We determined the structures of two ...human monoclonal antibodies-AZD8895 and AZD1061-which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor-binding domain (RBD) of SARS-CoV-2 to define the genetic and structural basis of neutralization. AZD8895 forms an 'aromatic cage' at the heavy/light chain interface using germ line-encoded residues in complementarity-determining regions (CDRs) 2 and 3 of the heavy chain and CDRs 1 and 3 of the light chain. These structural features explain why highly similar antibodies (public clonotypes) have been isolated from multiple individuals. AZD1061 has an unusually long LCDR1; the HCDR3 makes interactions with the opposite face of the RBD from that of AZD8895. Using deep mutational scanning and neutralization escape selection experiments, we comprehensively mapped the crucial binding residues of both antibodies and identified positions of concern with regards to virus escape from antibody-mediated neutralization. Both AZD8895 and AZD1061 have strong neutralizing activity against SARS-CoV-2 and variants of concern with antigenic substitutions in the RBD. We conclude that germ line-encoded antibody features enable recognition of the SARS-CoV-2 spike RBD and demonstrate the utility of the cocktail AZD7442 in neutralizing emerging variant viruses.
Neutralization assays are experimental surrogates for the effectiveness of infection- or vaccine-elicited polyclonal antibodies and therapeutic monoclonal antibodies targeting SARS-CoV-2. However, ...the measured neutralization can depend on the details of the experimental assay. Here, we systematically assess how ACE2 expression in target cells affects neutralization by antibodies to different spike epitopes in lentivirus pseudovirus neutralization assays. For high ACE2-expressing target cells, receptor-binding domain (RBD) antibodies account for nearly all neutralizing activity in polyclonal human sera. However, for lower ACE2-expressing target cells, antibodies targeting regions outside the RBD make a larger (although still modest) contribution to serum neutralization. These serum-level results are mirrored for monoclonal antibodies: N-terminal domain (NTD) antibodies and RBD antibodies that do not compete for ACE2 binding incompletely neutralize on high ACE2-expressing target cells, but completely neutralize on cells with lower ACE2 expression. Our results show that the ACE2 expression level in the target cells is an important experimental variable, and that high ACE2 expression emphasizes the role of a subset of RBD-directed antibodies.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein is the main target for neutralizing antibodies. These antibodies can be elicited through immunization or passively ...transferred as therapeutics in the form of convalescent-phase sera or monoclonal antibodies (MAbs). Potently neutralizing antibodies are expected to confer protection; however, it is unclear whether weakly neutralizing antibodies contribute to protection. Also, their mechanism of action in vivo is incompletely understood. Here, we demonstrate that 2B04, an antibody with an ultrapotent neutralizing activity (50% inhibitory concentration IC50 of 0.04 μg/ml), protects hamsters against SARS-CoV-2 in a prophylactic and therapeutic infection model. Protection is associated with reduced weight loss and viral loads in nasal turbinates and lungs after challenge. MAb 2B04 also blocked aerosol transmission of the virus to naive contacts. We next examined three additional MAbs (2C02, 2C03, and 2E06), recognizing distinct epitopes within the receptor binding domain of spike protein that possess either minimal (2C02 and 2E06, IC50 > 20 μg/ml) or weak (2C03, IC50 of 5 μg/ml) virus neutralization capacity in vitro. Only 2C03 protected Syrian hamsters from weight loss and reduced lung viral load after SARS-CoV-2 infection. Finally, we demonstrated that Fc-Fc receptor interactions were not required for protection when 2B04 and 2C03 were administered prophylactically. These findings inform the mechanism of protection and support the rational development of antibody-mediated protection against SARS-CoV-2 infections. IMPORTANCE The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by SARS-CoV-2, has resulted in the loss of millions of lives. Safe and effective vaccines are considered the ultimate remedy for the global social and economic disruption caused by the pandemic. However, a thorough understanding of the immune correlates of protection against this virus is lacking. Here, we characterized four different monoclonal antibodies and evaluated their ability to prevent or treat SARS-CoV-2 infection in Syrian hamsters. These antibodies varied in their ability to neutralize the virus in vitro. Prophylactic administration of potent and weakly neutralizing antibodies protected against SARS-CoV-2 infection, and this effect was Fc receptor independent. The potent neutralizing antibody also had therapeutic efficacy and eliminated onward aerosol transmission. In contrast, minimally neutralizing antibodies provided no protection against infection with SARS-CoV-2 in Syrian hamsters. Combined, these studies highlight the significance of weakly neutralizing antibodies in the protection against SARS-CoV-2 infection and associated disease.
This study presents a 234U enrichment meter that uses high energy gamma and neutron count rate as measured by a portable, high-purity germanium gamma ray detector. Twenty-one 30B cylinders containing ...UF6 of varying origin were analyzed with an HPGe detector for high-energy gamma ray and neutron counts. Excellent correlations (R2≥ 0.95) between various regions of ≥3.0 MeV gamma rays, neutron count rate, and uranium enrichment were found. These neutron and high-energy gamma data are used to create calibration-dependent enrichment meters for 234U. The 234U enrichment calculated from the neutron count rate and 4 – 6 MeV gamma count rate is more accurate than methods that rely on the 120.9 keV peak which is strongly attenuated inside commercial sized UF6 cylinders. These neutron and high-energy gamma enrichment calculators can also be used to determine a 235U enrichment, assuming mass-based enrichment from natural uranium, but the results are not as accurate as the traditional 185.7 keV peak enrichment meter.
We quantify the behavior of Cu, Ga, Ge, As, Mo, Ag, Cd, In, Sn, Sb, W, Tl, Pb, and Bi during the differentiation of a picritic magma in the Kilauea Iki lava lake, Hawaii, using whole rock and glass ...differentiation trends, as well as partition coefficients in Cu-rich sulfide blebs and minerals. Such data allow us to constrain the partitioning behavior of these elements between sulfide and silicate melts, as well as the chalcophile element characteristics of the mantle source of the Kilauea lavas. Nearly all of the elements are generally incompatible on a whole-rock scale, with concentrations increasing exponentially below ∼6wt% MgO. However, in-situ laser ablation data reveal that Cu, Ag, Bi, Cd, In, Pb, and Sn are chalcophile; As, Ge, Sb, and Tl are weakly chalcophile to lithophile; and Mo, Ga, and W are lithophile. The average Dsulfide/silicate melt values are: DAg=1252±1201 (2SD), DBi=663±576, DCd=380±566, DIn=40±34, DPb=34±18, DSn=5.3±3.6, DAs=2.4±7.6, DGe=1.6±1.4, DSb=1.3±1.5, DTl=1.1±1.7, DMo=0.56±0.6, DGa=0.10±0.3, and DW=0.11±0.1. These findings are consistent with experimental partitioning studies and observations of Ni-rich sulfide liquid in mid-ocean ridge basalts (MORB), despite the different compositions of the KI sulfides. The KI glasses and whole rocks are enriched in As, Ag, Sb, W, and Bi, relative to elements of similar compatibility (as established by abundances in MORB), mimicking enrichments found in basalts from the Manus back arc basin (Jenner et al., 2012) and the upper continental crust (UCC). These enrichments suggest the presence of terrigenous sediments in the Kilauea mantle source. The KI source is calculated to be a mixture of depleted MORB mantle (DMM) and 10–20% recycled crust composed of MORB and minor terrigenous sediments.
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