A new approach to estimating AIDS incubation times: results in homosexual infected men

Trends of HIV-1 incidence with credible intervals in Sweden 2002-09 reconstructed using a dynamic model of within-patient IgG growth

BACKGROUND

HIV-1 is a lifelong disease, often without serious symptoms for years after infection, and thus many infected persons go undetected for a long time. This makes it difficult to track incidence, and thus epidemics may go through dramatic changes largely unnoticed, only to be detected years later. Because direct measurement of incidence is expensive and difficult, several biomarker-based tests and algorithms have been developed to distinguish between recent and long-term infections. However, current methods have been criticized and demands for novel methods have been raised.

METHODS

We developed and applied a biomarker-based incidence model, joining a time-continuous model of immunoglobulin G (IgG) growth (measured by the IgG-capture BED-enzyme immunoassay) with statistical corrections for both sample size and unobserved diagnoses. Our method uses measurements of IgG concentration in newly diagnosed people to calculate the posterior distribution of infection times. Time from infection to diagnosis is modelled for all individuals in a given period and is used to calculate a sample weight to correct for undiagnosed individuals. We then used a bootstrapping method to reconstruct point estimates and credible intervals of the incidence of HIV-1 in Sweden based on a sample of newly diagnosed people.

RESULTS

We found evidence for: (i) a slowly but steadily increasing trend in both the incidence and incidence rate in Sweden; and (ii) an increasing but well-controlled epidemic in gay men in Stockholm. Sensitivity analyses showed that our method was robust to realistic levels (up to 15%) of BED misclassification of non-recently infected persons as early infections.

CONCLUSIONS

We developed a novel incidence estimator based on previously published theoretical work that has the potential to provide rapid, up-to-date estimates of HIV-1 incidence in populations where BED test data are available.

Serial cervicovaginal exposures with replication-deficient SIVsm induce higher dendritic cell (pDC) and CD4+ T-cell infiltrates not associated with prevention but a more severe SIVmac251 infection of rhesus macaques

OBJECTIVE

Intravaginal exposure to simian immunodeficiency virus (SIV) acutely recruits interferon-alpha (IFN-α) producing plasmacytoid dendritic cells (pDC) and CD4 T-lymphocyte targets to the endocervix of nonhuman primates. We tested the impact of repeated cervicovaginal exposures to noninfectious, defective SIV particles over 72 hours on a subsequent cervicovaginal challenge with replication competent SIV.

METHODS

Thirty-four female Indian Rhesus macaques were given a 3-day twice-daily vaginal exposures to either SIVsmB7, a replication-deficient derivative of SIVsmH3 produced by a T lymphoblast CEMx174 cell clone (n = 16), or to CEM supernatant controls (n = 18). On the fourth day, animals were either euthanized to assess cervicovaginal immune cell infiltration or intravaginally challenged with SIVmac251. Challenged animals were tracked for plasma viral load and CD4 counts and euthanized at 42 days after infection.

RESULTS

At the time of challenge, macaques exposed to SIVsmB7, had higher levels of cervical CD123 pDCs (P = 0.032) and CD4 T cells (P = 0.036) than those exposed to CEM control. Vaginal tissues showed a significant increase in CD4 T-cell infiltrates (P = 0.048) and a trend toward increased CD68 cellular infiltrates. After challenge, 12 SIVsmB7-treated macaques showed 2.5-fold greater daily rate of CD4 decline (P = 0.0408), and viral load rise (P = 0.0036) as compared with 12 control animals.

CONCLUSIONS

Repeated nonproductive exposure to viral particles within a short daily time frame did not protect against infection despite pDC recruitment, resulting instead in an accelerated CD4 T-cell loss with an increased rate of viral replication.

The relationship of reported HIV risk and history of HIV testing among emergency department patients

OBJECTIVE

Among a random sample of emergency department (ED) patients, we sought to determine the extent to which reported risk for human immunodeficiency virus (HIV) is related to ever having been tested for HIV.

