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1.
Heliyon ; 9(5): e15587, 2023 May.
Article in English | MEDLINE | ID: covidwho-2299164

ABSTRACT

The COVID-19 pandemic continues to threaten human health worldwide as new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerge. Currently, the predominant circulating strains around the world are Omicron variants, which can evade many therapeutic antibodies. Thus, the development of new broadly neutralizing antibodies remains an urgent need. In this work, we address this need by using the mRNA-lipid nanoparticle immunization method to generate a set of Omicron-targeting monoclonal antibodies. Five of our novel K-RBD-mAbs show strong binding and neutralizing activities toward all SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, Delta and Omicron). Notably, the epitopes of these five K-RBD-mAbs are overlapping and localized around Y453 and F486 of the spike protein receptor binding domain (RBD). Chimeric derivatives of the five antibodies (K-RBD-chAbs) neutralize Omicron sublineages BA.1 and BA.2 with low IC50 values ranging from 5.7 to 12.9 ng/mL. Additionally, we performed antibody humanization on broadly neutralizing chimeric antibodies to create K-RBD-hAb-60 and -62, which still retain excellent neutralizing activity against Omicron. Our results collectively suggest that these five therapeutic antibodies may effectively combat current and emerging SARS-CoV-2 variants, including Omicron BA.1 and BA.2. Therefore, the antibodies can potentially be used as universal neutralizing antibodies against SARS-CoV-2.

2.
J Biomed Sci ; 29(1): 108, 2022 Dec 22.
Article in English | MEDLINE | ID: covidwho-2266799

ABSTRACT

BACKGROUND: The variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harbor diverse spike (S) protein sequences, which can greatly influence the efficacies of therapeutics. Therefore, it would be of great value to develop neutralizing monoclonal antibodies (mAbs) that can broadly recognize multiple variants. METHODS: Using an mRNA-LNP immunization strategy, we generated several mAbs that specifically target the conserved S2 subunit of SARS-CoV-2 (B-S2-mAbs). These mAbs were assessed for their neutralizing activity with pseudotyped viruses and binding ability for SARS-CoV-2 variants. RESULTS: Among these mAbs, five exhibited strong neutralizing ability toward the Gamma variant and also recognized viral S proteins from the Wuhan, Alpha, Beta, Gamma, Delta and Omicron (BA.1, BA.2 and BA.5) variants. Furthermore, we demonstrated the broad reactivities of these B-S2-mAbs in several different applications, including immunosorbent, immunofluorescence and immunoblotting assays. In particular, B-S2-mAb-2 exhibited potent neutralization of Gamma variant (IC50 = 0.048 µg/ml) in a pseudovirus neutralization assay. The neutralizing epitope of B-S2-mAb-2 was identified by phage display as amino acid residues 1146-1152 (DSFKEEL) in the S2 subunit HR2 domain of SARS-CoV-2. CONCLUSION: Since there are not many mAbs that can bind the S2 subunit of SARS-CoV-2 variants, our set of B-S2-mAbs may provide important materials for basic research and potential clinical applications. Importantly, our study results demonstrate that the viral S2 subunit can be targeted for the production of cross-reactive antibodies, which may be used for coronavirus detection and neutralization.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Antibodies, Viral , Antibodies, Monoclonal/metabolism , Spike Glycoprotein, Coronavirus/genetics , Antibodies, Neutralizing
3.
iScience ; 26(2): 105995, 2023 Feb 17.
Article in English | MEDLINE | ID: covidwho-2179849

ABSTRACT

The coronavirus nucleocapsid (N) protein is known to bind to nucleic acids and facilitate viral genome encapsulation. Here we report that the N protein can mediate RNA or DNA entering neighboring cells through ACE2-independent, receptor (STEAP2)-mediated endocytosis, and achieve gene expression. The effect is more pronounced for the N protein of wild-type SARS-CoV-2 than that of the Omicron variant and other human coronaviruses. This effect is enhanced by RANTES (CCL5), a chemokine induced by N protein, and lactate, a metabolite produced in hypoxia, to cause more damage. These findings might explain the clinical observations in SARS-CoV-2-infected cases. Moreover, the N protein-mediated function can be inhibited by N protein-specific monoclonal antibodies or p38 mitogen-activated protein kinase inhibitors. Since the N-protein-mediated nucleic acid endocytosis involves a receptor commonly expressed in many types of cells, our findings suggest that N protein may have an additional role in SARS-CoV-2 pathogenesis.

