Why are animals used
in infectious disease
research?

From furthering our basic understanding of infectious organisms, such as bacteria, viruses, fungi and parasites (collectively known as pathogens), all the way to creating new treatments and even cures, animal research has been, and continues to be, a major contributor in our fight against infectious diseases, both to protect the health of humans and animals too. For now, the information gleaned from animal studies is crucial to the discovery of entirely new treatments and the development of improved ones, that have widespread effect and benefit.

Treatments for infectious organisms (collectively known as pathogens) are needed more than ever, as they are responsible for some of the most deadly and devastating diseases, and are capable of affecting virtually every part of the body, whether that is the blood or vital organs like the brain. Sometimes, it is the infection itself that does the most damage, or else it can trigger side effects or reactions from the body that range from mild to life-threatening.

For many types of infectious disease, we are unfortunately still lacking cures. The most recent reminder of that is, of course, the Covid-19 pandemic and the role of research using animals was at the core of both the fundamental research needed to understand the virus and then the development of effective vaccines that could meet this challenge. Thanks to such studies, these Covid vaccines were developed in record time (see box, Using animals in Covid-19 research).

This feature describes some of the key infectious diseases that have involved the study of animals, along with significant discoveries and breakthroughs, and how such research also serves to benefit animal health.

Man receives injection. (Credit: Unsplash)

How are animals used in infectious disease research?

Basic research is a key pillar of the study of infectious diseases and using a complex organism, such as a lab animal, can reveal an understanding of how a pathogen enters and infects the body, how it evades the body’s defences, and then infects other people.

One reason that non-animal methods have not completely replaced the use of animals in research into infectious diseases is that many animal species can be naturally infected by the same pathogens as humans, for instance hamsters and ferrets can catch Covid-19 and flu, which allows researchers to investigate how these agents progress to cause the disease.

Mice, in particular, are suited to having their genetics altered so that they can harbour a disease of interest, even if they are not normally affected by it in the wild. Genetic approaches also have the benefit of being able to make mice and rats ‘immunodeficient’ so that their immune systems do not act against the infection, which would hamper the study of disease pathogens.

Specific components of an animals’ immune system can also be ‘switched off’ to target the desired parts of the immune response to infections. Genetic approaches have been used in this way to model infections including HIV, Epstein-Barr virus, dengue and hepatitis.

Here are some other examples of how different species of animals have helped us understand more about infectious diseases.

Simian immunodeficiency virus (SIV) in monkeys is closely related to human immunodeficiency virus (HIV), and a study by EARA member the Biomedical Primate Research Centre (BPRC), Netherlands, discovered that the SIV virus damages the brain and can lead to neurological symptoms. This highlighted how HIV in people could also affect other parts of the body (not just the immune system) and helped identify other possible targets for research and treatments.

A study using rats at Trinity College Dublin, Ireland, showed the effect a protein has on the immune system and how it hampers the body’s response to tuberculosis.

And a recent zebrafish study, at the Paris Brain Institute, France, and UMC Amsterdam, Netherlands, identified that brain neurons that detect bitter tastes played a role in protecting against bacterial meningitis.

Developing vaccines also involves the use of animals, for example so that the right parts of the body, or bodily processes, are targeted, to successfully eliminate the infection. In turn, these new potential drugs and treatments are then tested on animals in preclinical studies, before they reach human trials.

The Worldwide Influenza Centre at the Francis Crick Institute, is monitoring the evolution of flu strains so as to create new vaccines as they are needed. The research involves using sheep to develop antibodies, and making antiserum from infected ferrets to analyse the infection properties of a specific virus. Fertilised eggs from chickens are then used to mass produce new vaccines.
Among the research on animals that have helped shed light on effective Covid-19 vaccines, was a study involving EARA members Ghent University and VIB, both Belgium, which found that antibodies from llamas could stop the coronavirus from breaking into host cells – watch the VIB video on the role of llamas in Covid-19 research below.

Researchers at Temple University, USA, used CRISPR gene editing to create a therapy for HIV that worked to eliminate the virus in mice, monkeys and human cells, which has now gone to clinical trials on humans. While another US team at Scripps Research developed an HIV vaccine, which improved the ability of mice, rabbits and monkeys to block the virus.

