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J Virol. 2010 January; 84(1): 492–502.
Published online 2009 October 14. doi:  10.1128/JVI.01743-09
PMCID: PMC2798410

Replicative Capacity of Human Immunodeficiency Virus Type 1 Transmitted from Mother to Child Is Associated with Pediatric Disease Progression Rate[down-pointing small open triangle]


Human immunodeficiency virus (HIV)-infected infants in the developing world typically progress to AIDS or death within the first 2 years of life. However, a minority progress relatively slowly. This study addresses the potential contribution of viral factors to HIV disease progression in eight infants selected from a well-characterized cohort of C clade HIV-infected infants, monitored prospectively from birth in Durban, South Africa. Three infants were defined as “progressors,” and five were defined as “slow progressors.” We observed that slow-progressor infants carry HIV isolates with significantly lower replicative capacity compared to virus from progressors. Furthermore, our data suggest a link between the attenuated viral phenotype and HLA-B* 57/5801 epitope-specific Gag mutational patterns of the transmitted virus and not to coreceptor usage or to the presence of Nef deletions or insertions. These data underline the importance of virus-host interactions and highlight the contribution of viral attenuation through Gag-specific CD8+ T-cell escape mutations, among other factors, in the control of pediatric HIV infection.

Untreated human immunodeficiency virus (HIV)-infected infants progress more rapidly to AIDS and death than older children or adults (35). This is particularly the case in resource-limited settings, where mortality exceeds 50% by 2 years of age. Viral loads during infancy remain strikingly high, and the rapid reduction in viremia from peak levels characteristic of acute adult infection occurs only slowly over the first few years of life in pediatric infection. This late reduction in viremia, compared to the establishment of viral setpoint within a few weeks in adult infection, may coincide with the normal maturation of infant adaptive immune responses.

There are several additional reasons for impaired virological control during infancy. First, HIV-induced T-cell depletion damages the developing immune system before an effective antiviral response can be mounted (13, 23). Second, HIV-infected infants are more likely to possess nonprotective HLA alleles, since at least 50% of the infant's HLA genotype is shared with the mother, and high maternal viremia is a risk factor for perinatal HIV transmission (35). Finally, the infecting virus may be adapted to maternally and paternally inherited HLA genes (19, 38). However, a minority of infants progress relatively slowly. The immune correlates of slow progression in pediatric HIV infection are still not well understood. In this context, the interactions between characteristics of the maternal virus transmitted but also the CD8+ T-cell responses generated by the child are likely to be important factors to HIV control in pediatric infection, as in adults (11, 28).

In certain cases described in the literature, the biological properties of the virus have been determined as the primary reason for effective HIV control. Presence of attenuated HIV variants with low replicative capacity (RC) has been linked to nonprogressive disease (12, 36) and elite control (28) in HIV-infected adults. Moreover, transmission of certain HIV Gag CD8+ T-cell escape variants to a recipient lacking the same HLA molecules leads to reduced viral set point in acute adult infection and contributes to higher CD4 counts and lower viral load (6, 14). In other cases, control of viremia has been strongly associated with CD8+ T-cell responses mediated by “protective” HLA alleles such as HLA-B*57 or B*27 (16). In HIV-infected children, as in adults, there is evidence that CD8+ T-cell responses can contribute to viral containment and that the “protective” effect of certain HLA alleles identified in adult HIV infection may also operate in pediatric infection (42). In addition, HIV-infected infants lacking protective HLA alleles but whose mothers express protective HLA alleles such as HLA-B*57, B*5801, or B*8101 tend to progress more slowly, for reasons hypothesized to relate to transmission of virus that has been attenuated by the selection of CD8+ T-cell escape mutants in the mother (41).

We therefore undertook the present study in perinatally HIV-infected infants in Durban, South Africa, the epicenter of the pediatric epidemic, to investigate the potential role of the viral RC of mother-to-child transmitted virus on pediatric HIV disease progression. We studied eight infants with clade C HIV infection: three defined as progressors (P) and five as slow progressors (SP). To characterize in detail biological properties of the virus, viral variants were isolated from plasma samples in both groups. The RC of viral isolates was measured in vitro in primary cells. In addition, viral tropism was determined for these isolates, together with the presence of polymorphisms in Nef, and of HLA-B*57/5801-associated Gag escape mutants, since these have been additional factors previously linked to viral attenuation and disease outcome.


