Distinct Geographical Clustering of HIV-1 and a Signature Amino Acid at Position 41 of the p24 Unveiled by gag Variability in India

Author(s): Arpan Acharya, Salil Vaniawala, Harsh Parekh, Anju Nagee, Rabindra N. Misra, Minal Wani, Pratap N. Mukhopadhyaya

Journal Name: Current HIV Research

Volume 11 , Issue 4 , 2013

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Abstract:

A portion of the gag gene cDNA for p24 protein from 30 Indian HIV-1 proviral DNA was amplified by PCR and sequenced. Phylogenetic analysis with reference samples of A1, A2, B, C, D, F1, F2, G, H, J, K, N and O subtypes revealed that 29 test samples aligned with subtype C reference strain while 1 matched with HIV-1 subtype A. Multiple alignment of predicted amino acid sequence of the Indian test samples and reference C subtype of HIV-1 samples from other countries indicated a molecular signature by way of rigid conservation of the amino acid ‘S’ at position 41 of the gag p24 protein in all Indian HIV-1 samples analyzed in this study as opposed to ‘T’in the same position in C subtype sequences from other parts of the world. A phylogenetic analysis and visualization of the resulting tree in radial position showed distinct clubbing of all Indian C subtypes and formation of a cluster when compared to C subtype sequences from other countries with a single Chinese sample as an exception which was found in the Indian cluster. The use of a portion of p24 gene sequence as tool for subtyping as well as phylogenetic grouping with special reference to its geographical location is discussed.

Keywords: HIV-1, gag, p24, phylogeny, subtype.

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Article Details

VOLUME: 11
ISSUE: 4
Year: 2013
Published on: 22 September, 2013
Page: [295 - 303]
Pages: 9
DOI: 10.2174/1570162X113119990044
Price: $65

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