The Journal of Immunology, 1999, 162: 6155-6161.
Copyright © 1999 by The American Association of Immunologists
Selection of HIV-Specific Immunogenic Epitopes by Screening Random Peptide Libraries with HIV-1-Positive Sera
Giuseppe Scala1,2,*,
,
Xueni Chen1,*,
Weimin Liu*,
Jean Noel Telles*,
Oren J. Cohen*,
Mauro Vaccarezza*,
Tatsu Igarashi
and
Anthony S. Fauci*
*
Laboratory of Immunoregulation, and
Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892; and
Dipartimento di Medicina Sperimentale e Clinica, Universita degli Studi di Catanzaro, Catanzaro, Italy
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Abstract
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Efforts to develop a protective HIV-1 vaccine have been hindered by
difficulties in identifying epitopes capable of inducing broad
neutralizing Ab responses. In fact, the high mutation rate occurring in
HIV-1 envelope proteins and the complex structure of gp120 as an
oligomer associated with gp41 result in a high degree of antigenic
polymorphism. To overcome these obstacles, we screened random peptide
libraries using sera from HIV-infected subjects to identify antigenic
and immunogenic mimics of HIV-1 epitopes. After extensive
counterscreening with HIV-negative sera, we isolated peptides
specifically recognized by Abs from HIV-1-infected individuals. These
peptides behaved as antigenic mimics of linear or conformational HIV-1
epitopes generated in vivo in infected subjects. Consistent with these
findings, sera of simian HIV-infected monkeys also recognized the
HIV-specific epitopes. The selected peptides were immunogenic in mice,
where they elicited HIV-specific Abs that effectively neutralized HIV-1
isolates. These results demonstrate that pools of HIV-1 mimotopes can
be selected from combinatorial peptide libraries by taking advantage of
the HIV-specific Ab repertoire induced by the natural
infection.
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Introduction
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A
number of studies in animal models demonstrate a protective role of Abs
against HIV-1 challenge (1, 2). In this regard, a strong correlation
was observed between protection against infection and levels of
neutralizing Abs in nonhuman primates infected with HIV-1 or simian HIV
(SHIV)3 (3, 4, 5). Adoptive immunotherapy with HIV-specific
Igs (6) and passive immunization with anti-HIV envelope mAbs in
chimpanzees and in PBL-SCID mice (7, 8) have also resulted in
protection against HIV challenge. Synergistic neutralization of HIV-1
by anti-HIV Igs combined with envelope-specific mAbs has also been
reported (9). These results suggest that an effective vaccine should
elicit an HIV-specific Ab response (10, 11). However, these studies
have failed to identify epitopes capable of inducing an effective
neutralizing Ab response. In fact, the identity of the immunogenic
epitopes has been determined in only a few mAbs and has remained
elusive in the case of the human polyclonal immune response to multiple
B cell epitopes, which are primarily conformational in nature and
cannot be identified from primary sequences (12). In the case of HIV-1,
the high mutation rate occurring in HIV-1 envelope proteins and the
complex structure of gp120 as an oligomer associated with gp41 (13, 14)
result in the generation of numerous epitopes. Moreover, some epitope
specificities may change during the course of disease as a result of
viral evolution, Ab affinity maturation, and viral escape (15). In
developing a protective vaccine, it would be advantageous to identify
those epitopes that are specifically recognized by Abs generated by
HIV-1-infected subjects. In fact, these epitopes might include a
substantial proportion of the epitope repertoire generated among a
large panel of HIV-infected subjects harboring different HIV-1
quasispecies over several years of infection. Moreover, these epitopes
would be immunogenic, since they have been selected for their binding
to serum Abs; in fact, they would function as antigenic mimics of HIV-1
and would induce Abs reacting with HIV-1 when utilized as immunogens.
This possibility was tested by screening random peptide libraries
(RPL) using HIV-positive sera as ligands. We
identified numerous epitopes that behaved as antigenic and immunogenic
mimics of HIV-1 or SHIV epitopes generated in the natural course of
infection. The selected epitopes induced a neutralizing Ab response
when used as immunogens in mice. These findings indicate that the
antigenic polymorphism of HIV can be matched by a collection of
epitopes selected for their affinity to human HIV-1 Abs.
