Discovering and characterizing emerging and re-emerging viruses in communities encroaching tropical hotspots.

Author(s)

Nicholas Di Paola

• Document type: Doctoral Thesis
• Press: São Paulo.
• Institution: Universidade de São Paulo (USP). Instituto de Ciências Biomédicas (ICB/SDI)
• Defense date: 2018-03-21

Examining board members

Paolo Marinho de Andrade Zanotto; Daniel José Galafasse Lahr; Carlos Frederico Martins Menck; Saulo Duarte Passos; Enrique Mario Boccardo Pierulivo

• Advisor: Paolo Marinho de Andrade Zanotto

Abstract

Fragmentation and encroachment of tropical rainforests and the growing concentration of human settlements have exponentially increased chances of exposure to re-emerging and emerging viruses. Given the large potential for pathogens to spillover and spread in a population, identifying and characterizing circulating human pathogens could improve the readiness and diagnostic capabilities for a future emergence. Molecular and metagenomic approaches using next-generation sequencing technologies have led to the discovery and characterization of many emerging viruses over the last decade. In complement, in silico approaches can also help identify emerging viruses using only publicly available sequencing data. Moreover, estimating the phylogenetic ancestry and even analyzing changes in codon usage are additional tools that can improve our understanding of an emerging or re-emerging virus. This project aimed to apply these tools to two viruses that could be circulating in Brazil: Parvovirus B19 and Yellow Fever virus. We also explored the applications of Hidden Markov models and codon adaptation index using publicly available data. We expect this work to provide a proof-of-concept for future metagenomic projects, and demonstrate the utility for several molecular and bioinformatics techniques in the study of emerging viruses. (AU)

• FAPESP's process: 13/22136-1 - Discovering novel viruses in communities encroaching tropical hotspots via a metagenomics approach
• Grantee: Nicholas Di Paola
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)