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Dr Emma Hodcroft Profile picture
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Aug 30 • 4 tweets • 4 min read
Submitting to @NCBI can be intimidating -- but no more! Getting your #monkeypox sequences up is as simple as following this guide!

Thanks to NCBI & of course to all scientists worldwide contributing to #opendata #openscience
Why is #opendata useful? It's much easier for scientists to share, create tools for, & publicly analyze open sequences.
For example, @Nextstrain creates the #monkeypox builds with open data & provides curated seqs+meta

nextstrain.org/monkeypox/hmpx…

github.com/nextstrain/mon…
@mpxv_lineages uses open data to designate lineages & @GenSpectrum uses open data for the API & website

github.com/mpxv-lineages/…

mpox.genspectrum.org
We absolutely have work remaining to do to ensure scientists can feel secure in sharing data openly without scooping fears, & I personally would love to see publishers be stronger here & the community decide on guidelines. I believe it's possible!

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More from @firefoxx66

Dr Emma Hodcroft Profile picture
Aug 26
Our paper on relabelling the internal clades of the #monkeypox to be non-geographical, & proposing a new lineage naming system within Clade IIb, is now out in @PLOSBiology 🙌🏻
This has been an international effort I'm humbled to be part of.

journals.plos.org/plosbiology/ar…

1/8
Because it seems like there's a lot of misunderstanding around this paper/proposal - our paper does *not* touch on renaming the #monkeypox virus itself.
We focus on switching to more structured, non-stigmatizing & standardized naming within the virus phylogeny.

2/8
Contrary to what many people believe, there are long-standing efforts to name new viruses, & re-label old virus-related terms (like clades/lineages/strains), to avoid potentially stigmatizing & often inaccurate names. But previously, you didn't hear of it in the media! 😁

3/8
Read 8 tweets
Dr Emma Hodcroft Profile picture
Aug 12
📣CoVariants.org Update!📣

To help your Friday be fantastic 😎, I'm happy to say that we've updated CoVariants with awesome new graphs that load on-demand, speeding up the browsing experience!

HUGE thanks to @richgoater for implementing! 🎉🙏🏻

1/3
With this new addition, graphs now load dynamically as you scroll, speeding up overall loading time & reducing the overhead (especially on older mobile devices 📱).
Check it out on covariants.org/per-country, or the Per Variant or Cases pages!

2/3
As we try to graph more data from more places over longer times, we're always interested in improving our graphs & website!
If you'd like to help, check out the issues on our Github or reach out with an idea - we love contributions! 🥰

3/3
github.com/hodcroftlab/co…
Read 4 tweets
Dr Emma Hodcroft Profile picture
Aug 5
Monkeypox:
- We've had warnings about it for years
- We have a vaccine
- We have antivirals
- We have experience w poxviruses

Pandemic Preparedness is a buzzword right now, but if we don't seem to be prepared to effectively combat #monkeypox... Is that what we want?

1/
I am not implying that combatting #monkeypox is easy - & the current outbreak has plenty new to figure out (cryptic transmission, new presentation & lesion locations, MSM spread, ABOBEC mutations).

But we've had so much opportunity to be better prepared than we seem to be.

2/
Very few viruses arrive with the headlines they do in movies.
But #monkeypox really did send heralds for years before the current outbreaks. 📣 The waning of smallpox vaccines. The signs of ongoing transmission.

So what should we be doing better?

3/
Read 6 tweets
Dr Emma Hodcroft Profile picture
Jul 27
🎉CoVariants.org Update!🎉

22D (BA.2.75) is now available on CoVariants! It's visible as part of Per Country & Per Variant plots, on the shared mutation page - and of course, has a page of its own!

1/8
#BA275 #centaurus

covariants.org/variants/22D.O…
This is in line with the recent addition of 22D (BA.2.75) as a @nextstrain clade - read more on that below! 👇🏻

2/8
On the 22D page, you can read about some initial 22D / BA.2.75 work on things like immune-evasion, see a list of defining mutations, a plot of the variant growth, link to Aquaria protein viz, & see a list of other mutations present in the variant.

3/8
covariants.org/variants/22D.O…
Read 8 tweets
Dr Emma Hodcroft Profile picture
Jul 22
📯CoVariants.org Update📯

As I mentioned yesterday, from today we switch the Per Variants page to 2-week intervals without smoothing & fixed the "New Year bug" - making interpretation clearer & cleaner! 🎉

covariants.org/per-variant

1/7
HUGE thanks to @MoiraZuber & @ivan_aksamentov for their work on this! 🙏🏻

Previously, Per Country was by 2-weeks (unsmoothed) & Per Variant was 1-week (smoothed) - this made reconciling numbers confusing & unintuitive. The change makes all of that easier!

2/7
As part of this, you'll notice the graphs look a little more jumpy & angular 📐. That's what happens when smoothing turns off!
But, it more closely represents the real data - I think this is a worthy trade-off!

3/7
Read 7 tweets
Dr Emma Hodcroft Profile picture
Jul 21
So far, #monkeypox seems generally mild (if sometimes very painful & physically scarring) - but is that enough not to worry?
I still think we need to consider our response carefully.

If it continues to be hard to contain, what are the medical *and* social risks?

1/14
At the moment, the #monkeypox outbreak impacts some parts of our world & society more than others - this is always dangerous as it makes dismissal easier. It's not threatening 'most of us' - at least not right now.



2/14
But if #monkeypox becomes widely endemic in MSM (men who have sex with men) populations, what might this mean?

1st, wider spread == more chance of spillover into other groups. Vulnerable, elderly, children - where outcomes may be different/worse.

3/14
Read 15 tweets

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