Introduction to phylogenetic inferences 2016 Workshop

Introduction to phylogenetic inferences 2016 Workshop



Generation and use of viral gene sequence information is pertinent in the understanding of viral epidemics and in the design of strategies for the control, treatment and eradication of viral diseases. With the advent of new sequencing and analyses tools, it is now possible to exploit viral gene sequences to answer a wide variety of questions, ranging from the determination of virus origin to the mixing of ‘generalized’ and key population epidemics. These advances in technology have now been widely adopted, albeit in well-resourced settings, to contribute to the understanding and control of viral epidemics.

Overall Aim

To facilitate capacity building for the increased use and improved understanding of HIV-1 sequence data from general and key populations in Africa.

Capacity Building

The International Collaboration on Acute HIV infection screening and ART initiation (ICAHI) – a collaboration of scientists from Oxford, Lund, Amsterdam, Durban, and Kilifi, are proposing a series of initiatives to strengthen the capacity for HIV-1 sequence analyses within Kenya and beyond. The first initiative is a workshop to introduce participants from collaborating sites to sequence analysis and phylogenetics.

Workshop Objectives

  • To determine origin of HIV-1 epidemics in a population
  • To estimate time of HIV-1 epidemic introduction into a population
  • To describe the spatial and temporal dispersion of HIV-1 epidemic in a population
  • To describe HIV-1 transmission networks and the role of high-risk populations, including MSM, in the propagation of HIV-1 epidemic.

The Workshop

This will be conducted from 12-16 September 2016, and include lectures and practical training sessions. Lectures will cover basic concepts of viral evolution, gene homology, sequence alignment and phylogenetic methodology and approaches. In the practical sessions, participants will interact with existing sequence datasets and have hands on sessions on sequence handling, sequence alignment and phylogenetic analyses. In addition, participants are encouraged to bring their own sequence datasets to work on and use to make simple phylogenetic inferences.

Target Population

Scientists (MA, PhD, or Post-Doc) from MSM health research consortium Kenya, IAVI-supported African Research Centres and Sub-Saharan African Network for TB/HIV Research Excellence – SANTHE (max – 15 participants).

Expected Outcomes

Increased capacity in using HIV-1 sequence data to better understand the HIV-1 epidemic in key populations and to inform control strategies.


KEMRI/Wellcome Trust Research Programme, Kilifi campus.


Course Coordinators


Dr. Eduard Sanders

KEMRI/Welcome Trust Research Programme, Kenya

Dr. Joakim Esbjörnsson

Dr. Joakim Esbjörnsson

Oxford University


Dr. Amin Hassan

KEMRI/Welcome Trust Research Programme, Kenya