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Materials and Methods
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Screening of phage-displayed RPL
Human sera were collected from HIV-1-positive or
HIV-1-negative control subjects. Criteria for definition of long-term
nonprogression or of AIDS were as previously described (16). Two
peptide libraries composed of random nonamers displayed on the N
terminus of pVIII major coat protein of filamentous phages, either
unconstrained (pVIII9aa) (17) or flanked by two cysteines
(pVIII9cys-aa-cys) (18), were screened as described (19). In the
immunoaffinity selection, serum IgG was linked to magnetic microbeads
(tosyl-activated Dynabeads M450; Dynal, Lake Success, NY) previously
coated with an anti-human (Fc-specific) polyclonal Ab (goat
anti-human IgG Fc-specific; Sigma, St. Louis, MO) at 200 µg/ml of
beads suspension. A total of 2 x 1011 transducing
units (TU) of phage particles were applied to IgG-coated beads and
incubated for 16 h at 4°C. After extensive washing, bound phages
were eluted with 0.1 M HCl/glycine buffer (pH 2.2) and neutralized.
Immunoscreening was performed as follows: TG-1 cells were infected with
eluted phages at a multiplicity of infection (MOI) of 1 x
10-3 and plated at a density of 1 x 104
TU/plate. The following day, bacterial colonies were collected,
amplified, and superinfected with M13K07 at an MOI of 50. A total
of 2 x 103 colonies were replated on a lawn of TG-1
cells in the presence of 35 µg/ml of
isopropyl-1-thio-ß-D-galactoside (IPTG). Plates were
layered with nitrocellulose filters for 16 h at 37°C. Filters
were incubated with serum at a 1:50 dilution in immunoscreening buffer
(5% nonfat dry milk, 0.1% Nonidet P-40, 3 x 1011
wild-type phages, 5 x 109 M13K07 UV-killed phages/ml,
10 µl of TG1 bacterial extract) for 16 h, at 4°C. Positive
colonies were detected by an anti-human (Fc-specific) alkaline
phosphatase-conjugated Ab (Sigma).
For ELISA, microtiter plates were coated with anti-M13 Ab
(Pharmacia, Piscataway, NJ) at 10 µg/ml overnight at 4°C in coating
buffer. A total of 50 µl of cleared phage supernatant with an
equal volume of blocking buffer were incubated for 1 h at
37°C. Plates were washed extensively and supplemented with human
serum at 1:100 dilution, followed by an overnight incubation at 4°C.
After washing, wells were coated with an anti-human (Fc-specific)
alkaline phosphatase-conjugated Ab. Plates were washed and
developed. Results were expressed as the difference between OD405
nm and OD620 nm by an ELISA reader.
Affinity purification of phagotope-specific human Abs
Dishes with a 60-mm diameter were coated with 5 x
1011 CsCl-purified phages overnight at 4°C. After washing
and blocking, human serum (1:100 dilution) was added and incubated for
16 h at 4°C. After extensive washing, bound Abs were eluted with
glycine-HCl buffer (pH 2.2). Ab concentration was determined by an in
house ELISA with a low detection level of 12 ng/ml.
Immunization of mice
Phages were CsCl-purified and used at a concentration of 6
x 1012 particles/ml in 0.9% NaCl with an equal volume of
CFA or IFA. Four- to five-wk-old female BALB/c and C57B1 mice were
immunized by i.p. injection of 200 µl of Ag emulsion at weeks 0, 3,
6, 9, 12 and bled on day 0 and days 710 after each additional
injection. Serum IgG were purified from mouse sera with T-Gel Adsorbent
(Pierce, Rockford, IL).
Virus neutralization
Neutralization of HIVIIIB and NL4-3 molecular clones
was measured in a MT-2 assay (20). Briefly, cell-free virus (500 tissue
culture-infective dose50/ml) and serial dilutions of mouse
IgG were incubated in triplicate at 37°C for 1 h before the
addition of MT-2 cells (5 x 104/well). At 68 days
postinfection, neutralization was quantified by staining viable cells
with neutral red, followed by colorimetric determination of uptake at
540 nm. In the case of AD8, neutralization assay was performed on
PHA-activated PBMC as described (21).
