- Open Access
Characterization of HIV-1 subtype C envelope glycoproteins from perinatally infected children with different courses of disease
© Zhang et al; licensee BioMed Central Ltd. 2006
- Received: 24 May 2006
- Accepted: 20 October 2006
- Published: 20 October 2006
The causal mechanisms of differential disease progression in HIV-1 infected children remain poorly defined, and much of the accumulated knowledge comes from studies of subtype B infected individuals. The applicability of such findings to other subtypes, such as subtype C, remains to be substantiated. In this study, we longitudinally characterized the evolution of the Env V1–V5 region from seven subtype C HIV-1 perinatally infected children with different clinical outcomes. We investigated the possible influence of viral genotype and humoral immune response on disease progression in infants.
Genetic analyses revealed that rapid progressors (infants that died in the first year of life) received and maintained a genetically homogeneous viral population throughout the disease course. In contrast, slow progressors (infants that remained clinically asymptomatic for up to four years) also exhibited low levels variation initially, but attained higher levels of diversity over time. Genetic assessment of variation, as indicated by dN/dS, showed that particular regions of Env undergo selective changes. Nevertheless, the magnitude and distribution of these changes did not segregate slow and rapid progressors. Longitudinal trends in Env V1–V5 length and the number of potential N-glycosylation sites varied among patients but also failed to discriminate between fast and slow progressors. Viral isolates from rapid progressors and slow progressors displayed no significant growth properties differences in vitro. The neutralizing activity in maternal and infant baseline plasma also varied in its effectiveness against the initial virus from the infants but did not differentiate rapid from slow progressors. Quantification of the neutralization susceptibility of the initial infant viral isolates to maternal baseline plasma indicated that both sensitive and resistant viruses were transmitted, irrespective of disease course. We showed that humoral immunity, whether passively acquired or developed de novo in the infected children, varied but was not predictive of disease progression.
Our data suggest that neither genetic variation in env, or initial maternal neutralizing activity, or the level of passively acquired neutralizing antibody, or the level of the de novo neutralization response appear to be linked to differences in disease progression in subtype C HIV-1 infected children.
- Viral Isolate
- Slow Progressors
- Infected Child
- Neutralization Susceptibility
- Ghost Cell Line
Mother to child transmission (MTCT) of human immunodeficiency virus type 1 (HIV-1) is the primary mode of pediatric HIV-1 infection  in sub-Saharan Africa. In this region, HIV-1 subtype C accounts for approximately 50% of infections. Pediatric HIV-1 disease progression has been most intensively studied for subtype B virus infections where it was found to be bimodal, with 15 to 20 % of untreated infants progressing rapidly to AIDS and death by 4 years of age , whereas the remaining 80% progress more slowly [3, 4]. The applicability of such findings to other subtypes remains to be substantiated.
HIV-1 disease progression in adults is a complex interplay between viral factors, host genetics, and host immune response  where all contribute to disease progression [5–20]. The survival time for HIV-1 infected children is shorter, on average, than that of infected adults , and could be explained by a number of factors including: immaturity of their immune system , failure to acquire passive immunity from the mother, timing of transmission [2, 22, 23] or maternal HIV-1 RNA levels [24, 25]. Other factors, such as viral replication rate, syncytium-induction, CD4+ T-cell depletion, and thymic infection have been shown to associate with early onset of pediatric AIDS [25–28]. As in adults, the emergence of X4 variants in infected children has been associated with disease progression [27–29], but this is unlikely to be a causal factor since most rapidly progressing children harbor viruses of the R5 phenotype . Moreover, shared HLA class I alleles between mother and infant was shown to influence clinical outcome . Humoral immunity has been suggested to play a role in the disease for both adults and children, but the function of neutralizing antibody responses in delaying disease progression or preventing HIV-1 infection, especially in children, has not been fully established [5, 19, 20, 31–33].
The determinants of many of the above biological properties map to the HIV-1 envelope glycoprotein (Env) or associate with Env receptor binding, tropism-definition, cytopathicity determinants or neutralization susceptibility [34–43], although other HIV-1 genes related to HIV-1 pathogenesis were also described [11, 44–50]. Studies on HIV-1 Env from both infected adults and children have indicated that viral populations exhibiting high rates of non-synonymous nucleotide substitutions and high antigen diversity usually associate with broad immune reactivity, slow CD4+ T cell decline, and slow rates of disease progression [33, 51–54]. However, others have shown a correlation between higher sequence diversity and a more rapid disease onset [28, 32]. Despite various associations with viral and host parameters, the mechanisms behind differential disease progression in HIV-1 infected children remain poorly defined.
As an extension of our efforts to better understand the characteristics of perinatally transmitted subtype C HIV-1 and to clarify the relationship between viral evolution, humoral immune responses and disease outcome in infected children , we analyzed the evolution of the env V1–V5 region from seven perinatally infected children with different disease courses. We also performed a longitudinal assessment of the infant neutralizing antibody responses against autologous primary viral isolates from various time points during disease progression. This study was designed to investigate the possible influence of genetic properties of subtype C envelope glycoproteins and humoral immune response on disease progression in infants.
Characteristics of seven HIV-1 infected children
Genetic variation, co-receptor usage and clinical information for the different infants included in this study
Cause of death
HIV-1 isolation was unsuccessful from all baseline (birth) samples and all infants were HIV PCR negative at birth, suggesting that they were infected either intrapartum or postpartum. HIV-1 env sequences were amplified from infant PBMC at different postpartum timepoints, as indicated in Table 1. Because the amount of sample from these children was limited, priority was given to virus isolation in lieu of PCR when necessary (e.g., infant 1084, viral isolation was positive by 4 month and the first PCR was performed 6 month after birth). A portion of the env gene from V1–V5 was amplified by PCR, cloned, and sequenced in order to longitudinally characterize Env genetic diversification and evolution.
Env sequence analyses
We sequenced a total of 711 infant clones (23 – 48 sequences per timepoint) derived from PBMC genomic DNA. When all sequences were aligned and included in a single phylogenetic analysis, sequences from each mother-infant pair formed a monophyletic group, indicating that maternal and infant sequences were epidemiologically linked (data not shown). Viral subtype determinations showed that all cases were subtype C in Env, except for mother-infant-pair 1449 which was a subtype A/C recombinant.
