Characterizing the zika virus genome – A bioinformatics study

Current Computer-Aided Drug Design

Volumn 12, Issue 2, 2016, Pages 87-97

  Nandy, Ashesh ^a   Dey, Sumanta ^a   Basak, Subhash C ^a,b   Bielińska Wąż, Dorota ^c   Wąż, Piotr ^c  

^a Centre for Interdisciplinary Research and Education   (India)

^b UNIVERSITY OF MINNESOTA DULUTH   (United States)

^c MEDICAL UNIVERSITY OF GDANSK   (Poland)

Author 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

Indexed keywords

BIOINFORMATICS; GENES; GRAPHIC METHODS; VIRUSES;

2D GRAPHICAL REPRESENTATION; AFRICAN AND ASIAN-AMERICAN CLADE; AMINO ACID CHANGE; AMINO-ACIDS; CLADEWISE TRANSITION-TRANSVERSION RATIO; DESCRIPTORS; ZIKA SEQUENCE DESCRIPTOR; ZIKA VIRUS; ZIKA VIRUS CHARACTERIZATION; ZIKA VIRUS PHYLOGENY;

AMINO ACIDS;

ADENINE; AMINO ACID; CYTOSINE; GUANINE; STRUCTURAL PROTEIN; THYMINE;

5' UNTRANSLATED REGION; ARTICLE; CODON USAGE; CONFORMATIONAL TRANSITION; DENGUE VIRUS; GENE SEQUENCE; HUMAN; MUTATION; NONHUMAN; PHYLOGENETIC TREE; SEQUENCE ALIGNMENT; STRUCTURAL BIOINFORMATICS; VIRION; VIRUS CHARACTERIZATION; VIRUS GENOME; ZIKA VIRUS; GENETICS; GENOMICS; PHYLOGENY; SPECIES DIFFERENCE;

GENOME, VIRAL; GENOMICS; PHYLOGENY; SPECIES SPECIFICITY; ZIKA VIRUS;

EID: 84981532068     PISSN: 15734099     EISSN: 18756697     Source Type: Journal    
DOI: 10.2174/1573409912666160401115812     Document Type: Article

References (27)

