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1.
Cell ; 183(1): 169-184.e13, 2020 10 01.
Article in English | MEDLINE | ID: mdl-32931734

ABSTRACT

The coronavirus disease 2019 pandemic has made deployment of an effective vaccine a global health priority. We evaluated the protective activity of a chimpanzee adenovirus-vectored vaccine encoding a prefusion stabilized spike protein (ChAd-SARS-CoV-2-S) in challenge studies with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and mice expressing the human angiotensin-converting enzyme 2 receptor. Intramuscular dosing of ChAd-SARS-CoV-2-S induces robust systemic humoral and cell-mediated immune responses and protects against lung infection, inflammation, and pathology but does not confer sterilizing immunity, as evidenced by detection of viral RNA and induction of anti-nucleoprotein antibodies after SARS-CoV-2 challenge. In contrast, a single intranasal dose of ChAd-SARS-CoV-2-S induces high levels of neutralizing antibodies, promotes systemic and mucosal immunoglobulin A (IgA) and T cell responses, and almost entirely prevents SARS-CoV-2 infection in both the upper and lower respiratory tracts. Intranasal administration of ChAd-SARS-CoV-2-S is a candidate for preventing SARS-CoV-2 infection and transmission and curtailing pandemic spread.


Subject(s)
Coronavirus Infections/immunology , Immunogenicity, Vaccine , Pneumonia, Viral/immunology , Viral Vaccines/immunology , Adenoviridae/genetics , Administration, Intranasal , Animals , Antibodies, Neutralizing/blood , Antibodies, Viral/blood , COVID-19 , COVID-19 Vaccines , Chlorocebus aethiops , Coronavirus Infections/pathology , Coronavirus Infections/prevention & control , Female , HEK293 Cells , Humans , Injections, Intramuscular , Mice , Mice, Inbred BALB C , Pandemics , Pneumonia, Viral/pathology , Respiratory Mucosa/immunology , Respiratory Mucosa/pathology , Respiratory Mucosa/virology , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology , Vero Cells , Viral Vaccines/administration & dosage
2.
Immunity ; 54(6): 1290-1303.e7, 2021 06 08.
Article in English | MEDLINE | ID: mdl-34022127

ABSTRACT

Dissecting the evolution of memory B cells (MBCs) against SARS-CoV-2 is critical for understanding antibody recall upon secondary exposure. Here, we used single-cell sequencing to profile SARS-CoV-2-reactive B cells in 38 COVID-19 patients. Using oligo-tagged antigen baits, we isolated B cells specific to the SARS-CoV-2 spike, nucleoprotein (NP), open reading frame 8 (ORF8), and endemic human coronavirus (HCoV) spike proteins. SARS-CoV-2 spike-specific cells were enriched in the memory compartment of acutely infected and convalescent patients several months post symptom onset. With severe acute infection, substantial populations of endemic HCoV-reactive antibody-secreting cells were identified and possessed highly mutated variable genes, signifying preexisting immunity. Finally, MBCs exhibited pronounced maturation to NP and ORF8 over time, especially in older patients. Monoclonal antibodies against these targets were non-neutralizing and non-protective in vivo. These findings reveal antibody adaptation to non-neutralizing intracellular antigens during infection, emphasizing the importance of vaccination for inducing neutralizing spike-specific MBCs.


Subject(s)
Antibodies, Viral/immunology , Antibody Formation/immunology , B-Lymphocytes/immunology , COVID-19/immunology , Host-Pathogen Interactions/immunology , Immunodominant Epitopes/immunology , SARS-CoV-2/immunology , Antibodies, Neutralizing/immunology , Antibody Formation/genetics , B-Lymphocytes/metabolism , Computational Biology/methods , Cross Reactions/immunology , Epitope Mapping , Female , Gene Expression Profiling , High-Throughput Nucleotide Sequencing , Host-Pathogen Interactions/genetics , Humans , Immunodominant Epitopes/genetics , Immunologic Memory , Male , Neutralization Tests , Single-Cell Analysis/methods , Spike Glycoprotein, Coronavirus/immunology , Transcriptome
3.
Immunity ; 53(4): 852-863.e7, 2020 10 13.
Article in English | MEDLINE | ID: mdl-32976769

