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1.
Heliyon ; 9(3): e14453, 2023 Mar.
Article in English | MEDLINE | ID: covidwho-2248738

ABSTRACT

COVID-19 is a severe acute respiratory syndrome that has caused a major ongoing pandemic worldwide. Imaging systems such as conventional chest X-ray (CXR) and computed tomography (CT) were proven essential for patients due to the lack of information about the complications that could result from this disease. In this study, the aim was to develop and evaluate a method for automatic diagnosis of COVID-19 using binary segmentation of chest X-ray images. The study used frontal chest X-ray images of 27 infected and 19 uninfected individuals from Kaggle COVID-19 Radiography Database, and applied binary segmentation and quartering in MATLAB to analyze the images. The binary images of the lung were split into four quarters; Q1 = right upper quarter, Q2 = left upper quarter, Q3 = right lower, and Q4 = left lower. The results showed that COVID-19 patients had a higher percentage of attenuation in the lower lobes of the lungs (p-value < 0.00001) compared to healthy individuals, which is likely due to ground-glass opacities and consolidations caused by the infection. The ratios of white pixels in the four quarters of the X-ray images were calculated, and it was found that the left lower quarter had the highest number of white pixels but without a statistical significance compared to right lower quarter (p-value = 0.102792). This supports the theory that COVID-19 primarily affects the lower and lateral fields of the lungs, and suggests that the virus is accumulated mostly in the lower left quarter of the lungs. Overall, this study contributes to the understanding of the impact of COVID-19 on the respiratory system and can help in the development of accurate diagnostic methods.

2.
Virology ; 573: 84-95, 2022 08.
Article in English | MEDLINE | ID: covidwho-1895491

ABSTRACT

The world health organization has announced that SARS-CoV-2 Omicron variant (B.1.1.529), including the three versions; 21K (BA.1), 21L (BA.2) and 21M (BA.3) as a variant of concern (VOC) on November 2022. In this study, we used the specialized computational platforms to predict the stability and flexibility of the spike protein of Omicron. The aim of this study was to investigate the expected effect of Omicron spike mutations on its physiochemical properties. Findings of this study revealed 16 stabilizing mutations that might explain a newly gained environmental stability. We expect the new mutations to play a crucial role in changing the physiochemical properties of epitopes of the spike protein. The notable finding of SuerPose work was the potential linear B-cells epitope G252 → S255 that has been changed in the spike protein of the Omicron 21L to a helix structure which might confer an escape from human monoclonal antibodies.


Subject(s)
COVID-19 , Epitopes, B-Lymphocyte , Amino Acid Sequence , Antibodies, Viral , Epitopes, B-Lymphocyte/genetics , Humans , Membrane Glycoproteins/genetics , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Viral Envelope Proteins/genetics
3.
Biochimie ; 191: 91-103, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1401244

ABSTRACT

The spike protein of SARS-CoV-2 plays a crucial role in binding with the human cell surface, which causes its pathogenicity. This study aimed to predict molecular dynamics change of emerging variants in the spike protein. In this study, several structural biology tools, such as SuperPose, were utilized to study spike protein structures' thermodynamics, superimposition, and the spike protein disulphide bonds. This questions the current vaccines efficacies that were based on the Nextstrain clade 19A that first documented in Wuhan and lacks any variants. The prediction results of this study have exhibited the stabilizing role of the globally dominant variant, the D614G; clade 20A, and other variants in addition to their role in increasing the flexibility of the spike protein of the virus. The SuperPose findings have revealed a conformational change impact of D614G in allowing the polybasic Furin cleavage site (682RRAR↓S686) to be closer to the receptor-binding domain (RBD) and hence more exposed to cleavage. The presence of D614G in any clade or subclade, such as 20A, B.1.1.7 (20I/501Y.V1) or Alpha, B.1.351 (20H/501Y.V2) or Beta, P.1 (20J/501Y.V3) or Gamma, B.1.617.2 (21A/478K.V1) or Delta, has increased its stability and flexibility and unified the superimposition among all clades which might impact the virus ability to escape the antibodies neutralization by changing the antigenicity drift of the protein three-dimensional (3D) structure from the wild type clade 19A; this is in agreement with previous study. In conclusion, a new design for the current vaccines to include at least the mutation D614G is immediately needed.


