Rational design of a booster vaccine against COVID-19 based on antigenic distance

Current COVID-19 vaccines are highly effective against symptomatic disease, but repeated booster doses using vaccines based on the ancestral strain offer limited additional protection against SARS-CoV-2 variants of concern (VOCs). To address this, we used antigenic distance to in silico select optimized booster vaccine seed strains effective against both current and future VOCs. Our model suggests that a SARS-CoV-1-based booster vaccine has the potential to cover a broader range of VOCs. Candidate vaccines including the spike protein from ancestral SARS-CoV-2, Delta, Omicron (BA.1), SARS-CoV-1, or MERS-CoV were experimentally evaluated in mice following two doses of the BNT162b2 vaccine. The SARS-CoV-1-based booster vaccine outperformed other candidates in terms of neutralizing antibody breadth and duration, as well as protective activity against Omicron (BA.2) challenge. This study suggests a unique strategy for selecting booster vaccines based on antigenic distance, which may be useful in designing future booster vaccines as new SARS-CoV-2 variants emerge.

Non-Neutralizing Epitopes Shade Neutralizing Epitopes against Omicron in a Multiple Epitope-Based Vaccine

The ongoing coronavirus disease 2019 pandemic has raised concerns about the risk of re-infection. Non-neutralizing epitopes are one of the major reasons for antibody-dependent enhancement. Past studies on the ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have revealed an infectivity-enhancing site on the ancestral SARS-CoV-2 spike protein. However, infection enhancement associated with the SARS-CoV-2 Omicron strain remains elusive. In this study, we examined the antibodies induced by a multiple epitope-based vaccine, which showed infection enhancement for the Omicron strain but not for the ancestral SARS-CoV-2 or Delta strain. By examining the antibodies induced by single epitope-based vaccines, we identified a conserved epitope, IDf (450-469), with neutralizing activity against ancestral SARS-CoV-2, Delta, and Omicron. Although neutralizing epitopes are present in the multiple epitope-based vaccine, other immunodominant non-neutralizing epitopes such as IDg (480-499) can shade their neutralizing activity, leading to infection enhancement of Omicron. Our study provides up-to-date epitope information on SARS-CoV-2 variants to help design better vaccines or antibody-based therapeutics against future variants.

Bacillus Calmette-Guérin-induced trained immunity protects against SARS-CoV-2 challenge in K18-hACE2 mice

SARS-CoV-2 has been confirmed in over 450 million confirmed cases since 2019. Although several vaccines have been certified by the WHO and people are being vaccinated on a global scale, it has been reported that multiple SARS-CoV-2 variants can escape neutralization by antibodies, resulting in vaccine breakthrough infections. Bacillus Calmette-Guérin (BCG) is known to induce heterologous protection based on trained immune responses. Here, we investigated whether BCG-induced trained immunity protected against SARS-CoV-2 in the K18-hACE2 mouse model. Our data demonstrate that i.v. BCG (BCG-i.v.) vaccination induces robust trained innate immune responses and provides protection against WT SARS-CoV-2, as well as the B.1.617.1 and B.1.617.2 variants. Further studies suggest that myeloid cell differentiation and activation of the glycolysis pathway are associated with BCG-induced training immunity in K18-hACE2 mice. Overall, our study provides the experimental evidence that establishes a causal relationship between BCG-i.v. vaccination and protection against SARS-CoV-2 challenge.

Heats of formation and stress-strain relationship of Fe-Cr solid solutions from a constructed Fe-Cr potential

A new Fe-Cr interatomic potential is constructed under the framework of the embedded-atom method and has better performances in predicting heats of formation and stress-strain relationship of Fe-Cr solid solutions than the Fe-Cr potentials already published in the literature. Based on the constructed Fe-Cr potential, molecular dynamics simulation reveals that the heats of formation of BCC Fe-Cr solid solutions at 1600 K are positive within the entire composition range, and the calculated values are in good agreement with corresponding experimental measurements in the literature. In addition, it is also found that the tensile strengths of BCC Fe-Cr solid solutions increase with the increase of the Cr composition, and that BCC Fe-Cr solid solutions are less ductile with smaller critical strains than both Fe and Cr. The simulated results are discussed and compared with the corresponding experimental and calculated evidence in the literature to validate the relevance of the newly constructed Fe-Cr potential.

