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Journal of Virology, June 2003, p. 6108-6116, Vol. 77, No. 11
0022-538X/03/$08.00+0 DOI: 10.1128/JVI.77.11.6108-6116.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Persistence of Extraordinarily Low Levels of Genetically Homogeneous Human Immunodeficiency Virus Type 1 in Exposed Seronegative Individuals
Tuofu Zhu,1,2* Lawrence Corey,1,2,3,4 Yon Hwangbo,1 Jean M. Lee,1 Gerald H. Learn,2 James I. Mullins,1,2 and M. Juliana McElrath1,3,4
Departments of Laboratory Medicine,1
Microbiology,2
and Medicine, University of Washington School of Medicine, Seattle, Washington 98195,3
Program in Infectious Diseases, Fred Hutchinson Cancer Research Center, Seattle, Washington 981094
Received 1 July 2002/
Accepted 27 September 2002

ABSTRACT
Some individuals remain inexplicably seronegative and lack evidence
for human immunodeficiency virus type 1 (HIV-1) infection by
conventional serologic or virologic testing despite repeated
high-risk virus exposures. Here, we examined 10 exposed seronegative
(ES) individuals exhibiting HIV-1-specific cytotoxicity for
the presence of HIV-1. We discovered HIV-1 DNA in resting CD4
+ T cells (mean, 0.05 ± 0.01 copies per million cells)
at multiple visits spanning 69 to 130 weeks in two ES individuals
at levels that were on average 10
4- to 10
6-fold lower than those
of other HIV-1-infected populations reported. Sequences of HIV-1
envelope and
gag genes remained markedly homogeneous, indicating
little to undetectable virus replication. These results provide
the evidence for HIV-1 infection in ES individuals below the
detection limit of standard assays, suggesting that extraordinary
control of infection can occur. The two HIV-infected ES individuals
remained healthy and were not superinfected with other HIV-1
strains despite continued high-risk sexual exposures to multiple
HIV-infected partners. Understanding the mechanisms that confer
diminished replicative capacity of HIV-1 in these hosts is paramount
to developing strategies for protection against and control
of HIV-1 infection.

INTRODUCTION
Rare individuals have been identified since early in the AIDS
pandemic who fail to seroconvert and lack evidence for human
immunodeficiency virus type 1 (HIV-1) infection despite high-risk
and/or multiple exposures to HIV-1. These exposed seronegative
(ES) individuals include infants born to HIV-1-infected mothers
(
11,
42), commercial sex workers in areas where the disease
is epidemic (
25,
43), hemophiliacs who received tainted factor
VIII preparations (
16), health care personnel with accidental
percutaneous exposure to infected blood (
9,
37), and sexual
partners of known HIV-1-infected persons (
17,
30). Transient
infection (
2,
6,
40) or silent infection (
20) was proposed to
explain the case of some ES individuals in whom HIV infection
had been detected either by culture or by PCR of peripheral
blood mononuclear cells (PBMCs). However, this pattern of HIV
infection has not been unambiguously confirmed by genetic analyses
(
32) and remains highly controversial (
15). Nevertheless, one-third
to one-half of ES individuals have detectable HIV-1-specific
T-cell responses (
16,
17,
30,
37,
42,
43) and, in some cases,
mucosal immunoglobulin A (IgA) antibodies (
30), suggesting that
some ES individuals may have acquired HIV-1 infection but that
the virus is either cleared or no longer detectable by routine
methods (
17,
30,
37).
An HIV-1 reservoir in resting CD4+ T cells has been identified as early as 5 days after infection (7, 8, 14, 49) and may persist over the patient's lifetime with highly active antiretroviral therapy (HAART) (13). We hypothesize that during initial active HIV-1 infection, a reservoir is established in quiescent cells of some ES individuals, who then fail to manifest clinical infections or laboratory evidence of infection by standard serologic or virologic testing. To examine this hypothesis, we screened for HIV-1 DNA sequences in purified resting CD4+ T cells from our ES cohort (17). The intense labor involved in these studies precluded assessment of a large number of ES individuals (see below). The present study was not designed to determine the frequency of HIV-1 infection in ES populations. Instead, our investigation focused on 10 ES individuals with detectable HIV-1-specific cytotoxic T lymphocytes (CTL), based on the assumption that memory T-cell responses were more likely to be present in persons with previous HIV-1 exposure or infection (16, 17, 30, 37, 42, 43). We demonstrate here the persistence of HIV-1 DNA at levels below the detection limit of conventional assays in 2 of these 10 persons: ES1 and ES38.

