Influence of CD4+ T cell counts on viral evolution in HIV-infected individuals undergoing suppressive HAART

Impact of Clinical Parameters in the Intrahost Evolution of HIV-1 Subtype B in Pediatric Patients: A Machine Learning Approach

Determining the factors modulating the genetic diversity of HIV-1 populations is essential to understand viral evolution. This study analyzes the relative importance of clinical factors in the intrahost HIV-1 subtype B (HIV-1B) evolution and in the fixation of drug resistance mutations (DRM) during longitudinal pediatric HIV-1 infection. We recovered 162 partial HIV-1B pol sequences (from 3 to 24 per patient) from 24 perinatally infected patients from the Madrid Cohort of HIV-1 infected children and adolescents in a time interval ranging from 2.2 to 20.3 years. We applied machine learning classification methods to analyze the relative importance of 28 clinical/epidemiological/virological factors in the HIV-1B evolution to predict HIV-1B genetic diversity (d), nonsynonymous and synonymous mutations (dN, dS) and DRM presence. Most of the 24 HIV-1B infected pediatric patients were Spanish (91.7%), diagnosed before 2000 (83.3%), and all were antiretroviral therapy experienced. They had from 0.3 to 18.8 years of HIV-1 exposure at sampling time. Most sequences presented DRM. The best-predictor variables for HIV-1B evolutionary parameters were the age of HIV-1 diagnosis for d, the age at first antiretroviral treatment for dN and the year of HIV-1 diagnosis for ds. The year of infection (birth year) and year of sampling seemed to be relevant for fixation of both DRM at large and, considering drug families, to protease inhibitors (PI). This study identifies, for the first time using machine learning, the factors affecting more HIV-1B pol evolution and those affecting DRM fixation in HIV-1B infected pediatric patients.

Clinical Determinants of HIV-1B Between-Host Evolution and their Association with Drug Resistance in Pediatric Patients

Understanding the factors that modulate the evolution of virus populations is essential to design efficient control strategies. Mathematical models predict that factors affecting viral within-host evolution may also determine that at the between-host level. Although HIV-1 within-host evolution has been associated with clinical factors used to monitor AIDS progression, such as patient age, CD4 cells count, viral load, and antiretroviral experience, little is known about the role of these clinical factors in determining between-host HIV-1 evolution. Moreover, whether the relative importance of such factors in HIV-1 evolution vary in adult and children patients, in which the course of infection is different, has seldom been analysed. To address these questions, HIV-1 subtype B (HIV-1B) pol sequences of 163 infected children and 450 adults of Madrid, Spain, were used to estimate genetic diversity, rates of synonymous and non-synonymous mutations, selection pressures and frequency of drug-resistance mutations (DRMs). The role and relative importance of patient age, %CD4, CD4/mm3, viral load, and antiretroviral experience in HIV-1B evolution was analysed. In the pediatric HIV-1B population, three clinical factors were primary predictors of virus evolution: Higher HIV-1B genetic diversity was observed with increasing children age, decreasing CD4/mm3 and upon antiretroviral experience. This was mostly due to higher rates of non-synonymous mutations, which were associated with higher frequency of DRMs. Using this data, we have also constructed a simple multivariate model explaining between 55% and 66% of the variance in HIV-1B evolutionary parameters in pediatric populations. On the other hand, the analysed clinical factors had little effect in adult-infecting HIV-1B evolution. These findings highlight the different evolutionary dynamics of HIV-1B in children and adults, and contribute to understand the factors shaping HIV-1B evolution and the appearance of drug-resistance mutation in pediatric patients.

Correlation between CD4 T cell counts and virus compartmentalization in genital and systemic compartments of HIV-infected females

The majority of infection by the human immunodeficiency virus (HIV-1) across the world occurs by heterosexual transmission and is likely mediated by virus present in genital secretions. In spite of this, infection is followed by clinical markers of the virus present in blood, which may not be representative of the virus involved in transmission. In fact, several studies have demonstrated that the genital tract represents a unique compartment for the virus. We assessed the relationship between immune system integrity, represented by CD4+ T cell counts, and the maintenance of viral compartmentalization between plasma and vaginal fluid virus in treatment naïve women from the Dominican Republic infected by the heterosexual transmission route. We cloned and sequenced cell free virus from plasma and genital fluid samples from six women to assess viral evolution, phylogenetic relatedness, and calculated co-receptor use for the C2V3 region of the envelope. Our analyses demonstrated plasma and vaginal fluid virus compartments remained intact only in samples from women with CD4+ T cell counts over 350 cells/μl. The majority of viral forms were predicted to use the CCR5 co-receptor, although several dual tropic forms were also identified. None of the clones were found to use the CXCR4 co-receptor even though many of the patients showed severe disease. Our findings lend further support to the role of an intact immune system in maintaining compartmentalization across blood and genital quasispecies and provide a compelling rationale to specifically consider genital tract viral forms in therapeutic and vaccine research.

Colon M, Porrata-Doria T, Johnston ICD, Lorenzo E. Characterization of HIV-1 RNA forms in the plasma of patients undergoing successful HAART

An assay to characterize plasma human immunodeficiency virus 1 (HIV-1) sequences for patients with low viral loads was developed by combining the selective binding of anti-CD44 MicroBeads with a nested RT-PCR targeting the env C2V4 region. Sequences were obtained from 10 of 20 HIV+ patients who had viral loads below 48 copies/ml. Sequences derived from plasma were compared to those from CD14+ CD16 +monocytes and CD4+ T cells. The plasma sequences were most closely related to those amplified from monocytes, suggesting that during successful antiretroviral therapy, the predominant plasma virus originates from myeloid cells. By characterizing HIV-1 RNA sequences from 8 ml of plasma while avoiding multiple steps, which can lead to contamination and deterioration, this method can help elucidate the viral forms in patients with therapeutically suppressed HIV-1. Understanding the source of residual viremia is crucial in developing approaches for viral eradication.