Patient cohort.

The study cohort has previously been described elsewhere (29, 34). Briefly, 63 HIV-infected infants who met the study criteria were randomized at diagnosis to one of three arms: deferred antiretroviral therapy (ART), started once clinical or immunological criteria were reached (arm A), immediate short-term ART given for 1 year and then stopped (arm B), or immediate short-term ART given with up to three structured treatment interruptions (STIs) to 18 months of age and then stopped (arm C). Arm B and C infants subsequently started long-term ART once they met World Health Organization (WHO) clinical or immunological criteria. Clinical criteria were pediatric stage III disease or advanced pediatric stage II disease, as defined in 2003 WHO guidelines. Immunological criteria of progression to AIDS were confirmed CD4 ≤20% (less than 18 months of age) or ≤15% (more than 18 months of age). For the present study, we categorized infants as P or SP based on these CD4 criteria, since viral load during infancy is not predictive of disease progression, whereas CD4 count (expressed as a percentage) is the best marker of disease outcome identified (8, 17). For the purposes of the present study, P subjects were defined as infants who reached the ART treatment initiation threshold (CD4 ≤ 20% if under 18 months; CD4 ≤ 15% if over 18 months) within the first 12 months of life (arm A) or within 12 months of stopping early ART (arms B and C). SP were defined as infants who had not reached treatment criteria by the study endpoint (3 years of age).

Virus extraction and titrations.

Viruses were isolated from cryopreserved plasma samples by using anti-CD44 beads, according to the manufacturer's protocol (Miltenyi Biotech, Germany). Prior to virus extraction, peripheral blood mononuclear cells (PBMC) from three healthy HIV-uninfected donors were isolated and CD8+ cells depleted with anti-CD8 beads (Dynabeads; Invitrogen, United Kingdom). Pooled CD8-depleted PBMC from three donors were then stimulated under three different conditions (3×3 Method; Miltenyi Biotech): low-dose phytohemagglutinin (PHA; 0.5 μg/ml), high-dose PHA (5 μg/ml), or plate-bound anti-CD3 monoclonal antibody (OKT3) at 37°C and 5% CO2. After 72 h, cells from the three different conditions were pooled, and 3 × 106 (cells/ml) were incubated with 200 μl of extracted virus for 2 to 4 h at 37°C and 5% CO2. After infection, cells were resuspended to a final concentration of 106 (cells/ml) in R10 supplemented with 100 U of interleukin-2 (Roche, United Kingdom)/ml. Cultures were fed weekly with 106 (cells/ml) fresh 3×3-stimulated CD8-depleted PBMC. Viral growth was monitored by p24 enzyme-linked immunosorbent assay (ELISA; Innogenetics) twice a week. Virus was harvested when the concentration of p24 in the supernatant was at least 104 (pg/ml) and stored at −80°C.

Sequencing, phylogenetic analyses, and subtype determination.

RNA was extracted from viral stocks (Qiagen, United Kingdom) and reverse transcribed to cDNA. Gag, Pol, and Nef fragments of the HIV genome were amplified and sequenced as previously described (24). RNA was also extracted from the original cryopreserved plasma samples (based on availability), reverse transcribed to cDNA, and sequencing was undertaken in the same manner in order to compare the sequences of population plasma virus and laboratory isolates. Gag sequences from plasma and viral stocks were edited and manually aligned with Seq-Al version 2. A maximum-likelihood phylogenetic tree was constructed with GARLI (genetic algorithm for rapid likelihood inference). Phylogenetic trees were edited with Fig-tree version 1.1.2. The virus subtype was determined by submitting isolates Gag and Nef sequences to the REGA HIV automated subtyping tool.

Titration and single-cycle infectivity assay.

Titers of virus stocks were determined in Ghost X4R5 cells, and 50% tissue culture infective doses were calculated based on the Spearman-Karber equation. Single-cycle infectivity assays were undertaken in Ghost X4R5 cells as previously described (33). Briefly, Ghost X4R5 cells were infected in triplicate by spinoculation with viral isolates to a multiplicity of infection (MOI) of 0.025. After 24 h, infectivity was measured by assessing the green fluorescent protein (GFP) expression by flow cytometry. The data were analyzed with FlowJo 8.6 software (Tree Star).

Replication kinetics in CD8-depleted PBMC.

