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Nature Medicine | Volume 30 | December 2024 | 3544–3554 3544
nature medicine
Article
https://doi.org/10.1038/s41591-024-03277-z
Sustained HIV remission after allogeneic
hematopoietic stem cell transplantation
with wild-type CCR5 donor cells
HIV cure has been reported for ve individuals who underwent allogeneic
hematopoietic stem cell transplantation (allo-HSCT) with cells from
CCR5Δ32 homozygous donors. By contrast, viral rebound has occurred
in other people living with HIV who interrupted antiretroviral treatment
after undergoing allo-HSCT, with cells mostly from wild-type CCR5 donors.
Here we report the case of a male individual who has achieved durable HIV
remission following allo-HSCT with cells from an unrelated HLA-matched
(9 of 10 matching for HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 alleles)
wild-type CCR5 donor to treat an extramedullary myeloid tumor. To date,
plasma viral load has remained undetectable for 32 months after the
interruption of antiretroviral treatment. Treatment with ruxolitinib has been
maintained during this period to treat chronic graft-versus-host disease.
Low levels of proviral DNA were detected sporadically after allo-HSCT,
including defective but not intact HIV DNA. No virus could be amplied in
cultures of CD4+ T cells obtained after antiretroviral treatment interruption,
while CD4+ T cells remained susceptible to HIV-1 infection in vitro. Declines
in HIV antibodies and undetectable HIV-specic T cell responses further
corroborate the absence of viral rebound after antiretroviral treatment
interruption. These results suggest that HIV remission could be achieved in
the context of allo-HSCT with wild-type CCR5.
Antiretroviral treatment (ART) efficiently blocks viral replication of
HIV but cannot eliminate infected cells, which persist in people with
HIV despite decades of treatment. These persistently infected cells
establish viral reservoirs that initiate rapid viral rebound if ART is inter-
rupted. A few exceptions have been reported for individuals who are
able to durably control HIV-1 infection after discontinuation of ART,
achieving a state of virological remission1,2. This outcome appears
to be favored by early ART initiation3,4, although the mechanisms
remain unknown. Notably, five individuals have seemingly achieved
an HIV cure after undergoing allogeneic hematopoietic stem cell trans-
plantation (allo-HSCT), for the treatment of different blood cancers,
with cells from CCR5Δ32/Δ32 donors5–9. These donors’ cells lack CCR5
expression on the cell surface, thus providing natural protection against
CCR5-tropic HIV-1 variants10.
Different studies have shown that allo-HSCT in people with
HIV consistently provokes a dramatic decrease in the frequency of
HIV-infected cells
11–14
. The reduction in the size of the HIV reservoir
is unrelated to the presence (or absence) of the CCR5Δ32 mutation in
donor cells15. Instead, it seems to result from a combination of cytotoxic
effects of the conditioning regimens, donor allogeneic immunity dur-
ing graft-versus-host reactions and the gradual dilution of the pool of
infected cells during immune cell replacement
12,16
. However, even such
pressure may not be sufficient to eliminate all infected cells. Cells car-
rying HIV DNA have been found after allo-HSCT in the blood of some
Received: 6 June 2024
Accepted: 27 August 2024
Published online: 2 September 2024
Check for updates
e-mail: asier.saez-cirion@pasteur.fr; alexandra.calmy@hug.ch
A list of authors and their afiliations appears at the end of the paper
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Article https://doi.org/10.1038/s41591-024-03277-z
(21 cycles of 5-azacytidine, 32.5 mg m−2 per day, days 1–5). Severe lym-
phopenia was initially detected after allo-HSCT. A rapid expansion of
NK cells and CD8+ T cells was then observed, followed by CD4+ T cells
and B cells (Fig. 1 and Supplementary Fig. 2a). Immune reconstitution
was incomplete with relatively low CD4
+
T cell counts and an inverse
CD4/CD8 ratio, consistent with what others and we have observed for
other people with HIV who underwent allo-HSCT19,21 (Fig. 1).
The individual developed hepatic acute GvHD 120 days after HSCT
and was treated with corticosteroids and tacrolimus. Following immu-
nosuppressive drug tapering in March 2019 (8 months after HSCT,
M8), he presented with a hepatic GvHD relapse, which was treated
with corticosteroids and cyclosporin. In July 2019 (M12), he further
developed a mild chronic skin GvHD, and in August 2019, a third-line
treatment with ruxolitinib 10 mg twice daily was initiated (Fig. 1 and
Supplementary Fig. 1b). Immunosuppressive drugs were then tapered
and stopped in early January 2021 (M30). Unfortunately, he had signs
of a second hepatic GvHD relapse in late January 2021 and resumed a
combined anti-GvHD treatment course including corticosteroid and
ruxolitinib, with both prescriptions continued until October 2022
(M51). In November 2022 (M52), an atypical neurological chronic GvHD
with neuropathy and small-fiber damage was diagnosed and ruxoli-
tinib 10 mg twice daily was again prescribed together with low-dose
prednisone (10 mg per day).
During the multiple episodes of GvHD, to reduce the risk of poten-
tial drug interactions, ART was further simplified to dolutegravir and
lamivudine dual therapy in December 2019 (M17) and to single dolute-
gravir, one 50 mg tablet daily, in August 2020 (M25). Finally, on 17
November 2021 (M40), all antiretrovirals were stopped following a
consensual decision between the participant and his physician to
evaluate the possibility of HIV remission. At the time of this report,
32 months after interruption of ART (M72), plasma HIV viremia has
remained undetectable despite frequent testing (at least monthly since
ART interruption) (Fig. 1).
Decline of virologic markers after allo-HSCT
We further examined virological markers to better characterize the
evolution of HIV-1 infection following allo-HSCT and ART interruption in
this individual. HIV RNA could be detected with the ultrasensitive viral
load assay in three plasma samples obtained before (1.33 RNA copies
per ml at M3), at the time of (4.18 RNA copies per ml) and immediately
after (2.22 RNA copies per ml at M1) allo-HSCT. A positive ultrasensi-
tive viral load value (4 copies per ml) was also detected at M19 after
allo-HSCT, but was undetectable (<1 copy per ml) in all the other sam-
ples analyzed, including eight samples analyzed after ART interruption
(Fig. 2a). Cell-associated HIV DNA could be detected in bone marrow
cells, peripheral blood mononuclear cells (PBMCs) and purified blood
CD4+ T cells before allo-HSCT (1,096, 202 and 457 copies per million
cells, respectively) (Fig. 3b). These frequencies rapidly decreased after
allo-HSCT. Viral DNA was still detectable (316 copies) in a bone mar-
row sample obtained at M1 after allo-HSCT, but was undetectable in
subsequent samples (Fig. 2b,c). HIV DNA was sporadically detected in
PBMCs with an ultrasensitive assay
22
(maximum of 5 copies per million
cells at M47) and purified CD4+ T cells (maximum of 40 copies at M19,
coinciding with positive ultrasensitive viral load) but was consecutively
undetectable by quantitative PCR in the last 6 samples obtained after
ART interruption. HIV DNA was not detected in small biopsies from the
small intestine; ascending, transverse, descending and sigmoid colon;
cecum; and rectum obtained at M54 (14 months after ART interruption)
(<20 copies of HIV DNA per 106 cells; 1.4 million cells tested).
We also investigated the presence of replication-competent
virus. The intact proviral DNA assay (IPDA)
23
detected potentially
intact proviruses in two samples that had been obtained during
ART-suppressed viremia 17 and 32 months before allo-HSCT in the
context of his participation in the Swiss HIV cohort study (Fig. 2c). By
contrast, potentially intact proviruses were never detected following
people with HIV who did not achieve full donor chimerism12,17 or in
tissue sanctuaries analyzed in necropsy studies
18
. Moreover, during
the weeks following allo-HSCT, a window of vulnerability occurs when
highly activated CD4+ T cells from both donor and recipient coexist19,
thereby increasing the risk of reservoir reseeding if infection of donor
cells is not prevented by pharmacological or genetic and host barriers.
Accordingly, and in contrast to the five individuals who have achieved
HIV cure, viral rebound has been reported so far in all cases of people
with HIV who interrupted ART after receiving allo-HSCT from wild-type
CCR5 donors11–15, and even in some individuals who received a transplant
from CCR5Δ32/Δ32 donors20. These observations strongly supported
the hypothesis that engraftment with CD4
+
T cells that remain resistant
to preexisting HIV-1 variants might be necessary to avoid HIV-1 relapse
from the few infected cells that may persist after allo-HSCT.
Challenging this assumption, we describe here the case of a male
individual living with HIV-1 for over 30 years who, 72 months after
undergoing allo-HSCT with cells from a wild-type CCR5 donor and
32 months after ART interruption, has not shown evidence of HIV-1
rebound or replicating virus despite carrying CD4
+
T cells that remain
fully susceptible to HIV-1 infection.
