Viral Diversity and Diversification of Major Non-Structural Genes vif, vpr, vpu, tat exon 1 and rev exon 1 during Primary HIV-1 Subtype C Infection

To assess the level of intra-patient diversity and evolution of HIV-1C non-structural genes in primary infection, viral quasispecies obtained by single genome amplification (SGA) at multiple sampling timepoints up to 500 days post-seroconversion (p/s) were analyzed. The mean intra-patient diversity was 0.11% (95% CI; 0.02 to 0.20) for vif, 0.23% (95% CI; 0.08 to 0.38) for vpr, 0.35% (95% CI; −0.05 to 0.75) for vpu, 0.18% (95% CI; 0.01 to 0.35) for tat exon 1 and 0.30% (95% CI; 0.02 to 0.58) for rev exon 1 during the time period 0 to 90 days p/s. The intra-patient diversity increased gradually in all non-structural genes over the first year of HIV-1 infection, which was evident from the vif mean intra-patient diversity of 0.46% (95% CI; 0.28 to 0.64), vpr 0.44% (95% CI; 0.24 to 0.64), vpu 0.84% (95% CI; 0.55 to 1.13), tat exon 1 0.35% (95% CI; 0.14 to 0.56 ) and rev exon 1 0.42% (95% CI; 0.18 to 0.66) during the time period of 181 to 500 days p/s. There was a statistically significant increase in viral diversity for vif (p = 0.013) and vpu (p = 0.002). No associations between levels of viral diversity within the non-structural genes and HIV-1 RNA load during primary infection were found. The study details the dynamics of the non-structural viral genes during the early stages of HIV-1C infection

HIV-1 subtype C phylogenetic relationship and diversity of HIV non-structural genes is consistent with the multiplicity of HIV-1 infection determined by analysis of the <i>env</i>/<i>gag</i> genes.

<p>A maximum likelihood phylogenetic tree was reconstructed using Fastree2 (Price <i>et al</i>., 2010) using the GTR+G model for nucleotide substitution and visualized in Figtree v.1.1.3 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035491#pone.0035491-Rambaut1" target="_blank">[54]</a>. Alternative likelihood ratio tests <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035491#pone.0035491-Anisimova1" target="_blank">[55]</a> >0.95 are shown by an asterisk. Subjects infected with multiple viral variants are colored red. Patient B and D subtrees (individual trees on grey background) show branching topology of earliest sampling (0–90 days p/s) and represent examples of single (subject B) and multiple (subject D) HIV-1 transmission.</p

HIV-1C diversity, mean and 95% confidence intervals for non-structural genes <i>vif</i>, <i>vpr</i>, <i>vpu</i>, <i>tat</i> exon 1 and <i>rev</i> exon 1 over the first 500 days p/s.

<p>Viral diversity for each subject was calculated using maximum composite likelihood model <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035491#pone.0035491-Tamura2" target="_blank">[56]</a>.</p

HIV-1 subtyping by analysis of phylogenetic relationships of HIV-1 non-structural genes.

<p>The analyzed region of HIV-1 genome corresponded to nucleotide positions 5,041 to 6,310 in HXB2. Three sequences were randomly selected for each study subject (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035491#s2" target="_blank">Methods</a>). A phylogenetic tree was inferred by Mr. Bayes using GTR model. The convergence was reached after 10 M MCMC run. The consensus tree was visualized in Figtree v.1.3.1 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035491#pone.0035491-Rambaut1" target="_blank">[54]</a>. Clade credibility values of >0.95 shown by asterisk, Subtype D cluster showed the support of 0.93 indicated by + symbol. HIV-1 subtype C reference sequences are shown as blue circles. All non-subtype C group M reference sequences are shown at the bottom of the phylogenetic tree. SIV sequence (CPZ.CM98.CAM3.AF115393) was used as an outgroup.</p

Individual distribution of pairwise distances for each of the non-stuctural genes,<i>vif</i> (HXB2 start 5041 to 5619), <i>vpr</i> (HXB2 start 5559 to 5850), <i>vpu</i> (HXB2 start 6062 to 6310), <i>tat</i> exon 1 (HXB2 start 5831 to 6045), and <i>rev</i> exon 1(HXB2 start 5970 to 6045).

<p>Individual distribution of pairwise distances for each of the non-stuctural genes,<i>vif</i> (HXB2 start 5041 to 5619), <i>vpr</i> (HXB2 start 5559 to 5850), <i>vpu</i> (HXB2 start 6062 to 6310), <i>tat</i> exon 1 (HXB2 start 5831 to 6045), and <i>rev</i> exon 1(HXB2 start 5970 to 6045).</p

Molecular characterisation of hepatitis B virus in HIV-1 subtype C infected patients in Botswana

