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1.
American Journal of Gastroenterology ; 117(10):S1996-S1996, 2022.
Article in English | Web of Science | ID: covidwho-2307142
2.
Vacunas ; 23:S18-31, 2022.
Article in English | PubMed Central | ID: covidwho-2132623

ABSTRACT

Background: The new coronavirus is still a life-threatening menace, because of its changing nature and capacity to produce many mutations to bypass the immune system. The vaccination is the first effective weapon against COVID-19. Aim: The study's goal was to design a multi-epitope peptide vaccine (MEPV) for a mix of Omicron and Delta Coronavirus strains using immuno-chemoinformatics tools. Methods: To create the vaccine epitopes, seven proteins from the Omicron and Delta coronavirus strains were selected (ORF1a, ORF3a, surface protein, membrane protein, ORF7a, ORF8, and nucleocapsid protein). Antigenicity, toxicity, and allergenicity of the epitopes were evaluated. Results: The designed vaccine is made up of 534 amino acids that are homogeneous, antigenic, and non-toxic. Sticky restriction enzymes (XhoI and XbaI) were used to incorporate the MEPV into the pmirGLO luciferase vector. SnapGene server was used to create primers for PCR testing. Developing the MEPV is a terrific cost-effective strategy. The created MEPV's physiochemical properties have been determined to be basic, hydrophobic, and stableImmunogenicity and immune response profiles of the developed vaccine candidate were better assessed using in silico immunological simulations. Conclusions: We advocate moving the built vaccine to the biological validation step, where it may test our findings using appropriate model organisms.

3.
VacciMonitor ; 31(3):127-134, 2022.
Article in English | EMBASE | ID: covidwho-2092366

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 genetic variation must be closely monitored. Viral transmission can inevitably result from mutations in the viral genome and functional proteins that aid in the virus's adaptation to the host. This study aimed to look for mutations in the E protein and see how they affected the ligands' molecular docking. Mathematical saturation mutagenesis and other informatics techniques were used. Fourteen severe acute respiratory syndrome coronavirus 2 isolates from Iraq were selected. Doxycycline and rutin were chosen as ligands. In four strains of severe acute respiratory syndrome coronavirus 2, the N15Y mutation was detected in the envelope protein. Depending on the calculation of the amount of energy of the atoms, this mutation is critical in modifying the shape of the protein as well as increasing protein stability. In the single-chain mutation, one pocket was determined, while all pentamer chains had two pockets. The N15Y mutation altered the degree of doxycycline binding by affecting the residue of attachment of the ligands. It also altered the position of the rutin's attachment to the E protein, which has a clear impact on the virion particle. Copyright © 2022, Finlay Ediciones. All rights reserved.

4.
Medical Immunology (Russia) ; 24(3):617-628, 2022.
Article in English | EMBASE | ID: covidwho-1979757

ABSTRACT

Rapid emergence and evolution of novel SARS-CoV-2 variants has raised concerns about their potential impact on efficiency of currently available vaccines. Among the most significant target mutations in the virus are those of the spike glycoprotein. Remdesivir, which inhibits the polymerase activity of the RNA-dependent RNA polymerase RdRp, is the only medicine approved by FDA for treatment of COVID-19 (nsp12). The docking features of the flexible ligand (remdesivir) with the stiff receptors was investigated in the present study (S protein and RdRp interaction). In various studies, the spike glycoprotein and RdRp mutations were found to have a significant influence upon viral behaviour and, as a result, affect human health. The docking position of remdesivir with the S and RdRp proteins was shown to be unaffected by mutations in the missing loops. The remdesivir can only bind the B and C chains of S protein. Some mutations can be transferred between variations, without changing the type of amino acid, such as K417N, L452R, N501Y, D614G, T716I, and S982A.

