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
Agenda
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
Afternoon:
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
Morning:
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
Afternoon:
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
Morning:
Short presentations by participants (plenary or break-out groups, depending on size)
Remaining analytical topics to be covered.
Afternoon:
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
Morning:
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
Morning:
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)
Afternoon:
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.