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1.
PLoS One ; 19(5): e0302579, 2024.
Article En | MEDLINE | ID: mdl-38722969

Since March 2020, the COVID-19 pandemic has swiftly propagated, triggering a competitive race among medical firms to forge vaccines that thwart the infection. Lebanon initiated its vaccination campaign on February 14, 2021. Despite numerous studies conducted to elucidate the characteristics of immune responses elicited by vaccination, the topic remains unclear. Here, we aimed to track the progression of anti-spike SARS-CoV-2 antibody titers at two-time points (T1: shortly after the second vaccination dose, T2: six months later) within a cohort of 201 adults who received Pfizer-BioNTech (BNT162b2), AstraZeneca, or Sputnik V vaccines in North Lebanon. Blood specimens were obtained from participants, and antibody titers against SARS-CoV-2 were quantified through the Elecsys-Anti-SARS-CoV-2 S assay (Roche Diagnostics, Switzerland). We used univariate analysis and multivariable logistic regression models to predict determinants influencing the decline in immune response and the occurrence of breakthrough infections among vaccinated patients. Among the 201 participants, 141 exhibited unchanging levels of antibody titers between the two sample collections, 55 displayed waning antibody titers, and only five participants demonstrated heightened antibody levels. Notably, age emerged as the sole variable significantly linked to the waning immune response. Moreover, the BNT162b2 vaccine exhibited significantly higher efficacy concerning the occurrence of breakthrough infections when compared with the AstraZeneca vaccine. Overall, our study reflected the immune status of a sample of vaccinated adults in North Lebanon. Further studies on a larger scale are needed at the national level to follow the immune response after vaccination, especially after the addition of the third vaccination dose.


Antibodies, Viral , COVID-19 , SARS-CoV-2 , Humans , Male , Lebanon/epidemiology , Female , Adult , COVID-19/prevention & control , COVID-19/immunology , COVID-19/epidemiology , Antibodies, Viral/blood , Antibodies, Viral/immunology , SARS-CoV-2/immunology , Middle Aged , Spike Glycoprotein, Coronavirus/immunology , COVID-19 Vaccines/immunology , COVID-19 Vaccines/administration & dosage , Vaccination , Aged , Young Adult , BNT162 Vaccine/immunology , Breakthrough Infections
3.
Sci Rep ; 14(1): 10772, 2024 05 10.
Article En | MEDLINE | ID: mdl-38730052

We aimed to determine SARS-CoV-2 antibody seropositivity among pregnant women and the transplacental transfer efficiency of SARS-CoV-2-specific antibodies relative to malaria antibodies among SARS-CoV-2 seropositive mother-cord pairs. This cross-sectional study was conducted in Accra, Ghana, from March to May 2022. Antigen- specific IgG antibodies against SARS-CoV-2 (nucleoprotein and spike-receptor binding domain) and malarial antigens (circumsporozoite protein and merozoite surface protein 3) in maternal and cord plasma were measured by ELISA. Plasma from both vaccinated and unvaccinated pregnant women were tested for neutralizing antibodies using commercial kit. Of the unvaccinated pregnant women tested, 58.12% at antenatal clinics and 55.56% at the delivery wards were seropositive for both SARS-CoV-2 nucleoprotein and RBD antibodies. Anti-SARS-CoV-2 antibodies in cord samples correlated with maternal antibody levels (N antigen rs = 0.7155, p < 0.001; RBD rs = 0.8693, p < 0.001). Transplacental transfer of SARS-CoV-2 nucleoprotein antibodies was comparable to circumsporozoite protein antibodies (p = 0.9999) but both were higher than transfer rates of merozoite surface protein 3 antibodies (p < 0.001). SARS-CoV-2 IgG seropositivity among pregnant women in Accra is high with a boost of SARS-CoV-2 RBD-specific IgG in vaccinated women. Transplacental transfer of anti-SARS-CoV-2 and malarial antibodies was efficient, supporting vaccination of mothers as a strategy to protect infants against SARS-CoV-2.


Antibodies, Viral , COVID-19 , Immunoglobulin G , SARS-CoV-2 , Humans , Female , Pregnancy , Ghana , SARS-CoV-2/immunology , COVID-19/immunology , COVID-19/prevention & control , Antibodies, Viral/immunology , Antibodies, Viral/blood , Adult , Cross-Sectional Studies , Immunoglobulin G/blood , Immunoglobulin G/immunology , Maternal-Fetal Exchange/immunology , Antibodies, Neutralizing/immunology , Antibodies, Neutralizing/blood , Infant , Infant, Newborn , Spike Glycoprotein, Coronavirus/immunology , Immunity, Maternally-Acquired , Young Adult , Fetal Blood/immunology , Antibodies, Protozoan/immunology , Antibodies, Protozoan/blood
4.
Int J Mol Sci ; 25(9)2024 Apr 24.
Article En | MEDLINE | ID: mdl-38731860

The COVID-19 pandemic has underscored the critical need for the advancement of diagnostic and therapeutic platforms. These platforms rely on the rapid development of molecular binders that should facilitate surveillance and swift intervention against viral infections. In this study, we have evaluated by three independent research groups the binding characteristics of various published RNA and DNA aptamers targeting the spike protein of the SARS-CoV-2 virus. For this comparative analysis, we have employed different techniques such as biolayer interferometry (BLI), enzyme-linked oligonucleotide assay (ELONA), and flow cytometry. Our data show discrepancies in the reported specificity and affinity among several of the published aptamers and underline the importance of standardized methods, the impact of biophysical techniques, and the controls used for aptamer characterization. We expect our results to contribute to the selection and application of suitable aptamers for the detection of SARS-CoV-2.


