Next-generation sequencing technology in clinical virology

Research output: Contribution to journalArticle

94 Citations (Scopus)

Abstract

Recent advances in nucleic acid sequencing technologies, referred to as 'next-generation' sequencing (NGS), have produced a true revolution and opened new perspectives for research and diagnostic applications, owing to the high speed and throughput of data generation. So far, NGS has been applied to metagenomics-based strategies for the discovery of novel viruses and the characterization of viral communities. Additional applications include whole viral genome sequencing, detection of viral genome variability, and the study of viral dynamics. These applications are particularly suitable for viruses such as human immunodeficiency virus, hepatitis B virus, and hepatitis C virus, whose error-prone replication machinery, combined with the high replication rate, results, in each infected individual, in the formation of many genetically related viral variants referred to as quasi-species. The viral quasi-species, in turn, represents the substrate for the selective pressure exerted by the immune system or by antiviral drugs. With traditional approaches, it is difficult to detect and quantify minority genomes present in viral quasi-species that, in fact, may have biological and clinical relevance. NGS provides, for each patient, a dataset of clonal sequences that is some order of magnitude higher than those obtained with conventional approaches. Hence, NGS is an extremely powerful tool with which to investigate previously inaccessible aspects of viral dynamics, such as the contribution of different viral reservoirs to replicating virus in the course of the natural history of the infection, co-receptor usage in minority viral populations harboured by different cell lineages, the dynamics of development of drug resistance, and the re-emergence of hidden genomes after treatment interruptions. The diagnostic application of NGS is just around the corner.

Original languageEnglish
Pages (from-to)15-22
Number of pages8
JournalClinical Microbiology and Infection
Volume19
Issue number1
DOIs
Publication statusPublished - Jan 2013

Fingerprint

Virology
Viral Genome
Viruses
Technology
Genome
Metagenomics
Cell Lineage
Drug Resistance
Hepatitis B virus
Hepacivirus
Nucleic Acids
Antiviral Agents
Immune System
HIV
Infection
Research
Population
Therapeutics

Keywords

  • Co-receptor usage
  • Metagenomics
  • Next-generation sequencing
  • Quasi-species
  • Resistance-associated mutations
  • Ultradeep pyrosequencing
  • Viral diversity

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases

Cite this

Next-generation sequencing technology in clinical virology. / Capobianchi, M. R.; Giombini, E.; Rozera, G.

In: Clinical Microbiology and Infection, Vol. 19, No. 1, 01.2013, p. 15-22.

Research output: Contribution to journalArticle

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