The development of a vaccine against human immunodeficiency virus type 1 (HIV-1) has been affected by the ability of HIV to acquire high levels of genetic heterogeneity, which is also expected to pose problems in expanding therapeutic intervention to resource-poor countries. We propose the use of C-PCR to facilitate rapid molecular epidemiologic characterization to aid vaccine and therapeutic strategies. 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 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. 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-κB sites encoded in the subtype C-specific fragment.
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. Here, we describe the development of a specific and sensitive PCR-based strategy to identify subtype C-viruses (C-PCR). 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. Subsequent reports identifying multiple subtypes suggest new introductions and/or their detection due to extended screening. Earlier reports from India identified the preponderance of subtype C and a small proportion of subtype A viruses. 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.
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