Results
Case study
We conducted a longitudinal virological and immunological characteri-
zation of a 53-year-old male (IciStem number 34, IciS-34), who is alive
and asymptomatic. This individual was diagnosed to be HIV-1 clade B
positive in May 1990 in Switzerland and presented with a CD4
+
T cell
count of 589 cells per microliter (32%) at the time of diagnosis (cat-
egory A1 according to US Centers for Disease Control and Prevention
classification). He immediately started ART after diagnosis, including
first-generation nucleoside reverse transcriptase inhibitors (Supple-
mentary Fig. 1). However, despite antiretroviral exposure, his CD4+ T cell
count decreased to 295 cells per microliter and the first available HIV-1
plasma viral load determination in October 1996 was 63,293 copies
per milliliter (Fig. 1). At this time, he began protease inhibitor-based
therapy, receiving sequentially boosted saquinavir and atazanavir, with-
out achieving full viral suppression (median (interquartile range), 1,150
(102–7,745) HIV RNA copies per milliliter) during this period that lasted
9 years. A Iopinavir-based therapy was initiated in October 2005, result-
ing in a continuously suppressed plasma viral load despite evidence of
multiresistance to components of three major classes of antiretrovirals
(Supplementary Table 1). A progressive increase in CD4+ T cell counts
and normalization of the CD4/CD8 ratio were also observed (Fig. 1). An
integrase-inhibitor-based ART regimen with dolutegravir and daruna-
vir/ritonavir (DRV/r) was initiated in January 2015. This individual has
been followed in the Swiss HIV cohort study since April 1992.
In January 2018, this person was diagnosed with a myeloid sarcoma
with lymph node and bone marrow involvement. He initially received
two cycles of induction chemotherapy based on anthracyclines,
fludarabine and cytarabine. To avoid drug–drug interactions, DRV/r
was switched to tenofovir alafenamide and emtricitabine (200/25 mg)
in March 2018 (Fig. 1 and Supplementary Fig. 1). He experienced a
short-term malignancy relapse in June 2018 and was treated with
a hypomethylating agent, followed by allo-HSCT in July 2018. The
donor was an unrelated nine-of-ten HLA-matched (Supplementary
Table 2) male with no CCR5Δ32 mutation. IciS-34 received one cycle of
a sequential conditioning regimen (clofarabine, cyclophosphamide,
fludarabine and a total body irradiation of 8 Gy) before the peripheral
stem cell (no T cell depletion) transplant. Graft-versus-host disease
(GvHD) prophylaxis after transplant comprised cyclophosphamide at
days 3 and 4, tacrolimus and mycophenolate mofetil. Full donor chi-
merism in granulocytes and mononuclear cells was achieved in blood
and bone marrow less than a month after the transplant. The myeloid
sarcoma remains in complete remission. A maintenance treatment
with 5-azacytidine was provided from January 2019 to September 2020
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Article https://doi.org/10.1038/s41591-024-03277-z
allo-HSCT. Traces of defective proviruses were detected in PBMCs
and/or bone marrow samples after allo-HSCT by IPDA, at levels over
40 times lower than those observed before allo-HSCT. Intracellular
HIV RNA was also not detected in samples obtained at multiple time-
points after ART interruption (Supplementary Table 3). Finally, viral
production could not be detected with an ultrasensitive p24 single
molecule Simoa assay24 in the supernatants of purified CD4+ T cells
from multiple samples that were cultured in the presence of a pool
of activated CD4
+
T cells from three different donors (Supplemen-
tary Table 3). Overall, these results indicate that the HIV-1 reservoir
markedly contracted after allo-HSCT in this individual and that,
although traces of viral DNA were found in some samples obtained
up to 57 months after the transplant, no potentially intact proviruses
or evidence of replication-competent viruses were detected after
allo-HSCT and ART discontinuation.
Sustained absence of detection of antiretroviral molecules
The participant reported using on-demand pre-exposure prophylaxis
during two episodes in January (M42) and November 2022 (M52), taking
it for only 2–3 days during these times. To document the ART interrup-
tion period more accurately, antiretrovirals were measured retrospec-
tively since November 2022 in all available plasma samples after ART
interruption and prospectively from that point onwards. Low concen-
trations of emtricitabine (2.8–78 ng ml
−1
) and tenofovir (1–4 ng ml
−1
)
were detected in samples obtained at M42 and M53 (Supplementary
Table 4), coinciding with the self-reported use of these molecules by
0
200
400
600
800
1,000
CD4
+
T cells (cells per
µ
l)
0
0.5
1.0
1.5
CD4/CD8
1990 1997 2004 2011 2018
1
2
3
4
5
2019 2020 2021 2022 2023 2 024
Viral load
(log(RNA copies per ml))
GvHD
ART
0 10 20 30 40 45 50 55 60 65 70
Months after allo-HSCT
Immuno-
suppressants
0 10 20 30 40 45 50 55 60 65 70
Months after allo-HSCT
Nucleoside reverse transcriptase inhibitors
Inosine monophosphate
May 1990, HIV diagnosis
Feb 2018, Myeloid sarcoma
Jul 2018, CCR5WT HSCT (M0)
Nov 2021, Stop ART (M40)
Jan 2022, ‘PreP‘
Nov 2022, ‘PreP‘
dehydrogenase inhibitor
Calcineurin inhibitors
Corticoids
Janus kinase inhibitors
Protease inhibitors
Integrase inhibitors
Non-nucleoside reverse transcriptase inhibitors
Positive analysis
Negative analysis (threshold)
Fig. 1 | Treatment course and immuno-virological evolution. Timeline of
clinical events, CD4+ T cell counts, CD4/CD8 ratio and plasma viral load since
HIV-1 diagnosis and until last follow-up. The successive immunosuppressants
and antiretroviral regimens are also shown (detailed information can be found
in Supplementary Fig. 1). Undetectable plasma viral load concentrations are
represented by empty symbols at the threshold of detection, which varied
throughout the follow-up. Hexagons represent different episodes of GvHD.
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Nature Medicine | Volume 30 | December 2024 | 3544–3554 3547
Article https://doi.org/10.1038/s41591-024-03277-z
the participant. This is consistent with the concentrations detected
being at or below the median plasma concentration levels at 24 h after
single oral dose of these molecules reported in the context of the ANRS
IPERGAY study25. Neither these nor other molecules were found in the
other samples analyzed prospectively. These results corroborate that
durable remission of HIV infection in this individual occurred in the
total absence of antiretroviral molecules for extensive periods of time.
CD4+ T cells remain susceptible to HIV-1 infection
Previous cases of HIV remission following allo-HSCT were associated
with the reconstitution of the CD4
+
T cell pool with cells that were resist-
ant to R5 HIV-1 due to the CCR5Δ32 mutation
5–9
. We wondered whether
the CD4
+
T cells that expanded after allo-HSCT in this individual may
possess some alternative mechanism of resistance to HIV-1 infection.
As previously reported for other individuals19, CD4+ T cells from samples
obtained early after allo-HSCT were characterized by high activation
frequencies (15.5% of HLA-DR+CD38+ cells at M4), which decreased in
later samples (2.81% of DR
+
CD38
+
cells at M53) without reaching the
basal levels observed in individuals without HIV (Fig. 3a). In agreement
with the wild-type CCR5 status of the donor, CCR5 could be detected on
the surface of the CD4
+
T cells that expanded after allo-HSCT (Fig. 3b).
These cells also expressed CXCR4, which is used by X4 HIV-1 variants.
Accordingly, purified CD4
+
T cells from IciS-34 obtained after allo-HSCT
were highly susceptible to infection in vitro with (R5) HIV-1
BaL
(Fig. 3c).
Moreover, we detected high levels of infected cells after their in vitro
exposure to HIV-1NL4-3ΔEnv particles pseudotyped with the pantropic
020 40 60
0
2
4
Ultrasensitive VL
Months after allo-HSCT
RNA copies per ml
020 40 60
0
100
200
HIV-1 DNA PBMCs
Months after allo-HSCT
DNA copies per 106
cells
DNA copies per 106 cells
DNA copies per 106 cells
020 40 60
0
200
400
HIV-1 DNA CD4+ T cells
Months after allo-HSCT
0 5 10 15 20
0
500
1,000
1,500
HIV DNA BM
Months after allo-HSCT
Positive analysis Negative analysis (threshold)
IPDA
Blood Bone marrow
Months
after allo-
HSCT
Cells
Intact
(copies
per 106
cells
Defective Cells Intact Defective
–32 681,000 Yes
(13)
Yes
(137/365,000
droplets)a
–17 965,000 Yes
(3)
Yes
(80/167,000
droplets)a
0 Allo-HSCT
1 6,000 No
Yes
(2/51,000
droplets)b
4 218,000 No
Yes
(4/52,000
droplets)a
709,000 No No
19 271,000 No
Yes
(9/27,000
droplets)a
0.9 million No
Yes
(3/42,000
droplets)b
40 ART interruption
52-1 480,000 No No
53 423,000 No
Traces
(1/151,000
droplets)b
55 479,000 No Traces
(1/98,000
droplets)b
56 559,000 No No
57 360,000 No
Traces
(1/75,000
droplets)b
59 695,000 No No
61 514,000 No No
65 738,000 No No
ab
c
ATI AT I AT I
Fig. 2 | Viral markers before and after allo-HSCT. a,b, Evolution of residual
low-level viremia measured with an ultrasensitive viral load (VL) assay in plasma
(a) and HIV DNA associated with PBMCs, purified blood CD4+ T cells or bone
marrow (BM) cells (b) before and after allogeneic HSCT. The empty symbols
represent undetectable levels and are shown at the threshold of the techniques,
which varied depending on the amount of material analyzed. The time of allo-
HSCT and of analytical treatment interruption (ATI) is indicated as a dashed
vertical line. c, Summary of the outcome of IPDA analyses in blood and tissues
at different timepoints before and after allo-HSCT. The number of cells per
amount of material tested is indicated for each analysis. aDefective in 3′ or 5′.
bDefective in 3′.
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Article https://doi.org/10.1038/s41591-024-03277-z
VSV-G envelope (Fig. 3d). These results refuted the presence of intrinsic
barriers preventing HIV-1 replication in the CD4+ T cells of this individual
after transplant.
