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Next-generation sequencing technology in clinical virology.
MedLine Citation:
PMID:  23279287     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
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.
Authors:
M R Capobianchi; E Giombini; G Rozera
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases     Volume:  19     ISSN:  1469-0691     ISO Abbreviation:  Clin. Microbiol. Infect.     Publication Date:  2013 Jan 
Date Detail:
Created Date:  2013-01-02     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9516420     Medline TA:  Clin Microbiol Infect     Country:  France    
Other Details:
Languages:  eng     Pagination:  15-22     Citation Subset:  IM    
Copyright Information:
© 2012 The Authors Clinical Microbiology and Infection © 2012 European Society of Clinical Microbiology and Infectious Diseases.
Affiliation:
National Institute for Infectious Diseases 'L. Spallanzani', Rome, Italy.
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