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Journal of Virology, January 2005, p. 860-868, Vol. 79, No. 2
0022-538X/05/$08.00+0 doi:10.1128/JVI.79.2.860-868.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Human Immunodeficiency Virus Type 1 Clade B Superinfection: Evidence for Differential Immune Containment of Distinct Clade B Strains
Otto O. Yang,1*
Eric S. Daar,2
Beth D. Jamieson,1
Arumugam Balamurugan,1
Davey M. Smith,3
Jacqueline A. Pitt,2
Christos J. Petropoulos,4
Douglas D. Richman,3,5,6
Susan J. Little,3 and
Andrew J. Leigh Brown7
Department of Medicine, UCLA Medical Center,1
Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center and the David Geffen School of Medicine at UCLA, Los Angeles,2
Departments of Medicine,3
Pathology, University of California, San Diego,5
VA San Diego Healthcare System, La Jolla,6
ViroLogic, Inc., South San Francisco, California,4
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland7
Received 21 June 2004/
Accepted 4 September 2004

ABSTRACT
Sequential infection with different strains of human immunodeficiency
virus type 1 (HIV-1) is a rarely identified phenomenon with
important implications for immunopathogenesis and vaccine development.
Here, we identify an individual whose good initial control of
viremia was lost in association with reduced containment of
a superinfecting strain. Subject 2030 presented with acute symptoms
of HIV-1 infection with high viremia and an incomplete seroconversion
as shown by Western blotting. A low set point of viremia (

1,000
HIV-1 copies/ml) was initially established without drug therapy,
but a new higher set point (

40,000 HIV-1 copies/ml) manifested
about 5 months after infection. Drug susceptibility testing
demonstrated a multidrug-resistant virus initially but a fully
sensitive virus after 5 months, and an analysis of
pol genotypes
showed that these were two phylogenetically distinct strains
of virus (strains A and B). Replication capacity assays suggested
that the outgrowth of strain B was not due to higher fitness
conferred by
pol, and
env sequences indicated that the two strains
had the same R5 coreceptor phenotype. Delineation of CD8
+-T-lymphocyte
responses against HIV-1 showed a striking pattern of decay of
the initial cellular immune responses after superinfection,
followed by some adaptation of targeting to new epitopes. An
examination of targeted sequences suggested that differences
in the recognized epitopes contributed to the poor immune containment
of strain B. In conclusion, the rapid overgrowth of a superinfecting
strain of HIV-1 of the same subtype raises major concerns for
effective vaccine development.

INTRODUCTION
The global distribution of circulating recombinant forms of
human immunodeficiency virus type 1 (HIV-1) M group strains
and the high prevalence of intersubtype recombinants in some
areas where multiple subtypes are common (reviewed in reference
35) demonstrate that dual infection with different strains of
HIV-1 occurs. However, specific examples of dual infection have
been documented clearly in only a few cases. Most of these examples
have been observations of chronically infected patients with
two different subtypes in countries where more than one subtype
is prevalent (
4,
7,
30,
37,
38), and a few examples of intrasubtype
B dual infections have been described (
14,
40,
41,
51). Whether
these dual infections occurred as coinfections or superinfections
is unknown, and the influence of cellular immunity on coexisting
viruses has been largely undefined.
A few cases of superinfection, usually involving superinfecting strains that differ in antiretroviral drug susceptibility from the initial variant, have been identified. One individual was initially infected with a strain of HIV-1 belonging to clade CRF01_AE and, after a series of therapy interruptions, became superinfected with a B subtype strain (21). Another individual was initially infected with a drug-resistant strain but became superinfected in the absence of therapy with a drug-sensitive strain of the same subtype (23). One study explored the possible role of cellular immune responses in an individual who was undergoing structured treatment interruptions and had achieved relatively stable control of viremia, subsequently becoming superinfected with another B subtype strain and suffering an acute rise in viremia (2). However, data regarding the role of cellular immunity in superinfection in the absence of drug therapy have been lacking.
We have studied a subject who was initially infected with a multiply drug-resistant strain of HIV-1 subtype B. He controlled the initial infection well in the absence of antiretroviral therapy but became superinfected 4 months later with a second, drug-sensitive strain and showed a marked rise in viremia. Detailed genetic and immunological characterization showed that cytotoxic T-lymphocyte (CTL) responses against the first strain waned with outgrowth of the second strain. The failure of immune containment of the second strain despite early infection and an initially effective HIV-specific CTL response exemplifies a significant challenge to the development of effective vaccines.