4.
Shanghai Journal of Preventive Medicine ; 34(4):303-308, 2022.
Article in Chinese | GIM | ID: covidwho-2155965

ABSTRACT

Objective: Based on the investigation of the core capacity development of health emergency response of Shanghai disease prevention and control institutions after the COVID-19 pandemic, to analyze the shortcomings of health emergency response capacity of Shanghai disease prevention and control institutions, and to put forward suggestions to improve the core capacity of Shanghai's disease prevention and control system in the face of public health emergencies.

5.
Front Med (Lausanne) ; 9: 941980, 2022.
Article in English | MEDLINE | ID: covidwho-2142049

ABSTRACT

Objectives: After the coronavirus disease 2019 (COVID-19) pandemic emerged, there has been a substantial decline in emergency department (ED) visits. However, the impact of the pandemic on pediatric ED (PED) visits has not been well discussed. This study aimed to compare the epidemiology and clinical characteristics of PED visits before and after the time of the COVID-19 outbreak. Methods: Data of pediatric patients admitted to the PED between February 2019 and January 2021 were retrospectively collected. All patients were divided into two groups: 1 year before the COVID-19 pandemic (group 1) and 1 year after the COVID-19 outbreak (group 2). Basic demographics, clinical characteristics, triage levels, categories of diagnosis at PED, disposition, and hospitalization rates (wards and intensive care units) were further analyzed and compared between the two groups. Results: During the study period, 48,146 pediatric patients were enrolled (30,823 in group 1, and 17,323 in group 2). PED visits represented a 43.8% annual decline. The most common diseases in the PED in group 1 were infectious diseases, whereas digestive system diseases were the most common diseases in group 2 (both P < 0.001). In group 2, shorter PED observational time, longer hospital stay, and higher admission rates were noted compared to those in group 1 (all P < 0.001). Conclusion: During the COVID-19 pandemic, the proportion of respiratory system diseases and infectious diseases sharply decreased in the PED, whereas the proportion of digestive system diseases relatively increased. The COVID-19 pandemic has impacted the nature of PED visits and we should pay more attention on digestive system diseases and the rates of out-of-hospital cardiac arrest and overall mortality.

6.
Sci Rep ; 12(1): 18640, 2022 Nov 04.
Article in English | MEDLINE | ID: covidwho-2106472

ABSTRACT

Disinfection eliminates pathogenic microorganisms and ensures a biosafe environment for human beings. The rapid spread of COVID-19 is challenging traditional disinfection methods in terms of reducing harmful side effects and conducting faster processes. Spraying large-scale chemical disinfectants is harmful to individuals and the environment, while UV lamp and light-emitting diode (LED) disinfection still requires a long exposure time due to the low irradiance and highly divergent beam characteristics. Given that a laser maintains a high irradiance over a long distance, we studied the effectiveness of lasers as a new disinfection method, and the results show the capability for ultrafast inactivation of SARS-CoV-2 virus with a 266 nm laser. This work confirms UV lasers as a good candidate for disinfection.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Ultraviolet Rays , Disinfection/methods , Lasers , Virus Inactivation
7.
J Pediatr Hematol Oncol ; 44(2): e450-e452, 2022 Mar 01.
Article in English | MEDLINE | ID: covidwho-2063086

ABSTRACT

In people with sickle cell disease (SCD), oral abscesses are concerning clinical conditions and carry a high risk of postoperative sickle cell complications. We present an unusual case of a 14-year-old girl with SCD whose initial presentation of facial swelling, headaches, jaw pain, and paresthesia mimicked an odontogenic abscess. She was diagnosed with vaso-occlusive crisis in the mandibular bone and successfully managed noninvasively. This is among the youngest cases of paresthesia in the lower lip in SCD, which provided a clue that postponing invasive aspiration or biopsy was possible under empiric antibiotics and close observation.


