ABSTRACT
Global infection and mortality rates have soared to millions due to SARS-CoV-2 human-to-human transmission via droplets which then declared as pandemic. This study examined the created cold plasma equipment (CPE) effectiveness in reducing COVID-19 transmission in a confined space. CPE sucked air using a fan in a test chamber then pushed it into a cold plasma reactor. The results indicated that it was able to terminate all SARS-CoV-2 variants along with bacteria and fungi indoors by keeping it turned on for 30 min' minimum. CPE was proven as safe and effective to hinder virus transmission with the acceptable ozone emission as the side effect. © 2022 University of Kerbala.
ABSTRACT
Context: SARS-CoV-2, a member of family Coronaviridae and the causative agent of COVID-19, is a virus which is transmitted to human and other mammals. Aims: To analyze the B-cell epitope conserved region and viroinformatics-based study of the SARS-CoV-2 lineage from Indonesian B.1.1.7 isolates to invent a vaccine nominee for overcoming COVID-19. Methods: The sequences of seven Indonesian B.1.1.7 isolates, Wuhan-Hu- 1 isolate, and WIV04 isolate were extracted from the GISAID EpiCoV and GenBank, NCBI. MEGA X was employed to understand the transformations of amino acid in the S protein and to develop a molecular phylogenetic tree. The IEDB was implemented to reveal the linear B-cell epitopes. In addition, PEP-FOLD3 web server was utilized to perform peptide modeling, while docking was performed using PatchDock, FireDock, and the PyMOL software. Moreover, in silico cloning was developed by using SnapGene v.3.2.1 software. Results: In this study, the changes of amino acid in all seven Indonesian B.1.1.7 isolates were uncovered. Furthermore, various peptides based on the B-cell epitope prediction, allergenicity prediction, toxicity prediction from S protein to generate a vaccine contrary to SARS-CoV-2 were identified. Furthermore, the development of in silico cloning using pET plasmid was successfully achieved. Conclusions: This study exhibits the transformations of amino acid in Indonesian B.1.1.7 isolates, and proposes four peptides ("LTPGDSSSGWTAG", "VRQIAPGQTGKIAD", "ILPDPSKPSKRS", and "KNHTSPDVDLG") from S protein as the candidate for a peptide-based vaccine. However, further advance trials such as in vitro and in vivo testing are involved for validation.
ABSTRACT
SARS-CoV-2 firstly emerged in China and sporadically transmitted worldwide. In March 2020, WHO announced that the infection was a pandemic. The outbreak and rapid transmission of COVID-19 have endangered the global health and the economy. This crisis has called for an extensive scientific mobilization of studies on SARS-CoV-2 concerning its clinical aspects, characteristics, and its mechanism of transmission. Although many scientists have published the treatment options against COVID-19, currently, there is not any approved medications against the virus yet. COVID-19 vaccine development has started in many research centers and pharmaceutical industries following the announcement of the agent and the full genome of SARS-CoV-2 recognized. Recently, the collected data described that COVID-19 vaccine candidates grouped into the following types: protein-based, epitope, inactivated or live-attenuated virus, virus-like particle, nucleic acid-based, and viral vectors. Therefore, the present review gives a sneak peek of recent updates on COVID-19 vaccine construction worldwide and COVID-19 vaccine’s acceptance in Indonesia. © 2020 EManuscript Technologies. All rights reserved.