MATERIALS AND METHODS
The subject.
Subject 2030 was a 33-year-old homosexual Asian-American male
with no significant past medical history who presented after
10 days of an acute illness. He reported multiple ongoing unprotected
sexual exposures as a risk factor for HIV-1 infection and was
subsequently found to be seropositive. These studies were conducted
with appropriate subject consent and approved by the Human Research
Protections Program at the Harbor-UCLA Medical Center Research
and Education Institute, University of California, Los Angeles,
Calif.
HLA typing.
High resolution HLA typing was performed by Pel-Freez Biologicals.
HIV-1 phenotyping.
Antiretroviral susceptibility was determined by PhenoSense (ViroLogic, Inc.) as previously described (36). In this assay, a region extending from p7gag to amino acid 300 in reverse transcriptase (RT) is RT-PCR amplified from plasma viral RNA and inserted into the test vector. This construct, after transfection into the target cells, is used in a single cycle assay in the presence of drug for assaying drug susceptibility; similarly, in the absence of drug, it is used for assaying endogenous replication capacity (9). In both assays, the replication rate is compared to the replication rate of the control strain HIV-1 clone NL4-3.
HIV-1 genomic sequencing and phylogenetics.
Sequencing of viral genomic regions containing CTL epitopes was performed after RT-PCR amplification of plasma viral RNA (extracted with Finnzyme one-step RT-PCR kit, MJ Research, Waltham, Mass., or RNA isolation kit, QIAGEN, Valencia, Calif.). Primers to sequence HIV-1 were those employed by Altfeld et al. (2) (except those for Env), including 737-F (GCG ACT GGT GAG TAC GCC), 2095-R (TTC CCT AAA AAA TTA GCC TG), 1232-F (ACC TAG AAC TTT AAA TGC ATG GG), 1754-R (CAA CAA GGT TTC TGT CAT CC), 1816-F (TAG AAG ACA TGA TGA CAG CAT G), 3018-R (GGT GAT CCT TTC CAT CC), and 2422-R (TCT TAC TTT GAT AAA ACC TCC) (Gag); 5040-F (ATG GAA AAC AGA TGG CAG G), 6455-R (GGG TCT GTG GGT ACA CA), and 5579-R (GGT CTT CTG GGG CTT GTT CC) (Vif); 5692-F (TAT CTA TGA AAC TTA TGG GGA TAC) and 6229-R (CTT TCA TTG CCA CTG TCT TC) (Tat/Rev); 7361-F (TTA ATT GTG GAG GAG AAT TTT T), 9403-R (ACT CCG GAT GCA GCT CTC GGG C), 8804-F (ATG GGT GGC AAG TGG TC), and 9239-R (ACT GGT ACT AGC TTG AAG CAC C) (Nef); V3-F out (CAA AGG TAT CCT TTG AGC CAA T), V3-B out (ATT ACA GTA GAA AAA TTC CCC T), V3-B in (GCG TTA AAG CTT CTG GGT CCC CTC CTG AG), and V3-F in (GAA CAG GAC CAG GAT CCA ATG TCA GCA CAG TAC AAT) (Env). DNA fragments were then gel purified (gel purification kit; QIAGEN) and cloned into the TOPO TA vector (Invitrogen Corp., Carlsbad, Calif.). For each fragment, a minimum of three individual clones were sequenced to obtain consensus sequences for each time point. PCR products were sequenced with Prism Dye terminator kits (ABI, Foster City, Calif.) on an ABI 3100 Genetic Analyzer. Sequences were compiled, aligned, and edited by using Sequencher 4.0 (Genecodes, Ann Arbor, Mich.) and BioEdit (17), and phylogenetic analysis was performed by using MEGA2 (26). Neighbor-joining phylogenetic trees for the reverse transcriptase and protease coding region were obtained from a matrix of synonymous nucleotide distances. This method is most appropriate in regions where there is strong selection on nonsynonymous changes, which otherwise can lead to incorrect trees (demonstrated at http://www.hiv.lanl.gov/content/hiv-db/CONTAM/contam_conserved.html).
ELISPOT analysis of HIV-1-specific CD8+-T-cell responses.
Nonspecifically expanded CD8+ T cells were screened to define HIV-1-specific responses by using a standard gamma interferon enzyme-linked immunospot (ELISPOT) assay as previously described (49). Briefly, cryopreserved peripheral blood mononuclear cells from the indicated times were polyclonally expanded to yield CD3+/CD8+ lymphocytes by using a CD3:CD4-bispecific antibody (50) and evaluated for reactivity against overlapping HIV-1 subtype B 15-mer peptide sets (most of which are based on a consensus sequence) obtained from the NIH AIDS Research and Reference Reagent Repository (ARRRR; catalogue numbers 6869, 6208, 6451, 5189, 5138, 6445, 6446, 6447, and 6444). Initial screening was performed on pools of 16 or fewer peptides, followed by analysis of 4-by-4 matrix pools and confirmation using individual peptides. This method is reported to result in a small but quantitatively consistent bias in the expansion of antigen-specific CD8+ T lymphocytes (3, 20), in agreement with our own experience comparing ELISPOT responses with fresh and expanded CD8+ peripheral blood mononuclear cells (r2 = 0.58 for comparisons within nine chronically infected persons; data not shown).

