Corporate report

APHA science and evidence review 2021

Updated 23 August 2022

This document sets out a summary of science highlights achieved throughout the year 2021 in support of the Animal and Plant Health Agency (APHA) Science Strategy 2021-2026.

Important achievements are also published regularly on the APHA science blog on GOV.UK which covers a range of scientific highlights from special interest stories on our scientists through to more detailed reports on the excellent science we do. Our aim through this document and the blog is to improve communication of our science to a wider audience.

A collection of 6 square photos:

• a hand wearing a sterile glove is holding a test tube with liquid inside
• a person standing in a large greenhouse full of flowers, they are holding a bunch in their hands
• a person wearing a face mask is collecting mosquitoes in the APHA insectary
• 3 turkeys standing outside in a flock
• an Asian hornet taken by a macro lens (photo by David Walker from Dungeness Bird Observatory)
• a herd of sheep are standing together under a tree at sunset

Foreword

“This has been another challenging year for APHA with the coronavirus (COVID-19) pandemic continuing to test us all both personally and at work. Concurrently we had the largest Avian Influenza outbreak ever seen in the UK.

“APHA led the national response to the UK Avian Influenza (AI) outbreak. Our teams have managed the on-farm operations of inspecting suspect diseased flocks and sampling birds and environment to confirm diagnoses. Our virologists provided novel results that improved the efficiency of testing and diagnosis and our epidemiologists analysed the outbreak over time and provided evidence to help control the outbreak. Our Ornithologists and Wildlife Management team contributed their specialist skills in recognising AI in wild birds and many colleagues in APHA were deployed into other roles than usual to support management of the AI outbreak. All these activities supported decisions to enable fast and effective control of the outbreak.

“Jenny Stewart joined APHA in September 2021 as Director of Science and Transformation. In the autumn of 2021, the National Science Capability for Animal Health (NSCAH) programme business case was approved by HM Treasury after the Major Projects Review Group. This enabled the programme to continue development of the new world-class facilities for APHA at the Weybridge site.

“Disease reporting requirements were introduced in 2021 for several animal diseases that were not previously reportable or notifiable to align domestic legislation with the EU Animal Health Regulation. APHA now holds National Reference Laboratory status for 49 diseases, 23 of which are international designations.

“Additional capability secured via the 2020 spending review has allowed us to deliver increased scientific responsibilities, enhance resilience and international links.”

Dr Kath Webster - APHA Director of Scientific Services

Animal and Zoonotic Viral Diseases Portfolio (AZVDP)

In 2021 this portfolio was appointed National or Designated Reference Laboratory for 27 viral diseases. This status means that APHA provides expert disease advice to control disease incursions into the UK, to advise countries globally on testing strategies and to act as a centre of excellence for disease research and diagnostic techniques.

Rabies screening and diagnosis

Rabies screening of wildlife and pets continues to pose policy challenges in the UK and abroad. APHA’s vital international outreach helps to tackle rabies around the world - APHA Science Blog.

In 2021, over 1000 bat lyssavirus (a genetic variant of the rabies virus) submissions were triaged with 481 priority cases tested in 2021, resulting in 4 positive cases (2 Serotine bats with EBLV-1 and 2 Daubenton’s bats with EBLV-2).

These viruses (known as European Bat Lyssaviruses (EBLVs), types 1 and 2) very rarely cross the species barrier from bats to humans and are different from the ‘classical’ rabies virus found in dogs and other animals. These viruses do however cause clinical rabies in humans. The presence of EBLV does not alter the UK rabies-free status.

A rabies diagnosis was excluded from 15 dogs and 8 cats, 7 of which were submitted following death in transit/quarantine as part of the Afghan Rescue cohort. Higher numbers of PETS (Pet Travel Scheme) Rabies serology submissions continue post EU Exit and because of policy changes in the USA.

SARS-CoV-2 screening and research

APHA established a system for receiving, screening (using accredited PCR tests) and reporting on animals (12) with suspected SARS-CoV-2 infection. The virus was confirmed in 3 dogs (Jersey, England) and 3 tigers (zoo, England) reported nationally and to the OIE.

The SARS-CoV-2 research and development programme continued in 2021 funded by Defra, the One Health European Joint Programme (OHEJP) joint innovation project COVRIN, UK Research and Innovation (UKRI) and Health Data Research UK (HDRUK).

