Patterns of early diversity of SARS-CoV-2

Richard Neher
Biozentrum & SIB, University of Basel

slides at

Do early patterns of diversity give us clues about the origin of SARS-CoV-2?

Maybe, but interpreting these patterns is hard an much uncertainty remains.

WHO report

Multi-market hypothesis

Garry,, 2021

Plausible roots of current SC2 diversity

  • 19A/lineage B: Huanan market cluster, favored by models without explicit outgroups, implies 2 reversions
  • 19B/lineage A: 2 mutations closer to bat viruses, would result in an earlier TMRCA
  • Guangdong cluster: 3 mutations closer to bat viruses, epidemiologically less plausible, still earlier TMRCA
  • Other viruses close to bat viruses: mostly one-offs, some reversions are expected by chance

Root inferred by Pekar et al

Pekar et al

Similarity to bat viruses

The 8782/28144 split

Homoplasies and Reversions to bat-like states

Homoplasies and Reversions to bat-like states (non-terminals only)


  • Both 19A/19B rootings are plausible
  • Early epidemiological dynamics is expected to be very stochastic, sampling focussed on 19A (lineage B, Huanan cluster)
    → epi-evidence weak in my opinion
  • Positions 8782 and 21844 are reasonably stable
    → points towards 19B (lineage A) as root
  • Some genomes need to be interpreted with caution


Trevor Bedford and his lab -- terrific collaboration since 2014

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

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

Data are shared and curated by GISAID