ABSTRACT

Influenza B virus (IBV) infections can cause severe disease in children and the elderly. Commonly used antivirals have lower clinical effectiveness against IBV compared to influenza A viruses (IAV). Neuraminidase (NA), the second major surface protein on the influenza virus, is emerging as a target of broadly protective antibodies that recognize the NA active site of IAVs. However, similarly broadly protective antibodies against IBV NA have not been identified. Here, we isolated and characterized human monoclonal antibodies (mAbs) that target IBV NA from an IBV-infected patient. Two mAbs displayed broad and potent capacity to inhibit IBV NA enzymatic activity, neutralize the virus in vitro, and protect against lethal IBV infection in mice in prophylactic and therapeutic settings. These mAbs inserted long CDR-H3 loops into the NA active site, engaging residues highly conserved among IBV NAs. These mAbs provide a blueprint for the development of improved vaccines and therapeutics against IBVs.


Subject(s)
Antibodies, Viral/immunology , Catalytic Domain/immunology , Influenza B virus/immunology , Neuraminidase/immunology , Viral Proteins/immunology , Animals , Antibodies, Monoclonal/immunology , Cell Line , Dogs , Female , HEK293 Cells , Humans , Influenza A virus/immunology , Influenza, Human/immunology , Leukocytes, Mononuclear/immunology , Madin Darby Canine Kidney Cells , Mice , Mice, Inbred BALB C , Middle Aged , Orthomyxoviridae Infections/immunology
4.
Proc Natl Acad Sci U S A ; 117(30): 17957-17964, 2020 07 28.
Article in English | MEDLINE | ID: mdl-32661157

ABSTRACT

There is a need for improved influenza vaccines. In this study we compared the antibody responses in humans after vaccination with an AS03-adjuvanted versus nonadjuvanted H5N1 avian influenza virus inactivated vaccine. Healthy young adults received two doses of either formulation 3 wk apart. We found that AS03 significantly enhanced H5 hemagglutinin (HA)-specific plasmablast and antibody responses compared to the nonadjuvanted vaccine. Plasmablast response after the first immunization was exclusively directed to the conserved HA stem region and came from memory B cells. Monoclonal antibodies (mAbs) derived from these plasmablasts had high levels of somatic hypermutation (SHM) and recognized the HA stem region of multiple influenza virus subtypes. Second immunization induced a plasmablast response to the highly variable HA head region. mAbs derived from these plasmablasts exhibited minimal SHM (naive B cell origin) and largely recognized the HA head region of the immunizing H5N1 strain. Interestingly, the antibody response to H5 HA stem region was much lower after the second immunization, and this suppression was most likely due to blocking of these epitopes by stem-specific antibodies induced by the first immunization. Taken together, these findings show that an adjuvanted influenza vaccine can substantially increase antibody responses in humans by effectively recruiting preexisting memory B cells as well as naive B cells into the response. In addition, we show that high levels of preexisting antibody can have a negative effect on boosting. These findings have implications toward the development of a universal influenza vaccine.


Subject(s)
Adjuvants, Immunologic , B-Lymphocytes/immunology , Cross Reactions/immunology , Immunologic Memory , Influenza A Virus, H5N1 Subtype/immunology , Influenza Vaccines/immunology , Influenza, Human/prevention & control , Antibodies, Viral/immunology , Antibody Formation/immunology , Antibody Specificity/immunology , B-Lymphocytes/metabolism , Epitopes, B-Lymphocyte/immunology , Female , Humans , Immunization, Secondary , Male , Plasma Cells/immunology , Plasma Cells/metabolism
5.
Proc Natl Acad Sci U S A ; 115(39): E9201-E9210, 2018 09 25.
Article in English | MEDLINE | ID: mdl-30194229

