Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

Deep sequencing technologies have the potential to transform the study of highly variable viral pathogens by providing a rapid and cost-effective approach to sensitively characterize rapidly evolving viral quasispecies. Here, we report on a high-throughput whole HIV-1 genome deep sequencing platform that combines 454 pyrosequencing with novel assembly and variant detection algorithms. In one subject we combined these genetic data with detailed immunological analyses to comprehensively evaluate viral evolution and immune escape during the acute phase of HIV-1 infection. The majority of early, low frequency mutations represented viral adaptation to host CD8+ T cell responses, evidence of strong immune selection pressure occurring during the early decline from peak viremia. CD8+ T cell responses capable of recognizing these low frequency escape variants coincided with the selection and evolution of more effective secondary HLA-anchor escape mutations. Frequent, and in some cases rapid, reversion of transmitted mutations was also observed across the viral genome. When located within restricted CD8 epitopes these low frequency reverting mutations were sufficient to prime de novo responses to these epitopes, again illustrating the capacity of the immune response to recognize and respond to low frequency variants. More importantly, rapid viral escape from the most immunodominant CD8+ T cell responses coincided with plateauing of the initial viral load decline in this subject, suggestive of a potential link between maintenance of effective, dominant CD8 responses and the degree of early viremia reduction. We conclude that the early control of HIV-1 replication by immunodominant CD8+ T cell responses may be substantially influenced by rapid, low frequency viral adaptations not detected by conventional sequencing approaches, which warrants further investigation. These data support the critical need for vaccine-induced CD8+ T cell responses to target more highly constrained regions of the virus in order to ensure the maintenance of immunodominant CD8 responses and the sustained decline of early viremia

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Tricks of the Trade: Sexual Health Behaviors, the Context of HIV Risk, and Potential Prevention Intervention Strategies for Male Sex Workers

Sex work is a significant risk for HIV and sexually transmitted infection (STI) among men who have sex with men (MSM); however, there is a dearth of knowledge about how to reduce risk in this group. MSM sex workers (N = 32) completed a semistructured qualitative interview and a close-ended quantitative assessment. Analyses focused on themes relevant to intervention development. Participants reported an average of 46 male sex partners in the prior 12 months; 31% of participants were HIV-infected. Male sex workers frequently used substances during sex and had elevated levels of psychological distress. Qualitative findings suggest that trauma-informed mental health and substance abuse treatment, ready access to HIV/STI testing and treatment and condoms/informational materials, support groups to address isolation/loneliness, skill-building for risk reduction with sex partners, and paid incentives as add-ons to effective behavior change interventions may be valuable intervention components. Targeting consumers of paid/exchanged sex may assist with changing community norms regarding the practice of transactional sex. Multipronged interventions to decrease sexual risk taking among male sex workers would also benefit from addressing the unique socioeconomic and legal needs of this population

Optimizing Pre-Exposure Antiretroviral Prophylaxis Adherence in Men Who Have Sex with Men: Results of a Pilot Randomized Controlled Trial of "Life-Steps for PrEP"

Antiretroviral pre-exposure prophylaxis (PrEP) has been demonstrated to decrease HIV acquisition in multiple efficacy trials, but medication adherence is critical, and was suboptimal in several studies. Fifty HIV-uninfected at risk men who have sex with men (MSM) were randomized to a cognitive behavioral intervention condition or a time and session-matched comparison counseling intervention. The experimental intervention entailed four nurse-delivered initial and two booster sessions based on Life-Steps, an ART treatment adherence intervention. The comparison condition provided information and supportive counseling. The primary analyses compared adherence (Wisepill and tenofovir plasma levels) at 3 and 6 months. Fifty-eight MSM were screened to enroll 50 participants. Median age was 38.2 years old, 86% were white; 64% had completed college. Wisepill adherence was high in both groups, and not statistically different. Plasma tenofovir levels were significantly higher in the intervention group at 6 months using mean substitution analysis (i.e., computing missing variables) (p = 0.037), however, in the completer analyses (i.e., using only those completing all study visits), there were no statistically significant differences between randomization conditions. Medication adherence was high across a cognitive-behavioral (Life-Steps) and time-matched counseling intervention for PrEP adherence, with some evidence suggesting superiority of Life-Steps in this pilot RCT. Further evaluation in a fully powered efficacy trial is warranted to assess the robustness of this intervention

Street Workers and Internet Escorts: Contextual and Psychosocial Factors Surrounding HIV Risk Behavior among Men Who Engage in Sex Work with Other Men

