Successfully appealed the biorxiv rejection and today our paper (co-authors @darrenmartin.bsky.social & Ravi Gupta) is posted. The paper's too long to do a single summary thread, but I'll do a cursory overview here, then more detailed subsection threads later. 1/16 www.biorxiv.org/content/10.6...

Coevolving Mutations in Chronic SARS-CoV-2 Infections

The SARS-CoV-2 pandemic has been marked by two outstanding features that have had major impacts on global public health: the repeated emergence and growth of highly divergent saltation variants with n...

biorxiv.org

Ryan Hisner@ryanhisner.bsky.social · 2mo ago

Spend 3+ years painstakingly working on a paper, doing original analysis, writing 10,000s of lines of custom code, etc, only to be rejected by a preprint server, which derides it as "automated/computational analyses of public data, facile database searches, sequence alignments"...

Excited to see @jonj-udd.bsky.social's fantastic work out @genetics-gsa.bsky.social. Selection in _heterozygotes_ is the primary force shaping allele frequencies of loss-of-function mutations in humans, even in genes only associated with purely recessive diseases. 🧪🧬 doi.org/10.1093/gene...

Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes

Abstract. The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model pred

doi.org

We just published our new paper about an active Helitron transposon in wheat 🌾🧬 We found that it can be mobilised by heat stress when DNA methylation is reduced. We document its full lifecycle: RNA -> circular DNA -> integration www.nature.com/articles/s41... #TEsky

An active Helitron transposon family in wheat - Nature Plants

Helitrons are a recently identified category of transposons. This study reveals that heat stress combined with reduced DNA methylation can mobilize a Helitron family in wheat. Its mobilization is gene...

nature.com

New preprint from us! 🦠 Clinical metagenomics is great for sequencing pathogens directly from patient samples but for some protocols sensitivity for RNA viruses lags behind bacteria & fungi. We have shown why, and how to fix it. www.medrxiv.org/content/10.6...

Library preparation strategy critically impacts RNA virus sensitivity in clinical metagenomics

Clinical metagenomics uses sequencing for culture-independent identification of pathogens directly from clinical specimens. While a number of protocols claim to be pathogen agnostic, sensitivity for R...

medrxiv.org

Dr. David Morens - who is 78 years old and served his country for nearly 50 years - used Gmail, which he shouldn't have done. However, "[he] was stripped and handcuffed [by] a half-dozen federal agents carrying guns and wearing tactical gear [..] and jailed". www.science.org/content/arti...

Guns and bulletproof vests: How federal agents arrested Fauci aide

David Morens, 78, was stripped and handcuffed for email violations

science.org

J. Craig Venter, genomics pioneer and founder of JCVI and Diploid Genomics, Inc., dies at 79 www.jcvi.org/media-center...

No light quite like that produced against gathering clouds after a day of sunshine. The pinky-hues drenching the road paving and walls of Pompeii are magical.

5/ Marthe Gautier played a crucial role in identifying trisomy 21 as the cause of Down syndrome. Working with minimal institutional support, she built a cytogenetics laboratory from scratch and produced the preparations that revealed an extra chromosome in affected children.

We've got ISSUES. Literally. We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do? arxiv.org/abs/2601.07563 A 🧵 1/n

We've been doing wastewater metagenomics for 2 years. In the first 20 months we never detected measles once. However, in the last 4 months we've detected it 10 times across numerous states. It's going endemic again; good reason to get vaccinated. health.hawaii.gov/news/newsroo...

DOH MONITORING FIRST WASTEWATER DETECTION OF MEASLES IN KAUAʻI COUNTY

HONOLULU — The Hawaiʻi Department of Health (DOH) is monitoring a positive wastewater sample for measles virus, the first wastewater detection of the virus for Kauaʻi County. The sample was collected ...

health.hawaii.gov

A viral clonality evenness score to predict progression to adult T-cell leukaemia in asymptomatic carriers of human T-lymphotropic virus type 1 in Japan: a retrospective longitudinal cohort study - The Lancet Microbe www.thelancet.com/journals/lan...

A viral clonality evenness score to predict progression to adult T-cell leukaemia in asymptomatic carriers of human T-lymphotropic virus type 1 in Japan: a retrospective longitudinal cohort study

The implementation of VCE scoring in clinical practice could inform early pre-emptive therapeutic interventions, exclusively targeting individuals with HTLV-1 at high risk and aiming to prevent progre...

thelancet.com

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

Digital Artist: In my work I invented the Gowl Detector as a cautionary tale Tech Company: At long last, we have created the Gowl Detector from classic art installation Don't Create The Gowl Detector

The Economist@economist.com · 9mo ago

A new paper suggests a photo can tell a recruiter much about an applicant’s personality

When Clare Daly launched her re-election bid last year, Catherine Connolly sat at her right hand. “I wish I could canvass every day for her on the streets,” Connolly said. Will Connolly use the presidential platform in a similar way to how Daly used hers? My piece: www.irishtimes.com/politics/202...

How is Catherine Connolly likely to approach foreign policy as president?

