Phylogenetic analysis of the p24-p7 region of the human immunodeficiency virus type 1 gag gene to determine subtype distribution among female sex workers in Calcutta, India

Abstract

Human immunodeficiency virus type 1 (HIV-1) subtype C, based on the envelope region, has been reported to be predominant in India. We sequenced the p24-p7 gag region from 51 HIV-1 seropositive female sex workers in Calcutta, India, for more-detailed molecular characterization. Subtype C was found to be prevalent, although no strong monophyletic cluster was observed.

FIG. 1.

Phylogenetic analysis of HIV-1 p24-p7 region of gag gene from 51 female sex workers in Calcutta, India. The construction of the tree is described in the text. Samples from Calcutta were designated “cal.” Reference isolates of different subtypes used were as follows: subtype A, UG029 and Q23_17; subtype B, Mstd101, HXB2 copy, and NC7; subtype C, mIDU101_3, 96ZM651, 98IS002, KER2010, 93IN101, 93IN9999, 95IN21068, 93IN904, 96BW01B03, 97ZA012, 98BR004, AA97202GP, and 97TZ04; subtype D, MB2059 and 99UGA07412; subtype F1, 93BR020_1 and BZ163; subtype G, 91ZR02 and X558; subtype H, 056 and VI991; subtype J, SE7887 and SE7022; and subtype K, EQTB11C and VI325.

FIG. 2.

Phylogenetic study of p24-p7 gene sequences of 51 HIV-1 seropositive strains from Calcutta, the eastern region of India, with 44 other C strains from different regions of India. The symbols used with the isolate names denote the origins of the strains as defined in the figure. Samples from Calcutta are designated “cal.” GenBank accession numbers of the Calcutta sequences are given in the text. The different isolates used for the study are as follows: NARI_GAG_1, NARI_GAG_2, NARI_GAG_3, NARI_GAG_4, NARI_GAG_5, NARI_GAG_6, 01IN565_10, 01IN565_11, 01IN565_13, 01IN565_14, 95IN21068, 93IN904, 94IN11246, 93IN101, 93IN905, 93IN9999, 98IN022, 94IN476, 98IN012, 50437, 60161, 60080, 60133, 60615, 50813, 50322, 49670, 50581, 33840, 33842, 49587, 80496, 50542, 70177, 50823, 50950, 50561, MYA1, IMP1, IMP3, IMP4, IMP5, IMP6, and C_GAG_221.