Sains Malaysiana 51(9)(2022): 2985-2997

http://doi.org/10.17576/jsm-2022-5109-19

 

Construction of Multi-Epitopes Vaccine Candidate against SARS-CoV-2 D614G Variant

(Pembinaan Calon Vaksin Epitop Pelbagai terhadap Varian D614G SARS-CoV-2)

 

SITI ASMAA MAT JUSOH, DANESH THANGESWARAN, MUHAMMAD SYAHIR HAKIMI MOHD HAZLI1, MOHD FIRDAUS RAIH3, NURULASMA ABDULLAH1 & SHAHARUM SHAMSUDDIN1,2,*

 

 1School of Health Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan Darul Naim, Malaysia

2Universiti Sains Malaysia (USM)-RIKEN Interdisciplinary Collaboration for Advanced Sciences (URICAS), 11700 Gelugor, Penang, Malaysia

3Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

 

Received: 28 November 2021/Accepted: 23 March 2022

 

ǂ These authors contributed equally to this work

 

Abstract

COVID-19 caused by the SARS-CoV-2 virus has become a real threat due to the emergence of new variants which are more deadly with higher infectivity. Vaccine constructs that target specific SARS-CoV-2 variants are needed for stemming COVID-19 fatality. The spike (S) glycoprotein is the major antigenic component that triggers the host immune response. Reverse vaccinology strategy was applied to the S protein of COVID-19 variant D614G to identify highly ranked antigenic proteins. In this study, a multi-epitope synthetic gene was designed using computational strategies for the COVID-19 D614G variant. The SARS-CoV-2 D614G variant protein sequence was retrieved from the NCBI database. The prediction of linear B-cell epitopes was carried out using Artificial Neural Network (ANN)-based ABCpred and BepiPred 2.0 software. The top 15 highly antigenic epitopes sequences were then selected. Propred 1 and Propred servers were used to identify major histocompatibility complex (MHC) class I and class II binding epitopes within pre-determined B-cell epitopes to predict T-cell epitopes. The top 5 MHC class I and class II were selected. Further in-silico testing for its solubility, allergenicity, antigenicity, and other physiochemical properties was analyzed using Bpred. The constructed gene was subjected to assembly PCR and the gene product was confirmed by Sanger sequencing. The findings from this study suggested that a highly antigenic specific region of the SARS-CoV-2 D614G variant can be predicted in-silico and amplified using the assembly PCR method. The designed synthetic gene was shown to elicit specific humoral and cell-mediated immune responses towards the SARS-CoV-2 variants.

 

Keywords: Assembly PCR; D614G variant; gene construct; multi-epitopes; SARS-CoV-2 spike

 

Abstrak

COVID-19 yang disebabkan oleh virus SARS-CoV-2 telah menjadi ancaman sebenar kerana kemunculan varian baharu yang lebih mematikan dengan jangkitan yang lebih tinggi. Pembinaan vaksin yang mensasarkan varian SARS-CoV-2 tertentu diperlukan untuk membendung kematian disebabkan COVID-19. Glikoprotein lonjakan (S) adalah komponen antigen utama yang mencetuskan tindak balas imun perumah. Strategi vaksinologi terbalik diterapkan pada protein S daripada varian D614G COVID-19 untuk mengenal pasti protein antigen kelas tinggi. Dalam kajian ini, gen sintetik epitop pelbagai direka bentuk menggunakan strategi komputasi untuk varian D614G COVID-19. Urutan protein varian SARS-CoV-2 D614G diambil daripada pangkalan data NCBI. Ramalan epitop sel B linear dilakukan dengan menggunakan perisian ABCpred dan BepiPred 2.0 berasaskan rangkaian neural tiruan (ANN). Lima belas urutan epitop antigen teratas kemudian dipilih. Perisian Propred 1 dan Propred digunakan untuk mengenal pasti epitop pengikat kelas I dan kelas II kompleks kehistoserasian utama (MHC) dalam epitop sel B yang telah ditentukan untuk meramalkan epitop sel T. Lima kelas I dan kelas II MHC teratas dipilih. Ujian in-sillico lebih lanjut untuk kelarutan, kealergenan, keantigenan dan sifat fisiokimia lain dianalisis menggunakan Bpred. Gen yang dibina dikenakan himpunan PCR dan produk gen tersebut disahkan oleh penjujukan Sanger. Hasil daripada kajian ini menunjukkan bahawa kawasan yang sangat khusus antigen varian SARS-CoV-2 D614G dapat diramalkan dalam silika dan dikembangkan menggunakan kaedah himpunan PCR. Gen sintetik yang dibangunkan menunjukkan penghasilan tindak balas imun khusus humoral dan sel yang dimediasi khusus terhadap varian SARS-CoV-2.

 

Kata kunci: Epitop pelbagai; himpunan PCR; pembinaan gen; peningkatan SARS-CoV-2; varian D614G

 

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*Corresponding author; email: shaharum1@usm.my

 

 

 

 

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