• JoomlaWorks Simple Image Rotator
  • JoomlaWorks Simple Image Rotator
  • JoomlaWorks Simple Image Rotator
  • JoomlaWorks Simple Image Rotator
  • JoomlaWorks Simple Image Rotator
  • JoomlaWorks Simple Image Rotator
  • JoomlaWorks Simple Image Rotator
  • JoomlaWorks Simple Image Rotator
  • JoomlaWorks Simple Image Rotator
  • JoomlaWorks Simple Image Rotator
 
  Bookmark and Share
 
 
Doctoral Thesis
DOI
https://doi.org/10.11606/T.42.2018.tde-26062018-095508
Document
Author
Full name
Nicholas Di Paola
Institute/School/College
Knowledge Area
Date of Defense
Published
São Paulo, 2018
Supervisor
Committee
Zanotto, Paolo Marinho de Andrade (President)
Lahr, Daniel José Galafasse
Menck, Carlos Frederico Martins
Passos, Saulo Duarte
Pierulivo, Enrique Mario Boccardo
Title in Portuguese
Descoberta e caracterização de vírus emergentes e reergentes em áreas peri-florestais.
Keywords in Portuguese
Evolução viral
Filogenia
Modelos Ocultos de Markov
Parvovírus B19
Uso do codão
Vírus da febre amarela
Vírus emergente
Abstract in Portuguese
A fragmentação e a invasão de florestas tropicais e a crescente concentração de assentamentos humanos aumentaram exponencialmente as chances de exposição a vírus emergentes e emergentes. Dado o grande potencial de espalhamento de patógenos em população humanas, a identificação e caracterização de agentes patogênicos circulantes podem melhorar a atenção primária e as capacidades de diagnóstico para um agente emergente futuro. As abordagens moleculares e metagenômicas que utilizam as tecnologias de sequenciação da próxima geração levaram a descoberta e caracterização de muitos vírus emergentes na última década. Além disso, as abordagens in silico também podem ajudar a identificar vírus emergentes usando apenas dados de sequenciamento publicamente disponíveis. Além disso, estimar a ascendência filogenética e até mesmo analisar as mudanças no uso de codons são ferramentas adicionais que podem melhorar a nossa compreensão de vírus emergentes ou reemergentes. Este projeto visou aplicar essas ferramentas em ambos os vírus que poderiam estar circulando no Brasil: Parvovírus B19 e vírus da Febre Amarela. Também exploramos as aplicações de modelos ocultos de Markov e índice de adaptação de codons usando dados publicamente disponíveis. Esperamos que este trabalho forneça uma prova de conceito para futuros projetos metagenômicos e demonstre a utilidade das várias técnicas moleculares e bioinformáticas no estudo de vírus emergentes.
Title in English
Discovering and characterizing emerging and re-emerging viruses in communities encroaching tropical hotspots.
Keywords in English
Codon usage
Emerging virus
Hidden Markov Models
Parvovirus B19
Phylogeny
Viral Evolution
Yellow Fever virus
Abstract in English
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.
 
WARNING - Viewing this document is conditioned on your acceptance of the following terms of use:
This document is only for private use for research and teaching activities. Reproduction for commercial use is forbidden. This rights cover the whole data about this document as well as its contents. Any uses or copies of this document in whole or in part must include the author's name.
Release Date
2020-06-25
Publishing Date
2018-06-27
 
WARNING: Learn what derived works are clicking here.
All rights of the thesis/dissertation are from the authors
CeTI-SC/STI
Digital Library of Theses and Dissertations of USP. Copyright © 2001-2020. All rights reserved.