Waning anti-HIV antibodies
Next, we studied whether the absence of viral rebound could be related
to immune control after ART interruption. Immunoblot analyses
confirmed the stable presence of anti-HIV antibodies over a period of
20 years preceding allo-HSCT. By contrast, anti-HIV antibodies began
to decrease after the intervention, starting with those recognizing
p17 and p31, as previously described for other PLWH who underwent
allo-HSCT
15
(Fig. 4a). Of note, anti-HIV antibodies continued to wane
after ART discontinuation. To characterize the antibody response more
thoroughly during this period, we measured the binding of purified IgG
antibodies from three plasma samples after ART interruption. IgG anti-
bodies binding to HIV-1 p24, BG505 SOSIP.664 and YU2 gp140 foldon
Env trimers, gp120 and gp41 protein subunits were detected in all three
samples at low levels, comparable to those found in people who are on
ART since primary HIV infection (Fig. 4b). These IgGs showed very weak
reactivity against consensus B Env overlapping peptides, including
those from gp120 V3 loop and gp41 immunodominant regions com-
monly detected in other people with HIV (Fig. 4c). Accordingly, puri-
fied IgGs showed no neutralizing activity against a panel of five clade
B viruses (Fig. 4d), and very weak capacity to bind to CEM.NKR-CCR5
target infected cells (Fig. 4e), and thus may have a limited potential
to promote antibody-dependent cellular cytotoxicity. Overall, these
results indicate that the absence of viral rebound after ART interrup-
tion was not related to an increased pressure by the antibody response.
Absence of detectable HIV-specific T cells
Allo-HSCT was performed with cells from a donor who was matched
for HLA-B*27 (Supplementary Table 2), an allele that has previously
been shown to favor HIV-1 control26. However, we could not detect, by
intracellular cytokine staining, CD4
+
or CD8
+
T cells responding to 6 h
of stimulation with pools of overlapping HIV-1 Gag, Nef or Pol peptides
in samples obtained after allo-HSCT (M10) or after ART interruption
HIVneg
HIV + ART
M4
M11
M51
M52-1
M52-2
M53
0
10
20
30
40
CCR5 cells among
CD4+ T cells (%)
IciS-34
Post allo-HSCT
HIVneg
HIV + ART
M4
M11
M51
M52-1
M52-2
M53
0
100
Normalized to mode
80
60
40
20
101102103
GFP
104105
0
20
40
60
80
100
CXCR4 cells among
CD4+ T cells (%)
IciS-34
Post allo-HSCT
3 7 10 14
1
10
100
1,000
Days after infection (in vitro)
p24 (ng ml−1)
EFS974
IciS-34
HIVBaL (R5) NL4-3∆Env-VSVG
HIVneg
HIV + ART
M4
M11
M51
M52-1
M52-2
M53
0
5
10
15
20
CD38+HLA-DR+ cells
among CD4+ T cells (%)
IciS-34
Post allo-HSCT
HIVneg
HIV + ART
M4
M11
M51
M52-1
M52-2
M53
0
0.5
1.0
1.5
2.0
Ki67+ cells among
CD4+ T cells (%)
IciS-34
Post allo-HSCT
a
b
cd
GFP+
57.4
GFP+
52.7
Fig. 3 | Phenotype and HIV susceptibility of CD4+ T cells. a,b, Percentage of
CD4+ T cells from IciS-34 expressing activation markers (CD38+HLA-DR+, Ki67+)
(a) and the HIV-1 coreceptors CCR5 and CXCR4 (b) at different times after
allo-HSCT (samples designated as the month after allo-HSCT when they were
obtained; purple). The proportions of CD4+ T cells from an independent HIV-
negative (HIVneg) blood donor (gray) and one person with HIV on ART (black) are
depicted for reference. c, Dynamics of viral replication in purified CD4+ T cells
from IciS-34 (M59, purple) and one unrelated blood donor upon infection in vitro
with HIV-1BaL. The data are shown as the mean ± s.d. (n = 3 replicates) of p24 levels
in culture supernatants. d, Proportion of infected (GFP+) CD4+ T cells from IciS-34
3 days after challenge with HIVNL4.3GFPΔEnv-VSV-G particles (purple). The negative
control is depicted as a dashed line. The rate of infected CD4+ T cells from one
unrelated blood donor is provided as a reference (gray).
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Nature Medicine | Volume 30 | December 2024 | 3544–3554 3549
Article https://doi.org/10.1038/s41591-024-03277-z
(M45 and M64) (Fig. 5a,c). No HIV-specific cells could be amplified
either after 6 days of stimulation or recall with HIV-1 peptides (Fig. 5b,c).
Moreover, we did not detect CD8
+
T cells binding to HLA-B*27 dex-
tramers carrying the immunodominant KRWIILGLNK Gag epitope
(Supplementary Fig. 3e). By contrast, cells responding to human cyto-
megalovirus (HCMV) pp65 peptides could be detected in the same
samples and amplified in 6 day cultures (Fig. 5a–c). In agreement with
the lack of detection of HIV-specific CD8+ T cells, purified CD8+ T cells
obtained at multiple timepoints after ART interruption could not sup-
press ex vivo HIV-1 infection of autologous CD4
+
T cells (Fig. 5d). These
results argue against a role of T cells in maintaining viral control in this
individual and confirm the overall lack of mobilization of the adaptive
response against HIV-1 in this person despite ART discontinuation.
Notably, we observed a relative lack of T cell reactivity in this
individual to short polyclonal stimulation when compared with
cells from different unrelated blood donors explored in these analy-
ses. We wondered whether this observation could be related to the
ruxolitinib-based immunosuppressive therapy27 that was administered
for extended periods of time to treat GvHD. We therefore analyzed the
T cell responses in samples taken before, during and after a brief period
of ruxolitinib discontinuation that occurred during the follow-up
(between M51 and M53; Fig. 5e). Poor polyclonal reactivity was again
observed in the M51 sample, when compared with cells from another
blood donor (EFS639). The frequency of responding cells sharply
increased in the samples taken 2 weeks (M52-1) and 4 weeks (M52-2)
after ruxolitinib was stopped. Ruxolitinib was reintroduced at this time
owing to relapse of GvHD, and a reduction in the frequency of respond-
ing T cells was observed 2 weeks later (M53). These results support
that ruxolitinib therapy may influence the reactivity of T cells to short
polyclonal stimulation. Of note, despite the stronger T cell reactivity
observed during ruxolitinib discontinuation, no HIV-specific T cells
could be identified during this period (Fig. 5e).
High frequency of CD16+CD56– NK cells
NK cells have been proposed to play an important role in mediating
the graft-versus-leukemia effect upon allo-HSCT, while their expan-
sion and interaction with T cells may also regulate acute and chronic
GvHD
28,29
. On the other hand, their implication in controlling HIV after
ART interruption is suggested by recent reports
30–32
. Of note, IciS-34
underwent allo-HSCT with cells from a nine-of-ten HLA-matched donor.
Among the matched alleles, there were three HLA class I alleles (A*24:02,
B*27:05 and B*44:02) that intrinsically express the Bw4 ligand that is
recognized by NK cells and whose presence has been associated with
lower levels of HIV-1 viremia33. We therefore analyzed the phenotype
and antiviral capacity of NK cells. While early after allo-HSCT, NK cells
were characterized by a high proportion of immature CD16
−
CD56
++
cells, a high proportion of experienced CD16
+
CD56
−
cells expressing
CD57 were observed at later timepoints (Fig. 6a,b). NK cells expressed
different killer-cell immunoglobulin-like receptors (KIRs; Fig. 6c), such
as KIR2DL1/S1, KIR2DL23 and, notably, KIR3DL1/S1, which are reported
NK cell receptors for Bw4 (refs. 34–36). NK cell maturation, loss of
CD56 and expression of CD57, was more preponderant among cells
expressing KIRs and, in particular, KIR3DL1/S1 (Fig. 6b,c), suggesting
a predominant activation of KIR-expressing cells in this case. The loss
of CD56 expression has been proposed to identify NK cells with adap-
tive traits that became exhausted owing to repeated inflammatory and
activating signals
37
. Although CD16
+
CD56
−
NK cells are expanded dur-
ing chronic HIV infection
38,39
, the frequency observed here was higher
than that in one person with HIV on ART whose cells were analyzed in
parallel for reference (Fig. 6a and Supplementary Fig. 4b). The dynam-
ics of NK cells in this case closely recapitulate the changes occurring
in people without HIV who underwent allo-HSCT and experienced
HCMV reactivation during the procedure40. Indeed, IciS-34 experienced
three episodes of HCMV reactivation between August 2018 and March
2019 requiring valganciclovir treatment. HCMV reactivation was also
detected between June 2019 and January 2020, but at levels that did
not require treatment. We did not observe significant changes in the
phenotype of NK cells during the brief period of ruxolitinib discontinu-
ation (Fig. 6b and Supplementary Fig. 4c). While CD16+CD56− NK cells
have been reported to have poor cytotoxic and antiviral potential38,39,
we found that NK cells from IciS-34 were able to partially inhibit HIV-1
infection in vitro of autologous CD4
+
T cells (Fig. 6d). Further analyses
will be needed to better understand the role that NK cells may have
played in decreasing the HIV reservoir through graft-versus-HIV res
-
ervoir or direct antiviral effects.
Discussion
We describe the case of a person who underwent allo-HSCT with cells
from a wild-type CCR5 donor and whose viral load remains undetect-
able 32 months after interruption of ART. Multiple virological and
immunological readouts confirm the absence of viral exposure since
ART discontinuation and support a profound and prolonged HIV-1
remission in this individual.
