Sign in

Sebastien Calvignac-Spencer

@scs22.bsky.social
652 followers 253 following 38 posts

Infectious disease ecology and evolution, pathogen genomics, environmental DNA, ancient DNA/RNA

PostsRepliesMedia
Reposted by Sebastien Calvignac-Spencer
Kevin Daly @gingerhowley.bsky.social · 02/09/2026
Our paper on ancient sheeppox virus genomes, including many found from parchment samples, is now published af Science Advances. Congrats to all our co-authors and particularly first author Louis. #aDNA share.google/JqVOTB2lvxcO...
share.google
Three thousand five hundred years of sheeppox virus evolution inferred from archaeological and codicological genomes
Sheeppox virus (SPPV) is a major livestock pathogen causing economic hardship through reduced production and death of vulnerable sheep, with written descriptions of sheeppox-like disease recorded sinc...
26028
Reposted by Sebastien Calvignac-Spencer
Helmholtz Institute for One Health (HIOH) @helmholtz-hioh.bsky.social · 21/05/2026
📣 Wir suchen Unterstützung! Du hast Erfahrung als Laborassistent_in für Biologie/Chemie? Dann komm zu uns ans Helmholtz-Institut für One Health in Greifswald! Wir suchen eine technische Assistenz (m/w/d). Weitere Infos unter: www.helmholtz-hioh.de/de/jobs/
022
Reposted by Sebastien Calvignac-Spencer
Jan Gogarten @jangogarten.bsky.social · 28/03/2026
Nice coverage by @kakape.bsky.social in @science.org of our preprint, where we present data showing orthopoxviruses, including MPXV, infect duikers, which are popular bushmeat in many mpox endemic regions. Highlights lots more about orthopoxvirus ecology to explore: www.science.org/content/arti...
science.org
These small African antelopes may help mpox spread
Researchers find evidence that duikers, hunted and eaten across sub-Saharan Africa, can harbor the deadly virus
22711
Reposted by Sebastien Calvignac-Spencer
Kevin Daly @gingerhowley.bsky.social · 25/02/2026
Can safely way this is the craziest and coolest study I have led. We chart the evolution of sheeppox virus, finding it in the Eurasian steppe ~3700 years ago, and also in a LOT of parchment from medieval Europe (made from a range of animals skins!) #aDNA
55524
Reposted by Sebastien Calvignac-Spencer
Jan Gogarten @jangogarten.bsky.social · 30/10/2025
A paper for the #eDNA crowd, in particular those using flies for terrestrial biomonitoring. We show that massive pooling works well, reducing costs + time, bringing us a step closer to scalable terrestrial eDNA biomonitoring. doi.org/10.1002/edn3...
doi.org
An Exploration of DNA Extraction Methods of Fly iDNA for Scalable Biodiversity Monitoring
Metabarcoding of invertebrate-derived DNA (iDNA) is an excellent tool for assessing terrestrial mammal diversity, but the time and costs associated with sample processing constrain its wider adoption....
1129
Sebastien Calvignac-Spencer @scs22.bsky.social · 16/10/2025
If you could take just one journalist with you to a polar archipelago, who would it be? 100% @kakape.bsky.social😉 Thanks for the extensive conversations and excellent reporting. Immer wieder gerne!
041
Reposted by Sebastien Calvignac-Spencer
Helmholtz Institute for One Health (HIOH) @helmholtz-hioh.bsky.social · 05/09/2025
New study by the Institut Pasteur de Bangui and HIOH examines CAR #mpox outbreaks via genomic #epidemiology. High frequencies of independent spillovers highlight the need to strengthen systematic surveillance & identify animal sources to prevent future outbreaks www.sciencedirect.com/science/arti...
Three researchers preparing samples for high-throughput sequencing in the laboratories of the Genomic Surveillance Platform of the Institut Pasteur de Bangui.
043
Sebastien Calvignac-Spencer @scs22.bsky.social · 02/07/2025
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).
000
Sebastien Calvignac-Spencer @scs22.bsky.social · 02/07/2025
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.
110
Sebastien Calvignac-Spencer @scs22.bsky.social · 02/07/2025
@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?
100
Sebastien Calvignac-Spencer @scs22.bsky.social · 02/07/2025
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.
110
Sebastien Calvignac-Spencer @scs22.bsky.social · 02/07/2025
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....
bmcbiol.biomedcentral.com
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 ...
1135
Sebastien Calvignac-Spencer @scs22.bsky.social · 09/04/2025
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
020
Sebastien Calvignac-Spencer @scs22.bsky.social · 09/04/2025
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
131
Sebastien Calvignac-Spencer @scs22.bsky.social · 09/04/2025
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
120
Sebastien Calvignac-Spencer @scs22.bsky.social · 09/04/2025
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
1157
Reposted by Sebastien Calvignac-Spencer
Schaufler Lab (GEAR@HIOH) @schauflerlab.org · 06/03/2025
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
helmholtz-hzi.de
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...
024
Reposted by Sebastien Calvignac-Spencer
RESTOREID @restoreideu.bsky.social · 23/01/2025
🧬 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
044
Reposted by Sebastien Calvignac-Spencer
Helmholtz Institute for One Health (HIOH) @helmholtz-hioh.bsky.social · 10/01/2025
🚨 #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
003
Reposted by Sebastien Calvignac-Spencer
Tulio de Oliveira @tuliodna.bsky.social · 12/01/2025
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
0810
Sebastien Calvignac-Spencer @scs22.bsky.social · 11/01/2025
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).
000
Sebastien Calvignac-Spencer @scs22.bsky.social · 11/01/2025
As others, including @psimmond.bsky.social have pointed at, the ICTV welcomes all views and proposals.
100
