Fedik Abdul Rantam, Viol Dhea Kharisma, Christrijogo Sumartono, Jusak Nugraha, Andi Yasmin Wijaya, Helen Susilowati, Suryo Kuncorojakti, Alexander Patera Nugraha
Background: An immunoinformatic approach may be useful to investigate the conserved region in the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Indonesia isolates. The aim of this study was to investigate Indonesian SARS-CoV-2 isolates based on B cell epitopes by targeting the conserved regions in the spike glycoprotein to trigger increased multi-variant virus neutralization and memory response for the development of vaccine seed candidates. Methods: SARS-CoV-2 spike glycoprotein gene sequences originating from Indonesia were compared with Wuhan (China), the United Kingdom, South Africa, India, the United States, and Brazil isolates obtained from the NCBI and GISAID databases. The recognition of antigens was carried out directly using B cells through the B cell receptor (BCR). An indirect B cell activation by Cluster of Differentiation (CD)4+ T cells and major histocompatibility complex (MHC)-II was predicted through the binding with human leukocyte antigen (HLA) based on IC 50 value. In addition, vaccine allergenicity and toxicity were investigated. During the molecular complex examination, the 3D peptide structure was investigated and the lowest amount of energy formed when the vaccine candidate peptide bound to BCR and MHC-II was calculated. Results: As a result, the spike glycoprotein sequences of Indonesian SARS-CoV-2 isolates had conserved regions which were very similar to reference countries such as China, the United Kingdom, South Africa, India, the United States, and Brazil. Conclusion: It was predicted that the conserved regions could be identified as the epitope of B and T CD4+ cells that produced the peptides for vaccine candidate with antigenic, non-allergen, and non-toxic properties. © 2021 Rantam FA et al.
Research Center for Vaccine Technology and Development, Institute of Tropical Disease, Universitas Airlangga, Surabaya, East Java, Indonesia; Virology and Immunology Laboratory, Department of Microbiology, Faculty of Veterinary Medicine, Airlangga University, Surabaya, East Java, 60132, Indonesia; Biology Department, Faculty of Mathematic and Natural Sciences, Universitas Brawijaya, Malang, East Java, Indonesia; Anasthesiology and Reanimation Department, Dr. Soetomo Gerneral Hospital and Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia; Clinical Pathology Department, Dr. Soetomo Gerneral Hospital and Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia; Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia; Department of Veterinary Anatomy, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia; Orthodontics Department, Universitas Airlangga, Surabaya, East Java, 60132, Indonesia