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1.
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
2.
J Integr Med ; 2022 Jun 24.
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.

3.
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
4.
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.

5.
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
6.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-335937

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) have emerged. 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 K417 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 IC 50 values that range from 5.7 to 12.9 ng/mL. Additionally, we performed antibody humanization on a broadly neutralizing chimeric antibody to create K-RBD-hAb-62, which still retains 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.

7.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-335816

ABSTRACT

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. In addition, 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.

8.
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
9.
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
10.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-324127

ABSTRACT

The black-box nature of machine learning models hinders the deployment of some high-accuracy models in medical diagnosis. It is risky to put one's life in the hands of models that medical researchers do not fully understand. However, through model interpretation, black-box models can promptly reveal significant biomarkers that medical practitioners may have overlooked due to the surge of infected patients in the COVID-19 pandemic. This research leverages a database of 92 patients with confirmed SARS-CoV-2 laboratory tests between 18th Jan. 2020 and 5th Mar. 2020, in Zhuhai, China, to identify biomarkers indicative of severity prediction. Through the interpretation of four machine learning models, decision tree, random forests, gradient boosted trees, and neural networks using permutation feature importance, Partial Dependence Plot (PDP), Individual Conditional Expectation (ICE), Accumulated Local Effects (ALE), Local Interpretable Model-agnostic Explanations (LIME), and Shapley Additive Explanation (SHAP), we identify an increase in N-Terminal pro-Brain Natriuretic Peptide (NTproBNP), C-Reaction Protein (CRP), and lactic dehydrogenase (LDH), a decrease in lymphocyte (LYM) is associated with severe infection and an increased risk of death, which is consistent with recent medical research on COVID-19 and other research using dedicated models. We further validate our methods on a large open dataset with 5644 confirmed patients from the Hospital Israelita Albert Einstein, at São Paulo, Brazil from Kaggle, and unveil leukocytes, eosinophils, and platelets as three indicative biomarkers for COVID-19.

11.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-323754

ABSTRACT

Background: The coronavirus disease-19 (COVID-19) and its variants have increased rapidly worldwide since December 2019, with respiratory disease being a prominent complication. As such, optimizing evaluation methods and identifying factors predictive of disease progress remain critical. The purpose of the study was to assess late phase (≥3 weeks) pulmonary changes using intensity-based computed tomography (CT) scoring in COVID-19 patients and determine the clinical characteristics predicting lung abnormalities and recovery. Methods: : We conducted a retrospective study on 42 patients (14 males, 28 females;age 65±10 years) with COVID-19. Only patients with at least 3 CT scans taken at least 3 weeks after initial symptom onset were included in the study. Two scoring methods were assessed: (1) area-based scoring (ABS) and (2) intensity-weighted scoring (IWS). Temporal changes in the average lung lesion were evaluated by the calculating the averaged area under the curve (AUC) of the CT score-time curve. Correlations between averaged AUCs and clinical characteristics were determined. Results: Using the ABS system, temporal changes in lung abnormalities during recovery were highly variable (P=0.934). By contrast, the IWS system detected more subtle changes in lung abnormalities during in COVID-19 patients, with consistent week-to-week relative reductions in IWS (P=0.025). Strong relationships were observed with D-dimer and C-reactive protein (CRP) levels on admission, with hazard ratios (HR)(95%CI) of 5.32 (1.25-22.6)(P=0.026) and 1.05 (1.10-1.09)(P=0.017), respectively. Conclusion: Our results suggest COVID-19-mediated pulmonary abnormalities persist well-beyond 3-weeks of symptom onset, with intensity-weighted rather than area-based scoring being more sensitive. Moreover, D-dimer and CRP levels were predictive of the recovery from the disease.

12.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-323753

ABSTRACT

Objectives: To assess the late phase CT changes of COVID-19 patients, and figure out factors predicting lung abnormality in late phase. Methods: : We conducted a retrospective study on 42 patients (14 males, 28 females;age 65±10 years) with COVID-19 admitted between February 7, 2020 and March 27, 2020. Only patients with at least 3 CT scans taken at least 3 weeks after initial symptom onset were included in the study. CT images were analyzed by 2 independent radiologists using different scoring: (1) area-based scoring (ABS);and (2) intensity-weighted scoring (IWS). Temporal changes in the average lung lesion were evaluated by averaged area under the curve (AUC) of the CT score-time curve. Correlations between averaged AUCs and clinical characteristics were determined. Results: Temporal changes in lung abnormalities during recovery (weeks 3 through 8) of CT findings using the ABS system were variable (P=0.934). By contrast, the IWS system detected more subtle changes in lung abnormalities during the late phase of recovery in COVID-19 patients, with consistent week-to-week relative reductions in IWS (P=0.025). In assessing the correlation between averaged AUCs and clinical characteristics, strong relationships were observed with D-dimer and C-reactive protein (CRP) levels on admission, with hazard ratios (HR)(95%CI) of 5.32 (1.25-22.6)(P=0.026) and 1.05 (1.10-1.09)(P=0.017), respectively. Conclusion: Our results suggest an intensity-weighted rather than area-based scoring system is more sensitive to detect subtle temporal CT changes in COVID-19, with D-dimer and CRP levels on admission being predictive of the time course of late phase recovery from the disease.

