Has the rate of progression to AIDS changed in recent years?

The phylogenomics of evolving virus virulence

How virulence evolves after a virus jumps to a new host species is central to disease emergence. Our current understanding of virulence evolution is based on insights drawn from two perspectives that have developed largely independently: long-standing evolutionary theory based on limited real data examples that often lack a genomic basis, and experimental studies of virulence-determining mutations using cell culture or animal models. A more comprehensive understanding of virulence mutations and their evolution can be achieved by bridging the gap between these two research pathways through the phylogenomic analysis of virus genome sequence data as a guide to experimental study.

Temporal trends in prognostic markers of HIV-1 virulence and transmissibility: an observational cohort study

BACKGROUND

Measures of CD4 T-cell count and HIV-1 plasma viral load before antiretroviral therapy are proxies for virulence. Whether these proxies are changing over time has implications for prevention and treatment. The aim of this study was to investigate those trends.

METHODS

Data were derived from the Concerted Action on SeroConversion to AIDS and Death in Europe (CASCADE) collaboration of mainly European seroconverter cohorts. Longitudinal CD4 cell counts and plasma viral load measurements before the initiation of antiretroviral therapy or AIDS onset were analysed by use of linear or fractional polynomials mixed models adjusting for all available potential confounders. Calendar time effects were modelled through natural cubic splines.

FINDINGS

15 875 individuals seroconverting from 1979 to 2008 fulfilled the inclusion criteria; 3215 (20·3%) were women; median follow-up was 31 months (IQR 14-62); dropout before starting antiretroviral therapy or AIDS onset was 8·1%. Estimated CD4 counts at seroconversion for a typical individual declined from about 770 cells per μL (95% CI 750-800) in the early 1980s to a plateau of about 570 cells per μL (555-585) after 2002. CD4 cell rate of loss increased up to 2002. Estimated set-point plasma viral loads increased from 4·05 log10 copies per mL (95% CI 3·98-4·12) in 1980 to 4·50 log10 copies per mL (4·45-4·54) in 2002 with a tendency of returning to lower loads thereafter. Results were similar when we restricted analyses to various subsets, including adjusting for plasma viral load assay, censored follow-up at 3 years, or used variations of the main statistical approach.

INTERPRETATION

Our results provide strong indications of increased HIV-1 virulence and transmissibility during the course of the epidemic and a potential plateau effect after about 2002.

FUNDING

European Union Seventh Framework Programme.

The contribution of viral genotype to plasma viral set-point in HIV infection

Disease progression in HIV-infected individuals varies greatly, and while the environmental and host factors influencing this variation have been widely investigated, the viral contribution to variation in set-point viral load, a predictor of disease progression, is less clear. Previous studies, using transmission-pairs and analysis of phylogenetic signal in small numbers of individuals, have produced a wide range of viral genetic effect estimates. Here we present a novel application of a population-scale method based in quantitative genetics to estimate the viral genetic effect on set-point viral load in the UK subtype B HIV-1 epidemic, based on a very large data set. Analyzing the initial viral load and associated pol sequence, both taken before anti-retroviral therapy, of 8,483 patients, we estimate the proportion of variance in viral load explained by viral genetic effects to be 5.7% (CI 2.8-8.6%). We also estimated the change in viral load over time due to selection on the virus and environmental effects to be a decline of 0.05 log10 copies/mL/year, in contrast to recent studies which suggested a reported small increase in viral load over the last 20 years might be due to evolutionary changes in the virus. Our results suggest that in the UK epidemic, subtype B has a small but significant viral genetic effect on viral load. By allowing the analysis of large sample sizes, we expect our approach to be applicable to the estimation of the genetic contribution to traits in many organisms.

Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission

OBJECTIVE

The potential for changing HIV-1 virulence has significant implications for the AIDS epidemic, including changing HIV transmission rates, rapidity of disease progression, and timing of ART. Published data to date have provided conflicting results.

