Sub-genomic analysis of Chikungunya virus E2 mutations in Pakistani isolates potentially modulating B-cell & T-Cell immune response

  • Bilal Ahmed Khan
  • Saif Ullah University of Karachi
  • Amanullah lail Dow University of Health Sciences
  • Saeed Khan Dow University of Health Sciences
Keywords: CHIKV, Epitopes, E2, Pakistan, E2 Mutation


Background & Objectives: The Chikungunya virus (CHIKV) transmitted to the humans through Aedes species of the mosquitoes. In December 2016, a severe outbreak reported from Pakistan. However, there is no vaccine or anti-viral treatment currently available so host immune response against CHIKV gained significant interest. Therefore, this study was conducted to identify the mutations in CHIKV E2 region of currently circulating Pakistani strains & determine their potential immunogenicity in Pakistani population.

Methods: It was a cross sectional study in which a total of 60 CHIKV PCR positive samples were collected from Molecular Department of Pathology, Dow University of Health Sciences (DUHS), Karachi during November 2017 to February 2018. CHIKV E2 gene was amplified by PCR & sequenced. Sequences were analyzed by using bioinformatic tools followed by epitope prediction in E2 sequences by In-silico immunoinformatic approach.

Results: Several single nucleotide variations (SNVs) were identified in Pakistani isolates with six novel mutations in E2 sequences. Immunoinformatic analyses showed more proteasomal sites, CTL & B-Cell epitopes in Pakistani strains with respect to S27 prototype with 69.4% population coverage against these epitopes in Pakistan. The study also identified key mutations responsible for generation of unique epitopes and HLA restriction in Pakistani isolates. The strain specific mutations revealed the current outbreak was caused by ESCA.IOL lineage of CHIKV.

Conclusion: The evolution of E2 protein in Pakistani strains has increased its immunogenicity in comparison to ancestral s27 strain. The identification of most immunogenic and conserved epitopes with high population coverage has high potential to be used in vaccine development against these local strains.


How to cite this:
Khan BA, Saifullah, Lail A, Khan S. Sub-genomic analysis of Chikungunya virus E2 mutations in Pakistani isolates potentially modulating B-cell & T-Cell immune response. Pak J Med Sci. 2021;37(1):93-98. doi:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

How to Cite
Khan, B. A., Ullah, S., lail, A., & Khan, S. (2020). Sub-genomic analysis of Chikungunya virus E2 mutations in Pakistani isolates potentially modulating B-cell & T-Cell immune response. Pakistan Journal of Medical Sciences, 37(1).