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:

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

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

  1. Rapid human-to-human spread in Wuhan beyond initial market outbreak
  2. Extensive local transmission while testing was rare
  3. 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

Data from

My favorite metric is number of sequences available from samples collected in the past 30 days

Data from

US, UK and Europe all have stunning genomic surveillance programs

Data from

Africa and South America have picked up dramatically but there are still geographic gaps

Data from

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.


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