PBMC were isolated from three healthy HIV-seronegative donors and CD8+ cells depleted using anti-CD8 beads (Dynabeads). CD8-depleted PBMC were then stimulated under two different conditions: low-dose PHA (0.5 μg/ml) and high-dose PHA (5 μg/ml). After 72 h, 2 × 106 CD8-depleted PBMC were infected with different viral isolates to an MOI of 0.002 for 4 h at 37°C and 5% CO2. After infection, cells were washed three times with 10 ml of phosphate-buffered saline (PBS) and resuspended to a final concentration of 106 (cells/ml) in R10 supplemented with 100 U of interleukin-2/ml. A total of 200 μl of supernatant was taken every day and replaced with 250 μl of fresh medium for 10 days. Viral growth was measured by p24 ELISA (Innogenetics) and viral infection was quantified as the amount of intracellular p24 at the end of the experiment by fluorescence-activated cell sorting (FACS).

Virus tropism.

Viral tropism was measured in U87 immortalized cell lines expressing CCR5 or CXCR4, as previously described with minor modifications (3, 11). 5000 cells were plated in a 96-well plate and infected with 2000 pg of p24 for each viral variant overnight. The next day, virus was washed three times with 200 μl of PBS and fresh media added to a final volume of 200 μl. Five days after infection, presence of syncytia was determined by nuclear DAPI (Invitrogen, United Kingdom) staining under microscope and viral growth measured by p24 ELISA. Virus were consider positive for a particular coreceptor usage (+++) by the presence of syncytia under the microscope and p24 quantification over 300 (pg/ml).

Construction of p24-Gag recombinant virus from isolates and replication kinetics.

In order to determine the importance of p24 polymorphism as a genetic determinant of viral replication, RNA was extracted from viral isolates of two P (197-B and 097-A) and three SP (517-A, 349-A, and 586-A). The p24 capsid coding region was PCR amplified from SapI to ApaI restriction sites (positions 1098 to 2021 in HXB2 sequence) and cloned into p83-2, as previously described (27). Recombinant clones were sequenced and selected based on the match of the p24-coding region between isolate and recombinant. Viral stocks were produced by contransfection of p83-2 derived p24 clones and p83-10EGFP in MT4 cells. The 50% tissue culture infective dose was determined in MT4 cells by the Reed and Muench method (30). For replication kinetics experiments Jurkat T cells were infected in triplicate to an MOI 0.005 with wild-type (WT) virus or variants at 37°C for 2 h. Pellets were washed twice with PBS and cultured at 37°C and 5% CO2. After infection, 150 μl of supernatant with at least 50,000 cells were harvested, and infectivity was determined by the percentage of GFP-positive cells by FACS. Infectivity rate was calculated as previously described (32).

ELISPOT assays.

A panel of previously defined optimal clade C peptides were synthesized on an automated peptide synthesizer (MBS 396; Advanced ChemTech). Ex vivo measurement of infant optimal HIV-specific cytotoxic-T-lymphocyte responses by gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assay was undertaken, as described elsewhere (42).


Clinical evolution and virus isolation.

Five infants were defined as SP, and three infants were defined as P. The median time to AIDS among P infants was 152 days. Two were arm A infants (197 and 641) who progressed to CD4 ≤20% on days 291 and 152 of life, respectively; the other (infant 097) was an arm B infant who met criteria to start treatment within 17 days of cessation of early ART. Of the NP, two were arm A infants (517 and 349) who remained untreated at 3 years of age; three were arm B infants (001, 586, and 114) who had not met criteria to restart treatment two years after cessation of early ART (Table (Table1).1). Details of the clinical course and sample time points for the eight infants are shown in (Fig. (Fig.1).1). Plasma viruses were isolated from a total of 19 time points from eight infants. In order to test whether the extracted viral isolates were representative of the plasma virus population, viral RNA was extracted from viral stocks and contemporaneous plasma samples. HIV gag was amplified by PCR, and a maximum-likelihood phylogenetic tree was constructed to compare virus isolates and plasma sequences. The phylogenetic tree (Fig. (Fig.2)2) showed that viral isolates were either identical or very closely related to the plasma sample sequences. These results demonstrate that the viral isolates that were extracted from cryopreserved plasma were indeed representative of circulating virus and not archaic viral strains.

