Avian Flu, from ‘FluWarning’ early alerts for virus spillovers

A system developed by Researchers at the Politecnico di Milano and the University of Milan detects changes that may indicate cross-species transmission and anticipate possible epidemics

Politecnico di Milano

FacebookXLinkedInWeChatBlueskyMessageWhatsAppEmail

 

image: 

Reassortant virus

view more 

Credit: Politecnico di Milano

How can we monitor the cross-species transmission of avian flu? The answer is FluWarning, a digital system that reports abnormal changes in flu viruses, developed by a research team from the Politecnico di Milano and the University of Milan. The system analyses the genetic code of flu viruses, looking for subtle but significant changes that could indicate cross-species transmission (for example, from birds to cattle or to humans), a process known as spillover.

The study, which was recently published in the prestigious journal Science Advances, was developed under the NRRP-funded PRIN 2022 – SENSIBLE project (Small-data Early warNing System for viral pathogens In puBLic hEalth). The FluWarning research team includes three members from DEIB – Department of Electronics, Information and Bioengineering at the Politecnico di Milano, SENSIBLE’s Principal Investigator Anna Bernasconi, Professor Stefano Ceri and Researcher Tommaso Alfonsi, along with Matteo Chiara, Professor in the Department of Biosciences at the University of Milan.

The study relied on data from GISAID, a platform for sharing virus sequences and the related metadata produced by laboratories all around the world. FluWarning was developed using data from the H1N1 swine flu pandemic in 2009, a well-documented example of a virus being transmitted from animals to humans. It was then applied to H5N1 bird flu, a highly pathogenic strain among birds, which in the past year has also begun to spread among US cattle.

The system uses a statistical method to recognise anomalies. Depending on the settings, it can be used to recognise individual anomalous sequences or groups of anomalous sequences. FluWarning learns the normal sequences of influenza viruses and issues an alert whenever the code of the sequences changes significantly. For each alert, virologists analyse the corresponding sequences and confirm or reject the presence of spillover.

‘With its simple installation and analysis that can be done for specific locations and over specific time periods, the FluWarning software can potentially be used by many laboratories or regional genomic surveillance institutions, enabling important discoveries on both small and large scales,’ Anna Bernasconi notes. ‘In fact, the system is perfectly operational. It can give feedback on these changes day by day.’

In 2024–2025, two H5N1 genotypes were linked to independent outbreaks in the US, where numerous heads of dairy cattle were found to be infected with bird flu. ‘FluWarning identified clusters of viral activity in several US states, particularly in California, where a state of emergency was declared on 18 December 2024 due to the risk of bird flu contamination in cattle. Surprisingly, some FluWarning alerts appeared before official reports were published. The system also detected specific mutations in the haemagglutinin (HA) gene, a key protein that affects the way the virus infects the host cells,’ Matteo Chiara says. The tool monitored the evolution of the virus and identified characteristic markers of the California strains.

‘FluWarning is an important step towards more effective detection of viral changes that could pose a risk to animals or humans. By making this technology widely available, we hope to strengthen global surveillance on a health issue of global significance’ Stefano Ceri concludes.

---

Journal

Science Advances

DOI

10.1126/sciadv.adz7312 

Method of Research

Data/statistical analysis

Subject of Research

Not applicable

Article Title

Lightweight multiscale early warning system for influenza A spillovers

LA REVUE GAUCHE - Left Comment: Search results for ZOONOSIS

Working together to combat the spread of antibiotic resistance

The BfR participates in an interdisciplinary monitoring approach.

BfR Federal Institute for Risk Assessment

FacebookXLinkedInWeChatBlueskyMessageWhatsAppEmail

OHIS stands for One Health Integrated Surveillance, i.e. the monitoring of antibiotic resistance in the sense of a holistic, interdisciplinary One Health strategy. In addition to the BfR, the Robert Koch Institute (RKI), the Friedrich Loeffler Institute (FLI), the Federal Environment Agency (UBA) and the German Federal Office of Consumer Protection and Food Safety (BVL) are also involved in the network.