Aptamers, Nucleotide , COVID-19 , Protein Binding , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Aptamers, Nucleotide/metabolism , Aptamers, Nucleotide/chemistry , Spike Glycoprotein, Coronavirus/metabolism , SARS-CoV-2/metabolism , SARS-CoV-2/drug effects , Humans , COVID-19/virology , COVID-19/metabolism , Interferometry/methods , Flow Cytometry/methods
5.
Int J Mol Sci ; 25(9)2024 Apr 25.
Article En | MEDLINE | ID: mdl-38731879

Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, SARS-CoV-2 variants capable of breakthrough infections have attracted global attention. These variants have significant mutations in the receptor-binding domain (RBD) of the spike protein and the membrane (M) protein, which may imply an enhanced ability to evade immune responses. In this study, an examination of co-mutations within the spike RBD and their potential correlation with mutations in the M protein was conducted. The EVmutation method was utilized to analyze the distribution of the mutations to elucidate the relationship between the mutations in the spike RBD and the alterations in the M protein. Additionally, the Sequence-to-Sequence Transformer Model (S2STM) was employed to establish mapping between the amino acid sequences of the spike RBD and M proteins, offering a novel and efficient approach for streamlined sequence analysis and the exploration of their interrelationship. Certain mutations in the spike RBD, G339D-S373P-S375F and Q493R-Q498R-Y505, are associated with a heightened propensity for inducing mutations at specific sites within the M protein, especially sites 3 and 19/63. These results shed light on the concept of mutational synergy between the spike RBD and M proteins, illuminating a potential mechanism that could be driving the evolution of SARS-CoV-2.


COVID-19 , Machine Learning , Mutation , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/chemistry , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , Humans , COVID-19/virology , COVID-19/genetics , Viral Matrix Proteins/genetics , Viral Matrix Proteins/chemistry , Coronavirus M Proteins/genetics , Protein Domains/genetics , Amino Acid Sequence , Protein Binding
6.
Virulence ; 15(1): 2351266, 2024 Dec.
Article En | MEDLINE | ID: mdl-38717195

Background: The COVID-19 pandemic has led to millions of fatalities globally. Kidney transplant (KT) patients, given their comorbidities and under immunosuppressant drugs, are identified as a high-risk group. Though vaccination remains pivotal for pandemic control, some studies indicate that KT exhibits diminished immune reactions to SARS-CoV-2 vaccines. Therefore, evaluating the vaccine responses in KT, especially the humoral responses against emergent variants is crucial.Methods: We developed a multiplexed SARS-CoV-2 variant protein microarray, incorporating the extracellular domain (ECD) and the receptor binding domain (RBD) of the spike proteins from the variants. This was employed to investigate the collective humoral responses after administering two doses of mRNA-1273 and AZD1222 vaccines in KT under immunosuppressive drugs and in healthy controls.Results: After two doses of either mRNA-1273 or AZD1222, the KT generally showed lower surrogate neutralizing and total antibodies against spike ECD in multiple variants compared to healthy controls. Although two doses of mRNA-1273 induced 1.5-2 fold more surrogate neutralizing and total antibodies than AZD1222 in healthy controls, the KT subjects with two doses of mRNA-1273 generally exhibited higher surrogate neutralizing but similar total antibodies against spike ECD in multiple variants. There were moderate to high correlations between the surrogate neutralizing and total antibodies against spike ECDs.Conclusion: This study offers pivotal insights into the relative vulnerability of KT concerning humoral immunity and the evolving mutations of SARS-CoV-2. Such findings are useful for evaluating vaccine responses and recommending vaccine episodes for KT.


2019-nCoV Vaccine mRNA-1273 , Antibodies, Neutralizing , Antibodies, Viral , COVID-19 Vaccines , COVID-19 , Immunity, Humoral , Kidney Transplantation , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Humans , SARS-CoV-2/immunology , SARS-CoV-2/genetics , COVID-19/prevention & control , COVID-19/immunology , COVID-19 Vaccines/immunology , COVID-19 Vaccines/administration & dosage , Antibodies, Viral/blood , Male , Middle Aged , Female , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/genetics , 2019-nCoV Vaccine mRNA-1273/administration & dosage , 2019-nCoV Vaccine mRNA-1273/immunology , Adult , Antibodies, Neutralizing/blood , Antibodies, Neutralizing/immunology , Immunosuppressive Agents/administration & dosage , Vaccination , Aged , Transplant Recipients
7.
Front Immunol ; 15: 1383612, 2024.
Article En | MEDLINE | ID: mdl-38742107

