Emergence, Evolution and Epidemiology

This is a website for collaborative analysis and discussion about the emergence, evolution and epidemiology of novel human viral pathogens. The site is divided into sections for different viruses. The aim is to present new analyses as data becomes available.

All content is publically viewable but adding content, comments or blog entries is restricted to account holders. 

Emerging viruses and new epidemics

Recently discovered and newly emerging viruses

coronavirus-1.pngMERS-CoV - Emerging human cases of a genotype 2c betacoronavirus currently spatially associated with the Arabian Peninsula


influenza.pngAvian H7N9 - Emerging human cases of a H7N9 influenza in the area of Shanghai, China


Major human pandemics

Ongoing work on the molecular epidemiology and evolution of major human pathogens. Influenza will be added first, others to follow.


Influenza A, B & C

Human immunodeficiency virus (HIV)

Hepatitis virus C (HCV)

Dengue virus

West Nile virus

Methods and techniques

Notes and tutorials on the methods used for molecular epidemiology and evolution

Introduction: How to read a phylogenetic tree

Interactive Tool: What is the probability of no changes in a pair of viruses sampled at different times?

Cook Book
Contributed questions and analyses for answering them

BEAST software
Bayesian MCMC software for analysing pathogen gene sequences

An older (now fossilized) site about the 2009 A/H1N1 influenza pandemic is available here. This was active during the pandemic and provides a useful prototype for this website.