Some crazy cool virus discovery!!!! Was lucky to see @julienmelade.bsky.social presenting this one at #VGEB24 a few weeks ago!

Heading back after a wonderful #VGEB24. Couldn't be happier having seen my favourite people again & being able to give my lab members an opportunity to see cutting edge science firsthand. Hope I can return in 2 years to deliver on my exquisite data vis promise. The last night was quite the blur!

At #VGEB24, @meerac.bsky.social is closing out the meeting by reminding us of strategy in surveillance, & the sacrifice that's made in where to put your resources:

"If you're doing one thing, you're not doing the other. So go hard when you need it, and pull back when you don't." 🎯

It’s our final plenary! @meerac.bsky.social discussing the future of genomic pathogen surveillance. No shortage of utopian visions to choose from! But in a resource limited scenario how do we prioritise pathogen genome surveillance? #VGEB24

Protein language models are definitely the Method of the Conference at #VGEB24 - Shasuke Kawakubo demonstrating their utility in predicting antigenic cartography

Learning the fitness dynamics of pathogens from phylogenies The dynamics of pathogen genetic diversity, including the emergence of lineages with increased fitness, is a foundational concept of disease ecology with key public health implications. However, the i...

Learning the fitness dynamics of pathogens from phylogenies from Naomi Lefrancq #VGEB24 www.medrxiv.org/content/10.1...

Learning from prepandemic data to forecast viral escape - Nature EVEscape, a flexible framework using deep learning and biophysical structural information, enables early identification of concerning mutations in viruses with pandemic potential, facilitating the dev...

Noor Yousef presenting Learning from prepandemic data to forecast viral escape #VGEB24 www.nature.com/articles/s41...

Next up Rachel Colquhoun - discussing the opportunities of using diagnostic metagenomics sequence data (such as respiratory) to build a continuous online metagenomics surveillance resource #VGEB24

Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus - Nature Communications The impact of other pathogens on disease outcome was studied in European infants with RSV infection. Additional viruses were commonly co-detected during infection but were weakly linked to severity. H...

Final day of #VGEB24 - it’s been great! First talk is from Tanya Golubchik discussing use of target capture for understanding pathogen co-infections: www.nature.com/articles/s41...

We've got another #enterovirus poster today at #VGEB24! Interested in EVA71, CVA6, CVA16, & HFMD? Be sure to stop by Nadia's poster P38!

Want to talk @pathoplexus.org ? Please come find me!

And remember, all of the Hodcrew have awesome stickers to share!

Delphy

Final talk of this session is Patrick Varilly presenting Delphy, an inbrowser real-time Bayesian tree builder delphy.fathom.info #VGEB24

Emma Hodcroft (@firefoxx66.bsky.social) is explaining the goals of @pathoplexus.org at #VGEB24

Determinants of SARS-CoV-2 within-host evolutionary rates in persistently infected individuals Understanding the within-host evolutionary dynamics of SARS-CoV-2, particularly in relation to variant emergence, is crucial for public health. From a community surveillance study, we identified 576 p...

Determinants of SARS-CoV-2 within-host evolutionary rates in persistently infected individuals from Mahan Ghafari www.medrxiv.org/content/10.1... #VGEB24

Evolutionary-scale prediction of atomic-level protein structure with a language model A protein language model enables structure prediction and analysis of more than 600 million metagenomic proteins.

ESM-2 - a protein language model is featuring a lot at this year’s meeting www.science.org/doi/10.1126/... #VGEB24

Using big sequencing data to identify chronic SARS-Coronavirus-2 infections The evolution of SARS-Coronavirus-2 (SARS-CoV-2) has been characterized by the periodic emergence of highly divergent variants, many of which may have arisen during chronic infections of immunocomprom...

Using big sequencing data to identify chronic SARS-Coronavirus-2 infections from Adi Stern www.biorxiv.org/content/10.1... #VGEB24

How fast are viruses spreading in the wild? Genomic data collected from viral outbreaks can be exploited to reconstruct the dispersal history of viral lineages in a two-dimensional space using continuous phylogeographic inference. These spatial...