RESULTS
Clinical presentation and course of subject 2030.
Subject 2030 presented with an acute syndrome of fever, rash,
myalgia, cervical lymphadenopathy, oral ulcers, and headache
of 10 days duration. Upon presentation, he had a positive serum
ELISA for HIV-1 antibodies, a borderline Western blot for HIV-1
(bands for gp160 and p24 only), a peripheral blood CD4
+-T-lymphocyte
count of 396 cells/µl, and viremia of approximately 300,000
HIV-1 copies of HIV RNA/ml of plasma. Subsequently, the viremia
decreased to an initial set point of approximately 1,000 copies/ml,
and the CD4
+-T-lymphocyte count rose to over 600 cells/µl
(Fig.
1). However, after this period of relative stability following
acute infection, plasma viremia rose sharply to a new plateau
of approximately 30,000 to 40,000 copies/ml at 5 months after
presentation, with a concomitant decline in the CD4
+-T-lymphocyte
count to about 450 cells/µl. Subject 2030 reported ongoing
high-risk sexual exposures, raising the possibility that this
acute change in set point could be due to HIV-1 superinfection.
Dramatic shift in HIV-1 phenotype and genotype indicating infection with two distinct strains.
Phenotypic testing revealed that the initial infecting virus
was resistant to multiple drugs (Fig.
2). The 50% inhibitory
concentration of drug (IC
50) of the baseline sample was 50-fold
higher than the wild-type control HIV-1
NL4-3 for zidovudine,
approximately 160-fold higher for delavirdine, and 13-fold higher
for nelfinavir. The
pol genotype revealed multiple resistance-associated
mutations in both protease (PR) and RT: V77I and L90 M in PR;
and M41L, K103N, Y181C, T215F, and an insertion of two serine
amino acids at position 69.
When viremia rose at month 5 (Fig.
1), this initially drug-resistant
phenotype abruptly shifted to a phenotype that was susceptible
to all tested drugs (Fig.
2). Genotyping at this point revealed
none of the prior drug resistance mutations and showed distinct
variations at polymorphic sites other than those associated
with drug resistance. A phylogenetic analysis of protease and
reverse transcriptase for this subject, and for control subjects
in the same area with acute HIV-1 infection within the year,
confirmed that the initial virus strain (A) and the subsequent
strain (B) were phylogenetically distinct (Fig.
3). The genetic
distance between strains A and B at synonymous sites within
the sequenced
gag-pol region was 15.42 ± 2.0%. This genetic
distance was greater than that seen in 95% of comparisons among
local acute HIV-1 infections involving subtype B (mean, 11.98%;
maximum, 16.8%). The
nef genes of the strains also were clearly
distinct, although not as divergent as
gag-pol. Within
nef,
nonsynonymous sites differed more, on average, between the two
than did synonymous sites (
dN = 5.7% and
dS = 4.5%, as estimated
by the modified Nei-Gojobori method with Jukes-Cantor correction
for multiple hits). In the C2V3 region of
env, however, there
is no difference between
dN and
dS43, and a single overall rate
was estimated. On the basis of 12 clonal sequences 409 bp in
length from each of the two strains (strain A, month 3; strain
B, month 7), the mean genetic distance was 19.2 ± 0.039%
(Tamura-Nei model with