Introduction: SARS-CoV-2, the cause of the COVID pandemic, is an RNA virus with a high propensity to mutate. Successive virus variants, including variants of concern (VOC), have emerged with increased transmission or immune escape. The original pandemic virus and early variants replicated poorly, if at all, in mice at least partly due to a mismatch between the receptor binding domain on the viral spike protein and the murine angiotensin converting enzyme 2 (ACE2). Omicron VOC emerged in late 2021 harboring > 50 new mutations, 35 of them in the spike protein. This variant resulted in a very large wave of infections, even in the face of prior immunity, albeit being inherently less severe than earlier variants. Reflecting the lower severity reported in humans, Omicron displayed attenuated infection in hamsters and also in the K18-hACE2 mouse model. K18-hACE2 mice express both the human ACE2 as well as the endogenous mouse ACE2. Methods: Here we infected hACE2 knock-in mice that express only human ACE2 and no murine ACE2, or C57BL/6 wildtype mice with SARS-CoV-2 D614G (first-wave isolate), Delta or Omicron BA.1 variants and assessed infectivity and downstream innate immune responses. Results: While replication of SARS-CoV-2 Omicron was lower in the lungs of hACE2 knock-in mice compared with SARS-CoV-2 D614G and VOC Delta, it replicated more efficiently than the earlier variants in C57BL/6 wildtype mice. This opens the opportunity to test the effect of host genetics on SARS-CoV-2 infections in wildtype mice. As a proof of principle, we tested Omicron infection in mice lacking expression of the interferon-alpha receptor-1 (IFNAR1). In these mice we found that loss of type I IFN receptor signaling resulted in higher viral loads in the lungs were detected. Finally, using a chimeric virus of first wave SARS-CoV-2 harboring the Omicron spike protein, we show that Omicron spike increase infection of C57BL/6 wildtype mice, but non-spike genes of Omicron confer attenuation of viral replication. Discussion: Since this chimeric virus efficiently infected C57BL/6 wildtype mice, and replicated in their lungs, our findings illustrate a pathway for genetic mapping of virushost interactions during SARS-CoV-2 infection.


Angiotensin-Converting Enzyme 2 , COVID-19 , Mice, Inbred C57BL , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Virus Replication , Animals , SARS-CoV-2/genetics , SARS-CoV-2/immunology , SARS-CoV-2/physiology , Mice , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/metabolism , COVID-19/immunology , COVID-19/virology , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/metabolism , Humans , Disease Models, Animal , Gene Knock-In Techniques , Mice, Transgenic
8.
J Infect Dev Ctries ; 18(4): 520-531, 2024 Apr 30.
Article En | MEDLINE | ID: mdl-38728643

INTRODUCTION: The coronavirus disease 2019 (COVID-19) pandemic caused global health, economic, and population loss. Variants of the coronavirus contributed to the severity of the disease and persistent rise in infections. This study aimed to identify potential drug candidates from fifteen approved antiviral drugs against SARS-CoV-2 (6LU7), SARS-CoV (5B6O), and SARS-CoV-2 spike protein (6M0J) using virtual screening and pharmacokinetics to gain insights into COVID-19 therapeutics. METHODOLOGY: We employed drug repurposing approach to analyze binding performance of fifteen clinically approved antiviral drugs against the main protease of SARS-CoV-2 (6LU7), SARS-CoV (5B6O), and SARS-CoV-2 spike proteins bound to ACE-2 receptor (6M0J), to provide an insight into the therapeutics of COVID-19. AutoDock Vina was used for docking studies. The binding affinities were calculated, and 2-3D structures of protein-ligand interactions were drawn. RESULTS: Rutin, hesperidin, and nelfinavir are clinically approved antiviral drugs with high binding affinity to proteins 6LU7, 5B6O, and 6M0J. These ligands have excellent pharmacokinetics, ensuring efficient absorption, metabolism, excretion, and digestibility. Hesperidin showed the most potent interaction with spike protein 6M0J, forming four H-bonds. Nelfinavir had a high human intestinal absorption (HIA) score of 0.93, indicating maximum absorption in the body and promising interactions with 6LU7. CONCLUSIONS: Our results indicated that rutin, hesperidin, and nelfinavir had the highest binding results against the proposed drug targets. The computational approach effectively identified SARS-CoV-2 inhibitors. COVID-19 is still a recurrent threat globally and predictive analysis using natural compounds might serve as a starting point for new drug development against SARS-CoV-2 and related viruses.


Antiviral Agents , COVID-19 , Drug Repositioning , Molecular Docking Simulation , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , SARS-CoV-2/drug effects , Humans , Antiviral Agents/pharmacokinetics , Antiviral Agents/pharmacology , Antiviral Agents/chemistry , Spike Glycoprotein, Coronavirus/metabolism , COVID-19/virology , Pandemics , Betacoronavirus/drug effects , COVID-19 Drug Treatment , Coronavirus 3C Proteases/antagonists & inhibitors , Coronavirus 3C Proteases/metabolism , Coronavirus 3C Proteases/chemistry
9.
Hum Vaccin Immunother ; 20(1): 2346963, 2024 Dec 31.
Article En | MEDLINE | ID: mdl-38745461