ABSTRACT

Murine norovirus (MNoV) is closely related to human norovirus (HNoV), an infectious agent responsible for acute gastroenteritis worldwide. Here we report the X-ray crystal structure of the dimeric MNoV VP1 protruding (P) domain in complex with its cellular receptor CD300lf. CD300lf binds the P domain with a 2:2 stoichiometry, engaging a cleft between the AB and DE loops of the P2 subdomain at a site that overlaps the epitopes of neutralizing antibodies. We also identify that bile acids are cofactors enhancing MNoV cell-binding and infectivity. Structures of CD300lf-P domain in complex with glycochenodeoxycholic acid (GCDCA) and lithocholic acid (LCA) reveal two bile acid binding sites at the P domain dimer interface distant from receptor binding sites. The structural determinants for receptor and bile acid binding are supported by numerous biophysical assays utilizing interface residue mutations. We find that the monomeric affinity of CD300lf for the P domain is low and is divalent cation dependent. We have also determined the crystal structure of CD300lf in complex with phosphocholine, revealing that MNoV engages its receptor in a manner mimicking host ligands including similar metal coordination. Docking of the cocomplex structures onto a cryo-EM-derived model of MNoV suggests that each virion can make multiple CD300lf engagements, and thus, infection may be driven by the avidity of cell surface clustered CD300lf. These studies identify multiple potential modulators of norovirus infection that may act to regulate the interaction between the viral capsid P domain and its cognate cellular receptor.


Subject(s)
Bile Acids and Salts/chemistry , Molecular Docking Simulation , Norovirus/chemistry , Receptors, Immunologic/chemistry , Virion/chemistry , Animals , Bile Acids and Salts/metabolism , Caliciviridae Infections , Cell Line , Cryoelectron Microscopy , Mice , Mutation , Norovirus/genetics , Norovirus/metabolism , Protein Domains , Protein Structure, Quaternary , Protein Structure, Secondary , Receptors, Immunologic/genetics , Receptors, Immunologic/metabolism , Virion/genetics , Virion/metabolism
6.
Glycobiology ; 26(5): 520-31, 2016 May.
Article in English | MEDLINE | ID: mdl-26692049

ABSTRACT

Formation of the heterocyst envelope polysaccharide (HEP) is a key process for cyanobacterial heterocyst differentiation. The maturation of HEP in Anabaena sp. strain PCC 7120 is controlled by a gene cluster termed HEP island in addition to an operon alr3698-alr3699, which encodes two putative proteins termed Alr3698/HepD and Alr3699/HepE. Here we report the crystal structures of HepE in the apo-form and three complex forms that bind to UDP-glucose (UDPG), UDP&glucose, and UDP, respectively. The overall structure of HepE displays a typical GT-B fold of glycosyltransferases, comprising two separate ß/α/ß Rossmann-fold domains that form an inter-domain substrate-binding crevice. Structural analyses combined with enzymatic assays indicate that HepE is a glucosyltransferase using UDPG as a sugar donor. Further site-directed mutageneses enable us to assign the key residues that stabilize the sugar donor and putative acceptor. Based on the comparative structural analyses, we propose a putative catalytic cycle of HepE, which undergoes "open-closed-open" conformational changes upon binding to the substrates and release of products. These findings provide structural and catalytic insights into the first enzyme involved in the HEP biosynthesis pathway.


Subject(s)
Anabaena/enzymology , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Glucosyltransferases/chemistry , Glucosyltransferases/metabolism , Polysaccharides, Bacterial/biosynthesis , Polysaccharides, Bacterial/chemistry , Anabaena/genetics , Bacterial Proteins/genetics , Glucosyltransferases/genetics , Multigene Family , Polysaccharides, Bacterial/genetics , Protein Domains , Uridine Diphosphate Glucose/chemistry , Uridine Diphosphate Glucose/genetics , Uridine Diphosphate Glucose/metabolism
7.
Acta Crystallogr D Biol Crystallogr ; 71(Pt 4): 873-81, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25849398

ABSTRACT

Microcystins, which are the most common cause of hepatotoxicity associated with cyanobacterial water blooms, are assembled in vivo on a large multienzyme complex via a mixed nonribosomal peptide synthetase/polyketide synthetase (NRPS/PKS). The biosynthesis of microcystin in Microcystis aeruginosa PCC 7806 starts with the enzyme McyG, which contains an adenylation-peptidyl carrier protein (A-PCP) didomain for loading the starter unit to assemble the side chain of an Adda residue. However, the catalytic mechanism remains unclear. Here, the 2.45 Šresolution crystal structure of the McyG A-PCP didomain complexed with the catalytic intermediate L-phenylalanyl-adenylate (L-Phe-AMP) is reported. Each asymmetric unit contains two protein molecules, one of which consists of the A-PCP didomain and the other of which comprises only the A domain. Structural analyses suggest that Val227 is likely to be critical for the selection of hydrophobic substrates. Moreover, two distinct interfaces demonstrating variable crosstalk between the PCP domain and the A domain were observed. A catalytic cycle for the adenylation and peptide transfer of the A-PCP didomain is proposed.