Short communication: Human blood dendritic cells are infected separately from monocytes in HIV type 1 patients

Monocytes serve as a systemic reservoir of myeloid precursors for the renewal of tissue macrophages and dendritic cells (DCs). Both monocytes and dendritic cells can be infected with HIV-1. Circulating DCs are believed to be derived from a common precursor of monocytes, or, in the case of inflammatory challenge, from monocytes directly. Because there are fewer infected blood monocytes than infected cells after differentiation, we hypothesized that the majority of HIV-1 infection in circulating DCs occurs via direct viral binding to their CD4 and coreceptors after differentiation. We isolated monocytes at one time point and circulating dendritic cells at a second time point from the blood of HIV-1-infected patients. Proviral DNA was isolated from DCs and monocytes, and the C2-V4 region of the HIV-1 env gene was cloned and sequenced. Phylogeny, nucleotide distances, and glycosylation patterns of the env gene were performed. The phylogenetic trees revealed that viral forms from the monocytes clustered distantly from the quasispecies derived from circulating DCs. The nucleotide distances and differing glycosylation patterns suggest that the infection of DCs is independent of the infection of the monocytes.

HIV-1 infection of monocytes is directly related to the success of HAART

Macrophages are recognized cellular compartments involved in HIV infection; however, the extent to which precursor monocytes are infected in vivo and its significance remains poorly understood. Our aim was to analyze the contribution of monocytes to HIV infection in vivo. PCR assays did not detect HIV-1 proviral DNA in monocytes of HAART-suppressed patients. Monocyte-derived macrophages from individuals under suppressive HAART did not show evidence of harboring HIV, thereby, minimizing the possibility of infection by the integration of sequestered virus after differentiation. These results suggest that the infection of permissive monocytes is directly related to the success of HAART (p<0.001). HIV-1 env was characterized from patients under sub-optimal HAART and hence, with infected monocytes. Sequence analyses showed a consistent relationship between monocytes and plasma virus. Altogether, we found that in suppressive HAART, neither monocytes nor Monocyte-derived macrophages-harbored HIV.

Correlation between SIV Tat evolution and AIDS progression in cerebrospinal fluid of morphine-dependent and control macaques infected with SIV and SHIV

Morphine abuse has been associated with higher virus replication and accelerated disease progression in a non-human primate model of AIDS. In our previous report, we have shown that 50% of morphine-addicted macaques progress rapidly and that 2/3 of the rapid progressors exhibit severe neuropathogenesis. In this report, we examined the sequence evolution of the SIV Tat protein, known to participate in AIDS neuropathology, in the cerebrospinal fluid (CSF) of morphine-dependent and control macaques over the first 20 weeks of infection. The CSF SIV Tat evolution was found to be inversely related with disease progression, and the highly neuropathogenic inoculum clone sequence was the prevalent CSF form in rapid progressors. Divergence from the inoculum clone was significantly greater in both morphine-dependent normal progressors and control macaques than in the morphine-dependent rapid progressors. Furthermore, we also found evidence of a trend that morphine alters the type of mutation, resulting in an enhanced ratio of transitions to transversions (Ts:Tv). Rapid disease exacerbates this trend and appears to influence the distribution of nonsynonymous changes in the first exon of SIV tat, with a clear majority of mutations occurring in the C-terminal half of the protein where the known functionally important domains reside. Thus, morphine abuse may change the nature and extent of mutations that drive viral evolution.

Virus replication and disease progression inversely correlate with SIV tat evolution in morphine-dependent and SIV/SHIV-infected Indian rhesus macaques

We analyzed the association between evolution of the 5' exon of tat and disease progression in an SIV/SHIV macaque model of opiate dependence and AIDS. Cloned tat sequences were obtained by RT-PCR amplification of 3 plasma viruses (recovered at different times) from 6 morphine-dependent and 2 control Indian rhesus macaques inoculated with SHIV(KU-1B) SHIV(89.6P) and SIV/17E-Fr. Approximately ten clones were sequenced for each animal per time point for use in phylogenetic analyses. We found a strong, significant inverse correlation between disease progression and tat diversity in plasma by 20 weeks post-infection. The morphine-dependent macaques developed 2 distinct disease patterns - rapid progressor (Group A) and slow progressor (Group B) - whereas control animals developed into slow progressor only (Group C). The three animals in Group A exhibited approximately 40% (P = 0.01) and approximately 50% (P = 0.028) less diversity than Group B and C animals, respectively, over the 20 weeks. Furthermore, the Group A macaques showed a prominent reemergence of the wild-type SV17E tat sequence used in the inoculum that coincided with disease progression. This suggests that the virus from the original infection represented the most pathogenic form among all animals in these cohorts throughout the first 20 weeks of infection. We were unable to support or rule out a role for immune pressure on tat evolution based on the spectrum of sequence changes in the data set. Thus, in the short duration of this study, the Tat-specific immune pressure cannot explain the different disease outcomes of the six morphine animals nor of the two controls. Our results also suggest that in vivo morphine dependence can contribute to the pathogenesis of SIV/SHIV infection and that it may do so in conjunction with the evolution of viral proteins, such as Tat.