Similar patterns of variation were observed at the amino acid level, although levels of polymorphism were higher relative to variation at the nucleotide level. Mean amino acid differences (AA% in Table 1) within the initial populations ranged from 0.6 to 2.4 % for the earliest samples, and from 1.0 to 8.9% for the later time-point samples. Mean genetic distance (DNA % in Table 1) within contemporaneous sequences were lower in rapid progressors than in slow progressors (Table 1), but this difference was not statistically significant. There was a trend towards increased levels of genetic diversity as time progressed, with some refractory periods. Accordingly, we observed the highest levels of genetic diversity (DNA% in Table 1) in samples collected at the latest time points in slow progressors (Table 1, 48- month samples from infants 1084, 1690 and 1984). However, the rates of change in genetic diversity and genetic divergence were similar for all patients (data not shown), although sample sizes precluded statistical tests of this observation.
Positive Darwinian selection is indicated when the estimated ratio of non-synonymous changes to synonymous changes (dN/dS) >1. We observed high dN/dS values for the env gene (Table 1), suggesting that positive selection was occurring in the infant env genes. The values ranged from 0.41 to 1.37, with a mean of 0.78 (Table 1). The significance of this finding is that higher dN/dS values have been linked to longer survival, and presumably, a higher dN/dS value is a consequence of a stronger and/or broader immune response [20, 55]. In the three slow progressor infants there was at least one time point where the dN/dS > 1; whereas a dN/dS > 1 was detected in only one of the rapid progressor infants (1449), but it is possible that this is a function of the duration of infection. Indeed, while we observed a higher level of non-synonymous substitutions in slow progressors (mean = 0.89) versus rapid progressors (mean = 0.78), this difference was not statistically significant.
Taken together, the higher diversity associated with later time points, in combination with the observed accumulation of amino acid substitutions in putatively exposed regions of the glycoprotein indicate that selective pressures, including humoral immunity, may be playing a substantial role in driving Env evolution.
V1–V5 length and putative glycosylation sites
Co-receptor usage and cell tropism
Since co-receptor usage switches to an X4-utilization phenotype with disease progression in some adults and children, we evaluated co-receptor usage and phenotype of viral isolates from the two groups. We found that all viral isolates exclusively used CCR5 as a co-receptor (Table 1), exhibited macrophage-tropism, and did not infect T cell lines or form syncytia in vitro. The only exception was the 48-month isolate from infant 1690. For 1690, R5 co-receptor tropism was maintained until 42 months; after this time, the viral isolate exhibited dual X4/R5 co-receptor usage (Table 1), and infected both macrophages and MT-2 T lymphoblasts, where it formed syncytia (data not shown). To date, this is the only X4-utilizing virus isolated from our cohort, implying that while X4-utilizing subtype C HIV-1 can develop in patients, such development is uncommon and disease pathogenesis is not dependent on such phenotypic switches. To test whether the characterized subtype C Env sequences possessed co-receptor usage properties consistent with those defined for the virus isolated by co-culture, we generated Env chimeras by introducing the subtype C V1–V5 region into a subtype B NL4-3 Env expression vector. The chimeric Env constructs were then used to make pseudoviruses for evaluation of co-receptor usage in Ghost cell lines that express different co-receptors. All chimeras tested exhibited CCR5 tropism and lacked appreciable X4 tropism (data not shown). These findings are consistent with those obtained from experiments using primary isolates.
Neutralization capacity of the baseline mother and infant plasma for the first infant viral isolate
Neutralization activity (%) of baseline plasma for infant first viral isolates1
Longitudinal humoral immune responses of infected children
Similarly, the autologous plasma neutralization of slow progressor infant early (4 or 6-month) and late (48-month) viral isolates was evaluated, and two representatives (1984 and 1084) are shown in Figure 4B. In the slow progressor 1084, a substantial amount of Nab was detected at birth, but decayed to zero by six months. Subsequently, the child developed an effective neutralizing response against both the earliest virus and the contemporaneous (12 and 48-month) viruses. In contrast, slow progressor 1984 received no detectable Nab from the mother, but mounted an effective neutralizing response by 6 months whose magnitude was directly correlated with the timepoint of virus isolation, with 6-month virus being more effectively neutralized than 12 and 48-month viruses. It is apparent that in slow progressors there are infants who passively acquired neutralizing activity (1084), while others (1984) did not. Therefore, it is unlikely that rapid progression is due to receipt of lower maternal Nab, or that slow progression is due to acquisition of high level of maternal Nab or the development of a higher or more durable de novo humoral response.
Replication of viral isolates from both rapid and slow progressors
Longitudinal changes in viral genetic variation, immune responses, and disease progression have rarely been investigated in HIV-1 subtype C infected children. We have previously characterized the evolution of the Env C2-V4 region of subtype C HIV-1 and the humoral immune response from one infected infant. In the present study, we expanded our study by correlating the changes of the Env longitudinally with disease outcome, in seven children, divided into two groups based on rapid or slow disease progression. In addition, with these two groups, we were able to examine the contribution of Env length and glycosylation in disease progression, and the role of humoral immunity, both passively acquired and developed de novo, to clinical outcomes.
Phylogenetic analyses show that maternal and infant viruses were epidemiologically linked in each of the seven pairs, and support the concept that selective transmission occurred [33, 59–61]. Rapid progressors, those who died in the first 12 months, received and maintained a genetically homogeneous viral population throughout the short disease course. Slow progressors initially also exhibited low levels of variation, but attained higher levels of diversity over time. These findings are consistent with previous studies that showed higher genetic diversity associated with slow disease progression in children [33, 53, 54].
In both groups of children, a large number of unique, but closely related haplotypes were sampled, matching predictions for a population that was exponentially growing in size from a homogeneous starting point. Estimates of dN/dS can be used to determine whether selective pressure, in addition to expanding population size, played a role in the diversification of the infant viral populations. Our data show that dN/dS values were high in all 7 individuals, exceeding 1.0 in 7 of 24 populations sampled. Values of dN/dS greater than 1.0 provide evidence of positive Dawinian selection .
One of the primary selective pressures acting on Env is neutralizing antibody. The earliest infant Nab responses are largely due to passive transfer from the mother. Passively acquired maternal immunity can play a critical role in protecting infants from infections; however, the specific contribution of maternal or passively-acquired neutralizing antibodies in limiting HIV-1 transmission or disease progression in children is not well understood. Our observations indicate that the neutralizing activity in maternal and infant baseline plasma varied in its effectiveness for the initial infant virus but did not differentiate rapid from slow progressors. Since our assays for Nab activity relied on co-cultured virus, and selection during co-culture may bias the results away from the main phenotype of virus in the original population, the lack of difference between groups should be taken as a tentative result. Nevertheless, consistent with other findings [33, 63, 64], all children developed de novo neutralizing responses within the first 6 months post-infection regardless of the disease course. But our results show that even when children develop effective de novo neutralization responses, they may still progress rapidly (Figure 4A). In contrast, we also observed children who failed to mount high neutralizing responses to later virus, yet have remained clinically asymptomatic throughout the study (Figure 4B). These findings indicate that the development of effective neutralizing responses in children fails to protect them from disease progression, but surprisingly, failure to develop effective responses is not predictive of rapid progression. Moreover, there is no association between the replication kinetics and disease progression, since viral isolates isolated from similar time points (4–8 month) from both rapid and slow progressors replicated with similar pattern (Figure 5A and 5B), even though the late viruses from slow progressors replicated slightly faster than early viruses from the same hosts (Figure 5B). Similarly, our study did not reveal any differences in cytopathicity of the viruses from either progressors or non-progressors from different time points, suggesting a lack of correlation between viral cytopathicity and disease progression among the viruses that were analyzed.