At the time of allo-HSCT, this individual had been living with HIV for
more than 30 years and had experienced several years of uncontrolled
viremia, leading to a drop in CD4
+
T cell counts, before the virus was
successfully controlled through an optimized protease inhibitor-based
ART regimen. IPDA confirmed the presence of replication-competent
virus in samples obtained during the period of suppressed viremia
under ART before allo-HSCT. Cells carrying HIV DNA were readily detect-
able in blood and bone marrow samples just before the intervention,
and residual viremia in the plasma was detected with an ultrasensi-
tive technique at this time. A drastic drop in all these parameters was
observed following allo-HSCT. However, previous cases of people with
HIV who interrupted ART after wild-type CCR5 allo-HSCT resulted in viral
rebound within weeks to months of treatment discontinuation
11,41
, con-
firming that the dramatic decline in the viral reservoirs associated with
allo-HSCT is generally not sufficient to achieve HIV remission or cure.
The factors underlying the absence of viral rebound in the case pre-
sented here remain unclear. Sporadic (twice) pre-exposure prophylaxis
use was reported by the participant and confirmed by pharmacological
analyses, but given the long-term viral remission (now getting close
to 3 years), we believe intermittent ART was not a major factor in the
outcome of this case. Unknown host factors may hinder HIV reseeding
and amplification from residual infected cells in this case. We found,
however, that CD4+ T cells obtained after ART interruption were fully
susceptible to HIV-1 infection. Moreover, we could not identify any
evidence of immune-driven control of infection. In particular, we could
not find neutralizing antibodies or CD8
+
T cells able to suppress HIV
infection. On the contrary, the lack of detectable HIV-specific T cells and
the weak and waning antibody levels observed after ART interruption
provide further evidence of the lack of viral reactivation events since
allo-HSCT in this individual. Nevertheless, we cannot rule out a poten-
tial role of NK cells in mediating viral control. The combination of Bw4
ligands and KIRs present in this person after the transplant has been
previously shown to favor natural viral control
35,36
, and NK cells have
the capacity to react to the expression of stress peptides on infected
cells42 before viral antigen production. Although the CD16+CD56− NK
population, highly abundant in this case, has been generally considered
as functionally impaired38,39, recent reports suggest that this population
may be more heterogeneous than previously thought and that at least
some of these cells possess diverse functionality, including cytotoxic
potential
43,44
. A more thorough analysis of this compartment in this
and other cases of people with HIV who required allo-HSCT will be
needed to better understand the potential role of NK cells in controlling
infection in this setting, either through graft-versus-reservoir effects
or antiviral activities.
The immunosuppressive environment provided by ruxolitinib
might contribute to the prevention of viral reactivation in this indi-
vidual. This inhibitor of the JAK–STAT pathway was used to treat GvHD
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Nature Medicine | Volume 30 | December 2024 | 3544–3554 3550
Article https://doi.org/10.1038/s41591-024-03277-z
and has been administered almost continuously since ART interrup-
tion. Of note, ruxolitinib has been shown to block HIV replication,
viral reactivation and reservoir reseeding in vitro and ex vivo and may
favor the decay of the viral reservoir
45,46
. We found that the presence
of ruxolitinib was indeed associated with a relative lack of reactivity
of T cells from this individual to short stimulation in vitro. Ruxolitinib
was briefly discontinued during the follow-up after ART interruption,
and this was accompanied by an increase in T cell reactivity in vitro. The
absence of ruxolitinib did not result in viral rebound or the appearance
of HIV-specific cells, suggesting that no HIV antigens were produced
during this period. It is possible, however, that the discontinuation
of ruxolitinib (4 weeks) was too short for stochastic viral reactivation
events to occur in a context in which potential remaining infected cells
would be extremely rare.
Finally, we can hypothesize that allogenic immunity during
repeated graft-versus-host events in this individual led to a deeper
elimination of infected cells than in previous cases, achieving HIV cure
through the complete purge of cells carrying replication-competent
gp120
gp41
p31
p24
p17
Stop ART (M40)
M–251
M–3
M3
M37
M44
M63
Allo-HSCT (M0)
gp120
gp41
p31
p24
p17
41 26 12 17 0
31 21 7 1 1 1
55 34 16 12 1
50 23 1 1 14 3
81 81 40 43 4
84 83 43 38 9
83 86 50 47 15
79 78 36 35 7
6 5 4 10 0
AD8
YU2
CH058
REJO
THRO
CO42
CO108
CO107
CO105
PTC005002
pt3
Ctr–
1
2
3
A
450 nm
CO108
CO107
PTC005002
pt3
Ctr–
21018516013511085603510
IciS-34
M55
IciS-34
M55
IciS-34
M65
IciS-34M53
IciS-34M53
IciS-34M53
IciS-34M55
gp120 gp41
V3 PID
0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
98 16 97 83 90
87 95 93 53 46
43 0 22 28 52
0 0 0 0 0
Bal.26
6535.3
YU2.DG
PVO.4
SC422661.8
pt3
PTC005002
CO107 (lART)
CO108 (eART)
OD405nm
log10[IgG (µg ml−1)]
AUC
p24
eART
lART
IciS-34
Ctr
SOSIP gp140 gp120 gp41
0
1
2
3
4
0
1
2
3
4
0
1
2
3
4
0
1
2
3
4
–2 –1 0 1 2
0
1
2
3
4
0
50
100
150
200
0
50
100
150
200
0
50
100
150
200
0
50
100
150
200
0
50
100
150
200
a
bc
de
3
Rating
2
1
+/–
–
Fig. 4 | Antibody response after ART interruption. a, Results of immunoblots
for HIV-1 antibodies in plasma samples from IciS-34 at different times before
and after allo-HSCT. The arrows indicate the antigens against which reactivity
was progressively lost. On the right are indicated the reactivity ratings that were
automatically attributed for each antigen on the strips. b, ELISA graphs (left)
comparing the reactivity of purified plasma IgG antibodies from IciS-34 (values
for samples obtained at three different timepoints (M53, M55, M65) are depicted)
and early- and late-treated PLWH (eART (n = 6) and lART (n = 6), respectively)
against HIV-1 p24 and Env proteins. HIV-1-seronegative (Ctr−) sera (n = 5) were
used as negative controls. Dot plots comparing the area under the curve (AUC)
values calculated from the titration curves are shown on the right (horizontal
lines indicate the median values). c, Heatmap showing the ELISA binding
analysis of purified serum IgG antibodies from IciS-34 at two timepoints against
consensus subtype B overlapping Env peptides. Darker colors indicate higher
reactivity (absorbance values); white, no binding. Sera from eART (CO108),
lART (CO107), post-treatment controller (PTC005002) and elite controller (pt3)
individuals were used as positive controls. d, Heatmap comparing the in vitro
neutralizing activity (as percentages) of purified serum IgG antibodies from
IciS-34 (3 timepoints), CO108, CO107, PTC005002 and pt3 against selected clade
B tier 1 and 2 viruses as measured in the TZM-bl assay. e, Heatmap comparing
the percentage of CEM.NKR-CCR5 cells infected by laboratory-adapted (YU2
and AD8) and transmitted/founder viruses (CH058, REJO and THRO) bound
by purified serum IgG antibodies from IciS-34 (2 timepoints), eART (CO42 and
CO108), lART (CO105 and CO107), PTC005002 and pt3. HIV-1-seronegative (Ctr−)
serum was used as negative control (c,e).
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Nature Medicine | Volume 30 | December 2024 | 3544–3554 3551
Article https://doi.org/10.1038/s41591-024-03277-z
HIV
PMA–iono
HCMV pp65
HIV Gag
HIV Nef
HIV Pol
EFS639
M51
M52-1
M52-2
M53 0.5
1.0
1.5
2.0
PMA–iono
HCMV pp65
HIV Gag
HIV Nef
HIV Pol
1
2
3
4
PMA–iono
HCMV pp65
HIV Gag
HIV Nef
HIV Pol
EFS639
M51
M52-1
M52-2
M53 0.05
0.10
0.15
0.20
0.25
PMA–iono
HCMV pp65
HIV Gag
HIV Nef
HIV Pol
0.5
1.0
CD4 CD8 CD4 CD8
+
Ruxolitinib
+
–
–
+
Ruxolitinib
+
–
–
IFNγTNF IFNγCD107
1.18
0.13
2.34
1.63
1.12
0.18
0.43
0.16
4.24
0.12
2.63
4.9
2.24
0.16
0.26
0.19
0.16
0.06
0.07
0.12
1.29
0.37
0.81
0.12
0.09
EFS889 6 h
M45 6 h
EFS889 6 d
M45 6 d
EFS1010 6 h
M64 6 h
EFS1010 6 d
M64 6 d
20
40
60
% of cells
% of cells
% of cells % of cells % of cells % of cells
Pos control
HCMV pp65
HIV Gag
HIV Nef
HIV Pol
EFS889 6 h
M45 6 h
EFS889 6 d
M45 6 d
EFS1010 6 h
M64 6 h
EFS1010 6 d
M64 6 d
20
40
60
IFNγTNF
IFNγCD107
35.1
3.7
0.13
0.16
0.21
1.14
3.28
22.8
64.8
63.1
21.6
2.72
22.8
26
5.59
0.34
0.06
0.15
0.21
1
2.28
15.4
58.5
60.4
9.2
1.42
14.9
18.9
IFNγ BV605
TNF PerP Cy5.5
IciS-34
IciS-34
HIVneg
Unstim
0
0
00.016 7.04 × 10−3 0.064 11.0
0.89
0.16
0.010
0.011
8.38 × 10−3
Gag Nef Pol HCMV pp65 PMA/ionomycin
CFSE
IFNγ BV605
HIVneg
Unstim Gag Nef Pol HCMV pp65 PMA/ionomycin
HIVneg
105
105
104
104
103
103
–103
–103
0
0
M51 M52-1 M52-2 M53
IFNγ BV605
CD8-BUV496
a c
b
d
e
CD4 CD4:CD8
0.1
1
10
100
1,000
p24 (ng ml−1)
0.013
9.30 × 10−3
4.89 0.28 3.29 6.94 3.78
4.29 × 10−3 3.20 × 10−3 1.25 57.5
0.046 0.02 0 0
0
0.34 61.8
HIV
Fig. 5 | T cell reactivity and HIV-specific T cell response. a, Percentage of
CD8+ T cells from IciS-34 (M45) and an HIV-negative donor producing IFNγ and
TNF after 6 h of stimulation with PMA/ionomycin, or with pools of HCMV pp65
peptides and HIV-1 Gag, Nef and Pol peptides. Unstimulated (Unstim) cells were
used as control. Results are depicted as standard pseudocolor dot plots.
