Molecular Evolution of Zika Virus by Phylogenetic Analysis of Individual Structural Capsid (C) Gene and Whole genome Sequences Worldwide
DOI:
https://doi.org/10.31580/pjmls.v4i04.2205Keywords:
Capsid gene; Full-length genome; Phylogenetic; zika virus;Abstract
Background: Zika virus was first discovered in Uganda in 1947 considered to be an emerging, arbovirus, mosquito-borne, Flavivirus, which is transmitted through Aedes mosquito possesses global health concerns. Distribution of zika virus all through much of Africa as well as Asia. In this study, using phylogenetic trees based analysis; we reported first full-length genome and partial capsid (C) gene of zika virus distributed over the globe.
Materials and Methods: Herein, 22 full-length genome including a Spondweni virus and partial capsid (C) gene sequences of geographically diverse zika virus strains were retrieved from GenBank database. Phylogenetic investigation and evolutionary distances from nucleotide and amino acid sequences were calculated by using maximum likelihood (ML) methods choosing best fitted model in MEGA X software.
Results: Phylogenetic and geographical distinct strains followed maximum-likelihood approach based full-length genome analysis showed that all strains fell into two main lineages which confined the genetically closeness. While, phylogenetic analysis of capsid (C) gene nucleotide and amino acid sequences revealed extensive differences in the topologies, followed by full genome sequences either in term of bootstrap support or distribution of the strains into various groups. These results propose significant distinction in the evolutionary trail of the studied genome and gene.
Conclusions: This data highlight the significance of studying the phylogenetic constructed viral evolution conferring to global perspective. This line of attack will expand our understanding the spread of zika virus to prevent their emergence as well as improve health surveillance.
References
2. Dick, G., S. Kitchen, and A. Haddow, Zika virus (I). Isolations and serological specificity. Transactions of the Royal Society of Tropical Medicine and Hygiene, 1952. 46(5): p. 509-520.
3. Lanciotti, R.S., et al., Genetic and serologic properties of Zika virus associated with an epidemic, Yap State, Micronesia, 2007. Emerging infectious diseases, 2008. 14(8): p. 1232.
4. Musso, D., E. Nilles, and V.M. Cao?Lormeau, Rapid spread of emerging Z ika virus in the P acific area. Clinical Microbiology and Infection, 2014. 20(10): p. O595-O596.
5. Haddow, A.D., et al., Genetic characterization of Zika virus strains: geographic expansion of the Asian lineage. PLoS neglected tropical diseases, 2012. 6(2): p. e1477.
6. Guerbois, M., et al., Outbreak of Zika virus infection, Chiapas State, Mexico, 2015, and first confirmed transmission by Aedes aegypti mosquitoes in the Americas. The Journal of infectious diseases, 2016. 214(9): p. 1349-1356.
7. Lazear, H.M. and M.S. Diamond, Zika virus: new clinical syndromes and its emergence in the western hemisphere. Journal of virology, 2016. 90(10): p. 4864-4875.
8. Weaver, S.C., et al., Zika virus: History, emergence, biology, and prospects for control. Antiviral research, 2016. 130: p. 69-80.
9. Calvez, E., et al., Differential transmission of Asian and African Zika virus lineages by Aedes aegypti from New Caledonia. Emerging microbes & infections, 2018. 7(1): p. 159.
10. Gu, S.H., et al., Whole-genome sequence analysis of Zika virus, amplified from urine of traveler from the Philippines. Virus Genes, 2017. 53(6): p. 918-921.
11. Tripathi, S., et al., A novel Zika virus mouse model reveals strain specific differences in virus pathogenesis and host inflammatory immune responses. PLoS pathogens, 2017. 13(3): p. e1006258.
12. Shrivastava, S., et al., Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains. Scientific reports, 2018. 8(1): p. 15843.
13. Kauffman, E.B. and L.D. Kramer, Zika virus mosquito vectors: competence, biology, and vector control. The Journal of infectious diseases, 2017. 216(suppl_10): p. S976-S990.
14. Poland, G.A., et al., Development of vaccines against Zika virus. The Lancet infectious diseases, 2018. 18(7): p. e211-e219.
15. Lednicky, J., et al., Zika virus outbreak in Haiti in 2014: molecular and clinical data. PLoS neglected tropical diseases, 2016. 10(4): p. e0004687.
16. Giovanetti, M., et al., Zika Virus spreading in South America: Evolutionary analysis of emerging neutralizing resistant Phe279Ser strains. Asian Pacific journal of tropical medicine, 2016. 9(5): p. 445-452.
17. Zhu, Z., et al., Comparative genomic analysis of pre-epidemic and epidemic Zika virus strains for virological factors potentially associated with the rapidly expanding epidemic. Emerging microbes & infections, 2016. 5(1): p. 1-12.
18. Hatcher, E.L., et al., Virus Variation Resource–improved response to emergent viral outbreaks. Nucleic acids research, 2016. 45(D1): p. D482-D490.
19. Thompson, J.D., D.G. Higgins, and T.J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research, 1994. 22(22): p. 4673-4680.
20. Tamura, K., G. Stecher, and S. Kumar, MEGA11: molecular evolutionary genetics analysis version 11. Molecular biology and evolution, 2021. 38(7): p. 3022-3027.
21. Wilder-Smith, A., Murray and Quam. Epidemiology of Dengue: Past, Present and Future Prospects Clin. Epidemiol, 2013. 299.
22. Weaver, S.C. and W.K. Reisen, Present and future arboviral threats. Antiviral research, 2010. 85(2): p. 328-345.
23. Calvet, G., et al., Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study. The Lancet infectious diseases, 2016. 16(6): p. 653-660.
24. Camacho, E., et al., Detection of autochthonous Zika virus transmission in Sincelejo, Colombia. Emerging infectious diseases, 2016. 22(5): p. 927.
25. Weber, D.S., K.A. Alroy, and S.M. Scheiner, Phylogenetic insight into Zika and emerging viruses for a perspective on potential hosts. Ecohealth, 2017. 14(2): p. 214-218.
26. Shrivastava, S., et al., Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains. Scientific reports, 2018. 8(1): p. 1-11.
27. Zanluca, C., et al., First report of autochthonous transmission of Zika virus in Brazil. Memórias do Instituto Oswaldo Cruz, 2015. 110(4): p. 569-572.
28. Buathong, R., et al., Detection of Zika virus infection in Thailand, 2012–2014. The American journal of tropical medicine and hygiene, 2015. 93(2): p. 380-383.
29. Alera, M.T., et al., Zika virus infection, Philippines, 2012. Emerging infectious diseases, 2015. 21(4): p. 722.
30. Hayes, E.B., Zika virus outside Africa. Emerging infectious diseases, 2009. 15(9): p. 1347.
31. Villamil-Gómez, W.E., et al., Zika, dengue, and chikungunya co-infection in a pregnant woman from Colombia. International Journal of Infectious Diseases, 2016. 51: p. 135-138.
32. Wang, A., et al., Zika virus genome biology and molecular pathogenesis. Emerging microbes & infections, 2017. 6(1): p. 1-6.