The group was formed in 2023 as part of the government's German Antibiotic Resistance Strategy (DART 2030). DART 2030 outlines six areas of action for halting the spread of antibiotic resistance at national level and through international cooperation. In addition to prevention, the appropriate use of antibiotics, research and development, "surveillance and monitoring" is one of the key areas of action. The aim of interdisciplinary surveillance is, among other things, to identify trends and developments in antibiotic resistance so that targeted measures can be taken at an early stage and subsequently assessed. One of the goals of DART 2030 is for the OHIS group to set up a website linking data from the individual sectors.

The BfR is involved in various aspects of the fight against antibiotic resistance. For example, the institute is home to the National Reference Laboratory (NRL) for Antibiotic Resistance. Its most important task is to collect comparable data on antibiotic resistance in zoonotic agents and other bacteria that pose a hazard to public health. The results are summarised in the annual zoonosis report and forwarded to the European Food Safety Authority (EFSA). Since 2023, this and other monitoring data has also been made available to experts and the interested public via the ZooNotify internet portal.

Another key activity of the BfR is the collection and assessment of antibiotic consumption quantities in cattle, pigs, chickens and turkeys, as well as the frequency of treatment in certain animal production types. The annual evaluation of the data forms the basis for the competent authorities to take measures to protect consumers.

The OHIS meeting, to which the Federal Ministry of Health (BMG), the Ministry of Agriculture (BMLEH) and the Ministry of the Environment (BMUKN) are also invited, is organised by the BVL and supports the motto of this year's WAAW, "Act Now: Secure Our Present, Protect Our Future."

Further information on the use of antibiotics and the development of resistance

Topic page on the use of antibiotics in livestock
https://www.bfr.bund.de/en/food-safety/assessment-of-microbial-risks-in-foods/use-of-antibiotics-in-livestock/

Topic page on antibiotic resistance
https://www.bfr.bund.de/en/research/research-fields/microbiology/antibiotic-resistance/

Zoonotify
https://zoonotify.bfr.berlin/explanations?lang=en

About the BfR

The German Federal Institute for Risk Assessment (BfR) is a scientifically independent institution within the portfolio of the German Federal Ministry of Agriculture, Food and Regional Identity (BMLEH). It protects people's health preventively in the fields of public health and veterinary public health. The BfR provides advice to the Federal Government as well as the Federal States (‘Laender’) on questions related to food, feed, chemical and product safety. The BfR conducts its own research on topics closely related to its assessment tasks.

ZOONOSIS

New study reveals not all bats carry equal viral risk

University of Oklahoma

FacebookXLinkedInWeChatBlueskyMessageWhatsAppEmail

NORMAN, OKLA. – A groundbreaking study published in Nature’s Communications Biology sheds new light on the relationship between bats and dangerous viruses. Led by researchers at the University of Oklahoma, the study shows that contrary to widespread assumptions, not all bats carry viruses with high epidemic potential, only specific groups of species.

Many high-consequence viruses — pathogens with significant potential to cause severe illness, death and widespread transmission — originate from wildlife. Bats have been identified as carriers of numerous viruses, including but not limited to SARS-like coronaviruses, Marburg virus, and Hendra and Nipah viruses.

However, bats are beneficial to their ecosystems, and different bat species provide distinct services to their environments. In Oklahoma, Mexican free-tailed bats consume agricultural pests, thereby helping to ensure that crops can flourish. Fruit bats, on the other hand, serve as pollinators in their communities.   

“If we lost bats, agricultural production would be negatively affected, and so would economies,” said Caroline Cummings, a doctoral student in the School of Biological Sciences and the lead author on the paper.