b, Percentage of CD8+ T cells from IciS-34 (M45) and an HIV-negative donor that
proliferated (CFSElow) after 6 days of stimulation with anti-CD3/CD28, pools
of HCMV pp65 peptides, and HIV-1 Gag, Nef and Pol peptides and were able to
produce IFNγ upon short polyclonal or antigen-specific restimulation.
c, Heatmap comparing the percentage of CD8+ T cells from IciS-34 (two samples)
and two HIV-negative donors that produced IFNγ and/or TNF and IFNγ and/or
expressed CD107 after 6 h or 6 days (d) of polyclonal (positive control, Pos) or
antigen-specific stimulation. Darker colors indicate higher percentages. White,
undetectable; gray, not done. The percentages are indicated after subtraction
of the background from the unstimulated condition. d, Comparison of the level
of infection of CD4+ T cells from IciS-34 (M45) infected in vitro with HIV-1BaL
cultured alone or in the presence of autologous CD8+ T cells (1:1 ratio). The results
are shown as the levels of p24 in culture supernatants at day 7 after infection
in vitro (mean ± s.d. of 3 experiments). Similar results were obtained at M54,
M56, M57 and M59. e, Percentage of CD8+ T cells from an HIV-negative donor
and IciS-34 at time of ruxolitinib discontinuation (M51), 15 days after ruxolitinib
discontinuation (M52-1), 4 weeks after ruxolitinib discontinuation, time of
reinitiation (M52-2) and 15 days after ruxolitinib reinitiation (M53), producing
IFNγ 6 h after polyclonal stimulation with PMA/ionomycin (top). Heatmap
comparing the percentages of CD4+ and CD8+ T cells from the HIV-negative donor
and IciS-34 at different timepoints that produced IFNγ and/or TNF and IFNγ and/
or expressed CD107 after 6 h of polyclonal or antigen-specific stimulation.
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Nature Medicine | Volume 30 | December 2024 | 3544–3554 3552
Article https://doi.org/10.1038/s41591-024-03277-z
viruses. In favor of an allogenic pressure on the HIV reservoir in this
case is the progressive rarefaction after the transplant of cells carrying
viral DNA, which were detected at trace levels in several samples in the
months that followed the transplant. The need for graft-versus-host
reactions to achieve HIV cure after allo-HSCT has been the subject
of debate: while its impact on the HIV reservoir is increasingly clear
(graft-versus-reservoir effects)
15,47
, the incidence of GvH in the reported
cases of HIV cure after allo-HSCT was variable5–9. Of note, a recent
study in a model of allo-HSCT in Simian immunodeficiency virus
(SIV)-infected macaques has shown that allogeneic immunity can in
some cases lead to the total clearance of the viral reservoir
16
. Recently,
a mathematical model was applied to data from IciStem participants,
including data from IciS-34 before ART interruption15. The model
supports the hypothesis that the main driver of the strong reservoir
reduction after allo-HSCT is graft-versus-reservoir effects rather than
conditioning regimens. It is tempting to assume that the repeated
graft-versus-host reactions in this case may have led to an efficient
elimination of reservoir cells in the absence of the barrier provided
by CCR5Δ32.
Allo-HSCT is not a therapeutic option for people with HIV who do
not have a cancer requiring this approach. Nevertheless, allo-HSCT is
the only medical intervention that has reproducibly led to profound
remission and potential cure of HIV-1 infection. The case presented
here is the first to achieve such outcome after receiving cells from a
ART IciS-34
CD16–CD56++ CD16+CD56+CD16+CD56–
a
b
0
1,000
2,000
3,000
4,000
5,000
CD57 (MFI)
2DL1/S1
2DL2/3
3DL1/S1
–
–
–
+
–
–
+
+
–
+
–
+
+
+
+
c
d
CD4
CD4:NK (1:1)
CD4:NK (1:3)
1
10
100
p24 (ng ml−1)
98.9
0
KIR2DL1/S1–BUV496
0
100
200
300
400
Count
29.3
0
KIR3DL1/S1–PerCPCy5.5
0
100
200
300
25.7
0
KIR2DL2/3–BUV396
0
50
100
150
200
32.2 2.52
3.3661.9
CD57–FITC
CD69–BV650
11.8 35.3
45.67. 28
12.2 32.5
40.015.3
15.1 1.6 8
1.9681.2
0
KIR3DL1/S1–PerCP–Cy5.5
0
KIR2DL2/3–BUV396
15.9 13 .1
27. 443 .7
17. 9 8.72
18.255.2
CD16
+
CD56
+
9.95
CD16+CD56–
13.8
CD16–CD56++
2.81
CD16–APC Cy7
CD56–BUV737
CD16+CD56+
37.6
CD16+CD56–
4.95
CD16–CD56++
3.34
0
CD16–APC Cy7
0
–103
–103
103
103
104
104
105
105
105
104
103
0 105
104
103
104
103
0
105
104
103
106
105105105
104104
103103
–103
104
0
–103
103
104
105
1050–103103104105
CD56–BUV737
ART
M4
M10
M51
M52-1
M52-2
M53
0
20
40
60
80
100
Follow-up after HSCT
Proportion among NK cells (%)
CD16–CD56++ CD16+CD56+CD16+CD56–
Fig. 6 | Phenotype and antiviral activity of NK cells. a, Expression of CD16
and CD56 on NK cells from one person with HIV on ART and IciS-34 (M52-2).
b, Proportion of CD16−CD56++, CD16+CD56+ and CD16+CD56− NK cells in the
sample from the person on ART and from IciS-34 at six different timepoints (left).
Expression of KIR2DL2/3 and/or KIR3DL1/S1 and CD69 and/or CD57 in the three
NK cell subsets from IciS-34 (M52-2) (right). c, Expression of CD57 on NK cell
subsets from IciS-34 (M52-2) defined on the absence or expression of different
combinations of KIRs. MFI, median fluorescence intensity. d, Comparison of
the level of infection of CD4+ T cells from IciS-34 (M59) infected in vitro with
HIV-1BaL cultured alone or in the presence of autologous NK cells (1:1 and 1:3
ratios). The results are shown as the levels of p24 in culture supernatants at day
3 after infection in vitro (mean ± s.d. of three experiments). Similar results were
obtained at M54.
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Article https://doi.org/10.1038/s41591-024-03277-z
wild-type CCR5 donor. It is unclear whether the status that this person
has achieved will be permanent. We cannot exclude that he may harbor
rare, infected cells with competent provirus or that viral rebound may
occur if immunosuppressive drugs are discontinued for longer periods
of time. Viral rebound can occur even after long periods of undetect-
able viremia without ART, as observed in the so-called Mississippi
baby48. Because of the absence of an intrinsic resistance to infection,
the risk of viral rebound may be considered higher than for the cases
of allo-HSCT with CCR5Δ32 cells. However, the duration of undetect-
able viremia is unprecedented in this context. This case opens new
perspectives for the development of HIV cure strategies, particularly
concerning allogeneic immunity and immunosuppressive drugs.
Online content
Any methods, additional references, Nature Portfolio reporting sum-
maries, source data, extended data, supplementary information,
acknowledgements, peer review information; details of author con-
tributions and competing interests; and statements of data and code
availability are available at https://doi.org/10.1038/s41591-024-03277-z.
