Immunogenicity Validation of Predicted HLA Class II-binding Peptides Derived …

SARS-CoV-2, the cause of the COVID-19 pandemic, prompted rapid vaccine development. However, emerging variants challenge antibody-mediated protection. Targeting T-cell immunity is promising due to its crucial role in eliminating infected cells and the difficulty of viral evasion via HLA diversity. Despite this potential, there is a lack of HLA studies and SARS-CoV-2 epitope mapping in the I…

Immunoinformatics Study of Potential Molecular Mimicry between Viral T-Cell E…

There have been reports regarding the autoimmunity induced by SARS-CoV-2 in COVID-19 patients, such as: GBS, SLE, multiple sclerosis, demyelinating neuropathies, and orthostatic tachycardia syndrome, narcolepsy, even vaccine-induced. However, the exact mechanism is still unclear. One of possible reason is molecular mimicry, a condition in which the T-cell epitopes come from the virus antige…

In Silico Design and ELONA Validation of an Aptamer for SARS- CoV-2 Omicron R…

COVID-19, caused by the SARS-CoV-2 virus, has resulted in a pandemic with 6.8 million confirmed cases in Indonesia as of December 2023. The high number of cases has necessitated the need for robust and specific diagnostic tools. Despite its effectiveness, the qRT-PCR suggested by the World Health Organization has a number of drawbacks, such as expensive costs, the need for trained personnel …

Lineage Tree: Visualization Platform for Exploring SARS-CoV-2 Pango Lineage N…

Public health surveillance plays a pivotal role in ending the COVID-19 emergency, especially monitoring the emergence of new lineages. A dynamic SARS-CoV-2 lineage naming system, known as the Pango nomenclature system currently being used to assist genomic epidemiology. Currently, researchers manually draw charts to visualize mutations found in major pango lineages that shape the evolutionar…

Validation Of Predicted Sars-cov-2 Nucleocapsid Protein Peptides (np104-122, …

This study investigates the potential of T-cell-mediated immunity in combating SARS-CoV-2, given the concerns about the high mutation rate in the virus's S protein and its potential impact on vaccine efficacy. The prevalent HLA class II alleles in the Indonesian population, namely HLA-DRB1*12:02, HLA-DRB1*15:02, and HLA-DRB1*07:01, play a crucial role in presenting viral peptide antigens to the…

Immunogenicity Validation Of The Predicted Hla Class Ii T-cell Epitope from S…

The emergence of SARS-CoV-2 variants is primarily attributed to mutations in the S protein, diminishing the efficacy of existing vaccines that aim to generate antibodies against this S protein. As antibodies become less efficient, T cell-mediated immune response becomes essential in eliminating the virus. Three predominant HLA Class II alleles in the Indonesian population; HLA-DRB1*12:02, HLA-D…

In Vitro Analysis Of The Effect Of Sars-cov-2 Orf9b Mutations On Type I Inter…

Persisting as a risk to public health worldwide, the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has prompted extensive global research efforts to unravel the dynamic of virus-host interplay contributing to disease severity. One of the SARS-CoV-2 accessory proteins, ORF9b, is recognized for its role in the alteration of host antiviral type I inte…

Peptidome Analysis of the SRS-CoV-2 Spike Protein Across variants

The continuing COVID-19 pandemic has brought to light how crucial it is to comprehend the SARS-CoV-2 virus and its proteins in order to develop efficient treatment and diagnostic approaches. However, there are difficulties with storage, processing, and analysis because of the enormous number of SARS-CoV-2 protein sequence data. In order to analyze SARS-CoV-2 data, this study examines the …

Prediction of T-cell Epitopes from SARS-CoV-2 and Human Common Cold Coronavir…

The COVID−19 pandemic has been going on for three years, and research on preventive and curative measures is continuously being made. Belonging to the same coronavirus family, human common cold coronaviruses (CCCs) like 229E, NL63, HKU1, and OC43 have been around for decades. However, unlike SARS−CoV−2, they do not manifest serious signs and symptoms. Reports on T−cell cross−reactivit…