Computation of Antigenicity Predicts SARS-CoV-2 Vaccine Breakthrough Variants

It has been reported that multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) including Alpha, Beta, Gamma, and Delta can reduce neutralization by antibodies, resulting in vaccine breakthrough infections. Virus–antiserum neutralization assays are typically performed to monitor potential vaccine breakthrough strains. However, experiment-based methods took several weeks whether newly emerging variants can break through current vaccines or therapeutic antibodies. To address this, we sought to establish a computational model to predict the antigenicity of SARS-CoV-2 variants by sequence alone. In this study, we firstly identified the relationship between the antigenic difference transformed from the amino acid sequence and the antigenic distance from the neutralization titers. Based on this correlation, we obtained a computational model for the receptor-binding domain (RBD) of the spike protein to predict the fold decrease in virus–antiserum neutralization titers with high accuracy (~0.79). Our predicted results were comparable to experimental neutralization titers of variants, including Alpha, Beta, Delta, Gamma, Epsilon, Iota, Kappa, and Lambda, as well as SARS-CoV. Here, we predicted the fold of decrease of Omicron as 17.4-fold less susceptible to neutralization. We visualized all 1,521 SARS-CoV-2 lineages to indicate variants including Mu, B.1.630, B.1.633, B.1.649, and C.1.2, which can induce vaccine breakthrough infections in addition to reported VOCs Beta, Gamma, Delta, and Omicron. Our study offers a quick approach to predict the antigenicity of SARS-CoV-2 variants as soon as they emerge. Furthermore, this approach can facilitate future vaccine updates to cover all major variants. An online version can be accessed at http://jdlab.online.

Cohesive properties of PbBi/Fe3O4 and PbBi/(Fe,Cr)3O4 interfaces

First principles calculations reveal that the effects of PbBi on the cohesive properties of Fe₃O₄ and (Fe,Cr)₃O₄: PbBi can reduce the cohesive strength of the oxides, and the contents of O and Cr on the O-terminated oxide side play a significant role in the cohesive properties of the PbBi/Fe₃O₄ and PbBi/(Fe,Cr)₃O₄ interfaces. Specifically, the performance of oxidation decreases more significantly under the conditions of insufficient oxygen, and a high ratio of Cr of the subsurface of oxides can lead to the reduction of the cohesive properties of O-terminated interfaces. Calculations also show that the Pb-O-terminated interfaces are energetically favorable and are more stable than the Bi-O-terminated surfaces due to the strong bond of Pb-O, while the Bi-Cr and Bi-Fe interfaces are more stable than the Pb-Cr and Pb-Fe interfaces. Moreover, it is found that the stability and cohesion of the PbBi/Fe₃O₄ and PbBi/(Fe,Cr)₃O₄ interfaces will decrease when the oxygen concentration is insufficient or the degree of wetting of PbBi of oxides is low, and the PbBi/Fe₃O₄ interface is more sensitive to these conditions. The bond-dissociation energies and electronic structures provide a deep understanding of various interface properties, and the obtained results are in good agreement with experimental measurements in the literature.

Atomistic modelling of the immiscible Fe-Bi system from a constructed bond order potential

An analytical bond-order potential (BOP) of Fe-Bi has been constructed and has been validated to have a better performance than the Fe-Bi potentials already published in the literature. Molecular dynamics simulations based on this BOP has been then conducted to investigate the ground-state properties of Bi, structural stability of the Fe-Bi binary system, and the effect of Bi on mechanical properties of BCC Fe. It is found that the present BOP could accurately predict the ground-state A7 structure of Bi and its structural parameters, and that a uniform amorphous structure of Fe_100-xBi_xcould be formed when Bi is located in the composition range of 26 ⩽x< 70. In addition, simulations also reveal that the addition of a very small percentage of Bi would cause a considerable decrease of tensile strength and critical strain of BCC Fe upon uniaxial tensile loading. The obtained results are in nice agreement with similar experimental observations in the literature.

Adenosine synthase A contributes to recurrent Staphylococcus aureus infection by dampening protective immunity

Background: Staphylococcus aureus is a common human pathogen capable of causing diverse illnesses with possible recurrent infections. Although recent studies have highlighted the role of cellular immunity in recurrent infections, the mechanism by which S. aureus evades host responses remains largely unexplored.