Subject(s)
Anemia, Sickle Cell , Jaw Diseases , Abscess/diagnosis , Abscess/etiology , Adolescent , Anemia, Sickle Cell/complications , Female , Humans , Mandible , Pain/diagnosis , Pain/etiology , Paresthesia/complications
8.
Int J Pharm ; 627: 122256, 2022 Nov 05.
Article in English | MEDLINE | ID: covidwho-2049315

ABSTRACT

Throughout the COVID-19 pandemic, many prophylactic and therapeutic drugs have been evaluated and introduced. Among these treatments, monoclonal antibodies (mAbs) that bind to and neutralize SARS-CoV-2 virus have been applied as complementary and alternative treatments to vaccines. Although different methodologies have been utilized to produce mAbs, traditional hybridoma fusion technology is still commonly used for this purpose due to its unmatched performance record. In this study, we coupled the hybridoma fusion strategy with mRNA-lipid nanoparticle (LNP) immunization. This time-saving approach can circumvent biological and technical hurdles, such as difficult-to-express membrane proteins, antigen instability, and the lack of posttranslational modifications on recombinant antigens. We used mRNA-LNP immunization and hybridoma fusion technology to generate mAbs against the receptor binding domain (RBD) of SARS-CoV-2 spike (S) protein. Compared with traditional protein-based immunization approaches, inoculation of mice with RBD mRNA-LNP induced higher titers of serum antibodies and markedly increased serum neutralizing activity. The mAbs we obtained can bind to SARS-CoV-2 RBDs from several variants. Notably, RBD-mAb-3 displayed particularly high binding affinities and neutralizing potencies against both Alpha and Delta variants. In addition to introducing specific mAbs against SARS-CoV-2, our data generally demonstrate that mRNA-LNP immunization may be useful to quickly generate highly functional mAbs against emerging infectious diseases.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Mice , Animals , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Antibodies, Neutralizing/chemistry , Antibodies, Neutralizing/metabolism , Pandemics , Antibody Formation , RNA, Messenger , COVID-19/prevention & control , Antibodies, Viral , Antibodies, Monoclonal/chemistry , Immunization
9.
J Biomed Sci ; 29(1): 68, 2022 Sep 12.
Article in English | MEDLINE | ID: covidwho-2021289

ABSTRACT

The novel coronavirus disease (COVID-19) pandemic remains a global public health crisis, presenting a broad range of challenges. To help address some of the main problems, the scientific community has designed vaccines, diagnostic tools and therapeutics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The rapid pace of technology development, especially with regard to vaccines, represents a stunning and historic scientific achievement. Nevertheless, many challenges remain to be overcome, such as improving vaccine and drug treatment efficacies for emergent mutant strains of SARS-CoV-2. Outbreaks of more infectious variants continue to diminish the utility of available vaccines and drugs. Thus, the effectiveness of vaccines and drugs against the most current variants is a primary consideration in the continual analyses of clinical data that supports updated regulatory decisions. The first two vaccines granted Emergency Use Authorizations (EUAs), BNT162b2 and mRNA-1273, still show more than 60% protection efficacy against the most widespread current SARS-CoV-2 variant, Omicron. This variant carries more than 30 mutations in the spike protein, which has largely abrogated the neutralizing effects of therapeutic antibodies. Fortunately, some neutralizing antibodies and antiviral COVID-19 drugs treatments have shown continued clinical benefits. In this review, we provide a framework for understanding the ongoing development efforts for different types of vaccines and therapeutics, including small molecule and antibody drugs. The ripple effects of newly emergent variants, including updates to vaccines and drug repurposing efforts, are summarized. In addition, we summarize the clinical trials supporting the development and distribution of vaccines, small molecule drugs, and therapeutic antibodies with broad-spectrum activity against SARS-CoV-2 strains.


Subject(s)
COVID-19 Drug Treatment , COVID-19 , Viral Vaccines , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , BNT162 Vaccine , COVID-19/prevention & control , Humans , SARS-CoV-2 , Viral Vaccines/therapeutic use
10.
Int J Environ Res Public Health ; 19(17)2022 Aug 26.
Article in English | MEDLINE | ID: covidwho-2006013