13.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-327285

ABSTRACT

The emerging SARS-CoV-2 variants of concern (VOC) harbor mutations associated with increasing transmission and immune escape, hence undermine the effectiveness of current COVID-19 vaccines. In late November of 2021, the Omicron (B.1.1.529) variant was identified in South Africa and rapidly spread across the globe. It was shown to exhibit significant resistance to neutralization by serum not only from convalescent patients, but also from individuals recieving currently used COVID-19 vaccines with multiple booster shots. Therefore, there is an urgent need to develop next generation vaccines against VOCs like Omicron. In this study, we develop a panel of mRNA-LNP-based vaccines using the receptor binding domain (RBD) of Omicron and Delta variants, which are dominant in the current wave of COVID-19. In addition to the Omicron- and Delta-specific vaccines, the panel also includes a Hybrid vaccine that uses the RBD containing all 16 point-mutations shown in Omicron and Delta RBD, as well as a bivalent vaccine composed of both Omicron and Delta RBD-LNP in half dose. Interestingly, both Omicron-specific and Hybrid RBD-LNP elicited extremely high titer of neutralizing antibody against Omicron itself, but few to none neutralizing antibody against other SARS-CoV-2 variants. The bivalent RBD-LNP, on the other hand, generated antibody with broadly neutralizing activity against the wild-type virus and all variants. Surprisingly, similar cross-protection was also shown by the Delta-specifc RBD-LNP. Taken together, our data demonstrated that Omicron-specific mRNA vaccine can induce potent neutralizing antibody response against Omicron, but the inclusion of epitopes from other variants may be required for eliciting cross-protection. This study would lay a foundation for rational development of the next generation vaccines against SARS-CoV-2 VOCs.

14.
J Biomed Sci ; 29(1): 1, 2022 Jan 04.
Article in English | MEDLINE | ID: covidwho-1605455

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic is an exceptional public health crisis that demands the timely creation of new therapeutics and viral detection. Owing to their high specificity and reliability, monoclonal antibodies (mAbs) have emerged as powerful tools to treat and detect numerous diseases. Hence, many researchers have begun to urgently develop Ab-based kits for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Ab drugs for use as COVID-19 therapeutic agents. The detailed structure of the SARS-CoV-2 spike protein is known, and since this protein is key for viral infection, its receptor-binding domain (RBD) has become a major target for therapeutic Ab development. Because SARS-CoV-2 is an RNA virus with a high mutation rate, especially under the selective pressure of aggressively deployed prophylactic vaccines and neutralizing Abs, the use of Ab cocktails is expected to be an important strategy for effective COVID-19 treatment. Moreover, SARS-CoV-2 infection may stimulate an overactive immune response, resulting in a cytokine storm that drives severe disease progression. Abs to combat cytokine storms have also been under intense development as treatments for COVID-19. In addition to their use as drugs, Abs are currently being utilized in SARS-CoV-2 detection tests, including antigen and immunoglobulin tests. Such Ab-based detection tests are crucial surveillance tools that can be used to prevent the spread of COVID-19. Herein, we highlight some key points regarding mAb-based detection tests and treatments for the COVID-19 pandemic.


Subject(s)
Antibodies, Monoclonal , COVID-19 , SARS-CoV-2/isolation & purification , Antibodies, Monoclonal/therapeutic use , Antibodies, Neutralizing , Antibodies, Viral , COVID-19/diagnosis , COVID-19/drug therapy , Humans , Pandemics , Reproducibility of Results , Spike Glycoprotein, Coronavirus/genetics
15.
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/drug therapy , COVID-19/genetics , Humans , Rabbits , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics
16.
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
17.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-291709

ABSTRACT

The black-box nature of machine learning models hinders the deployment of some high-accuracy models in medical diagnosis. It is risky to put one's life in the hands of models that medical researchers do not fully understand. However, through model interpretation, black-box models can promptly reveal significant biomarkers that medical practitioners may have overlooked due to the surge of infected patients in the COVID-19 pandemic. This research leverages a database of 92 patients with confirmed SARS-CoV-2 laboratory tests between 18th Jan. 2020 and 5th Mar. 2020, in Zhuhai, China, to identify biomarkers indicative of severity prediction. Through the interpretation of four machine learning models, decision tree, random forests, gradient boosted trees, and neural networks using permutation feature importance, Partial Dependence Plot (PDP), Individual Conditional Expectation (ICE), Accumulated Local Effects (ALE), Local Interpretable Model-agnostic Explanations (LIME), and Shapley Additive Explanation (SHAP), we identify an increase in N-Terminal pro-Brain Natriuretic Peptide (NTproBNP), C-Reaction Protein (CRP), and lactic dehydrogenase (LDH), a decrease in lymphocyte (LYM) is associated with severe infection and an increased risk of death, which is consistent with recent medical research on COVID-19 and other research using dedicated models. We further validate our methods on a large open dataset with 5644 confirmed patients from the Hospital Israelita Albert Einstein, at São Paulo, Brazil from Kaggle, and unveil leukocytes, eosinophils, and platelets as three indicative biomarkers for COVID-19.

