title: Coreceptor usage, diversity, and divergence in drug-naive and drug-exposed individuals from Malawi, infected with HIV-1 subtype C for more than 20 years.
abstract: There are few cohorts of individuals who have survived infection with HIV-1 for more than 20 years, reported and followed in the literature, and even fewer from Africa. Here we present data on a cohort of subtype C-infected individuals from rural northern Malawi. By sequencing multiple clones from long-term survivors at different time points, and using multiple genotyping approaches, we show that 5 of the 11 individuals are predicted as CXCR4 using (by ≥3/5 predictors) but only one individual is predicted as CXCR4 using by all five algorithms. Using any one genotyping approach overestimates the number of predicted CXCR4 sequences. Patterns of diversity and divergence were variable between the HIV-1 long-term survivors with some individuals showing very small amounts of variation and change, and others showing a greater amount; both patterns are consistent with what has been described in the literature.
authors.affiliation: 1 Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway , Galway, Ireland .
authors.forename: Ishla
authors.initials: I
authors.lastname: Seager
authors.forename: Simon A
authors.initials: SA
authors.lastname: Travers
authors.forename: Michael D
authors.initials: MD
authors.lastname: Leeson
authors.forename: Amelia C
authors.initials: AC
authors.lastname: Crampin
authors.forename: Neil
authors.initials: N
authors.lastname: French
authors.forename: Judith R
authors.initials: JR
authors.lastname: Glynn
authors.forename: Grace P
authors.initials: GP
authors.lastname: McCormack
mesh_terms: D019380:Anti-HIV Agents / Q000627:therapeutic use*; D001483:Base Sequence; D017931:DNA Primers; D015658:HIV Infections / Q000188:drug therapy / Q000378:metabolism* / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000302:isolation & purification*; D006801:Humans; D016013:Likelihood Functions; D008295:Malawi; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D019718:Receptors, CXCR4 / Q000378:metabolism*
chemical_list: D019380:Anti-HIV Agents; D017931:DNA Primers; D019718:Receptors, CXCR4