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1.
J Virol Methods ; : 114597, 2022 Aug 03.
Article in English | MEDLINE | ID: covidwho-1966905

ABSTRACT

Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has become disaster for human society. As the pandemic becomes more regular, we should develop more rapid and accurate detection methods to achieve early diagnosis and treatment. Antigen detection methods based on spike protein has great potential, however, it has not been effectively developed, probably due to the torturing conformational complexity. By utilizing cross-blocking data, we clustered SARS-CoV-2 receptor binding domain (RBD)-specific monoclonal antibodies (mAbs) into 6 clusters. Subsequently, the antigenic sites for representative mAbs were identified by RBDs with designed residue substitutions. The sensitivity and specificity of selected antibody pairs was demonstrated using serial diluted samples of SARS-CoV-2 S protein and SARS-CoV S protein. Furthermore, pseudovirus system was constructed to determine the detection capability against SARS-CoV-2 and SARS-CoV. 6 RBD-specific mAbs, recognizing different antigenic sites, were identified as potential candidates for optimal antibody pairs for detection of SARS-CoV-2 S protein. By considering relative spatial position, accessibility and conservation of corresponding antigenic sites, affinity and the presence of competitive antibodies in clinical samples, 6H7-6G3 was rationally identified as optimal antibody pair for detection of both SARS-CoV-2 and SARS-CoV. Furthermore, our results showed that 6H7 and 6G3 effectively bind to SARS-CoV-2 variants of concern (VOCs). Taken together, we identified 6H7-6G3 antibody pair as a promising rapid antigen diagnostic tool in containing COVID-19 pandemic caused by multiple VOCs. Moreover, our results also provide an important reference in screening of antibody pairs detecting antigens with complex conformation.

2.
Frontiers in pharmacology ; 13, 2022.
Article in English | EuropePMC | ID: covidwho-1897880

ABSTRACT

Objective: People suffering from coronavirus disease 2019 (COVID-19) are prone to develop pulmonary fibrosis (PF), but there is currently no definitive treatment for COVID-19/PF co-occurrence. Kaempferol with promising antiviral and anti-fibrotic effects is expected to become a potential treatment for COVID-19 and PF comorbidities. Therefore, this study explored the targets and molecular mechanisms of kaempferol against COVID-19/PF co-occurrence by bioinformatics and network pharmacology. Methods: Various open-source databases and Venn Diagram tool were applied to confirm the targets of kaempferol against COVID-19/PF co-occurrence. Protein-protein interaction (PPI), MCODE, key transcription factors, tissue-specific enrichment, molecular docking, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to clarify the influential molecular mechanisms of kaempferol against COVID-19 and PF comorbidities. Results: 290 targets and 203 transcription factors of kaempferol against COVID-19/PF co-occurrence were captured. Epidermal growth factor receptor (EGFR), proto-oncogene tyrosine-protein kinase SRC (SRC), mitogen-activated protein kinase 3 (MAPK3), mitogen-activated protein kinase 1 (MAPK1), mitogen-activated protein kinase 8 (MAPK8), RAC-alpha serine/threonine-protein kinase (AKT1), transcription factor p65 (RELA) and phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (PIK3CA) were identified as the most critical targets, and kaempferol showed effective binding activities with the above critical eight targets. Further, anti-COVID-19/PF co-occurrence effects of kaempferol were associated with the regulation of inflammation, oxidative stress, immunity, virus infection, cell growth process and metabolism. EGFR, interleukin 17 (IL-17), tumor necrosis factor (TNF), hypoxia inducible factor 1 (HIF-1), phosphoinositide 3-kinase/AKT serine/threonine kinase (PI3K/AKT) and Toll-like receptor signaling pathways were identified as the key anti-COVID-19/PF co-occurrence pathways. Conclusion: Kaempferol is a candidate treatment for COVID-19/PF co-occurrence. The underlying mechanisms may be related to the regulation of critical targets (EGFR, SRC, MAPK3, MAPK1, MAPK8, AKT1, RELA, PIK3CA and so on) and EGFR, IL-17, TNF, HIF-1, PI3K/AKT and Toll-like receptor signaling pathways. This study contributes to guiding development of new drugs for COVID-19 and PF comorbidities.