METHODS

A random sample of patients (aged 18-64 years) from an adult, urban, northeastern United States, academic ED were surveyed about their history of ever having been tested for HIV and their reported HIV risk behaviors. A reported HIV risk score was calculated from the survey responses and divided into 4 levels, based on quartiles of the risk scores. Pearson's X(2) testing was used to compare HIV testing history and level of reported HIV risk. Logistic regression models were created to investigate the association between level of reported HIV risk and the outcome of ever having been tested for HIV.

RESULTS

Of the 557 participants, 62.1% were female. A larger proportion of females than males (71.4% vs 60.6%; P < 0.01) reported they had been tested for HIV. Among the 211 males, 11.4% reported no HIV risk, and among the 346 females, 10.7% reported no HIV risk. The proportion of those who had been tested for HIV was greater among those reporting any risk compared with those reporting no risk for females (75.4% vs 37.8%; P < 0.001), but not for males (59.9% vs 66.7%; P < 0.52). However, certain high-risk behaviors, such as a history of injection-drug use, were associated with prior HIV testing for both genders. In the logistic regression analyses, there was no relationship between increasing level of reported HIV risk and a history of ever having been tested for HIV for males. For females, a history of ever having been tested was related to increasing level of reported risk, but not in a linear fashion.

CONCLUSIONS

The relationship between reported HIV risk and history of testing among these ED patients was complex and differed by gender. Among these patients, having greater risk did not necessarily mean a higher likelihood of ever having been tested for HIV.

Evolutionary history of HIV-1 subtype B and F infections in Brazil

OBJECTIVE

To reconstruct the onset date of the HIV-1 B and F epidemics in Brazil based on virus diversification over time.

DESIGN

We studied HIV-1 env V3 sequences (210 nt) with a known sampling year isolated from HIV-1 positive patients from Brazil between 1989 and 1997: 101 subtype B sequences and 41 subtype F sequences.

METHODS

HIV-1 V3 env sequences were grouped by year of collection and the relationship between the sampling years of HIV-1 sequences and their genetic distance to the reconstructed common ancestor (intra-population divergence) or to other sequences from the same year (intra-population diversity) was examined by using linear regression analysis.

RESULTS

Regression analysis of nucleotide distances, revealed a highly significant positive correlation between sampling years of subtype B and F V3 sequences and their intra-population divergence (P < 0.001) or diversity (P < 0.0001). In both subtype populations, the divergence and diversity increased at a rate of 0.5 and 0.9% per year, respectively. Considering these evolutionary rates, we estimate the onset of the subtype B and F HIV-1 epidemics in Brazil during early 1970s and early 1980s, respectively.

CONCLUSIONS

The consistent correlation between divergence and diversity of the V3 sequences with their sampling years indicates that the molecular clock is operational in the evolution of the HIV-1 in Brazil's epidemic, and show that subtypes B and F are evolving at a similar rate over time. The dating results suggest a discontinuous introduction of these subtypes in the Brazilian population.

Back-calculation and projection of the HIV/AIDS epidemic among homosexual/ bisexual men in three European countries: evalution of past projections and updates allowing for treatment effects

This study critically evaluates the quality of 1990 back-calculations and long-term projections of the HIV/AIDS epidemic for homosexual/bisexual men in France, the Federal Republic of Germany, and the UK. The projection captured the general pattern observed in all three countries although the observed AIDS incidence peaked 2-3 years later and declined faster than had been projected. Total AIDS incidences from 1989 to 2000 were overestimated by 38.5% in France, and underestimated by 23.9 and 17.5% in western Germany and the UK. Updated back-calculations and projections to 2020 use AIDS incidence data up to 2000. The procedure incorporates an asymmetric long-tailed cumulative HIV curve as well as the increase in the median incubation period brought about by new therapies introduced during the 1990s. The results suggest that: (i) The rapid decrease in cases during the late 1990s was caused by a median incubation period that increased from 10 years to 21-23 years by the late 1990s. (ii) An imminent bottoming out followed by a protracted increase in AIDS cases from 2000 to at least 2010 could be the consequence of a leveling off of the median incubation period. (iii) A low variant of the projections shows that at least 40,000 homosexual men could develop AIDS in the three countries after 2000.

