Genomic surveillance of seasonal and pandemic influenza

Trevor Bedford (@trvrb)
16 Apr 2018
Annual Symposium
Institute for Disease Modeling

Influenza virus

Flu pandemics caused by host switch events

Host switch events often occur through reassortment

Tang et al. 2010. Infect Dis Clin North Am.

Spread of swine flu in 2009

Sequencing to reconstruct pathogen spread

Epidemic process

Sample some individuals

Sequence and determine phylogeny

Sequence and determine phylogeny


Project to conduct real-time molecular epidemiology and evolutionary analysis of emerging epidemics

with Richard Neher, James Hadfield, Colin Megill,
Sidney Bell, John Huddleston, Barney Potter,
Charlton Callender, Emma Hodcroft

Pandemic influenza H1N1 2009

After pandemic, seasonal epidemic influenza distinguished by competition between strains

Post-pandemic seasonal influenza

Population turnover is extremely rapid

Clades emerge, die out and take over

Clades show rapid turnover

Dynamics driven by antigenic drift

Drift necessitates vaccine updates

H3N2 vaccine updates occur every ~2 years

Vaccine strain selection by WHO

Current H3N2 diversity

Current H3N2 diversity

Two clades have been growing rapidly

Clade A2 more recently increasing

Reassortment event appears to drive success of clade A2

Reassortment event appears to drive success of clade A2

Timely surveillance critical for effective seasonal vaccine

Pre-pandemic influenza

Ongoing surveillance of circulating avian and swine viruses essential

H5N1 diversifying across the globe

Li et al. 2014. Emerg Infect Diseases.

Repeated reverse zoonoses of human flu into swine population

Nelson and Vincent. 2015. Trends Microbiol.


Bedford Lab: Alli Black, Sidney Bell, Gytis Dudas, John Huddleston,
Barney Potter, James Hadfield, Louise Moncla

Influenza: WHO Global Influenza Surveillance Network, Richard Neher, Barney Potter, John Huddleston, James Hadfield, Colin Russell, Andrew Rambaut, Dave Wentworth, Becky Garten, Jackie Katz, Marta Łuksza, Michael Lässig, Richard Reeve

Nextstrain: Richard Neher, James Hadfield, Colin Megill, Sidney Bell, Charlton Callender, Barney Potter, John Huddleston, Emma Hodcroft