MOLECULAR PERSPECTIVES OF THE EPIDEMIOLOGY, EVOLUTION AND TAXONOMY OF HUMAN PAPILLOMAVIRUSES
type: CreativeWork
description: In this thesis, we demonstrate that the issues of DNA virus evolution, taxonomy, and identification of papillomaviruses are inextricably linked to the wider issues of papillomavirus epidemiology. In our studies, we have designed experiments and databases for the reliable assessment of HPV genomes from lesions, through the use of Polymerase Chain Reaction (PCR) and nucleotide sequencing. Conservation of 30 amino acids in a selected 450 bp L1 fragment unequivocally identifies fragments derived from HPV genomes. Nucleotide sequence alignments allow calculation of their phylogenetic relatedness. Furthermore, through our development of a quantitative criterium by which the concept of type, variant and subtype may be defined, we have established that sequence divergences of these PCR fragments that exceed 10% from any known HPV type suggest a potential novel HPV status. Applying these techniques and developments to a comprehensive study of some 700 samples from Brazil, of which 180 were derived from American Indian patients in the Amazon, we identified three novel HPV genomes. The hope that these three isolates would represent HPV genomes endemic to America's aboriginal populations proved unfounded when reiated HPV genomes were detected in North America, South-East Asia and in non-Indian Brazilians as part of a continuing worldwide search for novel papillomaviruses. Our studies of variants and subtypes concentrated mainly on HPV-18 and the sequence analysis of its Long Control Region (LCR). Our work demonstrated that diversity within HPV-18 correlates with patterns of the evolution and spread of Homo sapiens (substantiating a postulated African origin), similar to that observed in parallel HPV-16 studies. Furthermore, outgroup rooting of the HPV-18 tree against its closest relative HPV-45, identified African HPV-18 variants as the root of the tree. We estimated that diversity within HPV-18 and probably within other HPV types evolved over a period of more than 200,000 year…
abstract: In this thesis, we demonstrate that the issues of DNA virus evolution, taxonomy, and identification of papillomaviruses are inextricably linked to the wider issues of papillomavirus epidemiology. In our studies, we have designed experiments and databases for the reliable assessment of HPV genomes from lesions, through the use of Polymerase Chain Reaction (PCR) and nucleotide sequencing. Conservation of 30 amino acids in a selected 450 bp L1 fragment unequivocally identifies fragments derived from HPV genomes. Nucleotide sequence alignments allow calculation of their phylogenetic relatedness. Furthermore, through our development of a quantitative criterium by which the concept of type, variant and subtype may be defined, we have established that sequence divergences of these PCR fragments that exceed 10% from any known HPV type suggest a potential novel HPV status. Applying these techniques and developments to a comprehensive study of some 700 samples from Brazil, of which 180 were derived from American Indian patients in the Amazon, we identified three novel HPV genomes. The hope that these three isolates would represent HPV genomes endemic to America's aboriginal populations proved unfounded when reiated HPV genomes were detected in North America, South-East Asia and in non-Indian Brazilians as part of a continuing worldwide search for novel papillomaviruses. Our studies of variants and subtypes concentrated mainly on HPV-18 and the sequence analysis of its Long Control Region (LCR). Our work demonstrated that diversity within HPV-18 correlates with patterns of the evolution and spread of Homo sapiens (substantiating a postulated African origin), similar to that observed in parallel HPV-16 studies. Furthermore, outgroup rooting of the HPV-18 tree against its closest relative HPV-45, identified African HPV-18 variants as the root of the tree. We estimated that diversity within HPV-18 and probably within other HPV types evolved over a period of more than 200,000 year…
author: ONG CHI KEONG
date published: 1995
date modified: 2026-07-24T03:33:22Z
provider: National University of Singapore
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: National University of Singapore