Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains

Background The HIV virus is known for its ability to exploit numerous genetic and evolutionary mechanisms to ensure its proliferation, among them, high replication, mutation and recombination rates. Sliding MinPD, a recently introduced computational method [1], was used to investigate the patterns of evolution of serially-sampled HIV-1 sequence data from eight patients with a special focus on the emergence of X4 strains. Unlike other phylogenetic methods, Sliding MinPD combines distance-based inference with a nonparametric bootstrap procedure and automated recombination detection to reconstruct the evolutionary history of longitudinal sequence data. We present serial evolutionary networks as a longitudinal representation of the mutational pathways of a viral population in a within-host environment. The longitudinal representation of the evolutionary networks was complemented with charts of clinical markers to facilitate correlation analysis between pertinent clinical information and the evolutionary relationships. Results Analysis based on the predicted networks suggests the following:: significantly stronger recombination signals (p = 0.003) for the inferred ancestors of the X4 strains, recombination events between different lineages and recombination events between putative reservoir virus and those from a later population, an early star-like topology observed for four of the patients who died of AIDS. A significantly higher number of recombinants were predicted at sampling points that corresponded to peaks in the viral load levels (p = 0.0042). Conclusion Our results indicate that serial evolutionary networks of HIV sequences enable systematic statistical analysis of the implicit relations embedded in the topology of the structure and can greatly facilitate identification of patterns of evolution that can lead to specific hypotheses and new insights. The conclusions of applying our method to empirical HIV data support the conventional wisdom of the new generation HIV treatments, that in order to keep the virus in check, viral loads need to be suppressed to almost undetectable levels.

An evaluation of depression, self-efficacy, satisfaction with life and perceived access to medical care across stages of HIV infection

This survey was designed to identify the incidence and scope of depression, satisfaction with life, self-efficacy and perceived access to medical care for those who are infected with the HIV virus. It also determined whether or not factors such as sexual orientation, ethnicity and socioeconomic status are intervening variables with respect to mental health issues. Subjects were recruited through a purposive sample from South Florida. A total of 871 surveys were used in the analysis. The overall response rate was nearly 90%. The incidence of depression was found to be higher than 75% across all stages of HIV infection. Furthermore, the incidence of depression increased as HIV disease progressed. Satisfaction with life and for the most part, self efficacy were found to decrease slightly as HIV disease progressed. Significant variance in depression, life satisfaction and self efficacy were found across stages of HIV infection. No significant differences between groups that were HIV infected were found for depression, life satisfaction and self efficacy. The severity of depression was found to vary significantly with self efficacy, life satisfaction and access to medical care but not with socioeconomic status. Life satisfaction was found to vary significantly with socioeconomic status, depression and self efficacy but not with access to medical care. Self-efficacy was found to vary significantly with socioeconomic status, depression and life satisfaction but not with access to medical care. Gender and ethnicity were not found to be significant precedent variables in depression for HIV infected individuals. Sexual orientation was found to be a significant precedent variable for depression, life satisfaction and self efficacy.