Alex

A cattle-derived human H5N1 isolate suppresses innate immunity despite efficient replication in human respiratory organoids https://www.biorxiv.org/content/10.1101/2025.11.02.684669v1

Viral epidemic potential is not uniformly distributed across the bat phylogeny - Communications Biology Phylogenetic and machine learning analyses reveal that bats (order: Chiroptera) are not a group with uniform viral epidemic potential: virulence, transmissibility, and death burden cluster within dist...

Viral epidemic potential is not uniformly distributed across the bat phylogeny

www.nature.com/articles/s42...

A divergent betacoronavirus with a functional furin cleavage site in South American bats Bats are natural reservoirs for a wide range of RNA viruses. Members of the genus Betacoronavirus, including Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) and Middle East Respiratory Syndrome...

We’ve identified a highly divergent betacoronavirus from South American bat that encodes a functional furin cleavage site.
Another fascinating reminder of how diverse coronavirus evolution is in wildlife reservoirs.
#Virology #VirusEvolution #Bats #Coronavirus

www.biorxiv.org/content/10.1...

I beg to differ! If it's not a sequencing mistake—and it looks clean—one of these BA.3.2 has something completely novel in SARS-CoV-2 evolution: an FCS-adjacent deletion!

One of the two QT repeats appears to have been deleted. I've never seen anything like this before. BA.3.2 is a different beast.

Not turbo cancer but turbo cancer-immunotherapy!
Combining mRNA COVID vaccines with standard-of-care immune therapy overwhelms tumor defenses to improved survival in animal models and large cohorts of people with cancer @nature.com
www.nature.com/articles/d41...
www.nature.com/articles/d41...

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...

Ebola virus in Kasai revives 50-year-old questions on viral latency On Sept 4, 2025, DR Congo declared its 16th Ebola virus outbreak. The epicentre of this outbreak occurred in the Kasai province—the first resurgence in this region since 2008.1 Genomic analysis identi...

Ebola virus in Kasai revives 50-year-old questions on viral latency www.thelancet.com/journals/lan...

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.

MERS-CoV and SARS-CoV-2 infection in diverse human lung organoid-derived cultures | Journal of Virology The COVID-19 pandemic heralded the upsurge in human-derived lung organoid-based studies due to their cellular heterogeneity that partly emulates the cellular complexity of the respiratory tract. A maj...

journals.asm.org/doi/10.1128/...

Persistent SARS-CoV-2 Infection Lasting Over 750 Days Documented in Person With HIV William Hanage, PhD, discusses viral evolution, transmission risk, and clinical implications for immunocompromised patients.

Recently we published a report describing what I *think* is the longest known continuous case of Covid-19 to date.

For some reason I've not found time to post about it. While I get around to doing so you can read a summary here 👇

www.contagionlive.com/view/persist...

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

More details on #Ebola outbreak in DRC:
Index case was a pregnant woman (in third trimester), who came to Bulape General Reference Hospital on 20 August with fever, bleeding, bloody diarrhea. She died on August 25.
Then two health care workers, who first had contact with her, developed symptoms...

The cow udder is a potential mixing vessel for influenza A viruses The incursion of high pathogenicity avian influenza A virus (IAV) into US dairy cows is unprecedented in the era of molecular diagnosis and pathogen sequencing. This raises questions over the likeliho...

The cow udder may be a mixing vessel where different strains of influenza can recombine--"underscoring its potential role in generating novel influenza viruses with pandemic risk." [Preprint] www.biorxiv.org/content/10.1...

Macaques infected with human HPAI H5N1 virus. Cynomolgus macaques = severe pneumonia, 100% mortality at 7dpi. Rhesus macaques dose-dependent mortality, survivors had protective immunity. Immune dysregulation key mechanism of pathogenesis.
👉 www.cell.com/immunity/ful...

Review of key studies showing replication of influenza and other viruses in the mammary gland, outline experimental and natural H5N1 2.3.4.4b infections in dairy cows + small animal models, One Health implications.
👉 journals.asm.org/doi/10.1128/...

Immunopathogenesis of lethal H5N1 avian influenza virus clade 2.3.4.4b infection in macaques Andersen et al. report the immunopathogenesis of severe H5N1 avian influenza virus clade 2.3.4.4b infection in cynomolgus and rhesus macaques. Inflammation and immune dysregulation were key mechanisti...

Beautiful paper from Dan Barouch & team looking at H5N1 pathogenesis in rhesus & cynomolgus macaques.

Dan presented some of this work in Feb at a meeting at Scripps & the mortality data was striking. H5N1 is really pathogenic in macaques, but in species-specific ways. www.cell.com/immunity/ful...

Synchronized seasonal excretion of multiple coronaviruses coincides with high rates of coinfection in immature bats - Nature Communications Bats harbor diverse coronaviruses but temporal dynamics are less well studied. Here, the authors analyzed coronaviruses in Australian flying foxes over 3 years showing peak shedding and co-infections ...