New initiatives for 2021 included the UK - International Global Coronavirus Network (UK-ICN) and Med-Vet-Net Association Workshop, both bringing together researchers and stakeholders from across the globe to enhance knowledge of animal, human and zoonotic coronaviruses, helping us to better prepare for, respond and hopefully prevent, any future outbreaks.

Avian influenza outbreak

APHA science have been at the heart of the response for 2 avian influenza outbreak seasons (early 2021 H5N8 and late 2021 H5N1) providing all the testing, diagnosis and epidemiological advice. A science blog highlighted this outbreak: APHA at the heart of the biggest ever outbreak of bird flu in GB - APHA Science Blog. Earlier in 2021 the H5N8 season in the spring included transmission to seals (Phoca vitulina and Halichoerus grypus) and a fox (Vulpes vulpes). Although genetic analyses indicated no increased risk for human infection with the H5N8 viruses in this outbreak, the investigation shows how these viruses may have unexpected and severe health risks for mammalian ‘spill over host’ species.

PCR tests specific for highly pathogenic H5 viruses, and swine influenza subtyping have been developed, reducing the time for virus differentiation and assisting rapid typing results for policy decision making processes.

Professor Ian Brown, Head of Virology, was awarded an OBE for his services to animal health and welfare and co-directorship of the BBSRC/Defra funded UK International Coronavirus Network and its launch.

2 red hens, with a flock of hens in the background.

Bacterial diseases and food safety (BDFS) portfolio

The Bacterial Diseases and Food Safety Portfolio was appointed National Reference Laboratory and reporting requirements were implemented for 6 bacterial diseases to align domestic legislation with the EU Animal Health Regulation in 2021. Unrelated to the Animal Health Regulations, APHA was appointed NRL for Brucella canis and Salmonella was made reportable in dogs to address surveillance gaps.

One Health approach to detecting Brucella canis in imported dogs

APHA is working closely with UKHSA on an emerging public health and animal health and welfare issue in imported rescue dogs infected with Brucella canis, originating mainly from Eastern Europe. The new reporting requirement and communication on this emerging issue raised awareness and resulted in requests for information on test choice, diagnostic capabilities of tests, safe handling of samples and testing approaches and increased demand for diagnostic screening for Brucella canis.

APHA contributed to a risk statement on Brucella canis and published guidance on the APHA Veterinary Gateway to inform vets, owners and importers. APHA also led a European workshop on Brucella canis to discuss current knowledge and approaches to tackling this serious disease. An article was published on Detecting brucellosis in dogs - Veterinary Practice (veterinary-practice.com) and a science blog further highlighted this work A One Health approach to tackling Brucella canis cases in imported dogs - APHA Science Blog.

One health day, 3 Nov. Focus on: Brucella Canis. A puppy in a crate with its nose and paw poking through the bars.

Implementation of whole genome sequencing for Salmonella

A transition plan is underway to implement whole genome sequence (WGS) based typing of Salmonella to replace conventional serotyping to exploit the value of this technology for infection control. The pipeline can differentiate between the live vaccine strains that are licensed in UK for use in poultry and pigs, from wild type isolates in a single test.

A full-throughput parallel trial was successfully completed, and preparations for launching the new WGS-based serotyping service are underway. This is a great step forward in terms for public health and aligns with testing of human and food isolates by public health authorities in England and Scotland, and the European Salmonella Reference Laboratory. WGS-based typing is facilitating real-time detection of outbreaks, and, in future, it could replace most antimicrobial resistance (AMR) testing, phage typing, and molecular testing with a single, high throughput process.

Antimicrobial resistance

APHA has reported the first detection of transferable resistance to the antibiotic tigecycline in bacteria from livestock. Tigecycline is one of the last-resort critically important antimicrobials and is used to treat multidrug resistant bacterial infections in people. It is not authorised for use in livestock. A joint report was published with UKHSA: Detection of the transferable tigecycline resistance gene tet(X4) in Escherichia coli from pigs in the United Kingdom, Journal of Antimicrobial Chemotherapy, Oxford Academic (oup.com).