Cumming’s research uncovered that far fewer bats carry dangerous viruses than is commonly assumed. Using advanced machine learning, the team identified specific groups of bat species that are more likely to host highly virulent and transmissible viruses. The research found that, for some viruses, these traits tend to cluster among closely related species.

“Instead of all bats carrying all dangerous viruses, it’s only specific bats that have co-evolved with specific viruses, and that’s why they tend to live with them and not be sick,” Cummings said.

With the rate of infectious disease emergence increasing in humans, predicting which wildlife species may harbor viruses is useful for viral surveillance and conservation efforts. Cummings says viral surveillance is typically time-, labor- and cost-intensive, and these results can help mitigate some of that intensity by narrowing down what to sample. Efforts can be targeted to focus on high-risk groups of bat species.

To further help focus viral surveillance, Cummings also mapped how these groups of high-risk bats overlap with areas of high habitat disruption and human encroachment. Habitat disruption and human encroachment can increase virus transmission from bats to humans, both by increasing contact between species and by causing stress for bats, potentially taxing their immune systems and increasing viral shedding. A healthy, undisturbed bat colony maintains better immunological balance, effectively keeping viruses in check. Cummings says conservation efforts aimed at protecting bat habitats could reduce the risk of spillover and preserve the critical ecosystem services bats provide.

“This work brings much-needed nuance to discussions around bats and their role as viral hosts,” said Dr. Daniel Becker, assistant professor in the School of Biological Sciences and senior author on the paper. “The literature has often made broad, sweeping statements about bats and zoonotic risk. By being able to identify which particular groups of bat species carry dangerous viruses, and where they most overlap with human impacts, we can minimize negative human–bat interactions.”

Beyond conservation and viral surveillance, Cummings says future research into the immune systems of these groups of bats that harbor dangerous viruses could lead to interesting developments in therapeutics. Understanding the adaptations these species have made to coexist with these viruses could be used for future medical advancements.

---

Journal

Communications Biology

DOI

10.1038/s42003-025-08929-5 

Article Title

Viral epidemic potential is not uniformly distributed across the bat phylogeny

LA REVUE GAUCHE - Left Comment: Search results for SPILLOVER

ZOONOSIS

France raises bird flu alert to highest level after new outbreaks

France raised its bird flu alert to the highest level on Wednesday after a rise in new cases in poultry and backyard flocks, triggering stricter biosecurity rules including the confinement of birds.


Issued on: 22/10/2025 - RFI

France has raised its bird flu alert to the highest level following new outbreaks in poultry and wild birds. AP - Bob Edme

A government decree in the Journal officiel confirmed the risk level will move from “moderate” to “high”, the top tier in the national alert system.

The move means poultry must now be sheltered and protected from contact with wild birds – an early precaution compared with previous years.

Authorities said the decision was prompted by “the dynamic spread of highly pathogenic avian influenza (HPAI) in migratory flyways crossing France”, with new cases detected among migratory wild birds on French territory.

Officials warned these birds could pass the virus to domestic flocks.

In just 10 days, five outbreaks of HPAI have been confirmed across the country – two on commercial poultry farms and three in smaller backyard holdings. The new decree aims to “reinforce surveillance and prevention measures” to limit further spread.

Hundreds of geese slaughtered as bird flu grips France's Dordogne

Early warning

France classifies bird flu risk in three categories – negligible, moderate and high. The level had remained “negligible” since May before being raised to “moderate” last week.

This year’s shift to the highest alert comes earlier than usual. In previous seasons, it was typically activated in November or December.

Under the “high risk” designation, birds must be sheltered indoors or protected by nets. On larger farms with more than 50 birds, feeding and watering systems must also be covered to prevent contamination from wild species.

Smaller flocks must be either confined or kept under netting.

Since October 2023, France has slightly eased certain confinement rules to ease the strain on free-range producers.

Poultry farmers raising chickens and guinea fowl can, from eight weeks of age, and turkeys from 10 weeks, let their birds outside – but only in restricted areas and without needing prior approval from local authorities.