Subject(s)
Ligases/chemistry , Microcystins/metabolism , Microcystis/enzymology , Amino Acid Sequence , Crystallography, X-Ray , Ligases/metabolism , Microcystis/chemistry , Microcystis/metabolism , Models, Molecular , Molecular Sequence Data , Protein Conformation , Protein Structure, Tertiary , Sequence Alignment
8.
J Biol Chem ; 288(32): 22985-92, 2013 Aug 09.
Article in English | MEDLINE | ID: mdl-23818518

ABSTRACT

Saccharomyces cerevisiae Abz2 is a pyridoxal 5'-phosphate (PLP)-dependent lyase that converts 4-amino-4-deoxychorismate (ADC) to para-aminobenzoate and pyruvate. To investigate the catalytic mechanism, we determined the 1.9 Å resolution crystal structure of Abz2 complexed with PLP, representing the first eukaryotic ADC lyase structure. Unlike Escherichia coli ADC lyase, whose dimerization is critical to the formation of the active site, the overall structure of Abz2 displays as a monomer of two domains. At the interdomain cleft, a molecule of cofactor PLP forms a Schiff base with residue Lys-251. Computational simulations defined a basic clamp to orientate the substrate ADC in a proper pose, which was validated by site-directed mutageneses combined with enzymatic activity assays. Altogether, we propose a putative catalytic mechanism of a unique class of monomeric ADC lyases led by yeast Abz2.


Subject(s)
Molecular Dynamics Simulation , Oxo-Acid-Lyases/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae/enzymology , Crystallography, X-Ray , Escherichia coli/enzymology , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Oxo-Acid-Lyases/metabolism , Protein Structure, Tertiary , Saccharomyces cerevisiae Proteins/metabolism , Structure-Activity Relationship
9.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 11): 3013-22, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25372690

ABSTRACT

Gas vesicles are gas-filled proteinaceous organelles that provide buoyancy for bacteria and archaea. A gene cluster that is highly conserved in various species encodes about 8-14 proteins (Gvp proteins) that are involved in the formation of gas vesicles. Here, the first crystal structure of the gas vesicle protein GvpF from Microcystis aeruginosa PCC 7806 is reported at 2.7 Šresolution. GvpF is composed of two structurally distinct domains (the N-domain and C-domain), both of which display an α+ß class overall structure. The N-domain adopts a novel fold, whereas the C-domain has a modified ferredoxin fold with an apparent variation owing to an extension region consisting of three sequential helices. The two domains pack against each other via interactions with a C-terminal tail that is conserved among cyanobacteria. Taken together, it is concluded that the overall architecture of GvpF presents a novel fold. Moreover, it is shown that GvpF is most likely to be a structural protein that is localized at the gas-facing surface of the gas vesicle by immunoblotting and immunogold labelling-based tomography.


Subject(s)
Bacterial Proteins/chemistry , Microcystis/chemistry , Proteins/chemistry , Amino Acid Sequence , Crystallography, X-Ray , Microcystis/ultrastructure , Models, Molecular , Molecular Sequence Data , Protein Conformation , Proteins/ultrastructure , Sequence Alignment
10.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 8): 2085-92, 2014 Aug.
Article in English | MEDLINE | ID: mdl-25084328

ABSTRACT

Saccharomyces cerevisiae Coq5 is an S-adenosyl methionine (SAM)-dependent methyltransferase (SAM-MTase) that catalyzes the only C-methylation step in the coenzyme Q (CoQ) biosynthesis pathway, in which 2-methoxy-6-polyprenyl-1,4-benzoquinone (DDMQH2) is converted to 2-methoxy-5-methyl-6-polyprenyl-1,4-benzoquinone (DMQH2). Crystal structures of Coq5 were determined in the apo form (Coq5-apo) at 2.2 Šresolution and in the SAM-bound form (Coq5-SAM) at 2.4 Šresolution, representing the first pair of structures for the yeast CoQ biosynthetic enzymes. Coq5 displays a typical class I SAM-MTase structure with two minor variations beyond the core domain, both of which are considered to participate in dimerization and/or substrate recognition. Slight conformational changes at the active-site pocket were observed upon binding of SAM. Structure-based computational simulation using an analogue of DDMQH2 enabled us to identify the binding pocket and entrance tunnel of the substrate. Multiple-sequence alignment showed that the residues contributing to the dimeric interface and the SAM- and DDMQH2-binding sites are highly conserved in Coq5 and homologues from diverse species. A putative catalytic mechanism of Coq5 was proposed in which Arg201 acts as a general base to initiate catalysis with the help of a water molecule.