Preclinical animal research is an essential step in vaccine development, both for safety and efficacy. It is not possible to take a new experimental drug or vaccine into human testing without doing safety testing in animals first.

Professor Helen McShane, Jenner Institute, University of Oxford, UK

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Using animals in Covid-19 research
Animal research has played a critical role in helping researchers understand the SARS-CoV-2 virus itself, not only the mechanics of its transmission, but also the safety and efficiency of all the vaccines so far produced to bring the end of the pandemic a step closer. Watch this video by Americans for Medical Progress on how animal research led to Covid-19 vaccines in record time.

If the animal trials showed the vaccine was not safe, or not effective, we would not have wasted time preparing clinical trials that could not go ahead. This time, we did all the clinical trial preparation while the animal trials were still going on.

That way, it was within days of receiving the safety data from our animal trials that we were putting the vaccine into the arms of our first volunteers.

Professor Dame Sarah Gilbert, Oxford Vaccine Group, UK

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In an example of the value of fundamental research to lay the groundwork for potential treatments and cures, genetically altered mice were developed in 2007 at the University of Iowa, USA, as a suitable model to study coronaviruses, such as Middle Eastern Respiratory Disease (MERS). The availability of this model meant that the disease could quickly be studied in the context of how the SARS-CoV-2 virus would affect human cells.

Meanwhile, mRNA vaccines, that were a critical part of the treatment of Covid-19, had been under development for many years thanks to early research in mice, that led to the understanding that mRNA could be manipulated to produce an immune response in the body – the discoverers were recently awarded the 2023 Nobel Prize in Medicine for this vital work.

A leading member of the Oxford Vaccine Group, the developers of the Oxford-AstraZeneca Covid-19 vaccine (not based on mRNA), also described the contribution of animal studies in its success.

Pfizer-BioNTech Covid-19 vaccine. (Credit: Wikimedia Commons)

Animals are also useful for investigating new treatments that may prove more effective than existing treatments.

A study at Yale School of Medicine, USA, found that a nasal influenza vaccine could provide mice with better protection than administering it via injection, as well as demonstrating it could potentially protect against new Covid-19 variants.

Also, at Yale, another team used the same blueprint of a Covid-19 vaccine to develop one for Lyme disease, which protected guinea pigs against this tick-borne infection.

The Koch Institute for Integrative Cancer Research, at MIT, USA, has tested in rats a ‘self-boosting’ polio vaccine that means multiple vaccination shots are not required.

Using mice, researchers from the University of North Carolina School of Medicine, USA, found that an oral drug originally intended for hepatitis B could also prevent the hepatitis A virus.

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Guinea pig held by an animal technician. (Credit: Understanding Animal Research)

Breakthroughs & discoveries

Whether it is to help eradicate diseases that historically killed thousands, or coming up with effective strategies to combat existing ones that still affect people around the world, here are the key breakthroughs and discoveries about infectious diseases that have come about from the use of animals.

Respiratory infections

From the common cold to more serious infections such as tuberculosis (TB) and Covid-19 that affect the lungs and respiratory system, animal research has been involved every step of the way to bolster our knowledge of these diseases and come up with therapies.

A variety of mammals have been used to research influenza, which causes seasonal disease epidemics that result in up to 5 million cases of severe illness a year. Ferrets were the first animals used to study influenza-like illness and observe how it could spread between animals, as their lungs have a similar biological make-up to people. They have also been used for different variants, such as influenza A, for example by confirming that the virus was spread by aerosol transmission (via expelled infectious droplets).

Ongoing research at Imperial College London, UK, is using ferrets to investigate how the flu virus infects cells, as well as how to reduce flu transmission. For example, a 2020 study showed that a drug called baloxavir can reduce the risk of ferrets transmitting the virus to healthy animals, suggesting it could be used to control flu outbreaks. See also this video on Imperial's research with Prof Wendy Barclay (pictured below).

Meanwhile, studies in guinea pigs established the distances between two people that flu could be transmitted from, and monkeys infected with influenza have been important for making sense of historical outbreaks by clarifying how the virus spreads, for example.

