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Farmed carnivores may become ‘disease reservoirs’ posing human health risk

Tue, 24/08/2021 - 16:03

Farming large numbers of carnivores, like mink, could allow the formation of undetected ‘disease reservoirs’, in which a pathogen could spread to many animals and mutate to become a risk to human health.

Research led by the University of Cambridge has discovered that carnivores have a defective immune system, which makes them likely to be asymptomatic carriers of disease-causing pathogens.

Three key genes in carnivores that are critical for gut health were found to have lost their function. If these genes were working, they would produce protein complexes called inflammasomes to activate inflammatory responses and fight off pathogens. The study is published today in the journal Cell Reports.

The researchers say that the carnivorous diet, which is high in protein, is thought to have antimicrobial properties that could compensate for the loss of these immune pathways in carnivores – any gut infection is expelled by the production of diarrhoea. But the immune deficiency means that other pathogens can reside undetected elsewhere in these animals.

“We’ve found that a whole cohort of inflammatory genes is missing in carnivores - we didn’t expect this at all,” said Professor Clare Bryant in the University of Cambridge’s Department of Veterinary Medicine, senior author of the paper. 

She added: “We think that the lack of these functioning genes contributes to the ability of pathogens to hide undetected in carnivores, to potentially mutate and be transmitted becoming a human health risk.”

Zoonotic pathogens are those that live in animal hosts before jumping to infect humans. The COVID-19 pandemic, thought to originate in a wild animal, has shown the enormous damage that can be wrought by a novel human disease. Carnivores include mink, dogs, and cats, and are the biggest carriers of zoonotic pathogens. 

Three genes appear to be in the process of being lost entirely in carnivores: the DNA is still present but it is not expressed, meaning they have become ‘pseudogenes’ and are not functioning. A third gene important for gut health has developed a unique mutation, causing two proteins called caspases to be fused together to change their function so they can no longer respond to some pathogens in the animal’s body.

“When you have a large population of farmed carnivorous animals, like mink, they can harbour a pathogen - like SARS-CoV-2 and others - and it can mutate because the immune system of the mink isn’t being activated. This could potentially spread into humans,” said Bryant.

The researchers say that the results are not a reason to be concerned about COVID-19 being spread by dogs and cats. There is no evidence that these domestic pets carry or transmit COVID-19. It is when large numbers of carnivores are kept together in close proximity that a large reservoir of the pathogen can build up amongst them, and potentially mutate.

This research was funded by Wellcome.

Reference
Digby, Z. et al: ‘Evolutionary loss of inflammasomes in the Carnivora and implications for the carriage of zoonotic infections.’ Cell Reports, August 2021. DOI: 10.1016/j.celrep.2021.109614

 

Carnivorous animals lack key genes needed to detect and respond to infection by pathogens, a study has found.

Infectious diseasesCOVID-19Clare BryantDepartment of Veterinary MedicineCambridge Infectious DiseasesDepartment of MedicineQueens' CollegeSchool of the Biological SciencesSchool of Clinical MedicineWe’ve found that a whole cohort of inflammatory genes is missing in carnivores Clare Bryant Oikeutta elaimille on FlickrFarmed mink


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Trinity Challenge announces inaugural winners

Fri, 25/06/2021 - 15:43

The eight winners have been selected by an international panel of expert judges, out of a total of 340 applications from 61 countries. The competition has seen unprecedented collaborations between the private, public, charitable and academic sectors, and will drive a step-change in using data and analytics for pandemic preparedness.

The University of Cambridge joined a coalition of some of the world’s leading businesses and academic and tech institutions to launch The Trinity Challenge in September 2020. The global challenge, convened by Dame Sally Davies, Master of Trinity College, provides a £10m prize fund for breakthrough solutions to make sure one billion more people are better protected against health emergencies.

Participatory One Health Disease Detection (PODD), which empowers farmers to identify and report zoonotic diseases that could potentially pass from animals to humans, has been named the grand prize winner at the inaugural awards ceremony. The organisation is being awarded £1.3 million (US$1.8 million) in pledged funding.

Led by Susumpat Patipow, General Director at OpenDream, PODD has developed a platform for livestock owners to report suspected animal illness, and in return receive veterinary care to improve animal health. If it appears a disease outbreak is likely, local health officials will quarantine the sick animals, saving the remaining livestock and possibly preventing the next COVID-19-type outbreak.

Having already achieved significant success in Thailand, with a network of 20,000 farmers helping to detect and control disease outbreaks, PODD is looking to expand its operations to Cambodia, India, Indonesia, Laos, Uganda and Vietnam over the next three years.

BloodCounts! - an international consortium of scientists, led by Professor Carola-Bibiane Schönlieb from Cambridge’s Department of Applied Mathematics and Theoretical Physics (DAMTP) that has developed an innovative infectious disease outbreak detection system, was one of two second-prize winners, each awarded £1 million in pledged funding.