ABSTRACT

BACKGROUND: The severe and critical cases of COVID-19 had high mortality rates. Clinical features, laboratory data, and radiological features provided important references for the assessment of COVID-19 severity. The machine learning analysis of clinico-radiological features, especially the quantitative computed tomography (CT) image analysis results, may achieve early, accurate, and fine-grained assessment of COVID-19 severity, which is an urgent clinical need. OBJECTIVE: To evaluate if machine learning algorithms using CT-based clinico-radiological features could achieve the accurate fine-grained assessment of COVID-19 severity. METHODS: The clinico-radiological features were collected from 78 COVID-19 patients with different severities. A neural network was developed to automatically measure the lesion volume from CT images. The severity was clinically diagnosed using two-type (severe and non-severe) and fine-grained four-type (mild, regular, severe, critical) classifications, respectively. To investigate the key features of COVID-19 severity, statistical analyses were performed between patients' clinico-radiological features and severity. Four machine learning algorithms (decision tree, random forest, SVM, and XGBoost) were trained and applied in the assessment of COVID-19 severity using clinico-radiological features. RESULTS: The CT imaging features (CTscore and lesion volume) were significantly related with COVID-19 severity (p < 0.05 in statistical analysis for both in two-type and fine-grained four-type classifications). The CT imaging features significantly improved the accuracy of machine learning algorithms in assessing COVID-19 severity in the fine-grained four-type classification. With CT analysis results added, the four-type classification achieved comparable performance to the two-type one. CONCLUSIONS: CT-based clinico-radiological features can provide an important reference for the accurate fine-grained assessment of illness severity using machine learning to achieve the early triage of COVID-19 patients.


Subject(s)
COVID-19 , Algorithms , COVID-19/diagnostic imaging , Humans , Machine Learning , Neural Networks, Computer , Tomography, X-Ray Computed/methods
11.
Frontiers in medicine ; 9, 2022.
Article in English | EuropePMC | ID: covidwho-1989436

ABSTRACT

Objectives After the coronavirus disease 2019 (COVID-19) pandemic emerged, there has been a substantial decline in emergency department (ED) visits. However, the impact of the pandemic on pediatric ED (PED) visits has not been well discussed. This study aimed to compare the epidemiology and clinical characteristics of PED visits before and after the time of the COVID-19 outbreak. Methods Data of pediatric patients admitted to the PED between February 2019 and January 2021 were retrospectively collected. All patients were divided into two groups: 1 year before the COVID-19 pandemic (group 1) and 1 year after the COVID-19 outbreak (group 2). Basic demographics, clinical characteristics, triage levels, categories of diagnosis at PED, disposition, and hospitalization rates (wards and intensive care units) were further analyzed and compared between the two groups. Results During the study period, 48,146 pediatric patients were enrolled (30,823 in group 1, and 17,323 in group 2). PED visits represented a 43.8% annual decline. The most common diseases in the PED in group 1 were infectious diseases, whereas digestive system diseases were the most common diseases in group 2 (both P < 0.001). In group 2, shorter PED observational time, longer hospital stay, and higher admission rates were noted compared to those in group 1 (all P < 0.001). Conclusion During the COVID-19 pandemic, the proportion of respiratory system diseases and infectious diseases sharply decreased in the PED, whereas the proportion of digestive system diseases relatively increased. The COVID-19 pandemic has impacted the nature of PED visits and we should pay more attention on digestive system diseases and the rates of out-of-hospital cardiac arrest and overall mortality.

12.
J Biomed Sci ; 29(1): 49, 2022 Jul 07.
Article in English | MEDLINE | ID: covidwho-1923546

ABSTRACT

BACKGROUND: With the continuous emergence of new SARS-CoV-2 variants that feature increased transmission and immune escape, there is an urgent demand for a better vaccine design that will provide broader neutralizing efficacy. METHODS: We report an mRNA-based vaccine using an engineered "hybrid" receptor binding domain (RBD) that contains all 16 point-mutations shown in the currently prevailing Omicron and Delta variants. RESULTS: A booster dose of hybrid vaccine in mice previously immunized with wild-type RBD vaccine induced high titers of broadly neutralizing antibodies against all tested SARS-CoV-2 variants of concern (VOCs). In naïve mice, hybrid vaccine generated strong Omicron-specific neutralizing antibodies as well as low but significant titers against other VOCs. Hybrid vaccine also elicited CD8+/IFN-γ+ T cell responses against a conserved T cell epitope present in wild type and all VOCs. CONCLUSIONS: These results demonstrate that inclusion of different antigenic mutations from various SARS-CoV-2 variants is a feasible approach to develop cross-protective vaccines.


