Conservation and Variability of Dengue Virus Proteins: Implications for Vaccine Design

Abstract

BackgroundGenetic variation and rapid evolution are hallmarks of RNA viruses, the result of high mutation rates in RNA replication and selection of mutants that enhance viral adaptation, including the escape from host immune responses. Variability is uneven across the genome because mutations resulting in a deleterious effect on viral fitness are restricted. RNA viruses are thus marked by protein sites permissive to multiple mutations and sites critical to viral structure-function that are evolutionarily robust and highly conserved. Identification and characterization of the historical dynamics of the conserved sites have relevance to multiple applications, including potential targets for diagnosis, and prophylactic and therapeutic purposes.Methodology/Principal FindingsWe describe a large-scale identification and analysis of evolutionarily highly conserved amino acid sequences of the entire dengue virus (DENV) proteome, with a focus on sequences of 9 amino acids or more, and thus immune-relevant as potential T-cell determinants. DENV protein sequence data were collected from the NCBI Entrez protein database in 2005 (9,512 sequences) and again in 2007 (12,404 sequences). Forty-four (44) sequences (pan-DENV sequences), mainly those of nonstructural proteins and representing ∼15% of the DENV polyprotein length, were identical in 80% or more of all recorded DENV sequences. Of these 44 sequences, 34 (∼77%) were present in ≥95% of sequences of each DENV type, and 27 (∼61%) were conserved in other Flaviviruses. The frequencies of variants of the pan-DENV sequences were low (0 to ∼5%), as compared to variant frequencies of ∼60 to ∼85% in the non pan-DENV sequence regions. We further showed that the majority of the conserved sequences were immunologically relevant: 34 contained numerous predicted human leukocyte antigen (HLA) supertype-restricted peptide sequences, and 26 contained T-cell determinants identified by studies with HLA-transgenic mice and/or reported to be immunogenic in humans.Conclusions/SignificanceForty-four (44) pan-DENV sequences of at least 9 amino acids were highly conserved and identical in 80% or more of all recorded DENV sequences, and the majority were found to be immune-relevant by their correspondence to known or putative HLA-restricted T-cell determinants. The conservation of these sequences through the entire recorded DENV genetic history supports their possible value for diagnosis, prophylactic and/or therapeutic applications. The combination of bioinformatics and experimental approaches applied herein provides a framework for large-scale and systematic analysis of conserved and variable sequences of other pathogens, in particular, for rapidly mutating viruses, such as influenza A virus and HIV.

West Nile Virus T-Cell Ligand Sequences Shared with Other Flaviviruses: a Multitude of Variant Sequences as Potential Altered Peptide Ligands

“…The evolutionary conservation and variability of the identified T-cell ligand regions in the alignments of the recorded WNV sequences were measured by use of a modified Shannon's entropy computation function (16,56) in the Antigenic Variability Analyzer (AVANA) software (http://sourceforge.net /projects/avana/) (33). The entropy of a ligand sequence (15 to 19 aa) position in the alignment was measured as the average of the entropies of the (7 to 11) nonamer positions within the ligand sequence position.…”

Dengue vaccine–induced CD8+ T cell immunity confers protection in the context of enhancing, interfering maternal antibodies

“…We also demonstrated that maternal antibodies inhibit seroconversion upon PDK53 vaccination in pups born to PDK53-immune dams. However, we hypothesized that vaccination of these pups with PDK53 may still induce T cell-mediated protection, which usually targets the more conserved nonstructural proteins (17,18,38,39). It was indeed reported that the T cell response to vaccination was not impaired by maternal antibodies (29).…”

Dengue virus specific dual HLA binding T cell epitopes induce CD8+T cell responses in seropositive individuals

“…A number of DENV specific T cell activating epitopes have been reported; 4,5,[28][29][30] however, these epitopes have been generated using peptide prediction algorithms and therefore may not accurately represent the natural peptides presented on MHC class I molecules of the infected cells. In addition, in order for a vaccine formulation to be universally applicable (i.e.…”