An outbreak of gastroenteritis in Stegen, Germany, June 1998

You are using an outdated browser. Please upgrade your browser or activate Google Chrome Frame to improve your experience. Context On 26 June 1998, the St Sebastian High School in Stegen (school A), Germany, celebrated a graduation party, where 250 to 350 participants were expected. Attendants included graduates from that school, their families and friends, teachers, 12th grade students, and some graduates from a nearby school (school B). ...

How to create a new post for the site


In this article we explain how to contribute new posts and slidedecks for the website. General workflow for contributing If you’re new to git and GitHub check out this nifty guide. The general workflow would include the following steps: Fork the project from the GitHub RECON learn project: This will create a copy of the project in your own GitHub account. You will need to clone this archive, and make the modifications there. ...

Is this outbreak over?

#epicurve #outbreak #outbreak end

Motivation At which time point during an outbreak of a person-to-person transmitted disease can one declare the outbreak as having ended? Answering this question can be important in order to calm the population, re-attract tourists, stop export bans or reduce alertness status. The current WHO method for answering the above question is as follows: a period of two times the longest possible incubation time needs to pass without observing additional cases, before the outbreak can be declared as being over. ...


Ebola simulation part 2: outbreak reconstruction

#genetics #simulation #response #outbreaker2 #epicurve #reproduction number #ebola

This practical is the second part of the response to a simulated Ebola Virus Disease (EVD) outbreak taking place in the city of Ankh, Republic of Morporkia. While the first part focussed on early assessments of transmissibility, this part explores more methodological options for estimating transmissibility, and provides an introduction to outbreak reconstruction using outbreaker2. An update on the EVD outbreak in Ankh, Republic of Morporkia After some rather concerning preliminary results on the new EVD outbreak in the city of Ankh, Republic of Morporkia, Public Health Morporkia (PHM) has sent you updates of the linelists and contact data. ...

Introduction to phylogenetics

#genetics #evolution

This lecture introduces general concepts pertaining to phylogenetic tree reconstruction, as well as the main approaches used for building trees, including distance-based, maximum parsimony, and maximum likelihood methods. It also discusses phylogenetic uncertainty, bootstrap, and some caveats and bad practices. Slides Click on the image below to access the slides: About this document Contributors Thibaut Jombart: initial version Contributions are welcome via pull requests. The source files of this lecture can be found here. ...

Outbreak investigation using outbreaker2

#reconstruction #outbreaker2

This short lecture gives a primer on some methodological aspects of outbreak reconstruction using outbreaker2. Slides Click on the image below to access the slides: About this document Contributors Thibaut Jombart: initial version Finlay Campbell: figure on *outbreaker2*’s contact model Contributions are welcome via pull requests. The source file can be found here. Legal stuff License: CC-BY Copyright: Thibaut Jombart, 2017