FIG. 1.
Clinical evolution of progressor and slow progressor HIV-infected infants. Changes in viral load (○) and CD4+ count (•) in the study infants over the follow-up period. Arrows indicate the time points of plasma samples used for ...
FIG. 2.
Phylogenetic tree of Gag sequences from viral isolates and plasma samples. Viral RNA was extracted from viral isolates and available plasma samples and the Gag HIV gene amplified. A maximum-likelihood tree was constructed by analysis of more than 1,000 ...
Virologic and immunologic characteristics of subjects and viral isolates

HIV C clade isolates from SP and P infants differ in viral RC.

It has previously been shown that viral attenuation can be a strong determinant of long-term nonprogressive HIV infection in adults (12, 28, 36). In order to determine the contribution of viral attenuation in the setting of early pediatric infection, we measured the virus RC of 19 clade C viral isolates. After 72 h of activation, mixed CD8+ T-cell-depleted PBMC from three HIV-seronegative donors were infected to an MOI of 0.002 with the different isolates and viral production monitored over time by p24 ELISA. First, we compared early isolates that were obtained between 1 and 4 months after infection or ART interruption. These viruses represent the closest available variants to the original maternal virus transmitted. Our data show a significant reduction in virus RC taking into account only the early virus isolates from SP versus P (day 3, P = 0.0016; day 9, P = 0.0159 [Mann-Whitney test, data not shown]). In addition, when our initial analyses were extended to the total number of isolates (Fig. (Fig.3A)3A) (day 3, P = 0.0030; day 9, P = 0.0004 [Mann-Whitney test]) and viral growth rate compared between groups (P < 0.0001) (Fig. (Fig.3B),3B), statistical support was also obtained, further supporting the hypothesis that virus RC might be higher in P compared to SP. Analogous results were obtained in an independent experiment conducted at lower MOI of 0.0005 (data not shown). Moreover, as shown in (Fig. (Fig.3),3), viral isolates from P infants showed a consistent logarithmic growth, comparable to those of a typical laboratory strain in culture, while greater variability in the replication profile was seen for SP isolates. Together, these results show an association between transmission of virus with low RC and slower disease progression in perinatally infected infants.

FIG. 3.
Replication kinetics of viral isolates from P versus SP infants in CD8-depleted PBMC. CD8-depleted PBMC were stimulated for 72 h and infected with viral isolates from P and SP subjects in duplicates to an MOI of 0.002. After infection virus replication ...

Temporal changes in viral RC during pediatric HIV infection.

Little is known about the evolution of viral RC in HIV infection. Conflicting studies report either an increase or decrease in viral RC over time at either an individual or at population level (1, 37, 43). In order to evaluate changes in RC over the course of pediatric HIV infection, we compared viral isolates from each study subject at different time points after infection, measuring viral infectivity by assays of both single-cycle replication and multiple cycles of replication. In these studies, there was no clear tendency toward higher or lower RC between early and late isolates measured by either single-cycle or multiple rounds of infection (Fig. 4A to C). Viral RC within P and SP isolates was variable over time, but consistent between assays (Fig. 4A and C). There were no differences in viral infectivity in the single-cycle assay between SP and P isolates (P = 0.1223 [Mann-Whitney]; Fig. Fig.4B).4B). However, there was a statistically significant difference between subgroups measured by intracellular p24 accumulated during multiple rounds of infection (P = 0.0047 [Mann-Whitney]; Fig. Fig.4D),4D), which is consistent with results from the earlier kinetics experiment (Fig. (Fig.3).3). These data suggest that infants with slow-progressive HIV infection tend to have virus with lower viral RC. Furthermore, the lack of any trend between early and late samples demonstrates the fluctuating nature of virus RC overtime that is established not in a single cycle but multiple rounds of viral replication.

FIG. 4.
(A) Single-cycle infectivity assay in GhostX4R5 cells. A total of 40,000 cells were infected in triplicate at an MOI of 0.025, and the amount of GFP was measured by FACS 24 h after infection. (C) p24 intracellular staining at D9 after infection in CD8-depleted ...

Genotypic characterization of Nef and viral tropism in viral isolates.