Next-Generation Sequencing and Prediction of T-cell Epitopes from Structural …

The COVID-19 global pandemic caused by SARS-CoV-2 has been going on for almost two years and has negatively impacted the global population. The same as other viruses, SARS-CoV-2 is continuously mutating to adapt to the environment, and this may result in negative impacts, such as an increase in virus transmission, virulence, and even resistance to vaccines. Hence, questions regarding whether th…

Peptidome Analysis of the SARS-CoV-2 Spike Protein across Variants

The continuing COVID-19 pandemic has brought to light how crucial it is to comprehend the SARS-CoV-2 virus and its proteins in order to develop efficient treatment and diagnostic approaches. However, there are difficulties with storage, processing, and analysis because of the enormous number of SARS-CoV-2 protein sequence data. In order to analyze SARS-CoV-2 data, this study examines the …

Immunoinformatics Approach to a Multivalent and Multi-epitope Oral Vaccine De…

The currently available COVID-19 vaccine is thought to be sufficient in protecting against SARSCoV-2 infection, whilst the constant mutations of SARS-CoV-2 and the failure of the vaccine mto evoke protective mucosal immunity have remained problems. This condition has brought forward the idea of targeting nucleocapsid (N) protein as a more conserved region of SARS-CoV-2, in addition to the spike…

Immunoinformatics Pipeline for Multi-Epitope Peptide Vaccine Design Based on …

COVID-19 were identified as viral diseases which was caused by the Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2). The SARS-CoV-2 are known to be the family of coronaviridae. As we all know that patients that were infected by the COVID-19 has risen significantly since the very early outbreak that happens in the early December 2019 specifically at Wuhan, China. Researc…

A Combination Approach to Investigate Zingiber zerumbet (Bitter Ginger) Rhizo…

substantial global public health concern has been raised due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak in 2019. Flavonoids were reported to possess anti-SARS-CoV-2 properties by targeting 3-Chymotrypsin Like protease (3CLpro) which is the main enzyme involved in the life cycle of SARS-CoV-2. Zingiber zerumbet (bitter ginger) is a plant native to Indonesia …

Investigation on the potential inhibitory activity of Foeniculum vulgare Seed…

The CoronaVirus Disease 2019 (COVID-19) caused by SARS-CoV-2 continues to be a global pandemic with substantial socioeconomic damages. Exploration of bioactive compounds from herbal resources with potential anti SARS-CoV-2 effects are currently on the rise. In particular, naturally-derived flavonoids are reported for its capability to inhibit 3-chymotrypsin like-protease (3CL ), a promising…

Identification and Comparison of SARS-CoV-2 Peptides Binding to HLA-A*24:02 a…

LA-A*24:07 is unique to the Indonesian population, dominated by Sundanese and Javanese. As the Caucasian population handles the most worldwide research, a little study on the HLA-A*24:07 has been undertaken. Recently, the connection of SARS-CoV-2 peptides with HLA, notably HLAA* 24:02, has been investigated. The only distinction between HLA-A*24:02 and HLA-A*24:07 is the residue position 70…

Optimization of RT-LAMP Methods for SARS-CoV-2 Viral Load Detection: A System…

Prevention and detection of COVID-19 in most countries have been strictly constricted to detection via qRT-PCR. We need to find better and more efficient methods to detect respiratory viruses in case another outbreak like SARS-CoV-2 ever happens again. Quick identification and isolation is key to preventing the spread of respiratory viruses. The more convenient the methods, the more likely w…

Whole Genome Sequencing And T-Cell Epitope Prediction Of The Structural Acces…

SARS-CoV-2 began its outbreak in the late December of 2019 and was later declared as a global pandemic. It has led to the research of therapeutics and vaccines development for SARS-CoV-2 as a method of treatment. The target genes for the immunotherapeutic construct are usually the spike protein due to its crucial binding to the human ACE2 receptor via the RBD. Upon its entrance to the host …

