Thread by @CorneliusRoemer

Genetic diversity within #Omicron can give us clues about its age and growth rate.
Omicron's abundant spike mutations and deletions interfere with sequencing, sometimes leading to incomplete genomes.
As a result phylogenetic inference struggles, causing spurious diversity. 1/5

To explore diversity within Omicron while addressing these issues @richardneher and I built a tree ignoring
1. sites mutated with respect to reference in more than 90% of available Omicron sequences
2. homoplasic sites that often fall in dropout regions
nextstrain.org/groups/neherla… 2/

The resulting tree has one big polytomy and a small number of notable clades.
Most sequences are within one or two mutations of the main group.
Though masking might lead to underestimates of the diversity, the resulting tree suggests a recent common ancestor 1-2 months ago. 3/5

As one example for how this tree can be used, the recent Dutch sequences appear to span the globally observed diversity. 4/5
nextstrain.org/groups/neherla…

It is amazing that within one week after discovery, there are publicly available sequences from across the globe
A big thank you to all sequencing teams for sharing this data
We will keep this analysis updated and hope it is useful
Link to @nextstrain: nextstrain.org/groups/neherla… 5/5

Clarification:
The Dutch sequences were all from travellers from South Africa.
The observed diversity indicates this was not just one single group but that travellers had picked up Omicron a number of times independently from the community, presumably in South Africa.

The tree has been updated with 3 new international sequences from Spain, Czech Republic and Reunion
The Spanish sequence is on a branch with ORF1a:K564N, shared with 1 Dutch and 2 South African sequences.
Czech/Reunion have one extra mutation each that hasn't been observed so far