MISMS South Africa

Johannesburg, South, December 3-5, 2018

Meeting venue: National Institute for Communicable Diseases, National Health Laboratory Services, 1 Modderfontein Road, Sandringham, 2193, Johannesburg, South Africa

A Training Workshop on Infectious Diseases Dynamics and Evolution was co-hosted by the National Institute for Communicable Diseases (NICN). 


Participants from 12 countries convened for the 3-day workshop


Monday, December 3

Morning: Plenary session, main auditorium

9.00-9.15am: Welcome: Lynn Morris, NICD
Introduction and workshop goals: Cheryl Cohen, NICD & Cecile Viboud, FIC

9.15-10.45a Computational disease modeling at the Fogarty International Center (FIC) and the South African Center for Epidemiologic Modeling and Analysis (SACEMA).
Moderator: Anne Von Gottberg, NICD.

9.30-9.55am: Epidemiology and transmission dynamics of influenza, Cecile Viboud, FIC

9.55-10.20am: Animal-human interface and evolutionary dynamics and of acute viral infections, Martha Nelson, FIC

10.20-10.45am: Projecting the impact of a product recall on the South African Listeriosis outbreak: Juliet Pulliam, SACEMA.

10.45a-11.15a Coffee Break

11.15a-12.30p: Research highlights at NICD and HIV dynamics. Moderator: David Spiro, FIC

11.15-11.40am: Epidemiology of influenza and respiratory viruses: Cheryl Cohen, NICD 11.40am-12.05pm: HIV epidemic and phylogenetics: Dale Kitchin, NICD 12.05-12.30pm: Phylodynamics concepts and the origins of HIV: Philippe Lemey,

Catholic University of Leuven.

12.30-1.30p Lunch Break

Afternoon: Break for phylogenetics and epidemiology/modeling tracks


A. Phylogenetics Track: Monday, December 3

Presentation: Introduction to phylogenetics – Data, alignment, ML trees. Nidia Trovao, FIC Computer tutorial on data, alignment, ML trees:

Getting data from FluDB or LANL (depending on interest in flu or HIV). Alignment with MUSCLE/MAFFT, trees with FigTree?, view trees with FigTree.

Late afternoon: Software installation checks.


Nidia Trovao (FIC) teaches FigTree

Tuesday December 4: 101 talks and software demonstrations


Presentation: Introduction to phylodynamics – Clocks, temporal signal, basic coalescent, phylogeography.

Tempest tutorial. Nidia Trovao. http://beast.community/tempest_tutorial

Presentation: Introduction to BEAST. Running BEAST, interpreting output and diagnosing issues. BEAST tutorial


Phylodynamics of flu tutorial: http://beast.community/workshop_influenza_phylodynamics

HIV cluster phylodynamics: demo/tutorial.


Wednesday December 5: Presentations and hands-on practice with own data


Short presentations by participants (plenary or break-out groups, depending on size)

Remaining analytical topics to be covered.


Work with your own data in small groups, facilitated by instructors.


B. Epidemiology/Modeling Track:


Monday, December 3
Afternoon: 101 presentations of modeling concepts.

Introduction to time series, seasonality analyses, and transmission models: Cecile Viboud, FIC

Break (3.30pm)

Basics of R tutorial (reading data, formatting/reshaping, plotting): Amanda Perofsky, FIC Software installation checks


Tuesday, December 4: 101 modeling concepts, hands-on tutorial, participants presentations


9.00- 10.45a Comparison of HIV transmission models (Juliet Pulliam)

Break (10.45—11.15am)

11.15-12.15pm Short presentations by participants (1 slide/2mn per participant)

Lunch (12.30-1.30pm)

1.30p-2.30pm: Seasonality, heatmaps, and clustering tutorial in R: Cecile Viboud and Amanda Perofsky.

Break (2.30-3.00pm)

3.00-4.00pm: Transmission model and reproduction number tutorial

4.00-5.00pm: EpiPoi demo for seasonality analyses (if needed) and/or time on your own to start formatting your data for analysis


Richard Nyamota presents on SIV in Kenya

Wednesday December 5: Participant presentations and hands-on practice with own data


9.00-10.00am Short presentations by participants (cont’d)

10.00-10.30am Remaining analytical topics to be covered and question session (all instructors).

Break (10.30-11.00am)

Work with your own data in small groups, facilitated by instructors.

Lunch (12.30-1.30pm)


Work with your own data in small groups, facilitated by instructors.

Break (3.00-3.30pm)

Work with your own data in small groups, facilitated by instructors. 5pm: Adjourn.