IntroductionIndonesia kick-started the big project of COVID-19 vaccination program in January 2021 by employed vaccine to the president of Indonesia. The outbreak and rapid transmission of COVID-19 have endangered the global health and economy. This study aimed to investigate the full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates as 12 January 2021.MethodsAll data of isolates was extracted from the Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV database. CoVsurver was employed to investigate the full-length genome mutation analysis of all isolates. Furthermore, this study also focused on the unlocking of mutation in Indonesian SARS-CoV-2 isolates S protein. WIV04 isolate that was originated from Wuhan, China was used as a virus reference according to CoVsurver default. All data was visualized using GraphPad Prism software, PyMOL, and BioRender.ResultsThis study result showed that a full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates was successfully discovered. Every single mutation in S protein was described and then visualised by employing BioRender. Furthermore, it also found that D614G mutation appeared in 103 Indonesian SARS-CoV-2 isolates.ConclusionTo sum up, this study helps to observe the spread of the COVID-19 transmission. However, it would like to propose that the epidemiological surveillance and genomics studies might be improved on COVID-19 pandemic in Indonesia.
Background Indonesia has started the big project of COVID-19 vaccination program since 13 January 2021 by employing the first shot of vaccine to the President of Indonesia as the outbreak and rapid transmission of COVID-19 have endangered not only Indonesian but the global health and economy. This study aimed to investigate the full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates as of 12 January 2021. Results All data of the isolates were extracted from the Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV database. CoVsurver platform was employed to investigate the full-length genome mutation analysis of all isolates. This study also focused on the phylogeny analysis in unlocking the mutation of S protein in Indonesian SARS-CoV-2 isolates. WIV04 isolate that was originated from Wuhan, China was used as the virus reference according to the CoVsurver default. The result showed that a full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates was successfully generated. Every single mutation in S protein was described and then visualized by utilizing BioRender platform. Furthermore, it also found that D614G mutation appeared in 103 Indonesian SARS-CoV-2 isolates. Conclusions To sum up, this study helped to observe the spread of COVID-19 transmission. However, it also proposed that the epidemiological surveillance and genomics studies might be improved on COVID-19 pandemic in Indonesia.
Coronavirus disease (COVID-19) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was first reported in the city of Wuhan, China at the end of December 2019. In the case of SARS-CoV-2, antibody-mediated immunity and T cells are the most effective protection. This study aimed to analyze IFN-γ profile in people who were vaccinated and unvaccinated against COVID-19. This research was conducted at the Molecular Laboratory of the Professor Nidom Foundation (LM-PNF), Surabaya, Indonesia from February 2021 to March 2022 using 100 blood samples with details of 50 samples from people who had been vaccinated against COVID-19 and 50 samples from people who had unvaccinated against COVID-19. We divided into four: vaccination only, vaccination and had infected of COVID-19 or survivors, unvaccination only, and unvaccination but survivors. Furthermore, we used the ELISpot method to see the IFN-γ profile. The data analysed by using ANOVA. The results of this study showed that IFN-γ profile vary widely with the highest IFN-γ obtained in samples of people who are vaccinated and had infected of COVID-19 compared to other groups. In summary, we conclude that the cellular immune response (IFN-γ) profile in people who vaccinated and had infected of COVID-19 was better than unvaccinated.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the resulting coronavirus disease 2019 (COVID-19) have afflicted millions of people in a worldwide pandemic. Several vaccines have been developed to prevent infection and illness. The success of preventing and controlling the COVID-19 by using an effective and efficient vaccine. This study aimed to find out the profile of interferon-gamma (IFN-γ) after COVID-19 vaccination. This study conducted at Animal Laboratory Professor Nidom Foundation (ABSL-3) from December 2021 to February 2022. The present study is an experimental study with a post test only control group design using 90 mice (Mus musculus L.). The test group consisted of mice injected subcutan with 0.1 mL PBS (P1), 0.1 mL adjuvant 1 (P2), 0.1 mL adjuvant 2 (P3), 0.1 mL VLPs SARS-CoV-2 10 μg (P4), 0.1 mL VLPs SARS-CoV-2 dose 50 μg (P5), 0.1 mL VLPs SARS-CoV-2 10 μg + adjuvant 1 (P6), 0.1 mL VLPs SARS-CoV-2 10 μg + adjuvant 2 (P7), 0.1 mL VLPs SARS-CoV-2 50 μg + adjuvant 1 (P8), and 0.1 mL VLPs SARS-CoV-2 50 μg + adjuvant 2 (P9). The data analysed by using ANOVA.
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.
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