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
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/
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
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…
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
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 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
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
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