Diversity of HIV1 Subtype B: Implications to the Origin of BF Recombinants (original) (raw)
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Journal of Virology, 2007
Current knowledge of human immunodeficiency virus type 1 envelope (Env) glycoprotein structure and function is based on studies of clade B viruses. We present evidence of sequence and structural differences in viral glycoprotein gp120 between clades B and C. In clade C, the C3 region ␣2-helix exhibits high sequence entropy at the polar face but maintains its amphipathicity, whereas in clade B it accommodates hydrophobic residues. The V4 hypervariable domain in clade C is shorter than that in clade B. Generally, shorter V4 loops are incompatible with a glycine occurring in the ␣2-helix in clade C, an intriguing association that could be exploited to inform Env immunogen design.
International journal of genomics, 2017
Vpr is an HIV-1 accessory protein that plays numerous roles during viral replication, and some of which are cell type dependent. To test the hypothesis that HIV-1 tropism extends beyond the envelope into the vpr gene, studies were performed to identify the associations between coreceptor usage and Vpr variation in HIV-1-infected patients. Colinear HIV-1 Env-V3 and Vpr amino acid sequences were obtained from the LANL HIV-1 sequence database and from well-suppressed patients in the Drexel/Temple Medicine CNS AIDS Research and Eradication Study (CARES) Cohort. Genotypic classification of Env-V3 sequences as X4 (CXCR4-utilizing) or R5 (CCR5-utilizing) was used to group colinear Vpr sequences. To reveal the sequences associated with a specific coreceptor usage genotype, Vpr amino acid sequences were assessed for amino acid diversity and Jensen-Shannon divergence between the two groups. Five amino acid alphabets were used to comprehensively examine the impact of amino acid substitutions i...
AIDS Research and Human Retroviruses, 2010
HIV-1 epidemics in South America are believed to have originated in part from the subtype B epidemic initiated in the Caribbean/North America region. However, circulation of BF recombinants in similar proportions was extensively reported. Information currently shows that many BF recombinants share a recombination structure similar to that found in the CRF12_BF. In the present study, analyzing a set of 405 HIV sequences, we identified the most likely origin of the BF epidemic in an early event of recombination. We found that the subtype B epidemics in South America analyzed in the present study were initiated by a founder event that occurred in the early 1970s, a few years after the introduction of these strains in the Americas. Regarding the F/BF recombinant epidemics, by analyzing a subtype F genomic segment within the viral gene gag present in the majority of the BF recombinants, we found evidence of a geographic divergence very soon after the introduction of subtype F strains in South America. Moreover, through analysis of a subtype B segment present in all the CRF12_BF-like recombination structure, we estimated the circulation of the subtype B strain that gave rise to that recombinant structure around the same time period estimated for the introduction of subtype F strains. The HIV epidemics in South America were initiated in part through a founder event driven by subtype B strains coming from the previously established epidemic in the north of the continent. A second introduction driven by subtype F strains is likely to have encountered the incipient subtype B epidemic that soon after their arrival recombined with them, originating the BF epidemic in the region. These results may explain why in South America the majority of F sequences are found as BF recombinants.
A molecular study on the evolution of a subtype B variant frequently found in Brazil
In spite of the remarkable diversity of HIV-1 env genes, several amino acids are extremely conserved, probably due to functional constraints. One example is the proline found at the second position of the GPGR motif. Several viruses, however, bear substitutions at this site, for instance, GWGR subtype B variant. GWGR viruses are described in Brazil since the beginning of the epidemics, but the extent of their dispersion or the geographical origin of the variant remains unknown. In the present study, phylogenetic trees were constructed in order to study the origin and spread of this variant. All GWGR sequences as well as a subset of subtype B sequences available were included in the analyses. Analyses of differential selection were also performed on GWGR and non-GWGR sequences in order to unveil evolutionary novelties due to the action of positive selection. Although the GWGR variant was found at least in 23 countries, its expansion probably has a single origin, and Brazil is the epicenter.
PLOS One, 2011
HIV-1 CRF02_AG and subtype G (HIV-1G) account for most HIV infections in Nigeria, but their evolutionary trends have not been well documented. To better elucidate the dynamics of the epidemic in Nigeria we characterised the gag and env genes of North-Central Nigerian HIV-1 isolates from pregnant women. Of 28 samples sequenced in both genes, the predominant clades were CRF02_AG (39%) and HIV-1G (32%). Higher predicted proportion of CXCR4-tropic (X4) HIV-1G isolates was noted compared to CRF02_AG (p = 0.007, Fisher's exact test). Phylogenetic and Bayesian analysis conducted on our sequences and all the dated available Nigerian sequences on the Los Alamos data base showed that CRF02_AG and HIV-1G entered into Nigeria through multiple entries, with presence of HIV-1G dating back to early 1980s. This study underlines the genetic complexity of the HIV-1 epidemic in Nigeria, possible subtype-specific differences in co-receptor usage, and the evolutionary trends of the predominant HIV-1 strains in Nigeria, which may have implications for the design of biomedical interventions and better understanding of the epidemic.
Journal of Clinical & Cellular Immunology, 2017
Ethiopian HIV viruses were mainly HIV type C in all discordant positives and HIV/AIDS subjects. But other subtypes such as subtype A, B and recombinant A/G subtypes were also observed. Co-receptor utilization of discordant positive isolated viruses was both CCR5 and CXCR4 in equal proportion. The majority of HIV/AIDS patients used CXCR4, although about one third used CCR5 and a few also used dual co receptors. Our study showed that the majority of subtype C viruses were CXCR4/SI high/rapid subtype. And about one third was CCR5/NSI subtypes. The phylogenetic or evolutionary relationship showed that the majority of the viruses isolated from discordant positives showed sub clustering in one region and those isolated from concordant couples in another region, showing that discordant positive isolated viruses were evolving independently and were related with each other but this was not seen in viruses of concordant couples and HIV/AIDS subjects.
Journal of General …, 2011
Human immunodeficiency virus type 1 has several genetic subtypes and two coreceptor use phenotypes: R5 that uses CCR5, while X4 uses CXCR4. A high amino acid charge of the envelope glycoprotein 120 V3 region, common at positions 11 and 25, is important for CXCR4 use. We characterized charged V3 amino acids, retrieving all biologically phenotyped sequences from the HIV Sequence Database. Selecting individually unique ones randomly yielded 48 subtype A, 231 B, 180 C, 37 D and 32 CRF01_AE sequences; 482 were R5 and 46 were X4. Charged amino acids were conserved in both R5 and X4 with general and subtype-specific patterns. X4 viruses gained a higher charge from positive amino acids at positions other than in R5, and through the loss of negative amino acids. Other positions than 11/25 had a greater impact on charge (P,0.001). This describes how R5 evolves into X4 in a subtype-specific context, useful for computer-based predictions and vaccine design.