To add to the excitement of your Saturday evening, the focal S:N501 build is now updated with data from 8th Jan, including 48 new seqs in 501Y.V1 (B.1.1.7 #b117) & 501Y.V2.

1/12

https://t.co/AbdhO1rqpw

There are 46 new non-UK sequences in 501Y.V1, from the Netherlands, Italy, Israel, Ireland, Norway, Sweden, the USA, and Luxembourg.
And 2 new non-South African sequences in 501Y.V2, from Australia for the first time.

2/12
In 501Y.V1:

Ireland has 4 new sequences (orange). 2 sit separately but are identical, indicating an additional introduction. 2 link to a previous sequence (green), 1 mutation away each. This could indicate location transmission, unsampled diversity, or a common exposure.

3/12
The Netherlands has 10 new seqs (orange). Many sit apart on the tree, indicating additional introductions. 3 cluster together separated by a few mutations. 2 are identical to an older seq. 1 falls in a cluster of older seqs. Some of these could indicate local transmission.

4/12
Israel has 22 new sequences (orange). 1 links to an older sequence, but is separated by 3 mutations, so may be separate introductions. Another is identical to an older sequence. But most new sequences cluster together (blue), clearly indicating local transmission.

5/12
Norway has 3 new sequences (orange). 2 cluster together but differ by 1 mutation, making their relationship hard to confidently infer. The other sits separately and indicates an independent introduction.

6/12
Italy has 2 new sequences (orange). Zooming in (divergence view) we can see they are identical (yellow), so are likely a single introduction.

7/12
The USA has 2 new sequences, from Connecticut (orange). They sit separately from each other & other USA sequences on the three, indicating independent introductions.

8/12
Luxembourg has 2 new sequences (orange). They sit apart on the tree, indicating separate introductions.

Sweden has 1 new sequence (orange). It sits separately, indicating an additional introduction

9/12
In 501Y.V2:

Australia has sequences that fall into 501Y.V2 for the first time. Zooming in (divergence), we can see they are identical, indicating one introduction.

10/12
As always, the S:N501 "reduced UK" build is updated, & the country-graphs are also updated - remember: many places are preferentially sequencing S:N501 (hot pink), so the frequencies shown may not accurately reflect the true proportion of S:N501!

11/12

https://t.co/c7wlQOLRiq
Finally, the main CoVariants SARS-CoV-2 Variant Tracking page is updated with new links & a new section for S:E484 - but as always, I welcome Pull Requests & Issues in the repository, with papers or online resources I've missed!

12/12

https://t.co/6qBdWhREtl

More from Dr Emma Hodcroft

Each day brings new challenges, but here's an update to the dedicated S.N501 build, using data from 6 Jan 2021 to keep you going.

There are 42 new non-UK sequences in 501Y.V1 (B.1.1.7) & 7 new non-South-African sequences in 501Y.V2.

1/14

https://t.co/kT1gFsSZn0


There are 42 new non-UK sequences in 501Y.V1 from the Netherlands, Italy, Hong Kong, Finland, Sweden, Germany, USA, Switzerland, Brazil, and the first sequence from 501Y.V1 in Oman.

https://t.co/XA8VR8HiEq

2/14


Oman has their first sequence which falls into 501Y.V1:

3/14


Finland has 12 new sequences (orange), which mostly represent separate introductions. Zooming in (divergence view), we can see 3 of the new sequences are identical (red), which may indicate the cases are connected.

4/14


Sweden has 8 new sequences (orange), which indicate separate introductions.

5/14
🎉Happy New Year!🎉

To kick off 2021, here's an update on:
- S:N501 variants (501Y.V1/V2) with data from 31 Dec 2020
- 69/70del variants
- 20A.EU1 variant (most prevalent variant in Europe)

(Here are some fireworks that look a bit like phylogenies! 🎆)

1/23


The latest sequences from 31 Dec show new sequences in the S:N501Y.V1 variant (originating from SE England) from Netherlands, Denmark, Australia, Italy, Canada, the USA, Germany, Switzerland, & India.

2/23

S:N501 link
https://t.co/TfHfPgBEBS

Image link
https://t.co/3aCKv1pAcI


Canada, Germany, & Switzerland all have sequences that fall in 501Y.V1 for the first time, scattered across the tree.

3/23


The USA also has its first 2 sequences that fall in 501Y.V1, from Colorado & California. India also had its first 3 sequences, also from different regions.

In both cases, the sequences are not connected, indicating separate introductions.

4/23


In countries with previous sequences:

6 new sequences from Netherlands, in orange/yellow (green are older).
1 is clearly separate - zooming in (& in divergence view, coloured by country) it is harder to determine the relationship between the others.

5/23

More from For later read

#IDTwitter #IDFellows
Introducing our new series: “IDFN top 10 articles every fellow should read”🔖

#1: SAB management
by @mmcclean1 @LeMiguelChavez
Reviewers @KaBourgi, @IgeGeorgeMD, @Courtcita, @MDdreamchaser

We know is subjective & expect feedback/future improvements 👇

1. Clinical management of Staphylococcus aureus bacteremia: a review.
https://t.co/9tBCtp9mlP
👉 A must read written by Holland et al. where they review the evidence of the management of SAB.

2. Impact of Infectious Disease Consultation on Quality of Care, Mortality, and Length of Stay in Staphylococcus aureus Bacteremia: Results From a Large Multicenter Cohort Study.
https://t.co/XujO68pCuH
👉ID consult associated with reduced inpatient mortality.

3. Predicting Risk of Endocarditis Using a Clinical Tool (PREDICT): Scoring System to Guide Use of Echocardiography in the Management of Staphylococcus aureus Bacteremia
https://t.co/otcA1pxjAw
👉Predictive risk factors for infective endocarditis, and thus the need for TEE.

4. The Cefazolin Inoculum Effect Is Associated With Increased Mortality in Methicillin-Susceptible Staphylococcus aureus Bacteremia.
https://t.co/CQZiryVWZz
👉Presence of cefazolin inoculum effect in the infecting isolate was associated with an increase 30-day mortality.

You May Also Like

I’m torn on how to approach the idea of luck. I’m the first to admit that I am one of the luckiest people on the planet. To be born into a prosperous American family in 1960 with smart parents is to start life on third base. The odds against my very existence are astronomical.


I’ve always felt that the luckiest people I know had a talent for recognizing circumstances, not of their own making, that were conducive to a favorable outcome and their ability to quickly take advantage of them.

In other words, dumb luck was just that, it required no awareness on the person’s part, whereas “smart” luck involved awareness followed by action before the circumstances changed.

So, was I “lucky” to be born when I was—nothing I had any control over—and that I came of age just as huge databases and computers were advancing to the point where I could use those tools to write “What Works on Wall Street?” Absolutely.

Was I lucky to start my stock market investments near the peak of interest rates which allowed me to spend the majority of my adult life in a falling rate environment? Yup.