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Bioinformatics analysis of rhinovirus capsid proteins VP1-4 sequences for cross-serotype vaccine development

Alshrari AS 1 , Hudu SA 2 , Asdaq SMB 3 , Ali AM 4 , Kin CV 5 , Omar AR 6 Show all authors , Pei CP 7 , Sekawi Z 8

Affiliations 

  • 1 Medical Laboratory Technology, Faculty of Applied Medical Science, Northern Border University, Arar, Saudi Arabia. Electronic address: [email protected]
  • 2 Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, 840232 Sokoto State, Nigeria. Electronic address: [email protected]
  • 3 Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Dariyah, 13713, Riyadh, Saudi Arabia. Electronic address: [email protected]
  • 4 Department of Medical Laboratory Sciences, Sulaiman ALrajhi University, Albukairah, Saudi Arabia. Electronic address: [email protected]
  • 5 School of Biosciences, Taylor's University, No 1, Jalan Taylor's, 47500 Subang Jaya, Selangor, Malaysia. Electronic address: [email protected]
  • 6 Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, University Putra Malaysia, 43400 Serdang, Selangor, Malaysia. Electronic address: [email protected]
  • 7 Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia. Electronic address: [email protected]
  • 8 Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia. Electronic address: [email protected]
J Infect Public Health, 2021 Nov;14(11):1603-1611.
PMID: 34624714 DOI: 10.1016/j.jiph.2021.09.001

Abstract

BACKGROUND: Rhinoviruses (RV) are associated with the development and exacerbations of asthma and chronic obstructive pulmonary disease. They've also been linked to more severe diseases like pneumonia, acute bronchiolitis, croup, and otitis media. Because of the hypervariable sequences in the same serotypes, no effective vaccine against rhinoviruses has been developed to date. With the availability of new full-length genome sequences for all RV-A and RV-B serotyped strains, this study used bioinformatics to find a suitable RV strain with the highest similarity matrices to the other strains.

METHODS: The full genomic sequences of all known different RV-A and -B prototypes were downloaded from the National Centre for Biotechnology Information (NCBI) and divided into minor low-density lipoprotein receptor (LDLR) and major intercellular adhesion molecule groups (ICAM). The sequences were edited using Biological Sequence Alignment Editor, v 7.2.0 (BioEdit software) to study each capsid protein (VP1, VP2, VP3, and VP4) and analyzed using the EMBL-EBI ClustalW server and the more current Clustal Omega tool for the calculation of the identities and similarities.

RESULTS: We analyzed and predicted immunogenic motifs from capsid proteins that are conserved across distinct RV serotypes using a bioinformatics technique. The amino acid sequences of VP3 were found to be the most varied, while VP4 was the most conserved protein among all RV-A and RV-B strains. Among all strains studied, RV-74 demonstrated the highest degree of homology to other strains and could be a potential genetic source for recombinant protein production. Nine highly conserved regions with a minimum length of 9-mers were identified, which could serve as potential immune targets against rhinoviruses.

CONCLUSION: Therefore, bioinformatics analysis conducted in the current study has paved the way for the selection of immunogenic targets. Bioinformatically, the ideal strain's capsid protein is suggested to contain the most common RVs immunogenic sites.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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