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1.
Nature ; 619(7969): 403-409, 2023 Jul.
Article in English | MEDLINE | ID: covidwho-20242865

ABSTRACT

The entry of SARS-CoV-2 into host cells depends on the refolding of the virus-encoded spike protein from a prefusion conformation, which is metastable after cleavage, to a lower-energy stable postfusion conformation1,2. This transition overcomes kinetic barriers for fusion of viral and target cell membranes3,4. Here we report a cryogenic electron microscopy (cryo-EM) structure of the intact postfusion spike in a lipid bilayer that represents the single-membrane product of the fusion reaction. The structure provides structural definition of the functionally critical membrane-interacting segments, including the fusion peptide and transmembrane anchor. The internal fusion peptide forms a hairpin-like wedge that spans almost the entire lipid bilayer and the transmembrane segment wraps around the fusion peptide at the last stage of membrane fusion. These results advance our understanding of the spike protein in a membrane environment and may guide development of intervention strategies.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/chemistry , Cryoelectron Microscopy , Lipid Bilayers , Virus Internalization , Membrane Fusion , Protein Conformation
2.
HERD ; : 19375867231174238, 2023 May 10.
Article in English | MEDLINE | ID: covidwho-2319758

ABSTRACT

OBJECTIVES: Serious COVID-19 nosocomial infection has demonstrated a need to design our health services in a different manner. Triggered by the current crisis and the interest in rapid deployable hospital, this article discusses how hospital building layouts can be improved to streamline the patient pathways and thus to reduce the risk of hospital-related infections. Another objective of this work is to explore the possibility to develop flexible and scalable hospital building layouts through modular construction. This enables hospitals to better cope with different future demands and thereby enhance the resilience of the healthcare facilities. BACKGROUND: During the first wave of COVID-19, approximate one-seventh to one-fifth COVID-19 patients and majority of infected healthcare workers acquired the disease in NHS hospitals. Similar issues emerged during the Crimean War (1853-1856) when more soldiers died from infectious diseases rather than of battlefield casualties in Scutari Hospital. This led to an important collaborative work between Florence Nightingale, who looked into this problem statistically, and Isambard Kingdom Brunel, who designed the rapid deployment Renkioi Hospital which yielded a death rate 90% lower than that in Scutari Hospital. While contemporary medical research and practice have moved beyond Nightingale's concept of contagion, challenges of optimizing hospital building layouts to support healing and effectively combat nosocomial infections still pose elusive problems that require further investigation. METHODS: Through case study investigations, this article evaluates the risk of nosocomial infections of airborne transmissions under different building layouts, and this provides essential data for infection control in the new-build or refurbished healthcare projects. RESULTS: Improved hospital layout can be achieved through reconfiguration of rooms and concourse. Design interventions through evidence-based infection risk analysis can reduce congestion and provide extra separation and compartmentalization which will contribute the reduced nosocomial infection rate. CONCLUSIONS: A resilient hospital shall be able to cope with unexpected circumstances and be flexible to change when new challenges arise, without compromising the safety and well-being of frontline medical staff and other patients. Such an organizational resilience depends on not only flexible clinical protocols but also flexible hospital building layouts. The latter allows hospitals to get better prepared for rapidly changing patient expectations, medical advances, and extreme weather events. The reconfigurability of an existing healthcare facility can be further enhanced through modular construction, standardization of building components, and additional space considered.

3.
iScience ; 26(5): 106582, 2023 May 19.
Article in English | MEDLINE | ID: covidwho-2291978

ABSTRACT

The number of mutations in the omicron (B.1.1.529) BA.1 variant of concern led to an unprecedented evasion of vaccine induced immunity. However, despite rise in global infections, severe disease did not increase proportionally and is likely linked to persistent recognition of BA.1 by T cells and non-neutralizing opsonophagocytic antibodies. Yet, the emergence of new sublineage BA.2, which is more transmissible than BA.1 despite relatively preserved neutralizing antibody responses, has raised the possibility that BA.2 may evade other vaccine-induced responses. Here, we comprehensively profiled the BNT162b2 vaccine-induced response to several VOCs, including omicron BA.1 and BA.2. While vaccine-induced immune responses were compromised against both omicron sublineages, vaccine-induced antibody isotype titers, and non-neutralizing Fc effector functions were attenuated to the omicron BA.2 spike compared to BA.1. Conversely, FcγR2a and FcγR2b binding was elevated to BA.2, albeit lower than BA.1 responses, potentially contributing to persistent protection against severity of disease.