COVID-19, caused by SARS-CoV-2, and meningococcal disease, caused by Neisseria meningitidis, are relevant infectious diseases, preventable through vaccination. Outer membrane vesicles (OMVs), released from Gram-negative bacteria, such as N. meningitidis, present adjuvant characteristics and may confer protection against meningococcal disease. Here, we evaluated in mice the humoral and cellular immune response to different doses of receptor binding domain (RBD) of SARS-CoV-2 adjuvanted by N. meningitidis C:2a:P1.5 OMVs and aluminum hydroxide, as a combined preparation for these pathogens. The immunization induced IgG antibodies of high avidity for RBD and OMVs, besides IgG that recognized the Omicron BA.2 variant of SARS-CoV-2 with intermediary avidity. Cellular immunity showed IFN-γ and IL-4 secretion in response to RBD and OMV stimuli, demonstrating immunologic memory and a mixed Th1/Th2 response. Offspring presented transferred IgG of similar levels and avidity as their mothers. Humoral immunity did not point to the superiority of any RBD dose, but the group immunized with a lower antigenic dose (0.5 µg) had the better cellular response. Overall, OMVs enhanced RBD immunogenicity and conferred an immune response directed to N. meningitidis too.


Antibodies, Viral , COVID-19 , Immunoglobulin G , Neisseria meningitidis , SARS-CoV-2 , Animals , Mice , Immunoglobulin G/blood , Neisseria meningitidis/immunology , Female , Antibodies, Viral/blood , Antibodies, Viral/immunology , COVID-19/prevention & control , COVID-19/immunology , SARS-CoV-2/immunology , Adjuvants, Immunologic/administration & dosage , COVID-19 Vaccines/immunology , COVID-19 Vaccines/administration & dosage , Immunity, Cellular , Immunity, Humoral , Mice, Inbred BALB C , Meningococcal Infections/prevention & control , Meningococcal Infections/immunology , Spike Glycoprotein, Coronavirus/immunology , Adjuvants, Vaccine/administration & dosage , Aluminum Hydroxide/administration & dosage , Aluminum Hydroxide/immunology , Immunization/methods , Antibody Affinity , Antibodies, Bacterial/blood , Antibodies, Bacterial/immunology , Meningococcal Vaccines/immunology , Meningococcal Vaccines/administration & dosage , Immunologic Memory , Th1 Cells/immunology
10.
Clin Lab ; 70(5)2024 May 01.
Article En | MEDLINE | ID: mdl-38747914

BACKGROUND: Nucleic acid amplification testing is the gold standard for SARS-CoV-2 diagnostics, although it may produce a certain number of false positive results. There has not been much published about the characteristics of false positive results. In this study, based on retesting, specimens that initially tested positive for SARS-CoV-2 were classified as true or false positive groups to characterize the distribution of cycle threshold (CT) values for N1 and N2 targets and number of targets detected for each group. METHODS: Specimens that were positive for N-gene on retesting and accompanied with S-gene were identified as true positives (true positive based on retesting, rTP), while specimens that retested negative were classified as false positives (false positive based on retesting, rFP). RESULTS: Of the specimens retested, 85/127 (66.9%) were rFP, 16/47 (34.0%) specimens with both N1 and N2 targets initially detected were rFP, and the CT values for each target was higher in rFP than in rTP. ROC curve analysis showed that optimal cutoff values of CT to differentiate between rTP and rFP were 34.8 for N1 and 33.0 for N2. With the optimal cutoff values of CT for each target, out of the 24 specimens that were positive for both N1 and N2 targets and classified as rTP, 23 (95.8%) were correctly identified as true positives. rFP specimens had a single N1 target in 52/61 (85.2%) and a single N2 target in 17/19 (89.5%). Notably, no true positive results were obtained from any specimens with only N2 target detected. CONCLUSIONS: These results suggest that retesting should be performed for positive results with a CT value greater than optimal cutoff value for each target or with a single N1 target amplified, considering the possibility of a false positive. This may provide guidance on indications to perform retesting to minimize the number of false positives.


COVID-19 Nucleic Acid Testing , COVID-19 , SARS-CoV-2 , Humans , False Positive Reactions , SARS-CoV-2/genetics , COVID-19/diagnosis , COVID-19/virology , COVID-19 Nucleic Acid Testing/methods , COVID-19 Nucleic Acid Testing/standards , ROC Curve , Spike Glycoprotein, Coronavirus/genetics , Sensitivity and Specificity , Coronavirus Nucleocapsid Proteins/genetics , RNA, Viral/genetics , RNA, Viral/analysis
11.
Nat Commun ; 15(1): 4056, 2024 May 14.
Article En | MEDLINE | ID: mdl-38744813

The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we perform a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identify mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we show that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.


