Lots of tweets about this today!
Let's see what we can see in the focal S:E484 build!

Phylogenetics (what I do - making 'family trees' from virus genetics) can be very informative to see how different variants are spreading, and how cases

The focal S:N501 build is now updated with data from 13 Jan!

There are a total of 247 non-UK & non-South African sequences in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

I'll do an additional thread later on, covering S:E484 & the 'Ohio variants'.

1/18

https://t.co/3bdttjKVl4

There are 244 new sequences in 501Y.V1 (B.1.1.7) from Australia, Belgium, Denmark, Germany, India, Israel, Italy, Netherlands, New Zealand, Norway, Portugal, Singapore, Spain & USA, as well sequences as from Ecuador and Greece for the first time.

2/18

Greece has 3 new sequences in 501Y.V1 for the first time. They indicate 2 separate introductions.

Ecuador has 2 sequences for the first time. They also indicate 2 separate introductions.

3/18

The USA has 61 new sequences (orange), from Florida, Minnesota, California, Pennsylvania, & New York.

A few of these represent separate introductions. Others form distinct clusters that may indicate ongoing local transmission.

4/18

Israel has 35 new sequences (orange). Some of these show separate introductions, but many link with older sequences, indicating ongoing local transmission.

5/18

A brief update to the focal S:N501 builds to start your Friday off right! This one includes data from 7 Jan 21.

We have about 20 new sequences each in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

Let's take a look at the new sequences, starting with 501Y.V1

1/14

https://t.co/kT1gFsSZn0

There are 22 new non-UK sequences in 501Y.V1, including for the first time from Luxembourg (3), & additional seqs from Singapore (1), Australia (4), France (12), & Switzerland (2).

2/14

First, Luxembourg has 3 sequences in 501Y.V1 for the first time. Each represents a separate introduction.

3/14

France has 12 new sequences (orange). Many of these represent independent introductions.

Zooming in (divergence view), we can see 2 new sequences are identical (possible local transmission), & 2 differ by 2 mutations (1 each).

4/14

Australia has 4 new sequences (red and orange) which are spread across the tree, representing separate additional introductions.

5/14

The latest focal S:N501 build is now up! It includes data from 4 Jan 2021.

We have new sequences in 501Y.V1/B.1.1.7 from Denmark, Singapore, Australia, Italy, Spain, France, Portugal, Germany, Brazil, Jamaica, Luxembourg, Pakistan & the USA.

1/12

https://t.co/FTjvV7T7wL

Denmark has 43 new sequences (in orange). These indicate additional introductions, as well as further expansion of the existing large local transmission cluster we saw previously (shown in zoomed divergence view).

2/12

10 new sequences from Portugal (orange) indicate additional, separate introductions.

3/12

Singapore has 5 new sequences (yellow). These indicate at least 5 separate introductions for the total of 6 sequences, with two identical sequences likely being 1 introduction.

4/12

5 new sequences from the US, from Florida & California (older sequences crossed through).

Zooming in (divergence view) on the California cluster, the relationship between these samples is difficult to infer from phylogenies alone.

5/12

The latest S:N501 focal build is now up, with data from 28th Dec:

We can see new sequences from Italy, Israel, Spain, France, & Ireland in the SE England variant (501Y.V1) & Switzerland in the South African variant (501Y.V2).

1/8

https://t.co/PEU7dhptO6

In 501Y.V1 (SE England variant), we can see 1 new sequence from France & Spain, each. The French sample has a travel history to the UK.

3 new sequences are from Israel (marked 1 & 2). Zooming in on '2' (divergence view) shows they are identical, indicating 1 introduction.

2/8

There are 7 new sequences from Ireland, found roughly in 5 places on the tree (4 are singletons, 3 cluster together - 2nd 'group' from the top).

These indicate at least 5 introductions, but we need to zoom in on the 3 that cluster to see more clearly.

3/8

Zooming in to the 3 that cluster together (divergence view), shows it can be difficult to distinguish introductions sometimes, especially as we expect strong travel links between the UK & Ireland, & may only be sampling the total diversity present in Ireland.

4/8

14 new sequences from Italy are scattered across the tree - some alone & some clustering.

Zooming in on a few clusters shows some seem to be linked, while others are harder to determine.
4 seem to be clearly linked as 1 introduction.

5/8

r u abbreving less rn?

Since the switch to 280 characters a year ago, we've seen an increase in people writing out full words and phrases.

All about the please and thank you.

With 280 characters, people are saying 'please' (+54%) and ‘thank you’ (+22%) more.

THANKS!!!!

💬💬💬

280 characters later, there are more ? and replies to Tweets. More room, more conversations!

I think the UK trans debate has teased out the sticking points for feminists, and it might be useful to lay them out given that the battle in the US, with a very different legislative environment, is just starting.

The GRA of 2004 gave trans people the ability to change legal sex via a GRC, but only if they had a psychiatric diagnosis of dysphoria and only after having lived in role for 2 years. The spousal veto gave spouses a chance to annul or obtain a favourable divorce.

While this ultimately created the loophole in women's rights that we've been fighting against in the last few years, it catered for a tiny number of dysphoric transsexuals and so did not have an enormous impact.

Discussions with trans friends and allies make it clear that, although surgery wasn't a requirement for a GRC, the diagnostic procedures were expected to trap and exclude males who did not want surgery, thereby preventing fetishists and opportunists from exploiting a GRC.

The Equality Act of 2010 defined the various protected characteristics, including both sex and 'gender reassignment', and provided for sex-based exemptions, under the auspices of which it is legal to exclude trans people from some single-sex spaces and services.

1/14 How do e-cigarettes (ECs) affect cigarette smoking among youth? My new paper with @FloeFoxon simulates each scenario and finds out which one best matches actual trends... https://t.co/dBB7kcnTls @jgitchell @mikepesko @SwitchFinder @jkelovuori @TobPolicy @Clive_Bates

2/14 First, let's talk about why this question is so difficult to answer: COUNTERFACTUALS. We can't know the alternate-reality answers, like which smokers would have never started in a world without ECs, and which nonsmokers would now be smoking without ECs as an option.

3/14 So, the best we can do is use fancy/sophisticated methodologies to estimate what would have happened to youth smoking rates in the absence of ECs. In our case, simulation modeling

4/14 First, we look at the declining smoking trends *that were already happening* before ECs came (~2010), and project them into the present. This is our BASE-CASE SCENARIO about what smoking trends would be if ECs were never invented. Actual trends were LOWER than this base-case

5/14 Side note about terminology: We use the term “catalyst” instead of “gateway,” because “catalyst” is more precise about the claim we are modeling (that ECs are used first, and then causally lead to smoking). Whereas "gateway" can include other mechanisms like renormalization.

"this is not a third world country.."

"this is not a third world country.."

"this is not a third world country..."

"this is not a third world country.."

"this is not a third world country.."