Patterns and rates of viral evolution in HIV-1 subtype B infected females and males.

Biological sex differences affect the course of HIV infection, with untreated women having lower viral loads compared to their male counterparts but, for a given viral load, women have a higher rate of progression to AIDS. However, the vast majority of data on viral evolution, a process that is clearly impacted by host immunity and could be impacted by sex differences, has been derived from men. We conducted an intensive analysis of HIV-1 gag and env-gp120 evolution taken over the first 6-11 years of infection from 8 Women's Interagency HIV Study (WIHS) participants who had not received combination antiretroviral therapy (ART). This was compared to similar data previously collected from men, with both groups infected with HIV-1 subtype B. Early virus populations in men and women were generally homogenous with no differences in diversity between sexes. No differences in ensuing nucleotide substitution rates were found between the female and male cohorts studied herein. As previously reported for men, time to peak diversity in env-gp120 in women was positively associated with time to CD4+ cell count below 200 (P = 0.017), and the number of predicted N-linked glycosylation sites generally increased over time, followed by a plateau or decline, with the majority of changes localized to the V1-V2 region. These findings strongly suggest that the sex differences in HIV-1 disease progression attributed to immune system composition and sensitivities are not revealed by, nor do they impact, global patterns of viral evolution, the latter of which proceeds similarly in women and men

Antiretroviral activity of 5-azacytidine during treatment of a HTLV-1 positive myelodysplastic syndrome with autoimmune manifestations

Myelodysplastic syndromes (MDS) are often accompanied by autoimmune phenomena. The underlying mechanisms for these associations remain uncertain, although T cell activation seems to be important. Human T-lymphotropic virus (HTLV-1) has been detected in patients with myelodysplastic syndromes, mostly in regions of the world which are endemic for the virus, and where association of HTLV-1 with rheumatological manifestation is not rare. We present here the case of a 58 year old man who presented with cytopenias, leukocytoclastic vasculitis of the skin and glomerulopathy, and was diagnosed as MDS (refractory anemia with excess blasts - RAEB 1). The patient also tested positive for HTLV-1 by PCR. After 8 monthly cycles of 5-azacytidine he achieved a complete hematologic remission. Following treatment, a second PCR for HTLV-1 was carried out and found to be negative. This is the first report in the literature of a HTLV-1-positive MDS with severe autoimmune manifestations, which was treated with the hypomethylating factor 5-azacitidine, achieving cytogenetic remission with concomitant resolution of the autoimmune manifestations, as well as HTLV-1-PCR negativity. HTLV-1-PCR negativity may be due to either immune mediated clearance of the virus, or a potential antiretroviral effect of 5-azacytidine. 5-azacytidine is known for its antiretroviral effects, although there is no proof of its activity against HTLV-1 infection in vivo

5-Azacytidine Can Induce Lethal Mutagenesis in Human Immunodeficiency Virus Type 1▿ †

Ribonucleosides inhibit human immunodeficiency virus type 1 (HIV-1) replication by mechanisms that have not been fully elucidated. Here, we report the antiviral mechanism for the ribonucleoside analog 5-azacytidine (5-AZC). We hypothesized that the anti-HIV-1 activity of 5-AZC was due to an increase in the HIV-1 mutation rate following its incorporation into viral RNA during transcription. However, we demonstrate that 5-AZC's primary antiviral activity can be attributed to its effect on the early phase of HIV-1 replication. Furthermore, the antiviral activity was associated with an increase in the frequency of viral mutants, suggesting that 5-AZC's primary target is reverse transcription. Sequencing analysis showed an enrichment in G-to-C transversion mutations and further supports the idea that reverse transcription is an antiviral target of 5-AZC. These results indicate that 5-AZC is incorporated into viral DNA following reduction to 5-aza-2′-deoxycytidine. Incorporation into the viral DNA leads to an increase in mutant frequency that is consistent with lethal mutagenesis during reverse transcription as the primary antiviral mechanism of 5-AZC. Antiviral activity and increased mutation frequency were also associated with the late phase of HIV-1 replication; however, 5-AZC's effect on the late phase was less robust. These results reveal that the primary antiviral mechanism of 5-AZC can be attributed to its ability to increase the HIV-1 mutation frequency through viral-DNA incorporation during reverse transcription. Our observations indicate that 5-AZC can affect two steps in HIV-1 replication (i.e., transcription and reverse transcription) but that its primary antiviral activity is due to incorporation during reverse transcription

Patterns and rates of viral evolution in HIV-1 subtype B infected females and males.

