title: Deep sequencing: becoming a critical tool in clinical virology.
abstract: Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
authors.affiliation: University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.
authors.forename: Miguel E
authors.initials: ME
authors.lastname: Quiñones-Mateu
authors.affiliation: Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico.
authors.forename: Santiago
authors.initials: S
authors.lastname: Avila
authors.affiliation: Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Reyes-Teran
authors.affiliation: Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Martinez
mesh_terms: D014644:Genetic Variation; D015658:HIV Infections / Q000821:virology*; D019698:Hepatitis C, Chronic / Q000821:virology*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000639:trends; D006801:Humans; D007251:Influenza, Human / Q000821:virology*; D025202:Molecular Diagnostic Techniques / Q000379:methods / Q000639:trends; D014773:Virology / Q000379:methods / Q000639:trends; D014780:Viruses / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification
keywords: Deep sequencing; Hepatitis C virus (HCV); Human immunodeficiency virus (HIV); Influenza virus; Next generation sequencing (NGS)