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© The Author(s) 2024
Asier Sáez-Cirión 1,2 , Anne-Claire Mamez3, Véronique Avettand-Fenoel 4,5,6, Mitja Nabergoj 7, Caroline Passaes 1,2,
Paul Thoueille 8,9, Laurent Decosterd 8, Maxime Hentzien 10, Federico Perdomo-Celis 2, Maria Salgado 11,12,13,
Monique Nijhuis 14,15, Adeline Mélard 4, Elise Gardiennet 4, Valérie Lorin 16, Valérie Monceaux 1,2, Anaïs Chapel1,2,
Maël Gourvès 1, Marine Lechartier1, Hugo Mouquet16, Annemarie Wensing 17,18, Javier Martinez-Picado 11,12,13,19,20,
Sabine Yerly 21, Mathieu Rougemont22 & Alexandra Calmy 10
1Viral Reservoirs and Immune Control Unit, Université Paris Cité, Institut Pasteur, Paris, France. 2HIV Inlammation and Persistence Unit, Université Paris
Cité, Institut Pasteur, Paris, France. 3Division of Hematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland. 4Institut
Cochin—CNRS 8104/INSERM U1016/Université de Paris, Paris, France. 5LI2RSO, Université d’Orléans, Orléans, France. 6Virologie, CHU d’Orléans,
Orléans, France. 7Institut Central des Hôpitaux, Sion, Switzerland. 8Service of Clinical Pharmacology, Department of Laboratory Medicine and Pathology,
Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland. 9Service of Clinical Pharmacology, Department of Medicine, Lausanne
University Hospital and University of Lausanne, Lausanne, Switzerland. 10HIV/AIDS Unit, Division of Infectious Diseases, Geneva University Hospitals,
Geneva, Switzerland. 11IrsiCaixa, Badalona, Spain. 12Germans Trias i Pujol Research Institute, Badalona, Spain. 13CIBERINFEC, Instituto de Salud Carlos
III, Madrid, Spain. 14Translational Virology Research Group, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The
Netherlands. 15HIV Pathogenesis Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. 16Humoral
Immunology Unit, Inserm U1222, Université Paris Cité, Institut Pasteur, Paris, France. 17Translational Virology Research Group, Department of Global Public
Health & Bioethics, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands. 18Ezintsha, Faculty of
Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. 19UVic-UCC, Vic, Spain. 20ICREA, Barcelona, Spain. 21Laboratory of Virology,
Geneva University Hospitals, Geneva, Switzerland. 22Unafiliated, Geneva, Switzerland. e-mail: asier.saez-cirion@pasteur.fr; alexandra.calmy@hug.ch
Content courtesy of Springer Nature, terms of use apply. Rights reserved
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Article https://doi.org/10.1038/s41591-024-03277-z
Methods
Ethics
The described individual was enrolled in 1992 in the Swiss HIV Cohort
Study (SHCS; www.shcs.ch) and in 2018 as participant number 34
in the IciStem (IciS-34) program (www.icistem.org) at the Hôpitaux
Universitaires de Genève after giving signed consent. The SHCS was
approved by the Cantonal Ethics Commission at Zürich (the Central
Ethics Commission in Switzerland for the SHCS), and the IciStem study
by the ethical committee at the Universitair Medisch Centrum Utrecht.
HSCT was done in the context of the standard protocol at Hôpitaux
Universitaires de Genève. The individual signed a consent form for the
use of samples for research purposes according to the regulations of
the Hôpitaux Universitaires de Genève.
The decision to stop ART was reached consensually between the
participant and his attending physicians after a period of treatment
simplification, which was implemented to diminish the risk of interac-
tions with immunosuppressors used to treat GvHD. Analyses from unre-
lated HIV-negative blood donors from the Etablissement Français du
Sang (collaboration agreement with Institut Pasteur) and people with
HIV on ART (with undetectable viremia for >24 months) from the ANRS
EP36 XII mTOR study (approved by ethics committee Ile-de-France XI)
are provided as reference.
Sample processing
Peripheral blood was collected in EDTA tubes. Fresh blood samples
were centrifuged at 750g for 20 min to collect the plasma. A second
centrifugation was made at 2,000g for 30 min to eliminate platelets.
Plasma samples were stored at −80 °C. PBMCs were obtained by density
gradient centrifugation following Ficoll Plaque Plus separation (GE
Healthcare) and used fresh or cryopreserved in liquid nitrogen.
Ultrasensitive plasma viremia
Ultrasensitive HIV RNA quantifications were performed on large
volumes of plasma using the Generic (Biocentric) or Abbott HIV
real-time PCR assay (Abbott)
12,22
. In brief, 3.5–17.5 ml of plasma was
ultra-concentrated at 170,000g at 4 °C for 30 min, after which viral RNA
was extracted. HIV RNA was quantified with a validated in-house cali-
bration curve, set with a limit of detection of 0.56 copies per milliliter.
Cell-associated HIV DNA and RNA levels
Total DNA was isolated from frozen PBMCs or CD4+ T cells sorted
from PBMCs (StemCell Technologies) using the DNeasy Kit (Qiagen).
Total HIV DNA was quantified with an ultrasensitive method using the
real-time PCR GENERIC HIV-DNA assay (Biocentric)22,49
Cell-associated RNA was extracted from PBMCs with an AllPrep
DNA/RNA Mini Kit (Qiagen). During extraction, cell-associated HIV
RNA was treated using DNase I (Qiagen). Cell-associated HIV RNA was
quantified by semi-nested real-time PCR targeting the gag region with
previously described primers and probes50 shown in Supplementary
Table 5. Reverse transcription was performed with random hexamers
and SuperScript IV (Invitrogen). The first PCR was performed with
Taq ADN polymerase (Merck) for 15 cycles, then the product of the
first PCR was used as a template in the second PCR. The semi-nested
real-time PCR was performed with Platinum qPCR SuperMix-UDG
w/ROX (Invitrogen) for 50 cycles. To normalize cell-associated HIV
RNA per µg total RNA, ribosomal RNA was quantified from the same
cDNA by real-time PCR using the Ribosomal RNA Control Reagents kit
(Applied Biosystems).
IPDA
The presence of potentially intact DNA HIV-1 was determined in PBMCs
using a duplex droplet digital PCR (QX200 ddPCR system, Bio-Rad)
targeting two regions in the viral genome
23
: the packaging signal in
the 5′ and the Rev response element in env in the 3′. Genomic DNA
was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen) with
precautions to minimize DNA shearing. To normalize and calculate
DNA shearing, a second duplex droplet digital PCR was used, targeting
the human RPP30 gene. Primers and probes were previously described
and are shown in Supplementary Table 6.
CD4+ T cell culture for viral amplification
CD4+ T cells were isolated from fresh PBMCs after positive selec-
tion with magnetic beads (EasySep Human CD4 Positive Selection
Kit II, StemCell Technologies, 17852). Cells were stimulated with
phytohemagglutinin-L (2 µg ml−1, Sigma-Aldrich, L4144) and IL-2
(200 UI ml
−1
, Miltenyi Biotec, 130-097-746). After 3 days of stimu-
lation, cells from IciS-34 (1× 10
6
–2 × 10
6
cells) were put in culture
with a pre-activated pool of HIV-susceptible CD4+ T cells from 3
HIV-negative donors (1:3 ratio of total cells) at a final concentra-
tion of 106 ml−1 in RPMI 1640 with glutamax (Gibco, 61870-044) sup-
plemented with 10% heat-inactivated fetal calf serum and IL-2 at
200 UI ml
−1
. Culture supernatants were collected every 3 to 4 days
and fresh medium was added to the cultures. Supernatants were
stored at −80 °C before analysis.
HIV-1 p24 was analyzed by ultrasensitive digital ELISA (Simoa
Quanterix). Cell supernatants were thawed at room temperature and
centrifuged at 845g for 5 min; 200 µl was transferred into a SimOa
96-well plate and inactivated with 20 µl of Triton 20%. HIV-1 Gag p24
was determined on a Simoa HD-1 analyzer using the Simoa HIV p24
kit (Quanterix, 102215) following the manufacturer’s instructions.
Four-parameter logistic regression fitting was used to estimate the
concentration of p24. Samples below the limit of quantification were
based on the established cutoff (it was determined based on the p24
average number of enzymes per bead (AEB) signal in the standard 0
and calculated as 2.5 standard deviations from the mean of the p24
AEB signal).
CD4+ T cell susceptibility to HIV-1 infection
Productive HIV-1 infection in vitro was studied in activated CD4
+
T cells
(10
6
cells per ml in triplicate) exposed to the HIV-1
BaL
strain (R5; p24
10 ng ml−1). The cells were cultured in 96-U-well plates for 14 days.
Every 3–4 days, the culture supernatants were removed and replaced
with fresh culture medium. Viral replication was monitored in the
supernatants by p24 ELISA (XpressBio). Single-round infections were
performed with HIV-1 NL4.3ΔenvΔnef/GFP (ref. 51) pseudotyped with
the VSV-G envelope protein by transiently cotransfecting (SuperFect;
Qiagen) 293 T cells with the proviral vectors and the VSV-G expression
vector pMD2.G. Activated CD4+ T cells were infected in triplicate (5 × 104
cells per well, 200 µl) with 35 ng per 1 × 106 HIV-1 NL4.3Δnef/GFP/VSV-G.
Active HIV-1 infection was estimated by flow cytometry (BD Fortessa,
BD Biosciences) as the percentage of GFP-expressing CD4
+
T cells 72 h
after infection.
Flow cytometry phenotyping
T cell phenotyping. Frozen PBMCs were thawed and incubated over-
night in RPMI, 10% fetal bovine serum, 1% penicillin–streptomycin
and IL-15 (0.1 ng ml−1, Miltenyi Biotec). Cells were stained with a Live/
Dead Fixable Aqua Dead Cell Stain Kit (Life Technologies) followed by
surface staining (CD3–FITC (SK7, 344804, dilution 1:13, BioLegend),
CD4–BUV496 (OKT4, 750977, 1:65, BD Biosciences), CD8–BUV496
(RPA-T8, 612942, 1:65, BD Biosciences), CCR5–PECy7 (2D7, 557752,
1:7, BD Biosciences), CXCR4–PE (12G5, 555974, 1:7, BD Biosciences),
CD45RA–APC_H7 (HI100, 560674, 1:26, BD Biosciences), CCR7–PE_Daz-
zle_594 (G043H7, 353236, 1:13, BioLegend), CD27–APC_R700 (M-T271,
565116, 1:26, BD Biosciences), HLA-DR–BV786 (G46-6, 564041, 1:26, BD
Biosciences), CD38–BV605 (HIT2, 740401, 1:65, BD Biosciences) and
Brilliant Stain Buffer Plus (563794, 1:3, BD Biosciences)). For intranu-
clear staining, cells were fixed and permeabilized (Cytofix/Cytoperm,
BD Biosciences) and stained with anti-Ki67-eFluor450 (20Raj1, 48-5699-
42, 1:26, eBioscience). All samples were acquired on an LSRFortessa
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Article https://doi.org/10.1038/s41591-024-03277-z
flow cytometer (BD Biosciences). The differentiation into naive, central
memory, transitional memory, effector memory and late effector
T cells over time was analyzed via the expression of CCR7, CD27 and
CD45RA (Supplementary Fig. 3a).