Biological sex differences affect the course of HIV infection, with untreated women having lower viral loads compared to their male counterparts but, for a given viral load, women have a higher rate of progression to AIDS. However, the vast majority of data on viral evolution, a process that is clearly impacted by host immunity and could be impacted by sex differences, has been derived from men. We conducted an intensive analysis of HIV-1 gag and env-gp120 evolution taken over the first 6-11 years of infection from 8 Women's Interagency HIV Study (WIHS) participants who had not received combination antiretroviral therapy (ART). This was compared to similar data previously collected from men, with both groups infected with HIV-1 subtype B. Early virus populations in men and women were generally homogenous with no differences in diversity between sexes. No differences in ensuing nucleotide substitution rates were found between the female and male cohorts studied herein. As previously reported for men, time to peak diversity in env-gp120 in women was positively associated with time to CD4+ cell count below 200 (P = 0.017), and the number of predicted N-linked glycosylation sites generally increased over time, followed by a plateau or decline, with the majority of changes localized to the V1-V2 region. These findings strongly suggest that the sex differences in HIV-1 disease progression attributed to immune system composition and sensitivities are not revealed by, nor do they impact, global patterns of viral evolution, the latter of which proceeds similarly in women and men

Inter-participant <i>env-gp120</i> phylograms.

<p>(<b>A</b>) A Phylogenetic tree of <i>env-gp120</i> for all 8 WIHS participants was inferred using RAxML [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#pone.0182443.ref051" target="_blank">51</a>] with the GTR substitution model +I +G [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#pone.0182443.ref048" target="_blank">48</a>]. External branches from the first available timepoint after infection are colored black. Branches from participants F1, F2, F3, and F7 are shaded light and dark to indicate taxa from early and late infection, respectively, when sequences from early in infection are found at opposite sides of the root node. The scale at the bottom measures genetic distances in nucleotide substitutions per site. Phylograms from each individual were rooted based on outgroup. Bootstrap values are shown along branches extending to each participant’s clade.</p

No differences in HIV-1 subtype B <i>env-C2V5</i> evolutionary rates between females and males.

<p>Intra-host <i>env-C2V5</i> (<b>A</b>) diversity at the first time point and (<b>B</b>) substitution rates for both WIHS and MACS cohorts. Substitution rates for both WIHS and MACS participants were estimated using a relaxed molecular clock model using Bayesian inference (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#sec002" target="_blank">Methods</a>). A Mann-Whitney U test was used to test for sex differences. Horizontal bars show the median and interquartile range. 95% HPD is the highest posterior density interval. HPM mean is the evolutionary rate (and 95% HPD) estimated using a hierarchical phylogenetic model applied across the group. Evolutionary rates were defined as nucleotide substitutions/site/year. A non-parametric Mann-Whitney U test was used to test differences between unmatched groups. (<b>C</b> and <b>D</b>) Evolutionary rates from (B) broken out by individual. ESS values were > 200 for meanRate in the analysis of 8/8 <i>env-C2V5</i> WIHS and 10/11 <i>env-C2V5</i> MACS BEAST simulations.</p

Correlates of disease progression and patterns of selection in the WIHS cohort.

<p>(<b>A</b>) Average pairwise diversity in <i>env-gp120</i> was estimated for each timepoint and is shown relative to peak diversity in each participant. (<b>B</b>) CD4⁺ T cell counts were placed relative to the time to peak diversity in <i>env-gp120</i>. The dashed horizontal line indicates the 200 CD4⁺ T cell count per mm³ AIDS-defining threshold. (<b>C</b>) The association between the time CD4+ T cells dropped below 200 per mm³ and the time of peak <i>env-gp120</i> diversity. Participants F4 and F7 were not included as virus had no observable peak in average pairwise diversity during the period of follow up. (<b>D</b>) Average pairwise diversity in <i>gag</i> for each timepoint is shown relative to the time of peak diversity in each participant. No peak was observed except for Subject F3. (<b>E</b>, <b>F</b>) The average pairwise ratio of nonsynonymous (<i>d</i>_<i>N</i>) to synonymous (<i>d</i>_<i>S</i>) substitutions per site at each timepoint compared to the inferred founder strain (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182443#sec002" target="_blank">Methods</a> section) for <i>gag</i> and <i>env-gp120</i>, respectively, for each participant. Associations were assessed using the Spearman’s correlation test.</p