MATERIALS AND METHODS
Subjects studied.
We focused on 10 ES individuals (
17) with (i) detectable HIV-1-specific
CTL, (ii) higher frequencies of exposure to HIV-1, and (iii)
large volumes of samples from multiple time points, allowing
us to carry out extensive and repeated PCR analyses. Both ES1
and ES38 reported repeated exposures to HIV-infected sexual
partners (Fig.
1). These individuals, both Caucasians, had the
wild-type CCR5 coreceptor genotype (
17). Class I HLA DNA sequence-specific
primer typing showed that ES1 was HLA-A*02, -A*68, -B*44, -B*51,
-Bw4, -Cw*05, and -Cw*15, whereas ES38 was HLA-A*02, -A*11,
-B*07, -B*35, -Bw6, -Cw*04, and -Cw*07. Over the past 7 years,
ES1 and ES38 exhibited no evidence of active HIV-1 infection
when evaluated at 1- to 6-month intervals by serologic (enzyme
immunoassay and Western blot tests), standard DNA PCR, and PBMC
HIV-1 coculture (with or without CD8
+-T-cell depletion) assays
(
17). In addition, no HIV-1 RNA was detected by reverse transcription-PCR
(RT-PCR) in seminal plasma, blood plasma, or PBMC from either
ES individual. Both ES individuals entered the study with normal
CD4
+-T-cell counts (ES1, 1,391 cells/µl; ES38, 937 cells/µl),
remained healthy without HIV-1-associated opportunistic infections,
and maintained strong recall antigen responses by in vitro proliferation
(
17). ES1, but not ES38, also demonstrated T-cell lymphoproliferative
responses to HIV-1 p24, gp120, and gp160 antigens (
17). Cytolytic
activities recognizing HIV-1 Gag, Env, Pol, and Nef were detected
in ES1 and ES38 (
17).
Cell purification and DNA extraction.
Each sample of fresh blood or cryopreserved PBMC was divided
into three portions: one was sent to the University of Washington
laboratory, one was sent to the Fred Hutchinson Cancer Research
Center laboratory, and one was stored in liquid nitrogen for
confirmatory studies. Purification of the three cell populations
was performed separately in both laboratories (
51). Genomic
DNA was extracted separately from purified resting CD4
+ T cells,
activated CD4
+ T cells, and monocytes (
51), one sample per day,
in a biosafety cabinet housed in a "PCR-clean" room. The room,
hood, and equipment were decontaminated after each use. Experiments
with ES specimens were separated by intervals of at least 4
weeks to further avoid cross-contamination between specimens.
PCR and sequence analyses.
Limiting-dilution nested PCR was performed to amplify the env and gag of HIV-1 sequences with the following primers: C2-V3-C3 region outer P5-2 and PV3; C2-V3-C3 region inner P5 (50) and Bsu (residues 7341 to 7315 of HIV-1 HXB2 sequence in the Los Alamos Database, 5'-TTACAATTTCTGGGTCCCCTCCTGAGG-3'); V3-C3 region outer Pvu (residues 7061 to 7090, 5'-CAATGCTAAAACCATAATAGTACAGCTGAA-3') and PV3; V3-C3 inner Pvu and Bsu; gag p17 outer PG3 (residues 763 to 789, 5'-TGACTAGCGGAGGCTAGAAGGAGAGAG-3') and PG8 (residues 1326 to 1299, 5'-GGCTCCTTCTGATAATGCTGAAAACATG-3'); and gag p17 inner PG1 (residues 790 to 814, 5'-ATGGGTGCGAGAGCGTCAGTATTAA-3') and PG6 (residues 1262 to 1231, 5'-TCACCTAGAACTTTAAATGCATGGGTAAAAGT-3'). Extend High Fidelity PCR system (Roche Molecular Biochemicals) was used for PCR as described previously (50, 51) with 10 pmol of each primer. Amplification conditions for the first round PCR were 94°C for 2 min, 94°C for 30 s, 55°C for 30 s, and 72°C for 90 s for 32 cycles, followed by a final extension at 72°C for 10 min. Then, 4 µl of the first-round PCR products were used in a second-round PCR at 94°C for 20 s, 55°C for 20 s, and 72°C for 60 s for 35 to 40 cycles, followed by a final extension at 72°C for 10 min. All PCRs were performed in the Perkin-Elmer model 9600 thermocycler. Controls for PCR included genomic DNA containing 1, 4, 25, and 100 copies of HIV-1 DNA, as well as reagent and HIV-1-negative controls. PCR was sensitive to detect one copy per microgram of DNA per reaction and was specific for the detection of HIV-1 (data not shown). HIV-1 copy numbers were calculated based on limiting-dilution PCR and a computer program (QUALITY) described previously (39). PCR products were cloned and sequenced (51). All sequences were aligned by using CLUSTALW (46). Maximum-likelihood estimation (MLE) phylogram was constructed by using PAUP* (Sinauer Associates, Inc., Sunderland, Mass.). The models of evolution (GTR+G) were selected by using the AIC (1) in Modeltest version 3.06 (38). It was necessary to perform 600 or more independent limiting-dilution PCRs to identify the HIV-1 sequences in each sample. Similar intensive PCR assays with positive samples from the same time point but stored initially in another laboratory and or in liquid nitrogen were carried out for confirmatory studies. Typically, billions of PBMC through leukapheresis would be used for cell separation, PCR, and sequence analyses; however, there were not enough cells to perform similar intensive PCR sequence analyses in another laboratory.
