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Updated: May 29, 2026
Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
Published on: December 27, 2010
Diversity of HIV type 1 envelope (V3-V5) sequence in HIV type 1-infected Indian children
Somi Sankaran Prakash1, Rajesh Kalra, Rakesh Lodha
1Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
Insights
Sequence diversity in the HIV-1 envelope was assessed in 13 Indian children. All children had subtype C infections, with unique findings including coreceptor usage and V4 region deletion, highlighting significant viral diversity.
Area of Science:
- Virology
- Immunology
- Genetics
Background:
- Human Immunodeficiency Virus type 1 (HIV-1) infection remains a global health concern.
- Understanding viral genetic diversity is crucial for developing effective treatments and vaccines.
- Pediatric HIV-1 infection presents unique challenges in disease progression and management.
Purpose of the Study:
- To analyze the sequence diversity of the HIV-1 viral envelope (V3-V5 region) in Indian children.
- To identify specific genetic characteristics within the viral envelope, such as coreceptor usage and sequence variations.
- To characterize the genetic landscape of HIV-1 in a pediatric cohort from North India.
Main Methods:
- Viral RNA extraction from patient samples.
- Sequencing of the HIV-1 envelope V3-V5 region.
- Bioinformatic analysis including coreceptor usage prediction (Web PSSM, Geno2pheno).
- Phylogenetic analysis to determine HIV-1 subtype.
Main Results:
- All 13 children were infected with HIV-1 subtype C.
- One viral sequence showed predicted CXCR4 coreceptor usage, associated with a longer V3 region (37 amino acids) and a specific motif (GRGQ).
- A unique finding was the complete deletion of the V4 region in another viral sequence.
- High sequence diversity was observed across the viral envelope sequences in the cohort.
Conclusions:
- HIV-1 subtype C is prevalent in this cohort of Indian children.
- Significant genetic diversity exists within the viral envelope, including unusual features like coreceptor tropism and regional deletions.
- These findings underscore the importance of characterizing viral diversity in pediatric populations for targeted therapeutic strategies.
Abstract:
Abstract We assessed the viral envelope (V3-V5 region) sequence diversity from 13 HIV-1-infected Indian children from north India. All of the 13 children were found to be infected with subtype C viruses. One of the viral sequences exhibited usage of the CXCR4 coreceptor predicted by Web PSSM and Geno2pheno tools. This virus also had a longer V3 sequence with 37 amino acids, a GRGQ motif, and a methionine residue before it (AIIMS_307). A unique finding was the complete deletion of the V4 region of another virus (AIIMS_363). High sequence diversity was observed in the envelope of the HIV-1-infected Indian children.
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