How fast are viruses spreading in the wild? www.biorxiv.org/content/10.1... #VGEB24

Mapping glycoprotein structure reveals defining events in the evolution of the Flaviviridae Viral glycoproteins drive membrane fusion in enveloped viruses and determine host range, tissue tropism and pathogenesis. Despite their importance, there is a fragmentary understanding of glycoprotein...

Mapping glycoprotein structure reveals defining events in the evolution of the Flaviviridae by Spyros Lytraa #VGEB24 - a lot of interest this meeting in comparing outputs of protein language models for inferring (very!) distant homology in viral proteins www.biorxiv.org/content/10.1...

Protein Set Transformer: A protein-based genome language model to power high diversity viromics Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses a...

Protein Set Transformer: A protein-based genome language model to power high diversity viromics www.biorxiv.org/content/10.1... #VGEB24

A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution Long-term ecological studies are powerful tools to investigate microbiomes and ecosystem change but have mostly ignored viruses. Here, we leveraged a 20-year time-series of a freshwater lake to charac...

A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution presented by @karthik-a.bsky.social www.biorxiv.org/content/10.1... #VGEB24

Immuno-epidemiology and the predictability of viral evolution Understanding viral evolution depends on a synthesis of evolutionary biology and immuno-epidemiology

Immuno-epidemiology and the predictability of viral evolution www.science.org/doi/10.1126/... #VGEB24

Opportunities and challenges in modeling emerging infectious diseases The term “pathogen emergence” encompasses everything from previously unidentified viruses entering the human population to established pathogens invading new populations and the evolution of drug resi...

www.science.org/doi/10.1126/... Opportunities and challenges in modeling emerging infectious diseases #VGEB24 from Jess Metcalfe

At #VGEB24 & interested in #enteroviruses / #polio #poliovirus ? EVE group (Hodcroft Lab aka Hodcrew) has some great posters! 👀

First, today, stop by P53 with Keno to hear about recombination, EV-Cs, & vaccine-derived polio!

Bonus: All the Hodcrew have great stickers to share!

Learning from prepandemic data to forecast viral escape - Nature EVEscape, a flexible framework using deep learning and biophysical structural information, enables early identification of concerning mutations in viruses with pandemic potential, facilitating the dev...

EVEscape - predicting emergence of new viral escape lineages: www.nature.com/articles/s41... #VGEB24

If you're interested in learning more about #Loculus - the customizable, open source pathogen database - or about @pathoplexus.org - a community-focused, transparent way to share viral sequences - check out @
Chaoran Chen's Poster9 & demo today & my talk tomorrow! (Or come chat!) #VGEB24

If you're at #VGEB24 and interested in learning more about GenSpectrum, covered in Tanjas talk, be sure to stop by Chaoran Chen's poster and demo 008 tomorrow afternoon!

Excited to be back at #VGEB24! (Virus Genetics, Evolution & Bioinformatics) with a great talk line up & fantastic list of attendees - as always!

To kick things off, our own Tanja Stadler from Basel (ETHZurich DBSSE), talking about leveraging sequences for public health!

Decoding Genomes: From Sequences to Phylodynamics An introduction to the modern analysis of evolving populations.

Tanje Stadler kicking off #VGEB24 as our first keynote - Tanje has just published a fantastic free book covering in great detail phylogenetic and phylodynamic methods for studying epidemics: decodinggenomes.org

Impeccable timing? We’re all off to #VGEB24 tomorrow (Virus Genomics, Evolution and Bioinformatics) which I am sure will be so divertingly interesting so that everyone forgets about the US election.

Very excited to be travelling to #VGEB24! I gave an overhyped talk at the 1st VGE (thanks, Ebola animation) then missed 3 meetings & now I'm back to talk (Thu 7 Nov) about Wuhan mosquito virus 6 (WuMV-6). Members of my lab (Aistė Židonytė & Martynas Smičius) will also present posters. Come see us!