Laying hens kept outdoors may also continue to roam within a reduced enclosure, provided farmers obtain the green light from their regional prefecture.

Europe in midst of worst ever bird flu outbreak, authorities warn

A Europe-wide concern

According to the European health surveillance platform ESA, 37 outbreaks of avian influenza were reported in poultry holdings across the EU between 1 August and 12 October, with additional cases since then – including several in France.

While the jump to “high risk” status will add new constraints for French farmers, officials hope early action will prevent a repeat of the devastating waves of bird flu seen in recent years.

With tighter monitoring and earlier containment, authorities aim to keep both flocks and consumers safe as migratory birds begin their autumn journeys.

(with newswires)

Taiwan detects first cases of swine fever

Taipei (AFP) – Taiwan has culled dozens of pigs after detecting its first cases of African swine fever, with the agriculture ministry saying Thursday no other infections have been detected elsewhere on the island.


Issued on: 23/10/2025 - FRANCE24

A vendor cuts meat at a pork stall at a local traditional market in Keelung. Taiwan has culled dozens of pigs after detecting its first cases of African swine fever © I-Hwa Cheng / AFP

The virus -- which does not affect humans -- is highly contagious and fatal for pigs, and an outbreak is potentially devastating for the pork industry, experts say.

"No abnormalities have been observed (elsewhere) so far," Deputy Agriculture Minister Tu Wen-jane told a news conference in the central city of Taichung where the infections were detected.

Samples of dead pigs at a farm in Wuqi district tested positive for swine fever this month and 195 pigs were culled, the ministry said Wednesday.

Taichung authorities were tracing the whereabouts of 28 pigs from the farm that were sold in markets, Lin Nien-nung, from the ministry's Animal and Plant Health Inspection Agency, said Thursday.

The ministry said a three-kilometre (nearly two-mile) "control zone" was set up to prevent the infection from spreading, while the transport and slaughter of pigs across the island is banned for five days.

Taiwan has around five million pigs and the pork industry generates about NT$70 billion (US$2.3 billion) a year, official data show.

President Lai Ching-te has urged the public to "not panic" and called on local governments, livestock associations and pig farmers to be "highly vigilant".

"If any abnormal deaths or suspected animal infections are found among pigs, please immediately report them to the local animal quarantine authorities," Lai said in a Facebook post.

© 2025 AFP

LA REVUE GAUCHE - Left Comment: Search results for SPILLOVER

ZOONOSIS

Bird-to-human jump by trichomonas parasites illuminated in new study

Genomic analysis creates datasets for future research on one of the world’s most common STIs

Johns Hopkins Bloomberg School of Public Health

Facebook

XLinkedInWeChatBlueskyMessageWhatsAppEmail

A new study led by researchers at the Johns Hopkins Bloomberg School of Public Health reveals how genetic changes in the parasite responsible for one of the world’s most common sexually transmitted infections may have helped it adapt to human hosts. 

The parasite Trichomonas vaginalis is thought to be the result of adaptation to human hosts by Trichomonas parasites that lived in birds sometime in the past several thousand years. Previously, little was known about how the parasite made the jump from birds to humans.  

For their study, the researchers performed what is thought to be the most extensive genomic comparison of T. vaginalis and other Trichomonas species to date and identified T. vaginalis genes that were likely involved in the switch. 

The findings offer a robust dataset for further study, and help researchers start thinking about vulnerabilities in the parasite that future treatments might exploit. The drug metronidazole is currently the first-line treatment for trich infections, but some strains of the parasite are resistant to it. No vaccine is available.

The results were published online July 24 in Nature Communications.

“There is a strong interest these days in learning how microorganisms jump successfully from birds to humans, and these findings shed light on genes and biological mechanisms that are important for that adaptation in parasites like T. vaginalis,” says study senior author Jane Carlton, PhD, Bloomberg Distinguished Professor at the Bloomberg School.