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Results
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Affinity selection of HIV-1 mimotopes
To select for B cell epitopes specifically recognized by
serum Abs of HIV-1-infected subjects, RPLs displayed on phages were
screened with HIV-1-positive sera. Given the fact that sera from
long-term nonprogressor (LTNP) subjects show higher titers of
neutralizing Abs than sera from AIDS patients (22), initial
screening was performed with LTNP sera. To maximize the detection
of HIV-specific peptides, phagotopes were first selected by
immunoaffinity purification with the IgG of one HIV-1-positive
individual and then subjected to immunoscreening by using a second
HIV-1-positive serum. Positive colonies were tested by ELISA for
reactivity with sera from multiple HIV-infected individuals and
counterscreened with an equivalent number of sera from HIV-negative
subjects. In selection 1, LTNP sera 6090 and 3976 were utilized for
immunoaffinity and immunoscreening steps, respectively. Similarly,
selection 2 was performed by using LTNP sera 3872 and 8075. Selection
1, performed on a cysteine-constrained pVIII9cys-aa-cys library (18),
resulted in the identification of five HIV-specific clones; selection
2, conducted on an unconstrained pVIII9aa library (17), led to
isolation of five additional phagotopes (Fig. 1
a). All the selected clones
were found to react with 22 LTNP sera and 25 AIDS sera with a
recognition frequency (f) ranging from 23 to 64%; all clones tested
negative by ELISA with 50 HIV-negative sera. It was highly unlikely
that the frequency distribution of each phagotope between HIV-positive
and -negative sera could have occurred by chance
(p < 0.001, as determined by using the Fisher
exact test; p values were adjusted for multiple testing
using the Bonferroni method). Accordingly, the clones were considered
HIV-1-specific phagotopes. Each serum manifested a distinct pattern of
reactivity with the pool of phagotopes (Fig. 1
a). Some sera,
such as 8873 and 1276, recognized most phagotopes indicating a broad Ab
specificity, whereas sera 2214, 5223, and 8075 reacted with only one
phagotope. Clone p217 was restricted in its reactivity to a subset of
LTNP sera (f, 23); however, it was completely unreactive with a pool of
AIDS sera (Fig. 1
a). Analysis of the reactivities of sera
for each phagotope showed that Ab titers to p163, p217, and p335 were
significantly higher in sera from LTNPs than from AIDS patients
(p < 0.05; Fig. 1
b). These results
suggest that Ab responses to these epitopes might afford a degree of
protection against disease progression.
Characterization of HIV-1 mimotopes
The amino acid sequences of the phage-displayed peptides are shown
in Fig. 2
. A BLAST analysis revealed that
the p195 epitope shares sequence homology with the gp120 V1 region
(residues 112120) of HIV1-U16374, a primary isolate from an acute
seroconverter (23); the p217 sequence matched with the gp120 C2 region
(residues 198205) of HIV1-U116077, a primary isolate from an AIDS
patient (24) (Fig. 2
a). Residues within these regions have
been predicted to be immunologically accessible by selected mAbs and by
x-ray crystal structure (13, 14). Moreover, the p197 epitope mapped to
a region of gp41 (residues 602605) of the HIVANT70 primary isolate
(25). This region is conserved among primary isolates of HIV subtypes A
through G and defines a disulfide-bonded structure recognized by a
human mAb (Fig. 2
, a and b; and 26). Thus,
the peptides expressed on p195, p217, and p197 are antigenic mimics of
epitopes expressed in primary HIV isolates from subjects at different
stages of disease. No sequence homology with HIV proteins was found in
the remaining clones, suggesting that they may represent immunological
mimics of conformational HIV-1 epitopes (Fig. 2
c).

