title: Phylogenetic characterization of six full-length HIV-1 subtype C molecular clones from three patients: identification of rare subtype C strains containing two NF-κB motifs in the long terminal repeat.
abstract: Molecular surveillance is the backbone of HIV-1 vaccinology. Full-length HIV-1 sequences are useful tools that can provide a better understanding of the epidemiology in a given region. A limited number of full-length HIV-1 sequences are available from India, where >95% of the HIV infections are due to HIV-1 subtype C (HIV-1C), which is distinct from the prototype African HIV-1C. In this study, we sequenced six full-length clones isolated from three patients. Extensive phylogenetic analyses of the full-length viral sequences using bioinformatic tools identified a separate cluster of Indian strains, thus confirming the distinct phylogenetic identity of the Indian HIV-1C. Notably, the long terminal repeat (LTR) of two of the six molecular clones contained only two NF-κB binding sites. The sequences also displayed features characteristic of HIV-1C including a Tat dicysteine motif, a shortened Rev open reading frame, and a predicted CCR5 coreceptor tropism for gp120 of three of the proviral sequences.
authors.affiliation: 1 Department of Microbiology and Immunology, Albert Einstein College of Medicine , Bronx, New York.
authors.forename: Luke Elizabeth
authors.initials: LE
authors.lastname: Hanna
authors.forename: Ujjwal
authors.initials: U
authors.lastname: Neogi
authors.forename: Udaykumar
authors.initials: U
authors.lastname: Ranga
authors.forename: Soumya
authors.initials: S
authors.lastname: Swaminathan
authors.forename: Vinayaka R
authors.initials: VR
authors.lastname: Prasad
mesh_terms: D000328:Adult; D001665:Binding Sites; D016000:Cluster Analysis; D019295:Computational Biology; D005260:Female; D016679:Genome, Viral; D005838:Genotype; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D006801:Humans; D007194:India; D008297:Male; D008969:Molecular Sequence Data; D016328:NF-kappa B / Q000378:metabolism; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D015728:Receptors, HIV; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D020079:Terminal Repeat Sequences; D053585:Virus Attachment; D055815:Young Adult; D054321:rev Gene Products, Human Immunodeficiency Virus / Q000235:genetics; D054322:tat Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D016328:NF-kappa B; D012367:RNA, Viral; D015728:Receptors, HIV; D054321:rev Gene Products, Human Immunodeficiency Virus; D054322:tat Gene Products, Human Immunodeficiency Virus