NK cell phenotyping. Frozen PBMCs were thawed and incubated
overnight in RPMI, 10% fetal bovine serum, 1% penicillin–streptomycin
and IL-15 (0.1 ng ml−1, Miltenyi Biotec). Cells were stained with a Live/
Dead Fixable Aqua Dead Cell Stain Kit (L34957, 1:2,000, Life Tech-
nologies) followed by surface staining (KIR2DL2/L3–BUV395 (clone
CH-L, 743456, 1:40), KIR2DL1/S1–BUV496 (clone HP-MA4, 752510,
1:40), CD25–BUV661 (clone M-A251, 741608, 1:40), CD56–BUV737
(clone NCAM16.2, 612766, 1:20), CD14–V450 (clone M5E2, 558121,
1:250), CD19–V450 (clone HIB19, 560353, 1:20), NKG2A–BV605 (clone
131411, 747921, 1:80), CD69–BV650 (clone FN50, number 563835, 1:20),
DNAM1–BV711 (clone DX11, 564796, 1:20), NKG2C–BV786 (clone 134591,
748170, 1:25), CD57–FITC (clone NK-1, 555619, 1:5), NKp46–PECy7
(clone 9E2, 562101, 1:20), CD3–AF700 (clone UCHT1, 557943, 1:50),
CD16–APC Cy7 (clone 3G8, 560195, 1:20) (all from BD Biosciences);
CD85j/LILRB1–PE (clone REA998, 130-116-615, 1:50), NKG2D–PE Vio615
(clone REA1228, 130-124-352, 1:50), KIR3DL1/S1–PerCPVio700 (clone
REA168, 130-124-077, 1:50), NKp30–APC (clone REA823, 130-112-431,
1:50) (from Miltenyi)). The gating schemes applied to identify NK cells
are shown in Supplementary Fig. 4. Boolean gating was performed
with FlowJo (v10.9) and the following markers: KIR3DL1/S1, KIR2DL1/
S1 and KIRDL2/3. Data were acquired using an LSRFortessa X20 flow
cytometer (BD Biosciences).
T cell stimulation
Cryopreserved PBMCs were thawed in RPMI 1640 Medium, GlutaMAX
Supplement, complemented with 20% fetal bovine serum. Cells were
split and partly stained with carboxyfluorescein succinimidyl ester
(CFSE) at 1 µM (Invitrogen, C34554) for 6 days of stimulation experi-
ments. All cells were then kept overnight at 37 °C and 5% CO2.
6h of stimulation. PBMCs were resuspended in RPMI 1640 Medium,
GlutaMAX with 10% fetal bovine serum in the presence of anti-CD107a–
BUV396 (clone H4A3, 565113,1:200) and BD FastImmune Co-stimulatory
Antibodies CD28/CD49d (1 µg ml
−1
; BD, 347690) and left unstimulated
or stimulated with either hCMV pp65 peptide pool (2 µg ml−1), HIV Gag
peptides (2 µg ml−1), HIV Nef peptides (2 µg ml−1) (all of them obtained
through the NIH HIV reagents program) or soluble anti-CD3 (clone
OKT3, 1 µg ml
−1
, eBioscience, 16-0037-85) and anti-CD28 (clone CD28.2,
1 µg ml
−1
, eBioscience, 16-0289-85). After 30 min of incubation, brefel-
din A (10 µg ml
−1
; Invitrogen, 00-4506-51) and BD GolgiStop Protein
Transport Inhibitor (containing monensin) (1 µg ml−1, BD, 554724) were
added and cells were cultured for 5 h 30 min before flow cytometry
staining.
6days of stimulation. CFSE-labeled PBMCs were resuspended in
RPMI 1640 Medium, GlutaMAX Supplement, complemented with 10%
fetal bovine serum and left unstimulated or stimulated in the same
conditions as described above. Following 6 days of culture, cells were
resuspended with anti-CD107a_BUV395 (clone H4A3, BD Biosciences,
565113, 1:200), brefeldin A and BD GolgiStop Protein Transport Inhibi-
tor (containing monensin) and were left unstimulated or restimulated
overnight with hCMV pp65 peptide pool (2 µg ml−1), HIV Gag pep-
tides (2 µg ml−1), HIV Nef peptides (2 µg ml−1), or phorbol 12-myristate
13-acetate (PMA) (80 ng ml
−1
, Sigma-Aldrich, P8139-5MG) and ionomy-
cin (500 ng ml−1, Sigma-Aldrich, I0634-5MG).
In all conditions, samples were stained using the Live/Dead Fix
-
able Aqua Dead Cell Stain Kit (Invitrogen; L34957), then extracellular
staining was performed using CD3–APCe780 (clone UCHT1, 47-0038-
42, 1:9, Biolegend), CD4–BUV737 (clone OKT4, 750977, 1:36, BD Bio-
sciences), CD8–BUV496 (clone RPA-T8, 612942, 1:36, BD Biosciences),
CCR7–PEDazzle594 (clone G043H7, 353236, 1:7, Biolegend), CD45RA
PECy7 (clone 5H9, 561216, 1:14, BD Biosciences) and CD27 APCR700
(clone M-T271, 565116, 1:14, BD Biosciences) antibodies. The cells were
fixed and permeabilized with the BD Cytofix/Cytoperm Fixation/Per-
meabilization Kit (BD Biosciences) and stained for IFNγ BV605 (clone
B27, 560679, 1:6, BD Biosciences), and TNF PerCP Cy5.5 (clone Mab11,
560679, 1:6, BD Biosciences) before analysis with an LSRFortessa X20
flow cytometer (BD Biosciences).
Viral suppression assays
HIV-1 suppression was evaluated with fresh blood samples
52
. After
PBMC isolation from peripheral blood, CD4+ T cells were separated
by positive magnetic bead isolation (EasySep Human CD4 Positive
Selection Kit II, 17852) and the remaining cell fraction was split for
subsequent CD8+ T cell and NK cell negative selection (EasySep Human
CD8+ Cell Enrichment Kit, 19053; EasySep Human NK Enrichment
Kit, 19055) using a Robosep instrument (StemCell Technology). Puri-
fied cells were cultured in RPMI 1640 medium containing GlutaMAX,
10% fetal bovine serum, penicillin (10 UI ml−1) and streptomycin
(10 µg ml−1). After purification, CD4+ T cells were activated for 3 days
with 2 µg ml
−1
of phytohemagglutinin-L (Sigma, L4144) and 200 IU ml
−1
of IL-2 (human IL-2 IS, premium grade, Miltenyi Biotec, 130-097-745).
In parallel, CD8+ T cells and NK cells were cultured in complete RPMI
medium in the absence of cytokines (CD8+ T cells) or in the presence
of IL-15 at 0.1 ng ml
−1
(NK cells). Activated CD4
+
T cells were infected
with HIV-1
BaL
by spinoculation alone or with autologous CD8
+
T cells
(1:1 ratio) or NK cells (1:1 and 1:3 ratio). Cells were then cultured for
14 days in interleukin-2 (100 IU ml
−1
)-supplemented complete RPMI.
Supernatants were collected and fresh medium replenished every
3–4 days. Viral replication was measured in terms of p24 production
in the culture supernatants by means of ELISA (HIV-1 p24 ELISA kit,
XpressBio, XB-1000). The viral inhibitory capacity of NK cells was
calculated comparing p24 levels at day 3 after infection in the NK:CD4
co-cultures to CD4
+
T cells cultured alone. The viral inhibitory capacity
of CD8
+
T cells was calculated at day 7 after infection as the log drop
in p24 production when CD4+ T cells were cultured in the presence of
CD8+ T cells.
Analysis of anti-HIV antibodies
Initial screening for HIV antibodies in plasma samples was done using
INNO-LIA HIV Score immunoblot (Fujirebio). For deeper characteri-
zation, IgG antibodies were purified from plasma samples by affin-
ity chromatography using Protein G Sepharose 4 Fast Flow (Cytvia,
17061805) according to the manufacturer’s instructions. Purified
plasma antibodies were dialyzed against PBS using Slide-A-Lyzer Cas-
settes (10 K molecular weight cutoff, Thermo Fisher Scientific). Final
IgG concentrations were measured using a NanoDro One instrument
(Thermo Fisher Scientific). Previously purified plasma IgG antibodies
from early treated (eART), late treated (lART), elite controller (Pt3),
and post-treatment controller (PTC005002) donors53–55 were used as
controls in the following experiments.
Titration of antibody levels by ELISAs. High-binding 96-well ELISA
plates (Costar, Corning) were coated overnight with purified Env pro-
teins (His-tagged clade B YU2 trimeric gp140 and monomeric gp120
(ref. 56), BG505 SOSIP.664 (ref. 57), gp41 (group O HIV-1 and 2, 227-
20101, RayBiotech) and HxB2 p24 (produced from the expression
plasmid number ARP-13137, NIH AIDS reagent program; 125 ng per well
in PBS). After washing with 0.05% Tween 20-PBS (PBST), plates were
blocked for 2 h with 2% bovine serum albumin and 1 mM EDTA–PBST
(blocking solution), washed and incubated with 1:3 serially diluted puri-
fied IgG antibodies in PBS (maximum concentration of 50 µg ml−1). After
washing, plates were revealed by the addition of goat-HRP-conjugated
anti-human IgG (1:2,000, 109-035-098, Jackson ImmunoResearch)
and HRP chromogenic substrate (ABTS solution; Euromedex)58,59.