The genotypic and phenotypic parameters leading to preferential transmission of particular virus variants from donor to recipient remain unclear. In heterosexual transmission between discordant couples, it was found that subtype C viruses with shorter V1–V4 regions and fewer putative glycans were preferentially transmitted and were neutralization sensitive [57, 58]. In addition, another study of heterosexually acquired subtype A viruses suggested that transmitted viruses have shorter V1–V2 length and few N-linked glycosylation sites . An extension of these findings is that evolution in the newly infected individual would lead to longer and more glycosylated Env proteins with time. These patterns have not been confirmed in subtype B sexual transmission [65–67]. The genotypic and phenotypic parameters leading to preferential transmission of particular virus variants were also evaluated in mother to child transmission. An investigation of subtype A mother to child transmission has revealed that the transmitted viruses were more resistant to neutralization by maternal plasma although the viruses harbored fewer putative glycosylation sites . In our study, we have observed that both neutralization sensitive and resistant viruses were transmitted to both slow and rapid progressors. It is worth noting that contrasting results between sexual transmission and vertical transmission studies could be due to fundamental differences between these processes, since vertical transmission occurs in the presence of neutralizing antibodies, but in sexual transmission there are presumed to be no baseline antibodies present.
It has been hypothesized that the extensive glycosylation of the HIV-1 Env shields the protein from immunological recognition, or conversely, targets recognition to less functionally constrained domains where hypervariability can be tolerated . Interestingly, neither pattern was confirmed with later viruses in our infant samples, suggesting that lengthening of the V1–V5 domain and acquisition of glycosylation sites were not always a component of glycoprotein evolution in newly infected individuals (Figure 3 and Table 1). Only in one case (infant 1084), a pattern consistent with this hypothesis was obtained, with increasing V1–V5 length and number of PNGS (Figures 3). Collectively, our results highlight the necessity to refine our understanding of the relationships between viral genotype, viral phenotype and different routes of transmission. Our observations and those of others also stress the need to further explore genetic and immunologic correlates of mother to child transmission in non-B subtypes.
Comparison of the rates of non-synonymous and synonymous substitutions has been used as an index of selective pressure exerted by the immune system [20, 55, 69]. There are reports that higher dN/dS ratios are linked with long-term survival [20, 55]; however, we found that the highest dN/dS value was estimated for envelopes from a rapid progressor child at the final timepoint prior to death (Table 1, 8-month sample from infant 1449). In addition, dN/dS values were highly variable in both groups and not statistically different. Despite the variation in dN/dS values, the estimates were high in all cases, suggesting that natural selection is a strong determinant of the diversification and evolution in the Env glycoprotein. Further evidence of this selective pressure comes from the observation that amino acid replacements are not evenly distributed in the protein sequence, but occur in 'hot-spots' in particular domains (Figure 2). We can predict two broad mechanistic explanations for these changes; (1) they modulate glycoprotein function thus enhancing viral fitness (currently under investigation), (2) they modulate immune recognition of the viral glycoprotein by altering epitopes. Despite differences in timing of sampling, or in ultimate disease outcome, some hot spots are shared among all children, and no hot spot differentiates the rapid from the slow progressors. One example of these common hot-spots is the region in C3 just carboxy-terminal to the V3 loop. Structurally this domain corresponds to alpha helix 2 from the alignment of HXBC2 to the intact SIV atomic structure . This sequence, which is perpetually changing, is located on the silent face of the trimeric structure as determined for subtype B. The clustering of polymorphisms as well as the differential binding of antibodies from subtype B versus C infected individuals to this region points to this as a good candidate for a subtype C neutralizing epitope.
Genetic assessment of variation, as indicated by dN/dS, shows that the protein is undergoing selective changes in a non-random fashion. Nevertheless, the magnitude and distribution of these changes do not segregate slow and rapid progressors. In addition, the apparent clustering of positively selected residues in particular regions of the subtype C glycoprotein that are normally not subject to high levels of mutation in subtype B implies significant structural differences between the glycoprotein of the two subtypes.
The sole parameter that discriminates rapid and slow progressors appears to be time to death. We found that neither genetic variation in env, nor maternal neutralizing activity at parturition, nor the level of passively acquired neutralizing antibody, nor the level of the de novo neutralization response was linked to differences in disease progression in the children studied. However, characteristics of the transmitted viruses other than Nab and the genetic make up of viral populations could be linked to disease progression. Such factors might include, but are not limited to, the fitness of the transmitted viruses, binding affinity to CD4 and/or co-receptors, and cell mediated immunity. The potential role of these factors in predicting disease outcome in subtype C HIV-1 infected children will be the focus of further investigations.
In this study, we examined the evolution of Env V1–V5 region from seven subtype C HIV-1 perinatally infected children with different clinical outcomes. In addition, the humoral immune responses of the infected children during disease progression were also evaluated. Our findings demonstrate that neither the level of maternal baseline neutralizing antibody nor the portion passively transferred to the infant is predictive of disease outcome. Inspection of the neutralization susceptibility to maternal baseline plasma indicated that both neutralization sensitive and resistant viruses were transmitted to the infected children with different disease courses. Moreover, we showed that the development of effective de novo neutralization response in infected children did not differentiate rapid from slow progressors. Genetic analysis of Env V1–V5 region could not segregate rapid and slow progressors, suggesting that time to death may be the parameter that discriminates rapid and slow progressors.
Patient population and sample collection
Seven mother/infants pairs 1449, 2669, 2873, 2617, 1984, 1084 and 1690 were recruited into the study. Venous blood was obtained from the mother before delivery and from the infant within 24 hours of birth. Follow-up blood specimens were obtained at 2, 4, and 6 or 8 months (for rapid progressors) and at regular intervals through 48 months (for slow progressors). The baseline HIV-1 serological status of the mother was determined by two rapid assays, Capillus (Cambridge Biotech, Ireland) and Determine (Abbott laboratories, USA). Positive serological results were confirmed by immunofluorescence assay (IFA), as previously described . HIV-1 infection in the infants was detected by sequential viral isolation from the infants' peripheral blood mononuclear cells (PBMC), as previously described , and by PCR of the HIV-1 provirus env gene from genomic DNA. The first timepoint for positive PCR from each infant is indicated in Table 1.
