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Supplemental methods
Phylogenetic relationship of the Zika virus with other Flaviviruses
131 whole genome sequences were obtained from Genbank containing
representative member of Zika Virus, Japanese Encephalitis Virus, Yellow fever
Virus, West Nile virus and Dengue Virus. All sequences were aligned using the
MAFFT server using default parameters. A maximum likelihood tree was
reconstructed using the General Time Reversible model and the tree with the
highest log likelihood (-165576.1058) is shown. Initial tree(s) for the heuristic
search were obtained by applying the Neighbor-Joining method to a matrix of
pairwise distances estimated using the Maximum Composite Likelihood (MCL)
approach. A discrete Gamma distribution was used to model evolutionary rate
differences among sites (5 categories (+G, parameter = 1.1760)). Results were
validated using 100 bootstrap replicates and the tree was plotted using FigTree.
Molecular phylogenetic analysis of Zika viral evolution
29 unique whole genome sequences of Zika virus were obtained from
GenBank and aligned using the MAFFT server using default parameters.
Maximum Likelihood phylogenetic trees were reconstructed based on the
General Time Reversible model. All positions with less than 95% site coverage
were eliminated. That is, fewer than 5% alignment gaps, missing data, and
ambiguous bases were allowed at any position. There were a total of 10239
positions in the final dataset. The initial tree(s) for the heuristic search were
obtained by applying the Neighbor-Joining method to a matrix of pairwise
distances estimated using the Maximum Composite Likelihood (MCL) approach.
A discrete Gamma distribution was used to model evolutionary rate differences
among sites (5 categories (+G, parameter = 0.2856)). 1000 bootstrap replicates
were utilized to validate and generate a condensed tree (50 % cutoff value).
Evolutionary analyses were conducted in MEGA6.
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Supplemental Figures
Figure S1
Fig. S1. Phylogeny of the flavi-viruses
A cladogram representing the phylogenetic relationship of the Zika virus with
other closely related flaviviruses like Dengue, Japanese Encephalitis, Yellow
fever and West Nile Virus obtained using the Maximum Likelihood method based
on the General Time Reversible model. The tree is obtained from 100 bootstrap
replicates using Mega6 and drawn as a cladogram using Figtree.
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The individual virus types group into distinct clades and are colored for easy
visualization and the relevant sub-strain types are labelled accordingly.Among
the flavivirus family, the four groups have been suggested to be phylogeneticallyrelated to Zika viruses, including Dengue virus (in green), Yellow fever virus (in
blue), Japanese encephalitis virus (in black), and West nile virus (in purple). The
Zika virus group is in red, of which two subclades (Asian-American lineage and
African lineage) are proposed and highlighted in yellow background.
Figure S2
Fig. S2. Structures of envelope glycoproteins
The structures of West Nile Virus (a), Japanese Encephalitis Virus (b) and Zika
virus (c) envelope glycoproteins are colored cyan, magenta, and green. Domains
I, II and III are defined by orange lines and superposed (d), suggesting these
structures are highly similar to each other.
Figure S3
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Fig. S3. The electrostatic potential surfaces of the E protein of three
Flaviviruses
The electrostatic potential surfaces of West Nile Virus (a), Japanese Encephalitis
Virus (b) and Zika virus (c) envelope glycoproteins. Domain III of Zika virus
envelope glycoprotein is more positively charged than those of West Nile Virus
and Japanese Encephalitis Virus envelope glycoproteins.
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