Antibodies, Neutralizing , COVID-19 , Mutation , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Virus Internalization , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism , Humans , SARS-CoV-2/immunology , SARS-CoV-2/genetics , Antibodies, Neutralizing/immunology , COVID-19/virology , COVID-19/immunology , Animals , Antibodies, Viral/immunology , Serine Endopeptidases/genetics , Serine Endopeptidases/immunology , Serine Endopeptidases/metabolism , Chlorocebus aethiops , HEK293 Cells , Vero Cells , Epitopes/immunology , Epitopes/genetics , Cell Line , Mice
12.
Org Biomol Chem ; 22(19): 3986-3994, 2024 May 15.
Article En | MEDLINE | ID: mdl-38695061

Algae-based marine carbohydrate drugs are typically decorated with negative ion groups such as carboxylate and sulfate groups. However, the precise synthesis of highly sulfated alginates is challenging, thus impeding their structure-activity relationship studies. Herein we achieve a microwave-assisted synthesis of a range of highly sulfated mannuronate glycans with up to 17 sulfation sites by overcoming the incomplete sulfation due to the electrostatic repulsion of crowded polyanionic groups. Although the partially sulfated tetrasaccharide had the highest affinity for the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, the fully sulfated octasaccharide showed the most potent interference with the binding of the RBD to angiotensin-converting enzyme 2 (ACE2) and Vero E6 cells, indicating that the sulfated oligosaccharides might inhibit the RBD binding to ACE2 in a length-dependent manner.


Angiotensin-Converting Enzyme 2 , Antiviral Agents , Microwaves , Polysaccharides , SARS-CoV-2 , SARS-CoV-2/drug effects , Antiviral Agents/pharmacology , Antiviral Agents/chemical synthesis , Antiviral Agents/chemistry , Chlorocebus aethiops , Angiotensin-Converting Enzyme 2/metabolism , Angiotensin-Converting Enzyme 2/antagonists & inhibitors , Angiotensin-Converting Enzyme 2/chemistry , Vero Cells , Polysaccharides/chemistry , Polysaccharides/pharmacology , Polysaccharides/chemical synthesis , Humans , Animals , Spike Glycoprotein, Coronavirus/antagonists & inhibitors , Spike Glycoprotein, Coronavirus/metabolism , Spike Glycoprotein, Coronavirus/chemistry , Hexuronic Acids/chemistry , Hexuronic Acids/pharmacology , Hexuronic Acids/chemical synthesis , Sulfates/chemistry , Sulfates/pharmacology , Sulfates/chemical synthesis , COVID-19 Drug Treatment , Structure-Activity Relationship
13.
J Nanobiotechnology ; 22(1): 239, 2024 May 12.
Article En | MEDLINE | ID: mdl-38735951

Widespread distribution of porcine epidemic diarrhea virus (PEDV) has led to catastrophic losses to the global pig farming industry. As a result, there is an urgent need for rapid, sensitive and accurate tests for PEDV to enable timely and effective interventions. In the present study, we develop and validate a floating gate carbon nanotubes field-effect transistor (FG CNT-FET)-based portable immunosensor for rapid identification of PEDV in a sensitive and accurate manner. To improve the affinity, a unique PEDV spike protein-specific monoclonal antibody is prepared by purification, and subsequently modified on FG CNT-FET sensor to recognize PEDV. The developed FET biosensor enables highly sensitive detection (LoD: 8.1 fg/mL and 100.14 TCID50/mL for recombinant spike proteins and PEDV, respectively), as well as satisfactory specificity. Notably, an integrated portable platform consisting of a pluggable FG CNT-FET chip and a portable device can discriminate PEDV positive from negative samples and even identify PEDV and porcine deltacoronavirus within 1 min with 100% accuracy. The portable sensing platform offers the capability to quickly, sensitively and accurately identify PEDV, which further points to a possibility of point of care (POC) applications of large-scale surveillance in pig breeding facilities.


Biosensing Techniques , Nanotubes, Carbon , Porcine epidemic diarrhea virus , Porcine epidemic diarrhea virus/isolation & purification , Animals , Swine , Biosensing Techniques/methods , Biosensing Techniques/instrumentation , Nanotubes, Carbon/chemistry , Limit of Detection , Immunoassay/methods , Immunoassay/instrumentation , Antibodies, Monoclonal/immunology , Transistors, Electronic , Swine Diseases/diagnosis , Swine Diseases/virology , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/analysis , Coronavirus Infections/diagnosis , Coronavirus Infections/veterinary , Coronavirus Infections/virology , Antibodies, Viral/immunology , Equipment Design
14.
Signal Transduct Target Ther ; 9(1): 131, 2024 May 13.
Article En | MEDLINE | ID: mdl-38740785

Almost all the neutralizing antibodies targeting the receptor-binding domain (RBD) of spike (S) protein show weakened or lost efficacy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged or emerging variants, such as Omicron and its sub-variants. This suggests that highly conserved epitopes are crucial for the development of neutralizing antibodies. Here, we present one nanobody, N235, displaying broad neutralization against the SARS-CoV-2 prototype and multiple variants, including the newly emerged Omicron and its sub-variants. Cryo-electron microscopy demonstrates N235 binds a novel, conserved, cryptic epitope in the N-terminal domain (NTD) of the S protein, which interferes with the RBD in the neighboring S protein. The neutralization mechanism interpreted via flow cytometry and Western blot shows that N235 appears to induce the S1 subunit shedding from the trimeric S complex. Furthermore, a nano-IgM construct (MN235), engineered by fusing N235 with the human IgM Fc region, displays prevention via inducing S1 shedding and cross-linking virus particles. Compared to N235, MN235 exhibits varied enhancement in neutralization against pseudotyped and authentic viruses in vitro. The intranasal administration of MN235 in low doses can effectively prevent the infection of Omicron sub-variant BA.1 and XBB in vivo, suggesting that it can be developed as a promising prophylactic antibody to cope with the ongoing and future infection.