Cell tropism and chemokine co-receptor usage
The syncytium-inducing (SI) or non-syncytium-inducing (NSI) phenotype was determined by infecting MT-2 cells as described . Virus was scored as 'SI' if syncytia and increasing level of p24 antigen were observed within a 10-day period and as 'NSI' if syncytia failed to form within that time. To further define the viral tropism, viral replication was assessed in primary monocyte-derived macrophages (MDM) and in the MT-2 T-cell line, as described .
Co-receptor usage was defined using Ghost cell lines that express specific co-receptors (Ghost-CXCR4 cells [CXCR4], Ghost-CCR5 cells [CCR5] and Ghost-CCR3 cells [CCR3])(NIH AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH from Dr. Vineet KewalRamani and Dr. Dan Littman) with standard procedures as recommended by the supplier. Uninfected control produced only one to two GFP-expressing cells per well. HIV-1 strains NL4-3 and SF128A were used as positive controls for CXCR4 and CCR5 utilization, respectively.
Virus neutralization assay
Virus sensitivity to neutralization by maternal or infant plasma-derived antibody (1:20 dilution of plasma) was determined by infections of TZM-bl cells (NIH AIDS Research and Reference Reagent Program catalog no. 8129, TZM-bl) as described .
Viral replication assay
Two thousand TCID50 (Tissue Culture Infectious Dose) of the viral isolates from early or late time points were added to a T-25 flask containing 2 × 107 PHA-stimulated PBMC from a pool of two HIV-1 seronegative blood donors. The subtype B laboratory isolate SF 128A  was used as a control. After incubation at 37°C for 6 hours, cells were washed 3 times with PBS and replenished with fresh medium. All infected cultures were sampled and supplemented with fresh culture medium at days 1, 5, 9, 13, 17 and 21-postinfection. Virus titer (TCID50/ml) was measured by infection of TZM-bl cells (NIH AIDS Research and Reference Reagent Program catalog no. 8129, TZM-bl).
Polymerase chain reaction, gene cloning, sequencing and subtype identification
Genomic DNA was purified from uncultured patient PBMC using the Puregene kit (Gentra Systems). Primers used for amplification of the subtype C env gene were designed based on a reference alignment of all HIV-1 subtypes obtained from the Los Alamos Sequence Database. Nested PCR was used to amplify a 1100 bp fragment spanning the V1–V5 region of the env gene from samples collected at birth through 48 months. In order to minimize the PCR bias, Env V1–V5 region were amplified in duplicates in the first-round PCR of each maternal and infant sample. First-round PCR products were combined and used as template in a second-round PCR. Primers used in the first round PCR were: forward primer EnvF1: 5'-GATGCATGAGGATATAATCAGTTTATGGGA (corresponding to position 6533 to 6562 of HIV-1 HXB2 strain), reverse primer EnvR1: 5'-ATTGATGCT GCGCCCATAGTGCT (position 7828 – 7806). Internal primers used in the second round PCR were EnvF2: 5'-AGTTTATGGGACCAAAGCCTAAAGCCATGT (position 6552 to 6581) and EnvR2: 5'-ACTGCTCTTTTTTCTCTCTCCACCACTCT (position 7762 to 7734). First and second round PCR were carried out at 94°C for 2 min; 94°C for 30 sec, 55°C for 1 min, 68°C for 1 min for 35 cycles; 68°C for 7 min using a Perkin-Elmer thermocycler. Amplified fragments were cloned into the pGEM-T Easy vector (Promega) and sequenced in both directions with dideoxy terminators (ABI BigDye Kit). The V1–V5 region of the env gene was analyzed.
Subtype affiliation was determined by comparing patient env sequences to a reference panel from the HIV database. Maximum likelihood (ML), Minimum-Evolution (ME) and neighbor-joining (NJ) phylogenetic analyses were done to visualize how viral populations within patients change with time. Maximum likelihood searches were conducted in Treefinder  using an independent model of nucleotide substitution for each codon position (GTR+Γ). Minimum-Evolution and Neighbor-joining analyses were performed in MEGA  using the Kimura 2 parameter nucleotide substitution model to estimate genetic distances. Support for the nodes in ME and NJ was evaluated by running 1000 bootstrap pseudoreplicates.
For each infant, samples were grouped according to the time of collection, and analyzed independently. To keep a consistent set of sites in the analyses, positions where putative insertions or deletions were inserted for alignment purposes in any timepoint were excluded from population level comparisons. Variation in the pattern of genetic diversity for each time-point was explored using MEGA3.1 , DNAsp ver 4.10  and Datamonkey . The number and location of putative N-linked glycosylation sites (PNGS) was estimated using N-GlycoSite from the Los Alamos National Laboratory database. Within each infant, temporal changes in viral diversity and viral divergence from the earliest population were calculated. Viral diversity estimates correlate with the effective population size of viral populations and were estimated based on the average number nucleotide differences between sequences, whereas viral divergence was calculated as the average genetic distance relative to the earliest population collected.
The overall dN/dS (non-synonymous changes relative to synonymous changes) values for each contemporaneous data set were calculated using Datamonkey , and used to estimate the relative strength of natural selection in each set of sequences. In addition, the number of synonymous and non-synonymous substitutions observed per site in infant Env (V1–V5) domains was calculated by Datamonkey, and the distribution of non-synonymous substitutions along the sequence was plotted to identify regions that accumulate most variations ('hot spots'). These regions were mapped on the structural predictions from Chen et al.  using their alignment of the SIV Env structure with HIV.
This study was supported by PHS grants HD39620, CA76958, Fogarty Training grant TW01429, and NCRR COBRE grant RR15635 to C.W. and PO1 AI 48240 to R.M.R. and C.W. We thank Dr. Vineet KewalRamani and Dr. Dan Littman for Ghost-CXCR4, Ghost-CCR5 and Ghost-CCR3 cells through the NIH AIDS research and reference reagent Program, Division of AIDS.
