Jan 11: First five genomes showed that the outbreak was caused by a novel SARS-like coronavirus

Jan 19: First 12 genomes from Wuhan and Bangkok lack genetic diversity

Single introduction into the human population between Nov 15 and Dec 15 and human-to-human epidemic spread from this point forward


Dec/Jan: Emergence from Wuhan in ~Nov 2019

Jan/Feb: Spread within China and seeding elsewhere

Feb/Mar: Epidemic spread within North America and Europe

Mar/Apr: Decreasing transmission with social distancing

Epidemic in the USA was introduced from China in late Jan and from Europe during Feb

Once in the US, virus spread rapidly

Single introduction at the beginning of Feb quickly shows up throughout the country

Timely example: third wave in Hong Kong can be seen here

Sequencing immediately useful for epidemiological understanding, but selection and functional impacts should also be studied

Significant interest in spike mutation D614G

This mutation occurred in the initial European introduction

D614G is prevalent throughout Europe and mixed in US and Australia

D614G is increasing in frequency across states in US and Australia

D614G is increasing in frequency across states in US and Australia

The success of D614G can be explained by either:

  • D614G is more transmissible and has higher $R_0$
  • founder effects and epidemiological confounding

Neutralization data suggests that D614G won't interfere with vaccination

Moving forward

  • Better methods for large datasets
  • Distinguishing endogenous spread from importations
  • Tying genomic epidemiology together with richer epi data to better understand local transmission
  • Incorporating within-host variation to improve phylogenetic resolution
  • Integrating clinical data to look for mutations that impact clinical outcomes


Genomic epi: Data producers from all over the world and GISAID

The Nextstrain Team: Richard Neher, James Hadfield, Emma Hodcroft, Thomas Sibley, John Huddleston, Louise Moncla, Cassia Wagner, Miguel Parades, Misja Ilcisin, Kairsten Fay, Jover Lee, Allison Black, Colin Megill, Sidney Bell, Barney Potter, Charlton Callender