4.
Chinese Journal of Nosocomiology ; 32(24):3681-3686, 2022.
Article in Chinese, English | GIM | ID: covidwho-2254507

ABSTRACT

OBJECTIVE: To analyze the epidemiological characteristics of Omicron subvariant BA.2 represented mild/asymptomatic COVID-19 cases in makeshift hospitals. METHODS: The data of COVID-19 patients who were mild and asymptomatic admitted to Shanghai Shilong Road Temporary Capsule Hospital from Apr 8 to May 13, 2022 were retrospectively collected. The epidemiological history, general situation, length of stay, severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) vaccination, and cycle threshold (Ct) values of N and ORF1ab genes in the cases were analyzed. Univariate analysis and multivariate Logistic regression were used to analyze the risk factors for hospitalization > 14 days and the risk of not being vaccinated. RESULTS: A total of 2896 patients with Omicron variant infection were collected in this study. The average length of hospital stay was (10.79+or-4.31)days. The average Ct values of N gene and ORF1ab gene on admission were 28.63+or-6.55 and 29.45+or-5.50, respectively, and 13.05% of the patients were not vaccinated against COVID-19. The length of hospital stay of the patients with old age was more likely to surpass 14 days. The patients with more times of vaccination were more likely to discharge within 14 days. Nucleic acid testing for COVID-19 showed that the Ct values of the N and ORF1ab genes in the juvenile patients were higher than those in the adult patients, and the Ct values of the genes in the patients with common chronic diseases were lower than those in the uncomplicated patients. Correlation analysis showed that the length of hospital stay was negatively correlated with the Ct values of N gene (r=-0.362,P<0.001) and ORF1ab gene (r=-0.391, P<0.001). CONCLUSION: The age of Omicron subvariant BA.2 infection patients, co-morbidity, times of vaccination, and Ct values of SARS-CoV-2 nucleic acid are the risk factors for the length of stay in hospital. Isolation of asymptomatic and mild COVID-19 patients in makeshift hospitals can effectively control the social spread of the epidemic.

5.
J Med Virol ; 95(3): e28673, 2023 03.
Article in English | MEDLINE | ID: covidwho-2267686

ABSTRACT

Broadly neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are sought to curb coronavirus disease 2019 (COVID-19) infections. Here we produced and characterized a set of mouse monoclonal antibodies (mAbs) specific for the ancestral SARS-CoV-2 receptor binding domain (RBD). Two of them, 17A7 and 17B10, were highly potent in microneutralization assay with 50% inhibitory concentration (IC50 ) ≤135 ng/mL against infectious SARS-CoV-2 variants, including G614, Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Kappa, Lambda, B.1.1.298, B.1.222, B.1.5, and R.1. Both mAbs (especially 17A7) also exhibited strong in vivo efficacy in protecting K18-hACE2 transgenic mice from the lethal infection with G614, Alpha, Beta, Gamma, and Delta viruses. Structural analysis indicated that 17A7 and 17B10 target the tip of the receptor binding motif in the RBD-up conformation. A third RBD-reactive mAb (3A6) although escaped by Beta and Gamma, was highly effective in cross-neutralizing Delta and Omicron BA.1 variants in vitro and in vivo. In competition experiments, antibodies targeting epitopes similar to these 3 mAbs were rarely enriched in human COVID-19 convalescent sera or postvaccination sera. These results are helpful to inform new antibody/vaccine design and these mAbs can be useful tools for characterizing SARS-CoV-2 variants and elicited antibody responses.


Subject(s)
Antibodies, Monoclonal , COVID-19 , Animals , Mice , Humans , SARS-CoV-2/genetics , COVID-19 Serotherapy , Mice, Transgenic , Spike Glycoprotein, Coronavirus/genetics , Antibodies, Viral , Antibodies, Neutralizing , Neutralization Tests
6.
J Control Release ; 354: 316-322, 2023 02.
Article in English | MEDLINE | ID: covidwho-2180267

