CADDE Genomic Epidemiology Workshop

The CADDE Genomic Epidemiology Workshop (2 to 6 December 2019) is a training hands-on course based on integrating Oxford Nanopore MinION sequencing with genetic data analysis for outbreak investigation. Researchers wanting training in library preparation, running the MinION sequencer, and analysing sequencing data using bioinformatic and phylogenetic tools are welcome to attend.

The Oxford Nanopore MinION is a portable hand-held DNA sequencer that is capable of producing 20 Gbase of sequence data in near-real time. This system was used to track

Ebola spread in West Africa, monitor the Zika outbreak in northeast Brazil, the yellow

fever outbreak in Minas Gerais, and more recently Zika local transmission in Angola. Using novel protocols developed by the ZiBRA and CADDE project teams, researchers can now generate virus genomes in less than 24 hours.

Places are limited and will be allocated according to the following criteria: applicants must have a background in either biology, public health, bioinformatics and/or wet lab work, and be able to attend all five days of the course. The applicants will need to

submit a written statement and an abstract. We will have a limited number of spaces in our first edition. Successful applicants will be asked to present a poster on their research. Oxford Nanopore Starter Packs will be available for awarded posters.

Apply here.




Monday 2 Dec 2019

Morning (IMT-FMUSP)

09.00 Workshop Welcome (Nuno Faria)

09.30 Arbovirus epidemiology in Brazil (SVS, Rodrigo Said)

10.00 Arbovirus surveillance in São Paulo (Renato Souza, Adriano Pinter, CVE)

11.30 Genomic monitoring of arboviruses (Luiz Alcantara)

12.00 Oxford Nanopore Technology – brief talk (Leila Luheshi)

12.30 Transport to São Paulo Zoo

Afternoon (São Paulo Zoo)

13.00 Walking lunch and demonstration of lab in a suitcase (Luke Meredith)

14.00 Zoology of Sao Paulo tour (Adriano Pinter, Zoo team, SUCEN)

15.00 Diagnostic of epizootics in Brazil & Sao Paulo (Alessandro and Mariana Cunha)

16.00 An introduction to DNA sequencing during outbreaks (Nick Loman)


Tuesday 3 Dec 2019

Morning (IMT-FMUSP)

Nanopore Sequencing [group 1]

08.30 Introduction to Nanopore: from sample to sequence (Nick Loman) (Lecture Theatre)

09.30 Library Preparation (Part 1) (Wet Lab)

11.00 Library Preparation (Part 2) (Wet Lab)

Afternoon (IMT-FMUSP)

14.00 MinION Sequencing (Wet Lab)

16.00 Introduction to RAMPART (Wet Lab)

Demonstrators and lecturers:

Group 1: Sarah Hill, Darlan Candido, James Hadfield

Group 2: Jaqueline Jesus, Ingra Claro, Flavia Salles, James Hadfield


Wednesday 4 Dec 2019

Morning (IMT-FMUSP)


08.30 Introduction to command line (Sarah Hill)

10.00 Guide for nanopore sequencing (Sarah Hill)

Afternoon (IMT-FMUSP)


14.00 Consensus sequence calling (Nick Loman)

16.00 Real-time sequencing with Rampart (James Hadfield)

Demonstrators and lecturers:

Sarah Hill, Darlan Candido, Jaqueline Jesus, Ingra Claro, Flavia Salles, James Hadfield


Thursday 5 Dec 2019

Morning (IMT-FMUSP)

08.30 Introduction to Phylodynamics (Andrew Rambaut)

09.30 Assembling genomic datasets (Bernardo Gutierrez)

11.00 Multiple sequence alignment and tree reconstruction methods (Jayna Raghwani)

Afternoon (IMT-FMUSP)

14.00 Dated phylogenetics (Philippe Lemey)

15.30 Virus phylogeography (Philippe Lemey and Nuno Faria)

17.00 Free computer time

Demonstrators and lecturers:

Philippe Lemey, Nuno Faria, Andrew Rambaut, Jayna Raghwani, Bernardo Gutierrez


Friday 6 Dec 2019 – Phylodynamics in public health

Morning (IMT-FMUSP)

08.30 Visualizing and interpreting outbreak genomic data (Nuno Faria)

10.00 Real-time phylogenetics (James Hadfield)

11.30 Epidemiological data, from collection to interpretation (Moritz Kraemer and Carlos Prete)

Afternoon (IMT-FMUSP)

14.00 Visualizing epidemiological data in real-time (Rachel Oidtman)

15.00 Translating data into policy (UNICEF Brazil)

16.00 Closing remarks and drinks

Demonstrators and lecturers:

Philippe Lemey, Nuno Faria, James Hadfied, Mortiz Kraemer, Carlos Prete, Manuel, Rachel Oidtman