Sebastien Calvignac-Spencer

Thanks to Verena for involving us and to all those involved, including the curators of the collections in Zurich (who provided the new samples) and the Berlin Museum of Medical History of the Charite (who provided positive controls).

More data is definitely needed to understand the evolutionary genomics of the largest respiratory pandemic of the 20th century.
We don t expect a ton of specimens out there, but a few more can certainly be found.

@lemeylab.bsky.social (incl Bram Vrancken) kicked in to show that the small sample of 1918 IAVs seem to show higher diversity in HA, PA, and PB2 than matched 2009 H1N1pdm samples.
Perhaps helped transition to high pathogenicity, as HA and pol genes have been linked to 1918 IAV high pathogenicity?

The case was from the pre pandemic wave that hit Zurich in July 1918, and was sampled within a week of the first patient clearly identified as a flu case in the city.
The genome already shows human-like residues at key sites for adaptation to mammalian hosts.

An ancient influenza genome from Switzerland allows deeper insights into host adaptation during the 1918 flu pandemic in Europe - BMC Biology Background From 1918 to 1920, the largest influenza A virus (IAV) pandemic known to date spread globally causing between 20 to 100 million deaths. Historical records have captured critical aspects of ...

We were part of another viral aRNA study that was just published. In this work spearheaded by Christian Urban in the lab of Verena Schuenemann, a new protocol was assessed (good for short fragments) and a seventh 1918 flu genome was completely sequenced

bmcbiol.biomedcentral.com/articles/10....

Congrats to the two amazing PhD candidates who led this work @schlotterbeckj.bsky.social and Carme Riutord-Fe: terrific job! And many thanks to Fabian Leendertz, Liv Patrono, Ari Düx, @jangogarten.bsky.social and everyone involved for yet another exciting project together! 4/4

At first glance it may seem exaggerated to put so much emphasis on a single or a few ecosystems, but in the long run I think it is probably our best shot at disentangling the complex ecological processes that lead to the emergence of infectious diseases 3/4

This was only possible because of @helmholtz-hioh.bsky.social commitment to long term health monitoring of wild nonhuman primates, here at Taï (CIV) with our friends of the @taichimpproject.bsky.social 2/4

We just succeeded in formally linking a specific rodent species - the otherwise charming fire-footed rope squirrel - to the onset of a mpox outbreak in a primate species - sooty mangabeys. Here Kai’s report on the preprint we released yesterday 1/2

Das Helmholtz-Institut für One Health (HIOH) sucht eine_n Technische_n Assistent_in (w/m/d) Das Helmholtz-Institut für One Health (HIOH) Greifswald ist ein Standort des Helmholtz-Zentrums für Infektionsforschung (HZI). Hier werden die Zusammen...

We are looking for a dedicated replacement to work as a technical assistant.
www.helmholtz-hzi.de/karriere/job...
If you are interested, please send us your complete application documents in accordance with the job advertisement. @helmholtz-hioh.bsky.social

🧬 First update from the eDNA lab! 🪰

Extracting mammalian DNA from carrion flies collected in Tanzania for biodiversity studies.

A first trial using @helmholtz-hioh.bsky.social protocol for the flies collected by @uantwerpen.bsky.social + #Gecolab

Shoutout to @paulinevanl.bsky.social ! 📸

#eDNA

🚨 #Job Alert 🚨
Die Bewerbungsfrist für die Position als Institutssekretär:in am HIOH endet bald! 📅 Bewerbungsschluss: 22. Januar.
Eine spannende Chance, Teil eines internationalen Forschungsteams in Greifswald zu werden. Mehr Infos: www.helmholtz-hioh.de/fileadmin/HI...
#JobOpportunity #OneHealth

Excited to announce the African STARS Fellowship, one of the largest programs in Africa. In partnership with Mastercard Foundation, Institut Pasteur & Stellenbosch University, initial funding of 165 million rands. Press release ceri.org.za/news/?token=... Launch 15 Jan, Cape Town, SA

I also think that it does a pretty good job at publicizing important discussions and changes through multiple means (website, Arch Vir, JGV and articles in prominent journals, e.g. Nat Microbiol).

As others, including @psimmond.bsky.social have pointed at, the ICTV welcomes all views and proposals.

A very reasonable thread on this (a bit unnecessarily overheated) debate.

I d also like to be added. Thanks!

Hi
Related to your & the previous post, I looked it up and there are 120 Study Groups (SGs), with collectively more than 900 members. These are expert and typically quite experienced virologists, & should provide a reasonable cross-section of knowledge and expertise. So it's not a mad dictatorship!

An image with text describing the jobs, and the logo of the Royal Veterinary College. The text says: Title: Hiring two postdoctoral researchers. What? Improve identification and response to emerging and endemic virus threats. Where? Royal Veterinary College. How? Genomics, metagenomics, phylogenetics. Who: Working with Prof Oliver Pybus, Dr Sarah Hill, Dr Jayna Rahgwani, and GAP DC. When? Apply by 27th January 2025. Underneath this, there are two boxes describing the two roles: Role 1: Phylodynamics: Introduction, emergence and spread of viruses in farmed and wild animals. Role 2: Detect and understand threats to/from wildlife and their environments.

🦠 We are recruiting two 2-year postdocs to work at the intersection of virus genomics and infectious disease. jobs.rvc.ac.uk/vacancy.aspx... Please share widely!

This happens every year, which means the ICTV is de facto a permanent consultation body; however, it does not wait for the broader community engagement to enact taxonomy changes

These proposals are reviewed by the SG, then
subcommittees and finally the executive committee - a process starting in spring each year (SG send proposals to subcommittees at this point). Approved proposals are then ratified by the entire ICTV membership in the fall

All binomials have already been approved by the ICTV and therefore represent the current official taxonomy. The way it works: ICTV operates year-round, with taxonomy change proposals collected by (usually) family level study groups (SG) and subcommittees - each overseeing multiple SG

The new binomials can be found in the ICTV website‘s taxonomy browser, where a tabular master species list is also available

ictv.global/taxonomy

ictv.global/msl

Much like peer reviewing, it is the kind of community service that many of us add to their evenings and weekends workload. I believe it is now up to the community to engage more with the ICTV. The tools exist (proposals of taxonomic change can be filed by anyone).

I agree that there is significant room for improvement in viral taxonomies. That said, we cannot expect it will all happen via the work of virologists that accept to serve in ICTV study groups.

NCBI uses a single viral taxonomy at any given time. So it is only a problem when results from analyses conducted before and after taxonomic changed are combined. People should always keep this in mind, because there are taxonomic changes every year.

The evolutionary drivers and correlates of viral host jumps - PubMed Most emerging and re-emerging infectious diseases stem from viruses that naturally circulate in non-human vertebrates. When these viruses cross over into humans, they can cause disease outbreaks, epid...

and secondary authors using taxonomy as a direct reflection of evolutionary processes (to identify host-virus associations). With this respect, sequence-based analyses seem lile the way to go. Here a very nice example

pubmed.ncbi.nlm.nih.gov/38528191/

In passing, a large part of the nightmare when trying to work on patterns of viral diversity at large scales (eg macroecological metaanalyses😉) is not taxonomy per se, but primary authors not referring to it

And sometimes, sure, there will be inconsistencies (perhaps the example you mention) but they can easily be corrected. A taxonomy is a living tool with which the community should engage. Here a link to the templates for taxonomy proposals

ictv.global/taxonomy/tem...

It makes sense to align taxonomy with some aspects of evolution, but a taxonomy is not meant to be and cannot be a faithful evolutionary model