AccScience Publishing / MI / Online First / DOI: 10.36922/MI025450120
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ORIGINAL RESEARCH ARTICLE

Identification of conserved SARS-CoV-2 gene regions for diagnostic tool development through whole-genome sequencing

Getnet Hailu1,2 ,  Fisihatsion Tadesse3* ,  Molalegne Bitew4 ,  Kidist Zealiyas2 ,  Girmay Medhin1 ,  Andargachew Gashu2 ,  Mengistu Legesse1
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1 Department of Tropical and Infectious Diseases, Aklilu Lemma Institute of Health Research, Addis Ababa University, Addis Ababa, Ethiopia
2 Department of Infectious Diseases, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
3 Department of Internal Medicine, College of Health Science, Addis Ababa University, Addis Ababa, Ethiopia
4 Department of Health Biotechnology, Bio and Emerging Technology Institute, Addis Ababa, Ethiopia
MI, 025450120 https://doi.org/10.36922/MI025450120
Received: 5 November 2025 | Revised: 26 April 2026 | Accepted: 14 May 2026 | Published online: 5 June 2026
© 2026 by the Author(s). This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )
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Abstract

The high mutation frequency of the SARS-CoV-2 spike (S) gene undermines the reliability of S-based diagnostics. Identifying conserved protein epitopes that remain stable across SARS-CoV-2 variants is paramount in resource-limited settings. This study aims to identify conserved gene regions of SARS-CoV-2 using whole-genome sequencing and immunoinformatics to support the development of monoclonal antibody-based rapid diagnostics. SARS-CoV-2 positive samples (Ct ≤ 30) collected in Ethiopia (June–August 2022) from a retrospective study (n = 70) were sequenced using Illumina NextSeq-550. Conserved regions were identified via Multiple Alignment using Fast Fourier Transform, entropy plots, and mutation profiling. B-cell epitopes were predicted and assessed for antigenicity and cross-reactivity. Structural modeling was conducted using AlphaFold and visualization tools. High-quality whole-genome sequencing of 63 SARS-CoV-2 samples revealed conserved regions in the nucleocapsid gene across major variants. Three surface-exposed, antigenic, and non-allergenic B-cell epitopes were identified with low cross-reactivity to common human coronaviruses. Structural modeling and docking confirmed their accessibility and strong antibody binding, supporting their potential for robust diagnostic applications. In conclusion, conserved N protein epitopes identified in this study are promising targets for developing robust, variant-resistant rapid diagnostic tools.

Keywords
SARS-CoV-2
Conserved gene region
Diagnostic tool
Monoclonal antibody-based approach
Ethiopia
Funding
None.
Conflict of interest
The authors declare that there are no conflicts of interest regarding the publication of this paper.
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Microbes & Immunity, Electronic ISSN: 3029-2883 Print ISSN: 3041-0886, Published by AccScience Publishing
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