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Nature Medicine
Article https://doi.org/10.1038/s41591-024-03277-z
Overlapping linear HIV-1 Env peptides (n = 211, consensus Subtype B
Env peptide set, 9480, BEI Resources) were coated on high-binding
96-well ELISA plates (Costar, Corning) at 10 µg ml−1 in PBS overnight.
After washing with 0.1% Tween 20–PBS, plates were blocked for 2 h with
1% Tween 20, 5% sucrose and 3% milk–PBS (blocking solution); washed
with 0.1% Tween 20–PBS; and incubated with purified IgG antibodies
at 10 µg ml
−1
in 1% BSA and 0.1% Tween 20–PBS. Plates were revealed
by the addition of secondary antibody and substrate as described.
Experiments were performed using a HydroSpeed microplate washer
and Sunrise microplate absorbance reader (Tecan), with absorbance
measured at 450 nm (A
450 nm
). All antibodies were tested in duplicate in
at least two independent experiments.
HIV-1 neutralization assay. Pseudoviruses (BaL.26 (11446), 6535.3
(11017), YU2.DG (12133), SC422661.8 (11058) and PVO.4 (11022); Env
plasmids obtained from the NIH AIDS reagent program) were prepared
by co-transfection of HEK-293T cells (CRL-3216, ATCC) with pSG3Δenv
vector (11051, NIH AIDS Reagent Program) using FUGENE-6 transfection
reagent (Promega)
60,61
. Neutralization experiments were performed
by incubating in triplicate IgG antibodies at a final concentration of
250 µg ml
−1
with pseudoviruses for 1 h at 37 °C. The virus–IgG mixtures
were then used to infect 10,000 TZM-bl cells (8129, NIH AIDS Reagent
Program) in the presence of 10 µg ml−1 of diethylaminoethyl (DEAE)–
dextran. Infection levels were determined after 48 h by measuring the
luciferase activity of cell lysates.
Antibody binding to infected cells. The capacity of purified
antibodies to bind to HIV-1-infected cells was evaluated using
laboratory-adapted (AD8 (11346) and YU2 (1350)) and transmitted/
founder (CH058 (11856), REJO (11746) and THRO (11745)) viruses pro-
duced from infectious molecular clones (NIH HIV Reagent Program).
CEM.NKR-CCR5 cells (4376, NIH HIV Reagent Program) were infected
with inocula of selected viruses and adjusted to achieve 10–40% of Gag
+
cells at 48 h after infection. Infected cells were incubated with purified
IgG antibodies (50 µg ml
−1
final concentration) in staining buffer (0.5%
BSA, 2 mM EDTA–PBS) for 30 min at 37 °C, washed and incubated with
AF647-conjugated anti-human IgG antibodies (1:400; A-21445, Life
Technologies) for 30 min at 4 °C. Cells were then fixed with 4% para
-
formaldehyde and stained for intracellular Gag using FITC-conjugated
anti-HIV-1 core FITC KC57 (1:500, 6604665, Beckman Coulter)62. Data
were acquired using an Attune Nxt instrument (Life Technologies) and
analyzed using FlowJo software (v10.7.1; FlowJo LLC).
Screening of antiretrovirals
The screening of antiretrovirals in plasma samples was performed using
three distinct multiplex liquid chromatography coupled to tandem
mass spectrometry (LC–MS/MS) methods. Bictegravir, cabotegravir,
cobicistat, darunavir, dolutegravir, doravirine, elvitegravir, raltegravir,
rilpivirine and ritonavir (pool A) were analyzed using a Vanquish system
hyphenated to a TSQ Quantiva triple quadrupole MS. The chroma-
tographic column was a Waters Xselect HSS T3 3.5 µm, 2.1 × 75 mm,
kept at 35 °C in the LC oven. The mobile phase was made of water and
acetonitrile (ACN) with 0.1% formic acid in each. The gradient pro-
gram ranged from 10% to 95% ACN plus formic acid in 3.6 min, and the
total method duration (including equilibration for the next injection)
was 5.5 min. The flow rate and injection volume were 0.5 ml min−1 and
5 µl, respectively. For the analysis of atazanavir, efavirenz, etravirine,
lopinavir, maraviroc, nevirapine and saquinavir (pool B), the gradient
program ranged from 2% to 95% ACN plus formic acid in 2.81 min and
the total method duration (including equilibration for the next injec-
tion) was 4.5 min. The analysis of abacavir, emtricitabine, lamivudine,
tenofovir and zidovudine (pool C) was performed using a Vanquish
system hyphenated to a TSQ Altis triple quadrupole MS. The chroma-
tographic column was a Waters Xselect HSS T3 3.5 µm, 2.1 × 75 mm,
kept at room temperature. The gradient program ranged from 0 to 70%
ACN in 3 min, and the total method duration (including equilibration
for the next injection) was 5 min. The flow rate and injection volume
were 0.4 ml min−1 and 3 µl, respectively.
For the sample preparation, 150 µl of the precipitation solution
containing the isotopically labeled internal standards was added
to an aliquot of 50 µl of plasma for protein precipitation. For pools
A and B, the mixture was then centrifugated for 10 min at 14,000g (5 °C)
and the supernatant was directly injected. For pool C, the mixture was
centrifugated for 10 min at 12,700g (5 °C) and the supernatant was
diluted 1:1 with fresh Milli-Q water before injection.
Statistics and reproducibility
Graphs were generated using Prism version 10 (GraphPad Software).
Flow cytometry data were analyzed using FlowJo cytometry analysis
software v10.7 or v10.9 (Tree Star).
As this study was focused on one specific male individual, several
limitations need to be noted: influence of sex or gender could not be
considered; no statistical method was used to predetermine sample
size; the experiments were not randomized; the investigators were not
blinded to allocation during experiments and outcome assessment.
Samples at different timepoints (biological replicates) were meas-
ured in all experiments except HIV DNA determinations in gut biop-
sies. Technical triplicates were measured for viral suppression assays,
neutralization assays and CD4+ T cell susceptibility to HIV-1 infection,
and duplicates for antibody titers. All replication attempts produced
consistent results. No data were excluded from the analyses.
Reporting summary
Further information on research design is available in the Nature
Portfolio Reporting Summary linked to this article.
Data availability
The data that support the findings of this study are presented in the
main figures and Supplementary Information of this Article. Sup-
porting data will be available within 6 weeks upon request to the cor-
responding authors, except when there are constraints related to the
protection of the participant’s privacy.
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Acknowledgements
We warmly thank Romuald, also known as the Geneva patient,
described here, for his generosity and commitment. We also thank
the Swiss HIV Cohort Study (www.SHCS.ch) supported by the Swiss
National Science Foundation (grant number 201369), SHCS project
number P889 and the IciStem study for their helpful contribution.
The IciStem program (www.icistem.org) was funded through the
AmfAR Research Consortium on HIV Eradication (ARCHE) program
(AmfAR 109858-64-RSRL) and the Dutch Aidsfonds (P60802). A list of
all members can be found in Supplementary Information. F.P.-C. was
supported by Institut Pasteur’s Roux Cantarini program. A. Chapel
was supported by a grant from ANRS Emerging Infectious Diseases
(ANRS-MIE). M.G. was supported by UM1AI164562, co-funded by the
National Heart Lung and Blood Institute (NHLBI), National Institute of
Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute
of Neurological Disorders and Stroke (NINDS), National Institute on
Drug Abuse (NIDA), and the National Institute of Allergy and Infectious
Diseases (NIAID). J.M.P. is supported by the Spanish Ministry of
Science, Innovation and Universities (grants PID2022-139271OB-I00
and CB21/13/ 00063) and NIH/NIAID (1P01AI178376-01). The funders
had no role in the study design, data collection and analysis, decision
to publish or preparation of the paper.
Author contributions
A.S.-C. and A. Calmy coordinated this work. A.S.-C., A.-C.M., V.A.-F.,
M. Nabergoj, M.S., M. Nijhuis, A.W., J.M.P., S.Y., M.R. and A. Calmy
conceived and designed the study. A.S.-C., V.A.-F., C.P., P.T., L.D., M.H.,
F.P.-C., M.S., M. Nijhuis, A.M., E.G., V.L., V.M., A. Chapel, M.G., M.L.,
H.M., A.W., J.M.P. and S.Y. designed and/or performed the experiments.
A.S.-C., V.A.-F., C.P., P.T., L.D., M.S., M. Nijhuis, H.M., A.W., J.M.P., S.Y. and
A. Calmy performed the analyses and/or interpreted the data. A.-C.M.,
M. Nabergoj, M.H., S.Y., M.R. and A. Calmy were involved in the clinical
management of the patient and/or collected and handled patient
samples. A.S.-C., A.-C.M., V.A.-F., H.M. and A. Calmy wrote the draft of
the paper. All authors critically reviewed the paper and contributed
important intellectual content.
Competing interests
The authors declare no competing interests.
Additional information
Supplementary information The online version contains supplementary
material available at https://doi.org/10.1038/s41591-024-03277-z.
Correspondence and requests for materials should be addressed to
Asier Sáez-Cirión or Alexandra Calmy.
Peer review information Nature Medicine thanks Timothy Henrich and
the other, anonymous, reviewer(s) for their contribution to the peer
review of this work. Primary Handling Editors: Alison Farrell and Liam
Messin, in collaboration with the Nature Medicine team.
Reprints and permissions information is available at
www.nature.com/reprints.
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