T. vaginalis infection, also called trichomoniasis or “trich,” affects hundreds of millions of people around the world. In the U.S., trich is considered one of the most prevalent non-viral sexually transmitted infections. Although many trich infections go unnoticed, they can cause itching, discharge, and inflammation in the vagina and urethra. 

Trich infection can also enhance the transmission of other pathogens including HIV. Studies have linked trich infections to higher risks of infertility, prostate cancer, cervical cancer, and adverse pregnancy outcomes including low-weight babies.

Research suggests that Trichomonas parasites originated in Australasia and may have begun jumping from pigeons and doves to humans after the human colonization of the Americas. In the past two decades, researchers have found that T. vaginalis is closely related to a different species, Trichomonas stableri, that infects the GI tract of pigeons and doves.

“Traditionally, humans and birds have bathed in the same places, so that may have been one route of transmission,” Carlton says. “Also, some of our human ancestors used bird gullets as condoms, which may have offered a more direct route.”

In the new study, Carlton and her team sequenced the full genomes of seven different Trichomonas parasite species. These included T. vaginalis; T. tenax, which can colonize the human mouth; and pigeon-infecting T. stableri.

The researchers’ analysis revealed dozens of T. vaginalis genes that appear to be changing over time in ways that suggest adaptation to the human host. Carlton and her colleagues note that these genes have been associated in prior studies with several key parasite functions: “phagocytosis,” in which the parasite essentially eats cells in its host, in part to gain nutrients, and “exosomes”—tiny capsules, secreted by T. vaginalis, that are filled with various molecules capable of affecting surrounding tissues. Some of these genes were already considered “virulence factors” that help T. vaginalis establish infection or cause disease. 

The researchers also examined segments in Trichomonas genomes known as transposable elements that often move to a new genomic position or create copies of themselves at new positions. Trichomonas species have relatively large numbers of these “jumping genes,” and T. vaginalis has by far the most—they make up about half of its genome length.

The scientists’ analysis suggests that the expansion of these mobile elements in human-infecting Trichomonasspecies likely reflects an increase in genetic drift—causing a relaxation of evolutionary selection pressures—in the new human host environment.

“Studying how these elements move, what they disrupt, and how T. vaginalis clamps down on them should be broadly useful for understanding their biology,” says Carlton, who also directs the Johns Hopkins Malaria Research Institute at the Bloomberg School. “We also need to find chinks in the parasite’s armor so we can develop better ways of treating trich—though I don’t think we'll ever manage to eliminate it completely, as long as people are having sex.” 

“Comparative Genomics of the Parasite Trichomonas vaginalis Reveals Genes Involved in Spillover from Birds to Humans” was written by Steven A. Sullivan, Jordan C. Orosco, Francisco Callejas-Hernández, Frances Blow, Hayan Lee, T. Rhyker Ranallo-Benavidez, Andrew Peters, Shane R. Raidal, Yvette A. Girard, Christine K. Johnson, Krysta H. Rogers, Richard Gerhold, Hayley Mangelson, Ivan Liachko, Harsh Srivastava, Chris Chandler, Daniel Berenberg, Richard A. Bonneau, Po-Jung Huang, Yuan-Ming Yeh, Chi-Ching Lee, Hsuan Liu, Ting-Wen Chen, Petrus Tang, Cheng-Hsun Chiu, Michael C. Schatz, and Jane M. Carlton.

The study was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (R21AI149449 and U24AI183870); the NYU IT High Performance Computing (resources, services, and staff expertise); Chang Gung Memorial Hospital (CMRPD1M0571-2) and the National Science and Technology Council, Taiwan (NSTC–110–2320B–182–016–MY3) Taiwan; and the Australian Government Wildlife Exotic Disease Preparedness Program.

# # #

 

---

Journal

Nature Communications

LA REVUE GAUCHE - Left Comment: Search results for SPILLOVER