Background: Hepatitis B virus (HBV) is a major global health problem especially in sub-Saharan Africa and in East Asia. Ten hepatitis B virus genotypes have been described that differ by geographic distribution, disease progression, and response to treatment. Escape mutations within the surface open reading frame (ORF) affect HBV antigenicity leading to failures in diagnosis, vaccine and hepatitis B immunoglobulin therapy. However, the molecular characteristics of HBV in Botswana, a highly endemic country, are unknown. We describe the molecular characteristics of HBV and prevalence of escape mutants among HIV/HBV coinfected individuals Botswana. Methods: DNA was extracted from archived plasma samples from 81 HIV/HBV co-infected participants from various clinical studies at the Botswana Harvard AIDS Institute Partnership. A 415 base pair (bp) fragment of the polymerase gene was amplified by semi-nested PCR. In a subset of samples, a 2100 bp fragment was amplified. The PCR product was genotyped using Big Dye sequencing chemistry and the sequences were analysed for genotypes and mutations. Results: Of the 81 samples included, 70 (86 %) samples were successfully genotyped. Genotype A was found in 56 (80 %) participants, D in 13 (18.6 %), and 1 (1.4 %) was genotype E. Escape mutations previously linked with failure of diagnosis or escaping active vaccination and passive immunoglobulin therapy were detected in 12 (17.1 %) participants at positions 100, 119, 122, 123, 124, 126, 129, 130, 133, 134 and 140 of the S ORF. Genotypes and escape mutations were not significantly associated with aspartate aminotransferase (AST), alanine aminotransferase (ALT) and AST platelet ratio index (APRI). Conclusion: Genotypes A, D and E were found in this cohort of HIV coinfected patients in Botswana, consistent with the findings from the sub-Saharan Africa region. Some escape mutations which have previously been associated with diagnosis failure, escaping vaccine and immunoglobulin therapy were also observed and are important in guiding future policies related to vaccine implementation, therapeutic guidelines, and diagnostic guidelines. They are also important for identifying patients who are at an increased risk of disease progression and to choose optimal therapy. Future research should focus on determining the clinical significance of the different HBV genotypes and mutations found in this population

Slow CD4+ T-Cell Recovery in Human Immunodeficiency Virus/Hepatitis B Virus-Coinfected Patients Initiating Truvada-Based Combination Antiretroviral Therapy in Botswana

Background. Hepatitis B virus (HBV) and human immunodeficiency virus (HIV) coinfection has emerged as an important cause of morbidity and mortality. We determined the response to Truvada-based first-line combination antiretroviral therapy (cART) in HIV/HBV-coinfected verus HIV-monoinfected patients in Botswana. Methods. Hepatitis B virus surface antigen (HBsAg), HBV e antigen (HBeAg), and HBV deoxyribonucleic acid (DNA) load were determined from baseline and follow-up visits in a longitudinal cART cohort of Truvada-based regimen. We assessed predictors of HBV serostatus and viral suppression (undetectable HBV DNA) using logistic regression techniques. Results. Of 300 participants, 28 were HBsAg positive, giving an HIV/HBV prevalence of 9.3% (95% confidence interval [CI], 6.3–13.2), and 5 of these, 17.9% (95% CI, 6.1–36.9), were HBeAg positive. There was a reduced CD4+ T-cell gain in HIV/HBV-coinfected compared with HIV-monoinfected patients. Hepatitis B virus surface antigen and HBeAg loss was 38% and 60%, respectively, at 24 months post-cART initiation. The HBV DNA suppression rates increased with time on cART from 54% to 75% in 6 and 24 months, respectively. Conclusions. Human immunodeficiency virus/HBV coinfection negatively affected immunologic recovery compared with HIV-1C monoinfection. Hepatitis B virus screening before cART initiation could help improve HBV/HIV treatment outcomes and help determine treatment options when there is a need to switch regimens

In Silico Analysis of Hepatitis B Virus Occult Associated Mutations in Botswana Using a Novel Algorithm

Occult hepatitis B infections (OBI) represent a reservoir of undiagnosed and untreated hepatitis B virus (HBV), hence the need to identify mutations that lead to this phenotype. Functionally characterizing these mutations by in vitro studies is time-consuming and expensive. To bridge this gap, in silico approaches, which predict the effect of amino acid (aa) variants on HBV protein function, are necessary. We developed an algorithm for determining the relevance of OBI-associated mutations using in silico approaches. A 3 kb fragment of subgenotypes A1 and D3 from 24 chronic HBV-infected (CHB) and 24 OBI participants was analyzed. To develop and validate the algorithm, the effects of 68 previously characterized occult-associated mutations were determined using three computational tools: PolyPhen2, SNAP2, and PROVEAN. The percentage of deleterious mutations (with impact on protein function) predicted were 52 (76.5%) by PolyPhen2, 55 (80.9%) by SNAP2, and 65 (95.6%) by PROVEAN. At least two tools correctly predicted 59 (86.8%) mutations as deleterious. To identify OBI-associated mutations exclusive to Botswana, study sequences were compared to CHB sequences from GenBank. Of the 43 OBI-associated mutations identified, 26 (60.5%) were predicted by at least two tools to have an impact on protein function. To our knowledge, this is the first study to use in silico approaches to determine the impact of OBI-associated mutations, thereby identifying potential candidates for functional analysis to facilitate mechanistic studies of the OBI phenotype