Corporate report

Animal and Plant Health Agency (APHA) science strategy, 2021 to 2026 (web version)

Published 21 April 2021

Foreword

Our Science Strategy 2021 to 2026 underpins our Animal and Plant Health Agency (APHA) Mission Statement: Safeguarding animal and plant health for the benefit of people, the environment and the economy.

It builds on our Science Strategy 2015 to 2020 'Expertise with Impact'.

Since we launched our 2015 strategy, there have been significant changes including the:

• decision to leave the EU
• confirmed funding for the redevelopment of our science headquarters in Weybridge, Surrey
• global COVID-19 pandemic

Whilst our mission and vision for the agency has remained the same, these significant changes strengthen our ambition to have a global scientific influence with world class facilities to support and retain our internationally recognised expertise.

For example, in response to SARS CoV-2 (a variant of COVID-19), we have built upon our ability to provide an agile and flexible One Health approach, utilising our laboratory facilities and scientific expertise and will extend this to provide and support a national response for incidents and disease outbreaks.

Science continues to be fundamental to everything APHA does and we are committed to high quality science-based evidence for decision making and policy development. We will deliver this strategy over the next five years.

Kath Webster, Director of Science

Strategic context

APHA as an Executive Agency of the Department for Environment, Food and Rural Affairs (Defra) is responsible for responding to biosecurity threats to the UK, including:

• endemic or exotic animal diseases (including zoonotic diseases)
• pests
• diseases of plants
• bees
• invasive non-native species

These biosecurity threats can occur in three ways:

• deliberate
• accidental
• natural

Around 60% of all human diseases and 75% of all new and emerging infectious diseases are naturally transmitted from animals to people (zoonotic diseases) (that is naturally transmitted from animals to people).

APHA work

We provide the following services:

• high containment laboratory and animal facilities
• scientific expertise in a range of microbiological and analytical disciplines
• research and test development functions to diagnose known diseases
• develop tests and reagents to detect new diseases
• support outbreak control measures

Our laboratory testing portfolio is extensive and includes over 600 assays across a very broad range. We perform more than 800,000 tests annually.

APHA is one of the world’s leading research centres in the field of animal and veterinary public health. APHA hosts 17 of the 25 International Reference facilities located in the UK, which are designated by the:

• World Organisation for Animal Health (OIE)
• World Health Organisation (WHO)
• Food and Agriculture Organisation of the United Nations (FAO)

Our scientists hold these expert roles being at the cutting edge of knowledge, modern technology and at the forefront of their fields. We are the UK designated laboratory for over 35 diseases, with the majority having National Reference Laboratory (NRL) status and we continue to expand this capability. Jointly with the Centre for Environment, Fisheries and Aquaculture Science (Cefas) and the Veterinary Medicines Directorate (VMD) we are also now recognised by the FAO as the Reference Centre for Antimicrobial resistance (AMR) and the OIE Collaborating Centre for Risk Analysis and Modelling jointly with the Royal Veterinary College (RVC).

APHA undertakes surveillance for new, re-emerging, endemic, exotic animal and plant diseases and pests.

Surveillance is achieved through a combination of approaches including:

• statutory reporting
• targeted surveillance
• local intelligence
• horizon scanning
• risk analysis including monitoring and tracking developments
• tracking developments and changes around the world through our wider networks (national and international)
• analysis and assessment of disease data arising from material submitted for diagnostic purposes

Our work in these high-profile areas is critical to the economy, society and the environment. APHA provides specialist expertise to the UK’s Veterinary Risk Group (VRG). This group’s remit is to identify and assess how to manage new and re-emerging animal health and welfare threats in the UK.

The risks associated with animal diseases, particularly those that can be transmitted naturally between animals and humans feature highly on the government’s radar. This has been further highlighted by the global pandemic of COVID-19:

• more than 2 million people in the UK have been infected by SARS-CoV-2 by early January 2021
• it has caused more than 80,000 deaths
• the UK Gross Domestic Product (GDP) fell by 9.9% in 2020, the largest annual fall on record

The loss of biodiversity and increasing human wildlife interactions contributes to increased risk of new zoonotic diseases. The National Risk Register features animal diseases as a high risk which would have a detrimental effect on our environment and economy.

Many of these risks need a One Health approach, in achieving optimal health outcomes. We recognise the interactions between people, animals, plants, and their shared environment and ecosystems.

