As we pry open our inboxes & settle into 2022, it's temping to breathe a sigh of relief that we managed to navigate a high-risk, high-stress holiday season. πŸ₯΄

But it's critically important we keep a mask on for that sigh 😷, & remain watchful πŸ‘€ of the #COVID19 situation!

1/12
What are we facing, as we stand on the doorstep of Jan 2022? πŸšͺ

1. For many, cases are high & still rising πŸ“ˆ
2. Case detection may be impacted πŸ§‘πŸΎβ€πŸ€β€πŸ§‘πŸ»πŸ§‘πŸΌβ€πŸ€β€πŸ§‘πŸ»
3. Holiday infections are still being detected πŸŽ„
4. "Back to work" means new transmission chances 🀝

Let's walk through.

2/12
>1. For many, cases are high & still rising πŸ“ˆ

Holidays may have passed, but chances are they've only started leaving their mark - even before they started, cases were rising, & in many places are still shooting up.

(source @OurWorldInData 3Jan)

3/12
>1. For many, cases are high & still rising πŸ“ˆ

For comparison, here's the same period, same countries, last year (note X-axis scale change). Holidays sometimes even led to a drop in cases as 'usual' mixing decreased.
We aren't seeing this now - so must stay alert!

4/12
>2. Case detection may be impacted πŸ§‘πŸΎβ€πŸ€β€πŸ§‘πŸ»πŸ§‘πŸΌβ€πŸ€β€πŸ§‘πŸ»

Many people will have been extra-careful & tested frequently during the holidays to protect family & friends while celebrating 😷πŸ₯³. Now that things are 'back to normal' many may not be as careful, or as quick to test. πŸ€”

5/12
>2. Case detection may be impacted πŸ§‘πŸΎβ€πŸ€β€πŸ§‘πŸ»πŸ§‘πŸΌβ€πŸ€β€πŸ§‘πŸ»

Plus, often high cases = long queuesπŸ₯Ά! This can turn people off testing, or make them delay. Testing centres may also have been closed or had reduced hours. πŸ•‘

Combined: we could see fewer people getting tested than need to! 😟

6/12
>3. Holiday infections are still being detected πŸŽ„

With high cases, at least some coming home from holiday celebrations will have brought an unwelcome guest: #Omicron. But the holidays just ended - NYE was only 3 days ago πŸŽ†. Recent infections may not be testing βž• yet! 😳

7/12
>3. Holiday infections are still being detected πŸŽ„

With less urgency/ability to test (see 2), many may not realise they're infected until they develop symptoms πŸ€’ or hear from a contact about their positive test πŸ“ž. So further 'holiday cases' may still be incoming.

8/12
>4. "Back to work" means new transmission chances 🀝

Many places are work-from-home again, but not everywhere. Even where it is, things are likely less strict than before. And many important jobs simply can't! πŸ’»
But even outside of work, we resettle into our routines. πŸ›’

9/12
>4. "Back to work" means new transmission chances 🀝

Unfortunately, with every change in who & where we meet comes new contacts & new transmission opportunities. Previously 'contained' family πŸ‘¨β€πŸ‘©β€πŸ‘§β€πŸ‘¦ outbreaks could now spread to colleagues & friends. πŸ§‘πŸΏβ€πŸ€β€πŸ§‘πŸ»

10/12
We're all so tired of being careful. Particularly if you, like me, spent the holidays being ultra-careful. But now isn't the time to stop! πŸ™πŸ»

Winter is still here, cases are high, & #Omicron dominates.
Stay strong ⛓️ - stay careful 😷 - stay safe πŸ™πŸ».
We're not out yet.

11/12
There are reasons to hope! πŸ•―οΈ:
- Spring will come 🌷
- Boosters are rolling out & increase protection πŸ’‰
- #Omicron may hospitalize fewer cases πŸ₯
- Cases will hopefully peak & start declining soon πŸ“‰

But we'll get there faster - safer! - if we all do our part now! πŸ™πŸ»

12/12

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More from @firefoxx66

7 Dec 21
🧨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
Read 9 tweets
5 Dec 21
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/ πŸ˜›(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 21
✨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 21
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 21
✨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 21
✨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

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