Evolution of HIV-1 quasispecies and coreceptor use in cell reservoirs of patients on suppressive antiretroviral therapy.
OBJECTIVE
To track changes in the V3 env region of HIV-1 quasispecies and determine virus coreceptor use in cell reservoirs of patients on long-term suppressive antiretroviral therapy (ART).


METHODS
Ten patients whose plasma viraemia had been suppressed for a median of 5.5 years were followed for 5 years. The V3 env regions of viruses in peripheral blood mononuclear cells were analysed by ultra-deep sequencing (UDS). HIV-1 tropism was predicted using the geno2pheno 5.75 algorithm and a phenotypic assay.


RESULTS
The UDS and phenotypic assay data were concordant for predicting HIV-1 tropism. CXCR4-using viruses detected by UDS accounted for 14.7%-76.5% of the virus populations in samples from five patients at enrolment. Five patients harboured pure R5 virus populations and no X4 viruses emerged during the 5 years. The selection pressures estimated by the dN/dS ratio were acting on the V3 region to produce diversification of the quasispecies in CXCR4-infected patients and purification of the quasispecies in R5-infected patients on effective ART.


CONCLUSIONS
UDS showed that the virus quasispecies in cell reservoirs of patients on long-term suppressive ART continued to evolve. CXCR4-using variants became more diversified. Analysis of the selection pressures on the virus quasispecies could provide a clearer picture of virus persistence in patients on effective ART.
INSERM, U1043, Toulouse F-31300, France Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse F-31300, France CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France raymond.s@chu-toulouse.fr.
Stéphanie
S
Raymond
INSERM, U1043, Toulouse F-31300, France.
Adrien
A
Saliou
INSERM, U1043, Toulouse F-31300, France Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse F-31300, France CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse F-31300, France.
Pierre
P
Delobel
INSERM, U1043, Toulouse F-31300, France CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France.
Michelle
M
Cazabat
INSERM, U1043, Toulouse F-31300, France CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France.
Christophe
C
Pasquier
INSERM, U1043, Toulouse F-31300, France CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France.
Nicolas
N
Jeanne
INSERM, U1043, Toulouse F-31300, France Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse F-31300, France CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France.
Karine
K
Sauné
Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse F-31300, France CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse F-31300, France.
Patrice
P
Massip
Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse F-31300, France CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse F-31300, France.
Bruno
B
Marchou
INSERM, U1043, Toulouse F-31300, France Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse F-31300, France CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France.
Jacques
J
Izopet
D000328:Adult; D044966:Anti-Retroviral Agents / Q000627:therapeutic use*; D004279:DNA, Viral / Q000235:genetics; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D060005:Genotyping Techniques; D015658:HIV Infections / Q000188:drug therapy / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000821:virology; D008297:Male; D008875:Middle Aged; D010641:Phenotype; D015728:Receptors, HIV / Q000032:analysis*; D056189:Viral Tropism; D014776:Virus Cultivation; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics
D044966:Anti-Retroviral Agents; D004279:DNA, Viral; D015728:Receptors, HIV; D054299:env Gene Products, Human Immunodeficiency Virus
V3 envelope region; selection pressure; ultra-deep sequencing