Although multiple factors contribute to RC of a virus, certain genetic features have been particularly strongly associated with viral RC. These include the presence of Nef polymorphisms or deletions and the establishment of highly pathogenic CXCR4 virus in early infection (22, 26). Therefore, we next investigated the potential impact of these genetic factors on viral phenotype in our cohort. We sequenced Nef and measured viral tropism in U87 immortalized cell lines expressing CD4 and either the CCR5 or CXCR4 coreceptor. We observed no deletions or premature stop codons in Nef previously associated with slow progression (12, 44) that could be linked to disease progression in these infants. Insertions and deletions were found within the variable region of Nef in the first 50 amino acids (aa) (Table (Table2);2); however, variation at this region, either deletions at positions 25 and insertions between aa 9 and 17, was equally distributed between P and SP group and was not associated with disease progression, either in this small study or in an analysis of 500 adult subjects infected with C clade HIV-1 in Durban (P. Matthews et al., unpublished data). Consistent with previous published data in infant clade C and D HIV infection (5, 7), the majority of our isolates (89% [17/19]) showed CCR5 coreceptor use and only one subject (641, a P infant) showed dual tropism (Table (Table2).2). Thus, in this albeit small study, there were no significant differences in virus coreceptor use between groups or coreceptor switch during the follow-up period.

Genotypic characteristics and viral phenotypes of isolates

Mutations in HLA-B*57/5801 Gag CD8+ T-cell epitopes: importance of p24 protein as a genetic determinant of viral replication.

Recent data have shown that transmission of HLA-B*57/B*5801 p24 Gag CD8+ T-cell escape mutants to non-HLA-B*57/5801 individuals is associated with higher CD4 counts and contributes to a lower viral set point after acute infection in adults (6, 14). In addition, similar advantage has been described in infants carrying B*57/B5801 escape HIV variants even in the absence of CD8+ T-cell responses (40). Based on these findings, we investigated the relationship between the presence of mutations within HLA-B*57/5801-restricted p24 Gag CD8+ T-cell epitopes and disease progression in our group of infants. We analyzed mutations within four HLA-B*57/5801 p24 Gag epitopes (ISPRTLNAW, ISW9, Gag 147-155; KAFSPEVIPMF, KF11, Gag 162-172; TSTLQEQIAW, TW10, Gag 240-249; and QATQDVKNW, QW9, Gag 308-316) and the compensatory changes at positions H219, I223, and M228 in the cyclophilin A binding loop (CypA), linked to variation within TW10 (4). All viral isolates studied encoded polymorphisms in at least one of the four B*57/5801-restricted Gag epitopes, although none carry these alleles, and only subjects 349 and 114 had mothers with B*5702 (Tables (Tables33 and and4).4). In six of the eight study subjects, the early viral isolates contained variations within TW10 (at Gag-242 and Gag-247) that have previously shown to reduce RC (24, 27). Although study numbers are small, in two of the three P infants, mutations in TW10 were accompanied by upstream compensatory changes at positions H219Q, I223P, and M228I/L, suggesting the possibility that transmitted virus in these cases was already fully compensated, whereas compensatory changes at H219 and M228 were not observed in any of the three SP infants with transmitted TW10 mutants (Table (Table3)3) (2, 4).

Variation at HLA-B*57/58 CTL epitopes in viral isolates
HLA class I type of subjects and mothers in the study

In order to more fully examine the role of HLA-B*57/5801 epitope-specific mutations in viral RC in the absence of other confounding genetic factors, we cloned the p24 coding region of five isolates (two from P [197-B and 097-A] and three from SP [517-A, 349-A, and 586-A]) into a NL43 isogenic backbone with a GFP reporter gene. These viruses were therefore identical with the exception of the cloned region. To measure viral replication, Jurkat T cells were infected with WT and recombinant variants. Similar to the data obtained from analysis of complete HIV isolates shown above (Fig. (Fig.4),4), the viruses generated from the two P infants 197-B and 097-A, showed a higher RC than recombinant virus from SP subjects 349-A and 586-A (Fig. 5A to C). Infectivity of the virus recombinant generated from SP 517, however, was not dissimilar from the P infants, which is consistent with the absence of extensive mutations within Gag B*57/5801 epitopes other than T242S in this study subject. These findings suggest that the presence of HLA-B*57/5801-related mutations in p24 Gag epitopes such as TW10 may contribute to a low RC. In contrast, the presence of compensatory changes, in particular H219Q (097-A), may contribute to a higher RC in rapidly progressing infants. Moreover, the similarity of the data obtained from recombinant p24 virus to those obtained in complete HIV isolates highlights the importance of Gag p24 as an important genetic determinant of the virus RC.