GenBank nucleotide sequence accession numbers.
The nucleotide sequences described in the paper have been submitted to GenBank (sequence accession no. AY162341 through AY162373 and AY162474 through AY162825).

RESULTS
Persistence of extraordinarily low levels of HIV-1 DNA in peripheral blood.
We used a limiting-dilution PCR to detect and quantitate HIV-1
env and
gag DNA, and the viral copy numbers shown in Table
1 were derived from the results of hundreds or thousands of independent
PCRs performed on each sample (
39,
51). HIV-1 DNA was detected
at extraordinarily low levels (mean, 0.05 ± 0.01 per
million cells) in resting CD4
+ T cells isolated at different
times and appeared to decline slowly over a period of 137 (ES1)
and 69 weeks (ES38) (Table
1). When multiple cell fractions
(week 137 of ES1 and week 69 of ES38) were available for study,
resting CD4
+ T cells had a higher HIV-1 copy number than the
total PBMC, monocytes, and activated CD4
+ T cells (Table
1).
The levels of HIV-1 DNA in these ES individuals were remarkably
lower than those typically found in other HIV-1-infected populations
(Fig.
2). We detected HIV-1 DNA in resting CD4
+ T cells from
the sexual partner of ES1 at levels approximately 10
5 fold higher
than in ES individuals (Table
1). HIV-1 DNA levels in ES individuals
were, on average, 10
4-fold lower than those in patients with
undetectable plasma viremia during HAART (491.4 ± 123.5
copies per million resting CD4
+ T cells;
P < 0.0001), approximately
5
x 10
5-fold lower than those in long-term nonprogressors (LTNP)
(1,189 ± 301.10 copies per million PBMC,
P < 0.0001),
and up to 10
6-fold lower than in patients with typical HIV-1
infection without therapy (5,704 ± 1,016 copies per million
PBMC;
P < 0.0001) (Fig.
2) (
3-
5,
51).
View this table:
[in this window]
[in a new window]
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TABLE 1. Identification of HIV-1 in ES mononuclear cells and comparison of copy numbers to the HIV-1-infected sexual partner of ES1
|
Homogeneity of HIV-1 sequences in longitudinal samples: lack of viral evolution.
We then examined HIV-1
env V3-C3 coding sequences from each
time point. Deduced amino acid sequences of HIV-1 V3-C3 regions
were markedly similar in ES1 cells obtained from all six time
points over the 130 weeks of study (Fig.
3A). To confirm these
findings, we retrieved a third portion of frozen cells from
weeks 8 and 137 and used different primers to amplify by PCR
and sequence the HIV-1 C2-V3-C3 region (Fig.
3A). These sequences
were virtually identical to those generated previously by amplification
of the shorter envelope region (V3-C3). Moreover, HIV-1 sequences
in ES1 found in activated CD4
+ T cells and monocytes were extremely
homogeneous, as in the resting CD4
+ T cells. Homogeneous sequences
of HIV-1 V3-C3 region were also observed in the resting CD4
+ T cells from ES38 (Fig.
3B). Except for clone 35 of V3-C3 sequence
from ES1 activated CD4
+ T cells obtained at week 137 (Fig.
