Trevor Bedford and his lab -- terrific collaboration since 2014

James Hadfield, Emma Hodcroft and Tom Sibley have led the recent development

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
• SARS-CoV-2 spreads more easily than SARS-CoV-1 or MERS
• Relatives are found in many different animals
• Closest known relative is a virus isolated from bats
  (RaTG13, approx 96% identical)
• Coronavirus recombine: trees need to be interpreted with caution

• 29k linear (+)ssRNA genome -- one of largest RNA virus genomes
• the first 2/3 code for the replication machinery

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

About two mutations per month, but mutations are often clustered and overdispersed

SARS-CoV-2 is remarkably mixed geographically -- genomes connect outbreaks in different places

• SARS-CoV-2 was disseminated widely before travel restrictions
  → Border closures had little effect (maybe if earlier)
• The virus typically spread locally before it was noticed
  (while testing focussed on people with travel history to hotspots)
• Temporal resolution by mutation is about 4 weeks
  → too low to resolve direct transmissions or directionality
  → sufficient to connect outbreaks and identify clusters
• Currently no solid evidence for mutations with functional significance
  see Sergei Pond's analysis of signals of positive selection

WRONG:

LIKELY WRONG:

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

Original title mid February...

• humidity (e.g. dry air increases time before droplets fall down)
• temperature
• UV light
• behavior (e.g. time spent indoors, ventilation, heating)

Yellow: good fit -- Blue: poor fit

Counter-factual scenario without strong social distancing!

Trevor Bedford and his lab -- terrific collaborations since 2014

James Hadfield, Emma Hodcroft, and Tom Sibley have led the recent development