1. Elachola, H.; Gozzer, E.; Zhuo, J.; Memish, Z.A. A crucial time for public health preparedness: Zika virus and the 2016 Olympics, Umrah, and Hajj. Lancet, 2016, 387, 630-632.
2. Victoria, C.G.; Schuler-Faccini, L.; Matijasevic, A.; Ribeiro, E.; Pessoa, A.; Barros, F.C. Microcephaly in Brazil: How to interpret reported numbers? Lancet, 2016, 387, 621-623.
3. BBC. Zika virus triggers pregnancy delay calls. http://www.bbc.co.uk/news/world-latin-america-35388842/. (Accessed February 26, 2016).
4. Roa, M. Zika virus outbreak: Reproductive health and rights in Latin America. Lancet, 2016, 387, 843.
5. WHO. "WHO Director-General summarizes the outcome of the Emergency Committee regarding clusters of microcephaly and Guillain-Barré syndrome". World Health Organization. 1 February 2016. Retrieved 16th February 2016.
6. The Intergovernmental Panel on Climate Change. Chapter 8 Human health 8.2.8 Vector-borne, rodent-borne and other infectious diseases. IPCC 4th Assessment Report: Climate Change 2007, 403-405.
7. Shuman, E.K. Global climate change and infectious diseases. N. Engl. J. Med., 2010, 362, 1061-1063.
8. Horton, R. Offline: Brazil—the unexpected opportunity that Zika presents. Lancet, 2016, 387, 633.
9. Nandy, A.; Basak, S.C. Prognosis of possible reassortments in recent H5N2 epidemic influenza in USA: Implications for computer-assisted surveillance as well as drug/vaccine design. Curr. Comp.-Aided Drug Des., 2015, 11, 110-116.
10. Duffy, M.R.; Chen, T.-H.; Hancock, W.T.; Powers, A.M.; Kool, J.L.; Lanciotti, R.S.; Pretrick, M.; Marfel, M.; Holzbauer, S.; Dubray, C.; Guillaumot, L.; Griggs, A.; Bel, M.; Lambert, A.J.; Laven, J.; Kosoy, O.; Panella, A.; Biggerstaff, B.J.; Fischer, M.; Hayes, E.B. Zika virus outbreak on Yap Island, Federated States of Micronesia. N. Engl. J. Med., 2009, 360, 2536-2543.
11. Berthet, N.; Nakoune´, E.; Kamgang, B.; Selekon, B.; Descorps-Declére, S.; Gessain, A.; Manuguerra, J.-C.; Kazanji, M. Molecular characterization of three zika flaviviruses obtained from sylvatic mosquitoes in the central African republic. Vector Borne Zoonotic Dis., 2014, 14, 862-865.
12. Heymann, D.L.; Hodgson, A.; Sall, A.A.; Freedman, D.O.; Staples, J.E.; Althabe, F.; Baruah, K.; Mahmud, G.; Kandun, N.; Vasconcelos, P.F.C.; Bino, S.; Menon, K.U. Zika virus and microcephaly: Why is this situation a PHEIC? Lancet 2016, 387, 719-721.
13. Kuno, G.; Chang, G.-J.J. Full-length sequencing and genomic characterization of Bagaza, Kedougou, and Zika viruses. Arch. Virol., 2007, 152, 687-696.
14. Haddow, A.D.; Schuh, A.J.; Yasuda, C.Y.; Kasper, M.R.; Heang, V.; Huy, R.; Guzman, H.; Tesh, R.B.; Weaver, S.C. Genetic Characterization of Zika virus strains: Geographic expansion of the asian lineage. PLoS Negl. Trop. Dis., 2012, 6(2), e1477.
15. Faye, O.; Freire, C.C.M.; Iamarino, A.; Faye, O.; de Oliveira, J.V.C.; Diallo, M.; Zanotto, P.M.A.; Sall, A.A. Molecular evolution of zika virus during its emergence in the 20th century. PLoS Negl. Trop. Dis., 2014, 8(1), e2636.
16. Nandy, A. A new graphical representation and analysis of DNA sequence structure: I. Methodology and application to Globin genes. Curr. Sci., 1994, 66, 309-314.
17. Raychaudhury, C.; Nandy, A. Indexing scheme and similarity measures for macromolecular sequences. J. Chem. Inf. Comput. Sci., 1999, 39, 243-247.
18. Nandy, A.; Harle, M.; Basak, S.C. Mathematical descriptors of DNA sequences: Development and applications. ARKIVOC 2006, 9, 211-238.
19. Nandy, A.; Nandy, P. On the uniqueness of quantitative DNA difference descriptors in 2D graphical representation models. Chem. Phys. Lett., 2003, 368, 102-107.
20. Bielińska-Wąż, D.; Clark, T.; Wąż, P.; Nowak, W.; Nandy, A. 2Ddynamic representation of DNA sequences. Chem. Phys. Lett., 2007, 442, 140-144.
21. Bielińska-Wąż, D.; Nowak, W.; Wąż, P.; Nandy, A.; Clark, T. Distribution moments of 2D-graphs as descriptors of DNA sequences. Chem. Phys. Lett., 2007, 443, 408-413.
22. Sanjuan, R.; Nebot, M.R.; Chirico, N.; Mansky, L.M.; Belshaw, R. Viral mutation rates. J. Virol.; 2010, 84, 9733-9748.
23. Dey, S.; Nandy, A. Phylogenetic and genetic analysis of envelope gene of the prevalent dengue serotypes in india in recent years. SciForum Mol2Net, 2015, 1 (Section B, No 016). Proceedings 1 http://sciforum.net/conference/mol2net-1
24. Brown, W.M.; Prager, E.M.; Wang, A.; Wilson, A.C. Mitochondrial DNA sequences of primates: Tempo and mode of evolution. J. Mol. Evol., 1982, 18, 225-239.
25. Tamara, K.; Nei, M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol., 1993, 10(3), 512-526.
26. Nandy, A. Two dimensional graphical representation of DNA sequences and intron-exon discrimination in intron-rich sequences. Comput. Appl. Biosci., 1996, 12(1), 55-62.
27. Basak, S.C.; Nandy, A. Computer-assisted approaches as decision support systems in the overall strategy of combating emerging diseases: Some comments regarding drug design, vaccinomics, and genomic surveillance of the Zika virus. Curr. Comp.-Aided Drug Des., 2016 (in press).