Subject(s)
Crystallography, X-Ray/methods , Methyltransferases/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae/metabolism , Ubiquinone/biosynthesis , Catalysis , Methyltransferases/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Substrate Specificity , Ubiquinone/metabolism
11.
Adv Nutr ; 15(1): 100124, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37940476

ABSTRACT

A meta-analysis published in 2018 indicated a significant association between the dietary inflammatory index (DII) and risk of urologic cancers (UC). The number of included studies was limited, and more research has been published on this topic since then. The current study aimed to find a more precise estimate of the association between dietary inflammatory potential and risk of UC by updating the previous meta-analysis. The PubMed and Embase databases were searched between January 2015 and April 2023 to identify eligible articles. Combined relative risk (RR) and 95% confidence intervals (CI) were calculated by random-effects model to assess the association between dietary inflammatory potential and risk of UC by comparison of the highest versus the lowest category of the DII/empirical dietary inflammatory pattern (EDIP) or by using the continuous DII/EDIP score. The analysis, including 23 studies with 557,576 subjects, showed different results for UC. There was a significant association for prostate cancer among case-control studies (RR = 1.75, 95% CI: 1.34-2.28), whereas among cohort studies a null association was found (RR = 1.02, 95% CI: 0.96-1.08). For bladder cancer, a nonsignificant association was observed in both case-control (RR = 1.59, 95% CI: 0.95-2.64) and cohort studies (RR = 1.03, 95% CI: 0.86-1.24). Pooled RR from 3 case-control studies displayed a statistically significant association between the DII and risk of kidney cancer (RR = 1.27, 95% CI: 1.03-1.56). Although DII was positively associated with all types of UC, no association was found for EDIP. The present meta-analysis confirmed that an inflammatory diet has a direct effect on the development of prostate cancer and kidney cancer. Large-scale studies are needed to demonstrate the association between dietary inflammatory potential and risk of UC and provide effective nutritional advice for UC prevention. PROTOCOL REGISTRATION: The protocol was registered in the International Prospective Register of Systematic Reviews (CRD42023391204).


Subject(s)
Kidney Neoplasms , Prostatic Neoplasms , Urinary Bladder Neoplasms , Male , Humans , Risk Factors , Inflammation/complications , Systematic Reviews as Topic , Diet/adverse effects , Prostatic Neoplasms/epidemiology , Prostatic Neoplasms/etiology , Urinary Bladder Neoplasms/epidemiology , Urinary Bladder Neoplasms/etiology , Kidney Neoplasms/etiology , Kidney Neoplasms/complications
12.
Int J Ophthalmol ; 16(7): 1145-1154, 2023.
Article in English | MEDLINE | ID: mdl-37465496

ABSTRACT

AIM: To evaluate and compare the anatomical and functional outcomes and negative effects of the three anti-vascular endothelial growth factor (VEGF) drugs in the treatment of macular edema (ME) due to retinal vein occlusion (RVO) based on the evidence pooled from current clinical trials and observational studies. METHODS: A systematic literature search was conducted on nine online databases from inception until April 30, 2022. The main endpoints were best corrected visual acuity (BCVA), central macular thickness (CMT), and adverse events (AEs). Cumulative Meta-analysis was conducted to synthesize the outcomes of the drugs. The retrieved data were analyzed using Stata software (version 12.0). RESULTS: A total of 20 studies comprising 1674 eyes met the inclusion criteria to the Meta-analysis. It was observed that conbercept and aflibercept had better visual acuity effects compared with ranibizumab at 1mo [weight mean difference (WMD)=-0.03, P=0.001; WMD=-0.05, P=0.019], but the effects were not different from that of ranibizumab at 6mo. Moreover, there was not statistically significant difference in the proportion of patients gaining ≥15 letters at 12-24mo between aflibercept and ranibizumab [odds ratio (OR)=1.16, P=0.427]. Conbercept had higher mean CMT change effects at 1mo (WMD=-14.43, P=0.014) and 6mo (WMD=-35.63, P≤0.001) compared with ranibizumab. Meanwhile, the mean CMT change effects at 1mo (WMD=-10.14, P=0.170), 6mo (WMD=-26.98, P=0.140) and 12-24mo (WMD=-12.34, P=0.071) were comparable among the groups. Similarly, AEs were not significantly different among the treatments (OR=0.75, P=0.305; OR=1.04, P=0.89). The stability of effect size of mean BCVA and CMT improved with the increase in sample size. Aflibercept and conbercept required fewer injections compared with ranibizumab. CONCLUSION: This is the first study to evaluate the efficacy and AEs of intravitreal administration of conbercept, ranibizumab, and aflibercept in the treatment of RVO-ME. Intravitreal aflibercept or conbercept results in better mean change in vision and CMT reduction compared with ranibizumab. Conbercept can be considered to be a promising and innovative drug with good anti-VEGF effects.

