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1.
Brief Bioinform ; 2021 Sep 22.
Article in English | MEDLINE | ID: covidwho-1434365

ABSTRACT

MOTIVATION: The Estimation of Model Accuracy problem is a cornerstone problem in the field of Bioinformatics. As of CASP14, there are 79 global QA methods, and a minority of 39 residue-level QA methods with very few of them working on protein complexes. Here, we introduce ZoomQA, a novel, single-model method for assessing the accuracy of a tertiary protein structure/complex prediction at residue level, which have many applications such as drug discovery. ZoomQA differs from others by considering the change in chemical and physical features of a fragment structure (a portion of a protein within a radius $r$ of the target amino acid) as the radius of contact increases. Fourteen physical and chemical properties of amino acids are used to build a comprehensive representation of every residue within a protein and grade their placement within the protein as a whole. Moreover, we have shown the potential of ZoomQA to identify problematic regions of the SARS-CoV-2 protein complex. RESULTS: We benchmark ZoomQA on CASP14, and it outperforms other state-of-the-art local QA methods and rivals state of the art QA methods in global prediction metrics. Our experiment shows the efficacy of these new features and shows that our method is able to match the performance of other state-of-the-art methods without the use of homology searching against databases or PSSM matrices. AVAILABILITY: http://zoomQA.renzhitech.com.

2.
Brief Bioinform ; 22(6)2021 11 05.
Article in English | MEDLINE | ID: covidwho-1364739

ABSTRACT

The global pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, has led to a dramatic loss of human life worldwide. Despite many efforts, the development of effective drugs and vaccines for this novel virus will take considerable time. Artificial intelligence (AI) and machine learning (ML) offer promising solutions that could accelerate the discovery and optimization of new antivirals. Motivated by this, in this paper, we present an extensive survey on the application of AI and ML for combating COVID-19 based on the rapidly emerging literature. Particularly, we point out the challenges and future directions associated with state-of-the-art solutions to effectively control the COVID-19 pandemic. We hope that this review provides researchers with new insights into the ways AI and ML fight and have fought the COVID-19 outbreak.


Subject(s)
COVID-19 Vaccines/genetics , COVID-19/drug therapy , Drug Discovery , SARS-CoV-2/genetics , Artificial Intelligence , COVID-19/genetics , COVID-19/virology , COVID-19 Vaccines/chemistry , Drug Design , Humans , Machine Learning , Pandemics , SARS-CoV-2/chemistry , SARS-CoV-2/pathogenicity
3.
Nano Today ; 40: 101243, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1300951

ABSTRACT

The outbreak of SARS-coronavirus 2 (SARS-CoV2) has become a global health emergency. Although enormous efforts have been made, there is still no effective treatment against the new virus. Herein, a TiO2 supported single-atom nanozyme containing atomically dispersed Ag atoms (Ag-TiO2 SAN) is designed to serve as a highly efficient antiviral nanomaterial. Compared with traditional nano-TiO2 and Ag, Ag-TiO2 SAN exhibits higher adsorption (99.65%) of SARS-CoV2 pseudovirus. This adsorption ability is due to the interaction between SAN and receptor binding domain (RBD) of spike 1 protein of SARS-CoV2. Theoretical calculation and experimental evidences indicate that the Ag atoms of SAN strongly bind to cysteine and asparagine, which are the most abundant amino acids on the surface of spike 1 RBD. After binding to the virus, the SAN/virus complex is typically phagocytosed by macrophages and colocalized with lysosomes. Interestingly, Ag-TiO2 SAN possesses high peroxidase-like activity responsible for reactive oxygen species production under acid conditions. The highly acidic microenvironment of lysosomes could favor oxygen reduction reaction process to eliminate the virus. With hACE2 transgenic mice, Ag-TiO2 SAN showed efficient anti-SARS-CoV2 pseudovirus activity. In conclusion, Ag-TiO2 SAN is a promising nanomaterial to achieve effective antiviral effects for SARS-CoV2.

4.
J Med Virol ; 93(4): 2365-2373, 2021 04.
Article in English | MEDLINE | ID: covidwho-1217386

ABSTRACT

Coronavirus disease 2019 (COVID-19) is a newly emerging infectious disease. Our understanding of the clinical characteristics of liver damage and the relationship with disease severity in COVID-19 is still limited. To investigate the serum hepatic enzyme activities in different phenotypes of COVID-19 patients, evaluate their relationship with the illness severity and analyze the correlation of glycyrrhizin treatment and abnormal liver enzyme activities, one hundred and forty-seven patients with COVID-19 were enrolled in a retrospective study that investigated hepatic dysfunction. Liver alanine aminotransferase (ALT), aspartate aminotransferase (AST), lactic dehydrogenase (LDH), Y-glutamyl transferase (GGT), superoxide dismutase (SOD), and alkaline phosphatase (ALP) were analyzed in these patients. Patients with diammonium glycyrrhizinate (DG) treatment were further investigated. Of the 147 patients, 56 (38.1%) had abnormal ALT activity and 80 (54.4%) had abnormal AST activity. The peak of abnormal hepatic enzyme activities occurred at 3 to 6 days after on admission. Serum AST and LDH levels were elevated, while the SOD level was decreased in severe and critical patients, compared with mild cases. DG treatment may alleviate the abnormal liver enzyme activities in non-critical COVID-19 patients. Abnormal liver functions may be observed in patients with COVID-19, and were associated with SARS-CoV-2-induced acute liver damage. Glycyrrhizin treatment may be an effective therapeutic approach for the outcome of abnormal hepatic enzyme activities in severe COVID-19 cases. Serum hepatic enzyme tests may reflect the illness severity and should be monitored.


