Virologist at @ImperialInfect. Viruses, Influenza, SARS-CoV-2 and Variants.
5 added to My Authors
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
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...)
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!)
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.
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)
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
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.
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