ABSTRACT

The early and massive vaccination campaign in Israel with the mRNA-LNP Comirnaty® (Pfizer-BioNTech) vaccine against the SARS-CoV-2 virus made available large amounts of data regarding the efficacy and safety of this vaccine. Adverse reactions to mRNA-based SARS-CoV-2 vaccines are rare events, but due to large mediatic coverage they became feared and acted as a potential source of delay for the vaccination of the Israeli population. The experience with the reactogenicity of the polyethylene glycol (PEG) moiety of PEGylated liposomes, PEGylated proteins and other PEGylated drugs raised the fear that similar adverse effects can be associated with the PEG lipid which is an essential component of currently used mRNA-LNP vaccines against COVID-19. In this study we quantified the levels of anti-PEG IgG, IgM and IgE present in the blood of 79 volunteers immediately before and 3 weeks after receiving a first dose of Comirnaty® vaccine. Our in vitro results show that different humanized anti-PEG antibodies bind the PEGylated nano-liposomes in a concentration-dependent manner, but they bind with a lower affinity to the Comirnaty vaccine, despite it having a high mole% of neutral PEG2000-lipid on its surface. We found an increase in IgG concentration in the blood 3 weeks after the first vaccine administration, but no increase in IgM or IgE. In addition, no severe signs of adverse reactions to the Comirnaty vaccine were observed in the population studied despite the significant pre-existing high titers of IgG before the first dose of vaccine in 2 donors.


Subject(s)
COVID-19 Vaccines , COVID-19 , Humans , BNT162 Vaccine , SARS-CoV-2 , Vaccination , Liposomes , Polyethylene Glycols , RNA, Messenger , Lipids , Immunoglobulin E , Immunoglobulin G , Immunoglobulin M , Antibodies, Viral
7.
Sci Adv ; 8(49): eabq6527, 2022 12 09.
Article in English | MEDLINE | ID: covidwho-2152873

ABSTRACT

As severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolves to escape natural antibodies, it also loses sensitivity to therapeutic antibody drugs. By contrast, evolution selects for binding to ACE2, the cell-surface receptor required for SARS-CoV-2 infection. Consistent with this, we find that an ACE2 decoy neutralizes antibody-resistant variants, including Omicron, with no loss in potency. To identify design features necessary for in vivo activity, we compare several enzymatically inactive, Fc effector-silenced ACE2-Fc decoys. Inclusion of the ACE2 collectrin-like domain not only improves affinity for the S protein but also unexpectedly extends serum half-life and is necessary to reduce disease severity and viral titer in Syrian hamsters. Fc effector function is not required. The activity of ACE2 decoy receptors is due, in part, to their ability to trigger an irreversible structural change in the viral S protein. Our studies provide a new understanding of how ACE2 decoys function and support their development as therapeutics to treat ACE2-dependent coronaviruses.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans
8.
Science ; 369(6511): 1586-1592, 2020 09 25.
Article in English | MEDLINE | ID: covidwho-2038226

ABSTRACT

Intervention strategies are urgently needed to control the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. The trimeric viral spike (S) protein catalyzes fusion between viral and target cell membranes to initiate infection. Here, we report two cryo-electron microscopy structures derived from a preparation of the full-length S protein, representing its prefusion (2.9-angstrom resolution) and postfusion (3.0-angstrom resolution) conformations, respectively. The spontaneous transition to the postfusion state is independent of target cells. The prefusion trimer has three receptor-binding domains clamped down by a segment adjacent to the fusion peptide. The postfusion structure is strategically decorated by N-linked glycans, suggesting possible protective roles against host immune responses and harsh external conditions. These findings advance our understanding of SARS-CoV-2 entry and may guide the development of vaccines and therapeutics.


Subject(s)
Host-Pathogen Interactions/immunology , Spike Glycoprotein, Coronavirus/chemistry , Angiotensin-Converting Enzyme 2 , Cryoelectron Microscopy , HEK293 Cells , Humans , Peptidyl-Dipeptidase A/chemistry , Protein Domains , Protein Multimerization , Protein Structure, Secondary , Receptors, Virus/chemistry , Virus Internalization
9.
Sci Immunol ; 7(76): eadd5446, 2022 10 28.
Article in English | MEDLINE | ID: covidwho-1992933

