Tracking and forecasting influenza virus evolution
Trevor Bedford (@trvrb)
21 Nov 2019
CEIRR Meeting
University of Pennsylvania
Population turnover of A/H3N2 influenza is extremely rapid
Nextflu
Project to provide a real-time view of the evolving influenza population
All in collaboration with 
Richard Neher
Nextflu → Nextstrain
Real-time tracking of pathogen evolution
with
Richard Neher,
James Hadfield,
Emma Hodcroft,
Thomas Sibley,
Colin Megill,
John Huddleston,
Barney Potter,
Sidney Bell,
Louise Moncla,
Charlton Callender,
Misja Ilcisin,
Kairsten Fay,
Jover Lee
Current view of H3N2 from nextstrain.org/flu
Central outputs used by GISRS
- Antigenic phenotypes (biweekly selection of ferret sera)
- Frequencies (twice yearly selection of vaccine strain)
- Forecasts (twice yearly selection of vaccine strain)
Antigenic phenotypes from ferret HI/FRA data
Weighted clade frequencies
Forecasts of clade turnover
Future directions
Integrating DMS serological data into forecasting framework
Integrating geographic circulation patterns into forecasting framework
Integrating genomic evolution into forecasting framework
Extending Nextstrain to other zoonotic influenza viruses
Acknowledgements
Bedford Lab:
Alli Black,
John Huddleston,
James Hadfield,
Katie Kistler
Louise Moncla,
Maya Lewinsohn,
Tom Sibley,
Jover Lee,
Kairsten Fay,
Misja Ilcisin,
Nicola Müller
Influenza: WHO Global Influenza Surveillance Network, GISAID, Richard Neher, John Huddleston, Louise Moncla, Barney Potter, Dave Wentworth, Becky Garten, Jesse Bloom, Sarah Cobey
Nextstrain: Richard Neher, James Hadfield, Emma Hodcroft, Tom Sibley, John Huddleston, Sidney Bell, Barney Potter, Colin Megill, Charlton Callender, Alli Black, Jover Lee, Kairsten Fay, Misja Ilcisin