Subject(s)
COVID-19/prevention & control , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Antibodies, Neutralizing , COVID-19 Vaccines , Disulfides/chemistry , Molecular Dynamics Simulation , Mutation , Protein Binding , Protein Domains , Thermodynamics
4.
Patient Prefer Adherence ; 15: 677-690, 2021.
Article in English | MEDLINE | ID: covidwho-1186656

ABSTRACT

PURPOSE: The COVID-19 pandemic has affected physician-patient communication (PPC) in multiple ways. This study aims to report on the impact of physician-patient communication (PPC) skills on COVID-19 patients' psychology in Jordan. SAMPLE AND METHODS: In this study, two questionnaires were designed. The first questionnaire targeted physicians, with 72 responses, and the second questionnaire targeted patients, with 248 responses. Both questionnaires contained common sections covering nine aspects of communication such as empathy, honesty, optimism, simple and deliberateness. RESULTS: This study found that the psychological effect of physicians' positive communication skills on COVID-19 patients is significant. There were almost statistical agreement between physicians' and patients' questionnaire responses that the physicians' communication skills have positively affected the patients' psychological status; all patients' responses confirmed this finding. CONCLUSION: Based on this study's findings, appropriate and continuous training will advance physicians' communication skills in the form of exercises that could be as simple as class- or lecture-based activities, or using technology-based learning. Using a protocol or handbook to guide such communication is another essential strategy to enhance physician-patient communication (PPC). The study recommends that physicians must be aware that PPC skills required may vary depending on whether they are dealing with a pandemic or non-pandemic situation. Generally, appropriate or positive communication skills are considered one of the main factors effecting patients' psychological responses to their diagnosis.

6.
Biochem Biophys Rep ; 25: 100896, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1002348

ABSTRACT

BACKGROUND: Spike protein is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the entry of the virus via the transmembrane receptors of the human respiratory cells causing COVID-19 disease. AIM: Here, we aimed to predict the three-dimensional monomer structure of spike protein of SARS-CoV-2 from 20 Jordanian nasopharyngeal samples and to determine the percentage of single amino acid variants (SAV) in the spike protein of SARS-CoV-2. METHODS: The output of the Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) found four single amino acid variants in the spike gene. RESULTS: The first variant represented by 5% of samples that showed tyrosine deletion at Y144 located in the N terminal domain. The second and the dominant variant, represented by 62%, showed aspartate a coil amino acid substitution to glycine an extracellular amino acid at D614G located in the spike recognition binding site. The third variant, represented by 5%, showed aspartate substitution to tyrosine at D1139Y, and the fourth variant, represented by 5% glycine substitution to serine at G1167S. CONCLUSION: Our results have shown low mutational sensitivity in all variants except to D614G the one with the most likely neutral mutational sensitivity that all variants might not explicitly affect the function of spike glycoprotein. However, D614G might change the viral conformational plasticity and hence a potential viral fitness gain but one must be cautious about drawing any concrete conclusions about the severity of symptoms and viral transmission from genomic data only. GENERAL SIGNIFICANCE: Studying mutations such as D614G in deep is essential to control the pandemic in terms of immune systems, antibodies, or even vaccines.

7.
preprints.org; 2020.
Preprint in English | PREPRINT-PREPRINTS.ORG | ID: ppzbmed-10.20944.preprints202006.0184.v1

ABSTRACT

Spike protein is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the entry of the virus via the transmembrane receptors of the human endothelial cells of the respiratoty system for the virus to be engulfed causing COVID-19 disease after priming by type II transmembrane protease TMPRSS2 and then binding with the angiotensin-converting enzyme 2 (ACE2). Therefore, mutations and amino acid variants analysis are essential in understanding the mechanism of binding of spike protein with its receptor to have an insights on possibilities to design a peptide or nucleotide-based vaccine for COVID-19. Here, we employed Iterative Threading Assembly Refinement (I-TASSER) and Multiple Alignment using Fast Fourier Transform (MAFFT) to predict the three-dimensional monomer structure of spike protein of SARS-CoV-2 and to analyze the amino acid variants for protein sequences from GISAID database for samples collected from Jordan in a try to find an explanation for the low confirmed number of COVID-19 in Jordan. Our Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) findings showed four single amino acid variants (SAV) found in 20 samples of SARS-CoV-2. What is equal to 5% of samples showed tyrosine deletion at Y144 located in the SARS-CoV-like_Spike_S1_NTD (N terminal domain), 62% showed aspartate substitution to glycine at D614G located in the SARS-CoV-2_Spike_S1_RBD (spike recognition binding site), 5% showed aspartate substitution to tyrosine at D1139Y and 5% showed glycine substitution to serine at G1167S both located in the Corona_S2 domain. The findings have shown lower mutational sensitivity in all variants that might not affect the function of spike glycoprotein except for D614G, which has the highest mutational sensitivity score (5 out of 9) indicating a higher likelihood to affect the function of the spike protein. This might suggest, in general, a reduced transmitability of SARS-CoV-2 in Jordan.