ABSTRACT

SARS-CoV-2 Omicron subvariants have generated a worldwide health crisis due to resistance to most approved SARS-CoV-2 neutralizing antibodies and evasion of vaccination-induced antibodies. To manage Omicron subvariants and prepare for new ones, additional means of isolating broad and potent humanized SARS-CoV-2 neutralizing antibodies are desirable. Here, we describe a mouse model in which the primary B cell receptor (BCR) repertoire is generated solely through V(D)J recombination of a human VH1-2 heavy chain (HC) and, substantially, a human Vκ1-33 light chain (LC). Thus, primary humanized BCR repertoire diversity in these mice derives from immensely diverse HC and LC antigen-contact CDR3 sequences generated by nontemplated junctional modifications during V(D)J recombination. Immunizing this mouse model with SARS-CoV-2 (Wuhan-Hu-1) spike protein immunogens elicited several VH1-2/Vκ1-33-based neutralizing antibodies that bound RBD in a different mode from each other and from those of many prior patient-derived VH1-2-based neutralizing antibodies. Of these, SP1-77 potently and broadly neutralized all SARS-CoV-2 variants through BA.5. Cryo-EM studies revealed that SP1-77 bound RBD away from the receptor-binding motif via a CDR3-dominated recognition mode. Lattice light-sheet microscopy-based studies showed that SP1-77 did not block ACE2-mediated viral attachment or endocytosis but rather blocked viral-host membrane fusion. The broad and potent SP1-77 neutralization activity and nontraditional mechanism of action suggest that it might have therapeutic potential. Likewise, the SP1-77 binding epitope may inform vaccine strategies. Last, the type of humanized mouse models that we have described may contribute to identifying therapeutic antibodies against future SARS-CoV-2 variants and other pathogens.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Mice , Animals , Spike Glycoprotein, Coronavirus/genetics , Angiotensin-Converting Enzyme 2 , Membrane Fusion , Antibodies, Viral , Antibodies, Neutralizing , Epitopes , Receptors, Antigen, B-Cell
10.
J Med Virol ; 94(11): 5363-5374, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-1955920

ABSTRACT

The surface glycoprotein (S protein) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was used to develop coronavirus disease 2019 (COVID-19) vaccines. However, SARS-CoV-2, especially the S protein, has undergone rapid evolution and mutation, which has remained to be determined. Here, we analyzed and compared the early (12 237) and the current (more than 10 million) SARS-CoV-2 strains to identify the mutation features and geographical distribution of the S gene and S protein. Results showed that in the early strains, most of the loci were with relative low mutation frequency except S: 23403 (4486 strains), while in the current strains, there was a surge in the mutation strains and frequency, with S: 23403 constantly being the highest one, but tremendously increased to approximately 1050 times. Furthermore, D614 (S: 23403) was one of the most highly frequent mutations in the S protein of Omicron as of March 2022, and most of the mutant strains were still from the United States, and the United Kingdom. Further analysis demonstrated that in the receptor-binding domain, most of the loci with low mutation frequency in the early strains, while S: 22995 was nowadays the most prevalent loci with 3 122 491 strains in the current strains. Overall, we compare the mutation features of the S region in SARS-CoV-2 strains between the early and the current stains, providing insight into further studies in concert with emerging SARS-CoV-2 variants for COVID-19 vaccines.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , COVID-19 Vaccines , Humans , Membrane Glycoproteins/genetics , Mutation , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus
11.
Front Immunol ; 13: 946731, 2022.
Article in English | MEDLINE | ID: covidwho-1952336

ABSTRACT

Mitochondria get caught in the crossfire of coronavirus disease 2019 (COVID-19) and antiviral immunity. The mitochondria-mediated antiviral immunity represents the host's first line of defense against viral infection, and the mitochondria are important targets of COVID-19. However, the specific manifestations of mitochondrial damage in patients with COVID-19 have not been systematically clarified. This study comprehensively analyzed one single-cell RNA-sequencing dataset of lung tissue and two bulk RNA-sequencing datasets of blood from COVID-19 patients. We found significant changes in mitochondrion-related gene expression, mitochondrial functions, and related metabolic pathways in patients with COVID-19. SARS-CoV-2 first infected the host alveolar epithelial cells, which may have induced excessive mitochondrial fission, inhibited mitochondrial degradation, and destroyed the mitochondrial calcium uniporter (MCU). The type II alveolar epithelial cell count decreased and the transformation from type II to type I alveolar epithelial cells was blocked, which exacerbated viral immune escape and replication in COVID-19 patients. Subsequently, alveolar macrophages phagocytized the infected alveolar epithelial cells, which decreased mitochondrial respiratory capacity and activated the ROS-HIF1A pathway in macrophages, thereby aggravating the pro-inflammatory reaction in the lungs. Infected macrophages released large amounts of interferon into the blood, activating mitochondrial IFI27 expression and destroying energy metabolism in immune cells. The plasma differentiation of B cells and lung-blood interaction of regulatory T cells (Tregs) was exacerbated, resulting in a cytokine storm and excessive inflammation. Thus, our findings systematically explain immune escape and excessive inflammation seen during COVID-19 from the perspective of mitochondrial quality imbalance.


