After 2 long virtual years, *so happy* to be back at #UCSDdynamics Dynamics & Evolution of Human Viruses in person in beautiful San Diego! Brilliant sessions on everything from #HIV to #SARSCoV2 & many viruses in between, with fantastic global scientists & experts! Image
Opening the conference, @manonragonnet shows the relationship of drug & antibody treatment for #SARSCoV2 on the appearance of resistance mutations, as well as their ability to escape. These mutations are rare in the general pop; mostly assoc with treatment.
#UCSDdynamics ImageImage
@sarehchimeh gives an interesting talk on how & whether we can detect increased selection on surface-exposed areas of #HumanViruses - since these are exposed to the immune system, might we expect to see them evolving faster?
#UCSDdynamics ImageImage
Tying up the 1st session beautifully, @SheriHarari speaks on her work on adaptive evo of #SARSCoV2. Viral load rebound can be a red flag for resistance, & key mutations missing between chronically infected & VoC defining are of interest!

#UCSDdynamics
ImageImageImage
To open the next #UCSDdynamics session, @viralverity gives a great breakdown of the origin of #SARSCoV2 Variant of Concern Alpha, & what this may mean for other & future VoCs. It seems most likely that Alpha came from a chronic infection.

#HumanViruses ImageImage
Turning to HIV, @twoseventwo gives a very nice overview of looking into age & sex dynamics in HIV transmission, using two approaches to try and better understand who infects whom at what points. Including a lovely chart of the relationships!
#UCSDdynamics #HumanViruses ImageImage
And closing out a brilliant 1st day, @heather_eGrant takes us through the incredibly interesting historical HIV subtype A1 & D sequences in Uganda. The rise & fall of subtype D is very interesting, & possibly related to cell tropism!
#UCSDdynamics #HumanViruses ImageImageImage

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More from @firefoxx66

Jun 11
I'm honoured to have been part of the global & African-anchored group working on a new, non-stigmatizing naming scheme for #monkeypox.

We propose renaming 'Congo Basin' to Clade 1, & 'West African' to Clades 2 & 3 - to stop using harmful, geographical-based names.

1/4
These clades reflect deep diversity from years of circulation in the animal reservoir.

Additionally, we propose a placeholder name for the recent group which has likely been circulating in humans, hMPXV1.
Within that are further labels; the most recent outbreak clade is B.1

2/4
This wouldn't have happened w/o the leadership of @Tuliodna & @christian_happi, coordination w @WHO & @AfricaCDC & the Africa-based contributors: Ifedayo Adetifa, Placide Mbala, Richard Njouom, Emmanuel Nakoune, Anise Happi, Nnaemeka Ndodo, Oyeronke Ayansola, Gerald Mboowa.

3/4
Read 7 tweets
May 30
A change in mutation rate? 40 mutations in 4 years? After SC2, these things sound really scary for #monkeypox. So why are scientists saying that there's a good chance these mutations aren't adaptive? How could we know?
A layman's follow-up on @richardneher's great thread.

1/14
40 mutations sounds like a lot - & it is more than we would expect from the slower-evolving #monkeypox. But the *type* & *location* of these mutations - which are very specific - gives us a hint about how they may have come to be. 🔍🤔

2/14

We have a lot of defences against viruses (many of which we've become familiar with recently!), but one that is less well-known is an in-built sabotage system to try and trip up viruses as they replicate.🕵️
One example of this is 'APOBEC', which you might be seeing around.

3/14
Read 15 tweets
May 30
I'm going to keep repeating this until the world starts taking it seriously:

Without equitable global sequencing *all* of our pandemic preparedness is half-blind. We don't know what's circulating now, & we don't have eyes for the future.

Equitable👏 Global👏 Sequencing👏 Now👏
#Monkeypox is making many of us wish there were more sequences available. There's nothing wrong with that sentiment - more data = better understanding.
But this is another chance to reflect on *why* it might be that we don't have more data. And *how* we fix this in the future.
@HelenBranswell's (as always) fantastic article digs into this for #monkeypox:

"[T]here’s no interest in working together with the country from which the cases are coming to try and understand it a little bit more,” Ihekweazu said.

statnews.com/2022/05/26/war…
Read 4 tweets
May 23
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.
Read 12 tweets
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

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