Pigs are emerging as good models for human flu vaccine development because of their similar immune systems, with research at the Pirbright Institute, UK, finding that the animals can mimic the effects of vaccination against human flu, and identified ways to administer vaccines to provide better disease protection.

Monkeys have helped to develop more effective vaccines against TB than the currently-used BCG vaccine, which is not very effective, while research at Duke University, USA, used zebrafish to identify suitable medicines for disrupting the formation of granulomas – aggregates of immune cells that play a key role in the development of TB. Historically, guinea pigs, along with mice and chicks, were used for finding the first cure for TB, through the testing of the effectiveness of streptomycin, a natural bacteria-killing substance made by microorganisms in the soil.

Thanks to vaccine developments, polio has been virtually eradicated worldwide. Researchers at the Pasteur Institute, Paris, first replicated polio in monkeys, using spinal cord samples from a patient, and developed a vaccine in the 1950s after decades of work in not only monkeys, but mice and rats. See also the work of researcher Jonas Salk.

Brain diseases

A universal vaccine targeting a range of strains of meningitis B, which affects the brain, has been developed by EARA member Novartis, Switzerland, that used earlier research in mice and rats. Novartis researchers were able to create the vaccine by searching the genome of the Neisseria meningitides bacterium (the main cause of meningitis) for proteins that could be targeted by antibodies, before producing these antibodies in mice and testing whether they could kill the bacteria. Rats treated with the mouse antibodies confirmed that the vaccine worked and could be rolled out to protect thousands from disability and death.

HIV

Animals have been paramount to understanding HIV in terms of the virus itself, and to how to treat AIDS which occurs as a result of the virus attacking the immune system – see also this article.

Several preclinical studies have paved the way for developing antiretroviral therapy (ART), which involves a combination of medicines that suppress the virus’s replication – the earliest ART was tested in monkeys.

There is also a real possibility of an effective vaccine within reach the next decade, based on the success of trials in animals. In 2019, for example, the virus was eliminated from the genome of a mouse for the first time, by researchers at Temple University and the University of Nebraska Medical Center, both USA. Temple researchers also created a new HIV therapy using gene editing that worked to eliminate HIV from infected cells in humans, mice and monkeys.

Hepatitis

Non-human primates have played a central role in the research and treatment of hepatitis, a group of infections, usually caused by viruses, that affect the liver and result in inflammation. Chimpanzees are the only animal that can be infected with the hepatitis C virus (HCV) – a type that has long confounded researchers. Although other animals can model aspects of HCV infection (mice, for example, share some genes with human HCV), they do not always encapsulate the disease well.

The use of great apes in research, including chimpanzees, is generally prohibited in the EU, and is only permitted when a condition that endangers humans cannot be studied in other species, as is with the case with hepatitis C. The discoverers of hepatitis C, Harvey J. Alter, Michael Houghton and Charles M. Rice, were awarded the 2020 Nobel Prize in Medicine, with chimpanzees being an integral part of the work.

Mice are more commonly used to study hepatitis B, for example through the transplantation of human liver, other species such as ducks and groundhogs are infected by similar viruses, that also make them useful to hepatitis research.

Malaria

In the last decades, significant progress has been made in treating this mosquito-borne disease, thanks to US research that involved penguins, infected with an avian version of malaria, to study how it could be treated with an antimalarial drug, chloroquine.

However, malaria remains a significant health threat in regions including sub-Saharan Africa and southeast Asia (it caused more than 600,000 deaths in 2021), and what is urgently needed is an effective vaccine that can target the parasite, or the disease itself. The RTS, S vaccine, which entered large-scale trials in 2019 to treat thousands of young children in Africa, was developed with the use of mice in the 1960s. Those studies showed that vaccinating animals against the infective stage of plasmodium can protect against infection, and also identified that a specific protein that could be recognised by the immune system – this was incorporated into the RTS, S vaccine and in 2021, the World Health Organization recommended RTS, S for preventing malaria in children living in high-risk areas.