Over the last five years APHA has been involved in responding to over 800 suspected exotic notifiable animal disease threats of which many have a human health impact.

APHA scientists are members of the human animal infections and risk surveillance (HAIRS) group, this group is a multi-agency cross government horizon scanning and risk assessment group. They identify and discuss infections with potential for interspecies transfer (particularly zoonotic infections) which may pose a threat to UK public health. The multidisciplinary nature of the HAIRS group enables it to assess horizon scanning reports in an objective and scientific manner.

Endemic animal diseases such as bovine tuberculosis (bTB), cost theUK taxpayer in excess of £150 million per yearwith additional costs falling to industry.

These diseases can have severe impacts on the health and welfare of the wider rural economy. Within APHA, over 500 staff are involved in combating bTB. Left unchecked, bTB poses an increasing threat to:

• animal health and welfare
• agricultural economy
• public health

Following the Godfray review (the strategy for achieving bTB free status for England). Several of the recommendations were agreed as the government’s top priorities including:

• accelerating work to develop a deployable cattle bTB vaccine
• improving diagnostic testing
• surveillance and deployment of epidemiological tools to better understand disease sources enable better targeted disease control policies

Antimicrobial resistance (AMR) is recognised on the National Risk Register as a serious longer-term issue. The number of resistant infections is expected to increase markedly over the next 20 years. AMR is a global problem and the government is working with international partners on action at a global level.

In the UK, the national action plan on AMR promotes actions to reduce infection and responsible use of antibiotics. For example, by improving our understanding of the routes of transmission of resistance including the impact of the environment and food, by raising the health status of farmed animals and improving rapid diagnostics we will significantly reduce the need to use antibiotics.

The UK Plant Health Risk Register identifies in excess of 1,100 plant pests and diseases that could seriously damage crops and plants in the UK.

By maintaining and promoting a high plant health status, we can reduce this biosecurity threat and help protect the £9 billion annual value of our crops, horticulture and trees, which deliver benefits to our economy and society. Through a contract with Defra, Fera Science Ltd delivers the plant health laboratory capability working in partnership with APHA.

There are nearly 2,000 non-native species established in Great Britain (England, Wales and Scotland) with numbers increasing each year. Most are harmless but about 10 to 15% become invasive - causing harmful impacts on the environment, economy and our way of life. They cost the British economy over £1.8 billion a year(https://publications.parliament.uk/pa/cm201919/cmselect/cmenvaud/88/88.pdf). This is one of the key drivers of global biodiversity loss and some can even pose a risk to human health.

Our work helps to reduce the future impact of invasive non-native species by:

• preventing more species being introduced and becoming established
• better managing existing problem species

A recommendation from the Environmental Audit Committee in 2019 called for significant strengthening of our capability to improve biosecurity against invasive non-native species.

Defra’s strategic goal to increase the UK’s international influence after leaving the EU in the areas of animal health and welfare, plant and bee health, aligns with APHA’s cross cutting International Development work.

This adds value to core capability and links the agency’s activities through international appointments, partnerships, funding sources and supporting the development of International Trade. For example, Official Development Assistance (ODA) in One Health aims to increase the capabilities of priority ODA eligible countries and regional institutions to meet international commitments and delivery ambitions. By strengthening preparedness and respond to zoonotic threats, emergencies and potential pandemics, and enhancing animal and plant health.

Our disciplines

Discipline specific excellence is vital for our multidisciplinary approach and our ‘discipline champions’ are appointed to lead on the capability implementation plans in these key areas.

Following the most recent capability review, we identified a need for both greater breadth and to strengthen our cross-cutting expertise. We have therefore appointed discipline champions for Data Sciences (replacing Biomathematics) and Vector-Borne Diseases (to strengthen awareness and understanding of the potential impact of the climate emergency).

For other capabilities where we do not have the in-house expertise, we use specific partnerships to provide this. Scientific work continues to be delivered via a portfolio of projects led by our lead scientists. See the strategy annex for an overview of portfolio and discipline strategies.

Our current key science disciplines include:

• epidemiology
• virology
• bacteriology
• pathology
• parasitology
• molecular biology
• animal sciences
• data sciences
• vector borne diseases

Our partnerships

Partnerships are vital to the delivery of our science, increasing the pool of professional knowledge, raising the impact and quality and providing efficiencies, which are especially important during these economically challenging times.

