Identifying Candidate Targets of Immune Responses in Zika Virus Based on Homology to Epitopes in Other Flavivirus Species

Abstract

Introduction: The current outbreak of Zika virus has resulted in a massive effort to accelerate the development of ZIKV-specific diagnostics and vaccines. These efforts would benefit greatly from the definition of the specific epitope targets of immune responses in ZIKV, but given the relatively recent emergence of ZIKV as a pandemic threat, few such data are available.

Methods: We used a large body of epitope data for other Flaviviruses that was available from the IEDB for a comparative analysis against the ZIKV proteome in order to project targets of immune responses in ZIKV.

Results: We found a significant level of overlap between known antigenic sites from other Flavivirus proteins with residues on the ZIKV polyprotein. The E and NS1 proteins shared functional antibody epitope sites, whereas regions of T cell reactivity were conserved within NS3 and NS5 for ZIKV. Discussion: Our epitope based analysis provides guidance for which regions of the ZIKV polyprotein are most likely unique targets of ZIKV-specific antibodies, and which targets in ZIKV are most likely to be cross-reactive with other Flavivirus species. These data may therefore provide insights for the development of antibody- and T cell-based ZIKV-specific diagnostics, therapeutics and prophylaxis.

Table 1. ZIKV Sequence similarity

Table 2. Pairwise sequence comparison of the genome polyproteins (top), E proteins (middle) and NS1 proteins (bottom) from different Flaviviruses

Fig. 1A: The Flavivirus sequence identity and human antibody response frequency visualized along the entire ZIKV polyprotein. The sequence identity data (grey) shown represent a running average (window of 9 aa) of sequences for reference Flaviviruses to ZIKV, while the response frequency scores (blue) represent individual residues. Red and green dots along the x-axis represent untested and negative regions, respectively. Residues intervals along the x-axis of the polyprotein plot represent start sites of individual protein products in the polyprotein depicted also at the bottom of panel A.

Fig. 1B: The Flavivirus sequence identity and human antibody response frequency visualized along the E protein. The sequence identity data (grey) shown represent a running average (window of 9 aa) of sequences for reference Flaviviruses to ZIKV, while the response frequency scores (blue) represent individual residues. Red and green dots along the x-axis represent untested and negative regions, respectively. Residues intervals along the x-axis of the polyprotein plot represent start sites of individual protein products in the polyprotein depicted also at the bottom of panel A.

Fig. 1C: The Flavivirus sequence identity and human antibody response frequency visualized along the NS1 protein. The sequence identity data (grey) shown represent a running average (window of 9 aa) of sequences for reference Flaviviruses to ZIKV, while the response frequency scores (blue) represent individual residues. Red and green dots along the x-axis represent untested and negative regions, respectively. Residues intervals along the x-axis of the polyprotein plot represent start sites of individual protein products in the polyprotein depicted also at the bottom of panel A.

Table 3. Regions of high sequence identity and antibody reactivity along ZIKV polyprotein

Table 4. Unique regions on the ZIKV polyprotein with high RFscore against other Flaviviruses

Fig. 2A: 3D rendering of RFscore mapped on the ZIKV E protein using PDB structure 5IRE showing functional Flavivirus epitopes (neutralizing and/or protective) defined in humans and mapped onto the corresponding locations on ZIKV E protein. Colors represent high to low RF scores, where (blue>cyan>green>yellow>orange>red), where blue is highest and red is lowest.

Fig. 2B: 3D rendering of RFscore mapped on the ZIKV NS1 protein using PDB structure 5IY3. Colors represent high to low RF scores, where (blue>cyan>green>yellow>orange>red), where blue is highest and red is lowest.

Fig. 3A: Flavivirus sequence identity and human T cell reactivity visualized onto the ZIKV reference genomic polyprotein for CD8+/class I responses to administered antigen (experimental or commercial vaccines). The sequence identity data shown (grey) represent a running average (window of 9 aa) while the RFscores (blue) represent individual residues. Red and green dots along x-axis represent untested and negative regions, respectively. Residues intervals along the x-axis represent start sites of individual proteins.

Fig. 3B: Flavivirus sequence identity and human T cell reactivity visualized onto the ZIKV reference genomic polyprotein for CD4+/class II responses to administered antigen (experimental or commercial vaccines). The sequence identity data shown (grey) represent a running average (window of 9 aa) while the RFscores (blue) represent individual residues. Red and green dots along x-axis represent untested and negative regions, respectively. Residues intervals along the x-axis represent start sites of individual proteins.

Fig. 4A: Flavivirus sequence identity and human T cell reactivity visualized onto the ZIKV reference genomic polyprotein for CD8+/class I responses to natural exposure (documented DF, DHF, DSS or living in/travel to endemic region). The sequence identity data shown (grey) represent a running average (window of 9 aa) while the response frequency scores (blue) represent individual residues. Red and green dots along x-axis represent untested and negative regions, respectively. Residues intervals along the x-axis represent start sites of individual proteins.

Fig. 4B: Flavivirus sequence identity and human T cell reactivity visualized onto the ZIKV reference genomic polyprotein for CD4+/class II responses to natural exposure (documented DF, DHF, DSS or living in/travel to endemic region). The sequence identity data shown (grey) represent a running average (window of 9 aa) while the response frequency scores (blue) represent individual residues. Red and green dots along x-axis represent untested and negative regions, respectively. Residues intervals along the x-axis represent start sites of individual proteins.

Table 5. Regions of high sequence identity and T cell reactivity along the ZIKV polyprotein

Supplemental Fig. 1: The degree of sequence conservation for consensus residue at each position for ZIKV polyprotein. The red line represents the sequence identity and the blue represents the percentage of residue deletions (if any). Deletions present at N- or C- termini are possibly the result of incomplete sequences and thus may not have biological significance.