Andrew Rambaut

I used to do a class on the phylogenetics of the metazoan phyla. Every year as I was polishing up the slides I would find that another paper had come out in the previous year that flipped the Ctenophore/Porifera (occasionally Platyzoa) as basal phylum. Glad to hear it has been sorted.

Congratulations to Joe Felsenstein on being awarded the 2026 Mendel Medal!

On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5

As expected, unfortunately.

If ever you needed a reason for never using GISAID ever again (as a data producer or data user - we're both), look no further.

Time to move on to more trusted and transparent solutions.

Virological A discussion forum for analysis and interpretation of virus molecular evolution and epidemiology.

Thanks to @kgandersen.bsky.social for taking this on - for years I was paying for virological.org out of my own pocket (primarily because I couldn't work out how to get it funded).

Finally we speculate as to whether this phenomenon of persistence and latency might be an adaptive mechanism of the virus to maintain itself in a structured and geographically diverse reservoir.

Doing so changes our understanding of where the root of the EBOV tree lies, the amount of time that underlies the current distribution and diversity of the virus. This hopefully help to provide insight into the nature and composition of this thus-far elusive reservoir.

We model this process of going into and out of latency and see if it can explain the variation in the molecular clock observed in the phylogenetic tree that subtends the human outbreaks.

We ask if a process similar to that observed in humans (persistence and then recrudescence with little or no replication and accumulation of mutations) might also be at work in the reservoir (likely bats).

This paper has been many years in creation, derailed by a pandemic. Lead by JT McCrone, it is a collaboration with @msuchard.bsky.social, @guybaele.bsky.social, @ifeanyiomah.bsky.social , Eddy Kinganda-Lusamaki, Luiz Carvalho, @evogytis.bsky.social, and Placide Mbala-Kingebeni

Evidence of latency reshapes our understanding of Ebola virus reservoir dynamics Ebola virus (EBOV) has caused severe outbreaks of haemorrhagic fever in Central and West Africa since the first observed zoonotic epidemic in the late 1970s. While recent outbreaks have revealed much ...

Our paper on the phenomenon of persistence and latency in Ebola virus in an unobserved reservoir is finally out in preprint: www.biorxiv.org/content/10.1...

And now NextStrain as well.

Next up, will GISAID start charging open-source community tools to have access?

That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.

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!

I would imagine that EIT plans to offer this as a service to public health labs globally a bit like Microsoft has got their claws into just about every institution. So this is probably going to be Teams but for pathogen genomics. With everything that sentence implies.

And as you say, that is before we get to the point where people have to decided whether to upload it all to the next mad billionaire’s weekend project.

The EIT thing keeps banging on about ‘always on’ which kind of misses the point that it is the surveillance network, sample collection, testing infrastructure that needs to be ‘always on’.

Or the UKHSA for just one bit of the UK

Seems to be name convergence in Global Pathogen Analysis internet things: You can have GPAS (service) or GPAP (platform): eit-pathogena.com or www.dtu.dk/english/news...

Custom in-house pipeline

Seems like Bobby Kennedy Jr misunderstands placental mammal reproduction. Go figure.

It is almost a classic reply-guy reply. If this as the other place it would have been instant!

Cue replies saying "Actually Frankenstein was the creator not the recombinant person monster"

Damn, I forgot to put "Never going to give you up" on it. You all clicked it right?

I just registered the domain Pathogenomenick.ai - do you want it?

Terrific new feature presented by @theo.io on @pathoplexus.org called SeqSets for generating DOIs for sequence subsets used in publications, that can then be tracked for impact via CrossRef that will allow data generators to track impact! #IMMEMXiV

Picture of the milky way above a rock in Southern Spain with a small orange rectangle highlighting the location of the Cygnus Loop or Veil Nebula.

A long exposure picture of the Cygnus Loop or Veil Nebula taken over 5 nights in Southern Spain. 325mm telescope.

Wonderful picture. Same nights, exactly the same location, different scale - a zoom in on the orange rectangle -

The 16th Ebola Virus Disease Outbreak in Bulape Health Zone, Kasai, Democratic Republic of the Congo: A new spillover event from an unknown reservoir host Background The Democratic Republic of the Congo (DRC) is currently facing concurrent outbreaks including mpox, cholera and malaria (1-4). The Ministry of Public Health, DRC has declared the 16th Ebola...

Amid the concerning news of a new Ebola Zaire outbreak in DRC, teams on the ground have already managed to sample, sequence, and share data. This rapid turnaround is a testament to their commitment and capacity to respond.

Read more: virological.org/t/the-16th-e...

1/7

@zachhensel.bsky.social and I have a new paper on the origin of SARS-CoV-2! 🧪

There are a lot of reviews on the topic already, so we tried to do something different: characterize "lab leak" scenarios, and directly address those on SARS-CoV-2's furin cleavage site.▫️1/9

doi.org/10.5802/crbi...

Top science journal faced secret attacks from Covid conspiracy theory group | Computer Weekly One of the world’s most prestigious general science journals, was the target of a two-year long sustained and virulent secret attack by a conspiratorial group of extreme Brexit lobbyists with high-lev...

Also a character in this bizarre story: www.computerweekly.com/news/3665534...

Go home Evolution you're drunk