Sex work has been associated with elevated risk for HIV infection among men who have sex with men (MSM) in many settings. This mixed methods study examined sexual risk among MSM sex workers in Massachusetts, collecting formative data on HIV risk behavior by sex worker type in order to gain a better understanding of how to tailor prevention interventions to this unique and high-risk subgroup of MSM. Two groups of MSM sex workers were recruited between January and March 2008: street workers (n = 19) and internet escorts (n = 13). Participants completed a semistructured qualitative interview and quantitative psychosocial assessment battery; interviews were conducted until redundancy in responses was achieved. Almost one third (31%) were HIV-infected. The majority of participants (69%) reported at least one episode of unprotected serodiscordant anal sex (either insertive or receptive) with a mean of 10.7 (SD = 42.2) male sex partners of an unknown or different HIV serostatus in the past 12 months. Salient findings included: (a) internet sex workers reported being paid substantially more for sex than street sex workers; (b) inconsistent condom use, high rates of unprotected sex, and low rates of HIV status disclosure with sex work partners for both internet and street workers; general perceptions of a lack of trust on the part of sex work partners (i.e., telling them what they want to hear), offers of more money for unprotected sex; (c) contextual differences in risk taking: internet sex workers reported that they are more likely to engage in sexual risk-taking with noncommercial sex partners than sex partners who pay; (d) HIV status and STI history: two street workers became infected in the context of sex work, and 25% of the entire sample had never been tested for sexually transmitted infections (STI); and (e) motivations and reasons for doing sex work, such as the “lucrativeness” of sex work, as a means to obtain drugs, excitement, power, “why not?” attitude, and because social norms modeled this behavior. Study findings can be used to generate hypotheses for designing and providing tailored primary and secondary prevention interventions for this at-risk subgroup of MSM

Impacts of Climate Change on the Global Invasion Potential of the African Clawed Frog Xenopus laevis

International audienceBy altering or eliminating delicate ecological relationships, non-indigenous species are con- sidered a major threat to biodiversity, as well as a driver of environmental change. Global cli- mate change affects ecosystems and ecological communities, leading to changes in the phenology, geographic ranges, or population abundance of several species. Thus, predicting the impacts of global climate change on the current and future distribution of invasive species is an important subject in macroecological studies. The African clawed frog (Xenopus laevis), native to South Africa, possesses a strong invasion potential and populations have become established in numerous countries across four continents. The global invasion potential of X. laevis was assessed using correlative species distribution models (SDMs). SDMs were com- puted based on a comprehensive set of occurrence records covering South Africa, North America, South America and Europe and a set of nine environmental predictors. Models were built using both a maximum entropy model and an ensemble approach integrating eight algo- rithms. The future occurrence probabilities for X. laevis were subsequently computed using bioclimatic variables for 2070 following four different IPCC scenarios. Despite minor differ- ences between the statistical approaches, both SDMs predict the future potential distribution of X. laevis, on a global scale, to decrease across all climate change scenarios. On a conti- nental scale, both SDMs predict decreasing potential distributions in the species’ native range in South Africa, as well as in the invaded areas in North and South America, and in Australia where the species has not been introduced. In contrast, both SDMs predict the potential range size to expand in Europe. Our results suggest that all probability classes will be equally affected by climate change. New regional conditions may promote new invasions or the spread of established invasive populations, especially in France and Great Britain

Comparison of sequence variant quantification by 454 deep sequencing and by PCR cloning/sequencing.

<p>Orthogonal regression of variant frequency estimates obtained by 454 and clonal sequence data across the highly variable 1544 nucleotide region spanning Vif to Tat in subject 9213 (slope = 1.01; 95% CI, 0.73 to 1.40).</p

Rapidly expanding sequence diversity during HIV-1 infection.

<p>Heat maps illustrate sites exhibiting amino acid sequence diversity at days 0, 3, 59, 165, 476 and 1543 post-presentation. Plotted is the percentage of amino acid diversity at each position with respect to the dominant baseline (day 0) amino acid residue. All 3174 amino acids of HIV-1 are represented, with the first amino acid of Gag located in the top left corner of the grid and the last amino acid of Nef located in the bottom right corner. Completely conserved residues are <i>dark blue</i>, low-level variant residues (<10% divergent from baseline) are <i>light blue</i>, moderately variable residues (10–50%) in <i>orange</i>, and highly variant residues (>50%) in <i>red</i>. (<b>A</b>) 0 days p.p., (<b>B</b>) 3 days p.p., (<b>C</b>) 59 days p.p., (<b>D</b>) 165 days p.p., (<b>E</b>) 476 days p.p., (<b>F</b>) 1543 days p.p..</p

Limited evolution in the HIV-1 proteome prior to establishment of viral set point.

<p>Sequence diversity is plotted for all evolving codons in each HIV-1 protein as the percent of sequences with an amino acid residue different from the dominant baseline residue. Colored lines denote individual evolving amino acid residues within each protein. The time of infection prior to the establishment of viral set point (day 165) is highlighted in <i>grey</i>.</p

Viral escape from acute and chronic phase CD8+ T cell responses.

<p>Stacked heat-maps illustrate variant codon frequencies over time for each residue of the CD8 epitopes targeted by subject 9213. Shown are epitopes targeted during the acute (Day 59) and chronic (Day 476) phases of HIV-1 infection. The baseline sequence is shown at the top of each epitope, with non-HIV-1B consensus residues highlighted in <i>blue</i>. The magnitude of each response is shown in SFC per million PBMC.</p