Several of ANSES's laboratories have been working on animal coronaviruses for many years. For example, their teams took part in the ANR project EPICOREM from 2014 to 2018. This study, coordinated by the Caen University Hospital, revealed the great diversity of coronaviruses circulating in wild animal populations in France and Europe. New viral species were described in humans, domestic animals and wildlife. At the same time, researchers monitored the evolution of a betacoronavirus, a SARS-CoV sister group, within a bat colony. This part of the project has led to a greater understanding of the dynamics of the virus’s evolution within a host.
The Maisons-Alfort Laboratory for Animal Health is also conducting several research projects on coronaviruses, including one on the therapeutic potential of new antiviral drugs against coronaviruses in general. The study is focusing on a human coronavirus responsible for respiratory infections (HCoV-229E) as well as a feline coronavirus (feline infectious peritonitis virus) responsible for a fatal disease in cats. The most effective drugs are being tested in vivo in naturally infected cats for which no therapy is currently possible. The findings will enable the therapeutically effective dose against a given coronavirus to be assessed.
Meanwhile, in Ploufragan, the Virology, Immunology and Parasitology in Poultry & Rabbits (VIPAC) Unit has been working on avian coronaviruses for over 30 years. In particular, the unit has been studying the genetic evolution of avian coronaviruses in the presence or absence of vaccination. The results have shown that the genetic evolution of an avian coronavirus is very rapid (detected from the first passage in non-vaccinated subjects) and differs between vaccinated and non-vaccinated subjects. These results have shed light on how coronaviruses evolve in the presence of vaccine immunity. Lastly, the Viral Genetics and Biosafety (GVB) Unit is home to the National Reference Laboratory for porcine epidemic diarrhoea (PED), a disease caused by a porcine coronavirus, which appeared for the first time in 2013 in the United States. It can affect pigs of any age, but the mortality rate is highest in unweaned piglets (80 and 100% respectively ).
Work carried out since the start of the COVID-19 crisis
At the Laboratory for Animal Health
The Virology UMR (an ANSES-ENVa-INRAe joint research unit) has particularly been involved in initiating the following projects:
- a scientific study on the potential infection of pets, especially cats. Following international publications describing a few cases of contamination in domestic carnivores, the Virology UMR launched a scientific study on the possible transmission of the SARS-CoV-2 virus to cats. Veterinary practitioners from Île-de-France were invited to submit samples collected from suspect animals (cats in close contact with a person infected with COVID-19 or cats showing acute respiratory symptoms). The aim of this study was to improve existing knowledge on how SARS-CoV-2 is transmitted and how it behaves in cats. It led to detection of the first infected cat in France. This sick cat, which ended up recovering, had likely been contaminated by its owner. An article on the topic was accepted for the journal Transboundary and Emerging Diseases;
- the SARS2BlockEntry project (Engineering nanobinders to block SARS-CoV-2 entry). Financed by the National Research Agency (ANR) and coordinated by the National Research Institute for Agriculture, Food and Environment (INRAe), it aims to develop drugs to block SARS-CoV-2 entry into cells, using hamsters as the animal model;
- work on potential central nervous system infection with SARS-CoV-2. A large number of patients with severe forms of COVID-19 have presented with neurological symptoms, suggesting that the virus may invade the central nervous system. The virus’s ability to infect these cells will be studied using central nervous system cells handled in the laboratory;
- the MUSECoV project, selected by the ERA-Net ICRAD (International coordination of research on infectious animal diseases) call for projects; coordinated by Sophie Le Poder from the Alfort National Veterinary School and managed by the Virology UMR. It seeks to improve understanding of the diversity of coronavirus strains, including SARS-CoV-2, circulating in animal populations. The aim is to better understand the dynamics of coronavirus infections in various animal populations and therefore to rapidly detect the emergence of particularly pathogenic variants;
- the laboratory also published a study on the possibilities of detecting, immobilising and controlling coronavirus infection using lectins produced by certain plants, algae and cyanobacteria.
