Molecular Mechanisms of HIV-1 Vertical Transmission and Pathogenesis in Infants

Comparative Genetic Variability in HIV-1 Subtype C vpu Gene in Early Age Groups of Infants

OBJECTIVE

Identifying the genetic variability in vertically transmitted viruses in early infancy is important to understand the disease progression. Being important in HIV-1 disease pathogenesis, vpu gene, isolated from young infants was investigated to understand the viral characteristics.

METHOD

Blood samples were obtained from 80 HIV-1 positive infants, categorized in two age groups; acute (<6 months) and early (>6-18 months). A total of 77 PCR positive samples, amplified for vpu gene, were sequenced and analyzed.

RESULTS

73 isolates belonged to subtype C. Analysis of heterogeneity of amino acid sequences in infant groups showed that in the sequences of acute age group both insertions and deletions were present while in the early age group only deletions were present. In the acute age group, a deletion of 3 residues (RAE) in the first alfa helix in one sequence and insertions of 1-2 residues (DM, GH, G and H) in the second alfa helix in 4 sequences were observed. In the early age group, deletion of 2 residues (VN) in the cytoplasmic tail region in 2 sequences was observed. Length of the amino terminal was observed to be gradually increasing with the increasing age of the infants. Protein Variation Effect Analyzer software showed that deleterious mutations were more in the acute than the early age group. Entropy analysis revealed that heterogeneity of the residues was comparatively higher in the sequences of acute than the early age group.

CONCLUSION

Mutations observed in the helixes may affect the conformation and lose the ability to degrade CD4 receptors. Heterogeneity was decreasing with the increasing ages of the infants, indicating positive selection for robust virion survival.

Comparative genetic variability in HIV-1 subtype C nef gene in early age groups of infants

Targeting properties of vertically transmitted viruses in early infancy is important to understand disease progression. To investigate genotypic characteristics of transmitted viruses, blood samples were obtained from infants aged 6 weeks-18 months, categorized in two age groups, acute (<6 months) and early (>6-18 months). Nef having an important role in pathogenesis was selected to explore the viral characteristics. A total of 57 PCR positive samples, amplified by nef gene were sequenced. Analysis showed that 50 sequences belonged to subtype C. In one sequence of acute age group, a long insertion of 10 residues (AAERMRRAEP) in variable region and a 13 residues deletion (ATNNADCAWLEAQ) around proteolytic cleavage region of gene in another sequence was observed. Insertions were also observed in sequences of early age group, however, they ranged from two to eight residues only. In one sequence of early age group, 3/4 arginines at positions 19, 21, 22 of arginine cluster were mutated to glutamine, alanine, and glutamine, respectively. Entropy analysis of two age groups revealed presence of several residues with statistically significant differences in their variability. Among these, 15 (R18,R23,R24; A66,L68,Q71; E74,E77,E78; V87,M92; R119, P144, E167, and C176) belonged to functional motifs, out of which, 12 were in acute age group, suggesting that variability was greater in this group. Prediction of HLA binding peptide motif revealed that epitope LTFGWCFKL was present in >80% study sequences. This epitope was also present in maximum number of HLA types circulating in India and vaccine candidate sequences, suggesting that it may be helpful in designing an epitope-based vaccine.

Molecular Characterization of the Human Immunodeficiency Virus Type 1 in Women and Their Vertically Infected Children

Approximately 35 million people worldwide are infected with human immunodeficiency virus (HIV) around 3.2 million of whom are children under 15 years. Mother-to-child-transmission (MTCT) of HIV-1 accounts for 90% of all infections in children. Despite great advances in the prevention of MTCT in Brazil, children are still becoming infected. Samples from 19 HIV-1-infected families were collected. DNA was extracted and fragments from gag, pol, and env were amplified and sequenced directly. Phylogenetic reconstruction was performed. Drug resistance analyses were performed in pol and env sequences. We found 82.1% of subtype B and 17.9% of BF recombinants. A prevalence of 43.9% drug resistance-associated mutations in pol sequences was identified. Of the drug-naive children 33.3% presented at least one mutation related to protease inhibitor/nucleoside reverse transcriptase inhibitor/nonnucleoside reverse transcriptase inhibitor (PI/NRTI/NNRTI) resistance. The prevalence of transmitted drug resistance mutations was 4.9%. On env we found a low prevalence of HR1 (4.9%) and HR2 (14.6%) mutations.

