A brief report by Amin Hassan, Post-Doctoral Researcher at KEMRI-Wellcome Trust Research Programme (KWTRP)
Generation and use of viral gene sequence information is pertinent in the understanding of viral epidemics. Whilst a lot of viral sequence data is being generated from resource limited settings, little capacity exists to make optimal use of these data to inform strategies for the control, treatment and eradication of viral diseases.
With support from the International AIDS Vaccine Inititative (IAVI) and SANTHE, the International Collaboration on Acute HIV Infection (ICAHI) organised this workshop, aimed at strengthening the capacity for viral phylogenetic inferences amongst young African scientists. The workshop was facilitated by two local (KEMRI/Wellcome Trust Research Programme) and two visiting (Erasmus University Medical Center, Rotterdam and Lund University, Sweden) scientists. It brought together a unique mix of 17 participants from Kenya (9), Uganda (3), South Africa (2), Rwanda (1), Zambia (1) and the UK (1), with diverse viral pathogen interests and from varied qualifications - from undergraduates through to post-doctoral fellows.
The intensive four days training included lectures covering the basic concepts of evolution, sequence alignment, gene homology, substitution models and tree building methods. This was followed by hands-on practicals using different phylogenetic softwares, characterisation of unknown sequences, determining origins and dating of viral introductions into a population. The workshop culminated in a programme-wide seminar with two excellent presentations from the visiting scientists around studying intra-host viral evolution using phylogenetic inferences, and modelling cost-effectiveness of HIV pre-exposure prophylaxis.
Overall, all the participants rated the workshop as very good or excellent, that it met their expectations and that it should be offered again in the future. Specifically, most participants felt that the training was very practical and relevant to their projects: “Well done! The course was very practical, thoroughly enjoyable and very relevant in my own work.” workshop participant
It was therefore generally concluded, by both the facilitators and the participants, that the workshop contributed to some phylogenetic inferences capacity amongst the participants, thus a huge success!