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.
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.
Introductions can still matter in how fast something spreads - reducing them (particularly through travel-related testing) may buy time. But the variant is very likely in many places - 'keeping it out' isn't a realistic goal for most places around the world.
Important: We don't have to try & say that Omicron is widespread in US/Europe to highlight that travel bans are harmful, discourage sharing, & likely not as effective as people assume.
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✨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!
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.
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!
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.
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.
"What's the situation in Europe?"
Yes - cases are rising in many places 📈
But it's difficult to talk about 'Europe' 🌍 as one entity right now: as the pandemic continues, things are getting more heterogeneous. 📊
*What one country can manage, may not be true for another*
1/16
First, we have to look both at absolute case numbers & change in case numbers - some places with high cases may see a decrease but remain high 📉, others with lower numbers might be seeing a concerning sharp increase 📈
"Thing is, we have a chance to build office work from the ground up: to re-evaluate the old 9-to-5, to relocate city centre offices, to let people work tight 4-day weeks, to realise that working smart is better than the old-fashioned idea of working hard"
From chatting to people, I think the main reason those high up want people to come back to the office is simple: control.
Even when productivity metrics indicate all is well, bosses don't trust employees & like to be able to physically check on them. Not related to actual output.
I'd be super curious in any survey difference between how much superiors miss "stopping by to chat" vs how much their employees feel similarly.