DESIGN

We conducted a meta-analysis of changes in baseline CD4(+) T-cell counts and set point plasma viral RNA load over time in order to establish whether summary trends are consistent with changing HIV-1 virulence.

METHODS

We searched PubMed for studies of trends in HIV-1 prognostic markers of disease progression and supplemented findings with publications referenced in epidemiological or virulence studies. We identified 12 studies of trends in baseline CD4(+) T-cell counts (21, 052 total individuals), and eight studies of trends in set point viral loads (10 ,785 total individuals), spanning the years 1984-2010. Using random-effects meta-analysis, we estimated summary effect sizes for trends in HIV-1 plasma viral loads and CD4(+) T-cell counts.

RESULTS

Baseline CD4(+) T-cell counts showed a summary trend of decreasing cell counts [effect = -4.93  cells/μl per year, 95% confidence interval (CI) -6.53 to -3.3]. Set point viral loads showed a summary trend of increasing plasma viral RNA loads (effect = 0.013  log(10)  copies/ml per year, 95% CI -0.001 to 0.03). The trend rates decelerated in recent years for both prognostic markers.

CONCLUSION

Our results are consistent with increased virulence of HIV-1 over the course of the epidemic. Extrapolating over the 30 years since the first description of AIDS, this represents a CD4(+) T cells loss of approximately 148  cells/μl and a gain of 0.39  log(10)  copies/ml of viral RNA measured during early infection. These effect sizes would predict increasing rates of disease progression, and need for ART as well as increasing transmission risk.

No evidence of a change in HIV-1 virulence since 1996 in France

OBJECTIVE

We investigated temporal trends in the CD4 cell count and in plasma HIV RNA and total HIV DNA levels measured at the time of primary HIV infection, as proxies for HIV-1 virulence, taking changes in patient characteristics into account.

DESIGN

We studied 903 patients enrolled during primary HIV infection in the French multicenter ANRS PRIMO cohort from 1996 to 2007.

METHODS

Associations between the year of primary HIV infection and the values of the three markers were tested with regression models. The year of primary HIV infection was first introduced as a restricted cubic splines function in a regression model in order to explore the shape of the associations, and then as a continuous/categorical variable. The following confounders were considered in multiple regression analysis: time since infection and age (introduced as restricted cubic spline functions), sex, place of birth (Africa vs. others), symptomatic primary HIV infection, smoking, and virus-related factors (subtype B vs. non-B, and drug resistance mutations).

RESULTS

Multivariate analysis showed no temporal trends in the CD4 cell count (square-root) or in HIV-1 RNA and DNA levels (log10) measured at the time of primary HIV infection. We observed the well described associations between the prognostic markers and the time since infection, sex, symptomatic primary HIV infection, and smoking.

CONCLUSION

The CD4 cell count and HIV RNA and DNA levels measured at the time of primary HIV-1 infection remained stable across 12 consecutive years (1996-2007) in the ANRS PRIMO cohort, suggesting no major change in virulence, after taking into account changes in patient characteristics.

Improvement in survival among symptomatic AIDS patients by exposure category in Sao Paulo

OBJECTIVE

The study assesses AIDS survival time per AIDS-case definition and exposure category in Sao Paulo State, Brazil during the periods 1992 to 1995 and 1998 to 2001.

METHODS

Case-fatality rate per AIDS case, Cox proportional hazards analysis, and Kaplan-Meier survival time.

RESULTS

The case-fatality rate per AIDS case in 1998 to 2001 was 37.6% for symptomatic (Centers for Disease Control and Prevention/modified and/or Paho/Caracas) and 9.7% for the Brazilian asymptomatic CD4 count<350 cells/mm3 AIDS-case definitions. Heterosexual/female patients were diagnosed earlier and presented the lowest case-fatality rate, followed by homosexual/male patients, heterosexual/male patients, and injecting drug users. In the multivariate Cox proportional hazards model, the period of diagnosis (hazard ratio=2.66; 95% confidence interval [CI]: 2.58 to 2.74) and AIDS-case definition (hazard ratio=4.48; 95% CI: 4.53 to 5.16) were strong predictors of survival. For the total AIDS cases, excluding death definition and undetermined exposure category, the estimated first quarter survival time improved from 4 months in 1992 to 1995 to 50 months in 1998 to 2001. Considering only the symptomatic AIDS-case definition, however, the improvement was from 4 months in the period 1992 to 1995 to 14 months in the period 1998 to 2001.