3.
Frontiers in immunology ; 13, 2022.
Article in English | EuropePMC | ID: covidwho-1787312

ABSTRACT

Since the first outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, its high infectivity led to its prevalence around the world in an exceptionally short time. Efforts have been made to control the ongoing outbreak, and among them, vaccine developments are going on high priority. New clinical trials add to growing evidence that vaccines from many countries were highly effective at preventing SARS-CoV-2 virus infection. One of them is B cell-based vaccines, which were common during a pandemic. However, neutralizing antibody therapy becomes less effective when viruses mutate. In order to tackle the problem, we focused on T-cell immune mechanism. In this study, the mutated strains of the virus were selected globally from India (B.1.617.1 and B.1.617.2), United Kingdom (B.1.1.7), South Africa (B.1.351), and Brazil (P.1), and the overlapping peptides were collected based on mutation sites of S-protein. After that, residue scanning was used to predict the affinity between overlapping peptide and HLA-A*11:01, the most frequent human leukocyte antigen (HLA) allele among the Chinese population. Then, the binding free energy was evaluated with molecular docking to further verify the affinity changes after the mutations happen in the virus genomes. The affinity test results of three epitopes on spike protein from experimental validation were consistent with our predicted results, thereby supporting the inclusion of the epitope 374FSTFKCYGL382 in future vaccine design and providing a useful reference route to improve vaccine development.

4.
Anal Chem ; 94(6): 2926-2933, 2022 02 15.
Article in English | MEDLINE | ID: covidwho-1721378

ABSTRACT

Recombinase polymerase amplification (RPA) is a useful pathogen identification method. Several label-free detection methods for RPA amplicons have been developed in recent years. However, these methods still lack sensitivity, specificity, efficiency, or simplicity. In this study, we propose a rapid, highly sensitive, and label-free pathogen assay system based on a solid-phase self-interference RPA chip (SiSA-chip) and hyperspectral interferometry. The SiSA-chips amplify and capture RPA amplicons on the chips, rather than irrelevant amplicons such as primer dimers, and the SiSA-chips are then analysed by hyperspectral interferometry. Optical length increases of SiSA-chips are used to demonstrate RPA detection results, with a limit of detection of 1.90 nm. This assay system can detect as few as six copies of the target 18S rRNA gene of Plasmodium falciparum within 20 min, with a good linear relationship between the detection results and the concentration of target genes (R2 = 0.9903). Single nucleotide polymorphism (SNP) genotyping of the dhfr gene of Plasmodium falciparum is also possible using the SiSA-chip, with as little as 1% of mutant gene distinguished from wild-type loci (m/wt). This system offers a high-efficiency (20 min), high-sensitivity (6 copies/reaction), high-specificity (1% m/wt), and low-cost (∼1/50 of fluorescence assays for RPA) diagnosis method for pathogen DNA identification. Therefore, this system is promising for fast identification of pathogens to help diagnose infectious diseases, including SNP genotyping.


Subject(s)
Nucleic Acid Amplification Techniques , Recombinases , Interferometry , Nucleic Acid Amplification Techniques/methods , Nucleotidyltransferases , Plasmodium falciparum/genetics , Sensitivity and Specificity
5.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-318011

ABSTRACT

The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was initially reported in Wuhan, China since December, 2019. Here, we reported a timely and comprehensive resource named iCTCF to archive 256,356 chest computed tomography (CT) images, 127 types of clinical features (CFs), and laboratory-confirmed SARS-CoV-2 clinical status from 1170 patients, reaching a data volume of 38.2 GB. To facilitate COVID-19 diagnosis, we integrated the heterogeneous CT and CF datasets, and developed a novel framework of H ybrid-learning for U nbia S ed predic T ion of COVID -19 patients (HUST-19) to predict negative cases, mild/regular and severe/critically ill patients, respectively. Although both CT images and CFs are informative in predicting patients with or without COVID-19 pneumonia, the integration of CT and CF datasets achieved a striking accuracy with an area under the curve (AUC) value of 0.978, much higher than that when exclusively using either CT (0.919) or CF data (0.882). Together with HUST- 19, iCTCF can serve as a fundamental resource for improving the diagnosis and management of COVID-19 patients.Authors Wanshan Ning, Shijun Lei, Jingjing Yang, and Yukun Cao contributed equally to this work.

6.
Frontiers in public health ; 9, 2021.
Article in English | EuropePMC | ID: covidwho-1602671

ABSTRACT

Personal protective behaviors of healthcare workers (HCWs) and dynamic changes in them are known to play a major role in the hospital transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, 1,499 HCWs in Chinese hospitals completed an online survey about their knowledge on SARS-CoV-2 transmission and their personal protective behaviors before and after coronavirus disease 2019 (COVID-19) vaccination. Of all the respondents, 89% were vaccinated at the time of the survey and 96% believed that the vaccine was effective or highly effective. Further, 88% of the vaccinated HCWs expressed that they would get revaccinated if the vaccination failed. Compared with HCWs with a lower education level, those with a higher education level had less fear of being infected with SARS-CoV-2 and reported a lower negative impact of the pandemic on how they treated patients. Physicians and nurses were willing to believe that short-range airborne and long-range fomite are possible transmission routes. HCWs with a higher education level had a better knowledge of COVID-19 but worse personal protective behaviors. The fact that HCWs with a longer work experience had worse personal protective behaviors showed that HCWs gradually relax their personal protective behaviors over time. Moreover, vaccination reduced the negative effects of the COVID-19 pandemic on how the HCWs treated patients. Importantly, the survey revealed that after vaccination, HCWs in China did not relax their personal protective behaviors, and it may bring a low potential risk for following waves of variant virus (e.g., delta).