-distributed rates;

value, 0.4). Overall,
sequence data from across the genome clearly demonstrated infection
of this individual with two distinct HIV-1 strains.
Recombination between strains A and B.
Very little viral sequence diversity accumulated in the first
three months of infection, with the exception of amino acid
position 215 in RT. At month 4, the consensus sequence contained
a series of mixtures at both synonymous and nonsynonymous positions,
clustered between amino acids 190 and 300 in RT. These mixtures
generally contained one nucleotide identical to the consensus
sequence from the first 3 months (strain A) and another nucleotide
corresponding to the subsequently distinct consensus sequence
at 6 months (strain B; Fig.
4). The most parsimonious reconstruction
of the month 4
pol genotype therefore was a mixture of two distinct
sequences, one from strain A and a second recombinant of strains
A and B. Only at amino acid 215 in RT, where one of the parental
alternatives (T) was not detected, was this reconstruction ambiguous.
This was the first evidence of the presence of strain B in Subject
2030 and the only evidence of recombination between the two
infecting strains detected in this study.
Reduced replicative capacity of pol in strain A compared to strain B.
The phenotypes of the
pol genes from the two strains were compared
also by using the ViroLogic replication capacity assay (Fig.
5). This assay correlates significantly with in vitro fitness
and usually, in the context of drug resistance, with plasma
viremia (
9). The assay compares the number of infective particles
produced (in the absence of drug) by recombinant viruses containing
subject-derived gagp7-RT segments in an NL4-3 backbone. Normalized
to the average of subject-derived viruses, the mean replicative
capacity for strain A (i.e., before month 4) was 35% of wild-type
subject-derived virus isolates (range, 64 to 12%), while that
for strain B (after month 4) was 8% (12 to 1.5%) of wild-type
subject-derived virus isolates. The generally lower value for
strain B was consistent with the observation of protease hypersusceptibility
of this strain (data not shown), which has been associated with
low replicative capacity (
29). These data show that the in vivo
overgrowth of strain A by strain B was not a result of lower
intrinsic replicative ability of strain A associated with drug
resistance mutations in
pol, raising the question of differential
immune containment of the two viruses.
Coreceptor usage of strains A and B.
Because the coreceptor usage of HIV-1 determines the cells that
can serve as targets of infection and is associated with disease
pathogenesis, the usages of strains A and B were determined
by sequencing of the C2V3 region of Env. Clonal sequences obtained
from the plasma were assessed for amino acids at positions 11
and 25 of V3, because CXCR4 coreceptor usage is determined by
specific amino acid substitutions in the V3 region of
env, notably
basic amino acid substitutions (
16). Although the V3 loop sequences
of the strains were distinct (12 clonal sequences each from
the month 3 and month 12 time points, data not shown), 12 of
12 clones from strain A (month 3) and 11 of 12 clones from strain
B (month 12) had serine at position 11. Similarly, 12 of 12
strain A and 11 of 12 strain B sequences had an acidic residue
at position 25 (glutamic acid in strain A and aspartic acid
in strain B). One strain B clone had asparagine at position