Antibodies, Neutralizing , Antibodies, Viral , COVID-19 , Epitopes , Immunoglobulin M , SARS-CoV-2 , Single-Domain Antibodies , Spike Glycoprotein, Coronavirus , SARS-CoV-2/immunology , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/chemistry , Humans , Single-Domain Antibodies/immunology , Single-Domain Antibodies/genetics , Single-Domain Antibodies/chemistry , Single-Domain Antibodies/pharmacology , Epitopes/immunology , Epitopes/genetics , Epitopes/chemistry , Animals , COVID-19/immunology , COVID-19/virology , Antibodies, Viral/immunology , Antibodies, Viral/chemistry , Antibodies, Neutralizing/immunology , Antibodies, Neutralizing/chemistry , Antibodies, Neutralizing/genetics , Immunoglobulin M/immunology , Immunoglobulin M/genetics , Mice , Protein Domains , Cryoelectron Microscopy
15.
Carbohydr Polym ; 337: 122156, 2024 Aug 01.
Article En | MEDLINE | ID: mdl-38710572

Seaweeds represent a rich source of sulfated polysaccharides with similarity to heparan sulfate, a facilitator of myriad virus host cell attachment. For this reason, attention has been drawn to their antiviral activity, including the potential for anti-SARS-CoV-2 activity. We have identified and structurally characterized several fucoidan extracts, including those from different species of brown macroalga, and a rhamnan sulfate from a green macroalga species. A high molecular weight fucoidan extracted from Saccharina japonica (FSjRPI-27), and a rhamnan sulfate extracted from Monostroma nitidum (RSMn), showed potent competitive inhibition of spike glycoprotein receptor binding to a heparin-coated SPR chip. This inhibition was also observed in cell-based assays using hACE2 HEK-293 T cells infected by pseudotyped SARS-CoV-2 virus with IC50 values <1 µg/mL. Effectiveness was demonstrated in vivo using hACE2-transgenic mice. Intranasal administration of FSjRPI-27 showed protection when dosed 6 h prior to and at infection, and then every 2 days post-infection, with 100 % survival and no toxicity at 104 plaque-forming units per mouse vs. buffer control. At 5-fold higher virus dose, FSjRPI-27 reduced mortality and yielded reduced viral titers in bronchioalveolar fluid and lung homogenates vs. buffer control. These findings suggest the potential application of seaweed-based sulfated polysaccharides as promising anti-SARS-CoV-2 prophylactics.


Antiviral Agents , COVID-19 , Mannans , Polysaccharides , SARS-CoV-2 , Seaweed , Polysaccharides/chemistry , Polysaccharides/pharmacology , Animals , Humans , SARS-CoV-2/drug effects , Seaweed/chemistry , Antiviral Agents/pharmacology , Antiviral Agents/chemistry , HEK293 Cells , Mice , COVID-19/prevention & control , COVID-19/virology , COVID-19 Drug Treatment , Mice, Transgenic , Spike Glycoprotein, Coronavirus/metabolism , Deoxy Sugars/pharmacology , Deoxy Sugars/chemistry , Angiotensin-Converting Enzyme 2/metabolism
16.
Elife ; 122024 May 08.
Article En | MEDLINE | ID: mdl-38716629

SARS-CoV-2 vaccines have been used worldwide to combat COVID-19 pandemic. To elucidate the factors that determine the longevity of spike (S)-specific antibodies, we traced the characteristics of S-specific T cell clonotypes together with their epitopes and anti-S antibody titers before and after BNT162b2 vaccination over time. T cell receptor (TCR) αß sequences and mRNA expression of the S-responded T cells were investigated using single-cell TCR- and RNA-sequencing. Highly expanded 199 TCR clonotypes upon stimulation with S peptide pools were reconstituted into a reporter T cell line for the determination of epitopes and restricting HLAs. Among them, we could determine 78 S epitopes, most of which were conserved in variants of concern (VOCs). After the 2nd vaccination, T cell clonotypes highly responsive to recall S stimulation were polarized to follicular helper T (Tfh)-like cells in donors exhibiting sustained anti-S antibody titers (designated as 'sustainers'), but not in 'decliners'. Even before vaccination, S-reactive CD4+ T cell clonotypes did exist, most of which cross-reacted with environmental or symbiotic microbes. However, these clonotypes contracted after vaccination. Conversely, S-reactive clonotypes dominated after vaccination were undetectable in pre-vaccinated T cell pool, suggesting that highly responding S-reactive T cells were established by vaccination from rare clonotypes. These results suggest that de novo acquisition of memory Tfh-like cells upon vaccination may contribute to the longevity of anti-S antibody titers.