We already collaborate with many scientific institutions nationally and internationally and will strengthen our key partnerships. They present an indispensable mechanism for both developing existing expertise, embracing opportunities to exploit science innovation, acquiring new skills or additional elements to a project outside of direct scientific remit.

These include partnerships with other government agencies, such as:

• Public Health England (PHE)
• Defence Science and Technology Laboratory (DSTL)
• research institutes, for example, Moredun and Pirbright
• education providers, for example, Royal Veterinary College
• industry

We have diversified income streams to increase efficiency, resilience and improve our ability to maintain vibrant capability and critical mass. For example, APHA Scientific (the commercial brand of APHA) provides an interface between our commercial customers and our scientific project leaders.

Our specialist scientific and veterinary expertise, containment laboratories and animal accommodation facilities present a unique opportunity for collaborative partnerships worldwide.

Substantial funding has been allocated by the government to support the development of a new National Science Centre for Animal Health (NSCAH) at Weybridge. This investment directly supports several of our strategic goals ( for example, international science centre, global influencer and a great place to work) and enhances the site’s global reputation as a centre of excellence.

The APHA Science Advisory Board provides assurance through effective challenges on the quality, value for money and appropriateness of APHA’s science and research capability.

Our key outcomes align with Defra’s 25 year environment plan for enhancing biosecurity and compliment:

• Wales Animal Health and Welfare Framework
• Scotland's Animal Health and Welfare Framework
• Defra's Safeguarding our animals and plants
• UK Biological Security Strategy

Our strategy takes account of our role in mitigating these risks on behalf of the government and well as protecting the wider population as an international partner.

Strategic framework

Our mission: we work to safeguard animal and plant health for the benefit of people, the environment and the economy.

Our vision: To be at the forefront of animal and plant science and to use that to reduce bovine TB, improve welfare, maintain GB biosecurity and support industry to import and export.

Strategic goals

Our strategic goals are:

1. Great place to work: we want to retain and develop specialist skills and expertise, where staff are highly engaged within a culture of innovation, inclusion, equality and diversity.
2. Global influencer: we want to grow and maintain our world class animal, plant and invasive species expertise and international networks to influence disease and risk control at a global level and help to reduce the risk and consequences of their entry into the UK.
3. Trusted partner: we want to build on and strengthen our reputation of being the partner of choice for delivering high quality, objective, fit for purpose assured science for animal and plant health advice, knowledge exchange and outbreak control.
4. International Science Centre: we want to continue to be recognised nationally and internationally as an international centre of excellence for science innovation within a context of disease control.
5. Future proofing: we want to ensure we have an operational framework that allows for flexibility, including changing priorities, future threats and opportunities.

Strategic themes

Underpinning our strategic framework is a series of strategic themes.

1. Biosecurity

Natural and accidental threats associated with either animal or zoonotic diseases, plant diseases and pests or invasive non-native species, have the potential to cause devastating effects on the nation’s health, security and economy. The UK’s approach to biosecurity is internationally recognised for delivering the highest standards of protection from pests, disease and invasive non-native species.

Threat awareness

An understanding and awareness of the threats that are likely to impact animal, plant and public health in the UK, both now and in the future.

Maintaining surveillance mechanisms including networks (nationally and internationally for example, OIE, FAO and WHO) to ensure we have the expertise to be aware of threats to the UK and respond to any outbreaks.

Awareness and understanding of the climate emergency and the impact this has on animal and plant diseases and pests including the new drivers for understanding the emergence of zoonoses, working at international scale.

Threat definition

Characterisation of the threat and assessment of the level of threat it presents. A multi-disciplinary approach is imperative to understand:

• causation and the nature of the threat
• assessment of pathways of entry into the country
• likelihood of establishment in the country
• assessment of the impact
• the mechanism of transmission and speed of spread

Threat mitigation

Systematic reduction in the extent of exposure to either the threat and the likelihood of its occurrence. Through prevention where possible, for example vaccination, enhancing biosecurity, border controls or influencing behaviour. If prevention is not possible, working in partnership to develop effective response plans.

2. One Health

Recognise that human, animal and environmental health are tightly connected and studies the hazards that may cross species and environmental barriers to move between compartments.

Animal human interface

A greater understanding of the interfaces, potential barriers and pathogens to host interactions is required to create and implement effective preventative measures and management interventions.

