Your browser doesn't support javascript.
loading
Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.
Knyazev, Sergey; Hughes, Lauren; Skums, Pavel; Zelikovsky, Alexander.
Afiliação
  • Knyazev S; Georgia State University, Atlanta, GA, USA.
  • Hughes L; University of Georgia, Athens, GA, USA.
  • Skums P; Belarusian State University.
  • Zelikovsky A; Belarusian State University.
Brief Bioinform ; 22(1): 96-108, 2021 01 18.
Article em En | MEDLINE | ID: mdl-32568371
The unprecedented coverage offered by next-generation sequencing (NGS) technology has facilitated the assessment of the population complexity of intra-host RNA viral populations at an unprecedented level of detail. Consequently, analysis of NGS datasets could be used to extract and infer crucial epidemiological and biomedical information on the levels of both infected individuals and susceptible populations, thus enabling the development of more effective prevention strategies and antiviral therapeutics. Such information includes drug resistance, infection stage, transmission clusters and structures of transmission networks. However, NGS data require sophisticated analysis dealing with millions of error-prone short reads per patient. Prior to the NGS era, epidemiological and phylogenetic analyses were geared toward Sanger sequencing technology; now, they must be redesigned to handle the large-scale NGS datasets and properly model the evolution of heterogeneous rapidly mutating viral populations. Additionally, dedicated epidemiological surveillance systems require big data analytics to handle millions of reads obtained from thousands of patients for rapid outbreak investigation and management. We survey bioinformatics tools analyzing NGS data for (i) characterization of intra-host viral population complexity including single nucleotide variant and haplotype calling; (ii) downstream epidemiological analysis and inference of drug-resistant mutations, age of infection and linkage between patients; and (iii) data collection and analytics in surveillance systems for fast response and control of outbreaks.
Assuntos
Palavras-chave

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Infecções por Vírus de RNA / Vírus de RNA / Genômica / Sequenciamento de Nucleotídeos em Larga Escala / Monitoramento Epidemiológico Tipo de estudo: Screening_studies Limite: Humans Idioma: En Revista: Brief Bioinform Assunto da revista: BIOLOGIA / INFORMATICA MEDICA Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Infecções por Vírus de RNA / Vírus de RNA / Genômica / Sequenciamento de Nucleotídeos em Larga Escala / Monitoramento Epidemiológico Tipo de estudo: Screening_studies Limite: Humans Idioma: En Revista: Brief Bioinform Assunto da revista: BIOLOGIA / INFORMATICA MEDICA Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Estados Unidos