Phylogenesys and homology modeling in Zika virus epidemic: food for thought

References

• Calvet GA, Filippis AM, Mendonça MC, Sequeira PC, Siqueira AM, Veloso VG, et al. First detection of autochthonous Zika virus transmission in a HIV-infected patient in Rio de Janeiro, Brazil. J Clin Virol. 2016;74:1–3.10.1016/j.jcv.2015.11.014
   PubMed Web of Science ®Google Scholar
• Gatherer D, Kohl A. Zika virus: a previously slow pandemic spreads rapidly through the Americas. J Gen Virol. 2016;97(2):269–73.10.1099/jgv.0.000381
   PubMed Web of Science ®Google Scholar
• Kelser EA. Meet dengue’s cousin. Zika. 2016;18(3):163–6.
   Google Scholar
• Campos GS, Bandeira AC, Sardi SI. Zika virus outbreak, Bahia, Brazil. Emerg Infect Dis. 2015;21(10):1885–6.10.3201/eid2110.150847
   PubMed Web of Science ®Google Scholar
• Rodriguez-Morales AJ. Zika: the new arbovirus threat for Latin America. J Infect Dev Countries. 2015;9(6):684-5.
   PubMed Web of Science ®Google Scholar
• Higgs S. Zika virus: emergence and emergency. Vector Borne Zoonotic Dis. 2016;16(2):75–6.10.1089/vbz.2016.29001.hig
   PubMed Web of Science ®Google Scholar
• Petersen EE, Staples JE, Meaney-Delman D, Fischer M, Ellington SR, Callaghan WM, et al. Interim guidelines for pregnant women during a Zika virus outbreak – United States, 2016. MMWR Morb Mortal Wkly Rep. 2016;65:30–3.10.15585/mmwr.mm6502e1
   PubMed Web of Science ®Google Scholar
• Tetro JA. Zika and microcephaly: causation, correlation, or coincidence? Microbes Infect. 2016;18(3):167–8.
   PubMed Web of Science ®Google Scholar
• Ventura CV, Maia M, Bravo-Filho V, Góis AL, Belfort R, Jr. Zika virus in Brazil and macular atrophy in a child with microcephaly. Lancet. 2016;387(10015):228.10.1016/S0140-6736(16)00006-4
   PubMed Web of Science ®Google Scholar
• Faye O, Freire CC, Iamarino A, Faye O, de Oliveira JV, Diallo M, et al. Molecular evolution of Zika virus during its emergence in the 20(th) century. PLoS Negl Trop Dis. 2014;8(1):e2636.10.1371/journal.pntd.0002636
   PubMed Web of Science ®Google Scholar
• Ashfaq UA, Ahmed B. De novo structural modeling and conserved epitopes prediction of Zika virus envelop protein for vaccine development. Viral Immunol. 2016 Jul 20. Epub ahead of print.
   PubMedGoogle Scholar
• Cox BD, Stanton RA, Schinazi RF. Predicting Zika virus structural biology: challenges and opportunities for intervention. Antivir Chem Chemother. 2016 Jun 13. pii: 2040206616653873. Epub ahead of print.
   Google Scholar
• Weiskopf D, Angelo MA, de Azeredo EL, Sidney J, Greenbaum JA, Fernando AN, et al. Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells. Proc Natl Acad Sci USA. 2013 May 28;110(22):E2046–53.10.1073/pnas.1305227110
   PubMed Web of Science ®Google Scholar
• Wahala WM, Silva AM. The human antibody response to dengue virus infection. Viruses. 2011 Dec;3(12):2374–95.10.3390/v3122374
   PubMed Web of Science ®Google Scholar
• Lo Presti A, Ciccozzi M, Cella E, Lai A, Simonetti FR, Galli M, et al. Origin, evolution, and phylogeography of recent epidemic CHIKV strains. Infect Genet Evol. 2012;12(2):392–8.10.1016/j.meegid.2011.12.015
   PubMed Web of Science ®Google Scholar
• Bell BP, Boyle CA, Petersen LR. Preventing Zika virus infections in pregnant women: an urgent public health priority. Am J Public Health. 2016;106(4):589–90.10.2105/AJPH.2016.303124
   PubMed Web of Science ®Google Scholar
• Azarian T, Lo Presti A, Giovanetti M, Cella E, Rife B, Lai A, et al. Impact of spatial dispersion, evolution, and selection on Ebola Zaire virus epidemic waves. Sci Rep. 2015;5:10170.10.1038/srep10170
   PubMed Web of Science ®Google Scholar
• Pond SL, Frost SD, Muse SV. HyPhy: hypothesis testing using phylogenies. Bioinformatics. 2005;21(5):676–9.10.1093/bioinformatics/bti079
   PubMed Web of Science ®Google Scholar
• Nielsen R, Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 1998;148(3):929–36.
   PubMed Web of Science ®Google Scholar
• Kosakovsky Pond SL, Frost SD. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 2005;22(5):1208–22.10.1093/molbev/msi105
   PubMed Web of Science ®Google Scholar
• Ciccozzi M, Vujošević D, Lo Presti A, Mugoša B, Vratnica Z, Lai A, et al. Genetic diversity of HIV type 1 in Montenegro. AIDS Res Hum Retroviruses. 2011;27(8):921–4.10.1089/aid.2010.0323
   PubMed Web of Science ®Google Scholar
• Kelley LA, Sternberg MJ. Protein structure prediction on the web: a case study using the Phyre server. Nat Protoc. 2009;4(3):363–71.10.1038/nprot.2009.2
   PubMed Web of Science ®Google Scholar
• Van Durme J, Delgado J, Stricher F, Serrano L, Schymkowitz J, Rousseau F. A graphical interface for the FoldX forcefield. Bioinformatics. 2011;27(12):1711–2.10.1093/bioinformatics/btr254
   PubMed Web of Science ®Google Scholar
• Patronov A, Pirrò S, Grifoni A, Ilieva KM, Gallo C, Del Duca A, et al. 2016. NeutraCorp: a new tool for cross-model B-cell epitope prediction.
   Google Scholar
• Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, Purton KA, et al. Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics. 2005;57(5):304–14.10.1007/s00251-005-0798-y
   PubMed Web of Science ®Google Scholar
• Nielsen M, Lundegaard C, Lund O. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics. 2007;8:238–249.10.1186/1471-2105-8-238
   PubMed Web of Science ®Google Scholar
• Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K, Buus S, et al. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci. 2003;12(5):1007–17.10.1110/(ISSN)1469-896X
   PubMed Web of Science ®Google Scholar
• Peters B, Sette A. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics. 2005;6:132.10.1186/1471-2105-6-132
   PubMed Web of Science ®Google Scholar
• Salimi N, Fleri W, Peters B, Sette A. The immune epitope database: a historical retrospective of the first decade. Immunology. 2012;137(2):117–23.10.1111/imm.2012.137.issue-2
   PubMed Web of Science ®Google Scholar
• Sturniolo T, Bono E, Ding J, Raddrizzani L, Tuereci O, Sahin U, et al. Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat Biotechnol. 1999 Jun;17(6):555–61.
   PubMed Web of Science ®Google Scholar