Biodiversity

Major drivers of biodiversity loss include climate change, over-exploitation, habitat loss and microbial ecosystems.

Unforeseen consequences of such ecological shifts can result in hidden problems that are not readily observed until there is a spill-over event with great human, plant or animal health impacts.

A greater understanding of the drivers and subsequent micro and macro effects of biodiversity loss, and reversal, will give better foresight to institute targeted monitoring for potential threats.

Environmental impacts

The environment may be seen as the cradle for pathogen-interfaces and biodiversity. Changes in the environment can be drivers to change in the other two pillars of the One Health triad. Understanding how the environment is changing and the adaptations that are made as a consequence is necessary to further our understanding and work within pathogen-interfaces and biodiversity.

For example, the COVID-19 pandemic caused by SARS-CoV-2 has ‘shone a light’ on zoonotic diseases illustrating the impact of global health security on every sector of the economy and in particular, highlighting weaknesses in early warning, detection and response.

SARS CoV-2 has emphasised the importance of a One Health Approach:

• collaborative multisector or transdisciplinary international working
• efficiencies and economic benefits accrued from jointly developed systems and disease control strategies
• combined service delivery, shared logistics and infrastructure across international institutions to better prevent, detect and respond to emerging zoonoses
• other threats leading to foodborne illnesses, food insecurity and public health

3. Innovation

Using modern technology and infrastructure to be efficient, flexible and responsive.

Utilising APHA science to develop solutions to challenges in disease threat, definition and control through applying cutting edge innovative approaches to genomics, surveillance, diagnosis and vaccine research.

Using big data to find solutions

The most far reaching and impactful solutions to our goals can be achieved by the exploitation of ‘Big Data’. Supercomputer technologies will combine bioinformatics with machine-based-learning in utilising powerful digital management systems for handling complex data.

These developing technologies will be applied to the rapid detection of new threats, referred to as ‘Disease X’; and will provide timely and cost-effective insights into broadening our understanding of complex pathogen-host interactions. For example, unlocking the potential of pathogen biology through Whole Genome Sequencing (WGS) allows rapid identification and characterisation of threats for either plants or animals, rapid detection of AMR risks; as well as detailed epidemiology of outbreaks or epidemics through molecular technologies.

Development and facilitation of non laboratory diagnostics

The development and facilitation of field or remote non-laboratory based ‘penside’ diagnostics for disease surveillance will provide early detection systems for new and emerging pathogens.

Data will be linked to automated laboratory based systems for rapid data flow and reporting. Thereby reducing the overall costs while maintaining quality assurance systems. These non-laboratory based surveillance systems will also make use of innovative technological solutions including drone technology by monitoring:

• environmental changes
• habitat fragmentation
• the incursion of emerging infectious pathogens
• pest threats

For example, monitoring of the potato virus or animal populations like monitoring wild boar using drones and routine use of onsite diagnostics at border control posts. As well as using Genie® LAMP (Loop mediated isothermal amplification) machines for the detection of animal pathogens and plant pests.

Detection of pathogens

The detection of both endemic and exotic pathogens will be enhanced by utilising diagnostic tools that differentiate between infected from vaccinated animals (DIVA). These DIVA tests will enable vaccine deployment to prevent disease incursion and spread using automated and computerised outputs in support of disease preparedness and emergency response.

Alternative methodologies for animal modelling

Use of alternative methodologies for animal models addressing reduction, refinement and replacement by application of synthetic production systems. Vaccine design will be improved with the development of multivalent vaccines against disease syndromes in animals. This approach will be assessed in animal models and by developing in vitro models to replace the use of animals.

These developments will be complemented by utilising advancements in immunology that strengthen research at the pathogen-host interface.

Using innovative platforms

We validate and utilise our innovative platforms for investigating exotic disease and pathogen emergence. Through our international preparedness programmes to ascertain international hotspots.

Our innovative platforms and solutions are part of our pre- and postgraduate training of veterinary professionals and scientists ensuring a multi-disciplinary approach.

Enabling pillars

These five pillars underpin all of the work we carry out:

1. Core expertise and capability: competent and skilled people, retained, valued and engaged.
2. Partnerships and collaborations: key collaborations and partnerships to enable us to deliver in a One Health approach, achieving efficiencies, multidisciplinary and innovative outcomes.
3. Facilities and resources: flexible future proofed facilities that are fit for purpose and deployed to improve animal and One Health outcomes.
4. Technology and data: accessing modern technology and using data effectively.
5. Communication: using appropriate channels to facilitate and promote knowledge exchange.

