Scholarship 23/07688-0 - Filogenia, Filogeografia - BV FAPESP
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Comparative phylogenetics, phylogeography and epidemiology applied in understanding the evolution of COVID-19, Influenza, and Dengue viruses in Brazil

Grant number: 23/07688-0
Support Opportunities:Scholarships in Brazil - Post-Doctoral
Start date until: November 01, 2023
End date until: October 31, 2025
Field of knowledge:Biological Sciences - Genetics - Molecular Genetics and Genetics of Microorganisms
Principal Investigator:Maria Carolina Quartim Barbosa Elias Sabbaga
Grantee:Isabela Carvalho Brcko
Host Institution: Instituto Butantan. Secretaria da Saúde (São Paulo - Estado). São Paulo , SP, Brazil
Associated research grant:21/11944-6 - Continuous improvement of vaccines: Center for Viral Surveillance and Serological Assessment (CeVIVAS), AP.CCD
Associated scholarship(s):24/17895-5 - Phylodynamics, and Evolution of Influenza A/H1N1pdm09 in Brazil: Integrating Genetic, Epidemiological, and Temporal Data (2009-2024), BE.EP.PD

Abstract

Phylogeography complements phylogenetics by considering the geographic distribution of viral lineages, making possible to investigate and understand how viruses move and spread in geographic space, taking into account environmental factors, movement of people and migration patterns. Finally, comparative epidemiology is fundamental to understanding the evolution of viruses, as it involves comparing different epidemiological aspects, such as transmission rate, disease severity and immune response. The combination of these methods in a single statistical structure was coined as phylodynamics and has proven to be an important tool in the investigation of temporal and geographic origins, evolutionary history and ecological risk factors associated with the growth and spread of viruses. In Brazil, this approach has been applied, mainly, in the investigation of Dengue and Zika epidemics. In Influenza, this approach was timidly explored among the H1N1 and H3N2 subtypes of Influenza A. The main results obtained from these studies revealed low concordance between the current vaccine strain and the A/H3N2 viruses circulating in Brazil between 1999 and 2012, mainly in the South regions and Southeast, places where the sample size were larger. The analyzes also pointed out that the decrease in the effectiveness of the flu vaccine after 2009 and the increase of severe cases are the result of multiple nucleotide substitutions in antigenic sites of the hemagglutinin (HA) gene in A/H1N1. However, both in the study of H3N2 and H1N1, only the HA gene or part of it was included in the analyzes and, therefore, it was not possible to assess how the complete viral genome evolves and how this can influence the antigenic evolution of the viruses. The reduced total number of samples (<300 samples) and low coverage in other regions of Brazil, such as the Midwest, Northeast and Northern, left open important questions about the flow of virus transmission and the frequency of viral lineages in each region of the country. In this context, this project aims to use the phylodynamics approach to integrate genetic data from complete genomes and epidemiological data from Influenza A viruses circulating in Brazil between 2013 and 2024 from all regions of the country collected in GISAID and complemented through the CeVIVAS project. The main objective will be to clarify the dynamics of dispersion of Influenza A viruses in the country to improve the development of vaccines and improve surveillance systems. (AU)

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