Tom Peacock Profile picture
Virologist at @ImperialInfect. Viruses, Influenza, SARS-CoV-2 and Variants.
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Jan 19
As its been getting increasing attention recently, I'm going to write a short thread on what we currently know about BA.2.
-what is BA.2?
-what is BA.2 doing currently?
-Should we be concerned about it? First off - what is BA.2?

BA.2 is a sister lineage to BA.1. Currently both lineages are defined as the Omicron variant.

As @shay_fleishon shows - BA.2 shares a lot of mutations with BA.1, but it also has many differences
Read 15 tweets
Jan 9
If anyone wants to check our working out on this (and I encourage people to do so if you are able to!) heres the phylogenetic tree of the sequences not clustering at all: In comparison the actually real recombinant lineage XC (an Alpha/Delta recombinant found in Japan a few months back) forms a really nice, single cluster (in red)
nextstrain.org/fetch/genome.u…
Read 8 tweets
Jan 3
Lots of chat about B.1.640.2 in the last few days - just a few points to keep in mind:
- B.1.640.2 actually predates Omicron
- in all that time there are exactly... 20 sequences (compared to the >120k Omis in less time)
Def not one worth worrying about too much at the mo... and as @shay_fleishon pointed out there havent been any new sequences uploaded since before Christmas... this virus has had a decent chance to cause trouble but never really materialised (as far as we can tell at least...)
Read 4 tweets
Jan 1
Happy New Year!

New Omicron preprint from us about replication in primary cells, receptor usage and entry routes (can be found here while screening on biorxiv):
drive.google.com/file/d/1vam2PV…

Here are a couple of highlights We looked at replication of Omicron in different cell types including primary human nasal epithelial cells (hNECs) – it consistantly replicates really really fast in these cells – even faster than Delta (which itself replicates faster than anything before!)
Read 11 tweets
Dec 21, 2021
Lots of reports of Omicron sequences carrying Delta-like mutations (eg P681R or L452R). Although a subset of these might end up being real, the vast majority will most likely turn out to be contamination or coinfection. No clear signals of anything real or nasty happening (yet). To be sure a signal like this is real you really want multiple sequencing labs finding the same recombinant/homoplasy independently (or at least on different sequencing runs) - ideally you would look into the raw seq files as well and show no mixed bases.
Read 7 tweets
Dec 8, 2021
I've been thinking about this for a while but with B.1.637.1 being assigned I've decided to write a thread about 'second generation variants'.
- What are they?
- Why should we be bothered about them?
- How should we look for them?
github.com/cov-lineages/p… Disclaimer – B.1.637.1 is almost definitely nothing to be worried about – its an interesting lineage that has some convergent evolution with Delta – seqs might increase in the coming weeks but this is mostly due to it being an S-gene target failure virus (false positive for BA.1)
Read 13 tweets
Nov 23, 2021
Just spotted: very small cluster of variant associated with Southern Africa with very long branch length and really awful Spike mutation profile including RBD - K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505H

github.com/cov-lineages/p… Full Spike profile: A67V, Δ69-70, T95I, G142D/Δ143-145, Δ211/L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F
Read 9 tweets
Oct 11, 2021
We think we can see some evidence of circulating SARS-CoV-2 isolates which have picked up short sequences of human mRNAs and inserted them into thier genomes so we wrote a virological post about it.

virological.org/t/putative-hos… While substitutions and deletions are common and well described for SARS2, insertions are rarer, though several widespread lineages have unique insertions. Mu/B.1.621, A.2.5, B.1.214.2, and AT.1 all have insertions in Spike
Read 10 tweets