Daniela Bezemer

ORCID: 0000-0001-9304-0877
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About
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Research Areas
  • 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:...

10.1097/qad.0b013e3282fd167c article EN AIDS 2008-05-23

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.

10.1126/scitranslmed.aad1863 article EN Science Translational Medicine 2016-01-06

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...

10.1371/journal.pmed.1001898 article EN cc-by PLoS Medicine 2015-11-03

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...

10.1093/ve/vey007 article EN cc-by Virus Evolution 2018-01-01
Chris Wymant Daniela Bezemer François Blanquart Luca Ferretti Astrid Gall and 95 more Matthew Hall Tanya Golubchik Margreet Bakker Swee Hoe Ong Lele Zhao David Bonsall Mariateresa de Cesare George MacIntyre-Cockett Lucie Abeler‐Dörner Jan Albert Norbert Bannert Jacques Fellay M. Kate Grabowski Barbara Bartmeyer Huldrych F. Günthard Pia Kivelä Roger D. Kouyos Oliver Laeyendecker Laurence Meyer Kholoud Porter Matti Ristola Ard van Sighem Ben Berkhout Paul Kellam Marion Cornelissen Peter Reiss Christophe Fraser Vincent Aubert Manuel Battegay Enos Bernasconi Jürg Böni Dominique L. Braun H C Bucher Claudine Burton‐Jeangros Alexandra Calmy Matthias Cavassini G Dollenmaier Matthias Egger Luigia Elzi Jan Fehr Jacques Fellay Hansjakob Furrer Christoph A. Fux Meri Gorgievski Huldrych F. Günthard David Haerry Barbara Hasse Hans H. Hirsch Matthias Hoffmann Irène Hösli Christian R. Kahlert Laurent Kaiser Olivia Keiser Thomas Klimkait Roger D. Kouyos Helen Kovari Bruno Ledergerber G Martinetti Begoña Martínez de Tejada Catia Marzolini Karin J. Metzner Nicolas Müller David Nadal Dunja Nicca G Pantaleo Andri Rauch Stephan Regenass Christoph Rudin F. Schöni-Affolter Patrick Schmid R Speck M Stöckle Philip Tarr Alexandra Trkola Pietro Vernazza Rainer Weber Sabine Yerly Mark van der Valk Suzanne E. Geerlings Abraham Goorhuis Joppe W. Hovius B. Lempkes F.J.B. Nellen T. van der Poll Jan M. Prins Peter Reiss Michèle van Vugt W. Joost Wiersinga F.W.M.N. Wit Marlies van Duinen J. van Eden A. Hazenberg A M H van Hes F J J Pijnappel S Smalhout

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,...

10.1126/science.abk1688 article EN Science 2022-02-03
Elske Hoornenborg Liza Coyer Anders Boyd Roel Achterbergh Maarten Franciscus Schim van der Loeff and 95 more Sylvia M. Bruisten Henry J.C. de Vries Jelle Koopsen Thijs van de Laar Maria Prins Jan van Bergen Godelieve J. de Bree P. Brokx F. Deug M. Heidenrijk Maria Prins Peter Reiss Marc van der Valk Jan van Bergen Godelieve J. de Bree P. Brokx Udi Davidovich Suzanne E. Geerlings Elske Hoornenborg A. Oomen Ard van Sighem Wim Zuilhof M.L. Groot Bruinderink Roel Achterbergh Michiel A. van Agtmael Jintanat Ananworanich Diederik van de Beek G.E.L. van den Berk Daniela Bezemer A. van Bijnen W Blok S Bogers Marije K. Bomers Charles A. Boucher W. Brokking David M. Burger Kees Brinkman N. Brinkman Marijn de Bruin Sylvia M. Bruisten Liza Coyer Reinout van Crevel Ceranza G. Daans L. Dellemann Maartje Dijkstra Y. T. van Duijnhoven Arne van Eeden L. Elsenburg Mark A. M. van den Elshout Carmen Ester E. Ersan P. E. V. Felipa P. H. J. Frissen Teunis B. H. Geijtenbeek Mieke H. Godfried J. van Gool Abraham Goorhuis Marco R. de Groot Catherine Hankins A. Heijnen M Hillebregt A.A. Hogewoning M. Hommenga Joppe W. Hovius Y. J. H. Janssen K. De Jong Vita W. Jongen Neeltje A. Kootstra Richard A. Koup Frank P. Kroon Thijs van de Laar Fanny N. Lauw M.M. van Leeuwen Kamilla D. Lettinga Ineke Linde Dominique Loomans J. T. van der Meer T. Mouhebati Barbara J.M. Mulder Jan Mulder F.J.B. Nellen A. Nijsters H. Nobel Paul M. Oostvogel Eline Op de Coul Edgar J.G. Peters Inga Peters T. van der Poll Oliver Ratmann Casper Rokx Martijn S. van Rooijen Maarten F. Schim van der Loeff W.E.M. Schoute Gerard J.B. Sonder Jan A. Veenstra

10.1016/j.jhep.2019.11.022 article EN publisher-specific-oa Journal of Hepatology 2019-12-18

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...

10.1097/qad.0b013e328333ddee article EN AIDS 2009-12-21

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...

10.1371/journal.pone.0044819 article EN cc-by PLoS ONE 2012-09-14

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...

10.1097/qad.0000000000000854 article EN cc-by-nc-nd AIDS 2015-11-10

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...

10.1016/j.epidem.2010.04.001 article EN cc-by-nc-nd Epidemics 2010-04-10

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...

10.1371/journal.pone.0007365 article EN cc-by PLoS ONE 2009-10-06

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...

10.1089/aid.2013.0171 article EN AIDS Research and Human Retroviruses 2013-08-16

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...

10.1093/nar/gkm697 article EN cc-by-nc Nucleic Acids Research 2007-09-26

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...

10.1177/09622802241309750 article EN cc-by-nc Statistical Methods in Medical Research 2025-02-12

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...

10.1177/135965350601100208 article EN Antiviral Therapy 2006-02-01

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...

10.1016/j.virusres.2016.08.004 article EN cc-by Virus Research 2016-08-05

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...

10.1371/journal.pcbi.1006761 article EN cc-by PLoS Computational Biology 2019-02-26

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...

10.1089/aid.2009.0041 article EN AIDS Research and Human Retroviruses 2010-04-01

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....

10.1093/emph/eot019 article EN cc-by Evolution Medicine and Public Health 2013-01-01

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...

10.1097/qad.0000000000001592 article EN AIDS 2017-07-07

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...

10.1111/trf.14097 article EN Transfusion 2017-04-04

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...

10.1371/journal.pone.0064437 article EN cc-by PLoS ONE 2013-05-27

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...

10.1101/2022.05.15.22275117 preprint EN cc-by-nc-nd medRxiv (Cold Spring Harbor Laboratory) 2022-05-16

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.

10.1097/qad.0b013e3282f37489 article EN AIDS 2008-01-11
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