Phylogenetics And Networks for Generalised HIV Epidemics in Africa


News & Publications


The International Scientific Advisory Board provided valuable input at the PANGEA meeting in Durban, 16th July 2016 

The PANGEA Consortium met to update the International Scientific Advisory Board on operational progress and ongoing scientific analysis. The ISAB congratulated the PANGEA Consortium on the innovative and productive nature of the network which is at the cutting edge of new approaches to epidemiological investigation. It recognized the multidisciplinary nature of the Consortium which includes investigators leading African studies, sequencing projects and phylogenetic analyses. PANGEA provides a platform that allows scientists to combine classical epidemiological data with molecular methods to define risk factors and interventions.

collage durban

PANGEA Steering Committee is Striving for Output! 16th July 2016

Over 20 Consortium members were in attendance at the Steering Committee meeting which took place at the KwaZulu-Natal Research Institute for Tuberculosis and HIV in Durban, RSA on Saturday, 16th July 2016. The key focus of the meeting was on discussing past, current and future challenges of the project, including the number and speed at which analysis proposals are received and reviewed. It is anticipated that the revised procedures agreed at the meeting will greatly increase the output of the project, and we encourage applications with this regard. Further details on how to obtain access and approval for any analysis relating to the linked sequencing, clinical, epidemiological and demographic data that is generated within the PANGEA HIV project can be obtained by emailing pangea-hiv@ucl.ac.uk. We are looking forward to hearing from you!

deenan TD0

Sequencing Meeting Kicks Off PANGEA Collaborators Meeting in Durban, 15th July 2016 

The PANGEA_HIV Network kicked off its collaborators meeting in Durban with a productive Sequencing Meeting. Dr Siva Danaviah gave exciting updates in regards to work that has been completed at the University of KwaZulu-Natal RSA whilst Dr Astrid Gall and Dr Dan Frampton provided updates on the activities in the UK. Approximately 10,000 samples from Botswana, South Africa and Uganda have been sequenced to date and close to 8,000 genomes are available. Genomes are being assembled using three different assembly pipelines, namely Geneious, Shiver (developed at Imperial College) and a pipeline developed at UCL. The latter two pipelines have been advanced to assemble HIV genomes and will be published shortly. All unassembled raw reads and genomes will be made publicly available in 2017. 


PANGEA_HIV Meets Again at a Satellite Symposium of the HIV Dynamics & Evolution conference 27thApril 2016           

PANGEA_HIV will hold a satellite meeting as part of the 23rd International HIV Dynamics & Evolution conference to promote discussions between HIV modelling specialists with a keen interest and expertise in phylogenetics. Ongoing phylodynamic research analyses will be discussed in addition to the final results of the Phylodynamic Simulation Exercise. Analytical approaches to and individual results of the Phylodynamic Simulation Exercise were discussed at previous satellite meetings. We hope to see you there! 


PANGEA_HIV Network Holds Meeting in Boston  23rd February 2016                          

A PANGEA HIV breakfast meeting was held in Boston on 23rd February to discuss both ongoing scientific analyses and new research proposals.

Dr Kate Grabowski was first to provide a summary and progress report on her research examining the role of fishing and trading communities in sustaining HIV spread in the Rakai district in Uganda. Dr Gonzalo Yebra followed with an update on his ongoing research on preliminary analysis of whole genome HIV sequences. Finally, Prof Deenan Pillay provided an overview of Dr Oliver Ratman’s analysis of multiple infections in men and women at the core of regional HIV epidemics.

Several new research proposals were discussed including Assessing trends in HIV virulence (Dr Josh Herbeck), Genome-wide association study of set point viral load using HIV whole genome sequences (Dr Robert Power), Estimating the heritability of viral load in Subtype C (Prof Andrew Leigh Brown on behalf of Dr Emma Hodcroft) and Ethical considerations of performing phylogenetic analyses in African settings (Dr Anne Hoppe).

We look forward to the outcomes of the ongoing analyses and look forward to the advancement of the new research proposals.    


