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Genomic epidemiology of emerging arbovirus using heterogeneous data sources in the state of São Paulo

Grant number: 20/13395-7
Support Opportunities:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): March 01, 2021
Effective date (End): February 28, 2022
Field of knowledge:Health Sciences - Medicine - Medical Clinics
Principal Investigator:Ester Cerdeira Sabino
Grantee:Jaqueline Goes de Jesus
Supervisor: Nuno Miguel Rodrigues Pascoal Faria
Host Institution: Faculdade de Medicina (FM). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Research place: Imperial College London, England  
Associated to the scholarship:19/12000-1 - Modeling of the spatiotemporal dispersion of emergent arboviruses using heterogeneous data sources in the State of São Paulo, BP.PD


Recently, Brazil has been affected by unexpected and explosive epidemics of insect- transmitted viruses (arboviruses), most notably Zika, chikungunya, dengue, and yellow fever viruses. Those viruses have brought much concern in public health, and due to genetic changes, host and vector population dynamics and environmental factors, in addition to its capacity for adaptation are emerging and establishing in the country. This study intends to analyze the transmission patterns of emerging sylvatic arbovirus diseases such as DENV, YFV, CHIKV among others, simultaneously analyzing different available sources of information as genome sequences, human density and movements and vector/vertebrate hosts' natural history. By using real-time molecular analysis and generation of novel complete and/or partial genomic sequences our group is contributing to genomic surveillance of those viruses, making it possible to monitor the diversity and viral evolution, allowing a better understanding of the origin of outbreaks and epidemics and of their transmission patterns, in order to estimate the occurrence of future events, assisting in the adoption of more efficient preventive measures and contributing to faster diagnostic approaches and clinical management. Thus, we intend continue performing genomic surveillance for those viruses, including the sequencing of ~1000 (around a thousand) DENV-2 genomes from different locations in Brazil in order to study the phylogenetic diversity of DENV-2 circulating in the country and also to evaluate the lineage replacement previously detected in São Paulo; and the development of a de novo assembly pipeline for generation of Brazilian mosquitoes genomes which are not yet submitted to any database in order to expand the knowledge about those vectors in Latin America. By going abroad, the proponent will have the unique opportunity to be trained on data analysis such as phylogenetics and phylogeographic analysis in spatiotemporal dynamics approach by experts in these fields at Imperial College London and also at University of Oxford. (AU)

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