Subject(s)
COVID-19 , SARS-CoV-2 , Antiviral Agents/therapeutic use , Humans , Inflammation , Lung , Mitochondria , RNA
12.
Frontiers in psychology ; 13, 2022.
Article in English | EuropePMC | ID: covidwho-1918575

ABSTRACT

Livestreaming e-commerce has emerged as a highly profitable e-commerce that has revolutionized the retail industry, especially during the COVID-19 pandemic. However, research on livestreaming e-commerce is still in its infancy. This study sheds new light on impulsive purchase behavior in livestreaming e-commerce. Based on stimulus-organism-response (SOR) theory, this study introduces the “People-Product-Place” marketing strategy for livestreaming e-commerce from the perspective of consumer perception and aims to understand the impact of marketing strategy on impulsive purchase behavior in e-commerce livestreaming shopping scenes, and to examine the mediating effect of involvement. The study conducted SEM analysis, in Amos, on 437 response sets from an online anonymous survey. The results show that perceived e-commerce anchor attributes, perceived scarcity, and immersion positively influence impulsive purchase behavior;that “People-Product-Place” marketing strategy is important;and that effective marketing triggers impulsive purchase. Perceived e-commerce anchor attributes, perceived scarcity, and immersion positively influence involvement, which positively influences impulsive purchase. Involvement mediates between perceived e-commerce anchor attributes, perceived scarcity and immersion, and impulsive purchase. These findings guide marketers to improve the profitability of livestreaming e-commerce and provide some references of economic recovery for many other countries that also suffered from the impact of the COVID-19 pandemic.

14.
BMC Cardiovasc Disord ; 22(1): 262, 2022 06 11.
Article in English | MEDLINE | ID: covidwho-1886916

ABSTRACT

BACKGROUND: Previous studies have observed inconsistent associations between coronavirus disease 2019 (COVID-19) and heart failure (HF), but these studies were prone to bias based on reverse causality and residual confounding factors. We aimed to investigate genetic liability between COVID-19 and heart failure using a bidirectional Mendelian randomization study. METHODS: The causal relationship between COVID-19 (including COVID-19, hospitalized COVID-19 compared with the general population, and severe COVID-19) and HF are determined by using a bidirectional Mendelian randomization analysis. We drew on summary statistics from the largest HF genome-wide association study (GWAS) meta-analysis on individuals of European ancestry, which included 47,309 HF patients and 930,014 controls. The inverse variance weighted (IVW), an adaption of the Egger regression (MR-Egger), the weighted median, and weighted model were conducted for the Mendelian randomization analysis to estimate a causal effect. To confirm the stability, we performed a "leave-one-out" approach for the sensitivity analysis. RESULTS: Genetically predicted severe COVID-19 was not significantly associated with the risk of HF [odds ratio (OR), 1.003; 95% confidence interval (CI), 0.969-1.037; p = 0.867]. The IVW demonstrated that there was no association between genetically hospitalized COVID-19 infection and HF risk [OR, 1.009; 95% CI, 0.939-1.085; p = 0.797]. There was no evidence to support the association between genetically determined COVID-19 and the risk of HF [OR, 1.066; 95% CI, 0.955-1.190; p = 0.253]. In addition, genetically predicted HF was also not causally associated with COVID-19 [OR, 1.162; 95% CI, 0.824-1.639; p = 0.393]. MR-Egger analysis indicated no evidence of directional pleiotropy. CONCLUSION: The current bidirectional Mendelian randomization analysis overcomes the limitations of observational studies. Our findings indicated that there is no causal association between COVID-19 and HF.