The PANGEA_HIV network will be presenting CROI 2015

We are very excited that numerous abstracts of PANGEA_HIV and of partners involved in this network have been accepted for CROI 2015. Furthermore, Professor Christophe Fraser, Executive Committee member and co-lead of the analysis work

stream of PANGEA_HIV will be presenting at a plenary session at this conference which will be taking place in Seattle, USA from 23rd to 26th February 2015. More details will follow closer to the time.

First Annual Meeting of the PANGEA_HIV International Scientific Advisory Board and Steering Committee – 3rd December 2014

Prof Deenan Pillay chaired first annual PANGEA_HIV meeting of the members of the International Scientific Advisory Board and the Steering Committee, held at the Farr Institute in London on 3rd December 2014. The aims of the meeting were:

· To provide a summary of project and the achievements to date.

· To provide summaries and updates from the different cohorts and studies which are contributing samples and data to PANGEA_HIV.

· To provide more detailed reports from the different work-packages and the work package meetings which were held on 2nd December.

· To seek scientific advice from the Advisory Board on how to move forward.

The meeting was attended by representatives of all the different cohorts and study groups, as well as representatives from the Bill and Melinda Gates Foundation. Each cohort gave a brief summary of their work. Followed by informative output presentations on the following:

· Sampling Density, Sequence Length & and HIV Clustering; HIV Long-Range Genotyping using Proviral DNA – Vladimir Novitsky

· Transmission Networks within MRC Cohorts – Pontiano Kaleebu

· The Geography of Sexual Partner Networks in Rakai, Uganda – Kate Grabowski

· Phylogenetic Analysis at The Africa Centre – Tulio De Oliveira

· Initial Results of the Phylodynamic Methods Comparison Exercise – Christophe Fraser

There was lively debate during each session.

PANGEA_HIV Workshops - 02nd December 2014

where the sequencing technology that is being used in PANGEA_HIV has been developed and PANGEA_HIV samples are being sequenced.

SC-ISAB meeting 03Dec14

The workshops were a great success and we would like to thank all attendees for their valuable contributions.

Workshops were held at the Farr Institute in London, UK, on 2nd December 2014. The workshops commenced with a combined session before the teams split to discuss the outcome of the Phylodynamic Methods Comparison Exercise, future sampling and sample shipments as well as the sequencing that is being done as part of PANGEA_HIV. The latter workshop included a tour of the Sanger Institute in Hinxton, UK,

Invitation to join the Phylodynamic Methods Comparison Exercise - 6th October 2014

If you are a researcher with a keen interest in photodynamic methods we would like to invite you to join our Phylodynamic Methods Comparison Exercise. The blinded methods comparison exercise will be performed on simulated sequence data sets that capture different HIV transmission dynamics in generalized HIV-1 epidemics and aims to evaluate existing phylogenetic methods in their ability to identify recent changes in HIV incidence in order to inform HIV prevention efforts in sub-Saharan Africa. Secondary aims of the exercise are to evaluate the merits of full genome sequence data, and the impact of changing sequence coverage. With this exercise, PANGEA-HIV aims to direct further methods development in collaboration with participating research groups. 

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A world class sequencing laboratory has been successfully established at the Africa Centre - July 2014

We are pleased to announce that the first African world class sequencing laboratory has been successfully established at the Africa Centre at the University of KwaZulu-Natal (UKZN). The genomics laboratory will be used to generate high-quality genomic data and will become a core scientific resource of the University of KwaZulu-Natal (UKZN) and other universities within South Africa. Furthermore, the facility is essential to support the world-class genomics research which is being done as part of PANGEA_HIV.

The construction of the genomics laboratory can be witnessed via three short videos which can be accessed via http://www.bioafrica.net/videos.php

The PANGEA HIV network expands at the HIV Dynamics Meeting in Tucson - 10th May 2014

A PANGEA_HIV workshop was held in conjunction with the 21st International Workshop on HIV Dynamics & Evolution and attracted over 40 participants.  Many of the participants expressed an interest in joining the PANGEA_HIV consortium.

