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A Restriction Enzyme Based Cloning Method to Assess the In vitro Replication Capacity of HIV-1 Subtype C Gag-MJ4 Chimeric Viruses
Published on: August 31, 2014
Comparative genetic variability in HIV-1 subtype C nef gene in early age groups of infants
Uma Sharma1,2, Poonam Gupta1, Megha Singhal2
1Molecular Virology Laboratory, Department of Biotechnology, Jamia Millia Islamia, New Delhi, India.
Insights
Genotypic analysis of vertically transmitted viruses in infants revealed subtype C dominance. Greater viral variability was observed in acutely infected infants, with a specific epitope identified for potential vaccine development.
Area of Science:
- Virology
- Immunology
- Genetics
Background:
- Understanding vertically transmitted viruses in infants is crucial for disease progression insights.
- The nef gene plays a significant role in viral pathogenesis.
Purpose of the Study:
- To investigate the genotypic characteristics of vertically transmitted viruses in infants.
- To explore viral variations in the nef gene across different infant age groups.
Main Methods:
- Blood samples from 57 infants (6 weeks-18 months) were analyzed.
- The nef gene was amplified by PCR and sequenced.
- Sequence analysis included identifying insertions, deletions, mutations, and entropy variations.
Main Results:
- Fifty out of 57 sequences were identified as subtype C.
- Significant viral variability, including insertions and deletions, was observed, particularly in the acute (<6 months) age group.
- Entropy analysis indicated greater residue variability in the acute group, with 12 residues in functional motifs showing significant differences.
- A conserved epitope (LTFGWCFKL) was identified in over 80% of sequences, common across Indian HLA types and vaccine candidates.
Conclusions:
- Infant viral infections show a high prevalence of subtype C.
- Acute infant infections exhibit greater nef gene variability, suggesting distinct evolutionary pressures.
- The identified epitope presents a promising target for developing effective, epitope-based vaccines against vertically transmitted viruses.
Abstract:
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.