A new monitoring scheme has been implemented for the antibiotic susceptibility of key veterinary bacterial pathogens in food animals. The scheme was implemented in scanning surveillance in England and Wales and will provide high quality, robust AMR data for veterinary pathogens against commonly used antibiotics improving the usefulness of surveillance. The scheme was published to promote discussion and development towards this goal: A proposed scheme for the monitoring of antibiotic resistance in veterinary pathogens of food animals in the UK - Teale - 2021 - Veterinary Record - Wiley Online Library.

Linking surveillance and research allows us to exploit our capabilities to rapidly respond and control zoonoses and AMR threats, arising in animals. There is extensive collaboration with UKHSA and other organisations on zoonotic investigations of human cases linked to animal sources.

The research team has been heavily involved with a range of investigations of Salmonella in livestock and raw meat pet food and related infections in dogs and several strains of S. Typhimurium related to human outbreaks in cattle and sheep. An outbreak investigation was initiated with UKHSA and Food Standards Agency (FSA) in response to further cases of a strain of S. enteritidis in reptile feeder mice linked to human cases. Our scientific investigation and expert advice have helped to manage risks, thereby protecting public health.

Bovine Tuberculosis (bTB)

Three young cows with tags in their ears are stood together in a field.

Start of field trials for the CattleBCG vaccine

During 2021 we have secured funding, appointed a contract manufacturing organisation (CMO), and commenced field trials for the CattleBCG vaccine and companion skin test.

In September, we were notified of complications in the trials linked to skin test reactions and the trials were paused. Following investigation of the results, the Cattle TB Vaccine Steering Committee agreed to restart the field trials in January 2022, after making minor revisions to the field trial protocol. The protocol variation has since been agreed with the Veterinary Medicines Directorate and trails have recommenced.

APHA are currently evaluating tenders for a good manufacturing process (GMP) provider for the Differentiating Infected amongst Vaccinated Animals (DIVA) skin test reagent and remain on target for obtaining Marketing Authorisations for CattleBCG and the DIVA test by 2025. Phase 2 of the BCG and DIVA skin test field trials is due to start in 2022.

Implementation of whole genome sequencing

Implementation of whole genome sequencing (WGS) as the sole routine M. bovis isolate characterisation tool was completed in 2021 following UKAS accreditation of the bioinformatics part of WGS to ISO 17025.

This is the first data analysis pipeline to be accredited to this standard by UKAS and has enabled the traditional genotyping to be ‘switched off’ with significant cost savings and process streamlining. Phase 2 - ‘Enhancing the use of M. bovis WGS to inform the control of bTB in Great Britain’ has commenced.

APHA is now building increasingly more sophisticated tools to integrate genome data with epidemiological information, such as location and animal movement history, to enable visualisation of how disease is spreading, identifying key infection pathways and thus potential intervention points.

Detection of M. bovis directly from post-mortem tissues

A PCR test to detect M. bovis directly from post-mortem tissues has been validated and 3 laboratories (APHA Penrith, Starcross and Weybridge) equipped (liquid handling robots and extraction instruments), staff recruited and trained to begin phase 1 (slaughterhouse & and non-bovine submissions).

This will significantly reduce the time to confirm or negate bTB to under 2 weeks compared with the current time for confirmation of up to 3 months. The PCR test was approved by the UK TB Liaison Group in 2021 and is scheduled to be used from March 2022. A Phase 2, where all routine submitted samples are analysed using PCR is planned for 2023.

Changes in testing regimes following the Godfray Review

Following public consultation and call for views on the Godfray review, Service Delivery expanded its field team to collect blood samples for gamma interferon testing where a re-current tuberculosis (TB) breakdown has occurred. The purpose of this testing is to identify residual infection with TB within a herd to avoid a prolonged breakdown and movement restrictions of cattle which can cause animal welfare issues and hardship and emotional damage to those involved.

Customer services and field teams rolled out 6 monthly TB testing across the whole of the High Risk Area successfully. This was another recommendation in the Godfray review to identify infected animals at an earlier stage, again with a view to reducing the duration of a breakdown.