Sebastien Calvignac-Spencer @scs22.bsky.social · 11/01/2025
A very reasonable thread on this (a bit unnecessarily overheated) debate.
120
Sebastien Calvignac-Spencer @scs22.bsky.social · 10/01/2025
I d also like to be added. Thanks!
100
Reposted by Sebastien Calvignac-Spencer
Peter Simmonds @psimmond.bsky.social · 10/01/2025
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!
031
Reposted by Sebastien Calvignac-Spencer
sarah-c-hill.bsky.social @sarah-c-hill.bsky.social · 18/12/2024
🦠 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!
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.
12218
Sebastien Calvignac-Spencer @scs22.bsky.social · 17/12/2024
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
000
Sebastien Calvignac-Spencer @scs22.bsky.social · 17/12/2024
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
100
Sebastien Calvignac-Spencer @scs22.bsky.social · 17/12/2024
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
100
Sebastien Calvignac-Spencer @scs22.bsky.social · 17/12/2024
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
100
Sebastien Calvignac-Spencer @scs22.bsky.social · 16/12/2024
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).
311
Sebastien Calvignac-Spencer @scs22.bsky.social · 16/12/2024
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.
100
Sebastien Calvignac-Spencer @scs22.bsky.social · 16/12/2024
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.
100
Sebastien Calvignac-Spencer @scs22.bsky.social · 14/12/2024
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/
pubmed.ncbi.nlm.nih.gov
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...
000
Sebastien Calvignac-Spencer @scs22.bsky.social · 14/12/2024
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
100
Sebastien Calvignac-Spencer @scs22.bsky.social · 14/12/2024
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...
ictv.global
Proposal Template Files | ICTV
000
Sebastien Calvignac-Spencer @scs22.bsky.social · 14/12/2024
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
110
Sebastien Calvignac-Spencer @scs22.bsky.social · 14/12/2024
Yet I still think it is very useful to have species names, if you use them with their limitations in mind. The main function of species names (and taxonomy) is disambiguation („is there a good chance we are talking of the same set of organisms?“)
100
Sebastien Calvignac-Spencer @scs22.bsky.social · 14/12/2024
I think that by now everyone agrees that all life is hybrid in nature. There is gene flow everywhere between all sorts of (even extremely distant) organisms. Species based classification systems do not and cannot capture this complexity
120
Sebastien Calvignac-Spencer @scs22.bsky.social · 13/12/2024
And I would also think that the ICTV likely represents a reasonable sample of the community. I don t have exact numbers but it seems plausible that two or three hundred virologists contribute across all study groups
300
Sebastien Calvignac-Spencer @scs22.bsky.social · 13/12/2024
There was a broader consultation, with an open invitation to all virologists link.springer.com/article/10.1...
link.springer.com
Binomial nomenclature for virus species: a consultation - Archives of Virology
The Executive Committee of the International Committee on Taxonomy of Viruses (ICTV) recognizes the need for a standardized nomenclature for virus species. This article sets out the case for establish...
200
Sebastien Calvignac-Spencer @scs22.bsky.social · 12/12/2024
Full disclosure: I am an ICTV member😉 It is a very open organization that aims to serve our community and absolutely welcomes and values everyone s input. Let s be kind with it and the people that make it work 5/5
000
Sebastien Calvignac-Spencer @scs22.bsky.social · 12/12/2024
Also: viral species names (and taxonomy) will evolve over time. That is good and nothing new. Zoologists, botanists, bacteriologists, etc. have navigated such changes for decades/centuries: we will survive!4/5
100
Sebastien Calvignac-Spencer @scs22.bsky.social · 12/12/2024
In the long run, this benefits everyone, including those managing large databases. There is a reason seq databases use official taxonomies and ask submitters to refer to it: it is an absolutely unambiguous resource with perfect versioning 3/5
100
Sebastien Calvignac-Spencer @scs22.bsky.social · 12/12/2024
For those of us working in eg genomic epi this will be a very short extra mile to run. Simply include the new species name the first time you ref a virus in your next paper, and keep doing it until a potential change (while still using your favorite virus common name) 2/5
100
Sebastien Calvignac-Spencer @scs22.bsky.social · 12/12/2024
Here the article where the ICTV explains the transition to Latinized binomial species names. I think the rationale is compelling: this change brings coherence, aligning viral taxonomy with that of all other biological entities 1/5 www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
Guidance for creating individual and batch latinized binomial virus species names
The International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains option...
240
Sebastien Calvignac-Spencer @scs22.bsky.social · 04/12/2024
And I would also suggest to add @jangogarten.bsky.social
110
Sebastien Calvignac-Spencer @scs22.bsky.social · 04/12/2024
I d like to join this starter pack. Thanks for putting it together!
100
Reposted by Sebastien Calvignac-Spencer
Angie Rasmussen @angierasmussen.bsky.social · 04/12/2024
Grateful to @smritimallapaty.bsky.social for covering our analysis of host transcriptional infection signatures at the Huanan market! Still not the “smoking raccoon dog” but getting closer… www.nature.com/articles/d41...
nature.com
Sick animals suggest COVID pandemic started in Wuhan market
A preliminary analysis takes a closer look at genomic data collected at the market.
727697