- Luzuriaga K, Sullivan JL: Viral and immunopathogenesis of vertical HIV-1 infection. Pediatr Clin North Am. 2000, 47 (1): 65-78. 10.1016/S0031-3955(05)70195-4.View ArticlePubMedGoogle Scholar
- Mayaux MJ, Burgard M, Teglas JP, Cottalorda J, Krivine A, Simon F, Puel J, Tamalet C, Dormont D, Masquelier B, Doussin A, Rouzioux C, Blanche S: Neonatal characteristics in rapidly progressive perinatally acquired HIV-1 disease. The French Pediatric HIV Infection Study Group. Jama. 1996, 275 (8): 606-610. 10.1001/jama.275.8.606.View ArticlePubMedGoogle Scholar
- Galli L, de Martino M, Tovo PA, Gabiano C, Zappa M, Giaquinto C, Tulisso S, Vierucci A, Guerra M, Marchisio P, et al: Onset of clinical signs in children with HIV-1 perinatal infection. Italian Register for HIV Infection in Children. Aids. 1995, 9 (5): 455-461.View ArticlePubMedGoogle Scholar
- Auger I, Thomas P, De Gruttola V, Morse D, Moore D, Williams R, Truman B, Lawrence CE: Incubation periods for paediatric AIDS patients. Nature. 1988, 336 (6199): 575-577. 10.1038/336575a0.View ArticlePubMedGoogle Scholar
- Hogan CM, Hammer SM: Host determinants in HIV infection and disease. Part 1: cellular and humoral immune responses. Ann Intern Med. 2001, 134 (9 Pt 1): 761-776.View ArticlePubMedGoogle Scholar
- Connor RI, Mohri H, Cao Y, Ho DD: Increased viral burden and cytopathicity correlate temporally with CD4+ T-lymphocyte decline and clinical progression in human immunodeficiency virus type 1-infected individuals. J Virol. 1993, 67 (4): 1772-1777.PubMed CentralPubMedGoogle Scholar
- Schuitemaker H, Koot M, Kootstra NA, Dercksen MW, de Goede RE, van Steenwijk RP, Lange JM, Schattenkerk JK, Miedema F, Tersmette M: Biological phenotype of human immunodeficiency virus type 1 clones at different stages of infection: progression of disease is associated with a shift from monocytotropic to T-cell-tropic virus population. J Virol. 1992, 66 (3): 1354-1360.PubMed CentralPubMedGoogle Scholar
- Schellekens PT, Tersmette M, Roos MT, Keet RP, de Wolf F, Coutinho RA, Miedema F: Biphasic rate of CD4+ cell count decline during progression to AIDS correlates with HIV-1 phenotype. Aids. 1992, 6 (7): 665-669. 10.1097/00002030-199207000-00008.View ArticlePubMedGoogle Scholar
- Gottlieb GS, Nickle DC, Jensen MA, Wong KG, Grobler J, Li F, Liu SL, Rademeyer C, Learn GH, Karim SS, Williamson C, Corey L, Margolick JB, Mullins JI: Dual HIV-1 infection associated with rapid disease progression. Lancet. 2004, 363 (9409): 619-622. 10.1016/S0140-6736(04)15596-7.View ArticlePubMedGoogle Scholar
- Sagar M, Lavreys L, Baeten JM, Richardson BA, Mandaliya K, Chohan BH, Kreiss JK, Overbaugh J: Infection with multiple human immunodeficiency virus type 1 variants is associated with faster disease progression. J Virol. 2003, 77 (23): 12921-12926. 10.1128/JVI.77.23.12921-12926.2003.PubMed CentralView ArticlePubMedGoogle Scholar
- Deacon NJ, Tsykin A, Solomon A, Smith K, Ludford-Menting M, Hooker DJ, McPhee DA, Greenway AL, Ellett A, Chatfield C, Lawson VA, Crowe S, Maerz A, Sonza S, Learmont J, Sullivan JS, Cunningham A, Dwyer D, Dowton D, Mills J: Genomic structure of an attenuated quasi species of HIV-1 from a blood transfusion donor and recipients. Science. 1995, 270 (5238): 988-991. 10.1126/science.270.5238.988.View ArticlePubMedGoogle Scholar
- Lum JJ, Cohen OJ, Nie Z, Weaver JG, Gomez TS, Yao XJ, Lynch D, Pilon AA, Hawley N, Kim JE, Chen Z, Montpetit M, Sanchez-Dardon J, Cohen EA, Badley AD: Vpr R77Q is associated with long-term nonprogressive HIV infection and impaired induction of apoptosis. J Clin Invest. 2003, 111 (10): 1547-1554. 10.1172/JCI200316233.PubMed CentralView ArticlePubMedGoogle Scholar
- Yamada T, Iwamoto A: Comparison of proviral accessory genes between long-term nonprogressors and progressors of human immunodeficiency virus type 1 infection. Arch Virol. 2000, 145 (5): 1021-1027. 10.1007/s007050050692.View ArticlePubMedGoogle Scholar
- Alexander L, Weiskopf E, Greenough TC, Gaddis NC, Auerbach MR, Malim MH, O'Brien SJ, Walker BD, Sullivan JL, Desrosiers RC: Unusual polymorphisms in human immunodeficiency virus type 1 associated with nonprogressive infection. J Virol. 2000, 74 (9): 4361-4376. 10.1128/JVI.74.9.4361-4376.2000.PubMed CentralView ArticlePubMedGoogle Scholar
- Troyer RM, Collins KR, Abraha A, Fraundorf E, Moore DM, Krizan RW, Toossi Z, Colebunders RL, Jensen MA, Mullins JI, Vanham G, Arts EJ: Changes in human immunodeficiency virus type 1 fitness and genetic diversity during disease progression. J Virol. 2005, 79 (14): 9006-9018. 10.1128/JVI.79.14.9006-9018.2005.PubMed CentralView ArticlePubMedGoogle Scholar
- Quinones-Mateu ME, Ball SC, Marozsan AJ, Torre VS, Albright JL, Vanham G, van Der Groen G, Colebunders RL, Arts EJ: A dual infection/competition assay shows a correlation between ex vivo human immunodeficiency virus type 1 fitness and disease progression. J Virol. 2000, 74 (19): 9222-9233. 10.1128/JVI.74.19.9222-9233.2000.PubMed CentralView ArticlePubMedGoogle Scholar
- Samson M, Libert F, Doranz BJ, Rucker J, Liesnard C, Farber CM, Saragosti S, Lapoumeroulie C, Cognaux J, Forceille C, Muyldermans G, Verhofstede C, Burtonboy G, Georges M, Imai T, Rana S, Yi Y, Smyth RJ, Collman RG, Doms RW, Vassart G, Parmentier M: Resistance to HIV-1 infection in caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature. 1996, 382 (6593): 722-725. 10.1038/382722a0.View ArticlePubMedGoogle Scholar
