title: HIV-1 tropism dynamics and phylogenetic analysis from longitudinal ultra-deep sequencing data of CCR5- and CXCR4-using variants.
abstract: OBJECTIVE
  Coreceptor switch from CCR5 to CXCR4 is associated with HIV disease progression. The molecular and evolutionary mechanisms underlying the CCR5 to CXCR4 switch are the focus of intense recent research. We studied the HIV-1 tropism dynamics in relation to coreceptor usage, the nature of quasispecies from ultra deep sequencing (UDPS) data and their phylogenetic relationships.
  
  
  METHODS
  Here, we characterized C2-V3-C3 sequences of HIV obtained from 19 patients followed up for 54 to 114 months using UDPS, with further genotyping and phylogenetic analysis for coreceptor usage. HIV quasispecies diversity and variability as well as HIV plasma viral load were measured longitudinally and their relationship with the HIV coreceptor usage was analyzed. The longitudinal UDPS data were submitted to phylogenetic analysis and sampling times and coreceptor usage were mapped onto the trees obtained.
  
  
  RESULTS
  Although a temporal viral genetic structuring was evident, the persistence of several viral lineages evolving independently along the infection was statistically supported, indicating a complex scenario for the evolution of viral quasispecies. HIV X4-using variants were present in most of our patients, exhibiting a dissimilar inter- and intra-patient predominance as the component of quasispecies even on antiretroviral therapy. The viral populations from some of the patients studied displayed evidences of the evolution of X4 variants through fitness valleys, whereas for other patients the data favored a gradual mode of emergence.
  
  
  CONCLUSIONS
  CXCR4 usage can emerge independently, in multiple lineages, along the course of HIV infection. The mode of emergence, i.e. gradual or through fitness valleys seems to depend on both virus and patient factors. Furthermore, our analyses suggest that, besides becoming dominant after population-level switches, minor proportions of X4 viruses might exist along the infection, perhaps even at early stages of it. The fate of these minor variants might depend on both viral and host factors.
authors.affiliation: Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina; Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
authors.forename: Mariano M
authors.initials: MM
authors.lastname: Sede
authors.affiliation: Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina; Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
authors.forename: Franco A
authors.initials: FA
authors.lastname: Moretti
authors.affiliation: Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina; Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
authors.forename: Natalia L
authors.initials: NL
authors.lastname: Laufer
authors.affiliation: Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Laboratorio de Virología y Genética Molecular, Facultad de Ciencias Naturales, sede Trelew, Universidad Nacional de la Patagonia San Juan Bosco, Chubut, Argentina.
authors.forename: Leandro R
authors.initials: LR
authors.lastname: Jones
authors.affiliation: Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina; Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
authors.forename: Jorge F
authors.initials: JF
authors.lastname: Quarleri
mesh_terms: D000328:Adult; D005260:Female; D056914:Genomic Structural Variation / Q000235:genetics*; D005838:Genotype; D015658:HIV Infections / Q000235:genetics / Q000821:virology; D015497:HIV-1 / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D019713:Receptors, CCR5 / Q000235:genetics*; D019718:Receptors, CXCR4 / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D019562:Viral Load / Q000235:genetics; D056189:Viral Tropism / Q000235:genetics*
chemical_list: C584933:CCR5 protein, human; C527276:CXCR4 protein, human; D019713:Receptors, CCR5; D019718:Receptors, CXCR4