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FIGURE 2. Amino acid sequences of the HIV-specific phagotopes. The amino acid
sequences of peptides displayed on the HIV-specific phagotopes are
shown as single letter codes. a, Homology between the
amino acid sequences of p195, p217, and p197 and discrete regions of
HIV gp160. Gray boxes indicate identity; similarity among amino acid
residues is indicated as gray. b, Consensus homology of
p197 with a gp41 domain conserved between HIV-1 subtypes A trough G.
c, Amino acid sequences of epitopes with no obvious
sequence homology with HIV protein domains.
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The Ab reactivities shown in Fig. 1
a indicate that the
phage-displayed peptides behave as antigenic mimics of viral
determinants generated in the course of HIV infection. Therefore, it
should be possible to immunoaffinity-purify Abs specific for each
phagotope from sera of HIV-infected individuals by using single
phagotopes as ligands. To this end, p195, p197, p217, p287, and p335
were utilized to purify the phagotope-specific Abs from LTNP serum
6090. The phagotope-specific Abs, purified from serum to IgG
concentrations of 510 ng/ml, recognized HIV-1 proteins by ELISA (Fig. 3
a). This reactivity was
specifically displaced by the related phagotopes, but not by wild-type
or unrelated phages (Fig. 3
b, and data not shown). Moreover,
peptides corresponding to the epitopes displayed on phages p195, p197,
and p335 effectively displaced the binding of Abs to HIV-1, indicating
that these peptides acquire in solution a conformation similar to the
one expressed by both the phage-displayed peptides and the HIV epitopes
(Fig. 3
c). Only a partial competition was observed in the
case of peptide 217 and 287, indicating that expression of these
peptides on the surface of the phages is essential to acquire a
conformation mimicking HIV epitopes (Fig. 3
c), as previously
suggested (27). When the phagotope-specific Abs were tested in
immunoblotting, a distinctive reactivity was found. Ab-195 and Ab-217
recognized gp160 and gp120, consistent with the mapping of these
epitopes at envelope regions. In addition, Ab-287 and Ab-335 also
detected HIV-gp160 and gp120, indicating that they recognized
envelope-specific epitopes (Fig. 3
d). No bands were detected
by p197-specific Abs, indicating an intrinsic inability of these Abs to
bind to the cognate epitope under denaturing conditions (Fig. 3
d).

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FIGURE 3. Phagotope-specific Abs bind to HIV-1. a, ELISA
reactivities of immunoaffinity-purified Abs with HIV-1. Abs were
immunoaffinity-purified from LTNP serum 6090 using single phagotopes as
ligands and tested for ELISA reactivity against HIV-1 virions by using
a standard ELISA kit (Organon, West Orange, NJ). Purified Abs were
tested at 510 ng/ml; HIV-negative (CS) and serum 6090 (HIV-1S) were
tested at 1:100 dilution. Data are expressed as mean ± SEM of
four independent determinations. b, The binding of
phagotope-specific Abs to HIV-1 is specifically displaced by the
related phagotopes. ELISA reactivities of single immunopurified Abs to
HIV-1 were tested in the presence of the indicated concentrations of
p195 ( ), p197 ( ), p217 (), p287 ( ), and p335 ( ). The
binding of each Ab to HIV was also tested in presence of increasing
concentrations of wild-type phages (open symbols). c,
Displacement of HIV-1 binding by peptides corresponding to the
phage-displayed epitopes shown in Fig. 2 , a and
c. ELISA reactivities of single immunoaffinity-purified
Abs with the related phagotopes were tested in the presence of
increasing concentrations of peptides 195 ( ), 197 ( ), 217 ( ),
287 ( ), and 335 (). d, HIV-1 immunoblotting with
phagotope-specific human Abs. Immunoaffinity-purified Abs were tested
at 60 ng/ml for binding to HIV-1 proteins in Western blot analysis by a
diagnostic kit (Aquila Biopharmaceuticals, Framingham, MA); 6090 LTNP
serum was tested at 1:1000 dilution.
