Prevalence and evolution of low frequency HIV drug resistance mutations detected by ultra deep sequencing in patients experiencing first line antiretroviral therapy failure.
OBJECTIVE
Clinical relevance of low-frequency HIV-1 variants carrying drug resistance associated mutations (DRMs) is still unclear. We aimed to study the prevalence of low-frequency DRMs, detected by Ultra-Deep Sequencing (UDS) before antiretroviral therapy (ART) and at virological failure (VF), in HIV-1 infected patients experiencing VF on first-line ART.


METHODS
Twenty-nine ART-naive patients followed up in the ANRS-CO3 Aquitaine Cohort, having initiated ART between 2000 and 2009 and experiencing VF (2 plasma viral loads (VL) >500 copies/ml or one VL >1000 copies/ml) were included. Reverse transcriptase and protease DRMs were identified using Sanger sequencing (SS) and UDS at baseline (before ART initiation) and VF.


RESULTS
Additional low-frequency variants with PI-, NNRTI- and NRTI-DRMs were found by UDS at baseline and VF, significantly increasing the number of detected DRMs by 1.35 fold (p<0.0001) compared to SS. These low-frequency DRMs modified ARV susceptibility predictions to the prescribed treatment for 1 patient at baseline, in whom low-frequency DRM was found at high frequency at VF, and 6 patients at VF. DRMs found at VF were rarely detected as low-frequency DRMs prior to treatment. The rare low-frequency NNRTI- and NRTI-DRMs detected at baseline that correlated with the prescribed treatment were most often found at high-frequency at VF.


CONCLUSIONS
Low frequency DRMs detected before ART initiation and at VF in patients experiencing VF on first-line ART can increase the overall burden of resistance to PI, NRTI and NNRTI.
Université Bordeaux, Microbiologie fondamentale et Pathogé nicité, UMR 5234, Bordeaux, France ; Centre national de la recherche scientifique, Microbiologie fondamentale et Pathogé nicité, UMR 5234, Bordeaux, France ; Centre Hospitalier Universitaire de Bordeaux, Service de Médecine Interne et Maladies Infectieuses, Hôpital Saint-André, Bordeaux, France ; Université Bordeaux, ISPED, Centre Inserm U897-Epidémiologie-Biostatistique, Bordeaux, France ; Centre Hospitalier Universitaire de Bordeaux, COREVIH Aquitaine, Bordeaux, France.
Marie-Anne
MA
Vandenhende
Université Bordeaux, Microbiologie fondamentale et Pathogé nicité, UMR 5234, Bordeaux, France ; Centre national de la recherche scientifique, Microbiologie fondamentale et Pathogé nicité, UMR 5234, Bordeaux, France ; Centre Hospitalier Universitaire de Bordeaux, Laboratoire de virologie, Bordeaux, France.
Pantxika
P
Bellecave
Université Bordeaux, Microbiologie fondamentale et Pathogé nicité, UMR 5234, Bordeaux, France ; Centre national de la recherche scientifique, Microbiologie fondamentale et Pathogé nicité, UMR 5234, Bordeaux, France ; Centre Hospitalier Universitaire de Bordeaux, Laboratoire de virologie, Bordeaux, France.
Patricia
P
Recordon-Pinson
Université Bordeaux, Microbiologie fondamentale et Pathogé nicité, UMR 5234, Bordeaux, France ; Centre national de la recherche scientifique, Microbiologie fondamentale et Pathogé nicité, UMR 5234, Bordeaux, France ; Centre Hospitalier Universitaire de Bordeaux, Laboratoire de virologie, Bordeaux, France.
Sandrine
S
Reigadas
Centre Jean Perrin, Plateforme GINA, EA 4677 ERTICa, Clermont-Ferrand, France.
Yannick
Y
Bidet
Centre Hospitalier Universitaire de Bordeaux, COREVIH Aquitaine, Bordeaux, France ; Institut National de la Santé et de la Recherche Mé dicale, ISPED, Centre Inserm U897-Epidémiologie-Biostatistique, Bordeaux, France.
Mathias
M
Bruyand
Centre Hospitalier Universitaire de Bordeaux, Service de Médecine Interne et Maladies Infectieuses, Hôpital Saint-André, Bordeaux, France ; Université Bordeaux, ISPED, Centre Inserm U897-Epidémiologie-Biostatistique, Bordeaux, France ; Centre Hospitalier Universitaire de Bordeaux, COREVIH Aquitaine, Bordeaux, France.
Fabrice
F
Bonnet
Centre Hospitalier Universitaire de Bordeaux, Service de Médecine Interne et Maladies Infectieuses, Hôpital Haut-Lévêque, Bordeaux, France.
Estibaliz
E
Lazaro
Centre Hospitalier Universitaire de Bordeaux, Fédération de maladies infectieuses et tropicales, Hôpital Pellegrin, Bordeaux, France.
Didier
D
Neau
Université Bordeaux, Microbiologie fondamentale et Pathogé nicité, UMR 5234, Bordeaux, France ; Centre national de la recherche scientifique, Microbiologie fondamentale et Pathogé nicité, UMR 5234, Bordeaux, France ; Centre Hospitalier Universitaire de Bordeaux, Laboratoire de virologie, Bordeaux, France.
Hervé
H
Fleury
Université Bordeaux, ISPED, Centre Inserm U897-Epidémiologie-Biostatistique, Bordeaux, France ; Centre Hospitalier Universitaire de Bordeaux, COREVIH Aquitaine, Bordeaux, France ; Institut National de la Santé et de la Recherche Mé dicale, ISPED, Centre Inserm U897-Epidémiologie-Biostatistique, Bordeaux, France.
François
F
Dabis
Centre Hospitalier Universitaire de Bordeaux, Service de Médecine Interne et Maladies Infectieuses, Hôpital Saint-André, Bordeaux, France ; Université Bordeaux, ISPED, Centre Inserm U897-Epidémiologie-Biostatistique, Bordeaux, France ; Centre Hospitalier Universitaire de Bordeaux, COREVIH Aquitaine, Bordeaux, France.
Philippe
P
Morlat
Université Bordeaux, Microbiologie fondamentale et Pathogé nicité, UMR 5234, Bordeaux, France ; Centre national de la recherche scientifique, Microbiologie fondamentale et Pathogé nicité, UMR 5234, Bordeaux, France ; Centre Hospitalier Universitaire de Bordeaux, Laboratoire de virologie, Bordeaux, France.
Bernard
B
Masquelier
D000328:Adult; D044966:Anti-Retroviral Agents / Q000627:therapeutic use; D015331:Cohort Studies; D017931:DNA Primers / Q000235:genetics; D024882:Drug Resistance, Viral / Q000235:genetics*; D019143:Evolution, Molecular; D005260:Female; D015658:HIV Infections / Q000188:drug therapy / Q000453:epidemiology* / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008297:Male; D015995:Prevalence; D020133:Reverse Transcriptase Polymerase Chain Reaction; D019562:Viral Load
D044966:Anti-Retroviral Agents; D017931:DNA Primers