Methods: This study utilizes in vitro and in vivo infection experiments to investigate difference of pro-inflammatory responses and subsequent adaptive immune responses between adsA mutant and WT S. aureus strain infection.

Findings: We demonstrated that adenosine synthase A (AdsA), a potent S. aureus virulence factor, can alter Th17 responses by interfering with NLRP3 inflammasome-mediated IL-1β production. Specifically, S. aureus virulence factor AdsA dampens Th1/Th17 immunity by limiting the release of IL-1β and other Th polarizing cytokines. In particular, AdsA obstructs the release of IL-1β via the adenosine/A2aR/NLRP3 axis. Using a murine infection model, pharmacological inhibition of A2a receptor enhanced S. aureus-specific Th17 responses, whereas inhibition of NLRP3 and caspase-1 downregulated these responses. Our results showed that AdsA contributes to recurrent S. aureus infection by restraining protective Th1/Th17 responses.

Interpretation: Our study provides important mechanistic insights for therapeutic and vaccination strategies against S. aureus infections.

A novel linker-immunodominant site (LIS) vaccine targeting the SARS-CoV-2 spike protein protects against severe COVID-19 in Syrian hamsters

The Coronavirus Disease 2019 (COVID-19) pandemic is unlikely to abate until sufficient herd immunity is built up by either natural infection or vaccination. We previously identified ten linear immunodominant sites on the SARS-CoV-2 spike protein of which four are located within the RBD. Therefore, we designed two linkerimmunodominant site (LIS) vaccine candidates which are composed of four immunodominant sites within the RBD (RBD-ID) or all the 10 immunodominant sites within the whole spike (S-ID). They were administered by subcutaneous injection and were tested for immunogenicity and in vivo protective efficacy in a hamster model for COVID-19. We showed that the S-ID vaccine induced significantly better neutralizing antibody response than RBD-ID and alum control. As expected, hamsters vaccinated by S-ID had significantly less body weight loss, lung viral load, and histopathological changes of pneumonia. The S-ID has the potential to be an effective vaccine for protection against COVID-19.

Hydrogen solubility and diffusivity at Σ3 grain boundary of PdCu

First principles calculations have been performed to comparatively reveal hydrogen solubility and diffusivity at grain boundaries of BCC and FCC PdCu phases. It is found that the temperature-dependent hydrogen solubility at BCC Σ3 (112) GB of PdCu seems much higher than that in BCC PdCu bulk, while hydrogen solubility in FCC Σ3 (111) GB of PdCu is much lower than that in its corresponding FCC bulk. Calculations also reveal that grain boundary has an important effect on hydrogen diffusion of BCC and FCC PdCu, i.e., hydrogen diffusivities of BCC Σ3 (112) and FCC Σ3 (111) grain boundaries of PdCu seem much smaller and bigger than those of its corresponding bulks, respectively. The predicted results could deepen the comprehension of hydrogen solubility and diffusion of PdCu phases.

Sodium salicylate enhances neural excitation via reducing GABAergic transmission in the dentate gyrus area of rat hippocampus in vivo

Sodium salicylate, one of the non-steroidal anti-inflammatory drugs, is widely prescribed in the clinic, but a high dose of usage can cause hyperactivity in the central nervous system, including the hippocampus. At present, the neural mechanism underlying the induced hyperactivity is not fully understood, in particular, in the hippocampus under an in vivo condition. In this study, we found that systemic administration of sodium salicylate increased the field excitatory postsynaptic potential slope and the population spike amplitude in a dose-dependent manner in the hippocampal dentate gyrus area of rats with in vivo field potential extracellular recordings, which indicates that sodium salicylate enhances basal synaptic transmission and neural excitation. In the presence of picrotoxin, a GABA-A receptor antagonist, sodium salicylate failed to increase the initial slope of the field excitatory postsynaptic potential and the amplitude of the population spike in vivo. To further explore how sodium salicylate enhances the neural excitation, we made whole-cell patch-clamp recordings from hippocampal slices. We found that perfusion of the slice with sodium salicylate decreased electrically evoked GABA receptor-mediated currents, increased paired-pulse ratio, and lowered frequency and amplitude of miniature inhibitory postsynaptic currents. Together, these results demonstrate that sodium salicylate enhances the neural excitation through suppressing GABAergic synaptic transmission in presynaptic and postsynaptic mechanisms in the hippocampal dentate gyrus area. Our findings may help understand the side effects caused by sodium salicylate in the central nervous system.

