title: Distinct geographical clustering of HIV-1 and a signature amino acid at position 41 of the p24 unveiled by gag variability in India.
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.
authors.affiliation: Interdisciplinary Science, Technology and Research Academy, AISC, Hidayatullah Road, CAMP, Pune, India. pnm_d@yahoo.com.
authors.forename: Arpan
authors.initials: A
authors.lastname: Acharya
authors.forename: Salil
authors.initials: S
authors.lastname: Vaniawala
authors.forename: Harsh
authors.initials: H
authors.lastname: Parekh
authors.forename: Anju
authors.initials: A
authors.lastname: Nagee
authors.forename: Rabindra N
authors.initials: RN
authors.lastname: Misra
authors.forename: Minal
authors.initials: M
authors.lastname: Wani
authors.forename: Pratap N
authors.initials: PN
authors.lastname: Mukhopadhyaya
mesh_terms: D000328:Adult; D000595:Amino Acid Sequence; D016000:Cluster Analysis; D005260:Female; D015683:Gene Products, gag; D016655:HIV Core Protein p24 / Q000235:genetics*; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007194:India / Q000453:epidemiology; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D010865:Pilot Projects; D011446:Prospective Studies; D011498:Protein Precursors; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein / Q000379:methods; D055815:Young Adult
chemical_list: D015683:Gene Products, gag; D016655:HIV Core Protein p24; D011498:Protein Precursors; C514799:p24 protein, Human Immunodeficiency Virus Type 1; C059767:p55 gag precursor protein, Human immunodeficiency virus 1