Full-Length Genome Analysis of Human Immunodeficiency Virus Type 1 Subtype C in Brazil

Abstract

The most prevalent HIV-1 clade in the global epidemics is C, and this clade is also becoming important in the Brazilian epidemics. In this study, we characterized HIV-1 subtype C variants by sequencing their near full-length genomes. DNA was extracted from six samples previously classified in our laboratory as subtype C on the basis of partial genome sequencing. Amplification was carried out by overlapping PCR followed by direct sequencing. Phylogenetic analysis of full length genomes confirmed that all isolates belonged to subtype C, which formed a highly supported monophyletic cluster and showed a nucleotide distance of 5.4%. The core promoter of all isolates contained three NF-kappaB binding motifs. Our results suggest that subtype C viruses circulating in Brazil were likely introduced recently from a unique point source. The independent clustering of Brazilian subtype C on the phylogenetic tree suggests the profile of an ideal local candidate for the development of a single subtype vaccine.

Extensive Intrasubtype Recombination in South African Human Immunodeficiency Virus Type 1 Subtype C Infections

“…Using additional data and analyses compared to previous reports, we were also able to further identify evidence of geographic clustering within the subtype C epidemic (11,16,30,33,34,37,40,43,45,51,57,58,62). Vaccine candidates designed on regional HIV-1 subtype C strains may be able to provide greater sequence coverage than those designed on all subtype C sequences detected to date.…”

Origin and evolutionary history of HIV-1 subtype C in Brazil

“…It is interesting to note that several phylogenetic studies [26,29,30,37] had previously proposed that Brazilian subtype C began as a single founder event; however, none of these studies included sequences from Burundi among the reference sequences. This was probably because reference sequences were selected at random, showing that the use of appropriate reference sequences for phylogenetic analyses is crucial to trace global patterns of viral spread.…”

“…All phylogenetic studies [26,29,30,37] performed to date indicate that the introduction of subtype C in Brazil was likely a single event of one or a few genetically related viruses, probably through the south. However, the exact origin of such a founder strain remains unresolved.…”

Identification of a Novel HIV-1 Circulating Recombinant Form (CRF72_BF1) in Deep Sequencing Data from Blood Donors in Southeastern Brazil

“…The NFLGs from five overlapping fragments were obtained by PCR and determined by a previously reported method (5). The sequencing library was prepared as described previously (6).…”