Subject(s)
COVID-19 , SARS-CoV-2 , Animals , Antibodies, Neutralizing , Antibodies, Viral , Broadly Neutralizing Antibodies , COVID-19/prevention & control , Humans , Mice , SARS-CoV-2/genetics , Vaccines, Synthetic , mRNA Vaccines
13.
J Integr Med ; 20(5): 416-426, 2022 09.
Article in English | MEDLINE | ID: covidwho-1907343

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19) is a rapidly spreading disease that has caused an extensive burden to the world. Consequently, a large number of clinical trials have examined the efficacy of traditional Chinese medicine (TCM) for treating and preventing COVID-19, with coinciding proliferation of reviews summarizing these studies. OBJECTIVE: This study aimed to evaluate the methodological quality and evidence quality of systematic reviews and meta-analyses on the efficacy of TCM. SEARCH STRATEGY: Seven electronic databases, including PubMed, Cochrane Library, Web of Science, China National Knowledge Infrastructure, Chongqing VIP, Wanfang Data and SinoMed, were searched for systematic reviews and meta-analyses in October 2021. Search terms such as "Chinese medicine," "Lianhua Qingwen" and "COVID-19" were used. INCLUSION CRITERIA: Systematic reviews and meta-analyses of randomized controlled trials that evaluated the efficacy of TCM treatment of COVID-19 were included. DATA EXTRACTION AND ANALYSIS: A Measurement Tool to Assess Systematic Reviews Version 2.0 (AMSTAR 2) was used to evaluate the methodological quality. The quality of evidence was graded using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) system. Data extraction and analysis were performed by two reviewers independently. RESULTS: There were 17 meta-analyses included in our overview. The intervention group was defined as TCM combined with Western medicine, while the control group was Western medicine alone. The methodological quality of all the included studies was moderate to poor. A total of 89 outcome indicators were evaluated, of which, 8 were rated as moderate quality, 39 as low quality, and 41 as very low quality. Only one outcome measure was graded as being of high quality. The moderate quality of evidence indicated that, for the treatment of COVID-19, the clinical efficacy of TCM in combination with Western medicine was better, in terms of lung recovery, rate of conversion to severe/critical cases, symptom scores, duration of symptoms, mortality, and length of hospital stay. CONCLUSION: Evidence from the included studies shows that, compared with conventional Western medical therapy alone, the addition of TCM to COVID-19 treatment may improve clinical outcomes. Overall, the quality of evidence of TCM for COVID-19 was moderate to poor. Meta-analyses of the use of TCM in the treatment of COVID-19 can be used for clinical decision making by accounting for the experiences of clinical experts, medical policies, and other factors.


Subject(s)
COVID-19 Drug Treatment , Drugs, Chinese Herbal , Drugs, Chinese Herbal/therapeutic use , Humans , Medicine, Chinese Traditional , Meta-Analysis as Topic , Systematic Reviews as Topic , Treatment Outcome
14.
Front Public Health ; 10: 876615, 2022.
Article in English | MEDLINE | ID: covidwho-1903221

