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


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

Central outputs used by GISRS

  1. Antigenic phenotypes (biweekly selection of ferret sera)
  2. Frequencies (twice yearly selection of vaccine strain)
  3. Forecasts (twice yearly selection of vaccine strain)

Antigenic phenotypes from ferret HI/FRA data

Weighted clade frequencies

Forecasts of clade turnover

John Huddleston

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

Louise Moncla


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