- Altfeld M, Addo MM, Rosenberg ES, Hecht FM, Lee PK, Vogel M, Yu XG, Draenert R, Johnston MN, Strick D, Allen TM, Feeney ME, Kahn JO, Sekaly RP, Levy JA, Rockstroh JK, Goulder PJ, Walker BD: Influence of HLA-B57 on clinical presentation and viral control during acute HIV-1 infection. Aids. 2003, 17 (18): 2581-2591. 10.1097/00002030-200312050-00005.View ArticlePubMedGoogle Scholar
- Pilgrim AK, Pantaleo G, Cohen OJ, Fink LM, Zhou JY, Zhou JT, Bolognesi DP, Fauci AS, Montefiori DC: Neutralizing antibody responses to human immunodeficiency virus type 1 in primary infection and long-term-nonprogressive infection. J Infect Dis. 1997, 176 (4): 924-932.View ArticlePubMedGoogle Scholar
- Ross HA, Rodrigo AG: Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J Virol. 2002, 76 (22): 11715-11720. 10.1128/JVI.76.22.11715-11720.2002.PubMed CentralView ArticlePubMedGoogle Scholar
- Ahmad N: The vertical transmission of human immunodeficiency virus type 1: molecular and biological properties of the virus. Crit Rev Clin Lab Sci. 2005, 42 (1): 1-34. 10.1080/10408360490512520.View ArticlePubMedGoogle Scholar
- Blanche S, Tardieu M, Duliege A, Rouzioux C, Le Deist F, Fukunaga K, Caniglia M, Jacomet C, Messiah A, Griscelli C: Longitudinal study of 94 symptomatic infants with perinatally acquired human immunodeficiency virus infection. Evidence for a bimodal expression of clinical and biological symptoms. Am J Dis Child. 1990, 144 (11): 1210-1215.View ArticlePubMedGoogle Scholar
- Blanche S, Rouzioux C, Moscato ML, Veber F, Mayaux MJ, Jacomet C, Tricoire J, Deville A, Vial M, Firtion G, et al: A prospective study of infants born to women seropositive for human immunodeficiency virus type 1. HIV Infection in Newborns French Collaborative Study Group. N Engl J Med. 1989, 320 (25): 1643-1648.View ArticlePubMedGoogle Scholar
- Rouet F, Sakarovitch C, Msellati P, Elenga N, Montcho C, Viho I, Blanche S, Rouzioux C, Dabis F, Leroy V: Pediatric viral human immunodeficiency virus type 1 RNA levels, timing of infection, and disease progression in African HIV-1-infected children. Pediatrics. 2003, 112 (4): e289-10.1542/peds.112.4.e289.View ArticlePubMedGoogle Scholar
- Munoz-Fernandez MA, Navarro J, Obregon E, Arias RA, Gurbindo MD, Sampelayo TH, Fernandez-Cruz E: Immunological and virological markers of disease progression in HIV-infected children. Acta Paediatr Suppl. 1997, 421: 46-51.View ArticlePubMedGoogle Scholar
- Kopka J, Batalla M, Mangano A, Mecikovsky D, Bologna R, Sen L: Relevance of viral phenotype in the early AIDS outcome of pediatric HIV-1 primary infection. Pediatr Res. 2002, 52 (4): 475-480. 10.1203/01.PDR.0000028056.74614.E0.View ArticlePubMedGoogle Scholar
- Resino S, Gurbindo D, Cano JM, Sanchez-Ramon S, Muoz-Fernandez MA: Predictive markers of clinical outcome in vertically HIV-1-infected infants. A prospective longitudinal study. Pediatr Res. 2000, 47 (4 Pt 1): 509-515.View ArticlePubMedGoogle Scholar
- Strunnikova N, Ray SC, Livingston RA, Rubalcaba E, Viscidi RP: Convergent evolution within the V3 loop domain of human immunodeficiency virus type 1 in association with disease progression. J Virol. 1995, 69 (12): 7548-7558.PubMed CentralPubMedGoogle Scholar
- Casper C, Naver L, Clevestig P, Belfrage E, Leitner T, Albert J, Lindgren S, Ottenblad C, Bohlin AB, Fenyo EM, Ehrnst A: Coreceptor change appears after immune deficiency is established in children infected with different HIV-1 subtypes. AIDS Res Hum Retroviruses. 2002, 18 (5): 343-352. 10.1089/088922202753519124.View ArticlePubMedGoogle Scholar
- Goulder PJ, Pasquier C, Holmes EC, Liang B, Tang Y, Izopet J, Saune K, Rosenberg ES, Burchett SK, McIntosh K, Barnardo M, Bunce M, Walker BD, Brander C, Phillips RE: Mother-to-child transmission of HIV infection and CTL escape through HLA-A2-SLYNTVATL epitope sequence variation. Immunol Lett. 2001, 79 (1-2): 109-116. 10.1016/S0165-2478(01)00272-3.View ArticlePubMedGoogle Scholar
- Geffin R, Hutto C, Andrew C, Scott GB: A longitudinal assessment of autologous neutralizing antibodies in children perinatally infected with human immunodeficiency virus type 1. Virology. 2003, 310 (2): 207-215.View ArticlePubMedGoogle Scholar
- Hutto C, Zhou Y, He J, Geffin R, Hill M, Scott W, Wood C: Longitudinal studies of viral sequence, viral phenotype, and immunologic parameters of human immunodeficiency virus type 1 infection in perinatally infected twins with discordant disease courses. J Virol. 1996, 70 (6): 3589-3598.PubMed CentralPubMedGoogle Scholar
- Zhang H, Hoffmann F, He J, He X, Kankasa C, Ruprecht R, West JT, Orti G, Wood C: Evolution of subtype C HIV-1 Env in a slowly progressing Zambian infant. Retrovirology. 2005, 2: 67-10.1186/1742-4690-2-67.PubMed CentralView ArticlePubMedGoogle Scholar
- de Jong JJ, Goudsmit J, Keulen W, Klaver B, Krone W, Tersmette M, de Ronde A: Human immunodeficiency virus type 1 clones chimeric for the envelope V3 domain differ in syncytium formation and replication capacity. J Virol. 1992, 66 (2): 757-765.PubMed CentralPubMedGoogle Scholar
- Shioda T, Levy JA, Cheng-Mayer C: Small amino acid changes in the V3 hypervariable region of gp120 can affect the T-cell-line and macrophage tropism of human immunodeficiency virus type 1. Proc Natl Acad Sci U S A. 1992, 89 (20): 9434-9438. 10.1073/pnas.89.20.9434.PubMed CentralView ArticlePubMedGoogle Scholar