ABSTRACT

Background: Local governments in China took restrictive measures after the outbreak of COVID-19 to control its spread, which unintentionally resulted in reduced anthropogenic emission sources of air pollutants. In this study, we intended to examine the effects of the COVID-19 lockdown policy on the concentration levels of particulate matter with aerodynamic diameters of ≤1 µm (PM1), ≤2.5 µm (PM2.5), and ≤10 µm (PM10), nitrogen dioxide (NO2), sulfur dioxide (SO2), ozone (O3), and carbon monoxide (CO) and the potential subsequent reductions in the incidence of ischemic and hemorrhagic stroke in Shandong Province, China. Methods: A difference-in-difference model combining the daily incidence data for ischemic and hemorrhagic stroke and air pollutant data in 126 counties was used to estimate the effect of the COVID-19 lockdown on the air pollutant levels and ischemic and hemorrhagic stroke incident counts. The avoided ischemic stroke cases related to the changes in air pollutant exposure levels were further estimated using concentration-response functions from previous studies. Results: The PM1, PM2.5, PM10, NO2, and CO levels significantly decreased by -30.2, -20.9, -13.5, -46.3, and -13.1%, respectively. The O3 level increased by 11.5% during the lockdown compared with that in the counterfactual lockdown phase of the past 2 years. There was a significant reduction in population-weighted ischemic stroke cases (-15,315, 95% confidence interval [CI]: -27,689, -2,942), representing a reduction of 27.6% (95% CI: -49.9%, -5.3%). The change in the number of hemorrhagic stroke cases was not statistically significant. The total avoided PM1-, PM2.5-, PM10-, NO2-, and CO-related ischemic stroke cases were 739 (95% CI: 641, 833), 509 (95% CI: 440, 575), 355 (95% CI: 304, 405), 1,132 (95% CI: 1,024, 1,240), and 289 (95% CI: 236, 340), respectively. Conclusion: The COVID-19 lockdown indirectly reduced the concentration levels of PM1, PM2.5, PM10, NO2, and CO and subsequently reduced the associated ischemic stroke incidence. The health benefits due to the lockdown are temporary, and long-term measures should be implemented to increase air quality and related health benefits in the post-COVID-19 period.


Subject(s)
Air Pollutants , Air Pollution , COVID-19 , Hemorrhagic Stroke , Ischemic Stroke , Air Pollutants/analysis , Air Pollution/analysis , COVID-19/epidemiology , COVID-19/prevention & control , China/epidemiology , Communicable Disease Control , Humans , Incidence , Nitrogen Dioxide/analysis , Particulate Matter/analysis
15.
Front Pediatr ; 10: 846410, 2022.
Article in English | MEDLINE | ID: covidwho-1887120

ABSTRACT

Background: Out-of-hospital cardiac arrest (OHCA) in children is a critical condition with a poor prognosis. After the coronavirus disease 2019 (COVID-19) pandemic developed, the epidemiology and clinical characteristics of the pediatric emergency department (PED) visits have changed. This study aimed to analyze the impact of the COVID-19 pandemic on pediatric OHCA in the PED. Methods: From January 2018 to September 2021, we retrospectively collected data of children (18 years or younger) with a definite diagnosis of OHCA admitted to the PED. Patient data studied included demographics, pre-/in-hospital information, treatment modalities; and outcomes of interest included sustained return of spontaneous circulation (SROSC) and survival to hospital-discharge (STHD). These were analyzed and compared between the periods before and after the COVID-19 pandemic. Results: A total of 97 patients with OHCA (68 boys and 29 girls) sent to the PED were enrolled in our study. Sixty cases (61.9%) occurred in the pre-pandemic period and 37 during the pandemic. The most common age group was infants (40.2%) (p = 0.018). Asystole was the most predominant cardiac rhythm (72.2%, P = 0.048). Eighty patients (82.5%) were transferred by the emergency medical services, 62 (63.9%) gained SROSC, and 25 (25.8%) were STHD. During the COVID-19 pandemic, children with non-trauma OHCA had significantly shorter survival duration and prolonged EMS scene intervals (both p < 0.05). Conclusion: During the COVID-19 pandemic, children with OHCA had a significantly lower rate of SROSC and STHD than that in the pre-pandemic period. The COVID-19 pandemic has changed the nature of PED visits and has affected factors related to ROSC and STHD in pediatric OHCA.

16.
Front Immunol ; 13: 872047, 2022.
Article in English | MEDLINE | ID: covidwho-1855361

ABSTRACT

An effective COVID-19 vaccine against broad SARS-CoV-2 variants is still an unmet need. In the study, the vesicular stomatitis virus (VSV)-based vector was used to express the SARS-CoV-2 Spike protein to identify better vaccine designs. The replication-competent of the recombinant VSV-spike virus with C-terminal 19 amino acid truncation (SΔ19 Rep) was generated. A single dose of SΔ19 Rep intranasal vaccination is sufficient to induce protective immunity against SARS-CoV-2 infection in hamsters. All the clones isolated from the SΔ19 Rep virus contained R682G mutation located at the Furin cleavage site. An additional S813Y mutation close to the TMPRSS2 cleavage site was identified in some clones. The enzymatic processing of S protein was blocked by these mutations. The vaccination of the R682G-S813Y virus produced a high antibody response against S protein and a robust S protein-specific CD8+ T cell response. The vaccinated animals were protected from the lethal SARS-CoV-2 (delta variant) challenge. The S antigen with resistance to enzymatic processes by Furin and TMPRSS2 will provide better immunogenicity for vaccine design.