More recently, research at EARA member the Max Planck Institute for Infection Biology, Germany, and the University of Bristol, UK, was able to find what caused organ failure in malaria patients by infecting mice with a variant of the malaria parasite (as well as genetically altering mice), to protect against liver damage that is seen in severe cases of the disease.

Ebola

In countries particularly in Africa, such as the Democratic Republic of Congo (DRC), Ebola is a serious ongoing health emergency. However, thanks in part to research involving mice and monkeys, a real breakthrough was achieved in 2019 when two of four experimental treatments cured 90% of patients in a clinical trial. These therapies were pioneered by harvesting the antibodies from humanised mouse models that were exposed to proteins from the virus, which were then studied in combination with monkeys.

An outbreak in 2020 (the second most deadly to occur) also ended because of a rollout of the first successful vaccine and two antibody drugs developed in monkeys by the National Institute of Allergy and Infectious Diseases (NIAID) Vaccine Research Center (VRC), USA.

And a more recent NIAID study used monkeys to develop a vaccine against Sudan virus – one of the four types that cause Ebola and is similarly deadly in both monkeys and people, and that is also lacking a treatment.

Other infectious diseases

Animal research, in species such as monkeys, has also paved the way for human vaccine trials to begin for other viral diseases, such as the one caused by Zika virus, after work by the University of Liverpool and EARA member the University of Manchester, both UK.

Meanwhile, research led by Oregon Health & Science University, USA, developed an experimental drug for the Chikungunya virus that, when tested in mice, reduced the amount of virus by up to 1,000 times and stopped joint pain, with hopes to start clinical trials in the future. Chikungunya is a viral disease transmitted via mosquito bites, with one of its key symptoms being joint pain, which can often be severe and last months, or even years.

The first vaccine for chikungunya is likely to go onto the market in 2023, following ‘imminent’ approval by the Food and Drug Administration (FDA). Developed by biotechnology company, Valneva, France, monkeys were used to test antibodies that can neutralise the virus, with trials showing that the animals did not develop any symptomatic disease.

We have developed many tools to study immunity in pigs… These tools and experience make pigs an invaluable model to study immunity against respiratory infections for improvement of animal and human health.

Mucosal Immunology Group, Pirbright Institute, UK

Thanks to research in monkeys, HIV is no longer a death sentence.

Biomedical Primate Research Centre, Netherlands

HIV infection in the bloodstream. (Credit: Science Photo Library, Canva)

For the first time in history, the disease can now be cured, raising hopes of eradicating hepatitis C virus from the world population.

Nobel Prize Committee

Mosquitoes are the vectors for the malaria parasite. (Credit: MPI for Infection Biology)

Animal research allows us to make predictions on human pathology. When this happens, we solve another piece in the jigsaw puzzle that explains what goes wrong in disease.

Arturo Zychlinsky, Max Planck Institute for Infection Biology, Germany

From now on, we will no longer say that Ebola is incurable. These advances will help save thousands of lives

Jean-Jacques Muyembe, INRB (DRC’s biomedical research institute)

An animal model can be useful to, in a very short time sometimes, show proof of concept – of how the virus transmits, or how it causes disease – but also if you want to test interventions. It is difficult to test interventions that are focused on preventing infection in humans.

Koen van Rompay, California National Primate Research Center, USA,

in a Q&A with EARA about Zika (pictured below).

If further trials prove successful, baloxavir could dramatically change how we manage seasonal influenza outbreaks and pandemic influenza in the future

Prof Wendy Barclay, Imperial College London, UK

(Credit: Understanding Animal Research)

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Koen van Rompay studies the Zika virus in monkeys.

Which animals are used in infectious disease research?

Rodents

As the most common species of animals used in research around the world, rodents are indispensable to the understanding and treatment of infectious diseases. Animals more closely related to us, such as monkeys, catch more of the same diseases as humans, however rats and hamsters have many of the same health problems that are common to the human condition – they can also easily be given characteristics of a disease through genetic alterations.