7.
Micromachines (Basel) ; 12(12)2021 Dec 19.
Article in English | MEDLINE | ID: covidwho-1580576

ABSTRACT

A two-stage isothermal amplification method, which consists of a first-stage basic recombinase polymerase amplification (RPA) and a second-stage fluorescence loop-mediated isothermal amplification (LAMP), as well as a microfluidic-chip-based portable system, were developed in this study; these enabled parallel detection of multiplex targets in real time in around one hour, with high sensitivity and specificity, without cross-contamination. The consumption of the sample and the reagent was 2.1 µL and 10.6 µL per reaction for RPA and LAMP, respectively. The lowest detection limit (LOD) was about 10 copies. The clinical amplification of about 40 nasopharyngeal swab samples, containing 17 SARS-CoV-2 (severe acute respiratory syndrome coronavirus) and 23 measles viruses (MV), were parallel tested by using the microfluidic chip. Both clinical specificity and sensitivity were 100% for MV, and the clinical specificity and sensitivity were 94.12% and 95.83% for SARS-CoV-2, respectively. This two-stage isothermal amplification method based on the microfluidic chip format offers a convenient, clinically parallel molecular diagnostic method, which can identify different nucleic acid samples simultaneously and in a timely manner, and with a low cost of the reaction reagent. It is especially suitable for resource-limited areas and point-of-care testing (POCT).

8.
Remote Sensing of Environment ; : 112775, 2021.
Article in English | ScienceDirect | ID: covidwho-1510274

ABSTRACT

Ozone (O3) is an important trace and greenhouse gas in the atmosphere, posing a threat to the ecological environment and human health at the ground level. Large-scale and long-term studies of O3 pollution in China are few due to highly limited direct ground and satellite measurements. This study offers a new perspective to estimate ground-level O3 from solar radiation intensity and surface temperature by employing an extended ensemble learning of the space-time extremely randomized trees (STET) model, together with ground-based observations, remote sensing products, atmospheric reanalysis, and an emission inventory. A full-coverage (100%), high-resolution (10 km) and high-quality daily maximum 8-h average (MDA8) ground-level O3 dataset covering China (called ChinaHighO3) from 2013 to 2020 was generated. Our MDA8 O3 estimates (predictions) are reliable, with an average out-of-sample (out-of-station) coefficient of determination of 0.87 (0.80) and root-mean-square error of 17.10 (21.10) μg/m3 in China. The unique advantage of the full coverage of our dataset allowed us to accurately capture a short-term severe O3 pollution exposure event that took place from 23 April to 8 May in 2020. Also, a rapid increase and recovery of O3 concentrations associated with variations in anthropogenic emissions were seen during and after the COVID-19 lockdown, respectively. Trends in O3 concentration showed an average growth rate of 2.49 μg/m3/yr (p < 0.001) from 2013 to 2020, along with the continuous expansion of polluted areas exceeding the daily O3 standard (i.e., MDA8 O3 = 160 μg/m3). Summertime O3 concentrations and the probability of occurrence of daily O3 pollution have significantly increased since 2015, especially in the North China Plain and the main air pollution transmission belt (i.e., the “2 + 26” cities). However, a decline in both was seen in 2020, mainly due to the coordinated control of air pollution and ongoing COVID-19 effects. This carefully vetted and smoothed dataset is valuable for studies on air pollution and environmental health in China.

9.
Ann Transl Med ; 9(10): 883, 2021 May.
Article in English | MEDLINE | ID: covidwho-1257380

ABSTRACT

BACKGROUND: Cardiovascular involvement manifesting as arrhythmias has been confirmed in patients with coronavirus disease 2019 (COVID-19), so we aimed to explore the association between primary tachyarrhythmia and death in critically ill patients with COVID-19 in this retrospective study. METHODS: A total of 79 critically ill patients with COVID-19 were included. Demographic characteristics, clinical data (past history, vital signs, therapeutic management, and outcomes), and results of laboratory findings and cardiac investigations were collected. All statistical analyses were performed using SPSS 23.0 software (IBM, Armonk, NY, USA). RESULTS: The median age was 65±12 years, and 53 patients (67%) were male. A total of 57 (72%) patients died, and compared with survivors, these patients were older and had significantly higher Acute Physiology and Chronic Health Evaluation (APACHE) II score, Sequential Organ Failure Assessment (SOFA) score and fewer lymphocytes as well as higher heart rate (P<0.05). Autopsy findings did not suggest severe myocarditis. A total of 19 (24%) patients had tachyarrhythmias, including 10 (13%) with atrial fibrillation (AF) and 9 (11%) with ventricular tachycardia or fibrillation. The incidence of tachyarrhythmias in non-survivor was much higher than in survivors (P=0.04). In a Cox regression model, older patients with ventricular tachyarrhythmias (VTAs) age were at a higher risk of death, with hazard ratio (HR) of 3.302 [95% confidence interval (CI), 1.524-7.154, P=0.002] and 1.045 (95% CI, 1.020-1.071, P=0.000), respectively. The use of beta-blockers [HR, 0.219 (95% CI, 0.066-0.722); P=0.013] was associated with a lower risk of death. CONCLUSIONS: Critically ill patients with COVID-19 had a poor prognosis. VTA and older age were independent prognostic factors of death. Beta-blockers might be an effective therapy to improve survival.

