Genomic epidemiology during a pandemic: lessons learned
Fred Hutch Cancer Research Center, Seattle, Washington, USA
Chan Zuckerberg Initiative & CZBiohub, San Francisco, California, USA
Sidney M. Bell (@sidneymbell)
Introduction
- Genomic epidemiology
- Nextstrain
- COVIDTracker
Learnings
- Open-source development
- Data management
- Partnership building
ACG
AGG
AGT
Many viruses mutate and spread on similar time-scales
ACG
AGG
AGT
Genomic epidemiology contextualizes outbreaks and resolves ambiguous cases
Project to conduct real-time genomic epidemiology and evolutionary analysis of emerging epidemics
James Hadfield, Emma Hodcroft, Thomas Sibley,
John Huddleston, Louise Moncla, Cassia Wagner, Miguel Parades, Misja Ilcisin, Kairsten Fay, Jover Lee, Allison Black, Colin Megill, Barney Potter, Charlton Callender
Richard Neher
Trevor Bedford
Behind the scenes:
Nextstrain for SARS-CoV-2
- Labs contribute directly to GISAID (now have >63k full genomes)
- Nextstrain pulls a complete dataset from GISAID every 24 hours
- This triggers an automatic rebuild on Amazon Web Services
- We manually update new GPS coordinates, metadata, etc...
- We push this build online to nextstrain.org and tweet the update from @nextstrain
Early warning: Washington state
2 day turnaround
24 languages
~500k weekly readers
Early warning: Kinshasa
SARS-CoV-2 is everywhere.
The fight is now (hyper)local.
COVIDTracker
Project Leads: Josh Batson, David Dynerman, Amy Kistler
Genomic Epidemiology: Patrick Ayscue, Sidney Bell
Sequencing: Michelle Tan, Angela Detweiler, Renuka Kumar, Lienna Chan, Lusajo Mwakibete, Karan Bhatt
Data & Engineering: Shannon Axelrod, Sam Hao, Danielle Kain, Phoenix Logan, Jack Kamm, Aaron McGeever, Angela Pisco, Jonathan Sheu, Tony Tung, James Webber, Mark Zhang
Project to build capacity for genomic epidemiology in Departments of Health across California
Coverage in California
Genomic epidemiology in practice
-
Resolve ambiguous contact tracing
-
Link outbreaks together
-
Identify introductions to county
Learnings:
open-source development, data management & partnership building
Developing
open-source software
during a pandemic
Sidebar: if you intend for your code to ever be run by someone else, you're a developer
To grow, you need an 'architecture of participation'
Reuters/Christian Hartmann
README
Contributing guidelines
Groomed issue board
Code of conduct!!
Clear process for PR review
Continuous integration will save your bacon
(or: the boring stuff no one wants to think about but will bite you in the tuckus if you don't)
Data management
Context is everything
Equity: we have work to do
Data sharing: meeting people where they're at
JSON with public data
CSV with private (PII/PHI) metadata
Linking data is a huge challenge
| DOH ID | CZB ID | GISAID ID |
|---|---|---|
Queryable, version-controlled, single source of truth
ACTG...
ACTG...
ACTG...
Scripted, reproducible QC & disambiguation
Linking data is a huge challenge
Partnerships & teams
Impact requires trusted collaborators
CLIAHub
Lightweight "process" helps get things done
Standup + Expectations + Code review
Work yourself out of a job
Iteration, rest, appreciation
Takeaways
- Global progress is largely the sum of local progress
- Genomic epidemiology can provide key context and disambiguation during outbreaks
- Building an architecture of participation is an investment in project resilience
- A single, version-controlled source of truth will simplify your life
- "Process" can be lightweight and amplify efforts
- Partnerships and capacity building are required for long-term impact
Acknowledgements
COVIDTracker Project Leads: Josh Batson, David Dynerman, Amy Kistler
Genomic Epidemiology: Patrick Ayscue, Sidney Bell
Sequencing: Michelle Tan, Angela Detweiler, Renuka Kumar, Lienna Chan, Lusajo Mwakibete, Karan Bhatt
Data & Engineering: Shannon Axelrod, Sam Hao, Danielle Kain, Phoenix Logan, Jack Kamm, Aaron McGeever, Angela Pisco, Jonathan Sheu, Tony Tung, James Webber, Mark Zhang
Nextstrain: Trevor Bedford, Richard Neher,
James Hadfield, Emma Hodcroft
Thomas Sibley, John Huddleston, Louise Moncla, Cassia Wagner, Miguel Parades, Misja Ilcisin, Kairsten Fay, Jover Lee, Allison Black, Colin Megill, Barney Potter, Charlton Callender
Questions?
@sidneymbell
slides.com/sidneymbell
sbe-coronavirtual-2020
By Sidney Bell
