A5103138084- HIV Research and Treatment
- HIV/AIDS Research and Interventions
- HIV, Drug Use, Sexual Risk
- HIV/AIDS drug development and treatment
- Hepatitis C virus research
- Genomics and Phylogenetic Studies
- Hepatitis B Virus Studies
- HIV/AIDS Impact and Responses
- RNA and protein synthesis mechanisms
- Bayesian Methods and Mixture Models
- Data-Driven Disease Surveillance
- Sex work and related issues
- Bacteriophages and microbial interactions
- Mosquito-borne diseases and control
- Liver Disease Diagnosis and Treatment
- Syphilis Diagnosis and Treatment
- Chromosomal and Genetic Variations
- Evolution and Genetic Dynamics
- Census and Population Estimation
- Evolutionary Game Theory and Cooperation
- Pneumocystis jirovecii pneumonia detection and treatment
- Plant and animal studies
- Complex Network Analysis Techniques
- Molecular Biology Techniques and Applications
Stichting HIV Monitoring
2013-2025
Helsinki University Hospital
2017
Imperial College London
2013
ETH Zurich
2013
University Hospital of Zurich
2013
University of Zurich
2013
Institut de Recherche pour le Développement
2013
Centre National de la Recherche Scientifique
2013
Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle
2013
Johns Hopkins Medicine
2013
Objective: Reducing viral load, highly active antiretroviral therapy has the potential to limit onwards transmission of HIV-1 and thus help contain epidemic spread. However, increases in risk behaviour resurgent epidemics have been widely reported post-highly therapy. The aim this study was quantify impact that had on epidemic. Design: We focus among men who sex with Netherlands, which well documented over past 20 years within several long-standing national surveillance programs. Methods:...
Available antiretrovirals both for treatment and prevention more comprehensive HIV testing would have prevented the majority of past, annual transmissions among MSM in Netherlands, but none three interventions isolation.
The HIV-1 subtype B epidemic amongst men who have sex with (MSM) is resurgent in many countries despite the widespread use of effective combination antiretroviral therapy (cART). In this combined mathematical and phylogenetic study observational data, we aimed to find out extent which result newly introduced strains or growth already circulating strains.As November 2011, ATHENA HIV cohort all patients care Netherlands since 1996 included polymerase sequences from 5,852 patients. Patients...
Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar can be meaningfully interpreted. Despite its higher throughput more detailed minority variant next-generation sequencing has yet to widely adopted for HIV. The difficulty accurately reconstructing consensus a quasispecies from reads (short fragments DNA) in presence large between- within-host diversity, including frequent indels, may have...
We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this had 0.54 to 0.74 log 10 increase (i.e., ~3.5-fold 5.5-fold increase) viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 other strains. Without treatment, advanced HIV—CD4 counts below 350 cells per cubic millimeter, long-term clinical consequences—is expected be reached, on average, 9 months after diagnosis for their thirties variant. Age, sex,...
To obtain insight in the HIV-1 transmission networks among men having sex with (MSM) Netherlands.A phylogenetic tree was constructed from polymerase sequences isolated 2877 subtype B-infected patients monitored as part of AIDS Therapy Evaluation Netherlands (ATHENA) nationwide observational cohort.For MSM a known date infection, most similar were selected potential pairs when they clustered bootstrap value at least 99%. Time infection to onward estimated median time between dates for each...
New HIV infections in men who have sex with (MSM) increased Switzerland since 2000 despite combination antiretroviral therapy (cART). The objectives of this mathematical modelling study were: to describe the dynamics epidemic MSM using national data; explore effects hypothetical prevention scenarios; and conduct a multivariate sensitivity analysis.The model describes transmission, progression cART differential equations. was fitted Swiss AIDS surveillance data twelve unknown parameters were...
CD4 cell count is a key measure of HIV disease progression, and the basis successive international guidelines for treatment initiation. dynamics are used in mathematical econometric models evaluating public health need interventions. Here, we estimate rates decline, stratified by relevant covariates, form that clinically transparent can be directly such models.We analyse AIDS Therapy Evaluation Netherlands cohort, including individuals with date seroconversion estimated to within 1 year...
There has been increasing concern about a resurgent epidemic of HIV-1 amongst men having sex with in the Netherlands, which parallels similar epidemics now occurring many other countries.A transmission model applicable to epidemics, including use antiretroviral therapy, is presented set ordinary differential equations. The fitted by maximum likelihood national and AIDS diagnosis data from 1980 2006, estimating parameters on average changes unsafe time diagnosis. Robustness studied detailed...
HIV-1 RNA plasma concentration at viral set-point is associated not only with disease outcome but also the transmission dynamics of HIV-1. We investigated whether and CD4 cell count have changed over time in HIV epidemic Netherlands.We selected 906 therapy-naïve patients least one measured 9 to 27 months after estimated seroconversion. Changes were analysed using linear regression models. The ATHENA national observational cohort contributed all who seroconverted or 1996; Amsterdam Cohort...