10.
SciFinder; 2020.
Preprint | SciFinder | ID: ppcovidwho-4704

ABSTRACT

Our objective was to isolate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from nasal/throat swabs from coronavirus disease 19 (COVID-19) patients. Three nasal/throat swab samples from COVID-19 patients in Shanghai were treated with TPCK trypsin and inoculated Vero E6 cells in 96-well plates. When most of the cells showed obvious cytopathic effect, the supernatants of cell culture were collected and used to detect the viral nucleic acid by fluorescent quant. polymerase chain reaction (PCR) and amplify the gene fragment of the virus receptor binding domain (RBD) using reverse transcription-PCR. The replicated virus was inoculated into Vero E6 cells seeded in 96-well plates, the cytopathic effect was recorded by photograph and the viral proteins were detected by immunofluorescence method. The Vero E6 cells inoculated with two of three nasal/pharyngeal swab samples showed obvious cytopathic effect and newly synthesized viral nucleic acid was detected in the supernatants of cell culture. The amplified receptor binding domain (RBD) sequence was completely consistent with the corresponding fragment of SARS-CoV-2 isolated earlier. Virus-infected Vero E6 cells showed rapid cytopathy and can react with the monoclonal antibody against nucleocapsid protein (N protein) and spike protein (S protein) of SARS-CoV-2, and convalescence sera of COVID-19 patients. Two SARS-CoV-2 strains were isolated from nasal/throat swab samples of COVID-19 patients in Shanghai, providing the basis for the mechanism research on the infection and pathogenesis of SARS-CoV-2 as well as the development of drugs and vaccines against SARS-CoV-2.

11.
Respir Med ; 175: 106218, 2020 12.
Article in English | MEDLINE | ID: covidwho-912594

ABSTRACT

OBJECTIVE: There were COVID-19 patients with SARS-COV-2 nucleic acid long-term positive. This article aims to understand the relevant factors that affect SARS-COV-2 clearance time. METHODS: The clinical data of 115 COVID-19 patients with SARS-COV-2 nucleic acid positive time exceeding 14 days were collected retrospectively, and the relationship between clinical characteristics, chest CT scans, blood cells, biochemical indicators, and the time of viral nucleic acid turning negative were analyzed. RESULTS: The time from symptom onsets to nucleic acid turning negative was (32.5 ± 8.7) days in this group of patients. The time of nucleic acid turning negative: no fever group was longer than fever group, diabetes group was longer than no comorbidity group, elevated levels of ALT (alanine aminotransferase), or GLU (fasting blood glucose) group, decreased levels of ALB (albumin) group or HDLC (high-density lipoprotein cholesterol) group was longer than it's normal group separately (P < 0.05). Cox multivariate regression analysis showed that ALT [odds ratio (OR): 2.164 (95% CI: 1.276-3.670), P = 0.004], GLU [OR: 2.064 (95% CI: 1.195-3.566), P = 0.009] and HDLC [OR: 0.527 (95% CI: 0.307-0.907), P = 0.021] were independent factors which affected the time of nucleic acid turning negative. CONCLUSIONS: ALT, GLU and HDLC were independent factors that influenced the time of nucleic acid turning negative. Although diabetes or hyperglycemia is a known risk factor, HDLC is the first to be identified, clinicians should be aware of dyslipidemia in covid-19 patients.


Subject(s)
COVID-19/blood , COVID-19/diagnosis , Cholesterol, HDL/blood , SARS-CoV-2/genetics , Aged , Alanine Transaminase/analysis , Blood Glucose/analysis , COVID-19/epidemiology , COVID-19/virology , Case-Control Studies , China/epidemiology , Comorbidity , Fasting/blood , Female , Humans , Hypoalbuminemia/blood , Male , Middle Aged , RNA, Viral/isolation & purification , Retrospective Studies , Risk Factors , SARS-CoV-2/growth & development , Severity of Illness Index , Time Factors , Virus Shedding/genetics
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