title: Identification of subtype C human immunodeficiency virus type 1 by subtype-specific PCR and its use in the characterization of viruses circulating in the southern parts of India.
abstract: Human immunodeficiency virus type 1 (HIV-1) subtype C viruses are associated with nearly half of worldwide HIV-1 infections and are most predominant in India and the southern and eastern parts of Africa. Earlier reports from India identified the preponderance of subtype C and a small proportion of subtype A viruses. Subsequent reports identifying multiple subtypes suggest new introductions and/or their detection due to extended screening. The southern parts of India constitute emerging areas of the epidemic, but it is not known whether HIV-1 infection in these areas is associated with subtype C viruses or is due to the potential new introduction of non-subtype C viruses. Here, we describe the development of a specific and sensitive PCR-based strategy to identify subtype C-viruses (C-PCR). The strategy is based on amplifying a region encompassing a long terminal repeat and gag in the first round, followed by two sets of nested primers; one amplifies multiple subtypes, while the other is specific to subtype C. The common HIV and subtype C-specific fragments are distinguishable by length differences in agarose gels and by the difference in the numbers of NF-kappaB sites encoded in the subtype C-specific fragment. We implemented this method to screen 256 HIV-1-infected individuals from 35 towns and cities in four states in the south and a city in the east. With the exception of single samples of subtypes A and B and a B/C recombinant, we found all to be infected with subtype C viruses, and the subtype assignments were confirmed in a subset by using heteroduplex mobility assays and phylogenetic analysis of sequences. We propose the use of C-PCR to facilitate rapid molecular epidemiologic characterization to aid vaccine and therapeutic strategies.
authors.affiliation: Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.
authors.forename: Nagadenahalli B
authors.initials: NB
authors.lastname: Siddappa
authors.forename: Prashanta K
authors.initials: PK
authors.lastname: Dash
authors.forename: Anita
authors.initials: A
authors.lastname: Mahadevan
authors.forename: Narayana
authors.initials: N
authors.lastname: Jayasuryan
authors.forename: Fen
authors.initials: F
authors.lastname: Hu
authors.forename: Bethany
authors.initials: B
authors.lastname: Dice
authors.forename: Randy
authors.initials: R
authors.lastname: Keefe
authors.forename: Kadappa S
authors.initials: KS
authors.lastname: Satish
authors.forename: Bhuthiah
authors.initials: B
authors.lastname: Satish
authors.forename: Kuttan
authors.initials: K
authors.lastname: Sreekanthan
authors.forename: Ramdas
authors.initials: R
authors.lastname: Chatterjee
authors.forename: Kandala
authors.initials: K
authors.lastname: Venu
authors.forename: Parthasarathy
authors.initials: P
authors.lastname: Satishchandra
authors.forename: Vasanthapuram
authors.initials: V
authors.lastname: Ravi
authors.forename: Susarla K
authors.initials: SK
authors.lastname: Shankar
authors.forename: Raj
authors.initials: R
authors.lastname: Shankarappa
authors.forename: Udaykumar
authors.initials: U
authors.lastname: Ranga
mesh_terms: D000293:Adolescent; D000328:Adult; D001483:Base Sequence; D005260:Female; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods* / Q000592:standards