3A),
no HIV-1 sequence examined contains any stop codons or insertions
or deletions. It is unlikely that this homogeneity resulted
from repeated sequencing of only a few HIV-1 proviruses, since
up to 50 clonal sequences from 6 to 15 independent positive
PCRs were used for each ES specimen. Comparison of
env sequence
changes over time revealed estimated rates of viral evolution
not different from zero (-0.012% per site per year in ES1;
P = 0.22; 0.00013% in ES38,
P = 0.17). These results suggest that
HIV-1 sequences in the ES individuals had not evolved or were
evolving very slowly over the 69- to 130-week study period.
This finding stands in contrast to a higher evolution rate of
HIV-1 V3-C3 sequences (mean, 0.437% per site per year;
P <
0.001) in patients with typical disease progression (
45). The
large amounts of cells required to perform these experiments
precluded us from carrying out similar extensive studies in
another laboratory (see Materials and Methods). However, to
prevent contamination, we performed special procedures to process
samples throughout the study (see Materials and Methods) (
15,
51). To further exclude sample mislabeling or contamination,
we performed PCR typing of five genetic markers (Amplitype PM;
Perkin-Elmer Cetus, Branchburg, N.J.), which can discriminate
the relatedness between two individuals by a power of 0.9954.
All samples from a given ES individual had identical individual
genotypes for the five markers (Table
1). The genotype of ES1
was also distinct from his HIV-1-infected sexual partner (Table
1).
Phylogenetic relationships were estimated between HIV-1 sequences
from ES1, ES38, and the contemporaneous, HIV-1-infected, sexual
partner of ES1 (Fig.
4). Sequences from ES1 and ES38 were grouped
closely in separate monophyletic clusters. In contrast, pronounced
sequence variation was observed in the sexual partner of ES1,
who was diagnosed with HIV-1 infection 2 years after initial
contact with ES1. However, HIV-1 sequences from ES1 and his
sexual partner were not closely related, suggesting neither
was the source of infection of the other (
26). There was also
no evidence of superinfection in the ES individuals despite
repeated high-risk unprotected sexual activity with multiple
partners over the study period (Fig.
1), suggesting a possible
protection against new HIV infection. Sequences from ES1 and
ES38 were also distinct from those of prototypic laboratory
HIV-1 strains, as well as the full catalog of HIV-1 sequences
in the Los Alamos National Laboratory database (
24) and a database
of local sequences by using FASTA (
26).
We also amplified
gag p17 of HIV-1 sequences from resting CD4
+ T cells at weeks 8 and 137 of ES1. The copy numbers of HIV-1
provirus detected by HIV-1
gag PCR were 0.09 and 0.03 per million
resting CD4
+ T cells at weeks 8 and 137, respectively. The evolution
rate of HIV-1
gag p17 sequences was 0.012% per site per year
(95% confident interval, -0.051 to 0.028%), which is not significantly
different from zero (
P = 0.169). Further phylogenetic analysis
to determine the evolutionary relationships of sequences obtained
from ES1 and other sequences in the databases (
24,
26) excluded
any possible contamination of known HIV-1 strains (Fig.
5).
These results are consistent with findings derived from the
analyses on HIV-1
env in ES1, indicating that HIV-1 sequences
from ES1 and ES38 are remarkably fixed in evolution and do not
represent contaminants from any identified source (
24,
26).

DISCUSSION
These results shed new light on the puzzling observation that
some persons can repeatedly engage in unprotected sexual activities
with HIV-1-infected partners and yet fail to acquire overt HIV-1
infection. Our study indicates that HIV-1 infection can be demonstrated
at extremely low levels in these seronegative persons only by
sampling large cell numbers and by performing hundreds or thousands
of PCR amplifications and sequence analyses. One of the remarkable
findings in the present study is that the HIV-1 DNA levels in
ES1 and ES38 are, on average, 10
4- to 10
6-fold lower than those
of other HIV-1-infected populations studied and also typically
10
2-fold lower than could have been detected in a previous study
of possible transient HIV infection (
15). Both ES1 and ES38
have remained healthy and free of superinfection of other new
HIV strains despite the fact that they had engaged repeatedly
in unprotected sexual intercourse with multiple HIV-1-infected
partners over the study period. However, epidemiological data
supporting the possibility of recognizable HIV-1 infection from
a distant exposure or set of exposures do not exist. This issue
may be addressed only by prospective, longitudinal ES studies,
which are in progress.