Estimation of epidemic size and incubation time based on age characteristics of vCJD in the United Kingdom

The size of the variant Creutzfeldt-Jakob Disease (vCJD) epidemic in the United Kingdom is a major public health concern and a subject of speculation. The cases are young (mean age = 28). Assuming that the risk of developing the disease in susceptible exposed subjects decreases exponentially with age after age 15, that all infections occurred between 1980 and 1989, and that the distribution of the incubation period is lognormal, we estimate that the mean duration of the incubation period is 16.7 years [95% confidence interval (CI): 12.4 to 23.2] and that the total number of cases will be 205 (upper limit of the 95% CI: 403).

Using human immunodeficiency virus type 1 sequences to infer historical features of the acquired immune deficiency syndrome epidemic and human immunodeficiency virus evolution

In earlier work, human immunodeficiency virus type 1 (HIV-1) sequences were analysed to estimate the timing of the ancestral sequence of the main group of HIV-1, the virus that is responsible for the acquired immune deficiency syndrome pandemic, yielding a best estimate of 1931 (95% confidence interval of 1915-1941). That work will be briefly reviewed, outlining how phylogenetic tools were extended to incorporate improved evolutionary models, how the molecular clock model was adapted to incorporate variable periods of latency, and how the approach was validated by correctly estimating the timing of two historically documented dates. The advantages, limitations, and assumptions of the approach will be summarized, with particular consideration of the implications of branch length uncertainty and recombination. We have recently undertaken new phylogenetic analysis of an extremely diverse set of human immunodeficiency virus envelope sequences from the Democratic Republic of the Congo (the DRC, formerly Zaire). This analysis both corroborates and extends the conclusions of our original study. Coalescent methods were used to infer the demographic history of the HIV-1 epidemic in the DRC, and the results suggest an increase in the exponential growth rate of the infected population through time.

Antiretroviral medication use among injection drug users: two potential futures

OBJECTIVE

To model the potential impact of HIV infection rates and the use of antiretroviral medication on life expectancy and mortality in the Downtown Eastside of Vancouver, British Columbia, Canada, from 1999 to 2006.

DESIGN

Population projections were made to estimate the population of the Downtown Eastside in the year 2006.

METHODS

Two scenarios were modelled to predict the impact of HIV infection and antiretroviral use on mortality and life expectancy. The use of antiretroviral therapy was estimated to be 80% in the first scenario and 20% in the second. The prevalence of HIV by age and sex, and by year infected was estimated using data from the Vancouver Injection Drug User Study.

RESULTS

If the level of antiretroviral therapy use among HIV-positive individuals was 80% at baseline, then we estimate that the life expectancy at birth in the year 2006 will be 60.8 years for men and 72.8 years for women, and 172 AIDS deaths will occur between 1999 and 2006. In contrast, if the present level of antiretroviral medication use persists, the life expectancy at birth in the year 2006 will be 56.9 years for men and 68.6 years for women, and 503 AIDS deaths will occur between 1999 and 2006.

CONCLUSION

Our analysis suggests that if the low levels of antiretroviral therapy use persist, life expectancy in Vancouver's Downtown Eastside will soon be on a par with many of the world's least developed countries. Our findings highlight the large health status decline that can be expected in many inner city neighbourhoods if low levels of antiretroviral use persist. Although reasonable coverage targets for injection drug users (IDU) have not been established, the expanded use of antiretroviral medication is urgently needed to avert a drastic decline in health status.

Timing the ancestor of the HIV-1 pandemic strains

HIV-1 sequences were analyzed to estimate the timing of the ancestral sequence of the main group of HIV-1, the strains responsible for the AIDS pandemic. Using parallel supercomputers and assuming a constant rate of evolution, we applied maximum-likelihood phylogenetic methods to unprecedented amounts of data for this calculation. We validated our approach by correctly estimating the timing of two historically documented points. Using a comprehensive full-length envelope sequence alignment, we estimated the date of the last common ancestor of the main group of HIV-1 to be 1931 (1915-41). Analysis of a gag gene alignment, subregions of envelope including additional sequences, and a method that relaxed the assumption of a strict molecular clock also supported these results.