- Chesebro B, Wehrly K, Nishio J, Perryman S: Macrophage-tropic human immunodeficiency virus isolates from different patients exhibit unusual V3 envelope sequence homogeneity in comparison with T-cell-tropic isolates: definition of critical amino acids involved in cell tropism. J Virol. 1992, 66 (11): 6547-6554.PubMed CentralPubMedGoogle Scholar
- Hwang SS, Boyle TJ, Lyerly HK, Cullen BR: Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science. 1991, 253 (5015): 71-74. 10.1126/science.1905842.View ArticlePubMedGoogle Scholar
- Safrit JT, Andrews CA, Zhu T, Ho DD, Koup RA: Characterization of human immunodeficiency virus type 1-specific cytotoxic T lymphocyte clones isolated during acute seroconversion: recognition of autologous virus sequences within a conserved immunodominant epitope. J Exp Med. 1994, 179 (2): 463-472. 10.1084/jem.179.2.463.View ArticlePubMedGoogle Scholar
- Safrit JT, Lee AY, Andrews CA, Koup RA: A region of the third variable loop of HIV-1 gp120 is recognized by HLA-B7-restricted CTLs from two acute seroconversion patients. J Immunol. 1994, 153 (8): 3822-3830.PubMedGoogle Scholar
- Takahashi H, Nakagawa Y, Pendleton CD, Houghten RA, Yokomuro K, Germain RN, Berzofsky JA: Induction of broadly cross-reactive cytotoxic T cells recognizing an HIV-1 envelope determinant. Science. 1992, 255 (5042): 333-336. 10.1126/science.1372448.View ArticlePubMedGoogle Scholar
- Takahashi H, Germain RN, Moss B, Berzofsky JA: An immunodominant class I-restricted cytotoxic T lymphocyte determinant of human immunodeficiency virus type 1 induces CD4 class II-restricted help for itself. J Exp Med. 1990, 171 (2): 571-576. 10.1084/jem.171.2.571.View ArticlePubMedGoogle Scholar
- Rusche JR, Javaherian K, McDanal C, Petro J, Lynn DL, Grimaila R, Langlois A, Gallo RC, Arthur LO, Fischinger PJ, et al: Antibodies that inhibit fusion of human immunodeficiency virus-infected cells bind a 24-amino acid sequence of the viral envelope, gp120. Proc Natl Acad Sci U S A. 1988, 85 (9): 3198-3202. 10.1073/pnas.85.9.3198.PubMed CentralView ArticlePubMedGoogle Scholar
- Palker TJ, Clark ME, Langlois AJ, Matthews TJ, Weinhold KJ, Randall RR, Bolognesi DP, Haynes BF: Type-specific neutralization of the human immunodeficiency virus with antibodies to env-encoded synthetic peptides. Proc Natl Acad Sci U S A. 1988, 85 (6): 1932-1936. 10.1073/pnas.85.6.1932.PubMed CentralView ArticlePubMedGoogle Scholar
- Wellensiek BP, Sundaravaradan V, Ramakrishnan R, Ahmad N: Molecular characterization of the HIV-1 gag nucleocapsid gene associated with vertical transmission. Retrovirology. 2006, 3: 21-10.1186/1742-4690-3-21.PubMed CentralView ArticlePubMedGoogle Scholar
- Sundaravaradan V, Hahn T, Ahmad N: Conservation of functional domains and limited heterogeneity of HIV-1 reverse transcriptase gene following vertical transmission. Retrovirology. 2005, 2: 36-10.1186/1742-4690-2-36.PubMed CentralView ArticlePubMedGoogle Scholar
- Alexander L, Aquino-DeJesus MJ, Chan M, Andiman WA: Inhibition of human immunodeficiency virus type 1 (HIV-1) replication by a two-amino-acid insertion in HIV-1 Vif from a nonprogressing mother and child. J Virol. 2002, 76 (20): 10533-10539. 10.1128/JVI.76.20.10533-10539.2002.PubMed CentralView ArticlePubMedGoogle Scholar
- Binley JM, Jin X, Huang Y, Zhang L, Cao Y, Ho DD, Moore JP: Persistent antibody responses but declining cytotoxic T-lymphocyte responses to multiple human immunodeficiency virus type 1 antigens in a long-term nonprogressing individual with a defective p17 proviral sequence and no detectable viral RNA expression. J Virol. 1998, 72 (4): 3472-3474.PubMed CentralPubMedGoogle Scholar
- Wang B, Ge YC, Palasanthiran P, Xiang SH, Ziegler J, Dwyer DE, Randle C, Dowton D, Cunningham A, Saksena NK: Gene defects clustered at the C-terminus of the vpr gene of HIV-1 in long-term nonprogressing mother and child pair: in vivo evolution of vpr quasispecies in blood and plasma. Virology. 1996, 223 (1): 224-232. 10.1006/viro.1996.0471.View ArticlePubMedGoogle Scholar
- Kirchhoff F, Greenough TC, Brettler DB, Sullivan JL, Desrosiers RC: Brief report: absence of intact nef sequences in a long-term survivor with nonprogressive HIV-1 infection. N Engl J Med. 1995, 332 (4): 228-232. 10.1056/NEJM199501263320405.View ArticlePubMedGoogle Scholar
- Iversen AK, Shpaer EG, Rodrigo AG, Hirsch MS, Walker BD, Sheppard HW, Merigan TC, Mullins JI: Persistence of attenuated rev genes in a human immunodeficiency virus type 1-infected asymptomatic individual. J Virol. 1995, 69 (9): 5743-5753.PubMed CentralPubMedGoogle Scholar
- Wolinsky SM, Korber BT, Neumann AU, Daniels M, Kunstman KJ, Whetsell AJ, Furtado MR, Cao Y, Ho DD, Safrit JT: Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science. 1996, 272 (5261): 537-542. 10.1126/science.272.5261.537.View ArticlePubMedGoogle Scholar
- Lukashov VV, Kuiken CL, Goudsmit J: Intrahost human immunodeficiency virus type 1 evolution is related to length of the immunocompetent period. J Virol. 1995, 69 (11): 6911-6916.PubMed CentralPubMedGoogle Scholar
- Ganeshan S, Dickover RE, Korber BT, Bryson YJ, Wolinsky SM: Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J Virol. 1997, 71 (1): 663-677.PubMed CentralPubMedGoogle Scholar
- Halapi E, Leitner T, Jansson M, Scarlatti G, Orlandi P, Plebani A, Romiti L, Albert J, Wigzell H, Rossi P: Correlation between HIV sequence evolution, specific immune response and clinical outcome in vertically infected infants. Aids. 1997, 11 (14): 1709-1717. 10.1097/00002030-199714000-00007.View ArticlePubMedGoogle Scholar