International science development (ISD)

ODA (official development assistance) funding

APHA secured ODA funding for a follow-on 1-year (2021 to 2022) project entitled ‘Enhancing preparedness and detection of One Health threats in vulnerable communities and interfaces in Ghana, Bangladesh, Ethiopia & Nigeria’. This project will support APHA to understand the needs, capabilities and operating environments for enhancing animal health preparedness and response, in preparation for a One Health and Animal Health System strengthening proposal to be delivered between 2022 and 2025.

The ODA Pandemic Preparedness Project was completed on 31 March 2021 with outcomes including:

• strengthened international relationships with Ghana, Bangladesh, Ethiopia, Egypt
• development of an e-learning platform and 2 Continuous Professional Development courses: ‘Disease Outbreak Preparedness and Management’ and ‘Veterinary Public Health Interventions at the Human–Animal Interface’
• an on-line tool box comprised of more than 60 training materials and Standard Operating Protocols describing best practices for ex-situ application in all 4 countries
• the International Viral Hazards Monitoring GIS platform developed as part of this project constitutes a proof of concept that APHA can use publicly available data to provide useful intelligence for risk factors for novel diseases on demand. There is huge potential to build on this work in the future by considering other types of risk factors for other diseases
• supported research projects in Bangladesh and Ghana on risk factors and impacts of emerging zoonotic pathogens

APHA also received ODA project funding to improve biosecurity in 4 eligible UK Overseas Territories and held a successful series of invasive species outreach events.

Achieved 3-year’s ODA funding (2022 to 2025) for a research and development proposal entitled ‘Safe and Sustainable Food Systems’. Funding for a second proposal entitled ‘Animal Health Systems Strengthening’ has also been approved.

Global Biothreat Reduction programme

APHA secured funding from the Ministry of Defence and the Defence Science and Technology Laboratory Global Biothreat Reduction programme as part of a 4-year (2021 to 2025) funded international programme.

Plant and bee health

Inspections and detections

Over the last year, PHSI (Plant Health and Seeds Inspectorate) received advanced notification of 89,049 consignments from the EU and 156,751 from the rest of the world. This is 102,047 more consignments than in 2020. In addition, 38,604 phytosanitary certificates were produced for exports, a more than 3-fold increase on the previous year and a 20% increase of plant passporting clients from the previous year .

APHA launched the plant health audited trader scheme (PHEATS), a trade facilitation scheme for the export of fruit, vegetables and cut flowers to the European Union (EU) and Northern Ireland (NI). The scheme is designed to facilitate export trade whilst ensuring the requirements of the importing country are met, assisting with ‘just in time’ logistics.

In 2021 there were 2 confirmed incursions of Asian Hornet (Vespa velutina) into the UK. Both incursions were reported during October, relatively late in the year compared with previous years, but most likely due to the relatively late season (of confirmed incursions) in 2021. For the first time inspectors used a track and trace app, developed by APHA. This app provides real time mapping and in field data capture, delivering a far more efficient and effective outbreak response. The early location, destruction and removal of nests, in both instances within a few days of being reported, has proven the value of this new tool.

Five outbreaks of Tomato Brown Fruit Rugose Virus found in 2020 to 2021 at tomato production nurseries have been eradicated. Defra publicised this in late 2021. This good news set in the context of the worsening and widespread situation in Europe, involved stakeholder engagement and outputs from research to develop our response.

APHA detected the first UK finding of Thekopsera minima  (Blueberry Rust) at a recent outbreak at one nursery site and a commercial blueberry production site. Blueberry crops appear to be on the increase in the UK and are of high value . Initial surveillance detected the disease on imported plants in England and Scotland.

APHA also detected the first UK finding of Cinara shinjii  (aphid pest of Pine) and completed its eradication.

The first finding of Phytophthora pluvialis (a fungal like pathogen affecting Western Hemlock and Douglas Fir) in Europe, was discovered by the Forestry Commission on Western Hemlock and Douglas Fir in Southwest England, then in Cumbria and then by Natural Resources Wales and Scottish Forestry. APHA supported initial inspections of trade premises in proximity, and a review of direct imports data from New Zealand and the USA. Demarcated zones were implemented to control movement of timber and plants. APHA have contacted clients to signpost them to restrictions and placed the information on GOV.UK.