Attaching cells or tissues derived from humans into mice – a technique called a xenograft – is another useful way to make the animals more ‘human-like’ so that they better reflect human diseases and pathology. Immune cells have been xenografted and applied to the study of several types of infectious disease, such as viral haemorrhagic fevers, that include dengue, yellow fever and Ebola. Research at the German Centre for Infection Research showed that by transplanting human stem cells into mice, the animals exhibited features akin to Ebola, such as liver impairment.

Mouse receiving an injection. (Credit: UAR)

By analysing mouse stem cells, researchers at the Francis Crick Institute, UK, found that the ‘machinery’ needed to build an antiviral protein that could protect the body against both the Covid-19 and Zika virus.

Read more about how mice are used in research in our feature.

Monkeys

As well as being very biologically similar to people, monkeys are also natural hosts of many of the same pathogens that infect us, such as the parasite that causes malaria. Studying infections that progress naturally, and occur from wild-type pathogens that have not been altered in some way, has the advantage of being more reflective of human disease – monkeys are the best animal to study Ebola, for instance, because the virus causes serious illness that is akin to what happens in people.

Assessing how well a vaccine works (or at all) is especially crucial, and the use of research monkeys has led to the introduction of antiretroviral therapy for HIV and the approval of all Covid-19 vaccines. Studies in monkeys also serve to improve our understanding of how diseases may affect the body long term – the hidden effects of ‘long Covid’ was revealed in a study in macaques by EARA member the BPRC, which showed that even with no obvious signs of infection, the animals still had evidence of lung damage and active virus in the lymph nodes. Watch this BPRC video on testing a Covid-19 vaccine (in Dutch).

Without an animal model that closely replicates what goes on in humans, there’s potential for harm in a fast-moving pandemic response like the one [in 2020].

Jay Rapport, director of the Tulane National Primate Research Center, USA

Read more in this EARA article on the role of monkeys in Covid-19 research.

Dogs

Dogs share several similar features to people, such as in their anatomy (they have most of the same organs), which makes them suitable for studying human-relevant diseases. They also naturally catch some of the same infections we do, such as rabies.

Research in dogs was responsible for both veterinary and human rabies vaccines, by vaccinating them using weakened samples of the virus (made from rabbits). Vaccinating dogs, means people and animals are also much better protected from its spread, as found by a study led by Imperial College London and the University of Glasgow, both UK, and Ifakara Health Institute, Tanzania.

Rabbits

Rabbits have played an important role in the study of some infectious diseases, particularly the S. pneumoniae bacteria that cause pneumococcal disease, which are a diverse range of infections, from those of the ear to the bloodstream, and is spread through direct contact.

Rabbits have helped to identify new types of the disease, by studying how the bacteria infects, survives and progresses, while also being central to developing and testing a range of candidate drugs. For example, US research, led by the University of Buffalo, New York, used rabbits along with mice to test a vaccine that was effective against more than 70 types of S. pneumoniae.

The first type of papilloma virus was also discovered in rabbits, with research into human papilloma virus (HPV) that can cause different types of cancer, and that is the main cause of cervical cancer, benefiting from the use of various animal species.

Other animals

Infectious disease research benefits from studying a range of other animals, such as ferrets and guinea pigs which naturally catch strains of human flu, for example, and therefore display similar symptoms.

Meanwhile, the embryos of chickens develop in a way that is comparable to human foetuses and are therefore useful for studying early infection in diseases like Zika.

(Credit: UAR)

More unconventional species such as insects – from moths to mosquitos to honeybees – are also emerging as valuable models, since they can be easily manipulated, for example at the genetic level, to help understand the factors that contribute to infection mechanisms, disease progression and much more. Insects have additional value because certain pathogens (such as the plasmodium parasite for malaria) use insects as a host to infect other organisms, and can also be used to better understand antibiotic resistance (see box, What is antibiotic resistance?).

Animal health

It is not only human health that benefits from infectious disease studies in animals – such research is also important to help to minimise or prevent transmission between humans and other species, as well as protect farm animals. Diseases that can pass between people and animals are known as zoonotic diseases, such as Covid-19 and rabies, or the recent outbreak of the monkeypox virus.