🦇 NEW RESEARCH: Our 3-year study of Australian flying foxes identified six co-circulating coronaviruses, with highest rates of infection and co-infection in young bats, and evidence of circulating recombinants 🧪🌏 🧵

Available open access in @natcomms.nature.com

📄 www.nature.com/articles/s41...

Surveillance on California dairy farms reveals multiple sources of H5N1 transmission Transmission routes of highly pathogenic H5N1 between cows or to humans remain unclear due to limited data from affected dairy farms. We performed extensive air, farm wastewater, and milk sampling on ...

Bird flu is spreading a LOT in dairy farms now in US- now is the time for surveillance and stepping up action on vaccine- but US has Kennedy who seems to think infections are fine and has cancelled the contract for developing a mrna bird flu vaccine

After Years of Anger Directed at C.D.C., Shooting Manifests Worst Fears

“...disinformation, conspiracy theories & political violence is getting scarier by the day. I’m very worried about how this is now going beyond defunding of infectious diseases & public health to political violence against the people working in those fields."

www.nytimes.com/2025/08/09/u...

Quick thread on the WHO's SAGO report on the origins of COVID-19, highlighting key points and even *new* data.

Their summary is that a zoonotic origin of COVID-19 is best supported by available data. This is consistent with most scientific reviews and statements in the rest of the literature.

New leader coming to infectious disease lab in Winnipeg | CBC News A new leader is coming to the National Microbiology Laboratory in Winnipeg, after its head stepped down just months after taking over leadership of the embattled laboratory that was previously at the ...

A very exciting professional update below that I can now share:

www.cbc.ca/news/canada/...

Virological characteristics of the SARS-CoV-2 NB.1.8.1 variant After the spread of SARS-CoV-2 JN.1, its subvariants, such as KP.3 (JN.1.11.1.3)1 and KP.3.1.1 (JN.1.11.1.3.1.1),2 and XEC (a recombinant lineage of two JN.1 subvariants),3 emerged and rapidly spread ...

BREAKING🔔 The 53th paper from G2P-Japan🇯🇵 is out at Lancet Infectious Diseases @thelancetinfdis.bsky.social. We elucidated the virological characteristics of SARS-CoV-2 NB.1.8.1. Please repost🔥
www.thelancet.com/journals/lan...

Overview of avain influenza vaccines out there, and where they are being trialled or implemented.
👉 www.mdpi.com/2076-393X/13...

Dynamic mechanisms of time-of-day-dependent adaptive immunity and vaccination responses
www.biorxiv.org/content/10.1...

Diverse bat organoids provide pathophysiological models for zoonotic viruses Bats are important reservoirs of zoonotic pathogens, but suitable model systems for comprehensively exploring host-pathogen interactions and assessing spillover risks remain limited. To address this g...

Diverse bat organoids provide pathophysiological models for zoonotic viruses | Science www.science.org/doi/10.1126/...

New @nature.com
Nasal vaccines for respiratory infections
Best review I've seen on this important topic and a big unmet need
www.nature.com/articles/s41...

Emergence and interstate spread of highly pathogenic avian influenza A(H5N1) in dairy cattle in the United States Highly pathogenic avian influenza (HPAI) viruses cross species barriers and have the potential to cause pandemics. In North America, HPAI A(H5N1) viruses related to the goose/Guangdong 2.3.4.4b hemagg...

Emergence and interstate spread of highly pathogenic avian influenza A(H5N1) in dairy cattle in the United States

Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections Evolution of SARS-CoV-2 in long-term persistent infections is hypothesised to be a major source of variants of concern (VOC). However, the linkage of intra-host variants into haplotypes that reflect v...

New preprint from Luke Snell from GSTT, Suzanne Pickering in my lab and Rui Galao, my colleague at KCL.

Here we examine in detail the evolution of the SARS CoV-2 spike in persistent infections, and essentially catch a potential variant in the act of developing. 1/n

www.biorxiv.org/content/10.1...

An updated dataset of early SARS-CoV-2 diversity supports a wildlife market origin The origin of SARS-CoV-2 has been intensely scrutinized, and epidemiological and genomic evidence has consistently pointed to Wuhan’s Huanan Seafood Wholesale Market as the epicenter of the COVID-19 p...

Exciting new data reported this month on the earliest #SARS2 #COVID sequences from early 2020. Big implications on #covidorigins, as 187 sequences have never before been included in analysis 1/n 🧪

www.biorxiv.org/content/10.1...

Bovine H5N1 binds poorly to human-type sialic acid receptors - Nature Nature - Bovine H5N1 binds poorly to human-type sialic acid receptors

After 8 months of peer review, our manuscript was published today @nature.com showing that bovine H5N1 viruses bind poorly to human-type sialic acid receptors. We now know that the virus is only 1 HA substitution away from efficiently binding human receptors.

www.nature.com/articles/s41...