A precedent for outspokenness, set by Michael D Higgins, now seems to be a baseline minimum

irishtimes.com

He must love infections and cancer. A short list of what’s been achieved or is in active development with this tech: – Seasonal flu (Phase 3) – RSV (FDA-approved, 2024) – CMV (Phase 3) – HIV (early trials) – Rapid-response design for emerging pathogens www.theguardian.com/us-news/2025...

RFK Jr’s health department to halt $500m in mRNA vaccine research

Agency to end 22 federal contracts, questioning safety of technology credited with helping end Covid pandemic

theguardian.com

Mass murderer. (gift link)

Kennedy Withdraws U.S. Funding Pledge to International Vaccine Agency

nytimes.com

MUST SEE: Congresswoman Schrier nails conspiracy theorist and unfortunate HHS Secretary, RFK Jr., on the value of vaccines—and it’s glorious. Schrier also happens to be the first pediatrician in Congress.

www.bbc.co.uk/news/article...

Our sister died because of our mum's cancer conspiracy theories, say brothers

Paloma Shemirani’s brothers say she refused chemotherapy because of their mother’s beliefs.

bbc.co.uk

New piece on why it’s unhelpful to characterise COVID debate as ‘lockdowns are bad’ vs ‘lockdowns are good’ when it was really about people who claimed that COVID was 100x less fatal than it was + optimal to have a massive epidemic immediately before vaccine… vs those who sense checked these claims.

Restrictions had unequal impacts, but the pandemic itself did too. - Boston Review

Adam Kucharski responds to Stephen Macedo and Frances Lee.

bostonreview.net

“This is an unmitigated public health disaster,” said Dr. Sean O’Leary, chair of the infectious disease committee for the American Academy of Pediatrics. Story by @apoorvanyt.bsky.social Gift link: nyti.ms/4mV37YK

RFK Jr. Removes All CDC Vaccine Panel Experts (Gift Article)

The U.S. health secretary chose to “retire” members of a committee that makes significant decisions about who receives immunizations, including the vaccines for children.

nyti.ms

📣 Latest from the lab: Performance of deep-learning-based approaches to improve polygenic scores www.nature.com/articles/s41... Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.

Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...

Ambitious project to develop low-cost genome sequencing for pathogens known and unknown - University of Birmingham

Project will build on research that helped diagnostic labs to adopt sequencing capacity for COVID-19 and permit characterisation of future infectious threats

birmingham.ac.uk

www.microbe.tv/twiv/twiv-12... Latest This week in virology has a nice discussion of the recent cell paper from @sdellicour.bsky.social and colleges on bat viruses ancestral to SARS-CoV-2

Just to be clear, this is a violation of the fundamental ethical principle in clinical trial design called "equipoise." Equipoise means that no-one is exposed to excess risk just to test the therapy. That's specifically *why* vaccine trials don't use placebo arms. Ethical violation as POLICY.

Robert F. Kennedy Jr will require all new vaccines to undergo placebo testing, WaPo reports

U.S. Health and Human Services Secretary Robert F. Kennedy Jr intends to shift the way vaccines are tested, The Washington Post reported on Wednesday, citing a spokesperson from the HHS.

reuters.com

I can't believe we're still allowing completely inadequate and uninterpretable Epigenome-Wide Association Studies (EWAS) to be published. I don't care that this study is probably well-intentioned, and probably trying to draw attention to awful events in Syria. www.nature.com/articles/s41...

Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees - Scientific Reports

Scientific Reports - Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees

nature.com

@charles_h_martin, not on #Bluesky, on #23andMe

"Angry, disappointed, frustrated"--Scientists were making progress on vaccines and antivirals for the next pandemic--until this week, when the Trump administration abruptly told them to stop. Here's my story with @apoorvanyt.bsky.social Gift link: nyti.ms/43Xz77q

H.H.S. Scraps Studies of Vaccines and Treatments for Future Pandemics (Gift Article)

Federal officials cited the end of the Covid-19 pandemic in halting the research. But much of the work was focused on preventing outbreaks of other pathogens.

nyti.ms

The Trump administration’s Department of Health and Human Services terminated around 60 federal grants supporting HIV and HIV prevention-related research over the past five weeks www.notus.org/health-scien...

HHS Pulled Funds for HIV Research at 22 Universities

The Trump administration pulled around $34 million in HIV-related grants.

notus.org

People do forget how common zoonotic exposure is. In this study 12% of people working in the guano industry in Myanmar were seropositive for sarbecoviruses: pmc.ncbi.nlm.nih.gov/articles/PMC...

Exposure to diverse sarbecoviruses indicates frequent zoonotic spillover in human communities interacting with wildlife

Sarbecoviruses are a subgenus of Coronaviridae that mostly infect bats with known potential to infect humans (SARS-CoV and SARS-CoV-2). Populations in Southeast Asia, where these viruses are most like...

pmc.ncbi.nlm.nih.gov

(((Bexzex)))@bexzex.bsky.social · last yr.

Zoonosis is not rare. They just don't always turn into outbreaks and they rarely turn into pandemics just like earthquakes are rarely devastating. www.abc.net.au/news/2008-08-21/qld-vet-dies-of-hendra-virus/484684 www.nature.com/articles/s43016-021-00362-1