GENEtic deteRminants of dengue virus escape from homotypic immune neutralisATION

"Dengue is the most important arbovirus disease worldwide. Constantly on the rise, the disease has a heavy burden in many developing countries in the South and in most French overseas territories. Historically, immunity acquired against one DENV serotype has been considered to confer 'homotypic' protective immunity against all strains of the same serotype. However, several factors indicate that homotypic protection (vaccine-induced or natural) may vary within the same serotype. A perspective that has strategic implications for two key aspects of DENV prevention and surveillance: (i) the gradual adoption by large countries in the intertropical belt of live-attenuated vaccines against the four serotypes of the dengue virus (DENV) and (ii) our inability to predict the capacity of a given DENV variant to penetrate a population with pre-existing immunity, which is currently natural but will be mixed (vaccine and/or natural) in the future. The main objective of this project is to identify the determinants of escape to homotypic protection against DENV infection, with a focus on a key component of immunity against DENV, immune neutralisation. This will pave the way for improved vaccine protection and surveillance of populations exposed to dengue. To answer this question, we propose a multi-disciplinary approach linking virus strains sequencing and phylodynamic investigations of virus lineage dynamics, to their experimental characterisation in vitro, and the modeling of the links between amino acid changes and antigenic divergence combined with the assessment of resulting structural changes in the envelope protein. To analyse the genetic evolution of DENV and identify variants that escape homotypic immunity, we will set up an observatory of the genetic diversity of strains circulating worldwide. We will create a panel of paired virus strains and anti-serums representative of DENV global diversity that will enable us to analyse intra-serotype antigenic variability within DENV2 (used as a model for this study) with seroneutralisation experiments. Using a combination of substitution-based model, structural impact assessment, and experimental validations based on reverse-genetics, we will finally identify the mutations involved in antigenic divergence in vitro. In parallel to this agnostic approach, we will also use a combination of phylodynamic assessment of locally circulating clades and directed in vitro evolution to identify putative homotypic immune escape variants that will also be characterised at the genetic, structural and antigenic levels. This work will serve as a prelude to the in vivo evaluation of the impact of the most extreme antigenic variations on the ability to protect against homotypic reinfection in vivo following vaccination or infection with a wild-type strain. This project will reinforce genomic monitoring of the virus through a network of national and international partners, renew our understanding of homotypic immune protection (natural and vaccineinduced) against DENV, and ultimately enable the optimisation of epidemiological surveillance and vaccine prevention strategies for dengue epidemics."