Subject(s)
COVID-19 , Furin , SARS-CoV-2 , Serine Endopeptidases , Animals , COVID-19/immunology , COVID-19/prevention & control , COVID-19/virology , COVID-19 Vaccines , Furin/genetics , Furin/metabolism , Humans , Immunity, Cellular , SARS-CoV-2/immunology , Serine Endopeptidases/genetics , Serine Endopeptidases/immunology , Spike Glycoprotein, Coronavirus/immunology
17.
Int J Mol Sci ; 23(6)2022 Mar 17.
Article in English | MEDLINE | ID: covidwho-1760649

ABSTRACT

For tiling of the SARS-CoV-2 genome, the ARTIC Network provided a V4 protocol using 99 pairs of primers for amplicon production and is currently the widely used amplicon-based approach. However, this technique has regions of low sequence coverage and is labour-, time-, and cost-intensive. Moreover, it requires 14 pairs of primers in two separate PCRs to obtain spike gene sequences. To overcome these disadvantages, we proposed a single PCR to efficiently detect spike gene mutations. We proposed a bioinformatic protocol that can process FASTQ reads into spike gene consensus sequences to accurately call spike protein variants from sequenced samples or to fairly express the cases of missing amplicons. We evaluated the in silico detection rate of primer sets that yield amplicon sizes of 400, 1200, and 2500 bp for spike gene sequencing of SARS-CoV-2 to be 59.49, 76.19, and 92.20%, respectively. The in silico detection rate of our proposed single PCR primers was 97.07%. We demonstrated the robustness of our analytical protocol against 3000 Oxford Nanopore sequencing runs of distinct datasets, thus ensuring high-integrity sequencing of spike genes for variant SARS-CoV-2 determination. Our protocol works well with the data yielded from versatile primer designs, making it easy to determine spike protein variants.


Subject(s)
COVID-19/virology , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Computational Biology , Genome, Viral , Genomics/methods , Humans , Mutation , Mutation Rate , Phylogeny , SARS-CoV-2/classification , Sequence Analysis, DNA
18.
Front Immunol ; 13: 796682, 2022.
Article in English | MEDLINE | ID: covidwho-1731771

ABSTRACT

In the ongoing coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), natural killer T (NKT) cells act as primary initiators of immune responses. However, a decrease of circulating NKT cells has been observed in COVID-19 different stages, of which the underlying mechanism remains to be elucidated. Here, by performing single-cell RNA sequencing analysis in three large cohorts of COVID-19 patients, we found that increased expression of Tim-3 promotes depletion of NKT cells during the progression stage of COVID-19, which is associated with disease severity and outcome of patients with COVID-19. Tim-3+ NKT cells also expressed high levels of CD147 and CD26, which are potential SARS-CoV-2 spike binding receptors. In the study, Tim-3+ NKT cells showed high enrichment of apoptosis, higher expression levels of mitochondrial genes and caspase genes, with a larger pseudo time value. In addition, Tim-3+ NKT cells in COVID-19 presented a stronger capacity to secrete IFN-γ, IL-4 and IL-10 compared with healthy individuals, they also demonstrated high expression of co-inhibitory receptors such as PD-1, CTLA-4, and LAG-3. Moreover, we found that IL-12 secreted by dendritic cells (DCs) was positively correlated with up-regulated expression of Tim-3 in NKT cells in COVID-19 patients. Overall, this study describes a novel mechanism by which up-regulated Tim-3 expression induced the depletion and dysfunction of NKT cells in COVID-19 patients. These findings not only have possible implications for the prediction of severity and prognosis in COVID-19 but also provide a link between NKT cells and future new therapeutic strategies in SARS-CoV-2 infection.


