Homology and conservation of amino acids in E-protein sequences of dengue serotypes

Venkatachalam, Ramesh; Vijayakumar, Sekar

doi:10.1016/s2222-1808(14)60681-2

Cited by 13 publications

(10 citation statements)

References 8 publications

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“…DENV4 was packed with the most number of HCSS nonamers (832 nonamers, ~ 35.85%), while DENV1 was least packed (459 nonamers; ~ 19.78%) (Table 2). This is in agreement with phylogenetic analysis of the four serotypes, with DENV4 generally the most distinct and highly conserved [78].…”

Section: Discussionsupporting

confidence: 88%

Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design

Khan

2019

BMC Genomics

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BackgroundThe sequence diversity of dengue virus (DENV) is one of the challenges in developing an effective vaccine against the virus. Highly conserved, serotype-specific (HCSS), immune-relevant DENV sequences are attractive candidates for vaccine design, and represent an alternative to the approach of selecting pan-DENV conserved sequences. The former aims to limit the number of possible cross-reactive epitope variants in the population, while the latter aims to limit the cross-reactivity between the serotypes to favour a serotype-specific response. Herein, we performed a large-scale systematic study to map and characterise HCSS sequences in the DENV proteome.MethodsAll reported DENV protein sequence data for each serotype was retrieved from the NCBI Entrez Protein (nr) Database (txid: 12637). The downloaded sequences were then separated according to the individual serotype proteins by use of BLASTp search, and subsequently removed for duplicates and co-aligned across the serotypes. Shannon’s entropy and mutual information (MI) analyses, by use of AVANA, were performed to measure the diversity within and between the serotype proteins to identify HCSS nonamers. The sequences were evaluated for the presence of promiscuous T-cell epitopes by use of NetCTLpan 1.1 and NetMHCIIpan 3.2 server for human leukocyte antigen (HLA) class I and class II supertypes, respectively. The predicted epitopes were matched to reported epitopes in the Immune Epitope Database.ResultsA total of 2321 nonamers met the HCSS selection criteria of entropy < 0.25 and MI > 0.8. Concatenating these resulted in a total of 337 HCSS sequences. DENV4 had the most number of HCSS nonamers; NS5, NS3 and E proteins had among the highest, with none in the C and only one in prM. The HCSS sequences were immune-relevant; 87 HCSS sequences were both reported T-cell epitopes/ligands in human and predicted epitopes, supporting the accuracy of the predictions. A number of the HCSS clustered as immunological hotspots and exhibited putative promiscuity beyond a single HLA supertype. The HCSS sequences represented, on average, ~ 40% of the proteome length for each serotype; more than double of pan-DENV sequences (conserved across the four serotypes), and thus offer a larger choice of sequences for vaccine target selection. HCSS sequences of a given serotype showed significant amino acid difference to all the variants of the other serotypes, supporting the notion of serotype-specificity.ConclusionThis work provides a catalogue of HCSS sequences in the DENV proteome, as candidates for vaccine target selection. The methodology described herein provides a framework for similar application to other pathogens.

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Section: Discussionsupporting

confidence: 88%

Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design

Khan

2019

BMC Genomics

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“…This taken in the context of another recent study, which demonstrated that neutralizing antibodies need to be homotypic to preclude the possibility of ADE [ 12 ], strongly suggests that it is important for a safe and effective dengue vaccine to elicit type-specific neutralizing antibodies to each of the four prevalent DENV serotypes. This situation warrants a continued search for alternate non-replicating vaccine candidates that may hopefully eliminate interference and the associated potential safety concerns [ 34 ].…”

Section: Discussionmentioning

confidence: 99%

Virus-like particles derived from Pichia pastoris-expressed dengue virus type 1 glycoprotein elicit homotypic virus-neutralizing envelope domain III-directed antibodies

et al. 2016

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BackgroundFour antigenically distinct serotypes (1–4) of dengue viruses (DENVs) cause dengue disease. Antibodies to any one DENV serotype have the potential to predispose an individual to more severe disease upon infection with a different DENV serotype. A dengue vaccine must elicit homotypic neutralizing antibodies to all four DENV serotypes to avoid the risk of such antibody-dependent enhancement in the vaccine recipient. This is a formidable challenge as evident from the lack of protective efficacy against DENV-2 by a tetravalent live attenuated dengue vaccine that has completed phase III trials recently. These trial data underscore the need to explore non-replicating subunit vaccine alternatives. Recently, using the methylotrophic yeast Pichia pastoris, we showed that DENV-2 and DENV-3 envelope (E) glycoproteins, expressed in absence of prM, implicated in causing severe dengue disease, self-assemble into virus-like particles (VLPs), which elicit predominantly virus-neutralizing antibodies and confer significant protection against lethal DENV challenge in an animal model. The current study extends this work to a third DENV serotype.ResultsWe cloned and expressed DENV-1 E antigen in P. pastoris, and purified it to near homogeneity. Recombinant DENV-1 E underwent post-translational processing, namely, signal peptide cleavage and glycosylation. Purified DENV-1 E self-assembled into stable VLPs, based on electron microscopy and dynamic light scattering analysis. Epitope mapping with monoclonal antibodies revealed that the VLPs retained the overall antigenic integrity of the virion particles despite the absence of prM. Subtle changes accompanied the efficient display of E domain III (EDIII), which contains type-specific neutralizing epitopes. These VLPs were immunogenic, eliciting predominantly homotypic EDIII-directed DENV-1-specific neutralizing antibodies.ConclusionsThis work demonstrates the inherent potential of P. pastoris-expressed DENV-1 E glycoprotein to self-assemble into VLPs eliciting predominantly homotypic neutralizing antibodies. This work justifies an investigation of the last remaining serotype, namely, DENV-4, to assess if it also shares the desirable vaccine potential manifested by the remaining three DENV serotypes. Such efforts could make it possible to envisage the development of a tetravalent dengue vaccine based on VLPs of P. pastoris-expressed E glycoproteins of the four DENV serotypes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12896-016-0280-y) contains supplementary material, which is available to authorized users.

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“…We recognize that arboviruses outbreaks result from a complex interaction among several factors, such as environmental determinants, mosquito ecology, viral genetics, behavior and immunological background of the population 5 , 6 , 16 - 19 . However, it is important that the immunological studies are redesigned and carried out taking into account the multiple variables capable of influencing the cross-reaction between DENV and ZIKV: a) existence of different DENV serotypes, mainly DENV-4, which forms a group considerably distant from DENV-1, -2 and -3 20 ; b) animal model for in vivo studies; c) naïve populations or with history of previous flaviviruses infections; d) coinfection or immunity to other flaviviruses (e.g. Yellow fever virus and West Nile virus ); e) existence of antibodies against conserved or flavivirus-specific regions of the envelope protein; f) genetic diversity of individuals’ immune responses; g) intrinsic factors related to the viruses, such as possible mutations, mainly in the gene sequence coding for the envelope.…”

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confidence: 99%

Dengue in Brazil in 2017: what happened?

Lopes

Silva

Pastor

et al. 2018

Rev. Inst. Med. trop. S. Paulo

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Homology and conservation of amino acids in E-protein sequences of dengue serotypes

Cited by 13 publications

References 8 publications

Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design

Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design

Virus-like particles derived from Pichia pastoris-expressed dengue virus type 1 glycoprotein elicit homotypic virus-neutralizing envelope domain III-directed antibodies

Dengue in Brazil in 2017: what happened?

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