Subject(s)
COVID-19/enzymology , Liver/enzymology , Adult , Aged , Aged, 80 and over , Alanine Transaminase/blood , Alkaline Phosphatase/blood , Aspartate Aminotransferases/blood , COVID-19/blood , COVID-19/metabolism , Female , Humans , Liver/metabolism , Liver Function Tests , Male , Middle Aged , Phenotype , Retrospective Studies , SARS-CoV-2 , Severity of Illness Index , Superoxide Dismutase/blood , Young Adult
5.
Clin Chim Acta ; 517: 48-53, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1101132

ABSTRACT

OBJECTIVE: Coronavirus Disease 2019 (COVID-19) caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still spreading worldwide, which may progress to pulmonary fibrosis (PF), leading to the worsen outcome. As the markers of lung injury, the correlation of Krebs von den Lungen-6 (KL-6) and fibronectin (Fn) with pulmonary fibrosis in COVID-19 was still unclear. METHODS: 113 patients diagnosed as COVID-19 were enrolled in this retrospective study, and divided into three categories as mild, moderate and severe cases. The concentrations of serum KL-6 and Fn at hospital admission were tested using the method of latex agglutination assay and immunoturbidimetic assay, respectively. RESULTS: Compared with that in the non-severe COVID-19 cases and normal control subjects, serum KL-6 concentration on admission was significantly higher in the severe group, which was positively correlated with C-reactive protein, and negatively correlated with lymphocytes count. Whereas, no obvious elevation in serum Fn concentration was investigated in COVID-19 patients with the different phenotypes. The severe cases displayed the higher incident rate of pulmonary fibrosis at hospital discharge. Compared with non-PF patients, the COVID-19 cases with PF had the higher serum KL-6 values. CONCLUSION: Serum KL-6 concentration was significantly elevated in severe COVID-19 patients, which may be useful for evaluating the disease severity. For early prevention of the development of pulmonary fibrosis, high concentrations of serum KL-6 in the early stage of COVID-19 should be paid close attention.


Subject(s)
COVID-19 , Fibronectins/blood , Mucin-1/blood , Pulmonary Fibrosis , Adolescent , Adult , Aged , Aged, 80 and over , Biomarkers , COVID-19/diagnosis , Female , Humans , Male , Middle Aged , Pulmonary Fibrosis/blood , Pulmonary Fibrosis/diagnosis , Retrospective Studies , Young Adult
7.
Medicine (Baltimore) ; 99(44): e23064, 2020 Oct 30.
Article in English | MEDLINE | ID: covidwho-990918

ABSTRACT

Coronavirus disease 2019 (COVID-19) is the most important global public health issue that we currently face. We aimed to explore the clinical features of patients with COVID-19 and compared them with those of hospitalized community-acquired pneumonia (CAP) patients caused by influenza virus during the same period.From Jan 1, to Mar 4, 2020, patients with COVID-19 or CAP caused by influenza virus who were admitted to the First Affiliated Hospital of Xiamen University were consecutively screened for enrollment.A total of 35 COVID-19 patients and 22 CAP patients caused by influenza virus were included in this study. Most of COVID-19 patients had characteristics of familial clustering (63%), however, in the other group, there was no similar finding. The percentages of patients with a high fever (the highest recorded temperature was ≥39.0°C; 11% vs 45% [COVID-19 vs CAP groups, respectively]), dyspnea (9% vs 59%), leukocytosis (3% vs 32%), elevated C-reactive protein concentrations (>10 mg/L, 48% vs 86%), elevated procalcitonin levels (>0.1 ng/ml, 15% vs 73%), PaO2/FiO2 <200 mm Hg (4% vs 22%), and infiltration on imaging (29% vs 68%) in the COVID-19 group were less than those same indices in the hospitalized CAP patients caused by influenza virus. Ground-glass opacity with reticular pattern (63%) and interlobular septal thickening (71%) in chest CT were commonly observed in the COVID-19 group.COVID-19 and CAP caused by influenza virus appear to share some similarities in clinical manifestaions but they definitely have major distinctions. Influenza infection remains a health problem even during COVID-19 pandemic.