13.
mSphere ; 7(3): e0016422, 2022 06 29.
Article in English | MEDLINE | ID: mdl-35607948

ABSTRACT

Bourbon virus (BRBV) was first discovered in 2014 in a fatal human case. Since then it has been detected in the tick Amblyomma americanum in the states of Missouri and Kansas in the United States. Despite the high prevalence of BRBV in ticks in these states, very few human cases have been reported, and the true infection burden of BRBV in the community is unknown. Here, we developed two virus neutralization assays, a vesicular stomatitis virus (VSV)-BRBV pseudotyped rapid assay and a BRBV focus reduction neutralization assay, to assess the seroprevalence of BRBV neutralizing antibodies in human sera collected in 2020 in St. Louis, MO. Of 440 human serum samples tested, three (0.7%) were able to potently neutralize both VSV-BRBV and wild-type BRBV. These findings suggest that human infections with BRBV are more common than previously recognized. IMPORTANCE Since the discovery of the Bourbon virus (BRBV) in 2014, a total of five human cases have been identified, including two fatal cases. BRBV is thought to be transmitted by the lone star tick, which is prevalent in the eastern, southeastern, and midwestern United States. BRBV has been detected in ticks in Missouri and Kansas, and serological evidence suggests that it is also present in North Carolina. However, the true infection burden of BRBV in humans is not known. In the present study, we developed two virus neutralization assays to assess the seroprevalence of BRBV-specific antibodies in human sera collected in 2020 in St. Louis, MO. We found that a small subset of individuals are seropositive for neutralizing antibodies against BRBV. Our data suggest that BRBV infection in humans is more common than previously thought.


Subject(s)
Thogotovirus , Ticks , Animals , Antibodies, Neutralizing , Humans , Missouri/epidemiology , Seroepidemiologic Studies , United States
14.
Spectrochim Acta A Mol Biomol Spectrosc ; 259: 119918, 2021 Oct 05.
Article in English | MEDLINE | ID: mdl-33991814

ABSTRACT

Molecular dynamics simulations and DFT calculations were performed for the demonstration of the structural dynamics and vibrational feature of N-Acetyl-d-glucosamine (NAG) in solution phase. The interactions between NAG and solvent molecules were evaluated through spatial distribution function and radial distribution function, and the preferred conformations of NAG in aqueous solution were revealed by cluster analysis. Results from normal mode analysis show that the solvent induced structural fluctuation of NAG could be reflected in the vibrational feature of specific chromophores, thus we can evaluate the molecular structure with the help of its vibrational signature based on the built correlation between molecular structure and vibrational frequencies of specific groups.


Subject(s)
Acetylglucosamine , Glucosamine , Molecular Dynamics Simulation , Vibration , Water
15.
Cell Rep ; 34(4): 108682, 2021 01 26.
Article in English | MEDLINE | ID: mdl-33503432

ABSTRACT

Novel influenza A virus (IAV) strains elicit recall immune responses to conserved epitopes, making them favorable antigenic choices for universal influenza virus vaccines. Evaluating these immunogens requires a thorough understanding of the antigenic sites targeted by the polyclonal antibody (pAb) response, which single-particle electron microscopy (EM) can sensitively detect. In this study, we employ EM polyclonal epitope mapping (EMPEM) to extensively characterize the pAb response to hemagglutinin (HA) after H5N1 immunization in humans. Cross-reactive pAbs originating from memory B cells immediately bound the stem of HA and persisted for more than a year after vaccination. In contrast, de novo pAb responses to multiple sites on the head of HA, targeting previously determined key neutralizing sites on H5 HA, expanded after the second immunization and waned quickly. Thus, EMPEM provides a robust tool for comprehensively tracking the specificity and durability of immune responses elicited by novel universal influenza vaccine candidates.