FIG. 5.
Replication kinetics in Jurkat T cells. (A) Patterns of HLA-B*57/5801-related mutations in p24 epitopes present in recombinant virus tested. (B) Jurkat T cells were infected in triplicate with WT virus or recombinant variants. Viral infectivity ...

HIV-specific CD8+ T-cell responses in pediatric HIV infection.

There is evidence that CD8+ T-cell responses can contribute to viral containment in HIV-infected children, as in adults (18, 21). We assessed CD8+ T-cell responses by using the IFN-γ ELISPOT assays with a panel of optimal HLA (Table (Table4)4) HIV peptides to determine the contribution of CD8+ specific responses to immune control in the small group of study subjects in whom virus isolates were evaluated (Fig. (Fig.6).6). Although the study numbers are small, the CD8+ T-cell responses in the two groups do not suggest clear-cut differences either in breath or magnitude that would explain the differences observed in disease progression.

FIG. 6.
IFN-γ ELISPOT responses in PBMC measured against a panel of optimal clade C HIV epitopes corresponding to HLA class I alleles of the study infants. Bars represent different time points per subject and colors represent different protein specificities ...


The data presented here represent the first analysis of viral RC in a group of P and SP infants with C clade HIV infection. Our data, which include analysis of the HIV-specific CD8+ T-cell responses made by these study subjects, support the hypothesis that the presence of attenuated HIV variants in SP infants, together with long-term establishment of efficacious CD8+ responses (41), contributes to viral control and influences disease progression during early pediatric HIV infection.

In perinatally infected infants, in contrast to HIV-infected adults, viral loads remain high after acute infection, and reduction of viremia occurs only slowly over the first few years of life. Although CD8+ T-cell responses can be detected shortly after birth in HIV-infected infants (42), they appear not to be efficacious in most of the infants in early life. Gradual reduction in viremia may be related to the maturation of CD8+ T-cell response (18). Thus, the biological characteristics of the maternal virus transmitted early on could have a great impact in allowing subsequent development of a mature immune system and thus on disease outcome. These studies demonstrate that early virus isolates from plasma samples within the first 4 months of life in P and SP infants have marked differences in viral RC. We show that SP infants typically have virus with a low RC, which is consistent with an important influence of viral attenuation on pediatric HIV progression and is consistent with recently published data in D clade infected infants showing an association between viral infectivity and survival during infancy (7).

Although in general there was a concordance between measurements of the RC and infectivity determined by replication kinetics and single-cycle infectivity, in some instances this was not the case. The discrepancies in the total number of infected cells for 197-B, 586-A/B, or 641-A/B (comparing Fig. Fig.4A4A and and4C)4C) between assays may be explained by the number of replication cycles in cell culture. Small differences in virus infectivity measured by a single cycle of infection are magnified through multiple rounds of virus infection in the kinetics experiments. That is reflected by the increase number of p24-positive cells compared to the number of GFP cells.

Multiple viral genetic factors may account for the differences in RC (15, 22, 44), we here focused on the presence of Nef polymorphism, virus tropism, and mutations in HLA-B*5703/58 Gag CD8+ T-cell epitopes. Our data did not reveal major differences in viral tropism or presence of Nef polymorphisms to account for differences in viral RC and disease outcome between groups. As anticipated, we observed a preferential use of CCR5 coreceptor in this C clade infected cohort, with no changes in the coreceptor use over time.