Subject(s)
Coronavirus Infections/epidemiology , Influenza, Human/epidemiology , Pneumonia, Viral/epidemiology , Adult , Aged , Aged, 80 and over , COVID-19 , China/epidemiology , Community-Acquired Infections , Coronavirus Infections/blood , Coronavirus Infections/diagnostic imaging , Coronavirus Infections/drug therapy , Coronavirus Infections/therapy , Cross-Sectional Studies , Female , Humans , Influenza, Human/blood , Influenza, Human/diagnostic imaging , Influenza, Human/therapy , Male , Middle Aged , Pandemics , Pneumonia, Viral/blood , Pneumonia, Viral/diagnostic imaging , Pneumonia, Viral/therapy , Radiography, Thoracic , Retrospective Studies
8.
J Biophotonics ; 14(3): e202000338, 2021 03.
Article in English | MEDLINE | ID: covidwho-908749

ABSTRACT

The appearance of antibodies in blood is a critical signal to suggest the infection. A rapid and accurate detection method for the antibody is significant to the disease diagnosis, especially for the epidemic. To this end, a highly sensitive whispering-gallery-mode (WGM) optical testing kit is designed and fabricated for detecting the specific immunoglobulin antibodies. The key component of the kit is a silica self-assembled microsphere decorated with the nucleocapsid proteins (N-proteins) of the SARS-CoV-2 virus. After the N-protein antibody immunoglobulin G (N-IgG) and immunoglobulin M (N-IgM) solutions being injected into the kit, the WGM red-shifts due to the antigen-antibody reaction. The wavelength displacement rates are proportional to the concentrations of these two antibodies from 1 to 100 µg/mL. A good specificity of the kit is demonstrated by the nonspecific human immunoglobulin G (H-IgG) and immunoglobulin M (H-IgM).


Subject(s)
Antibodies, Viral/immunology , COVID-19 Serological Testing , COVID-19/diagnosis , Microspheres , Silicon Dioxide/chemistry , Antigens/immunology , Biosensing Techniques , COVID-19/immunology , Coronavirus Nucleocapsid Proteins/immunology , Epidemics , Humans , Immunoglobulin G/immunology , Immunoglobulin M/immunology , Optics and Photonics , Phosphoproteins/immunology , Polymethyl Methacrylate/chemistry , SARS-CoV-2 , Silanes
9.
Eur Respir J ; 56(2)2020 08.
Article in English | MEDLINE | ID: covidwho-744959

ABSTRACT

BACKGROUND: Timely diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a prerequisite for treatment and prevention. The serology characteristics and complement diagnosis value of the antibody test to RNA test need to be demonstrated. METHOD: Serial sera of 80 patients with PCR-confirmed coronavirus disease 2019 (COVID-19) were collected at the First Affiliated Hospital of Zhejiang University, Hangzhou, China. Total antibody (Ab), IgM and IgG antibodies against SARS-CoV-2 were detected, and the antibody dynamics during the infection were described. RESULTS: The seroconversion rates for Ab, IgM and IgG were 98.8%, 93.8% and 93.8%, respectively. The first detectible serology marker was Ab, followed by IgM and IgG, with a median seroconversion time of 15, 18 and 20 days post exposure (d.p.e.) or 9, 10 and 12 days post onset (d.p.o.), respectively. The antibody levels increased rapidly beginning at 6 d.p.o. and were accompanied by a decline in viral load. For patients in the early stage of illness (0-7 d.p.o), Ab showed the highest sensitivity (64.1%) compared with IgM and IgG (33.3% for both; p<0.001). The sensitivities of Ab, IgM and IgG increased to 100%, 96.7% and 93.3%, respectively, 2 weeks later. When the same antibody type was detected, no significant difference was observed between enzyme-linked immunosorbent assays and other forms of immunoassays. CONCLUSIONS: A typical acute antibody response is induced during SARS-CoV-2 infection. Serology testing provides an important complement to RNA testing in the later stages of illness for pathogenic-specific diagnosis and helpful information to evaluate the adapted immunity status of patients.


Subject(s)
Betacoronavirus , Clinical Laboratory Techniques , Coronavirus Infections/blood , Coronavirus Infections/diagnosis , Pneumonia, Viral/blood , Pneumonia, Viral/diagnosis , Adult , Aged , COVID-19 , COVID-19 Testing , China , Coronavirus Infections/complications , Female , Hospitalization , Humans , Infectious Disease Incubation Period , Male , Middle Aged , Pandemics , Pneumonia, Viral/complications , SARS-CoV-2 , Sensitivity and Specificity , Seroconversion , Symptom Assessment , Time Factors , Viral Load
12.
Disaster Med Public Health Prep ; : 1-7, 2020 Aug 12.
Article in English | MEDLINE | ID: covidwho-712002

ABSTRACT

Since the outbreak of 2019 novel coronavirus (2019-nCoV) infection in Wuhan City, China, pediatric cases have gradually increased. It is very important to prevent cross-infection in pediatric fever clinics, to identify children with fever in pediatric fever clinics, and to strengthen the management of pediatric fever clinics. According to prevention and control programs, we propose the guidance on the management of pediatric fever clinics during the nCoV pneumonia epidemic period, which outlines in detail how to optimize processes, prevent cross-infection, provide health protection, and prevent disinfection of medical staff. The present consideration statement summarizes current strategies on the pre-diagnosis, triage, diagnosis, treatment, and prevention of 2019-nCoV infection, which provides practical suggestions on strengthening the management of pediatric fever clinics during the nCoV pneumonia epidemic period.

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