Dr Emma Hodcroft Profile picture
May 23 12 tweets 11 min read
This morning's session at the #Nobel Symposium starts with Michael Farzan explaining ACE2 binding in #SARSCoV2 & #SARSCoV1, including a great timeline comparison between how long steps took between the two (much faster in SC2) & asking if we can improve vaccines.
@MichaelWorobey follows, speaking to the importance of digging into the evidence of #SARSCoV2 outbreak sources & Hunan market.
He opens with a remark about how this beautiful location with so many great people to talk to is pretty close to heaven - he's not wrong!
Hyeryun Choe closes the first session with a great talk on how #SARSCoV2 adapted to humans, and the importance of the D615G mutation, to stabilizing the protein. With a great graphic reminder of how quickly G614 dominated.
Eric Snijder opens the second session with the reminder that "there are more proteins that are exciting than just Spike!" He points out that comparing similarities and differences across larger families can be very informative - and tells us about double membrane vesicles.
Last before lunch is @unibern's own @ProfVolkerThiel! Giving a fantastic overview of how to reconstruct #SARSCoV2 viruses, including VoC, and using them in human cell & animal models to evaluate differences. And another great visualisation of the advantage of G614.
No chance of falling asleep after lunch as @McLellan_Lab takes us through a fantastic talk on stabilizing prefusion spike proteins for vaccine development - critical for our current SC2 vaccines! And some exciting hints in the search for a universal beta-coronavirus vaccine.
And before coffee, @GuptaR_lab takes us through some great examples of discerning the impact of mutations in #SARSCoV2 VoCs - including careful inspection of the differences between Delta & Omicron in cell entry.
To close out the invited speakers today, @Tuliodna gives a brilliant talk on how South Africa managed in the pandemic & what was key: previous epidemic experience, holistic collaboration, communication with govt, being resilient, & giving back to the scientific community!
PhD student @robert_dyrdak outlines detection of mixed #SARSCoV2 BA.1 & BA.2 infections, and occasional misclassification of them as BA.3
Getting us going this morning at the #Nobel symposium is @florian_krammer excellently walking us through immune responses after #SARSCoV2 immunization & infection, including the impact of boosters & interesting observations on binding, non-neutralising antibodies!
@PennyMo70026063 battles disappearing p-values in uncooperative slides but delivers a great overview of the differences in immune profiles by vaccination & variant infection, & reminds us of the unique position of South Africa both in #SC2 history & due to people living with HIV
Fallen behind in tweeting, but Lindsey Baden gives an excellent overview of the challenges of the vaccine, including the importance of community inclusion, building public trust, & science communication. But he started with his takeaway: "The vaccine works."

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More from @firefoxx66

May 22
🎉VERY excited🎊 to share news of the shiny new #monkeypox @GenSpectrum (previously CoV-Spectrum) website & API - allowing lightning-fast ⚡️ queries to get info on metadata & sequence information.
As more #opendata sequences come in, this will be incredibly powerful!
To give an example of a couple of queries:

Number of #monkeypox sequences per country as JSON:
mpox-lapis.gen-spectrum.org/v1/sample/aggr…

Nucleotide mutations of #monkeypox sequences from this year as CSV:
mpox-lapis.gen-spectrum.org/v1/sample/nuc-…
I hinted at this coming a little earlier today 😉 - but want to really emphasize: this is what truly #opendata looks like.
Enabling development of tools that are able to benefit everyone to do fast & effective research to underpin response & understanding

Read 4 tweets
May 22
Feels very timely today to be on the way to the #Nobel Symposium in Stockholm: The First Great Pandemic of the 21st Century.
Though I do not believe the #monkeypox outbreak will be a pandemic, it's a reminder there are many pathogens that can rear their heads in different ways.
Tomorrow, I'll talk about how phylogenetics played a critical role in #COVID19 #SARSCoV2 - but also outline what challenges we face when we look to tomorrow's pandemics. In particular we have to ensure: sequencing, sharing, software & sufficient background.
A lot of pandemic preparedness focuses on detecting a new pathogen, or what to do once we know it's bad news. But a lot of the critical work is a little more boring: encouraging #openscience, ensuring credit, maintaining & advancing software & building up our virus knowledge.
Read 8 tweets
May 6
🎉Another new feature available on CoVariants.org!🎉

In collaboration with Aquaria.app @AquariaApp, you can now link directly to interactive protein structures for every variant!

1/4

covariants.org/variants/22A.O… Image
You can find these links in a dedicated box, just above the gif protein structures - just click on any of the available proteins (any with mutations) to go straight through to Aquaria.app!

2/4 Image
For details on how this works, check out @aSchaFu's fantastic thread, including some of the amazing things you can investigate using Aquaria.app:



3/4
Read 4 tweets
May 4
🎉New Variants on CoVariants.org!🎉

In line with the recent addition of 22A (BA.4), 22B (BA.5), & 22C (BA.2.12.1) as @nextstrain clades, you can now find these three variants on CoVariants.org!

1/9

As usual, each new variant has their own page, where you can see defining mutations (left), a per-variant plot (bottom) and read about the variant, its mutations, & studies done so far!

2/9

covariants.org/variants/22A.O…
And of course, these variants now show up on the Per Country & Cases pages.

22A & 22B are quickly overtaking 22L in South Africa, and we can see 22C on the rise in the USA.

In the USA Cases plot, we can also see 22C.

3/9

covariants.org/per-country
covariants.org/cases
Read 9 tweets
Apr 21
🎊BIG new update to CoVariants.org!🎊

Using cases from @OurWorldInData, we're now generating plots showing cases by variant! 📊🤯

This has been much-requested & in-the-works since Nov 2021. Let's take a look!

HUGE 🙏 to @MoiraZuber & @ivan_aksamentov!

1/7
Click the new 'Cases' link at the top of any CoVariants.org page, or go straight to covariants.org/cases!

Note that these are *estimates* of the proportion of cases by variant. Only a small % of cases are sequenced - we're extrapolating, so interpret with care!!

2/7
Currently we only show countries that have sequenced at least 3% cases for >=50% of the 2-week period CoVariants tracks (since May 2020). This tries to avoid plotting data that may not represent cases well.

If you think a country has good data & is missing - let me know!

3/7
Read 7 tweets
Mar 30
🗒️CoVariants.org Update!📝

CoVariants now filters out more data that can lead to misleading or confusing variant trends! Thanks to eagle-eyed users 🔎 & @MoiraZuber!

1/5
1 - CoVariants now only displays variant data from sequences that have come from humans.

A variant may circulate longer in animals than in people, & focused sampling of those animals can thus give a misleading picture. See mink EU1 samples in Latvia, before & after!

2/5
2 - Many people had flagged strange pockets of recent 'other' sequences in countries like Italy, India, Chile & others.
Was this a new variant?

No: most of these are just bad sequences where a clade can't be assigned! CoVariants now filters these out entirely!

3/5
Read 5 tweets

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