Developed by Dr Michael Roberts and Dr Nicholas Gleadall, the BloodCounts! Solution uses data from routine blood tests and powerful AI-based techniques to provide a ‘tsunami-like’ early warning system for new disease outbreaks.

“Since the beginning of the pandemic I have been developing AI-based methods to aid in medical decision making for COVID-19 patients, starting with analysis of Chest X-ray data,” said Roberts, who is affiliated with DAMTP and the Cambridge Mathematics of Information in Healthcare (CMIH) Hub. “Echoing the observations made by the clinical teams, we saw profound and unique differences in the medical measurements of infected individuals, particularly in their full blood count data. It is these changes that we can train models to detect at scale.”

Unlike many current test methods, their approach doesn't require any prior knowledge of a specific pathogen to work, instead, they use full blood count data to exploit the pathogen detecting abilities of the human immune system by observing changes in the blood measurements associated with infection.

As the full blood count is the world’s most common medical laboratory test, with over 3.6 billion being performed worldwide each year, the BloodCounts! team can rapidly apply their methods to scan for abnormal changes in the blood cells of large populations - alerting public health agencies to potential outbreaks of pathogen infection.

This solution is a demonstration of how the application of AI-based methods can lead to healthcare benefits. It also highlights the importance of strong collaboration between leading organisations, as the development of these algorithms was only possible due the EpiCov data sharing initiative pioneered by Cambridge University Hospitals. 

“Hundreds of millions of full blood count tests are being performed every day worldwide, and this meant that we could apply our AI methods at population scale,” said Gleadall, from the University of Cambridge and NHS Blood and Transplant. “Usually the rich measurement data are discarded after summary results have been reported, but by working with Cambridge University, Barts Health London, and University College London NHS Hospitals we have rescued throughout the pandemic the rich data from 2.8 million full blood count tests.”

The Sentinel Forecasting System is the other second-prize winner, and will explore the emergence of new infectious diseases in West Africa, beginning with Lassa fever. The system will combine data from ecology, social science, genomics and epidemiology to provide real-time disease risk for haemorrhagic fevers, such as Lassa and Ebola.

Lassa is a virus usually passed to humans through exposure to food or household items contaminated by infected rats. It is endemic in West African countries including Benin, Ghana, Guinea, Liberia, Mali, Sierra Leone, Togo and Nigeria.

Around 80% of people who become infected with Lassa virus have no symptoms, and the overall case-fatality rate is 1%. 1 in 5 infections can result in severe disease affecting the liver, spleen and kidneys.

The UCL team will partner with the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria, Nigeria Centre for Disease Control, Zoological Society of London, London School of Hygiene and Tropical Medicine, Microsoft, and Cambridge’s Laboratory of Viral Zoonotics (LVZ) to produce the system.

“This Trinity Challenge project brings new multidisciplinary technologies together to anticipate climatic, human, animal population, agricultural impacts on the likelihood of spill overs of infections from animals to humans,” said Professor Jonathan Heeney, who leads LVZ at Cambridge’s Department of Veterinary Medicine.

Additionally, five 3rd prize winners are each being awarded £480,000 (US$ 660,000) in pledged funding.

Dame Sally Davies said: “It was crystal clear at the beginning of this pandemic that the world had a lack of data, a lack of access to data, and a lack of interoperability of data, presenting a challenge. While others talked, we took action. The solutions we have discovered in the course of the Challenge will be a link between systems and countries.”

In addition to financial support, The Trinity Challenge will provide connections to the right organisations to maximise the impact of these solutions. Since its inception nine months ago, TTC has united early applicants with partners from the private, academic and social sectors to receive access to digital platforms, data, and technical advice, to scale-up the use of data and analytics to protect the world from future health emergencies. The Trinity Challenge has helped form over 200 connections between applicants and its members.

The Trinity Challenge has announced the winners of its inaugural competition, and is investing a £5.7 million (US$8 million) charitable pledged prize fund into one grand prize winner, two 2nd prize winners, and five 3rd prize winners.

medicinehealthPublic healthCarola-Bibiane SchönliebMichael RobertsNicholas GleadallJonathan HeeneySally DaviesDepartment of Applied Mathematics and Theoretical PhysicsCambridge Mathematics of Information in HealthcareDepartment of Veterinary MedicineSchool of the Physical SciencesSchool of Clinical MedicineSchool of the Biological SciencesTrinity CollegeJesus CollegeWhile others talked, we took action. The solutions we have discovered in the course of the Challenge will be a link between systems and countriesDame Sally DaviesThe Trinity ChallengeCollage of Trinity Challenge finalists


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