Facilitating trade

APHA launched the plant health audited trader scheme (PHEATS), a trade facilitation scheme for the export of fruit, vegetables and cut flowers to the European Union (EU) and Northern Ireland (NI). The scheme is designed to facilitate export trade whilst ensuring the requirements of the importing country can be met, assisting with ‘just in time’ logistics.

Surveillance intelligence

Expanding our network

From January 2021, 3 additional post mortem examination (PME) providers joined APHA’s scanning surveillance network. These are the universities of Cambridge, Liverpool, and Nottingham. This adds to the previous PME providers - The Royal Veterinary College, University of Bristol, University of Surrey, Wales Veterinary Science Centre and SRUC (St Boswells) - that work together with the 6 APHA Veterinary Investigation Centres. The addition of these new PME providers expands the capacity of scanning surveillance in England and Wales and brings some livestock premises closer to a post-mortem site, giving vets and farmers the benefit of increased capacity and expertise in this network.

Small-Animal Species Expert Group (SASEG)

A SASEG was established in 2021, expanding the current (livestock species and wildlife) expert groups to 7. The SASEG will operate on similar lines to the other species expert groups, providing a network between government and a wide range of key stakeholders in the small animal sector, enabling risks to be identified and evaluated in a more structured way. Members include expert representatives from small animal charities, academia, the British Small Animal Veterinary Association, APHA and other government departments.

Diagnostic testing

Differential diagnostic testing of negated notifiable disease report cases has continued in 2021, most notably in cases of high mortality in broiler chickens. Detailed investigation showed that all were attributed to Avian Pathogenic E. coli (APEC) ST1564. ST1564 is a newly identified threat not previously recognised in disease outbreaks in Great Britain.

Project work

The Thin Ewe Project examined a total of 198 sheep from 76 holdings to investigate potential causes of poor condition, specifically to see if the ‘iceberg diseases’ (Johne’s disease, Maedi Visna, caseous lymphadenitis, ovine pulmonary adenomatosis and border disease) were present in the flocks. The project has demonstrated the value of PME in identifying causes of chronic disease by allowing for examination of all body systems, targeted testing, and histopathological confirmation. Outcomes from the project were communicated via a presentation to the Sheep Veterinary Society, a Focus article in the Veterinary Record and an article in the National Sheep Association Sheep Farmer magazine.

A Bovine Babesiosis project was undertaken throughout the 2021 grazing season. The project aimed to investigate a variety of aspects of bovine babesiosis, and other bovine tick-borne disease. Over 100 submissions were received. Preliminary findings have suggested differences in geographical spread of cases, from those recorded over recent years. This is important not only to the cattle and sheep industries, but also from a zoonotic aspect in relation to tick-borne diseases.

Surveillance

APHA undertook enhanced surveillance for disease associated with porcine circovirus 3 (PCV3), a recently discovered virus in pigs. Findings from this disease surveillance indicate there is currently a low incidence of myocarditis associated with PCV3 in individual post-natal pigs, and occasional fetopathy and neonatal disease outbreaks of varying severity occur in breeding herds. This knowledge of the current status of PCV3 in the national pig herd will assist interpretation of investigations in the event of a change in the frequency of disease incidents associated with PCV3.

Four pigs standing together with their snouts poking through the metal rails of their pen.

Enhancing surveillance and improving outbreak response

Outbreak response

During 2021 many of the key personnel that work on the portfolio were involved in National Emergency Epidemiology Group (NEEG) response work for the Highly Pathogenic Avian Influenza (HPAI) outbreak of winter 2020 to 2021 (H5N8) and winter 2021 to 2022 (H5N1). These personnel included experts in risk assessment, epidemiology, mathematical modelling and project management. The AI outbreak experienced in winter 2020 to 2021 was particularly large and of extended duration compared to previous years, with the NEEG only standing down in May 2021 after 20 (HPAI H5N8), 2 (HPAI H5N1) and 2 LPAI infected premises. The 2021/22 outbreak has far surpassed the 2020/21 number of confirmed cases.

Exotic disease simulation exercises and training

NEEG members have also been involved in preparing and participating in a number of exotic disease simulation exercises in 2021. Exercise Holly, in July 2021, simulated an outbreak of African Swine Fever (ASF) and a Disease Emergency Response Committee (DERC) exercise for Contagious Equine Metritis (CEM) was held in August 2021. The NEEG members were involved in all aspects of the exercises, including scenario drafting, co-ordination, planning and facilitation of the events. The purpose of the exercises is to test coverage of contingency plans, assess whether they are fit for purpose and test resilience and capability in the event of an outbreak. NEEG’s involvement ensures we maintain our preparedness and capability in areas where we rarely experience real events.