Subject(s)
COVID-19 , Heart Failure , COVID-19/genetics , Genome-Wide Association Study , Heart Failure/diagnosis , Heart Failure/genetics , Humans , Mendelian Randomization Analysis , Polymorphism, Single Nucleotide
15.
Am J Obstet Gynecol ; 227(3): 493.e1-493.e7, 2022 09.
Article in English | MEDLINE | ID: covidwho-1872911

ABSTRACT

BACKGROUND: SARS-CoV-2 infection is associated with enhanced disease severity in pregnant women. Despite the potential of COVID-19 vaccines to reduce severe disease, vaccine uptake remained relatively low among pregnant women. Just as coordinated messaging from the Centers for Disease Control and Prevention and leading obstetrics organizations began to increase vaccine confidence in this vulnerable group, the evolution of SARS-CoV-2 variants of concerns, including the Omicron variant, raised new concerns about vaccine efficacy because of their ability to escape vaccine-induced neutralizing antibodies. Early data point to a milder disease course following infection with the Omicron variant in vaccinated individuals. Thus, these data suggest that alternate vaccine-induced immunity beyond neutralization may continue to attenuate Omicron variant-induced disease, such as Fc-mediated antibody activity. OBJECTIVE: This study aimed to test whether vaccine-induced antibodies raised during pregnancy continue to bind to and leverage Fc receptors to protect against variants of concern including the Omicron variant. STUDY DESIGN: The receptor binding domain or whole spike-specific antibody isotype binding titers and Fc gamma receptor binding directed toward variants of concern, including the Omicron variant, were analyzed in pregnant women after receiving the full dose regimen of either the Pfizer/BioNTech BNT62b2 (n=10) or Moderna mRNA-1273 (n=10) vaccination using a multiplexing Luminex assay. RESULTS: Reduced isotype recognition of the Omicron receptor binding domain was observed following administration of either vaccine with relatively preserved, albeit reduced, recognition of the whole Omicron spike by immunoglobulin M and G antibodies. Despite the near complete loss of Fc receptor binding to the Omicron receptor binding domain, Fc receptor binding to the Omicron spike was more variable but largely preserved. CONCLUSION: Reduced binding titers to the Omicron receptor binding domain aligns with the observed loss of neutralizing activity. Despite the loss of neutralization, preserved, albeit reduced, Omicron spike recognition and Fc receptor binding potentially continue to attenuate disease severity in pregnant women.


Subject(s)
COVID-19 , Pregnancy Complications, Infectious , Vaccines , Antibodies, Viral , COVID-19/prevention & control , COVID-19 Vaccines , Female , Humans , Membrane Glycoproteins/genetics , Membrane Glycoproteins/metabolism , Pregnancy , Pregnancy Complications, Infectious/prevention & control , RNA, Messenger , Receptors, Fc , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/genetics , Vaccination , Viral Envelope Proteins/genetics , Viral Envelope Proteins/metabolism
16.
Sci Immunol ; : eabp8328, 2022 May 12.
Article in English | MEDLINE | ID: covidwho-1846319

ABSTRACT

Key features of immune memory are greater and faster antigen-specific antibody responses to repeat infection. In the setting of immune-evading viral evolution, it is important to understand how far antibody memory recognition stretches across viral variants when memory cells are recalled to action by repeat invasions. It is also important to understand how immune recall influences longevity of secreted antibody responses. We analyzed SARS-CoV-2 variant recognition, dynamics of memory B cells and secreted antibody over time after infection, vaccination, and boosting. We find that a two-dose SARS-CoV-2 vaccination regimen given after natural infection generated greater longitudinal antibody stability and induced maximal antibody magnitudes with enhanced breadth across Beta, Gamma, Delta and Omicron variants. A homologous 3rd mRNA vaccine dose in COVID-naïve individuals conferred greater cross-variant evenness of neutralization potency with stability that was equal to the hybrid immunity conferred by infection plus vaccination. Within unvaccinated individuals who recovered from COVID, enhanced antibody stability over time was observed within a subgroup of individuals that recovered more quickly from COVID and harbored significantly more memory B cells cross-reactive to endemic coronaviruses early after infection. These cross-reactive clones map to the conserved S2 region of SARS-CoV-2 spike with higher somatic hypermutation levels and greater target affinity. We conclude that SARS-CoV-2 antigen challenge histories in humans influence not only the speed and magnitude of antibody responses, but also functional cross-variant antibody repertoire composition and longevity.

