Characterizing the zika virus genome – A bioinformatics study

Ashesh Nandy, Sumanta Dey, Subhash C. Basak, Dorota Bielińska-Wąż, Piotr Wąż

Research output: Contribution to journalArticlepeer-review

11 Scopus citations

Abstract

Background: The recent epidemic of Zika virus infections in South and Latin America have raised serious concern on its ramifications for the population in the Americas and spread of the virus worldwide. The Zika virus disease is a relatively new phenomenon for which sufficient and comprehensive data and investigative reports have not been available to date. Objective: To carry out a bioinformatics study of the available Zika virus genomic sequences to characterize the virus. Method: 2D graphical representation method is used for visual rendering and compute sequence parameters and descriptors of the African and Asian-American groups of the Zika viruses to characterize the sequences. We also used MEGA5.2 and other software to compute various biological properties of interest like phylogenetic relationships, transition-transversion ratios, amino acid usage, codon usage bias and hydropathy index of the Zika genomes and virions. Results: The phylogenetic relationships show that the African and Asian-American Zika virus genomes are grouped in two clades. The 2D plots of typical genomes of these types also show dramatic differences indicating that the gene sequences at the 5’-end coding regions for the structural proteins are rather strongly conserved. Among other characteristics, the transition/transversion ratio matrices for the sequences in each of the two clades show that analogous to the dengue virus, the transition rates are about 10 to 15 times the transversion rates. Conclusion: These findings are important for computer-assisted approaches towards surveillance of emerging Zika virus strains as well as in the design of drugs and vaccines to combat the growth and spread of the Zika virus.

Original languageEnglish (US)
Pages (from-to)87-97
Number of pages11
JournalCurrent computer-aided drug design
Volume12
Issue number2
DOIs
StatePublished - Jun 1 2016

Keywords

  • 2D graphical representation
  • African and Asian-American clades
  • Amino acid changes
  • Cladewise transition-transversion ratios
  • Zika sequence descriptors
  • Zika virus
  • Zika virus characterization
  • Zika virus phylogeny

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