Key outcomes

Our key outcomes are:

1. Science based evidence used for policy development.
2. Reduced risk from new and emerging threats.
3. Rapid control of pest and disease outbreaks.
4. Enhanced biosecurity and food safety.
5. Decreased spread of zoonotic diseases.
6. Improved international trade and agricultural economy.

Our purpose

Our key science outcomes are aligned with the overall APHA purpose:

Why we do it

Safeguarding animal and plant health for the benefit of people, the environment and the economy.

How we do it

• collaboration and partnership across the science community
• applied expert advice to decision makers
• high quality scientific services and research
• international science centre for animal health
• threat surveillance and risk assessment
• rapid emergency response
• manage import and export of animals and plants
• inspection, certification and enforcement
• engagement with farmers and industry groups

What we have achieved

• improved agricultural economy
• informed policy making
• decreased spread of zoonotic diseases
• reduced risk from new and emerging threats
• enhanced food security
• rapid control of pest and disease outbreaks
• enhanced biosecurity
• improved international trade
• improved animal welfare and plant health
• decreased incidence of bTB

All of these lead to a great place to work where all staff feel respected, included, supported and engaged.

Challenges and approaches

We face many challenges and have had to find new approaches, including:

• recognising that many of the challenges require long term investment, whether targeting eradication of specific diseases or maintaining expertise and capability in the face of declining budgets to deal with novel and evolving pathogens and threats. Longer term research programmes that support and develop key skills, disciplines and partnership working (at a national and international level) are an important mechanism to address these challenge
• investing in national capability in respect of epidemiology, mathematical modelling and surveillance methodology, including to support links between Public Sector Research Establishment (PSREs) and the academic sector.
• research funding to support the development of vaccines and disease intervention agents and diagnostic technologies
• development and maintenance our bio-informatics and supporting skills, capabilities and infrastructure, for example when utilising Whole-Genome-Sequencing (WGS), data analyses and contextual interpretation and other technologies.
• a common digital backbone across government and partners, including the NHS to facilitate easier transfer of data enabling flexible deployment of capability supporting a One Health approach
• the redevelopment and investment into Weybridge, due to the complexities, scale and increase to the risks of maintaining our business critical activities and ensuring a smooth transition
• loss of some EU funding due to the UK leaving the EU, resulting in additional challenge of maintaining the networks and intelligence sharing

Measures of success

We have successfully met our strategic goals in the following ways:

Great place to work

• reward and pay structure for scientists established and implemented
• established programme of apprenticeships, postgraduate studentships (MSc, PhDs) and science fellowships
• improve inclusion, diversity and equality
• fit for purpose equipment and facilities

Global influencer

• maintain or exceed annual publication targets and expanded use of other knowledge exchange formats
• maintain or increase numbers of staff on International committees or working groups
• maintain or enlarge our international portfolio including extending our Official Development Assistance (ODA) programme by working with others to develop and submit proposals for funding
• extend our international influence on invasive non-native species including in the British Overseas Territories

Trusted partner

• maintain or increase delivery of a broad range of laboratory services (including testing and analysis) and epidemiological activities, in support of bTB control, improved biosecurity and to facilitate international trade - areas of expertise including animal and zoonotic diseases (broad range of pathogens), and plant and bee health
• maintain our quality standards and accreditations
• develop key partnerships and utilise strategically
• scanning surveillance network expanded, harmonise data for trade assurance and better integrated One Health surveillance
• maintain expertise to support work towards achieving negligible Bovine spongiform encephalopathy (BSE) status
• support the ambitions of the government’s response to the Godfray Review (England), the eradication strategy of Wales and continued Officially TB Free status of Scotland

International Science Centre

• maintain or extend our National and International Reference Centre designations
• Science Capability for Animal Health (SCAH) programme of re-development at Weybridge on track
• support the UK’s 20-year vision and 5-year national action plan on AMR expanding the influence of APHA in this area

Future proofing

• strengthened succession planning for science leadership and specialists
• improve diversification of our funding streams to maintain vibrant capability and critical mass
• expertise in bioinformatics, genomic technologies, including genomic epidemiology discipline increased
• respond flexibly to future animal epizootics and human pandemics, based on the philosophy of Disease X