Inferring the Clonal Structure of Viral Populations from Time Series Sequencing.
PLoS Comput Biol
; 11(11): e1004344, 2015 Nov.
Article
em En
| MEDLINE
| ID: mdl-26571026
ABSTRACT
RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We would like to identify the underlying evolutionary structures. We utilize two sources of information to attempt this; within segment linkage information, and mutation prevalence. We demonstrate that clone haplotypes, their prevalence, and maximum parsimony reticulate evolutionary structures can be identified, although the solutions may not be unique, even for complete sets of information. This is applied to a chain of influenza infection, where we infer evolutionary structures, including reassortment, and demonstrate some of the difficulties of interpretation that arise from deep sequencing due to artifacts such as template switching during PCR amplification.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Vírus de RNA
/
RNA Viral
/
Análise de Sequência de RNA
/
Evolução Molecular
Tipo de estudo:
Risk_factors_studies
Idioma:
En
Revista:
PLoS Comput Biol
Assunto da revista:
BIOLOGIA
/
INFORMATICA MEDICA
Ano de publicação:
2015
Tipo de documento:
Article
País de afiliação:
Reino Unido