Subject(s)
COVID-19/immunology , Hepatitis A Virus Cellular Receptor 2/immunology , Natural Killer T-Cells/immunology , SARS-CoV-2/immunology , Humans , Interferon-gamma/immunology , Interleukin-10/immunology , Interleukin-4/immunology , Signal Transduction/immunology
19.
J Biomed Sci ; 28(1): 80, 2021 Nov 23.
Article in English | MEDLINE | ID: covidwho-1533257

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an RNA virus with a high mutation rate. Importantly, several currently circulating SARS-CoV-2 variants are associated with loss of efficacy for both vaccines and neutralizing antibodies. METHODS: We analyzed the binding activity of six highly potent antibodies to the spike proteins of SARS-CoV-2 variants, assessed their neutralizing abilities with pseudovirus and authentic SARS-CoV-2 variants and evaluate efficacy of antibody cocktail in Delta SARS-CoV-2-infected hamster models as prophylactic and post-infection treatments. RESULTS: The tested RBD-chAbs, except RBD-chAb-25, maintained binding ability to spike proteins from SARS-CoV-2 variants. However, only RBD-chAb-45 and -51 retained neutralizing activities; RBD-chAb-1, -15, -25 and -28 exhibited diminished neutralization for all SARS-CoV-2 variants. Notably, several cocktails of our antibodies showed low IC50 values (3.35-27.06 ng/ml) against the SARS-CoV-2 variant pseudoviruses including United Kingdom variant B.1.1.7 (Alpha), South Africa variant B.1.351 (Beta), Brazil variant P1 (Gamma), California variant B.1.429 (Epsilon), New York variant B.1.526 (Iota), and India variants, B.1.617.1 (Kappa) and B.1.617.2 (Delta). RBD-chAb-45, and -51 showed PRNT50 values 4.93-37.54 ng/ml when used as single treatments or in combination with RBD-chAb-15 or -28, according to plaque assays with authentic Alpha, Gamma and Delta SARS-CoV-2 variants. Furthermore, the antibody cocktail of RBD-chAb-15 and -45 exhibited potent prophylactic and therapeutic effects in Delta SARS-CoV-2 variant-infected hamsters. CONCLUSIONS: The cocktail of RBD-chAbs exhibited potent neutralizing activities against SARS-CoV-2 variants. These antibody cocktails are highly promising candidate tools for controlling new SARS-CoV-2 variants, including Delta.


Subject(s)
Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/immunology , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , Animals , Antibodies, Neutralizing/therapeutic use , Antibodies, Viral/therapeutic use , COVID-19/genetics , Humans , Rabbits , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , COVID-19 Drug Treatment
20.
Int J Mol Sci ; 22(22)2021 Nov 17.
Article in English | MEDLINE | ID: covidwho-1524025

ABSTRACT

Mitigation strategies of the coronavirus disease 2019 (COVID-19) pandemic have been greatly hindered by the continuous emergence of SARS-CoV-2 variants. New sensitive, rapid diagnostic tests for the wide-spectrum detection of viral variants are needed. We generated a panel of 41 monoclonal antibodies against the SARS-CoV-2 nucleocapsid protein (NP) by using mice hybridoma techniques. Of these mAbs, nine exhibited high binding activities and were applied in latex-based lateral flow immunoassays (LFIAs). The LFIAs utilizing NP-mAb-7 and -40 had the best sensitivity and lowest limit of detection: 8 pg for purified NP and 625 TCID50/mL for the authentic virus (hCoV-19/Taiwan/4/2020). The specificity tests showed that the NP-mAb-40/7 LFIA strips did not cross-react with five human coronavirus strains or 20 other common respiratory pathogens. Importantly, we found that 10 NP mutants, including alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2) variants, could be detected by NP-mAb-40/7 LFIA strips. A clinical study (n = 60) of the NP-mAb-40/7 LFIA strips demonstrated a specificity of 100% and sensitivity of 90% in infected individuals with cycle threshold (Ct) values < 29.5. These anti-NP mAbs have strong potential for use in the clinical detection of SARS-CoV-2 infection, whether the virus is wild-type or a variant of concern.


Subject(s)
Antibodies, Monoclonal/immunology , COVID-19/diagnosis , Immunoassay/methods , Nucleocapsid Proteins/immunology , SARS-CoV-2/metabolism , Adolescent , Adult , Aged , Aged, 80 and over , Antigen-Antibody Reactions , COVID-19/virology , Coronavirus/metabolism , Cross Reactions , Female , Humans , Male , Middle Aged , Point-of-Care Systems , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Young Adult
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