Cross-Reactivity Analysis between SARS-CoV-2 T Cell Epitopes with Epitopes fr…

Nearly all countries worldwide have been affected by the enormity of COVID-19 caused by SARS-CoV-2, including Indonesia. This pandemic has a variation in symptoms and the number of deaths among Indonesian COVID-19 patients, which could be explained by the nonspecific immunity provided by the cross-reactive epitopes from LAVs (BCG, OPV, and MMR). However, there is still a lack of base eviden…

Optimization of Rapid Turnaround SARS-CoV-2 Sequencing Protocol with Multiple…

Amidst a pandemic caused by the SARS-CoV-2 virus, rapid genomic surveillance of the virus is much needed to support epidemiology monitoring of the pathogen. Oxford Nanopore Technologies (ONT) has allowed scalable and high-throughput SARS-CoV-2 sequencing. However, a considerable coverage drop in certain genome regions has been observed in experiments using the ARTIC V3 Classic Protocol (ARTIC V…

Tracing The Racing The Changes to the T-Cell Epitopes of SARS-COV-2: From Wuh…

The SARS-CoV-2 has been subjected to mutation resulting in the appearance of VOC which are Alpha, Beta, Gamma, Delta and Omicron variants. T-cell is involved in viral infection control and providing immunological memory that is important for long-term protection against the infection. Analyses of conserved epitope, nonconserved epitopes, and phylogenetic trees of T-cells epitope are conduct…

Immunoinformatics Approach for Designing SARS-CoV-2 Multi Epitope Vaccine Bas…

SARS-CoV-2 pandemic is still ongoing in Indonesia, and multiple variants are identified to emerge along the progress. Study of vaccines found out that the newer variants had mutations within the target sites of currently available vaccines, especially on the spike region of the genome, thus reducing most vaccines effectiveness. Thus as precaution for possible future mutation, a multi-epitope va…

Genome Sequencing and T-cell Epitopes Prediction of SARS-CoV-2 Non-structural…

Nowadays, the various variants of SARS-CoV-2 have been found along with the time. It has been marked down that the antigenic drift takes a part of those occurrences. In genome mapping, SARS-CoV-2 has the largest Open Reading Frame (ORF) called ORF1ab which translates 16 different Non-Structural Protein (NSP) for viral replication. This project aims to predict the conservancy of the ORF1ab d…

Designing Plasmid for Expression of SARS-COV-2 3C Like Protein

The COVID-19 pandemic began in late 2019, when a cluster of patients began to experience shortness of breath and fever. This disease became a world pandemic by March 2020. The internship project focused on designing a plasmid to express the 3CLpro protein from the virus SARS-COV-2 in order to aid in a larger project that aims to research flavonoid compounds that inhibit the function of 3CLpro. …

In silico Analysis of SARS-CoV-2 T Cell Epitope-Based Vaccine Design for Indo…

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BM 22-033

IN SILICO STUDY OF ALKALOID COMPOUNDS WITH COMPUTATIONAL APPROACH FOR SELECTI…

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virulent source of the COVID-19 disease. As a result of the rapid transmission of the viral agent and deficiency of specific drugs against the virus, a worldwide pandemic ensued with a terrifying death toll. Thus there is tremendous urgency to discover substances for the development of specific COVID-19 drugs. With in…

IN SILICO STUDY OF FLAVONOID COMPOUNDS: UTILIZATION OF COMPUTATIONAL APPROACH…

The emergence of a new human betacoronavirus strain called Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as the causative agent of CoronaVirus Disease 19 (COVID-19) has caused a pandemic. According to previous experiments, it is known that the 3C-like protease of SARS-CoV-2 plays an important role in the pathogenicity of the virus. Flavonoids are a group of natural substances bel…

Comparison of Bioinformatics Pipeline for Enrichment Illumina Next Generation…

Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) is a newly emerging virus well known as the major cause of worldwide pandemic due to Coronavirus Disease 2019 (COVID-19). Major breakthroughs in the Next Generation Sequencing (NGS) field were elucidated following the first release of a full length SARS-CoV-2 genome in January 10th 2020, with the hope to turn the table against worseni…

Comparison of Lateral Flow Immunochromatographic Assays (LFAs) and Nucleic Ac…

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xi, 53p; 30cm;illus

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BM 21-003