The PANGEA-HIV workshop commenced with three talks in the area of phylodynamics from people working at the forefront of technical development in the area: Denise Kühnert , ETH Zurich, Switzerland, David Rasmussen, Duke University , Durham, NC, and Eben Kenah, University of Florida, Gainesville, FL. The presentations by the invited speakers were all of high quality and well received. Following the PANGEA presentations an open floor discussion was held to discuss simulation-based studies and their relevance to PANGEA_HIV. [AH1]

[AH1]Andy/Christophe to re-phrase appropriately 

PANGEA meets at CROI 2014 - March 2014

A short PANGEA_HIV meeting was in Boston, USA, on Tuesday, 4th March 2014 to coincide with the 21st Conference on Retroviruses and Opportunistic Infections. The meeting attracted 25 members of the PANGEA_HIV consortium as well as external advisors and served to strengthen new collaborations. A detailed overview of the projects and the proposed analysis were provided and these were followed by some lively discussions. 

Kick off of PANGEA HIV - 08-09th January 2014

The official start of the PANGEA HIV project was marked with a kick-off meeting which took place at University College London from 08th to 09th January 2014. The meeting was a great success and partners from all collaborating institutions were involved in determining the governance of the project and in discussing in details on how the project goals could most effectively be achieved. 


Oliver Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain M, Joy JB, Michelle Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon A, Rasmussen DA, Stadler T, Volz E,  Weis C,  Leigh Brown AJ, Fraser C on behalf of the PANGEA-HIV Consortium. Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison. Mol Biol Evol, 2016. doi: 10.1093/molbev/msw217


Yebra G, Hodcroft EB, Ragonnet-Cronin M, Pillay D, Leigh Brown AJ on behalf of the PANGEA_HIV Consortium and the ICONIC Project. Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic


Pillay D, Herbeck J, Cohen MS, de Oliveira T, Fraser C, Ratmann O, Leigh Brown A, Kellam P on behalf of the PANGEA-HIV Consortium. PANGEA-HIV: phylogenetics for generalised epidemics in Africa. Lancet Infect Dis, 2015. 15(3): p. 259-61.


Yebra G, Ragonnet-Cronin M, Ssemwanga D, Parry CM, Logue CH, Cane PA, Kaleebu P, Leigh Brown AJ. Analysis of the history and spread of HIV-1 in Uganda using phylodynamics. J Gen Virol, 2015. 96(Pt 7): p. 1890-8.


Dennis AM, Herbeck JT, Brown AL, Kellam P, de Oliveira T, Pillay D, Fraser C, Cohen MS. Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest? J Acquir Immune Defic Syndr, 2014. 67(2): p. 181-95.


Accepted Abstracts:

Frampton D, Hoppe A, Kellam P, Kremyda-Vlachou M, Gallo Cassarino T, Fraser C, Pillay D on behalf of the PANGEA-HIV Consortium. Successes and Challenges in High Throughput Whole Genome Sequencing of HIV Samples from Sub-Saharan Africa. Virus Genomics & Evolution Conference 2016; Hinxton, Cambridge, UK.

Danaviah S, Manasa J, Wilkinson E, Pillay S, Sibisi Z, Msweli S, Pillay D, de Oliveira T on behalf of the PANGEA_HIV Consortium. Near Full Length HIV-1 Sequencing to Understand HIV Phylodynamics in Africa in Real Time. CROI 2015; Seattle, USA. Abstract: 256         

Hodcroft E, Ratmann O, Cori A, Pickles M, Lycett S, Ragonnet M, Hall M, Leigh Brown A and Fraser C on behalf of the PANGEA_HIV Consortium. Detecting changes in incidence using phylogenetic tools: simulation-based studies within the PANGEA_HIV Initiative. CROI 2015; Seattle, USA. Abstract: 249

Wilkinson E, Danaviah S, Manasa J, Tanser T, Herbst K, Pillay D, de Oliveira T on behalf of the PANGEA_HIV Consortium. Exploring transmission dynamics of HIV in rural KwaZulu-Natal, using phylogenetics. CROI 2015; Seattle, USA. Abstract: 248