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HIV-1 mimotopes react specifically with sera of SHIV-infected
monkeys
SHIV recombinant viruses expressing HIV env on the
backbone of SIV isolates are a useful model of HIV-1 infection in
primates (28). SHIV-infected monkeys raise high titers of neutralizing
Abs that correlate with long-lasting protection from subsequent
challenge with pathogenic SHIV (29) or SIV-mac239 (30). Since the
HIV-specific phagotopes are immunogenic mimics of HIV-1 env proteins
(
Figs. 13

), they should be recognized by Abs of SHIV-infected
animals. To test this hypothesis, sera of nine SHIV-infected monkeys
and of four uninfected control animals were tested for ELISA reactivity
with the pool of HIV mimotopes. As in the case of HIV-1-infected
subjects (Fig. 1
a), sera of SHIV-infected monkeys recognized
the HIV-1 phagotopes with variable frequencies (Fig. 4
). As previously noted, phagotopes p32,
p54, and p689 did not match any HIV sequences in the database (Fig. 2
c). The fact that certain SHIV sera recognized these
phagotopes suggests that they are conformational mimics of discrete
regions of gp160, Nef, Tat, or Vpu, since these are the only
HIV-specific sequences within SHIV. Phagotope p163 and p483, which were
consistently recognized by LTNP and AIDS sera (Fig. 1
a), did
not react with SHIV sera, suggesting that they are antigenic mimics of
HIV-1 epitopes encoded for by gag or pol genes.
Sera from uninfected monkeys tested negative in ELISA (Fig. 4
).

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FIGURE 4. ELISA reactivities of monkey sera with HIV-specific phagotopes. Sera of
naive monkeys (SHIV Negative) and SHIV-infected animals were tested for
binding to HIV-1 phagotopes. Results are expressed as fold increase of
OD405 nm values of tested phagotope over the OD405
nm values of wild-type phage. Cutoff values were set as detailed
in the legend to Fig. 1 a. All the preinfection sera of
SHIV-positive animals tested negative by ELISA (data not shown). A125,
42C, E50, and AK98 are Rhesus macaques; 4138, 4150, and 79 are
cynomologous macaques; these animals were infected with
SHIVMD1 (38). 17860 and 17846 are pigtail macaques infected
with SHIVMD14YE (38).
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HIV-1 mimotopes induce neutralizing Abs in mice
HIV-1-binding Abs may exert neutralizing activity in vitro if
directed to accessible epitopes of infectious virions. As antigenic
mimics of HIV-1 epitopes, HIV-1 phagotopes have a conformation that
fits in the Ag-binding site of the related serum Abs, and would be
expected to elicit Abs in vivo with specificities similar to the
original serum IgG utilized to select them. To test this possibility,
HIV-1 phagotopes p195, p197, p217, p287, and p335 were used to
immunize BALB/c or C57B/6 mice. All mice developed comparable titers of
Abs against wild-type phages and a strong Ab response to the original
phagotopes used as immunogens (data not shown). Purified IgG from mice
immunized with HIV-1 phagotopes exerted a significant inhibition of
infection by HIV-1IIIB and NL4-3 isolates over a wide range
of IgG concentrations in an in vitro acute infection system, with 50%
protection observed at IgG concentrations of 0.83 µg/ml in
neutralization assays with HIVIIIB or NL4-3, respectively
(Fig. 5
, a and b).
Consistent levels of viral neutralization were also obtained in the
case of the AD8 primary isolate, with the exception of p335-specific
Abs, which exerted partial protection only at the highest
concentrations (Fig. 5
c).