5.
Cardiovascular Journal of Africa ; 33(SUPPL):61, 2021.
Article in English | EMBASE | ID: covidwho-1766887

ABSTRACT

Introduction: Studies show that children account for only 1-5% of diagnosed COVID-19 cases, they have milder disease than adults and deaths are extremely rare. The complete clinical picture of pediatric COVID-19 has not yet been fully reported or defined. Additionally, the South African pediatric population has unique clinical characteristics and risk implications and needs investigating. We aimed to characterize COVID-19 in Cape Town children. Methods: The UCT COVID-19 pediatric repository is a prospective cohort recruited via convenience sampling at 3 Western Cape Hospitals. All patients ≤ 18 years who test COVID-19 positive are eligible for inclusion in the study. Results: To date 227 participants, 56%(125/227) male with median age 2 years (IQR:0-6), have been enrolled. Only 28(12%) participants were in contact with a confirmed COVID-19 positive case, 67% of these, were first degree relatives, 28% second degree relatives and 6% health care workers. Comorbidities were present in 125(56%) participants. Of 32 recorded comorbidities, congenital heart disease (CHD), found in 7% of participants, ranked third. CHD subtypes included PDA (4), Tetralogy of Fallot (3), AVSD (2), Pulmonary atresia with VSD (2), truncus arteriosus (1), Coarctation of the Aorta (1), Congenital aortic valve stenosis (1), and ASD (1). Other cardiac comorbidities were, cardiomyopathy (2), primary pulmonary hypertension (1) and rhabdomyoma (1). On presentation 173 (76%) were symptomatic. Predominant symptoms included cough 40%, history of fever 36%, documented fever 34%, difficulty breathing 28%, and nausea or vomiting 20%. On examination, 65% had abnormal heart rates, 47% abnormal respiratory rates, 35% were in respiratory distress and 24% were hypoxic. Of the 227 patients, 169(74%) were admitted to hospital and 33 (15%) were admitted to ICU. In the ICU 79% of patients required non-invasive and 24% invasive ventilation, median length of ICU admission was 3 days (IQR:2-7.5). During admission 38(17%) patients developed COVID-19 complications: secondary infection 10%, sepsis 4%, MIS-C 2%, and myocarditis or new onset heart failure 1%) and 2(0.9%) died, including one patient with AVSD, who presented with severe pulmonary hypertension and acute heart failure post cardiac surgery. Conclusion: We present the initial findings of the UCT pediatric COVID-19 registry. We anticipate that these data will help to complete the clinical picture of COVID-19 in the South African pediatric population.

6.
1st International Conference on Intelligent Systems and Network, ICISN 2021 ; 243:674-685, 2021.
Article in English | Scopus | ID: covidwho-1296921

ABSTRACT

In December 2019 COVID-19, a viral disease originated in Wuhan (China), spread through China, and break out through the rest of the world, the disease is called coronavirus. The world health organisation (WHO) declared this disease as pandemic in March 2020. The recommended measures in almost every infected country was to enforce social distance. In 17 March 2020 Iraq declared curfew “Social distance” and provinces lockdown for the entire country as a precautious measure to control the spread of the disease. The daily reports data collected from JHU can be represented as time series, thus it can be analysed using time series analysis methods. The challenges in this pandemic include the short in data points for each vital pointer, the current continuous exponential trend in confirmed cases, and the randomness as the dominant phenomenon in observations. Those reasons made it very hard to predict or forecast long periods in the future. This paper suggests short periods for forecasting and an online updated state space model. The model records high accuracy with low error percentages comparing with other statistical models, which indicate that this rank of predictors is more suitable than other statistical models. The proposed model based on state space model, which is a technique to forecast time series with unobserved parameter, seasonal and unseasonal. The exponential behaviour of the time series assists in the good performance of the predictors. © 2021, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

7.
Mikrobiolohichnyi Zhurnal ; 83(2):82-92, 2021.
Article in English | EMBASE | ID: covidwho-1264711

ABSTRACT

SARS-CoV-2 remains life-threatening human pathogen witnessed in the present world. Purpose. The key objective of this research was to incorporate a bioinformatics technique to forecast the molecular docking of the ACE2-associated SARS-CoVs nucleocapsid protein. Methods. Different bioinformatics tools were used in this study in order to compare the chemical structures with their biological behaviour at the levels of atoms and the ligand-binding affinity. This research sought to investigate new data analysis. Results. It was computed the basic 2D structure that occurs in all models, requiring ion ligand binding sites to be predicted. The highlights of the analysis and the associated characteristics are largely responsible for nucleocapsid protein and ACE2 receptor that can be further changed for improved binding and selectivity. Conclusions. The precise functional importance of protein-protein docking cannot be established. But the detection of molecular docking can aid in self-association proteins in our summary, serving as a regulatory switch for the protein’s localization.