Subject(s)
Amino Acid Metabolism, Inborn Errors , COVID-19 , Coronavirus Infections
8.
researchsquare; 2020.
Preprint in English | PREPRINT-RESEARCHSQUARE | ID: ppzbmed-10.21203.rs.3.rs-33156.v1

ABSTRACT

Spike protein (approx. 180 kDa) is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the interaction of the virus with human endothelial cell receptors on the cell membrane to be engulfed causing COVID-19 disease after binding with the angiotensin-converting enzyme 2 (ACE2) with an evident activation by type II transmembrane protease TMPRSS2 . Therefore, mutations and amino acid variants analysis are essential in characterizing the mechanism of binding of spike protein with its receptor, which totally gives insights on possibilities to design a peptide or nucleotide-based vaccine for COVID-19. Here, we employed Iterative Threading Assembly Refinement (I-TASSER) and Multiple Alignment using Fast Fourier Transform (MAFFT) to predict the three-dimensional structure and to analyze the amino acid variants for spike protein sequences of SARS-CoV-2 from GISAID database of samples collected from Jordan to try to find a justification for low number of confirmed COVID-19 in Jordan, Middle East. Our findings showed the molecules structurally close to the spike glycoprotein from the Enzyme Commission (EC) numbers and active sites included Isoleucyl-tRNA synthetase, Crystal structure of the tricorn protease (hydrolase); Crystal structure of the T. Thermophilus RNA polymerase holoenzyme (transferase); Crystal structure of the complex between pyruvate-ferredoxin oxidoreductase from Desulfovibrio africanus and pyruvate (oxidoreductase); and Reovirus core (virus). Our MAFFT findings showed that Four Amino Acid Variants (SAV) founded in 20 samples of SARS-CoV-2 were not conserved residues in spike glycoprotein. What is equal to 5% of samples showed tyrosine (polar) deletion at Y144 , 62% of samples showed aspartate (polar, acidic) substitution to glycine (nonpolar) at D614G, 5% of samples showed aspartate (polar, acidic) substitution to tyrosine (polar) at D1139Y and 5% of samples showed glycine (nonpolar) substitution to serine (polar) at G1167S respectively. By using Phyre2, our findings have shown lower sensitive mutational that cannot affect the pocket region or alpha and beta-sheet in all mutations except for D614G, which has the highest mutational sensitivity score (5 out of 9) indicating a bigger effect on the function of spike protein. This might suggest, in general, a reduced transmitability of SARS-CoV-2 in Jordan, Middle East. As the crystal structure of spike protein is not revealed yet, it was not possible to compare the predicted modes versus each other.


Subject(s)
COVID-19 , Coronavirus Infections
9.
researchsquare; 2020.
Preprint in English | PREPRINT-RESEARCHSQUARE | ID: ppzbmed-10.21203.rs.3.rs-28866.v1

ABSTRACT

Initial epidemiological studies inform the central COVID-19 disease prophet. Some papers have been studying miRNA and viral RNA interaction target predictions over the past few years. In this work, via the miRDB database, we determined the target scores of predicted miRNA to bind with the ss-RNA of SARS-CoV-2 in general and spike gene in specific. Our predicted miRNA targets of the ss-RNA of SARS-CoV-2 might destabilize and hence inhibit the ss-RNA translation of SARS-CoV-2 and prevent viral replication that has been established by more than 80% of asymptomatic infected cases in Jordan due to host miRNA interactions. In respiratory epithelial cells, the high scoring miRNAs prediction covers the RNA from 5' to 3' that explain successful antiviral defenses against ss-RNA of SARS-CoV-2 and lead to new nucleotide deletion mechanisms. The exciting finding here that the substitution 1841A>G at the viral genomic RNA level or the D614G at spike protein level showed a change in the predicted miRNA sequence and an increase in the target score (from 91 to 92) (hsa-miR-4793-5p to hsa-miR-3620-3p).


Subject(s)
COVID-19
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