17.
Nat Methods ; 19(4): 381-383, 2022 04.
Article in English | MEDLINE | ID: covidwho-1784010
18.
Cell Rep ; 39(4): 110729, 2022 04 26.
Article in English | MEDLINE | ID: covidwho-1783229

ABSTRACT

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), bearing an unusually high number of mutations, has become a dominant strain in many countries within several weeks. We report here structural, functional, and antigenic properties of its full-length spike (S) protein with a native sequence in comparison with those of previously prevalent variants. Omicron S requires a substantially higher level of host receptor ACE2 for efficient membrane fusion than other variants, possibly explaining its unexpected cellular tropism. Mutations not only remodel the antigenic structure of the N-terminal domain of the S protein but also alter the surface of the receptor-binding domain in a way not seen in other variants, consistent with its remarkable resistance to neutralizing antibodies. These results suggest that Omicron S has acquired an extraordinary ability to evade host immunity by excessive mutations, which also compromise its fusogenic capability.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/genetics , Humans , Mutation/genetics , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus
19.
Sci Transl Med ; 14(642): eabn9243, 2022 04 27.
Article in English | MEDLINE | ID: covidwho-1741565

ABSTRACT

The Omicron variant of SARS-CoV-2 has been shown to evade neutralizing antibodies elicited by vaccination or infection. Despite the global spread of the Omicron variant, even among highly vaccinated populations, death rates have not increased concomitantly. These data suggest that immune mechanisms beyond antibody-mediated virus neutralization may protect against severe disease. In addition to neutralizing pathogens, antibodies contribute to control and clearance of infections through Fc effector mechanisms. Here, we probed the ability of vaccine-induced antibodies to drive Fc effector activity against the Omicron variant using samples from individuals receiving one of three SARS-CoV-2 vaccines. Despite a substantial loss of IgM, IgA, and IgG binding to the Omicron variant receptor binding domain (RBD) in samples from individuals receiving BNT162b2, mRNA-1273, and CoronaVac vaccines, stable binding was maintained against the full-length Omicron Spike protein. Compromised RBD binding IgG was accompanied by a loss of RBD-specific antibody Fcγ receptor (FcγR) binding in samples from individuals who received the CoronaVac vaccine, but RBD-specific FcγR2a and FcγR3a binding was preserved in recipients of mRNA vaccines. Conversely, Spike protein-specific antibodies exhibited persistent but reduced binding to FcγRs across all three vaccines, although higher binding was observed in samples from recipients of mRNA vaccines. This was associated with preservation of FcγR2a and FcγR3a binding antibodies and maintenance of Spike protein-specific antibody-dependent natural killer cell activation. Thus, despite the loss of Omicron neutralization, vaccine-induced Spike protein-specific antibodies continue to drive Fc effector functions, suggesting a capacity for extraneutralizing antibodies to contribute to disease control.


Subject(s)
COVID-19 Vaccines , COVID-19 , Antibodies, Neutralizing , Antibodies, Viral , BNT162 Vaccine , COVID-19/prevention & control , Humans , Immunoglobulin G , RNA, Messenger/genetics , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , mRNA Vaccines
20.
Frontiers in bioengineering and biotechnology ; 10, 2022.
Article in English | EuropePMC | ID: covidwho-1733087

ABSTRACT

In the fight against the worldwide pandemic coronavirus disease 2019 (COVID-19), simple, rapid, and sensitive tools for nucleic acid detection are in urgent need. PCR has been a classic method for nucleic acid detection with high sensitivity and specificity. However, this method still has essential limitations due to the dependence on thermal cycling, which requires costly equipment, professional technicians, and long turnover times. Currently, clustered regularly interspaced short palindromic repeats (CRISPR)-based biosensors have been developed as powerful tools for nucleic acid detection. Moreover, the CRISPR method can be performed at physiological temperature, meaning that it is easy to assemble into point-of-care devices. Microfluidic chips hold promises to integrate sample processing and analysis on a chip, reducing the consumption of sample and reagent and increasing the detection throughput. This review provides an overview of recent advances in the development of CRISPR-based biosensing techniques and their perfect combination with microfluidic platforms. New opportunities and challenges for the improvement of specificity and efficiency signal amplification are outlined. Furthermore, their various applications in healthcare, animal husbandry, agriculture, and forestry are discussed.

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