Impact of human immunodeficiency virus infection on the histological features of chronic hepatitis C: a case-control study. The MULTIVIRC group

Hepatitis C virus (HCV) is frequently encountered in human immunodeficiency virus (HIV)-infected patients because of common routes of transmission. Previous studies suggested that HIV infection impaired the natural course of chronic hepatitis C, with a more rapid progression to cirrhosis. However, these studies did not assess the HIV infection impact on chronic hepatitis C by taking into account the risk factors for liver fibrosis progression: alcohol, sex, age at the contamination, and duration of HCV infection. We studied liver biopsy specimens of 2 groups of 58 patients that were infected by both HCV and HIV or by HCV alone. The 2 groups were matched according those risk factors, and liver biopsy responses were evaluated with the METAVIR items. The METAVIR activity was higher in HIV-positive than HIV-negative patients. Cirrhosis was more frequent: (1) in HIV-positive patients with CD4 < or = 200 cells/microL (45%) than in HIV-negative patients (10%) (P = .003), (2) in HIV-positive patients with CD4 < or = 200 cells/microL (45%) than in HIV-positive patients with CD4 > 200 cells/microL (17%) (P = .04). These differences, which were linked to HIV status, might be related to the enhanced HCV replication during HIV infection or other immune mechanisms that need further studies.

[AIDS-free time and survival of an injecting drug users HIV seroconvertors cohort]

OBJECTIVE

To analyze AIDS free time, survival and the pre-AIDS survival for a injecting drug users cohort (IDU) of HIV seroconvertors.

SUBJECT AND METHODS

Interval for seroconversion was available for 276 IDUs from Centers for AIDS Information and Prevention (CIPS) recruited between 1987 and until June of 1996. AIDS diagnosis and vital status dates were obtained by follow up at hospitals, mortality and AIDS registries, and CIPS visits. The end of follow up was December of 1996. Seroconversion date was estimated as the middle point between last HIV- and first HIV+. Kaplan-Meier extension and Cox regression for truncated data were fitted to estimate AIDS-free and survival times and to observe differences by sex, age consumption time and year of seroconversion. Weibull, and Log-normal parametric models were fitted to estimate median and percentiles of AIDS-free and survival times distribution.

RESULTS

34 cases have been identified as AIDS, 24 as deaths, 9 of them being before AIDS. 63.5% of the individuals were AIDS-free 7 years after seroconversion, and the probability of death was 25.50. Pre-AIDS mortality is around 8.7%. There were not significant differences by sex, age, consumption time and year of seroconversion. Log-normal model fitted better estimating an AIDS-free median time of 10.93 years and 13.67 survival years.

CONCLUSION

The incubation period of HIV infection in a cohort of seroconvertors in our environment was around 11 years, not different from that observed out of the Mediterranean area as Holland, Scotland or United States

The effect of CMV infection on progression of human immunodeficiency virus disease is a cohort of haemophilic men followed for up to 13 years from seroconversion

The effect of prior infection with cytomegalovirus (CMV) on progression of HIV disease in a cohort of 111 men with haemophilia was studied after 13 years follow-up. The relative hazards associated with CMV positivity on progression to AIDS, death and a CD4 count of 0.05 x 10(9)/l were 2.28, 2.42 and 2.34, respectively. CMV seropositive patients were significantly older than the seronegative and this was controlled for by using a Cox proportional hazards model. The relative hazards for the three endpoints decreased to 1.89, 1.82 and 1.93 respectively and were marginally non-significant (P = 0.05, 0.08 and 0.08 for the three endpoints respectively). We conclude that this cohort continues to show evidence of a 'co-factor' effect associated with prior infection with CMV which is confounded by age but not completely explained by age differences. The potential biological significance of these results is discussed in the context of recent controlled clinical trials which show a survival benefit from long-term high-dose acyclovir, a drug with activity in vivo against CMV and other herpesviruses.