Paper # 567 
Ultradeep Sequencing Refines Phenotypic Predictions to Darunavir, Etravirine, and Other Protease and Reverse Transcriptase Inhibitors in Heavily Pre-treated Subjects Infected with Multidrug Resistant HIV-1
Francisco Codoñer*1, C Pou1, A Thielen2, F García3, R Delgado4, D Dalmau5, M Álvarez-Tejado6, B Clotet1,7, L Ruiz1, R Paredes1,7, and the PRIUS Study Group
1Fndn irsiCaixa, Autonomous Univ of Barcelona, Spain; 2Max Planck Inst for Informatics, Saarbrücken, Germany; 3Hosp San Cecilio, Granada, Spain; 4Hosp 12 de Octubre, Madrid, Spain; 5Mútua de Terrassa, Spain; 6Roche Diagnostics SL, Sant Cugat del Vallès, Spain; and 7Fndn Lluita contra la SIDA, Hosp Germans Trias i Pujol, Badalona, Spain
Background: The
role of ultradeep sequencing (UDS) in deep-salvage therapy (DST) is unknown. We
sought to explore the feasibility of UDS as a tool to inform treatment
decisions in heavily pre-treated HIV-1 infected subjects.
Methods: This proof-of-concept study analyzed paired
plasma samples from subjects infected with HIV-1 resistant to PI, NRTI and
NNRTI, who developed virological failure (VF) to DST including, at least,
darunavir, tipranavir, etravirine or raltegravir. Samples were obtained within 6
months before DST initiation (T1) and at the time of virological failure (T2) (i.e.
VL>400 copies/mL 24 weeks after DST initiation). The pol gene (PR,
RT, IN) was genotyped by population sequencing (PS) and UDS, using a predefined
cutoff for UDS of 1%. Viral phenotype was inferred from genotypes using the
HIVdb program.
Results: In
this study, 7 subjects previously exposed to a median of 15 antiretrovirals
during a median of 13 years were included. Median (IQR) VL (copies/mL)
and CD4 counts (cells/mm3) were, respectively, 110600 (46550,
370000) and 50 (12, 126) at T1; and 36700 (2895, 205000) and 150 (27, 247) at
T2. Median (IQR) UDS coverage was 1966 (1244, 2765) sequences. UDS detected all
mutations found by PS. The Table shows the additional mutations detected by UDS
relative to PS and the predicted phenotypic change (PPC) due to the additional
UDS findings.
|
SUBJECT
|
ADHERENCE (qualitative)
|
ART
|
T1
|
T2
|
|
UDS*
|
PPC*
|
UDS*
|
PPC*
|
|
1
|
GOOD
|
TDF FTC DRV RTV
ETR RAL
|
PR: I54T, A71V,
V82F, V82L, V82I
|
DRV: I to H
|
PR: I54A, A71V,
V82F, V82L, V82I
RT: V179D, Y181C
|
DRV, ETR: I to H
|
|
2
|
GOOD
|
TDF FTC DRV RTV
RAL
|
PR: I13V, V32I,
F53L, Q58E, A71I, V77I, V82I, I85V, L89V
|
none
|
PR: L10V, I54T,
A71V, V82I
RT: K101E, Y181C,
T215F
|
ETR: L to H
|
|
3
|
GOOD
|
TDF TPV RTV RAL
|
PR: I62V
RT: T215F
|
none
|
NRTI: D67N
|
ABC, DDI: L to I
|
|
4
|
GOOD
|
TDF FTC TPV RTV
RAL
|
none
|
none
|
RT: A62V
|
none
|
|
5
|
BAD
|
DRV RTV TDF FTC T20
|
PR: I62V
RT: T215F
|
none
|
RT: K103N, T215F
|
ABC, DDI: S to I
AZT, D4T: I to H
TDF: L to I
EFV: I to H
|
|
6
|
BAD
|
ZDV 3TC ABC ATV RAL
|
PR: M36I, I64L,
I64V
RT: K219Q
|
none
|
none
|
none
|
|
7
|
BAD
|
STOPS DRV RTV
TDF FTC, FROM T1 TO T2
|
PR: M36I, I54L,
V82A
RT: M41L, T215Y
|
ABC, ZDV, D4T, DDI,
TDF, FAPV, LPV: L to I
IDV, SQV: I to H
|
RT: T215Y
|
ABC, DDI, TDF: S to L
AZT, D4T: S to I
|
*additional mutations detected
by UDS relative to PS; degree of resistance: S: susceptible; L: low-level; I:
intermediate; H: High-level
Conclusions:
UDS refines phenotypic predictions to DRV, ETR, other PI, and RT-inhibitors in
heavily pre-treated MDR HIV-1-infected subjects by detecting minority mutants
at levels >1% in the virus population.
|