18.
PLoS Pathog ; 17(10): e1009704, 2021 10.
Article in English | MEDLINE | ID: covidwho-1484866

ABSTRACT

Development of effective therapeutics for mitigating the COVID-19 pandemic is a pressing global need. Neutralizing antibodies are known to be effective antivirals, as they can be rapidly deployed to prevent disease progression and can accelerate patient recovery without the need for fully developed host immunity. Here, we report the generation and characterization of a series of chimeric antibodies against the receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Some of these antibodies exhibit exceptionally potent neutralization activities in vitro and in vivo, and the most potent of our antibodies target three distinct non-overlapping epitopes within the RBD. Cryo-electron microscopy analyses of two highly potent antibodies in complex with the SARS-CoV-2 spike protein suggested they may be particularly useful when combined in a cocktail therapy. The efficacy of this antibody cocktail was confirmed in SARS-CoV-2-infected mouse and hamster models as prophylactic and post-infection treatments. With the emergence of more contagious variants of SARS-CoV-2, cocktail antibody therapies hold great promise to control disease and prevent drug resistance.


Subject(s)
Antibodies, Neutralizing/pharmacology , Antibodies, Viral/pharmacology , COVID-19/immunology , COVID-19/prevention & control , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , Animals , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , Cricetinae , Disease Models, Animal , Female , Male , Mice
19.
Nat Struct Mol Biol ; 28(9): 731-739, 2021 09.
Article in English | MEDLINE | ID: covidwho-1356577

ABSTRACT

The B.1.1.7 variant of SARS-CoV-2 first detected in the UK harbors amino-acid substitutions and deletions in the spike protein that potentially enhance host angiotensin conversion enzyme 2 (ACE2) receptor binding and viral immune evasion. Here we report cryo-EM structures of the spike protein of B.1.1.7 in the apo and ACE2-bound forms. The apo form showed one or two receptor-binding domains (RBDs) in the open conformation, without populating the fully closed state. All three RBDs were engaged in ACE2 binding. The B.1.1.7-specific A570D mutation introduces a molecular switch that could modulate the opening and closing of the RBD. The N501Y mutation introduces a π-π interaction that enhances RBD binding to ACE2 and abolishes binding of a potent neutralizing antibody (nAb). Cryo-EM also revealed how a cocktail of two nAbs simultaneously bind to all three RBDs, and demonstrated the potency of the nAb cocktail to neutralize different SARS-CoV-2 pseudovirus strains, including B.1.1.7.


Subject(s)
COVID-19/prevention & control , Mutation , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme 2/metabolism , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , Binding Sites/genetics , COVID-19/metabolism , COVID-19/virology , Cryoelectron Microscopy , Humans , Models, Molecular , Protein Binding , Protein Domains , Receptors, Virus/chemistry , Receptors, Virus/metabolism , SARS-CoV-2/immunology , SARS-CoV-2/physiology , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism
20.
PLoS Pathog ; 17(8): e1009758, 2021 08.
Article in English | MEDLINE | ID: covidwho-1352713

ABSTRACT

Since the pandemic of COVID-19 has intensely struck human society, small animal model for this infectious disease is in urgent need for basic and pharmaceutical research. Although several COVID-19 animal models have been identified, many of them show either minimal or inadequate pathophysiology after SARS-CoV-2 challenge. Here, we describe a new and versatile strategy to rapidly establish a mouse model for emerging infectious diseases in one month by multi-route, multi-serotype transduction with recombinant adeno-associated virus (AAV) vectors expressing viral receptor. In this study, the proposed approach enables profound and enduring systemic expression of SARS-CoV-2-receptor hACE2 in wild-type mice and renders them vulnerable to SARS-CoV-2 infection. Upon virus challenge, generated AAV/hACE2 mice showed pathophysiology closely mimicking the patients with severe COVID-19. The efficacy of a novel therapeutic antibody cocktail RBD-chAbs for COVID-19 was tested and confirmed by using this AAV/hACE2 mouse model, further demonstrating its successful application in drug development.


Subject(s)
COVID-19 , Communicable Diseases, Emerging , Disease Models, Animal , 3T3 Cells , Angiotensin-Converting Enzyme 2/genetics , Animals , Antibodies, Viral/immunology , Antibodies, Viral/therapeutic use , COVID-19/immunology , COVID-19/pathology , COVID-19/physiopathology , Chlorocebus aethiops , Dependovirus/genetics , Humans , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Transduction, Genetic , Vero Cells
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