Molecular mechanisms of HIV-1 infection in neonatal target cells

HIV-1-infected neonates and infants have a higher viral load and progress to symptomatic AIDS more rapidly than their own infected mothers, as well as other infected adults, with differences in clinical manifestations, recurrent bacterial infections and CNS disorders. Two major reasons have been attributed to this differential HIV pathogenesis and disease; the relative immaturity of the neonate’s immune system and it’s inability to contain the highly replicating and mutating HIV-1, and the more efficient replication of HIV-1 in neonatal cells than in adult target cells. In this context, it has been demonstrated that HIV-1 replicates more efficiently in neonatal (cord) blood monocytes/macrophages and T lymphocytes – including naive and memory T lymphocytes – compared with adult blood cells. We have also determined the mechanisms of the differential HIV-1 replication in cord versus adult blood monocytes/macrophages and T lymphocytes (naive and memory), finding that it was influenced at the level of HIV-1 gene expression. The increased HIV-1 gene expression in neonatal versus adult target cells was regulated by differential expression of host factors, transcription factors (NF-κB, E2F, HAT-1, TFIIE, Cdk9 and Cyclin T1), signal transducers (STAT3 and STAT5A) and cytokines (IL-1β, IL-6 and IL-10). We also showed that nuclear extracts from cord cells interacted with HIV-1 long terminal repeat cis-acting sequences, including NF-κB, NFAT, AP1 and NF-IL6, to a greater extent when compared with adult peripheral blood mononuclear cell nuclear extracts. Additionally, shRNA of retroviral origin for STAT3 and IL-6 downregulated both their own gene expression as well as that of HIV-1, indicating that these factors influenced the differential expression of HIV-1 genes in cord cells compared with adult cells. In addition, HIV-1 integration plays an important role in differential HIV-1 replication and gene expression in neonatal versus adult cells by integrating into more actively transcribed genes in neonates compared with adults. We characterized 468 HIV-1 integration sites within cord and adult blood T lymphocytes and monocytes/macrophages, including genes coding for cellular components, and those involved with maintenance of the intracellular environment, enzyme regulation, cellular metabolism, catalytic activity and cation transport, as well as several potential transcription factor binding sites at the sites of integration. Additionally, the genes at the integration sites, transcription factors and transcription binding sites were expressed at higher levels in cord than adult target cells. In summary, the increased HIV-1 gene expression and replication in neonatal target cells due to differential expression of host factors all contribute to an increased viral load and faster disease progression in neonates and infants when compared with similar situations in adult patients. Based on these findings, it may be possible to identify new viral and host targets for use in developing strategies for the treatment and prevention of HIV-1.

Diversity of HIV type 1 long terminal repeat (LTR) sequences following mother-to-child transmission in North India

We genetically characterized the extent of variation in HIV-1 LTR sequences from 11 mother-to-child transmission (MTCT) pairs from HIV-1-infected individuals from North India. Nine pairs were found to be infected with subtype C virus whereas two pairs were infected with subtype B virus. They harbored the characteristic three and two NF-κB sites, respectively. The analysis of intrasubtype divergence between B and C revealed greater diversity with subtype B LTR sequences than subtype C (p < 0.005). Significant evolutionary divergence of subtype C and subtype B was found in NFAT-III (p < 0.000001), NFAT-II (p < 0.0001), and USF (p < 0.005) transcription factor binding sites (TFBS). NF-κB-I, Sp I and II, Ets-I, AP-I and II, and TATA Box TFBS were highly conserved in both the subtypes. An alternate secondary structure of Tar was detected in the VT5 sample due to the point mutation from G to C (position +21) and T to C (position +38).

Molecular mechanisms of HIV-1 mother-to-child transmission and infection in neonatal target cells

HIV-1 mother-to-child transmission (MTCT) occurs mainly at three stages, including prepartum, intrapartum and postpartum. Several maternal factors, including low CD4+ lymphocyte counts, high viral load, immune response, advanced disease status, smoking and abusing drugs have been implicated in an increased risk of HIV-1 MTCT. While use of antiretroviral therapy (ART) during pregnancy has significantly reduced the rate of MTCT, selective transmission of ART resistant mutants has been reported. Based on HIV-1 sequence comparison, the maternal HIV-1 minor genotypes with R5 phenotypes are predominantly transmitted to their infants and initially maintained in the infants with the same properties. Several HIV-1 structural, regulatory and accessory genes were highly conserved following MTCT. In addition, HIV-1 sequences from non-transmitting mothers are less heterogeneous compared with transmitting mothers, suggesting that a higher level of viral heterogeneity influences MTCT. Analysis of the immunologically relevant epitopes showed that variants evolved to escape the immune response that influenced HIV-1 MTCT. Several cytotoxic T-lymphocyte (CTL) epitopes were identified in various HIV-1 genes that were conserved in HIV-1 mother-infant sequences, suggesting a role in MTCT. We have shown that HIV-1 replicates more efficiently in neonatal T-lymphocytes and monocytes/macrophages compared with adult cells, and this differential replication is influenced at the level of HIV-1 gene expression, which was due to differential expression of host factors, including transcriptional activators, signal transducers and cytokines in neonatal than adult cells. In addition, HIV-1 integration occurs in more actively transcribed genes in neonatal compared with adult cells, which may influence HIV-1 gene expression. The increased HIV-1 gene expression and replication in neonatal target cells contribute to a higher viral load and more rapid disease progression in neonates/infants than adults. These findings may identify targets, viral and host, for developing strategies for HIV-1 prevention and treatment.

Mutations generated in human immunodeficiency virus type 1 long terminal repeat during vertical transmission correlate with viral gene expression

We determined the effect of mutations generated in HIV-1 LTR on viral gene expression in six mother-infant pairs following vertical transmission. We show that the functional domains critical for LTR function, the promoter (TATAA), enhancers (three SpI and two NFkappaB sites), the modulatory region (two AP-I sites, two NFAT, one NF-IL6 site, one Ets-1, and one USF-1) and the TAR region were generally conserved among mother-infant pairs, although we observed several patient and pair specific mutations in these important domains. We then determined the promoter activity of our mother-infant LTR sequences by measuring CAT gene expression, which was driven by these LTRs and found that most of these HIV-1 LTRs derived from 6 mother-infant pairs were functional. However, mutations in the important transcription factor binding sites, including TATAA, SpI, NFkappaB, AP-I, NFAT, NF-IL6, Ets-1, USF-1 and TAR resulted in reduced LTR driven CAT gene expression. Taken together, conservation of functional domains in the LTR during vertical transmission supports the notion that a functional LTR is critical in viral replication and pathogenesis and mutations generated during the course of infection correlated with HIV-1 gene expression.