Challenges in dengue research: A computational perspective

Abstract

The dengue virus is now the most widespread arbovirus affecting human populations, causing significant economic and social impact in South America and South‐East Asia. Increasing urbanization and globalization, coupled with insufficient resources for control, misguided policies or lack of political will, and expansion of its mosquito vectors are some of the reasons why interventions have so far failed to curb this major public health problem. Computational approaches have elucidated on dengue's population dynamics with the aim to provide not only a better understanding of the evolution and epidemiology of the virus but also robust intervention strategies. It is clear, however, that these have been insufficient to address key aspects of dengue's biology, many of which will play a crucial role for the success of future control programmes, including vaccination. Within a multiscale perspective on this biological system, with the aim of linking evolutionary, ecological and epidemiological thinking, as well as to expand on classic modelling assumptions, we here propose, discuss and exemplify a few major computational avenues—real‐time computational analysis of genetic data, phylodynamic modelling frameworks, within‐host model frameworks and GPU‐accelerated computing. We argue that these emerging approaches should offer valuable research opportunities over the coming years, as previously applied and demonstrated in the context of other pathogens.

MVSE: An R‐package that estimates a climate‐driven mosquito‐borne viral suitability index

“…Due to ongoing human and climatic trends that favour the establishment of mosquitoes and movement of infectious hosts, these pathogens are becoming increasingly detrimental for human health and local economies (Jaenisch et al., ; Schwarz et al., ; Stanaway et al., ). For instance, in the last 5 years, Europe has witnessed its first DENV and CHIKV sustained outbreaks (Guzzetta et al., ; Lourenço et al., ). At the same time, ZIKV and CHIKV have recently taken a toll on the populations of island nations (Cauchemez et al., ; Duffy et al., ), South America and the Caribbean (Faria et al., ,, ; Louren¸co et al., ).…”

Portable sequencing in the field and the classroom: a retrospective examination of the circulation of DENV1 and DENV2 in Brazil

“…Dengue serotypes universally present temporal dynamics with an oscillatory behaviour characterized by recurrent peak prevalence of each serotype every 8-11 years. 32 Due to limitations in local testing capacity, inferring the relative prevalence of DENV1-4 with high spatio-temporal resolution in Brazil is often difficult. Our limited data (Table S3) suggests that between 2015 and 2016 DENV1 was the dominant serotype in the MW, NE, and SE regions ( Figure S6).…”

Evolutionary perspectives on human infectious diseases: Challenges, advances, and promises

“…Lourenço et al. () review and analyze the biological and epidemiological background of dengue, together with the major achievements of computational approaches including highlighting critical knowledge gaps and research underachievements that call for an urgent renewed focus. The authors argue that possible advancements based on new processing strategies, including real‐time computational analysis of genetic data, phylodynamic modeling frameworks, within‐host model frameworks and GPU accelerated computing already implemented for other pathogens, are already at reach of the Dengue research community.…”