The NEEG leadership team members have provided expertise and evaluation in developing an online teaching module on outbreak disease preparedness and management as part of the APHA ODA Pandemic Preparedness Project 2020/21. Expertise gathered from years of NEEG involvement in exotic disease outbreaks in the UK has been included in the teaching module designed to help other countries put methods in place to enhance and improve epidemiological response to disease outbreaks.

The Field Epidemiology team were heavily involved in the training of APHA’s field veterinarians in England, Scotland and Wales in veterinary risk assessment and undertaking epidemiological investigations of notifiable diseases, whether endemic or exotic. A major task was also running a further EU FMD training package in conjunction with IAH Pirbright which trained 115 veterinarians in all aspects of FMD control.

Livestock Demographic Data Groups (LDDGs)

The 2020 population reports for sheep, goats, poultry and pigs were published internally and online through the ‘VetGateway’ website. There has been an increasing interest and several requests for further information from the Livestock Demographic Data Groups (LDDGs), including groups within Defra and the Welsh and Scottish Government, academia and species-specific veterinary societies. These requests are assessed on a case-by-case basis and indicate the interest in the work and maps developed by the LDDGs.

TSEs (Transmissible Spongiform Encephalopathies)

Scrapie surveillance

Eleven atypical scrapie cases were identified through active surveillance with the rapid screening test and confirmed by confirmatory tests at APHA. Atypical scrapie is believed to be sporadic and the prevalence is consistent with previous results in the UK and other European countries. Two sheep and one cow were reported as clinical suspects for TSEs but were negated on clinical grounds. One deer was reported by the public with neurological signs, which resulted in examination of brain and lymphoid tissue but with a negative result. As TSEs are notifiable diseases it is encouraging that they are still being reported for further investigation.

The face of a white sheep with a curly fleece and small curled horns.

Confirmed case of classical BSE

One fallen stock cow was positive for BSE by rapid screening test and classical BSE was confirmed by confirmatory testing at APHA. Mathematical modelling by APHA researchers in 2016 had suggested that there was indeed a low probability of further cases of BSE occurring up to 2026. This result required a rapid response by APHA staff, tracing 60 cohort animals and offspring from the confirmed case (all tested negative) and identifying the possible cause of exposure, which was published in an epidemiology report. APHA’s management of the case received praise from OIE for the speed of implementation of control measures. England and Wales retain controlled BSE risk status.

Wildlife

Support to outbreak response

As reported in previous sections, the 2020 to 2021 Avian Influenza (AI) season was the worst on record. This was followed by the 2021 to 2022 season with even more outbreaks. Ornithology support for these cases was adjusted in 2020 to ensure we can respond effectively, and this change has become even more important in 2021. In addition to desk-top reports, NWMC (The National Wildlife Management Centre) staff have attended several difficult cases to help with removal of unusual species.

Invasive species inspectorate scoping study

The GB non-native species secretariate (NNSS) developed and trialled a scoping study for an invasive species inspectorate. During the year the staff visited and evaluated various falconry centres, garden centres, online sales, pet shops, deliberate releases, accidental escapes, inspections of angling and boating equipment, etc. The NNSS also received ODA project funding to improve biosecurity in 4 eligible UK Overseas Territories and held a successful series of invasive species outreach events which also resulted in reports of possible raccoon dog escapes in England.

Wildlife-related policy-support services

During 2021, NWMC’s Woodchester Park unit continued to provide a range of wildlife-related policy-support services and research for Defra’s TB team. Studies to monitor badger movement and contact patterns during the fourth year of badger culling were extended. This will be used to analyse social perturbation both during and after official culling occurs nearby.