Viral attenuation through the selection of Gag CD8+ T-cell escape variants has also emerged as an important factor contributing to HIV control in individuals with protective alleles such as B*5703, B*27, and B*13 (4, 10, 32, 39). HIV Gag CTL escape variants have been also associated with the control of viral replication after transmission to individuals lacking the restricting alleles (6, 14). Moreover, presence of HLA-B*57 Gag escape variants have been show to be a relevant factor associated with HIV control in B*57 haploidentical infants, even in the absence of CD8+ T-cell responses (40). We therefore evaluated the impact of mutations within HLA-B*57/5801-restricted epitopes in Gag and compensatory changes in the CypA binding loop associated with an increased RC. Despite none of the study subjects having HLA-B*57 or 5801, and only two mothers having HLA-B*57/5801, we found a high prevalence of mutations in these Gag epitopes in our isolates. The observed accumulation of HLA-B*57 related mutations in the non-B*57 population may be related to the rapid accumulation and fixation of B*57 escape variants in sub-Saharan Africa. The accumulation of escape variants will be favored by transmission events and virus adaptation to the prevalent HLA molecules in the region (20). Consistent with previous studies (24), we observed reversion of T242N in subject 114 between early and late time points, indicating the fitness cost associated with this mutation. Reversion of T242N takes many months and sometimes years (20, 24), and the reason for this long delay in reversion remains unclear. Reversion of T242N in subject 114 was accompanied by selection of A248T and the CypA loop changes at I223 and M228, together previously described as compensatory mutations for T242N (4). It has been shown that, although these CypA loop mutants do partially compensate for the fitness cost of T242N, this compensation is not sufficient to prevent reversion (24). In addition, in subject 114, the viral load had, prior to reversion, reduced from 174,000 to only 5,050 copies/ml of plasma (Fig. (Fig.1),1), and it is possible that it was the increasing immune pressure imposed on the virus by the child's developing immune responses that drove the selection at this time, not only of the compensatory mutants I223N/M228I/A248T but also of T242N reversion, all of which would be expected to increase the viral RC. Consistent with this hypothesis and with other studies documenting an increase in viremia following reversion (9), the next measured viral load in the child following reversion was 249,000 copies/ml.

These data suggest that the presence of mutations, frequently in the TW10 epitope, in early transmitted virus of SP infants may contribute to a low RC. Meanwhile, the presence of upstream compensatory changes in the CypA biding loop, mainly H219Q, may contribute to the higher RC in progressors, as previously reported (4, 27). Our in vitro RC studies, based on p24 recombinant virus, support our initial observations and demonstrate the importance of HLA-B*5703/58 p24 escape mutations as a major determinant of viral RC in certain genetic backgrounds. However, it is noteworthy that, in the case of 517, the Gag recombinant virus showed an increase in RC compared to the isolate counterpart. Factors that might account for these discrepancies observed include the fact that gag from the study subjects was cloned into a highly replicative NL4-3 backbone, so that detrimental mutations present in non-gag regions of the virus genome would not contribute to measurements of RC. For example, subject 517 isolates carry an insertion of 2 aa in position 25 of Nef that evolves into a 4-aa insertion over time, suggesting a role of Nef in RC of the isolates in this particular subject: this would be consistent with data showing a relatively high RC for 517-Gag-NL4-3 recombinant viruses and yet relatively low RCs for the whole-virus isolates from subject 517.

Although some CD8+ T-cell responses may seem to be efficacious in pediatric infection (25, 31), the immune correlates of HIV control in pediatric infection remain unclear. Previous studies in adult infection have demonstrated the importance of protein specificity of the CD8+ T-cell response in the control of HIV replication (21), revealing a negative association between the number of Gag responses and the viral load and a positive association between the number of Env responses and the viral load. Study of the CD8+ T-cell responses in the entire study cohort of 63 HIV-infected infants showed an association between relative slow progression and magnitude of the Gag-specific CD8+ T-cell response (41). In the small subset of eight infants studied here, however, there is no clear-cut evidence that disease progression was related to the CD8+ T-cell response. Indeed, in one of the SP infants, 349, no CD8+ T-cell responses whatsoever could be detected. These data are therefore consistent with a significant role for viral RC in influencing the rate of disease progression in pediatric HIV infection.

In summary, this study highlights the importance of virus-host interactions in mother-to-child HIV transmission, where transmission of early attenuated HIV variants together with the long-term establishment of infant immune responses are crucial factors to differences in HIV control. These data support the hypothesis that a Gag-specific CD8+ T-cell response is beneficial in facilitating immune control of HIV in the transmission recipient, where the transmitted virus may incorporate CD8+ T-cell escape mutations in Gag that reduce viral RC.


This project was funded by the Doris Duke Charitable foundation (2001 1031 to P.G.), the Wellcome Trust (P.G.), and Bristol Myers Squibb Secure the Future (RES 16/01 to P.G.). J.G.P. holds Marie Curie contract 41811 (IEF-FP6). T.N. holds the South African Department of Science and Technology/National Research Foundation Chair in Systems Biology of HIV/AIDS.

We thank all of the participants of the study, the clinical team at St. Mary's Hospital antenatal clinic, Mariannhill and Prince Mshiyeni Hospital, Umlazi, and the HIV Pathogenesis Programme team. We thank J. M. Picado for helpful discussions.


[down-pointing small open triangle]Published ahead of print on 14 October 2009.


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