Antibodies, Viral , BNT162 Vaccine , COVID-19 Vaccines , COVID-19 , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Vaccination , Humans , Antibodies, Viral/immunology , Antibodies, Viral/blood , Spike Glycoprotein, Coronavirus/immunology , SARS-CoV-2/immunology , COVID-19/immunology , COVID-19/prevention & control , BNT162 Vaccine/immunology , BNT162 Vaccine/administration & dosage , COVID-19 Vaccines/immunology , COVID-19 Vaccines/administration & dosage , Female , Male , Epitopes, T-Lymphocyte/immunology , Adult , T-Lymphocytes, Helper-Inducer/immunology , Middle Aged
17.
J Med Virol ; 96(5): e29664, 2024 May.
Article En | MEDLINE | ID: mdl-38727137

The causative agent of coronavirus disease 2019 (COVID-19), known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread accumulatively to 240 countries and continues to evolve. To gain a comprehensive understanding of the epidemiological characteristics of imported variants in China and their correlation with global circulating variants, genomic surveillance data from 11 139 imported COVID-19 cases submitted by Chinese provincial CDC laboratories between 2021 and 2022 were analyzed. Consensus sequences underwent rigorous quality checks, followed by amino acid mutations analysis using Nextclade. Sequences with satisfactory quality control status were classified according to the Pango nomenclature. The results showed that the dominant variants in imported cases reflected the global epidemic trend. An increase in the number of imported SARS-CoV-2 lineages monitored in China in the second half of 2022, and the circulating Omicron subvariants changed from the ancestral lineages of BA.5 and BA.2 into the lineages containing key amino acid mutations of spike protein. There was significant variation in the detection of Omicron subvariants among continents (χ2 = 321.968, p < 0.001) in the second half of 2022, with four lineages (BA.2.3.7, BA.2.2, BA.5.2.7, and XBB.1.2) identified through imported surveillance mainly prevalent respectively in Taiwan, China, Hong Kong SAR, China, Russian Federation, and Singapore. These findings revealed the alterations in circulating imported variants from 2021 to 2022 in China, reflecting the higher diversity of lineages in the second half of 2022, and revealed the predominant lineages of countries or regions that are in close contacts to China, providing new insights into the global prevalence of SARS-CoV-2.


COVID-19 , SARS-CoV-2 , Humans , China/epidemiology , COVID-19/epidemiology , COVID-19/virology , SARS-CoV-2/genetics , SARS-CoV-2/classification , Prevalence , Spike Glycoprotein, Coronavirus/genetics , Phylogeny , Mutation , Genome, Viral/genetics , Genetic Variation
18.
Sci Rep ; 14(1): 10297, 2024 05 04.
Article En | MEDLINE | ID: mdl-38704475

The ideal vaccines for combating diseases that may emerge in the future require more than simply inactivating a few pathogenic strains. This study aims to provide a peptide-based multi-epitope vaccine effective against various severe acute respiratory syndrome coronavirus 2 strains. To design the vaccine, a library of peptides from the spike, nucleocapsid, membrane, and envelope structural proteins of various strains was prepared. Then, the final vaccine structure was optimized using the fully protected epitopes and the fynomer scaffold. Using bioinformatics tools, the antigenicity, allergenicity, toxicity, physicochemical properties, population coverage, and secondary and three-dimensional structures of the vaccine candidate were evaluated. The bioinformatic analyses confirmed the high quality of the vaccine. According to further investigations, this structure is similar to native protein and there is a stable and strong interaction between vaccine and receptors. Based on molecular dynamics simulation, structural compactness and stability in binding were also observed. In addition, the immune simulation showed that the vaccine can stimulate immune responses similar to real conditions. Finally, codon optimization and in silico cloning confirmed efficient expression in Escherichia coli. In conclusion, the fynomer-based vaccine can be considered as a new style in designing and updating vaccines to protect against coronavirus disease.


COVID-19 Vaccines , COVID-19 , Computational Biology , Molecular Dynamics Simulation , SARS-CoV-2 , SARS-CoV-2/immunology , SARS-CoV-2/genetics , COVID-19 Vaccines/immunology , Humans , Computational Biology/methods , COVID-19/prevention & control , COVID-19/immunology , COVID-19/virology , Epitopes/immunology , Epitopes/chemistry , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/chemistry , Immunoinformatics
19.
Oncotarget ; 15: 275-284, 2024 May 03.
Article En | MEDLINE | ID: mdl-38709242

