BEEHIVE brings together information from a number national cohorts of patients. We are deeply indebted to the patients in these cohorts for consenting to provide their data, and to those who run the cohorts. The Netherlands ATHENA Cohort: Peter Reiss. Antwerp Cohort: Katrien Fransen, Guido Vanham. The French ANRS PRIMO Cohort: Laurence Meyer. Swiss HIV Cohort Study (SHCS): Huldrych Günthard, Roger Kouyos. German HIV-1 Seroconverter Cohort: Norbert Bannert, Barbara Gunsenheimer-Bartmeyer, Claudia Kücherer. UK Register of HIV Seroconverters: Kholoud Porter. Swedish InfCare HIV Cohort: Jan Albert. Helsinki IDU sc Cohort: Pia Kivelä, Kirsi Liitsola, Matti Ristola. Rakai Community Cohort: M. Kate Grabowski, Oliver Laeyendecker.
The cohort leads send the relevant clinical data to the team at the HIV Monitoring Foundation in Amsterdam - Daniela Bezemer, Mariska Hillebregt, Ard van Sighem, Sima Zaheri - who combine and curate this data from all the cohorts.
The cohort leads send the blood samples to the virology wet lab in Amsterdam Medical Centre, where the virus’ RNA (genetic material) is extracted. The AMC team is Margreet Bakker, Ben Berkhout, and Marion Cornelissen.
Following extraction, the viral RNA needs to be sequenced (i.e. we want to know what each virus’ sequence is). For most of the BEEHIVE data this was done by the Virus Genomics group formerly based at the Wellcome Sanger Institute: Astrid Gall, Swee Hoe Ong and Paul Kellam.
The Analysis Advisory Group is Samuel Alizon, Sebastian Bonhoeffer, Gabriel Leventhal, Andrew Rambaut, Oliver Pybus, and Gil McVean.
Other people who have contributed to the project in various capacites: François Blanquart, David Bonsall, Nick Croucher, Jacques Fellay, Tanya Golubchik, Martin Hunt, Oliver Ratmann, David van de Vijver, Frank de Wolf.
The Oxford team
The home of the analysis part of BEEHIVE is the Big Data Institute, part of the Nuffield Department of Medicine at the University of Oxford.
Christophe is the Principal Investigator of BEEHIVE. He is Senior Group Leader in Pathogen Dynamics at the Big Data Institute, and Professor in the Nuffield Department of Medicine. Christophe is interested in studying the population dynamics and epidemiology of pathogens, and translating this knowledge to public health.
Chris is a Senior Researcher on the BEEHIVE project. He has mainly been developing and applying bioinformatic methods for processing and analysing the genetic sequence data - leading development of the methods phyloscanner (with Matthew) and shiver, described under the Publications tab.
Matthew is focussing on the reconstruction of transmission patterns within the BEEHIVE dataset. He is a researcher in pathogen phylodynamics, with a particular interest in inference of who infected who. He is also interested in investigating the effects of sampling bias in molecular epidemiological studies.
Rob is a Sir Henry Wellcome postdoctoral fellow at the Big Data Institute (Oxford) and the Africa Health Research Institute (UCL/Durban). Rob’s main research interest is the application of statistical tools to the viral genomes in order to identify the underlying genetic variants that control infectiousness and transmission.
Michelle is a senior researcher in statistical genetics and pathogen dynamics. With a background in phylogenetics, she is particularly interested in developing tree-based methods for answering statistical questions about HIV genotypic variation within and between patients.
Lele is a researcher in statistical genetics and pathogen dynamics. She is interested in the within- and between-host evolution of viral infectious diseases. She uses various methods including phylogenetics and bayesian statistics to study the HIV transmission interface and the transmitted/founder variant.
THE STICHTING HIV MONITORING TEAM
Peter Reiss is Professor of Medicine at the Academic Medical Center in Amsterdam, the Netherlands, where he holds a joint appointment in the Department of Global Health and the division of Infectious Diseases. He is also the director of Stichting HIV Monitoring (the Netherlands’ HIV Monitoring Foundation). His research focuses primarily on the complications of HIV and HIV treatment, and more particularly in relation to ageing.
Sima Zaheri is the deputy director of Stichting HIV Monitoring (SHM) and manager of SHM’s Data Unit. Sima studied medical biology at the University of Amsterdam and, since 2002, has focused on setting up and driving the systems for data collection, data processing, quality improvement and quality maintenance. Sima works closely with the HIV-treating physicians, researchers, nurse consultants and others who use SHM’s data in the 26 HIV treatment centres in the Netherlands to ensure that important developments in the HIV and AIDS field are translated into processes, and to monitor the quality and efficiency of these processes on an ongoing basis.
Ard van Sighem
Ard van Sighem is a researcher at Stichting HIV Monitoring, where he investigates the changes in the HIV epidemic in the Netherlands in various at-risk groups, looking at how these groups have changed over the course of time. He is also interested in the more patient-specific side of the HIV epidemic. In addition, Ard is collaborating with cohorts from other countries to investigate changes in causes of death in people living with HIV. Lastly, Ard works together with the European Centre for Disease Control and Prevention to estimate the size of the population of people living with HIV, including those as yet undiagnosed, in Europe, and on nationwide and regional levels.
Daniela Bezemer is a researcher at Stichting HIV Monitoring. She specializes in evolutionary epidemiology. Her research aims to better understand HIV-1 transmission dynamics and evolution by mathematical modelling of epidemiological data and molecular phylogenetic analysis.
Mariska Hillebregt has a background in health science and epidemiology and has been a data manager at Stichting HIV Monitoring (SHM) since 2012. As the coordinator of SHM’s data management department, she is responsible for standardising, merging and documenting SHM’s data and safeguarding and improving the quality of data in SHM’s data warehouse. Mariska is also responsible for data management for Beehive.
The Rakai Community Cohort team
Oliver is a Staff Scientist at NIAID and holds joint appointments as an Assistant Professor of Medicine in the Division of Infectious Diseases and in Epidemiology at the Johns Hopkins University. His primary areas of interest are the development of methods for estimating incidence from cross-sectional surveys, the impact of HIV subtype on disease progression, and the development of serologic and molecular tools to investigate questions related to infectious disease epidemiology. He works closely with the Rakai Health Sciences Program and the HIV Preventions Trials Network.