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Introduction: SARS-CoV-2 is a rapidly spreading virus that poses a major burden on global human health and the economy. Therefore, it is essential to develop COVID-19 vaccines. Vaccine construction might not be easy, as a consequence of mutations and antibody-dependent enhancement (ADE). Objective: We first reported the D614G mutation and ADE sequences in Indonesian SARS-CoV-2 isolates and compared these isolates to those from other Southeast Asian countries. Methods: In this study, we extracted the SARS-CoV-2 genome of 40 Indonesian isolates from the GISAID EpiCoV database and the Wuhan-Hu-1 isolate (reference sequence) from GenBank, NCBI. We used BioEdit v7.2.5 to identify the D614G mutation and ADE sequences in the spike protein. Then, we rendered the spike protein using the SWISS-MODEL web server and PyMOL v2.4. Results: We identified the D614G missense mutation in 23 Indonesian SARS-CoV-2 isolates and isolates from six other Southeast Asian countries. In addition, we identified the ADE sequence 611LYQDVNC617 in the Wuhan-Hu-1 isolate, which had changed into 611LYQGVNC617 in recent mutated isolates. Conclusion: We conclude that the D614G mutation might affect ADE activities. A rapid but cautious approach to the vaccine development and other therapies developed for COVID-19 seems needed until we have more data on the risks of the D614G mutation and ADE. However, further studies including in vitro and in vivo assessments are relevant for validation of these results.
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Introduction: SARS-CoV-2, a new member of the coronavirus family that originated from Wuhan, China, is the agent of COVID-19 pandemic and has rapidly spread globally. Objective: We characterized the spike (S) glycoprotein gene from the Indonesian SARS-CoV-2 isolates to investigate its genetic composition, predict the B cell epitopes, and construct the molecular phylogenetic among Indonesian SARS-CoV-2 isolates. Methods: We employed Wuhan-Hu-1 isolate available in GenBank, NCBI and fourteen Indonesian SARS-CoV-2 isolates acquired from the database (GISAID EpiCoV). We performed using the MEGA X for genetic and amino acid mutations and construct molecular phylogenetic tree. We used IEDB web server to predict epitopes, evaluated allergenicity by applying AllerTOP v.2.0 web server, and non-toxic antigens applying the ToxinPred web server. Results: Interestingly, we discovered that the Indonesian SARS-CoV-2 isolates genetic composition do not have significant changes compared with the reference sequence based on the S glycoprotein gene. In addition, we proposed NSASFSTFKCYGVSPTKLNDLCFTNV as a candidate for a peptide-based vaccine against COVID-19. Furthermore, we also presented the molecular phylogenetic of Indonesian SARS-CoV-2 isolates and other coronaviruses. Conclusion: In summary, this study supplied data regarding mutations in the S glycoprotein and we proposed a candidate for peptide-based vaccine against COVID-19. However, this research still requires further genetic analysis and we recommend improvement in the molecular epidemiological surveillance on COVID-19 in Indonesia. © 2020 EManuscript Technologies. All rights reserved.
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Introduction: SARS-CoV-2 has crossed the species barrier to infect human. It is a rapidly spreading virus that has poses a significant public threat and is a considerable burden on the global economy and human health. Objective: We characterized the nucleocapsid phosphoprotein (N), membrane protein (M), and envelope protein (E) genes of Indonesian isolates to investigate genetic composition, predict B-cell epitopes, and construct a molecular phylogenetic tree. Methods: In the present work, we retrieved the sequences of 16 Indonesian isolates from the GISAID EpiCoV and the Wuhan-Hu-1 isolate (reference sequence) from GenBank, NCBI. We used MEGA X to identify mutations in the three structural protein genes and to construct a molecular phylogenetic tree. The IEDB was employed to reveal the linear B-cell epitopes and other parameters. Allergenicity prediction was evaluated using AllerTOP and ToxinPred was performed to analyze non-toxic antigen prediction. Results: In this study, we report the genetic composition of three structural protein genes in Indonesian SARS-CoV-2 isolates. Furthermore, we identified the peptide RRGPEQTQGNFGDQELIRQGTDYK from nucleocapsid phosphoprotein to generate a peptide-based vaccine contrary to SARS-CoV-2. Conclusion: In summary, we propose a candidate for a peptide-based vaccine contrary to SARS-CoV-2. However, advance trials such as in vitro and in vivo testing are involved for validation. © 2020 EManuscript Technologies. All rights reserved.