Analysis of viral diversity for vaccine target discovery

Asif M. Khan, Yongli Hu, Olivo Miotto, Natascha M. Thevasagayam, Rashmi Sukumaran, Hadia Syahirah Abd Raman, Vladimir Brusic, Tin Wee Tan, J. Thomas August

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Background: Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets. Results: This work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples. Our methodology has been implemented as an analytical pipeline that brings significant advancement to the field of reverse vaccinology, enabling systematic screening of known sequence data in nature for identification of vaccine targets. This includes key steps (i) comprehensive and extensive collection of sequence data of viral proteomes (the virome), (ii) data cleaning, (iii) large-scale sequence alignments, (iv) peptide entropy analysis, (v) intra- and inter-species variation analysis of conserved sequences, including human homology analysis, and (vi) functional and immunological relevance analysis. Conclusion: These steps are combined into the pipeline ensuring that a more refined process, as compared to a simple evolutionary conservation analysis, will facilitate a better selection of vaccine targets and their prioritization for subsequent experimental validation.

Original languageEnglish
Article number78
JournalBMC Medical Genomics
Volume10
DOIs
Publication statusPublished - Dec 21 2017

Fingerprint

Viral Vaccines
Vaccines
Hepatitis A
Dengue
Conserved Sequence
Sequence Alignment
Public Sector
Influenza A virus
Entropy
Adaptive Immunity
Proteome
Computational Biology
HIV-1
Immune System
Viruses
Peptides

Keywords

  • Bioinformatics
  • Database
  • Reverse vaccinology
  • Target discovery
  • Tools
  • Vaccine design
  • Viral diversity

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Khan, A. M., Hu, Y., Miotto, O., Thevasagayam, N. M., Sukumaran, R., Abd Raman, H. S., ... Thomas August, J. (2017). Analysis of viral diversity for vaccine target discovery. BMC Medical Genomics, 10, [78]. https://doi.org/10.1186/s12920-017-0301-2

Analysis of viral diversity for vaccine target discovery. / Khan, Asif M.; Hu, Yongli; Miotto, Olivo; Thevasagayam, Natascha M.; Sukumaran, Rashmi; Abd Raman, Hadia Syahirah; Brusic, Vladimir; Tan, Tin Wee; Thomas August, J.

In: BMC Medical Genomics, Vol. 10, 78, 21.12.2017.

Research output: Contribution to journalArticle

Khan, AM, Hu, Y, Miotto, O, Thevasagayam, NM, Sukumaran, R, Abd Raman, HS, Brusic, V, Tan, TW & Thomas August, J 2017, 'Analysis of viral diversity for vaccine target discovery', BMC Medical Genomics, vol. 10, 78. https://doi.org/10.1186/s12920-017-0301-2
Khan AM, Hu Y, Miotto O, Thevasagayam NM, Sukumaran R, Abd Raman HS et al. Analysis of viral diversity for vaccine target discovery. BMC Medical Genomics. 2017 Dec 21;10. 78. https://doi.org/10.1186/s12920-017-0301-2
Khan, Asif M. ; Hu, Yongli ; Miotto, Olivo ; Thevasagayam, Natascha M. ; Sukumaran, Rashmi ; Abd Raman, Hadia Syahirah ; Brusic, Vladimir ; Tan, Tin Wee ; Thomas August, J. / Analysis of viral diversity for vaccine target discovery. In: BMC Medical Genomics. 2017 ; Vol. 10.
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