11 and another had asparagine at position 25, but no clone had
negatively charged amino acids at both positions. Thus, there
was no significant difference between the two strains with respect
to predicted coreceptor usage, with both strains being the R5
phenotype.
Evolution of CD8+ cellular immune responses suggesting differential recognition of the viruses.
The initially low set point of viremia followed by the subsequent sharp increase (in the absence of antiretroviral therapy) suggested a change in immune control over time. We therefore analyzed the HIV-1-specific CD8+-T-lymphocyte responses by gamma interferon ELISPOT assays (Table 1). Recognition of epitopes in Gag, Nef, and Vif was observed as early as 17 days after the onset of symptoms of acute infection. These early responses generally persisted during the subsequent 3 months, accompanied by broadening to recognize additional epitopes in Gag and Tat. However, after the fifth month, the early responses waned, and new responses were noted in Nef and Rev by the ninth month. Classifying CTL responses as those detected at the first time point ("early responses") or only afterwards ("late responses") demonstrated a clear pattern of evolution (Fig. 6), with the magnitude of early responses declining consistently starting in the third month and the magnitude of late responses rising sharply starting in the fifth month. In the context of superinfection and overgrowth of strain A by strain B, these data strongly suggest that the initial CTL responses were specific to strain A and poorly recognized strain B; while there was adaptive retargeting of responses, this retargeting was inadequate to contain strain B to the degree that the initial responses had contained strain A.
Differences in strain A and strain B CTL epitopes.
To examine whether sequence differences might account for differential
immune control of the two viruses, regions targeted by CTL were
sequenced from strains A and B (Table
2). The in vivo viral
sequences corresponding to the recognized screening peptides
were compared in the context of the HLA type of the subject
(A*03, A*24, B*35, and B*40). Of responses that exceeded 100
spot-forming cells (SFC)/10
6 CD8
+ T lymphocytes, the majority
that waned after superinfection contained potentially significant
differences in strain B compared to strain A. These differences
included an insertion of four amino acids flanking a predicted
epitope (Table
2, row 4) and changes within the TCR-binding
region (Table
2, rows 6 and 8) or HLA-binding motif (Table
2,
row 9) of the predicted epitopes in four of six examples. Two
of these six examples (Table
2, rows 1 and 2) showed no difference
between the strains. However, it is clear that this waning of
the initial responses was not due to generalized immune deficiency,
because a vigorous new response against Rev was generated after
superinfection (Table
2, row 8). The recognized region of Rev
contained two amino acid differences in the TCR-binding region
of the predicted epitope in strain A compared to strain B, and
the screening peptide was identical to strain B in this sequence.
Furthermore, the persistence of an early response recognizing
a predicted epitope that was identical in strains A and B (Table
2, row 5) indicated that the decay of the early responses was
selective. Overall, these findings are consistent with significant
epitope differences in the two viruses having a central role
in differential immune containment by CTL and persistence of
the CTL response.