At the Laboratory for Rabies and Wildlife
- the Timing project, funded by the ANR and coordinated by INRAe. This ongoing project is studying the beneficial or deleterious effect of type I interferons (IFNs). These are small proteins produced naturally in the body in response to a viral infection. Numerous studies have shown that the body’s failure to produce type I IFNs may be associated with the development of severe forms of COVID-19. However, type I IFNs are not always beneficial, as they can cause excessive inflammation. The balance between the beneficial and detrimental effects of type I IFNs needs to be studied in the case of COVID-19. The objective of the Timing project is to determine the appropriate moment to administer IFN treatment, in order to eliminate the infection and reduce the development of COVID-19 symptoms and lesions, without causing excessive inflammation. The results have shown that the treatment is only effective when administered in the very early stages of infection;
- the study of anosmia, or loss of sense of smell, which is one of the symptoms often encountered in patients with COVID-19. Using the laboratory's experimental hamster model, and in collaboration with INRAe, the teams were able to demonstrate that the virus infects other cells in the nasal mucosa, but not the olfactory nerves. This infection of the mucosal cells was associated with desquamation of the nasal mucosa, which led to a loss of the olfactory neurons responsible for detecting odours. Their work was published in the journal Brain Behaviour and Immunity;
- the laboratory is responsible for the EvoZOOne project, selected by the World Health Organization as part of its R&D Blueprint call for projects. Its aim is to increase knowledge on SARS-CoV-2 at the human-animal interface relating to the evolution of the virus and the assessment of its zoonotic potential. The laboratory is also involved in a second WHO R&D Blueprint project on viral persistence under different environmental conditions, led by the ANSES Laboratory for Hydrology: persistence and behaviour of SARS-COV-2 particles in aqueous environmental matrices;
- study of mink in French farms: the laboratory analysed the sequences of viruses found in an infected mink farm in France. This study ruled out a direct link to the SARS-CoV-2 variants identified in mink farms in the Netherlands before the summer of 2020 and in Denmark in late 2020, and determined that the animals had been infected by humans carrying the virus;
- The laboratory is taking part in three projects as part of the Emergen consortium (coordinated by the French National Research Agency and Santé Publique France), which uses microbial genomics to carry out surveillance and research on infections caused by emerging pathogens:
- the RATVAR project, whose objective is to assess the receptivity and susceptibility of rats to the SARS-CoV-2 variants;
- the BIOVAR project, which aims to biologically characterise the different variants, by assessing their transmissibility, pathogenicity and fitness (ability to multiply in certain tissues and degree of aggressiveness);
- the PRODEVAR project, which will study the capacity of SARS-CoV-2 to evolve in laboratory settings, in particular with the constraints of vaccination, natural immunity and antiviral therapies.
The laboratory will also receive funding to strengthen its infrastructure.
At the Ploufragan-Plouzané-Niort Laboratory
The Virology, Immunology and Parasitology in Poultry & Rabbits (VIPAC) Unit and the Viral Genetics and Biosafety (GVB) Unit have been working to acquire the knowledge needed to combat the pandemic in several areas:
- identifying coronavirus inactivation treatments for surgical face masks: in a collaboration with Grenoble University Hospital, the French defence procurement agency (DGA), Tours Hospital and various private partners, and thanks to access to the facilities of the Dupuy de Lôme Research Institute (University of Southern Brittany), a partner of ANSES within the AgriFood Transition Carnot Institute, the Ploufragan Laboratory is currently assessing the efficacy of various virucidal treatments applicable to respiratory masks, using two animal coronavirus models (avian infectious bronchitis virus and porcine epidemic diarrhoea virus). The goal of this work is to help identify safe solutions that can be implemented by both professionals and private individuals, to sanitise their masks and make them fit for reuse. This work led to the filing of a patent application for a UV treatment process;
- developing a new specific serological test for European turkey coronavirus: this project is receiving financial support from the AgriFood Transition Carnot Institute. Ultimately, it will be possible to apply this knowledge to the development of tests for detecting other coronaviruses;
- studying the persistence of coronaviruses in coastal waters: as part of the ANR's RA-COVID-19 call for projects and in collaboration with the French Research Institute for Exploitation of the Sea (Ifremer), the DISCO project has been submitted with a view to studying the survival and persistence of coronaviruses in coastal waters, as well as their bioaccumulation in molluscs. Porcine coronaviruses will be used as models to replace the SARS-CoV-2 coronavirus for the preliminary studies;
- conducting diagnostic testing for SARS-CoV-2: as public veterinary research laboratories, the virology units on the Ploufragan site have been called on by the Brittany Regional Health Agency to build SARS-CoV-2 diagnostic capacities in Brittany. If needed, the laboratory will be able to perform up to 360 RT-PCR analyses per day. This mobilisation of veterinary laboratories to control the COVID-19 pandemic supports the concept to focus efforts on "One Health" combining veterinary and human health;
- within the Emergen consortium, the laboratory is involved in the CoVEvol project, dealing with the evolutionary dynamics of the SARS-CoV-2 variants under the influence of vaccination. This project is using the methodology and tools developed by the laboratory to analyse the genetic variability of avian coronaviruses in terms of their response to vaccination. The results may guide public health decisions, in particular with regard to the composition of vaccines, so as to not promote the emergence of new variants.
At the Laboratory for Food Safety
The Enteric Virus (EV) Unit has been working to advance knowledge and assess potential non-airborne routes of SARS-CoV-2 transmission, as well as the risks associated with the presence of the virus in the environment. It led the Impedance SARS-CoV-2 project, funded by the WHO as part of its R&D Blueprint. The aim was to increase knowledge of SARS-CoV-2 and viral persistence under different environmental conditions, including methods of food packaging and transport. The project led to development of a rapid and reliable real-time test to detect and quantify SARS-CoV-2 infectious particles.
