title: Using ultradeep pyrosequencing to study HIV-1 coreceptor usage in primary and dual infection.
abstract: HIV-1 dual infection (DI) and CXCR4 (X4) coreceptor usage are associated with accelerated disease progression but frequency and dynamics of coreceptor usage during DI is unknown. Ultradeep sequencing was used to interrogate for DI and infer coreceptor usage in longitudinal blood samples of 102 subjects. At baseline, X4 usage was high (23 subjects harbored X4 variants) and was not associated with infection duration or DI. Coreceptor usage changed over time in 12 of 47 participants, and X4 usage emerged in 4 of 41 monoinfections vs 2 of 5 superinfections (P = .12), suggesting a weak statistical trend toward occurrence of superinfection and acquiring X4 usage.
authors.affiliation: University of California San Diego, La Jolla, CA 92093, USA. gawagner@ucsd.edu
authors.forename: Gabriel A
authors.initials: GA
authors.lastname: Wagner
authors.forename: Mary E
authors.initials: ME
authors.lastname: Pacold
authors.forename: Edgar
authors.initials: E
authors.lastname: Vigil
authors.forename: Gemma
authors.initials: G
authors.lastname: Caballero
authors.forename: Sheldon R
authors.initials: SR
authors.lastname: Morris
authors.forename: Sergei L
authors.initials: SL
authors.lastname: Kosakovsky Pond
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Little
authors.forename: Douglas D
authors.initials: DD
authors.lastname: Richman
authors.forename: Sara
authors.initials: S
authors.lastname: Gianella
authors.forename: Davey M
authors.initials: DM
authors.lastname: Smith
mesh_terms: D000328:Adult; D015658:HIV Infections / Q000276:immunology / Q000821:virology*; D015497:HIV-1 / Q000235:genetics* / Q000276:immunology; D006801:Humans; D008297:Male; D019718:Receptors, CXCR4 / Q000235:genetics / Q000276:immunology; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D019718:Receptors, CXCR4
keywords: HIV-1 coinfection; HIV-1 dual infection; HIV-1 superinfection; coreceptor tropism; coreceptor usage; genotypic coreceptor usage prediction; genotypic tropism prediction; next-generation sequencing; ultradeep pyrosequencing