We performed a molecular phylogenetic study on HIV-1 polymerase sequences of men who have sex with (MSM) and heterosexual patient samples in Kenya to characterize any observed transmission networks. were obtained from Nairobi coastal 84 MSM, 226 other men, 364 women 2005 2010. Using Bayesian phylogenetics, we tested whether clustered by sexual orientation geographic location. In addition, used trait diffusion analyses identify significant epidemiological links quantify the number...
In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to non-redundant analysis and evolutionary-based classification elements. first version, contemplate eukaryotic Ty3/Gypsy Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on gag-pro-pol internal region commonly presented by these two groups strongly support a certain number previously described lineages originally reported from...
In stopping the spread of infectious diseases, pathogen genomic data can be used to reconstruct transmission events and characterize population-level sources infection. Most approaches for identifying pairs do not account time passing since divergence variants in individuals, which is problematic viruses with high within-host evolutionary rates. This prompted us consider possible terms phylogenetic additional estimates infection derived from clinical biomarkers. We develop Bayesian mixture...
Sequence analysis of HIV-1 from 440 therapy-naive individuals included within the CASCADE study, who seroconverted 18 months last negative test, identified 65 persons infected with a strain carrying resistance-associated mutations. Population-based sequencing was performed for 20 these during therapy-free follow-up period. The median time 15 (interquartile range 10 to 23 months). Of individuals, 12 showed subsequent evolution at resistance positions, whereas virus 8 people stable this In...
The BEEHIVE (Bridging the Evolution and Epidemiology of HIV in Europe) project aims to analyse nearly-complete viral genomes from >3000 HIV-1 infected Europeans using high-throughput deep sequencing techniques investigate virus genetic contribution virulence. Following development a computational pipeline, including new de novo assembler for RNA genomes, generate larger contiguous sequences (contigs) abundance short sequence reads that characterise data, another area determines genome...
The relationship between the underlying contact network over which a pathogen spreads and phylogenetic trees that are obtained presents an opportunity to use sequence data learn about networks difficult study empirically. However, this is not explicitly known usually studied in simulations, often with simplifying assumption static time, though human dynamic. We simulate on dynamic Erdős-Renyi random two skewed degree distribution, of one additionally clustered. tree shape features explore...
Whether temporary antiretroviral treatment during primary HIV infection (PHI) lowers the viral set point or affects subsequent CD4 count decline remains unclear. The objectives of this study were to analyze clinical, viral, and immunological effects early HAART PHI. This is a cohort patients with laboratory evidence Independent predictors analyzed using multiple regression analysis. Plasma HIV-1 RNA (pVL) trajectories linear mixed models. A total 332 included in Sixty-four started within 180...
Background and objectives: The severity of HIV-1 infection, measured by set-point viral load (SPVL), is highly variable between individuals. Its heritability infections quantifies the control pathogen genotype has over disease severity. Heritability estimates vary widely studies, but differences in methods make comparison difficult. Phylogenetic comparative analysis offers measures phylogenetic signal, it unclear how to interpret them terms fraction variance SPVL controlled virus genotype....
Objective: MSM are at increased risk for infection with HIV-1 and hepatitis C virus (HCV). Is HIV/HCV coinfection confined to specific HIV transmission networks? Design methods: A phylogenetic tree was constructed 5038 subtype B polymerase (pol) sequences obtained from in the AIDS therapy evaluation Netherlands cohort. We investigated existence of clusters HCV prevalence, density (i.e. number potential partners) HIV/HCV-coinfected compared HIV-infected without HCV, overlap phylogenies using...
BACKGROUND Separate transmission networks for human immunodeficiency virus (HIV) coexist. Molecular typing of viral genomes can provide insight in HIV routes donors whom risk behavior–based donor selection failed. STUDY DESIGN AND METHODS This study includes all HIV‐infected Dutch and Flemish the period 2005 to 2014 (n = 55). Part polymerase (pol) gene was amplified, sequenced, compared with more than 10,000 strains obtained from patients. The most likely route determined based on phylogeny...
Introduction Studies suggest that the HIV-1 epidemic in Netherlands may have become more virulent, leading to faster disease progression if untreated. Analysis of CD4 cell count decline before antiretroviral therapy (ART) initiation, a surrogate marker for progression, be hampered by informative censoring as ART initiation is likely with steeper decline. Methods Development from 9 48 months after seroconversion was analyzed using mixed-effects model and 2 models jointly modeled counts time...
Abstract Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in global epidemic. Most methods determining duration of classify samples into recent and non-recent are unable to give more granular TSI estimates. These binary classifications have a limited recency window several months, therefore requiring large sample sizes, cannot assess cumulative impact an intervention. We developed Random Forest Regression model, HIV-phyloTSI, that combines...
In addition to development or selection of resistance, failure continuously suppress HIV-1 production while still using initially effective combination antiretroviral therapy (cART) may result from super-infection with a drug-resistant strain. Both transmission drug resistant HIV and have been demonstrated. We analysed pol genes obtained before start successful cART during on in 101 patients. Difference precART sequences were explained by evolution not super-infection.