The 2020 badger removal post mortem results from the Cumbria TB outbreak area were all negative for TB. As a result, there was very little change in the management and in 2021 badger vaccination (using APHA staff) took place in the outer ring, while the cull was repeated in the core area. The cull in the Low Risk Area (LRA) in the Lincolnshire area reported some positive badgers as expected, and an extension to culling was granted to the area.

iMammalia app

The European Food Safety Authority (EFSA) funded ENETwild project continues to link multiple European mammal research institutes and engage citizen scientists. A new version of the iMammalia mammal recording smartphone app was launched that can record all mammals in all European countries and is now available in 12 languages. This has now reported over 14,000 sightings across Europe and the data set has been used at least 29 times. In addition, the citizen science camera trapping web site MammalWeb had over 96,000 images sequences uploaded from cameras at about 100 sites in 10 European countries.

A phone screen shows the iMammalia app on an app store. It shows its paw print logo and screenshots of the app.

Epidemiology

The dedicated National Bovine TB Epidemiology Group brings together specialists from data science, policy advice, statistics, modelling, analytical and field epidemiology to share knowledge and tackle specific bovine TB issues. Epidemiological understanding of the bovine TB epidemic has also been communicated more widely, including through the England, LRA, Edge Area and Wales TB Epidemiology Reports and GB Data Report and through seminars and presentations to facilitate knowledge transfer. Input continued into the development of approaches to monitoring and evaluation of the effects of control policies and risk factor identification as well as the roll out of WGS. Further activities are described under the TB portfolio.

Food safety and zoonoses

Within the area of food safety and zoonoses, epidemiological input continued to be provided on surveillance design and reporting as well as outbreak investigations in livestock linked with human illness with UKHSA. Epidemiological input also contributed to scanning surveillance activities for emerging and endemic diseases. This included analysis of post-mortem and laboratory submission data to provide routine surveillance reports, interactive dashboards and support to the Species Expert Groups. Input was also provided to the development of methods to aggregate and analyse outputs from diverse data sources to enhance scanning surveillance, including the use of abattoir meat inspection results provided by the Food Standards Agency, antimicrobial resistance data from private diagnostic laboratories, wildlife disease submissions, and mandatory monthly reporting by private laboratories of named endemic livestock diseases to meet new Animal Health Regulation requirements. Linked to this, the identification and assessment of new and emerging diseases was reviewed through monthly cross-administration UK Veterinary Risk Group meetings co-ordinated by the Epidemiology Policy Advice team.

OIE Collaborating Centre

The APHA is part of an OIE Collaborating Centre in Risk Analysis and Modelling in collaboration with the Royal Veterinary College (RVC). As part of this centre, work is ongoing to extend our international collaborations and impact.

Epidemiology Oversight Group

The aim of this APHA group is to enable an integrated approach to training, skills development and resourcing to provide the best quality epidemiological evidence, investigation and advice. In 2021, the epidemiology discipline has been a growing area within APHA due to EU Exit (in particular the newly formed UK Office for SPS & Trade Assurance), strengthening of TB epidemiology and international development activities.

Publications, representation and qualifications

Publishing in scientific journals is a key objective for APHA scientists and is almost always an important objective in any research project we work on. Whilst we aim to publish in top scientific journals wherever possible we are also mindful that APHA’s science is predominantly applied, translational and customer focused. This means that some of our work will be published in trade journals or as information booklets etc. – essentially somewhere that is accessible to our wide range of stakeholders.

In terms of peer reviewed publications, we have maintained a good publication rate with the publication of 239 papers across all our science portfolios. This is a 13% increase on 2020. Of the 239 we were lead author on 35.5%.

We have continued with our apprenticeship programme and currently have 25 people undertaking an apprenticeship. These include level 7 Bioinformatics, level 3 and 5 Leadership and management, level 6 Data Scientist, Digital and Marketing and level 2 Animal Technician. We have added to the programme this year other apprenticeship standards such as: Level 7 Systems Design Thinking, Level 3 Animal Technician, Level 3 Laboratory Technician.

Currently, 23 staff from APHA or studentships linked with APHA are undertaking PhDs, 18 were already registered before 2021 and 4 new PhDs were registered in 2021. In addition, 24 are undertaking MScs including 8 registered in 2021.

We continue to develop our representation on appropriate national committees (275 representatives on 158 committees) and international committees (158 representatives on 135 committees) demonstrating the strong scientific reputation of APHA and our scientists. Appropriate representation and influence at international level is increasingly important particularly now that the UK has left the EU.