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

MERS-CoV - Emerging human cases of a genotype 2c betacoronavirus currently spatially associated with the Arabian Peninsula

• Spatial, temporal and epidemiological information
• Phylogenetic Analysis
• Molecular Evolutionary Analysis
• MERS-CoV potential reservoir and related viruses in non-human hosts
  |Genetic evidence of a camel reservoir of MERS-CoV
  |Speculation and evidence for a camel source of human MERS-CoV
  |MERS-CoV-like fragment in bat in Saudia Arabia
• Genome Mutations of Novel Human Betacoronavirus 2c

• A rough analysis of case data

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

• Background information - Geography and temporal
• Molecular Phylogenetic Analysis

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