🧨NO! There is no new variant that isn't detectable by PCR😤

The a new set of sequences, closely related to #Omicron has been detected & we *absolutely can* detect cases with PCR. What we can't tell as easily is /that they are Omicron or Omicron-like/.

theguardian.com/world/2021/dec…
First things first - I'm a huge @guardian fan & immensely disappointed by this irresponsible headline. This kind of alarmist headline causes panic & makes *the work of scientists like myself 10 times harder*.

Please do better.

2/N
So what is this all about then? Well, one 'nice' thing about Omicron is that it has what we call S:69/70del - a deletion that means it has S-gene-drop-out (SGTF), meaning that some PCR tests can see straight away that it might be Omicron. This makes helps surveillance!

3/N
You can read more about SGTF, what it is, and how we can use it to help with detecting Omicron in this great thread. Not all SGTF is Omicron, but it's a handy tool to help us find Omicron. (And as Omicron cases ⬆️, it's more likely to be Omicron)



4/N
Scientists have now identified another cluster of seqs which share many of the same mutations as 'original' Omicron (BA.1) - but is missing some, & has some other new ones. You can read a bit more about this here. The new seqs are called BA.2.



5/N
One key mutation that BA.2 is missing is the S:69/70del -- the one that causes the SGTF/S-drop-out. This means we can't use this 'shortcut' to find possible Omicron cases *for BA.2 only*. However, *the PCR test itself still works!* You'd test + for SARS-CoV-2.

6/N
You can see where the BA.2 sequences are relative to BA.1 on this older 21K #Omicron build - I'm working on getting them incorporated into newer builds. The BA.2 is in blue.
You can mouseover the branches to see different mutations leading to each.

7/N

nextstrain.org/groups/neherla…
Looks like the preview for this has updated - which is great! But my tweet now makes less sense. Here's a screenshot of the original, just so the original has some context!

• • •

Missing some Tweet in this thread? You can try to force a refresh
 

Keep Current with Dr Emma Hodcroft

Dr Emma Hodcroft Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @firefoxx66

5 Dec
I've gotten a few Qs lately about what the odds are that a SGTF (S-gene-drop-out) is Omicron vs another variant with S:69-/70-

I track S:69- routinely for CoVariants.org, so I pulled out data from 30 Aug - 7 Nov (pre Omicron) as a baseline:
github.com/hodcroftlab/co…

1/5
This only includes countries CoVariants tracks - so at least 500 seqs in any variant or mutation.

As @CorneliusRoemer illustrated a few days ago, knowing this can help you get an idea of whether an SGTF is Omicron or /nOmicron/ 😛(seq to confirm!)

2/5

VERY Importantly: This is going to change quickly now -- for a lot of countries the odds that they're detecting Omicron are rising markedly.

But particularly if looking back at SGTF data from the last few weeks, knowing your 'baseline' can be helpful.

3/5
Read 6 tweets
2 Dec
CoVariants.org is updated with new data, & a new 21K #Omicron build is up as well.✨
I won't continue tweeting every time there's an update - I'm currently trying to update both daily, as much as possible. Just keep checking back!

1/4
We can now start to see a hint of Omicron appearing in recent sequencing from countries with recent imported cases, with Netherlands as an example below. (#Omicron is in purple, top right)

2/4
In the focal build, we can see more #Omicron sequences coming in from more countries, thanks to hard work by labs worldwide, & #opendata.
These builds lag behind the latest data in GISAID, so countries may take 1-2 days to appear!

3/4
Read 5 tweets
1 Dec
Important to put stories like this in context: given the apparent prevalence of Omicron in South Africa & relatively high travel connections with Europe, it's not very surprising that introductions may have happened a few weeks ago.

npr.org/2021/11/30/106…
It does *not* mean that Omicron originated in Europe or is widespread here (as I've read in a few tweets) - our genetic surveillance suggests strongly that's not the case.

We *don't know* where Omicron originated right now, though it was first detected in Botswana/S Africa.
This may be because their own great surveillance efforts picked it up after it arrived there from elsewhere, with less ability to do this surveillance. But that place isn't Europe.

What this does illustrate is that travel bans come after some introductions have already happened.
Read 5 tweets
28 Nov
✨New CoVariants.org @nextstrain focal build for (21K) Omicron now up✨
nextstrain.org/groups/neherla…

This includes all 125 sequences that were available on GISAID this morning.

1/4
We can take a closer look at the cluster and see where sequences have been generated around the world - so far, from South Africa, Botswana, Hong Kong, Israel, Australia, Italy, & Belgium.

2/4

nextstrain.org/groups/neherla…
We need to interpret the genetic diversity of the Omicron cluster with caution - some sequences are better quality than others, which can lead to artefacts. Example, here Australian & Italy sequences are ancestral - erroneous & likely because of missing seq data!

3/4
Read 4 tweets
26 Nov
CoVariants.org Now Updated✨
B.1.1.529 is designed @nextstrain clade 21K & is now included on covariants.org/variants/21K

Note that data is still incoming! I currently only have the first sequences detected & will update as soon as I have additional sequences.

1/4
The 21K (B.1.1.529) page offers some information about some of the observed mutations - but I'd welcome contributions to link to more research!

On the right you can see the defining mutations - note that nonsynonymous mutations aren't yet available - I'll add them soon.

2/4
You can also see 21K (B.1.1.529) on the Shared Mutations page (& too big to screenshot!) to compare what Spike mutations we also see in other variants.

covariants.org/shared-mutatio…

3/4
Read 5 tweets
25 Nov
Lots of headlines about B.1.1.529 today.

Thoughts: Yes, this variant has a high # of spike mutations, & a few known to cause changes. But, we've seen previous variants that looked worrying & never took off. We should watch & wait for more data to estimate how concerning this is.
As a catch-up for those who haven't seen said headlines, I think this @guardian article on it gives a fair summary, with some level-headed quotes from scientists.
theguardian.com/world/2021/nov…
We got some additional information this afternoon from a press conference with @Tuliodna & @rjlessells. You can watch it below. A brief touch on some of the new information.

Read 12 tweets

Did Thread Reader help you today?

Support us! We are indie developers!


This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Too expensive? Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal

Or Donate anonymously using crypto!

Ethereum

0xfe58350B80634f60Fa6Dc149a72b4DFbc17D341E copy

Bitcoin

3ATGMxNzCUFzxpMCHL5sWSt4DVtS8UqXpi copy

Thank you for your support!

Follow Us on Twitter!

:(