Subject(s)
Antibody Formation/immunology , Epitope Mapping/methods , Influenza A Virus, H5N1 Subtype/pathogenicity , Influenza Vaccines/therapeutic use , Humans , Influenza Vaccines/pharmacology
16.
mSphere ; 6(1)2021 02 03.
Article in English | MEDLINE | ID: mdl-33536325

ABSTRACT

Reported coronavirus disease 2019 (COVID-19) case counts likely underestimate the true prevalence because mild or asymptomatic cases often go untested. Here, we use a sero-survey to estimate the seroprevalence of IgG antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the St. Louis, MO, metropolitan area in a symptom-independent manner. Five hundred three adult and 555 pediatric serum/plasma samples were collected from patients presenting to Barnes-Jewish Hospital or St. Louis Children's Hospital between 14 April 2020 and 12 May 2020. We developed protocols for in-house enzyme-linked immunosorbent assays (ELISAs) using spike and nucleoprotein and used the assays to estimate a seroprevalence rate based on our samples. Overall IgG seropositivity was estimated to be 1.71% (95% credible interval [CI], 0.04% to 3.38%) in pediatric samples and 3.11% (95% CI, 0.92% to 5.32%) in adult samples. Seropositivity was significantly lower in children under 5 years of age than in adults, but rates between adults and children aged 5 or older were similar. Of the 176 samples tested from children under 4 years of age, none were positive.IMPORTANCE This study determined the percentages of both children and adult samples from the greater St. Louis metropolitan area who had antibodies to SARS-CoV-2 in late April to early May 2020. Approximately 1.7 to 3.1% of the tested individuals had antibodies, indicating that they had previously been infected by SARS-CoV-2. These results demonstrate that the extent of infection was about 10 times greater than the number of confirmed cases at that time. Furthermore, it demonstrated that by 5 years of age, children were infected to an extent similar to that of adults.


Subject(s)
Antibodies, Viral/blood , Antibodies, Viral/immunology , COVID-19/blood , COVID-19/immunology , SARS-CoV-2/immunology , Adolescent , Adult , COVID-19/epidemiology , Child , Child, Preschool , Enzyme-Linked Immunosorbent Assay/methods , Female , Humans , Immunoglobulin G/blood , Immunoglobulin G/immunology , Infant , Male , Middle Aged , Missouri/epidemiology , Seroepidemiologic Studies , Young Adult
17.
mSphere ; 6(4): e0045021, 2021 08 25.
Article in English | MEDLINE | ID: mdl-34346705

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seropositivity was assessed for 3,066 individuals visiting hospitals in St. Louis, Missouri, during July 2020, November 2020, or January 2021. Seropositivity in children increased from 5.22% in July to 21.16% in January. In the same time frame, seropositivity among adults increased from 4.52% to 19.03%, prior to initiation of mass vaccination. IMPORTANCE This study determined the percentage of children and adult samples from the St. Louis metropolitan area in Missouri with SARS-CoV-2 antibodies during three collection periods spanning July 2020 to January 2021. By January 2021, 20.68% of the tested individuals had antibodies. These results show the evolution of the SARS-CoV-2 pandemic in St. Louis, Missouri, and provide a snapshot of the extent of infection just prior to the start of mass vaccination.