CONCLUSION

The survival improvement in Sao Paulo State was attributable to the introduction of antiretroviral therapy with free universal access in 1996 and to earlier diagnosis associated with the introduction in 1998 of the Brazilian asymptomatic CD4 count<350 cells/mm3 AIDS-case definition with superior sensitivity compared with the symptomatic AIDS-case definitions.

Do HIV Disease Progression and HAART Response Vary among Injecting Drug Users in Europe?

Prior to HAART availability, there was no evidence of a geographical variation in HIV disease progression among injecting drug users (IDU) from different European regions. Nowadays, factors of importance regarding HIV disease progression in the face of HAART availability, such as HAART access, adherence, and the organization of care for IDU may differ across Europe. Therefore we studied HIV disease progression in a European study of IDU with known dates of HIV-seroconversion. Results show that with ongoing HAART availability, the risk of HIV disease progression has continued to decrease. When accounting for pre-AIDS death (in AIDS analyses) and non-natural deaths (suicide, overdose, accidents and homicide, in analyses of death) which are common among IDU, the risk of AIDS and death has decreased by as much as 65% and 75%, respectively, in 2000/2001. Results show little geographic variation in progression to AIDS. All-cause mortality was higher in IDU from Glasgow than elsewhere, while in the Valencian region (Spain) IDU were at a significantly lower risk of non-natural deaths. The timing of HAART initiation by treatment-naïve IDU likewise differed across Europe: IDU in Amsterdam, Innsbruck, and Edinburgh started at significantly lower CD4 counts than IDU in Paris, Geneva, Glasgow, and the Valencian region, but the subsequent short-term immune response was similar. In conclusion, the risk in progression to AIDS or natural death is similar across western Europe although IDU across Europe differ in other factors, such as the risk of non-natural death and the timing of HAART initiation.

HLA allele sharing and HIV type 1 viremia in seroconverting Zambians with known transmitting partners

Rapid HIV type 1 (HIV-1) mutation coupled with immune evasion poses a major obstacle to effective interventions. In particular, transmission of HIV-1 from a donor partner (transmitter) to a recipient (seroconverter) with similar antigen-presenting molecules (i.e., human leukocyte antigens, HLA) may favor or expedite viral adaptation to host immune responses. Our PCR-based HLA-A, HLA-B, and HLA-DRB1 genotyping for 115 Zambian couples with documented intracouple HIV-1 (mostly clade C) transmission revealed that single-locus HLA allele sharing ranged from 28 to 36%. Different degrees of allele sharing, at single or multiple HLA loci between donor-recipient pairs, were associated with only modest increases in seroconverter RNA level (+0.04 to + 0.24 log(10) copies/mL, p > 0.25). Thus, partial HLA allele sharing commonly seen in Zambian couples did not appear to confer unequivocal early advantage for viral replication in the newly seroconverting subjects. However, correlation of virus loads in seroconverters with those of their known index partners (adjusted Pearson r = 0.21, p = 0.03) did imply that viral characteristics can independently contribute to variability in plasma virus load.

[Prognostic factors of mortality during the episode of pneumonia due to Pneumocystis carinii in patients with HIV infection]

BACKGROUND

Despite a steady decrease in its incidence, pneumonia caused by Pneumocystis carinii (PCP) are still diagnosed, and they occur frequently in patients unaware of being infected with the human immunodeficiency virus (HIV). Since it is a disease with a high mortality risk, its early diagnosis and therapy would allow these patients to benefit from the advantages afforded Pneumocystis carinii, neumonía, infecciones oportunistas relacionadas con el sida, pronóstico.by anti-retroviral therapy.

