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!)
We could see the same doing competition assays (using variant specific RT-qPCR probes). No matter which isolates we used we could see Omicron replicates incredibly fast in primary nasal cells.
We confirmed Omicron likes to use human ACE2 then looked at which other species ACE2s it can use well - as others have found mouse ACE2 is very compatibly but so is horseshoe bat as well as some of the avian ACE2s which other variants haven't ever shown any usage of.
As others have described Omicron Spike is just not very fusogenic, this is in contrast to all previous SARS-CoV-2 variants...
...and is puzzling as in our hands N679K and P681H alone both enhance S1/S2 cleavage. It appears something quite strange is going on here with Omicron - maybe some sort of epistatic interaction somewhere else in Spike?
We describe evidence that Omicron Spike is more able to use the endosomal entry route than previous variants, being less sensitive to TMPRSS2-mediated entry and more sensitive to inhibitors of endosomal entry.
In live virus in primary cells, although TMPRSS2 inhibitors slow down Omicron, it eventually caught back up while Delta is completely inhibited. Despite being able to enter via the endosome Omicron live virus also appears completely resistant to endosomal IFITM inhibition.
Therefore we propose a model where Omicron has become less specialised in its entry route and become more of a 'generalist' - this allows it to efficiently infect a greater number of cells in the upper respiratory tract and may mean it even has a lower infectious dose?
Encouragingly, this work is very consistant with virological data on Omicron from our colleagues at @CVRinfo, @GuptaR_lab, @SystemsVirology, HKU, and more!
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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.
As far as I understand it these are appearing now for two reasons: 1) Lots of Delta and Omicron circulating in the same areas 2) Some older sequencing primer sets being less effective at picking up parts of Omicron so low level contamination with Delta being selectively picked up
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)
So what are 2nd gen variants? I’m defining them as variant lineages (ie long branch lengths, no intermediates) that are derived from previous variant lineages. B.1.637.1 is the first clear example of one of these that been assigned by @PangoNetwork
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
For those interested this has an NTD insertion at the NTD insertion hotspot (at aa214) which shows high likelihood of being host-derived (from host TMEM245 mRNA)
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
We looked at where insertions cluster in Spike and found they mostly fall in the NTD or near the S1/S2 site. This is very similar to where deletions are found.