The global EU-funded consortium, VACDIVA (pictured below), involving EARA member the Complutense University of Madrid, Spain, is at the forefront of developing a vaccine for African swine fever (ASF) – a high contagious disease affecting pigs that has resulted in millions of the animals being culled.

Research at The Roslin Institute at the University of Edinburgh, UK, found that vaccinating calves against bovine TB in their first few weeks of life boosted the level of protection against the disease, which presents a major health challenge in cattle, but can also be spread occasionally to humans.

VACDIVA team. (Credit: VACDIVA)

What is antibiotic resistance?
Antibiotics have been a dependable and highly effective way to combat infectious diseases. They come in many different types, but all work by disrupting some process in bacteria that is vital to their survival, or by preventing the bacteria from spreading.

However, in recent years, with the over-frequent use of antibiotics for both humans and animals, a phenomenon in bacteria known as antibiotic resistance is becoming a major global health threat. This has already rendered many drugs ineffective and is only set to get worse. Ultimately completely new ways will be needed to treat bacterial infections.

Animal studies will be essential for testing alternatives to antibiotics. Phage therapy, which uses viruses to infect and kill bacteria, is emerging as a promising alternative to antibiotics, but before it can be trialled in humans, animals have been essential to testing, refining and improving this approach so it can be used in the clinic.

Species ranging from mice to rabbits to chickens have been used to investigate phage therapy in a range of organ systems (such as the gastrointestinal) and bacterial strains. As farm animals like cows and pigs are given many antibiotics (even when they may be healthy). they are of particular interest in the study of antibiotic resistance, where diseases such as bovine tuberculosis and avian or swine flu are prevalent and pose a major health and economic burden.

Researchers at EARA members University Libre des Bruxelles and GSK, Belgium, have also looked to making existing antibiotics effective again, using mice to show that a molecule could reverse resistance against tuberculosis bacteria.

A lot of stuff can be done in Petri dishes, but then when it comes to testing the efficacy and potency of antibiotics, one has to look at animals models.

Professor Gad Frankel, Imperial College London

Care of animals

The use of animals in infectious disease research is tightly regulated to ensure that such studies are justified and that a non-animal method cannot be used to achieve the same results. In the EU, researchers must follow the 3Rs principle of replacement, reduction, refinement, with EU Directive 2010/63 ensuring that a high standard of animal welfare takes place and ethical considerations are addressed, while alternative methods to complement, and in some cases replace, animal research are being developed, where possible (see next section).

In the case of animal welfare, a range of aspects are important to maximise the well-being of animals, and the accuracy and reliability of experiments – from good experimental design to housing enrichment to harm-benefit analysis (whether the harms that animals are expected to experience justify the benefits of the research).

Technician checks rabbit. (Credit: UAR)

Can we use alternatives to animals in infectious disease research?

Increasingly, as with certain other areas of research, non-animal approaches are emerging that have the capacity to replace, reduce or refine (3Rs) animals used in some infectious disease studies. Although we are still not at a point where these methods can fully replace animals in studying and treating infections and diseases – owing to limitations in research and development, and regulatory approval – alternatives are nonetheless proving valuable for complementing aspects of animal research and providing insights.

Organoids created from human cells and tissue, and that can be grown and cultured in the lab, are useful for studying certain processes and testing the effect of drugs by mimicking what happens in specific organs in the body. For example, a study at the University of California, Irvine, USA, created a tonsil organoid that was successfully used to model respiratory infections, such as Covid-19 and the flu, and study the development of immunity in response to vaccination.

Human cells can also be used through organ-on-chip technology, where natural or engineered tissues are grown on a microfluidic chip. These also provide a way to simulate the body and to better understand what happens to organs when they are infected and inflamed, for instance. A variety of organs that are susceptible to infection can be mimicked, including the lungs, kidney and gut. However, before any studies based on these findings can progress to humans, animals still need to be used to assess the safety and effectiveness on a living organism.

Meanwhile, computer modelling can forecast diseases using existing data on factors such as transmission and symptoms, to provide estimates on how widespread or deadly a disease could be. Computation has also helped to model the dynamics of infections within hosts and between hosts for diseases like malaria and influenza.

Covid-19

antibiotic resistance