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and COVID-19 infection has led to worsened outcomes for patients with cancer. SARS-CoV-2 spike protein mediates host cell infection and cell-cell fusion that causes stabilization of tumor suppressor p53 protein. In-silico analysis previously suggested that SARS-CoV-2 spike interacts with p53 directly but this putative interaction has not been demonstrated in cells. We examined the interaction between SARS-CoV-2 spike, p53 and MDM2 (E3 ligase, which mediates p53 degradation) in cancer cells using an immunoprecipitation assay. We observed that SARS-CoV-2 spike protein interrupts p53-MDM2 protein interaction but did not detect SARS-CoV-2 spike bound with p53 protein in the cancer cells. We further observed that SARS-CoV-2 spike suppresses p53 transcriptional activity in cancer cells including after nutlin exposure of wild-type p53-, spike-expressing tumor cells and inhibits chemotherapy-induced p53 gene activation of p21(WAF1), TRAIL Death Receptor DR5 and MDM2. The suppressive effect of SARS-CoV-2 spike on p53-dependent gene activation provides a potential molecular mechanism by which SARS-CoV-2 infection may impact tumorigenesis, tumor progression and chemotherapy sensitivity. In fact, cisplatin-treated tumor cells expressing spike were found to have increased cell viability as compared to control cells. Further observations on γ-H2AX expression in spike-expressing cells treated with cisplatin may indicate altered DNA damage sensing in the DNA damage response pathway. The preliminary observations reported here warrant further studies to unravel the impact of SARS-CoV-2 and its various encoded proteins including spike on pathways of tumorigenesis and response to cancer therapeutics. More efforts should be directed at studying the effects of the SARS-CoV-2 spike and other viral proteins on host DNA damage sensing, response and repair mechanisms. A goal would be to understand the structural basis for maximal anti-viral immunity while minimizing suppression of host defenses including the p53 DNA damage response and tumor suppression pathway. Such directions are relevant and important including not only in the context of viral infection and mRNA vaccines in general but also for patients with cancer who may be receiving cytotoxic or other cancer treatments.


Cell Survival , Cyclin-Dependent Kinase Inhibitor p21 , Proto-Oncogene Proteins c-mdm2 , Receptors, TNF-Related Apoptosis-Inducing Ligand , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Tumor Suppressor Protein p53 , Humans , Proto-Oncogene Proteins c-mdm2/metabolism , Tumor Suppressor Protein p53/metabolism , Cyclin-Dependent Kinase Inhibitor p21/metabolism , Spike Glycoprotein, Coronavirus/metabolism , Spike Glycoprotein, Coronavirus/genetics , Cell Survival/drug effects , Receptors, TNF-Related Apoptosis-Inducing Ligand/metabolism , Receptors, TNF-Related Apoptosis-Inducing Ligand/genetics , SARS-CoV-2/physiology , Cell Line, Tumor , Neoplasms/metabolism , Neoplasms/drug therapy , Antineoplastic Agents/pharmacology , Transfection , COVID-19/virology , COVID-19/metabolism
20.
Am J Reprod Immunol ; 91(5): e13861, 2024 May.
Article En | MEDLINE | ID: mdl-38716765

BACKGROUND: Maternal-fetal immunology is intricate, and the effects of mRNA-S maternal vaccination on immune regulation at the maternal-fetal interface require further investigation. Our study endeavors to elucidate these immunological changes, enhancing our comprehension of maternal and fetal health outcomes. By analyzing immune profiles and cytokine responses, we aim to provide valuable insights into the impact of mRNA-S vaccination on the delicate balance of immune regulation during pregnancy, addressing critical questions in the field of reproductive pharmacology. OBJECTIVES: This investigation sought to examine the prospective influence of mRNA-S-based vaccines and extracellular vesicles (EVs) containing the Spike (S) protein at the maternal-fetal interface. Our primary emphasis was on evaluating their effects on maternal decidua cells and fetal chorion trophoblast cells (hFM-CTCs). METHODS: We validated the generation of EVs containing the S protein from small human airway epithelial cell lines (HSAECs) following mRNA-S vaccine exposure. We assessed the expression of angiotensin-converting enzyme 2 (ACE2) gene and protein in fetal membranes and the placenta, with specific attention to decidual cells and fetal membrane chorion cells. To assess cellular functionality, these cells were exposed to both recombinant S protein and EVs loaded with S proteins (eSPs). RESULTS: Our findings revealed that cells and EVs subjected to mRNA-S-based vaccination exhibited altered protein expression levels of S proteins. At the feto-maternal interface, both placental and fetal membrane tissues demonstrated similar ACE-2 expression levels. Among individual cellular layers, syncytiotrophoblast cells in the placenta and chorion cells in the fetal membrane exhibited elevated ACE-2 expression. Notably, EVs derived from HSAECs activated the MAPK pathway in decidual cells. Additionally, decidual cells displayed a substantial increase in gene expression of chemokines like CXCL-10 and CXCL-11, as well as proinflammatory cytokines such as IL-6 in response to eSPs. However, the levels of Ccl-2 and IL-1ß remained unchanged in decidual cells under the same conditions. Conversely, hFM-CTCs demonstrated significant alterations in the proinflammatory cytokines and chemokines with respect to eSPs. CONCLUSION: In conclusion, our study indicates that mRNA-S-based maternal vaccination during pregnancy may influence the maternal-fetal interface's COVID-19 interaction and immune regulation. Further investigation is warranted to assess safety and implications.


Extracellular Vesicles , Trophoblasts , Humans , Female , Pregnancy , Trophoblasts/immunology , Extracellular Vesicles/immunology , Extracellular Vesicles/metabolism , Decidua/immunology , Spike Glycoprotein, Coronavirus/immunology , Cytokines/metabolism , Vaccination , Angiotensin-Converting Enzyme 2/metabolism , Angiotensin-Converting Enzyme 2/genetics , Maternal-Fetal Exchange , SARS-CoV-2/immunology , COVID-19/prevention & control , COVID-19/immunology , Cell Line , COVID-19 Vaccines/immunology , RNA, Messenger/metabolism , RNA, Messenger/genetics
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