PATIENTS AND METHODS

Retrospective study, in which all adult HIV infected patients with microbiologically demonstrated PCP diagnosed at two tertiary-level hospitals in our country between 1985 and 1996 were included. The clinical records of patients were used as information source. The relative risks (RR) of death were estimated by the multivariant logistic regression.

RESULTS

PCP was the first AIDS indicating disease in approximately 70 % of cases. Thirteen percent of patients died during the episode. Patients aged over 45 years had a death RR during the episode of 3.15 (95 % CI from 0.8 to 12.2); patients previously diagnosed of AIDS had a death RR of 3.4 (95 % CI from 1.3 to 9), and those with an alveolar-arterial oxygen gradient (pA-aO2) > 50 mmHg, a death RR of 3 (95% CI from 1.1 to 8).

CONCLUSIONS

Factors independently related to survival to the PCP episode are age below 45 years, not to have had another AIDS indicating disease, and to have a pA-aO2 below 50 mmHg at diagnosis.

Cytomegalovirus seroconversion as a cofactor for progression to AIDS

OBJECTIVE

To study the impact of cytomegalovirus (CMV) seroconversion on HIV-1 disease progression.

DESIGN

Follow-up of CMV-seronegative subjects enrolled in the French SEROCO/HEMOCO cohorts of HIV-infected subjects.

METHODS

A total of 290 subjects were CMV-seronegative at enrolment in the cohort. Serological testing for CMV infection was done at enrolment and then every 6 months in CMV-seronegative subjects. The person-years method was used to calculate the incidence of CMV seroconversion. After adjustment for age, the CD4+ cell count at enrolment and the HIV exposure group in a Cox model, we studied CMV seroconversion as a time-dependent variable in progression to a CD4+ cell count below 200 x 10(6) cells/l and to clinical AIDS.

RESULTS

Overall, 61 CMV seroconversions were observed. The overall incidence rate was 4.4 per 100 person-years [95% confidence interval (CI), 3.3-5.5]. The risk of progression to a CD4+ cell count below 200 x 10(6) cells/l was not increased in CMV seroconverters. However, the risk of progression to AIDS was increased two-fold in CMV seroconverters compared with subjects who remained CMV-seronegative [relative risk (RR) = 2.09; 95% CI, 1.16-3.74; P = 0.01].

CONCLUSION

This analysis of 61 CMV seroconversions, the largest study in the literature, confirms the impact of recent CMV infection on progression to AIDS.

Evaluating the effect of year of seroconversion on HIV progression in cohort studies. Italian Seroconversion Study

OBJECTIVES

To show how a spurious association between the calendar year of seroconversion and HIV progression arises as a result of censoring the follow-up of individuals at their last visit, when the individuals' visits are intermittent.

DESIGN

A notional cohort of 1140 seroconverters and a cohort study of 1270 HIV-infected individuals seroconverted between 1985 and 1994, and followed up to December 1995 (the Italian Seroconversion Study cohort).

METHODS

Failure times and rate of the patients attending the clinic over the study period were simulated for the notional cohort. Three separate scenarios with different probabilities of making a visit were considered. Standard survival analysis techniques were used to assess the effect of the year of seroconversion on HIV progression. The progression to a CD4 cell count of 200 x 10(6)/l according to the calendar year of seroconversion in the Italian Seroconversion Study was assessed using different censoring strategies.

RESULTS

A spurious effect of the year of seroconversion consistently appeared in 100 repeated simulations. When ignoring the visits occurring after the first year of follow-up in the Italian Seroconversion Study cohort, results supported the hypothesis of no effect of the year from seroconversion.

CONCLUSIONS

The choice of the censoring strategy is crucial when assessing the effect of year of seroconversion using survival analysis in cohort studies with intermittent visit structure. Different censoring strategies should be considered before firmly concluding that more virulent strains or the use of treatment are modifying the natural history of HIV disease from cohort studies of this nature.