DISCUSSION
Previous studies of the evolution of the HIV-1 quasispecies
within infected individuals led to the widespread belief that
superinfection is a rare event (
5,
10-
13,
18,
27,
28,
31,
33,
34,
39,
42-
48). While dual infection was demonstrated to be
possible (
51), only recently have clear examples of superinfection
emerged (
2,
21). These two cases demonstrated superinfection
in subjects who underwent structured treatment interruptions
with partial control of viremia, presumed to be immunologically
mediated. Other recent studies, including a third case in which
coinfection or superinfection occurred in the absence of therapy
(
23), suggest that it can occur in the setting of natural infection
without alteration of immunity by pharmacologic intervention.
The case described here extends these novel findings and clearly
documents superinfection after an initial infection reaching
a stable set point in the absence of antiretroviral treatment
as a confounding factor.
It is impossible to entirely exclude the possibility that a superinfecting strain was present as an initial coinfection. In the case of subject 2030, however, overgrowth by strain B occurred rapidly and completely once it was detected, showing that its overall growth advantage in vivo was great. If present during acute infection, this overgrowth should have occurred much earlier than 4 months after infection. This example is striking because superinfection was clearly documented after a stable viremia set point was established, in contrast to most published reports. The subject had developed a broad and stable CTL response to the first virus and reached an equilibrium of viremia, suggesting efficient immune suppression of viral replication. Strain B, which was highly genetically distinct from strain A, was detectable only at 4 months after primary infection, but it rapidly overgrew strain A with a substantial increase in viremia set point. A fitness assessment of the pol genes showed a lower replication capacity for strain B than strain A, suggesting that substantially greater intrinsic replicative fitness due to differences in pol was not the mechanism of this overgrowth. Although fitness differences due to genes other than pol have not been excluded, the high level of viremia during primary infection suggested that strain A was not generally defective in replicative capacity. Furthermore, an evaluation of coreceptor usage revealed that both strains were predominately the R5 phenotype, making it unlikely that a difference in tropism could account for differences in replication in vivo. This finding indicates that differential immune containment of strain B versus strain A could be the key factor.
Consistent with the report on immune responses of a subject who had superinfection after structured treatment interruption (2), we found that our subject had developed a stable and broadening repertoire of CTL responses against the initial virus, which failed to prevent or contain infection with the second virus. Sampling of epitope sequences revealed significant differences between the viruses, suggesting that the mechanism of immune failure was nonrecognition of the second strain. Strikingly, the majority of CTL responses decayed rapidly after superinfection, similar to the observed loss of CTL after epitope mutation and escape occurring in chronically infected persons (19). Furthermore, while new CTL responses were detected after superinfection, these were fewer and failed to contain the second virus. This result could have been a consequence of the divergent sequence of the superinfecting strain or might imply a role for a mechanism, such as original antigenic sin (22), limiting the adaptability of CTL responses after initial infection.
The marked rise in viremia after superinfection is consistent with another detailed study of superinfection in the setting of immune control achieved by structured treatment interruption therapy in early infection (2). This phenomenon is also reminiscent of the increased viremia that has been observed with escape occurring during natural infection (15, 32) and reinfusion of an ex vivo expanded CTL clone (24) and associated with SIV vaccine failure in macaques (6). The ability of CTL to recognize the challenging viral sequences thus appears to be a crucial determinant of immune control.
Superinfection and loss of immune control in this subject, despite apparently effective CTL responses to the initial strain, may have serious implications for vaccine design. The determinants of an effective CTL response against HIV-1 remain unknown, and attempts to correlate the magnitude or breadth of the response (8) to control of viremia generally have been disappointing (1). Our data, in agreement with those of Altfeld et al. (2), indicate that protective CTL targeting against HIV-1 may vary not only by subtype of virus but even by individual strains. Given the great variability of HIV-1, this phenomenon may pose a significant obstacle to generating protective immunity with a fixed vaccine sequence.

ACKNOWLEDGMENTS
This work was supported by grants AI27670, AI38858, AI43638,
AI43203, AI41224, AI27660, AI055276, UCSD Center for AIDS Research
grant AI36214, and grant AI29164 from the National Institutes
of Health, the Research Center for AIDS and HIV Infection of
the San Diego Veterans Affairs Healthcare System, and General
Clinical Research Center, National Center for Research Resources
grant M01-RR00425.

FOOTNOTES
* Corresponding author. Mailing address: 37-121 Center for Health Sciences, Division of Infectious Diseases, 10833 LeConte Ave., UCLA Medical Center, Los Angeles, CA 90095. Phone: (310) 794-9491. Fax: (310) 825-3632. E-mail:
oyang{at}mednet.ucla.edu.


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Journal of Virology, January 2005, p. 860-868, Vol. 79, No. 2
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