From Mosquitos to Humans: Genetic Evolution of Zika Virus

Abstract

Initially isolated in 1947, Zika virus (ZIKV) has recently emerged as a significant public health concern. Sequence analysis of all 41 known ZIKV RNA open reading frames to date indicates that ZIKV has undergone significant changes in both protein and nucleotide sequences during the past half century.

Figure 1. Evolutionary relationships of Zika virus

All full-length Zika virus (ZIKV) ORF nucleotide and amino acid sequences (at least 10,100 bp) were obtained from the NIAID Virus Pathogen Database and Analysis Resource (ViPR) (http://www.viprbrc.org/) and NCBI GenBank (details listed in Table S1). (A) Phylogenetic tree constructed from nucleotide data from 41 viral complete ORF sequences of ZIKV strains by the maximum likelihood method logarithm in MEGA7 based on the Tamura-Nei model. A bootstrap percentage for 1000 replicates was shown on the left. Branches corresponding to partitions reproduced in less than 70% bootstrap replicates are not shown. Strains isolated from human, mosquito and monkey (NIH reference strain) were labeled with blue, orange, and black circles respectively. The two subtypes were labeled on the right side of the tree. The new strains Rio-U1 and Rio-S1 were highlighted using (*). (B) Nucleotide alignments were made using MUSCLE from ViPR. Alignment comparisons were made using Jalview V2.9. Graphical representation of unique nucleotide mutations (blue circle) in Natal_RGN, ZKV2015, Rio-U1, and Rio-S1 strains amongst all (29 total) current human strains within Asian lineage by using pairwise comparisons.

Figure 2. Genetic evolution of the Asian lineage and structural changes in pre-membrane protein (prM)

Graphical illustration of comparison between of Zika virus (ZIKV) from both linages. Amino acid comparisons were made between African (8 mosquito strains and 1 monkey strain) and Asian lineages (25 human strains). The sequences are aligned using MUSCLE. Conserved mutations were selected using meta-CATS from ViPR. Graphical map (top bar) of conserved amino acids, shown in blue line. These sites were in the table below, with the addition of an African human isolate (IbH-30656) and an Asian mosquito isolate (P6-740) for reference. Conserved sites from African and Asian lineages were highlighted in orange and blue, whereas non-related substitutions were highlighted in yellow. (B) Amino acid substitutions were made from pairwise comparisons of P6-740 against all Asian lineage isolates from humans. All mutations in P6-740 were labeled in orange. Using P6-740 as a reference, identical amino acid substitutions in the human isolates were also highlighted orange, and differences labeled in blue. (C) PrM protein of ZIKV shows significant structural alterations. Amino acid substitutions between strains are shown in the table inset. The cartoon representation of the predicted overall tertiary structural comparison of ZIKV PrM proteins from Rio-U1 (cyan) and ARB13565 (yellow). The automated server program CPHmodels-3.0 was employed to build the model according to the homology modeling method. The model was submitted to the Swiss-Model Workspace to obtain the 3D structure. Then verified using PROCHECK and by Verify3D Structure Evaluation Server and QMEAN. The figure was created in PyMol. The structural templates for the PrM protein query sequences were DENV 1 PrM Protein (PDB_ID: 4b03), which shared 48.35% and 50.55% primary sequence identity with the ZIKV PrM proteins from Rio-U1 and ARB13565, respectively. The N and C termini of the structures were labeled with letters. The differences between these two virus strains were shown in sticks.