Real-time genomic surveillance for public health response
Trevor Bedford (@trvrb)
Fred Hutchinson Cancer Center / Howard Hughes Medical Institute
13 Apr 2022
Africa PGI Webinar Series
Africa CDC
Slides at: bedford.io/talks
Sequencing to reconstruct pathogen spread
Epidemic process
Sample some individuals
Sequence and determine phylogeny
Sequence and determine phylogeny
Pathogen genomes may reveal
- Evolution of new adaptive variants
- Epidemic origins
- Patterns of geographic spread
- Animal-to-human spillover
- Transmission chains
Influenza: Forecasting spread of new variants for vaccine strain selection
Zika: Uncovering origins of the epidemic in the Americas
Ebola: Revealing spatial spread and persistence in West Africa
MERS: Repeated spillover into the human population from camel reservoir
TB: Tracking individual transmission chains
Genomic epidemiology during the COVID-19 pandemic
Over 10M SARS-CoV-2 genomes shared to GISAID and evolution tracked in real-time at nextstrain.org
Richard Neher,
Emma Hodcroft,
James Hadfield,
Thomas Sibley,
John Huddleston,
Ivan Aksamentov,
Moira Zuber,
Jover Lee,
Cassia Wagner,
Denisse Sequeira,
Cornelius Roemer,
Victor Lin,
Jennifer Chang
Three key insights that genomic epi provided during pandemic
- Rapid human-to-human spread in Wuhan beyond initial market outbreak
- Extensive local transmission while testing was rare
- Identification of variants of concern and mapping of increased transmission
Jan 11: First five genomes from Wuhan showed a novel SARS-like coronavirus
Jan 19: First 12 genomes from Wuhan and Bangkok showed lack of genetic diversity
Single introduction into the human population between Nov 15 and Dec 15 and subsequent rapid human-to-human spread
Rapid global epidemic spread from China
Epidemic in the USA was introduced from China in late Jan and from Europe during Feb
Seattle Flu Study detects local circulation and charts early epidemic in Washington State
Direct introduction from China ~Feb 1 responsible for the majority of the epidemic
Mitigation efforts visible in virus genetic diversity
After initial wave, with mitigation
efforts and decreased travel,
regional clades emerge
Repeated emergence of variant of concern viruses
Genetic relationships of globally sampled SARS-CoV-2 to present
Rapid displacement of existing diversity by emerging variants
Rapid displacement of existing diversity by emerging variants
Genomic surveillance
Sequences generated and shared at an unprecedented pace with >1M genomes shared in Mar 2022 alone
My favorite metric is number of sequences available from samples collected in the past 30 days
US, UK and Europe all have stunning genomic surveillance programs
Africa and South America have picked up dramatically but there are still geographic gaps
Global genomic surveillance aimed at rapid turnaround times important to catch new variants early, additional sequences from Africa or South Amerca would be far more valuable than additional sequences from the US or Europe
In depth genomic surveillance tied to data systems allows investigation of variant severity, secondary attack rate, etc...
Future perspectives
Response to the pandemic has spurred sequencing capacity across the world. This sequencing capacity should shift to non-SARS-CoV-2 pathogens of local public health concern as acute impacts of pandemic dissipate.
Acknowledgements
SARS-CoV-2 genomic epi: Data producers from all over the world, GISAID and the Nextstrain team
Bedford Lab:
John Huddleston,
James Hadfield,
Katie Kistler,
Louise Moncla,
Maya Lewinsohn,
Thomas Sibley,
Jover Lee,
Cassia Wagner,
Miguel Paredes,
Nicola Müller,
Marlin Figgins,
Denisse Sequeira,
Victor Lin,
Jennifer Chang