Understanding the mechanisms that account for the control of HIV infection, and the potential protection against new infection in these ES individuals should be of great interest to efforts to develop an effective vaccine. First, the low viral copy numbers may be the result of exposure to a low viral inoculum, reaching a minimum threshold to establish latency but insufficient to result in overt systemic infection. In support of this possibility, transient infection or occult systemic low-level infection was found in macaques challenged with low doses of simian immunodeficiency virus (SIV) (12, 31, 34, 36, 47, 48). In all of these studies, the animals did not seroconvert to SIV antigens by conventional assays, and most of these animals did not develop any signs of SIV-associated disease. Second, ES individuals may have encountered attenuated HIV-1 strains, an idea that in accord with observations of silent infection in monkeys inoculated with attenuated SIVmac strains (29). This may explain our inability to isolate infectious HIV-1 in vitro. Coculture of up to 600 million resting CD4+ T cells and CD8-depleted PBMC of ES individuals with different mitogens, such as phytohemagglutinin, anti-CD3, and tumor necrosis factor alpha alone or in combination, was carried out repeatedly without detection of virus (data not shown). In contrast, infectious virus was consistently isolated from seropositive donor cell controls. However, given that the HIV-1 proviral copy numbers in cells from ES individuals were extremely low (ranging from 1 per 10 to 100 million cells), the sensitivity of this technique might not have been adequate to identify a rare infectious virus. Nevertheless, based upon the extreme homogeneity of HIV-1 sequences over the study period, the repeatedly undetectable HIV-1 RNA in plasma, and the failure to isolate infectious virus in vitro, the HIV-1 in the resting CD4+ T cells from ES1 and ES38 may be attenuated or replication defective. Third, acquired T-cell immunity may play an important role in the control of HIV-1 infection (16, 17, 23, 30, 35, 37, 41-43). This is supported in a recent study (21, 22) by events surrounding the acquisition of HIV-1 infection in Nairobi HIV-1 exposed women who had resisted infection for many years, which the investigators believe may be linked to waning HIV-1-specific cytotoxic responses. Although we observed that the trend of the HIV-1 DNA decline in ES1 paralleled the fall in pCTL frequencies (17), we could not determine whether CTL were involved in controlling viral replication at such low levels. It is possible that T-cell responses in ES individuals only denote previous HIV-1 exposure or perhaps even cross-priming from exposure to their partner's infected cells. The capacity to maintain detectable CTL in the setting of such low levels of antigen exposure is an issue that will require further prospective analysis in order to understand their functional relevance in this population.
In summary, it is likely that more than one mechanism can account for the sustained, extraordinary control of infection and that both viral and host factors, including inheritance of genetic defects and distinct HLA or major histocompatibility complex types may contribute to this outcome (10, 18, 19, 27, 28, 33, 44). Key unresolved issues include (i) the proportion of ES individuals with low levels of HIV-1 infection, (ii) the likelihood that these individuals will subsequently manifest clinical HIV-1 disease, and (iii) the probability that they can transmit HIV-1 infection to their sexual partners. Because the HIV-1 copy number is extremely low and the effort to document low levels of infection is substantial, routine assessment of infection in resting CD4+ T cells is not likely to be feasible by current methodologies. Thus, although our findings provide new insight into protection against active HIV-1 infection, the challenge ahead lies in better understanding the long-term sequelae in these ES individuals and in translating the mechanisms underlying these circumstances to therapeutic and immunization strategies.

ACKNOWLEDGMENTS
We thank E. Wakabayashi, F. Feng, J. Kim, H. Liu, K. Diem, C.
Alef, and R. Akridge for technical assistance; Y. Wang and A.
J. Rossini for advice on statistical analyses; and the study
participants for their time and commitment.
This work is supported by NIH grants AI45402, AI41535, AI45206, AI35605, AI26503, RR00166, and AI49109; the Burroughs-Wellcome Clinical Scientist Award; and the University of Washington Center for AIDS Research Young Investigator Award (NIH AI27757).

FOOTNOTES
* Corresponding author. Mailing address: Department of Laboratory Medicine, University of Washington School of Medicine, Box 358070, 1959 N.E. Pacific St., Seattle, WA 98195-8070. Phone: (206) 732-6079. Fax: (206) 732-6055. E-mail:
tzhu{at}u.washington.edu.


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Journal of Virology, June 2003, p. 6108-6116, Vol. 77, No. 11
0022-538X/03/$08.00+0 DOI: 10.1128/JVI.77.11.6108-6116.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
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