Atomic structure, tensile property, and dislocation behavior of Fe-W interfaces from molecular dynamics simulation

Molecular dynamic simulations based on a recently constructed potential reveal that quasi-repeating patterns could appear in both Fe(110)/W(110) and W(110)/Fe(110) interfaces, and that three kinds of atomic displacements of Fe atoms because of the Fe-W interaction intrinsically bring about the interesting quasi-repeating patterns of the Fe-W interfaces. It is also found that the Fe-W interface becomes more brittle with less critical strains under tensile loading than pure Fe or W, which is fundamentally attributed to the movement of the interface dislocations as a result of the lattice mismatch between Fe and W. Interestingly, the dislocation loops could be formed in the Fe-W interface under tensile loading due to the pinning of the100edge dislocations by the edge dislocations of1/2111, whereas no dislocation loop would be generated in pure Fe or W.

Intradermal delivery of receptor-binding domain of SARS-CoV-2 spike protein with dissolvable microneedles to induce humoral and cellular responses in mice

The S1 subunit of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) spike protein contains an immunogenic receptor‐binding domain (RBD), which is a promising candidate for the development of a potential vaccine. This study demonstrated that intradermal delivery of an S‐RBD vaccine using a dissolvable microneedle skin patch can induce both significant B‐cell and significant T‐cell responses against S‐RBD. Importantly, the outcomes were comparable to that of conventional bolus injection.

Magnetic ground state of face-centered-cubic structure of iron

First principles calculations reveal that the antiferromagnetic double layer (AFMD) along the magnetization direction of 〈0 0 1〉 is the magnetic ground state of face-centered-cubic (FCC) structure of iron (Fe) due to its lowest total energy among all the studied magnetic states. This magnetic ground state of AFMD-〈0 0 1〉 is fundamentally due to a stronger chemical bonding in terms of electronic structure, and could be confirmed by its mechanical properties for the first time. Calculations also show that lattice constant has an important effect to determine the magnetic state of FCC Fe, and a transition of magnetic state between AFMD-〈0 0 1〉 and ferromagnetic happens at the critical lattice constant of 3.666 Å. The derived results are in good agreement with experimental and theoretical observations, and could clarify the controversy regarding magnetic ground state of FCC Fe in the literature.

Strain-stress relationship and dislocation evolution of W-Cu bilayers from a constructed n-body W-Cu potential

An n-body W-Cu potential is constructed under the framework of the embedded-atom method by means of a proposed function of the cross potential. This W-Cu potential is realistic to reproduce mechanical property and structural stability of WCu solid solutions within the entire composition range, and has better performances than the three W-Cu potentials already published in the literature. Based on this W-Cu potential, molecular dynamics simulation is conducted to reveal the mechanical property and dislocation evolution of the bilayer structure between pure W and W_0.7Cu_0.3 solid solution. It is found that the formation of the interface improves the strength of the W_0.7Cu_0.3 solid solutions along tensile loading perpendicular to the interface, as the interface impedes the evolution of the dislocation lines from the W_0.7Cu_0.3 solid solutions to the W part. Simulation also reveals that the interface has an important effect to significantly reduce the tensile strength and critical strain of W along the tensile loading parallel to the interface, which is intrinsically due to the slip of the edge or screw dislocations at low strains as a result of the lattice mismatch.

Effects of trigonal deformation on electronic structure and thermoelectric properties of bismuth

First principles calculation and Boltzmann transport theory have been used to reveal the effects of trigonal deformation on electronic structure and thermoelectric properties of bulk bismuth. It is found that the semimetal-semiconductor transition would happen at the critical c/a points of 2.41 and 2.51, and that such a transition should be ascribed to the opposite changes of band edges at T and L points during trigonal deformation. Calculations also reveal that trigonal deformation has an important effect on various temperature-dependent thermoelectric properties, and that carrier density plays a decisive role in determining the magnitude of Seebeck coefficient and figure of merit. The semimetal  →  semiconductor transition as a result of trigonal compression with the decrease of c/a fundamentally induces the best performance of the thermoelectric properties of bismuth at the c/a ratio of 2.45. The present results agree well with experimental observations in the literature, and provide a deep understanding of the intrinsic relationship between trigonal deformation, band structure, and thermoelectric properties of bismuth.