Title:Distinct Geographical Clustering of HIV-1 and a Signature Amino Acid at Position 41 of the p24 Unveiled by gag Variability in India
VOLUME: 11 ISSUE: 4
Author(s):Arpan Acharya, Salil Vaniawala, Harsh Parekh, Anju Nagee, Rabindra N. Misra, Minal Wani and Pratap N. Mukhopadhyaya
Affiliation:Interdisciplinary Science, Technology and Research Academy, AISC, Hidayatullah Road, CAMP, Pune
Keywords:HIV-1, gag, p24, phylogeny, subtype.
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.