Subject(s)
COVID-19/immunology , SARS-CoV-2/immunology , Adolescent , Adult , Aged , Antibodies, Viral/immunology , COVID-19 Serological Testing/methods , Child , Child, Preschool , Female , Humans , Male , Middle Aged , Missouri , Pandemics/prevention & control , Seroepidemiologic Studies , Young Adult
18.
Cell Rep ; 36(3): 109400, 2021 07 20.
Article in English | MEDLINE | ID: mdl-34245672

ABSTRACT

The development of an effective vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 2019 (COVID-19), is a global priority. Here, we compare the protective capacity of intranasal and intramuscular delivery of a chimpanzee adenovirus-vectored vaccine encoding a prefusion stabilized spike protein (chimpanzee adenovirus [ChAd]-SARS-CoV-2-S) in Golden Syrian hamsters. Although immunization with ChAd-SARS-CoV-2-S induces robust spike-protein-specific antibodies capable of neutralizing the virus, antibody levels in serum are higher in hamsters vaccinated by an intranasal compared to intramuscular route. Accordingly, against challenge with SARS-CoV-2, ChAd-SARS-CoV-2-S-immunized hamsters are protected against less weight loss and have reduced viral infection in nasal swabs and lungs, and reduced pathology and inflammatory gene expression in the lungs, compared to ChAd-control immunized hamsters. Intranasal immunization with ChAd-SARS-CoV-2-S provides superior protection against SARS-CoV-2 infection and inflammation in the upper respiratory tract. These findings support intranasal administration of the ChAd-SARS-CoV-2-S candidate vaccine to prevent SARS-CoV-2 infection, disease, and possibly transmission.

19.
mBio ; 12(1)2021 01 19.
Article in English | MEDLINE | ID: mdl-33468695

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently causing a global pandemic. The antigen specificity of the antibody response mounted against this novel virus is not understood in detail. Here, we report that subjects with a more severe SARS-CoV-2 infection exhibit a larger antibody response against the spike and nucleocapsid protein and epitope spreading to subdominant viral antigens, such as open reading frame 8 and nonstructural proteins. Subjects with a greater antibody response mounted a larger memory B cell response against the spike, but not the nucleocapsid protein. Additionally, we revealed that antibodies against the spike are still capable of binding the D614G spike mutant and cross-react with the SARS-CoV-1 receptor binding domain. Together, this study reveals that subjects with a more severe SARS-CoV-2 infection exhibit a greater overall antibody response to the spike and nucleocapsid protein and a larger memory B cell response against the spike.IMPORTANCE With the ongoing pandemic, it is critical to understand how natural immunity against SARS-CoV-2 and COVID-19 develops. We have identified that subjects with more severe COVID-19 disease mount a more robust and neutralizing antibody response against SARS-CoV-2 spike protein. Subjects who mounted a larger response against the spike also mounted antibody responses against other viral antigens, including the nucleocapsid protein and ORF8. Additionally, this study reveals that subjects with more severe disease mount a larger memory B cell response against the spike. These data suggest that subjects with more severe COVID-19 disease are likely better protected from reinfection with SARS-CoV-2.


Subject(s)
COVID-19/immunology , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , Adult , Antibodies, Neutralizing/immunology , Antibodies, Viral/blood , Antibodies, Viral/immunology , Antigens, Viral/immunology , B-Lymphocytes/immunology , COVID-19/blood , COVID-19/virology , Coronavirus Nucleocapsid Proteins/immunology , Cross Reactions , Epitopes/immunology , Female , Humans , Immunity, Humoral/immunology , Male , Middle Aged , Phosphoproteins/immunology
20.
J Phys Chem B ; 124(41): 9154-9162, 2020 10 15.
Article in English | MEDLINE | ID: mdl-32965118

ABSTRACT

The specific host-guest interactions in the corresponding complexes of K+ and NH4+ with typical crown ethers were investigated by using FTIR and ultrafast IR spectroscopies. The counteranions, i.e., SCN-, were employed as a local vibrational probe to report the structural dynamics of the complexation. It was found that the vibrational relaxation dynamics of the SCN- was strongly affected by the cations confined in the cavities of the crown ethers. The time constant of the vibrational population decay of SCN- in the complex of NH4+ with the 18-crown-6 was determined to be 6 ± 2 ps, which is ∼30 times faster than that in the complex of K+ with the crown ethers. Control experiments showed that the vibrational population decay of SCN- depended on the size of the cavities of the crown ethers. A theoretical calculation further indicated that the nitrogen atom of SCN- showed preferential coordination to the K+ ions hosted by the crown ethers, while the NH4+ can form hydrogen bonds with the oxygen atoms in the studied crown ethers. The geometric constraints formed in the complex of crown ethers can cause a specific interaction between the NH4+ and SCN-, which can facilitate the intermolecular vibrational energy redistribution of the SCN-.

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