- Williamson S: Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol Biol Evol. 2003, 20 (8): 1318-1325. 10.1093/molbev/msg144.View ArticlePubMedGoogle Scholar
- Chen B, Vogan EM, Gong H, Skehel JJ, Wiley DC, Harrison SC: Structure of an unliganded simian immunodeficiency virus gp120 core. Nature. 2005, 433 (7028): 834-841. 10.1038/nature03327.View ArticlePubMedGoogle Scholar
- Derdeyn CA, Decker JM, Bibollet-Ruche F, Mokili JL, Muldoon M, Denham SA, Heil ML, Kasolo F, Musonda R, Hahn BH, Shaw GM, Korber BT, Allen S, Hunter E: Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science. 2004, 303 (5666): 2019-2022. 10.1126/science.1093137.View ArticlePubMedGoogle Scholar
- Li B, Decker JM, Johnson RW, Bibollet-Ruche F, Wei X, Mulenga J, Allen S, Hunter E, Hahn BH, Shaw GM, Blackwell JL, Derdeyn CA: Evidence for potent autologous neutralizing antibody titers and compact envelopes in early infection with subtype C human immunodeficiency virus type 1. J Virol. 2006, 80 (11): 5211-5218. 10.1128/JVI.00201-06.PubMed CentralView ArticlePubMedGoogle Scholar
- Ahmad N, Baroudy BM, Baker RC, Chappey C: Genetic analysis of human immunodeficiency virus type 1 envelope V3 region isolates from mothers and infants after perinatal transmission. J Virol. 1995, 69 (2): 1001-1012.PubMed CentralPubMedGoogle Scholar
- Scarlatti G, Leitner T, Halapi E, Wahlberg J, Marchisio P, Clerici-Schoeller MA, Wigzell H, Fenyo EM, Albert J, Uhlen M, et al: Comparison of variable region 3 sequences of human immunodeficiency virus type 1 from infected children with the RNA and DNA sequences of the virus populations of their mothers. Proc Natl Acad Sci U S A. 1993, 90 (5): 1721-1725. 10.1073/pnas.90.5.1721.PubMed CentralView ArticlePubMedGoogle Scholar
- Wolinsky SM, Wike CM, Korber BT, Hutto C, Parks WP, Rosenblum LL, Kunstman KJ, Furtado MR, Munoz JL: Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants. Science. 1992, 255 (5048): 1134-1137. 10.1126/science.1546316.View ArticlePubMedGoogle Scholar
- Yang Z, Bielawski JP: Statistical methods for detecting molecular adaptation. Trends In Ecology And Evolution. 2000, 15 (12): 496-503. 10.1016/S0169-5347(00)01994-7.View ArticlePubMedGoogle Scholar
- Pollack H, Zhan MX, Ilmet-Moore T, Ajuang-Simbiri K, Krasinski K, Borkowsky W: Ontogeny of anti-human immunodeficiency virus (HIV) antibody production in HIV-1-infected infants. Proc Natl Acad Sci U S A. 1993, 90 (6): 2340-2344. 10.1073/pnas.90.6.2340.PubMed CentralView ArticlePubMedGoogle Scholar
- Wu X, Parast AB, Richardson BA, Nduati R, John-Stewart G, Mbori-Ngacha D, Rainwater SM, Overbaugh J: Neutralization escape variants of human immunodeficiency virus type 1 are transmitted from mother to infant. J Virol. 2006, 80 (2): 835-844. 10.1128/JVI.80.2.835-844.2006.PubMed CentralView ArticlePubMedGoogle Scholar
- Chohan B, Lang D, Sagar M, Korber B, Lavreys L, Richardson B, Overbaugh J: Selection for human immunodeficiency virus type 1 envelope glycosylation variants with shorter V1-V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels. J Virol. 2005, 79 (10): 6528-6531. 10.1128/JVI.79.10.6528-6531.2005.PubMed CentralView ArticlePubMedGoogle Scholar
- Frost SD, Liu Y, Pond SL, Chappey C, Wrin T, Petropoulos CJ, Little SJ, Richman DD: Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. J Virol. 2005, 79 (10): 6523-6527. 10.1128/JVI.79.10.6523-6527.2005.PubMed CentralView ArticlePubMedGoogle Scholar
- Frost SD, Wrin T, Smith DM, Kosakovsky Pond SL, Liu Y, Paxinos E, Chappey C, Galovich J, Beauchaine J, Petropoulos CJ, Little SJ, Richman DD: Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc Natl Acad Sci U S A. 2005, 102 (51): 18514-18519. 10.1073/pnas.0504658102.PubMed CentralView ArticlePubMedGoogle Scholar
- Wei X, Decker JM, Wang S, Hui H, Kappes JC, Wu X, Salazar-Gonzalez JF, Salazar MG, Kilby JM, Saag MS, Komarova NL, Nowak MA, Hahn BH, Kwong PD, Shaw GM: Antibody neutralization and escape by HIV-1. Nature. 2003, 422 (6929): 307-312. 10.1038/nature01470.View ArticlePubMedGoogle Scholar
- Bonhoeffer S, Holmes EC, Nowak MA: Causes of HIV diversity. Nature. 1995, 376 (6536): 125-10.1038/376125a0.View ArticlePubMedGoogle Scholar
- Mantina H, Kankasa C, Klaskala W, Brayfield B, Campbell J, Du Q, Bhat G, Kasolo F, Mitchell C, Wood C: Vertical transmission of Kaposi's sarcoma-associated herpesvirus. Int J Cancer. 2001, 94 (5): 749-752. 10.1002/ijc.1529.View ArticlePubMedGoogle Scholar
- Liu ZQ, Wood C, Levy JA, Cheng-Mayer C: The viral envelope gene is involved in macrophage tropism of a human immunodeficiency virus type 1 strain isolated from brain tissue. J Virol. 1990, 64 (12): 6148-6153.PubMed CentralPubMedGoogle Scholar
- Jobb G, von Haeseler A, Strimmer K: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol. 2004, 4 (1): 18-10.1186/1471-2148-4-18.PubMed CentralView ArticlePubMedGoogle Scholar
- Kumar S, Tamura K, Nei M: MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform. 2004, 5 (2): 150-163. 10.1093/bib/5.2.150.View ArticlePubMedGoogle Scholar
- Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R: DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 2003, 19 (18): 2496-2497. 10.1093/bioinformatics/btg359.View ArticlePubMedGoogle Scholar
- Pond SL, Frost SD: Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics. 2005, 21 (10): 2531-2533. 10.1093/bioinformatics/bti320.View ArticlePubMedGoogle Scholar
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