Real-time, rapid detection and sequencing of arboviruses in Brazil: Zika, dengue, Chikungunya and yellow fever

Abstract

Arbovirus infections in Brazil including Zika, chikungunya, dengue and Yellow Fever result inconsiderable morbidity and mortality and are pressing public health concerns. However ourunderstanding of these outbreaks is hampered by limited availability of epidemiologicalsurveillance data. Typically these data are generated by molecular diagnostic assays that are expensive to setup and lack specificity. Consequently we have limited understanding of the interplay and interactions between arboviruses in both human and mosquito populations in Brazil, as demonstrated by Zika virus in Brazil where detection was delayed by at least a year from the true start of the outbreak. Recently we pioneered a new approach to surveillance of arboviruses using portable, real-time nanopore sequencing - so-called 'genomic epidemiology'.This permits sensitive detection and assignment of viruses into genotypes. However, at present,the costs and complexity of this powerful technique (around $100) currently precludes its use as a routine surveillance tool in research and public health laboratory environments. In this proposal we aim to solve three pressing problems with portable sequencing for arbovirusdetection. This continues a highly productive collaboration between the University of São Paulo, the University of Birmingham and the University of Nottingham that has already resulted in very high impact publications in Nature and Nature Protocols [in press] (Faria et al. 2017; Quick et al. 2017). By training a talented early career scientist, Ingra Morales, during a three-month research visit in the UK Midlands and then applying the results of this research to large extant high-quality sample collections at the University of São Paulo, this project will have an immediate impact on the surveillance of arboviruses in Brazil and our understanding of this pressing public health problem. (AU)