Trevor Bedford and his lab -- terrific collaboration since 2014

especially James Hadfield, Emma Hodcroft, Ivan Aksamentov, Moira Zuber, and Tom Sibley

Data we analyze are contributed by scientists from all over the world

Data are shared and curated by GISAID

• SARS-CoV-2 is in the same family as SARS-CoV-1, MERS and
  two seasonal coronavirus
• The latter cause mild disease, the former severe
• Relatives are found in many different animals
• Closest known relative of SARS-CoV-2 is a virus isolated from bats
  (RaTG13, approx 96% identical)
• SARS-CoV-2 spreads more easily than SARS-CoV-1 or MERS;
  pre-symptomatic transmission makes it hard to control

• 29k linear (+)ssRNA genome -- one of largest RNA virus genomes
• the first 2/3 code for the replication machinery
• While it spreads, it accumulates about 2 mutations per month

Early genomes differed by only a few mutations, suggesting very recent emergence

• The outbreak originated from one source
  → not repeated zoonoses from a diverse reservoir.
• The common ancestor of all samples was Nov - early Dec 2019.
• Family clusters showed up as identical genomes (expected)
• A second clade emerged that will continue to spread

• Clade 20A (and its daughters 20B and 20C) have essentially taken over
• With them, several mutations, including S:D614G have become prevalent.
• There are reports that S:D614G increases transmission
  (equivocal in my view)
• Overall no strong signal that the virus has changed in meaningful ways
• But mutations are very useful to reconstruct how the virus spreads

Prior to travel restrictions, SARS-CoV-2 is spread widely across the globe

• comprehensive global analysis kept up-to-date by us
• data curation done by GISAID

• Focus on local analyses by Public Health Departments
• Necessity to subsample sequences
• Often little experience with command line tools
• Large data sets → computational challenges
• Challenging to interpret

Trevor Bedford and his lab -- terrific collaboration since 2014

especially James Hadfield, Emma Hodcroft, Ivan Aksamentov, Moira Zuber, and Tom Sibley

Data we analyze are contributed by scientists from all over the world

Data are shared and curated by GISAID

WRONG:

Low genetic diversity combined with very biased sampling → no directionality can be inferred