The unit is also involved in the ANR's SACADA project, which will study SARS-CoV-2 transmission in food preparation facilities, with the emphasis on meat-processing plants.
As part of the Emergen consortium, the Laboratory is carrying out the DIVA project in conjunction with the Laboratory for Animal Health. Its objective is to identify the routes of infection of the various SARS-CoV-2 variants that cause intestinal diseases. It will also explore their role in possible viral transmission via the faecal-oral route, using in vivo and in vitro models.
At the Nancy Laboratory for Hydrology
As part of its research activities, the laboratory's Microbiology Unit has also been working to advance knowledge of SARS-CoV-2. It led the project on persistence and behaviour of SARS-CoV2 particles in aqueous environmental matrices, funded by the WHO as part of its R&D Blueprint. This project aims to develop knowledge on the viral persistence of SARS-CoV-2 under different environmental conditions and to understand the persistence and behaviour of SARS-CoV-2 particles in aqueous environmental matrices.
The Microbiology Unit is also involved in the European COVRIN One Health EJP, which will, among other things identify the factors governing the spread of SARS-CoV-2 in the environment, including in wastewater. Although the infectivity of excreted SARS-CoV-2 is still a topic of debate, the abundant release of the virus in faeces during this pandemic period could determine its accumulation in wastewater and its release into the environment. Neither foodborne nor waterborne transmission can be considered the main routes of transmission, but indirect contamination of foods such as leafy vegetables, soft fruits or bivalve molluscs could occur through indirect faecal contamination, i.e. via irrigation water or the water from which bivalves are harvested. Collection of water samples, followed by concentration of the dispersed biological material, has been recommended as an environmental monitoring method by the WHO, as well as by the European Commission, through the publication on 17 March 2021 of its Recommendation (EU) 2021/472 on a common approach to establish a systematic surveillance of SARS-CoV-2 and its variants in wastewaters in the EU.
In the Risk Assessment Department
ANSES is leading the SACADA project (from the French acronym for "transmission of SARS-CoV-2 in food preparation facilities with the emphasis on meat processing plants"). Its objective is to better understand how the virus circulates in these plants and to suggest appropriate preventive measures. It is being subsidised by the National Research Agency (ANR) and conducted in collaboration with the Institut Pasteur, INRAe, Santé Publique France and the National Veterinary Schools of Alfort (ENVa) and Nantes (Oniris).
Interesting animal models for studying new therapeutic approaches
The Nancy, Lyon, Ploufragan and Maisons-Alfort Laboratories have responded to various calls for projects, in collaboration with hospital, INRAe and veterinary school research teams, to develop ferret and hamster animal models in order to test new therapeutic approaches and investigate host-pathogen relationships. The results obtained with ferret models in Nancy and hamster models in Lyon are highly relevant and complementary. The effects in ferrets resemble those observed in humans, especially in the upper airways, with clinical effects visible seven to 10 days post-inoculation. This animal model is also advantageous in that samples such as nasal wash fluids can be collected without having to sacrifice the animals; moreover, it enables viral loads to be monitored over time.
Conversely, the hamster model shows very rapid and strong signs of lung damage, from two days post-inoculation. This model is not as conducive as the ferret model to sampling without sacrificing; however, it is an excellent model that is easy to implement using short protocols (lasting around one week) to analyse candidate drugs having a possible therapeutic effect on SARS-CoV-2.
The validation of these animal models has led the Nancy and Lyon Laboratories to submit several requests and projects seeking to better understand the pathogenesis of COVID-19 and test therapeutic compounds and vaccines in collaboration with numerous institutes.
Prepare for the emergence of other coronaviruses
The Nancy, Ploufragan and Maisons-Alfort Laboratories are also working together to study under what conditions and for what reasons coronaviruses may cross the species barrier and thus jump from one animal species to another. This will help them better prepare for the emergence of new coronaviruses. This subject will be addressed within the framework of the One Health EJP, with the forthcoming organisation of a Joint Integrative Project (JIP) entitled "COVRIN-SARS-CoV-2" Research Integration & Preparedness for Future Coronavirus Outbreaks". This JIP aims to integrate the coronavirus research activities of all the One Health EJP partners. It will have two main operational objectives: to identify the factors determining emergence and spread of SARS-CoV-2, and to generate data and build models for assessing coronavirus risks.
Lastly, the Agency's work for the "One Health" project – based on the three pillars of human, animal and environmental health – and its involvement in scientific management of the One Health field of major interest (DIM) have sustained dynamic research into coronaviruses in domestic carnivores and supported new anti-coronavirus therapeutic approaches. They have also helped raise one million euros to support research during this crisis.