Discussing with @edwardcholmes, @arambaut, and BGarry, is it possible that B.1.1.7 and E484K_K417T/N lineages are all 'successful', but for different reasons?

The latter being inherently more transmissible, with the others due to _some_ level of immune escape?
We know the B.1.1.7 lineage is inherently more transmissible, but we don't have the same strong data for the E484K_K417T/N lineages - just that they appear to be expanding (rapidly) in the areas they're found.
We DON'T have any direct evidence that the E484K_K417T/N lineages _do_ indeed escape immunity though - it's purely a hypothesis, but I think worth testing.

Also, even if they _do_ escape _some_ immunity, it's unlikely to be complete - but even small effect = advantageous.
And since this always comes up - we (I) don't know if/how this might affect vaccine efficacy, but unlikely to render them non-functional.

But to @pfizer @moderna_tx, let's get the spikes from these SARS-CoV-2 lineages cloned and into animals so we can get early data.
*Latter = obviously I meant former (B.1.1.7) here!
Adding this recent preprint from CMMID where they consider these hypotheses for the 501Y.V2 lineage in South Africa (a E484K_K417N lineage).


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More from @K_G_Andersen

6 Jan
Additional cases of B.1.1.7 in San Diego. While worrying, these were found via targeted measures and not representative - we think the current prevalence is ~1%.

This will increase in coming weeks and the genomics suggest substantial local transmission.

As I mentioned at a presser last week, the presence of this strain does not change what we need to do - but we *do* need to do it better. Distance, avoid crowds, work from home, and wear facemasks.

I strongly suggest N95s when in public. You can buy here: clinicalsuppliesusa.com
Some more background on these cases in @sdut with a few comments from me.

Read 5 tweets
30 Dec 20
We just detected the first evidence of the UK lineage / B.1.1.7 circulating in California as mentioned by @GavinNewsom an hour ago. More details to follow via @SanDiegoCounty press conference at 2:30pm.

Data here: github.com/andersen-lab/H…

@scrippsresearch @UCSanDiego
For context, no history of travel and here's the timeline on test/sequencing (@nanopore for speed...).
Here’s a link to the consensus sequence in @NCBI: ncbi.nlm.nih.gov/nuccore/MW4222…
Read 5 tweets
20 Dec 20
It's important to be skeptical, but don't say there's "ZERO evidence" for a theory only to present a theory there's ZERO evidence for (and in this case, not plausible).

The emerging evidence is very suggestive that the N501Y lineages in UK and S. Africa are more transmissible.
To be clear, the observation so far is that there are lineages with N501Y *associated* with more rapid spread. Additionally, the UK lineage has more associated mutations than expected. The concern is that the mutations may be causing the more rapid spread, but we don't know yet.
To me - and I'm very skeptical when it comes to this - the data are highly suggestive that the observed association is indeed a causal relationship. A lot of very good scientists hard at work figuring it out.

Relevance (if any) to immunity/vaccines/clinical features, all unknown
Read 4 tweets
18 Dec 20
Lawyers making public health decisions is about as crazy as it gets. History will not be kind.

Strip Clubs: Open and 100% capacity
Restaurants: Open and 100% capacity
ICUs: Crushed and 0% capacity
Schools: Closed

This is not rational San Diego.

Just to make this absolutely clear - as I say in the UT article, I'm not suggesting throwing the restaurants and strip clubs under the bus. We need the county, the state of California, and the federal government to help them get through this with massive-scale programs...
... Largely such programs have been insufficient and have failed - this *has* to change and it has to change *now*. Continue to support restaurants ability to offer takeout, get it more often, tip more if you have the means...
Read 5 tweets
15 Dec 20
Interesting paper discussing the difficulty of rooting the SARS-CoV-2 tree - which is something we have been interested in too.

Most analyses root on e.g., Hu-1, but it appears that e.g., WA1 (lineage) may actually be a more appropriate root IMO.


One critical issue with the paper - they mention that rooting on non-Wuhan sequences would be inappropriate as that is inconsistent with epidemiological evidence (see 👇). That's not true - there's a very strong sampling bias early in the epidemic...

... which means that (early) sequences observed outside Wuhan could very likely have circulated (uncaptured) in Wuhan as well.

Read 5 tweets
12 Dec 20
The @CDCgov put out their interim guidelines for SARS-CoV-2 antigen testing and the document is exemplary - clear, concise, and with a lot of relevant information.

Short 🧵 on other useful documents for e.g., workplace and university testing 👇


General overview of different ways of testing for COVID-19.


FAQ from CDC on how to interpret testing results (as well as other FAQs).


Read 7 tweets

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