title: In-depth characterization of viral isolates from plasma and cells compared with plasma circulating quasispecies in early HIV-1 infection.
abstract: BACKGROUND
  The use of in vitro models to unravel the phenotypic characteristics of circulating viral variants is key to understanding HIV-1 pathogenesis but limited by the availability of primary viral isolates from biological samples. However, overall in vivo genetic variability of HIV-1 within a subject may not be reflected in the viable viral population obtained after isolation. Although several studies have tried to determine whether viral populations expanded in vitro are representative of in vivo findings, the answer remains unclear due to the reduced number of clonal sequences analyzed or samples compared. In order to overcome previous experimental limitations, here we applied Deep Pyrosequencing (DPS) technology in combination with phenotypic experiments to analyze and compare with unprecedented detail the composition of viral isolates and in vivo quasispecies.
  
  
  RESULTS
  We amplified by DPS HIV-1 genomic regions covering gag, protease, integrase and env-V3 to characterize paired isolates from plasma and peripheral blood mononuclear cells and compare them with total plasma viral RNA in four recently HIV-1 infected subjects. Our study demonstrated the presence of unique haplotypes scattered between sample types with conservation of major variants. In addition, no differences in intra- and inter-population encoded protein variability were found between the different types of isolates or when these were compared to plasma viral RNA within subjects. Additionally, in vitro experiments demonstrated phenotypic similarities in terms of replicative capacity and co-receptor usage between viral isolates and plasma viral RNA.
  
  
  CONCLUSIONS
  This study is the first in-depth comparison and characterization of viral isolates from different sources and plasma circulating quasispecies using DPS in recently HIV-1 infected subjects. Our data supports the use of primary isolates regardless of their plasma or cellular origin to define genetic variability and biological traits of circulating HIV-1 quasispecies.
authors.affiliation: AIDS Research Institute IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain.
authors.forename: Judith
authors.initials: J
authors.lastname: Dalmau
authors.forename: Francisco M
authors.initials: FM
authors.lastname: Codoñer
authors.forename: Itziar
authors.initials: I
authors.lastname: Erkizia
authors.forename: Maria
authors.initials: M
authors.lastname: Pino
authors.forename: Christian
authors.initials: C
authors.lastname: Pou
authors.forename: Roger
authors.initials: R
authors.lastname: Paredes
authors.forename: Bonaventura
authors.initials: B
authors.lastname: Clotet
authors.forename: Javier
authors.initials: J
authors.lastname: Martinez-Picado
authors.forename: Julia G
authors.initials: JG
authors.lastname: Prado
mesh_terms: D004279:DNA, Viral / Q000235:genetics; D014644:Genetic Variation; D005838:Genotype; D015658:HIV Infections / Q000097:blood / Q000175:diagnosis*; D015497:HIV-1 / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000166:cytology; D010641:Phenotype; D010802:Phylogeny; D011237:Predictive Value of Tests; D012367:RNA, Viral / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D004279:DNA, Viral; D012367:RNA, Viral