Introduction to Genomic Epidemiology

Sidney M. Bell (@sidneymbell)

Chan Zuckerberg Initiative

Mini workshop: California Departments of Public Health

September 10, 2020

Agenda

• Introduction to genomic epidemiology
   
• How to build and interpret trees
   
• Case studies: what kinds of questions can we answer with genomic epi?
   
• Discussion and questions

Genomic epidemiology

Using pathogen genomic sequences to understand the distribution and spread of infectious disease

Genomic epidemiology

• Complement contact-tracing efforts
   
• Infer prevalence over time
   
• Identify introductions, sources and sinks
   
• Predict severity and size of future outbreak seasons
   
• Determine drivers and determinants of spread

Viruses evolve and spread on similar timescales

Grubaugh, Nature Micro, 2019

Outbreak spread

Sample some individuals

Sequence and identify mutations

Determine phylogeny

Determine phylogeny

How to read a tree

Change (mutations, time)

How to read a tree

F

E

A

C

D

A

C

D

E

F

Common ancestor with A

What kinds of questions can we answer with a tree?

• Tracking introductions
   
• Resolve ambiguous contact tracing
   
• Understand relationships between outbreaks

(NBC)

Questions?

@sidneymbell

Many thanks to the Bedford lab,
Nextstrain team, and Biohub Data Science