Generation of intersubtype human immunodeficiency virus type 1 recombinants in env gene in vitro: influences in the biological behavior and in the establishment of productive infections

Genetic Consequences of Antiviral Therapy on HIV-1

A variety of enzyme inhibitors have been developed in combating HIV-1, however the fast evolutionary rate of this virus commonly leads to the emergence of resistance mutations that finally allows the mutant virus to survive. This review explores the main genetic consequences of HIV-1 molecular evolution during antiviral therapies, including the viral genetic diversity and molecular adaptation. The role of recombination in the generation of drug resistance is also analyzed. Besides the investigation and discussion of published works, an evolutionary analysis of protease-coding genes collected from patients before and after treatment with different protease inhibitors was included to validate previous studies. Finally, the review discusses the importance of considering genetic consequences of antiviral therapies in models of HIV-1 evolution that could improve current genotypic resistance testing and treatments design.

The detection of in vivo and in vitro HIV type 1 B/F profiles in Brazil using a real-time PCR assay for five HIV type 1 genomic regions

We sought to determine the frequency and profile of HIV-1 BF recombinants in vitro and in vivo. Laboratory HIV-1 strains from subtypes B and F were cocultured and evaluated. Clinical samples from the city of Santos, Brazil, where the first HIV-1 B/F circulating recombinant forms (CRF) were described, were also assessed. Five real-time PCR assays were developed to equally amplify subtypes B and F, and subtype-specific probes were developed and optimized. To validate the PCR systems, clinical samples from Santos were sequenced and phylogenetically analyzed. The real-time PCR assays were performed on these samples and on the supernatant of an in vitro competition assay to assess emergent recombinant strains. Out of 157 clinical samples, 62.1% were defined as subtype B, 3.0% were subtype F, 16.7% presented the CRF28_BF profile, and 13.6% of the samples presented the CRF29_BF profile. The specificity and sensitivity in the discrimination assay for this sample panel were 93% and 92%, respectively. The HIV that emerged from the coinfected cell culture closely resembled the CRF28_BF profile. The first-described CRFs are still fixed in this geographic region of Brazil, and the in vitro emerging strains detected by real-time PCR suggest that in addition to the shaping of recombinant strains by immune selection, viral structures may also play an important role in emerging CRFs.

Common genetic arrangements among human immunodeficiency virus type 1 subtype A and D recombinant genomes vertically transmitted in Tanzania

Human immunodeficiency virus type 1 (HIV-1) subtypes A, C, and D are cocirculating in Tanzania, and large numbers of recombinant genomes have been reported from this region. Here we describe full-length sequences of six unlinked HIV-1 subtype A and D recombinants. The samples came from newborns, indicating that the recombination patterns were vertically transmitted and were functionally competent. All six genomes had different recombination patterns with one to eight cross-over points frequently located at the beginning or end of functionally defined regions. In five of the six viruses most of gag, pol, tat, and rev and the intracytoplasmic domain of gp41 were classified as subtype D. In all but one genome, the external domain of gp41 and the majority of gp120 belonged to subtype A. A recombination site common to four of the six genomes was located at the transmembrane domain of gp41, at the end of the rev response element. The identification of subtype patterns among intersubtype recombinant genomes from recently infected individuals may reveal genetic determinants of improved viral fitness or advantage for transmission.