8.
Mikrobiolohichnyi Zhurnal ; 83(1):78-86, 2021.
Article in English | Scopus | ID: covidwho-1168247
9.
Open Access Macedonian Journal of Medical Sciences ; 8(T1):129-133, 2020.
Article in English | Scopus | ID: covidwho-914584

ABSTRACT

BACKGROUND: SARS-CoV-2 outbreaks remains a medical and economic challenge, due to the lack of a suitable drug or vaccine. The glycan in some proteins plays an important role in protein folding, sorting, transport, and oligomerization, so the hindering of N-linked glycosylation of glycoproteins will prevent assembly of the virion. Tunicamycin anticancer drug inhibits the N-linked glycan. AIM: This study aimed to find out the mechanism action of tunicamycin on the viral glycoproteins. RESULTS: The growth of the virus in the presence of tunicamycin conducted in the production of non-infectious and absence of spike protein (spikeless virions). Tunicamycin inhibits E2, S, and M glycoproteins of coronaviruses. Tunicamycin has also diminished glycosylation of PTMs such as HE, and 8ab of SARS-CoV. Finally, CONCLUSION: This study recommends using this drug to treat the SARS-CoV-2. © 2020 Ali Adel Dawood, Haitham Abdul-Malik Alnori.

10.
Vacunas ; 22(2): 114-118, 2021.
Article in English | MEDLINE | ID: covidwho-880624

ABSTRACT

Since the first period of the virus's emergence in Iraq, the government and health-related authorities have rushed to impose home quarantine and suspend work in all facilities of the country besides prescribed the sear measures for doubtful cases. From that time, the detected cases elevated with the number of mortality. Our study aims to take an overview of the disease during the past seven months, and a general review of the effects of quarantine measures that have resulted in an altitude graphic curve for both injuries and deaths. Data were analyzed using statistical software with significant values. The number of cases and mortality was elevated in a linear curve. The quarantine has been a factor for containing the virus in the early stages, but on the contrary, no impact was observed recently. The World Health Organization has warned that Iraq will face a second wave of coronavirus next fall, due to the lack of commitment of citizens to the comprehensive implementation of the ban and shortcomings rules of social spacing, proceed to hold special events, and increased activity in the markets. To see the country free from COVID-19, the responsible necessity to focus on the indigence to meet the public health requirements at a proper time.


Desde la primera aparición del virus en Irak, el gobierno y las autoridades sanitarias se apresuraron a imponer cuarentena domiciliaria y suspender el trabajo en todas las instancias del país, además de prescribir medidas de búsqueda para casos dudosos. Desde ese momento, los casos detectados se elevaron, al igual que el número de muertes. El objetivo de nuestro estudio es establecer una visión de la enfermedad durante los últimos siete meses, así como una revisión general de los efectos de las medidas sobre cuarentena, que han derivado en una curva gráfica de incremento de lesiones y muertes. Se analizaron los datos utilizando software estadístico con valores significativos. El número de casos y muertes se elevó en una curva lineal. La cuarentena ha sido un factor de contención del virus en las primeras etapas, pero, por el contrario, no se ha observado impacto alguno recientemente. La Organización Mundial de la Salud ha advertido que Irak se enfrentará a una segunda ola de coronavirus el próximo otoño, debido a la falta de compromiso de los ciudadanos con la implementación amplia de la prohibición y la carencia de normas sobre distanciamiento social, celebración de eventos especiales e incremento de actividad en los mercados. Para ver al país libre de COVID-19, existe la necesidad responsable de centrarse en la indigencia para satisfacer los requisitos sobre salud pública en el momento adecuado.

11.
Vacunas ; 22(1): 56-57, 2021.
Article in English | MEDLINE | ID: covidwho-801074
12.
New Microbes New Infect ; 35: 100673, 2020 May.
Article in English | MEDLINE | ID: covidwho-87552

ABSTRACT

Coronavirus disease 2019 SARS-CoV-2 (COVID-19) is a zoonotic virus causing a variety of severe respiratory diseases. SARS-CoV-2 is closest to SARS-CoV and MERS-CoV in structure. The high prevalence of COVID-19 is a result of a lack of symptoms at onset. Our study aimed to present an overview of the virus in terms of structure, epidemiology, symptoms, treatment and prevention. Whole genome sequences and some viral proteins were investigated to determine gaps and changes in alternation of nucleotides and amino acid sequences. We evaluate 11 complete genome sequences of different coronaviruses using BAST and MAFFT software. We also selected seven types of structural proteins. We conclude that COVID-19 might produce new mutations, specifically in glycoproteins, so caution and complete preparation by health authorities is required.

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