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Discussion
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The quest for a prophylactic HIV vaccine has been
frustrated in part by the high variability of HIV envelope sequences
and by its complex oligomeric structure. Furthermore, a vaccine
formulation should take into account the subtype prevalence in
different geographic regions as well as the insurgence of new HIV
isolates (31). Combinatorial peptide libraries express a large
collection of peptide sequences (108 or more) that mimic
both linear and conformational epitopes of folded protein domains, and
even carbohydrate structures (32) that contribute to the generation of
viral escape variants (33). Such libraries might offer a unique
opportunity to overcome the complexity of the HIV epitope repertoire by
allowing the selection of a pool of HIV-specific mimotopes using
HIV-specific Abs generated in representative cohorts of HIV-infected
subjects. To this end, we screened phage-displayed RPLs and selected
numerous epitopes that behaved as antigenic and immunogenic mimics of
HIV epitopes generated in the natural course of infection in humans as
well as in SHIV-infected monkeys. In further support of the
HIV-specificity of the selected phagotopes, sera from six HIV-infected
chimpanzees also recognized HIV phagotopes (G.S. et al., unpublished
observations) with a pattern similar to the reactivities of human
sera. Of interest, LTNP sera manifested higher Ab titers to certain
epitopes compared with AIDS sera, suggesting that the immune response
to these epitopes might afford some degree of protection against
disease progression.
Although the above phagotopes were selected by using Abs from
HIV-infected subjects likely carrying different isolates, the
neutralization data shown in Fig. 5
indicate that the specific Abs
induced in mice bind to HIVIIIB, NL4-3, and AD8 virus
isolates. This is consistent with the data shown in Fig. 3
, where Abs
that had been immunoaffinity purified from patients sera by using
single epitopes as ligands reacted with HIVIIIB proteins in
ELISA and in Western blot analysis (Fig. 3
, a and
d). This indicates that the epitopes displayed on the
pVIII coat of the phages could mimic HIV-1 epitopes from different
strains. This possibility is further supported by the data shown in
Fig. 4
, where epitopes reacted with Abs from monkeys infected with
chimeric SHIVs displaying an envelope from DH12, a dual-tropic strain
of HIV-1 (34). Moreover, as shown in Fig. 1
a, epitopes
selected for reactivity with a given serum were recognized by Abs from
numerous subjects likely infected with different HIV-1 quasispecies.
The above evidence underscores the capacity of a phage displayed
peptide to mimic multiple HIV epitopes present in vivo on glycosylated
gp120 without the constraint of a high sequence homology. Consistent
with this possibility, phage mimotopes of hypervariable region 1 of
hepatitis C virus induces Abs cross-reacting with a large number or
viral variants (35). Although the selected phagotopes were recognized
by most of the HIV-positive sera, it is unclear at present to what
extent they represent the complexity of the epitope repertoire of HIV
envelope proteins. In this regard, we are extending the pool of HIV-1
mimotopes by screening peptide libraries with additional HIV-positive
sera.
The selected phagotopes fulfilled the requirement for an effective
immunogen. In fact, Abs from phagotope-immunized mice neutralized HIV-1
strains in vitro, suggesting that they bind well to the virus under
physiologic conditions and could possibly prevent or inhibit HIV
infection when induced in phagotope-immunized primates. In support of
this possibility, serum Abs of SHIV-infected monkeys showed a strong
reactivity with the phage-displayed epitopes. In addition,
bacteriophages are excellent immunogens that induce a specific T
cell-dependent Ab response by parenteral as well as oral administration
(36, 37).
Taken together, our results indicate that a collection of HIV-1
mimotopes can be retrieved from combinatorial phage libraries by taking
advantage of the specific Ab repertoire induced by natural infection,
and thus may be useful in the development of effective HIV-1 vaccines.
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Acknowledgments
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We thank D. C. Montefiori for advice in viral
neutralization assays; C. Allahan for statistical analysis; T.-W.
Chun, J. Arthos, and B. Mathieson for critical reading of
the manuscript; M. A. Martin for discussing and reviewing the
manuscript; R. Cortese for providing the RPLs; P. Monaci,
A. Nicosia, and C. Prezzi for helpful discussions; and P.
Walsh for excellent editorial assistance.
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Footnotes
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1 These authors contributed equally to this work. 
2 Address correspondence and reprint requests to Dr. Giuseppe Scala, Laboratory of Immunoregulation/National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 6A08, 10 Center Drive, Bethesda, MD 20892-1576. E-mail address: 
3 Abbreviations used in this paper: SHIV, simian HIV; RPL, random peptide libraries; LTNP, long-term nonprogressor; f, recognition frequency. 
Received for publication December 21, 1998.
Accepted for publication March 3, 1999.
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