title: Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing.
abstract: Rapid evolution and high intrahost sequence diversity are hallmarks of human and simian immunodeficiency virus (HIV/SIV) infection. Minor viral variants have important implications for drug resistance, receptor tropism, and immune evasion. Here, we used ultradeep pyrosequencing to sequence complete HIV/SIV genomes, detecting variants present at a frequency as low as 1%. This approach provides a more complete characterization of the viral population than is possible with conventional methods, revealing low-level drug resistance and detecting previously hidden changes in the viral population. While this work applies pyrosequencing to immunodeficiency viruses, this approach could be applied to virtually any viral pathogen.
authors.affiliation: University of Wisconsin-Madison, Madison, WI 53711, USA.
authors.forename: Benjamin N
authors.initials: BN
authors.lastname: Bimber
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Dudley
authors.forename: Michael
authors.initials: M
authors.lastname: Lauck
authors.forename: Ericka A
authors.initials: EA
authors.lastname: Becker
authors.forename: Emily N
authors.initials: EN
authors.lastname: Chin
authors.forename: Simon M
authors.initials: SM
authors.lastname: Lank
authors.forename: Haiying L
authors.initials: HL
authors.lastname: Grunenwald
authors.forename: Nicholas C
authors.initials: NC
authors.lastname: Caruccio
authors.forename: Mark
authors.initials: M
authors.lastname: Maffitt
authors.forename: Nancy A
authors.initials: NA
authors.lastname: Wilson
authors.forename: Jason S
authors.initials: JS
authors.lastname: Reed
authors.forename: James M
authors.initials: JM
authors.lastname: Sosman
authors.forename: Leandro F
authors.initials: LF
authors.lastname: Tarosso
authors.forename: Sabri
authors.initials: S
authors.lastname: Sanabani
authors.forename: Esper G
authors.initials: EG
authors.lastname: Kallas
authors.forename: Austin L
authors.initials: AL
authors.lastname: Hughes
authors.forename: David H
authors.initials: DH
authors.lastname: O'Connor
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D014644:Genetic Variation; D016679:Genome, Viral; D006678:HIV / Q000737:chemistry / Q000235:genetics* / Q000276:immunology; D015658:HIV Infections / Q000276:immunology / Q000821:virology; D006801:Humans; D008253:Macaca mulatta; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D016097:Simian Acquired Immunodeficiency Syndrome / Q000276:immunology / Q000821:virology; D015302:Simian Immunodeficiency Virus / Q000737:chemistry / Q000235:genetics* / Q000276:immunology; D013045:Species Specificity; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D014764:Viral Proteins