October 2020
COVID-19 work
Since the start of the COVID-19 pandemic, CVERA colleagues have contributed to the work of the IEMAG (Irish Epidemiological Modelling Advisory Group), one of the 9 subgroups of the National Public Health Emergency Team (NPHET). IEMAG provides advice and expertise in support of national decision-making in the area of epidemiological data and modelling. This support has reduced substantially in recent months, but continues particularly in the area of spatial analysis. Several scientific papers have been published in support of this work, mainly in relation to estimates of epidemiological parameters, including Byrne et al., (opens in a new window)BMJ Open 10, e039856 (infectious period duration), McAloon et al., (opens in a new window)BMJ Open 10, e039652 (incubation period), Griffin et al. (opens in a new window)BMJ Open 10, e040263 (generation time, serial interval) and Häsler et al. (opens in a new window)Frontiers in Veterinary Science, 6, 23 (One Health in action).
Modelling forum
The first of an ongoing series of six-monthly meetings for those involved in modelling livestock diseases in Ireland took place on 28th September. Presentations were given by researchers at UCD, UCC, UFZ (Leipzig, Germany), Oniris (Nantes, France) and the University of Limerick. We expect that these meetings will foster collaboration amongst these groups as well as between them and DAFM/AHI.
Managing herd risk in the national bTB eradication programme
In recent weeks, there has been renewed interest in risk-based approaches to managing bovine TB, as part of the national programme. In particular, the TB herd history risk statement and report generated considerable debate in the national rural media letters. As part of this discussion, Simon More wrote two articles in the Irish Farmers Journal, including ‘(opens in a new window)TB risk categories ‘next logical step’ to eradication’ and ‘(opens in a new window)Lessons to learn on TB eradication from Australia and NZ’.
Spatial and network characteristics of Irish cattle movements
This study by Tratalos et al. examined the spatial and network characteristics of cattle movements between herds in the Republic of Ireland (ROI), to inform policy and research of relevance to the surveillance and management of disease in Irish cattle. The distances moved away from the herd were on average greater for herds in the west of ROI whereas distances moved to a herd were generally greater for destinations in the centre-east and the north-west. Approximately half of transfers were conducted within a single county, but the number and distance of between county movements varied considerably by county of origin and county of destination, with the proportion of moves completed within a single county correlated with its size. Herds exchanging cattle via a market were generally further apart than when moves were made directly herd to herd. Some herds took part in a relatively large number of movements whilst also retaining their cattle for long periods (> 100 days) between moves. Mart moves resulted in longer range displacements than those directly from farm to farm. The frequency distributions of a variety of herd-level movement metrics were heavily right skewed but, in contrast to similar studies, were not found to follow a power law. Different measures of the amount of movement experienced by a herd were often poorly correlated. The paper is available at (opens in a new window)Preventive Veterinary Medicine 183, 105095. Further to the above study, a follow-on project will examine the relationship between network derived cattle movement metrics and TB.
Raw milk cheese produced from M. bovis infected herds: what is the risk?
The recent rise in consumer demand for speciality cheeses, which are often produced using raw milk, and the persistence of M. bovis in Irish cattle herds has highlighted the potential risk of human Mycobacterium bovis (bTB) infection from consuming cheese produced from raw milk from bTB infected herds. Currently, published data quantifying this risk is lacking. Hence, the aim of this study which is being led by Áine Collins is to develop a risk assessment method to estimate the risk of human bTB infection from consuming cheese produced from raw milk originating in bTB infected herds.
Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland
Research conducted by Crispell et al. used whole-genome sequencing of M. bovis sourced from infected cattle, deer and badgers in County Wicklow to evaluate whether the epidemiological role of deer could have shifted from spillover host to source. The analyses reveal that cattle and deer share highly similar M. bovis strains, suggesting that transmission between these species is occurring in the area. In addition, the high level of diversity observed in the sampled deer population suggests deer may be acting as a source of infection for local cattle populations. These findings have important implications for the control and ultimate eradication of bTB in Ireland. For the full study, please see (opens in a new window)Microbial Genomics.
Risk factors for African swine fever incursion in Romanian domestic farms during 2019
The spread of African swine fever (ASF) has continued across Europe, most recently with the incursion of ASF into Germany. As a member of the ASF working group in the European Food Safety Authority (EFSA), Simon More contributes to ongoing work in support of decision-making on this issue in the European Commission. In most affected member states, the wild boar-habitat cycle has dominated ASF spread, with occasional spillover to domestic farms. In Romania, in contrast, there have been many outbreaks in domestic farms, primarily with low levels of biosecurity, and relatively few cases in wild boar. This study investigated possible risk factors for ASF incursion in commercial and backyard pig farms in Romania. A number of factors were found to be important, relating to herd size, to exposure from other outbreak farms and cases in wild boar, and to human activity and management. The paper by Boklund et al. is available in (opens in a new window)Scientific Reports 10, 10215.
Epidemiology of age-dependent prevalence of Bovine Herpes Virus Type 1 (BoHV-1) in dairy herds with and without vaccination
A national programme to control BoHV-1 does not currently exist in Ireland but is under active discussion. In collaboration with the Helmholtz Centre for Environmental Research in Germany, Animal Health Ireland (AHI) is developing age-structured epidemiological models to support consideration of possible control or eradication options. In support of this work, there is a need for an understanding of the age-related dynamics of BoHV-1 seroprevalence in seasonal calving Irish dairy herds. This paper by Brock et al., which introduces the concept of age-threshold cohorts, is published in (opens in a new window)Veterinary Research 51, 124.
Johne’s disease in Irish dairy herds: considerations for an effective national control programme
Over the last 10 years, there has been detailed discussion in support of an effective national Johne’s disease control programme. This paper provides an overview of this discussion, and
of the conclusions drawn. The discussion was supported by a narrative review of the scientific literature on the epidemiology of Johne’s disease and of selected control programmes throughout the world. Further, two modelling studies specifically commissioned to assess testing methods used to demonstrate confidence of freedom in herds and to evaluate a range of possible surveillance strategies provided additional information. The paper provides a rationale for the inclusion of a Veterinary Risk Assessment and Management Plan (VRAMP), including voluntary whole herd testing to identify infected herds and to support assurance-based trading through repeated rounds of negative testing, national surveillance for herd-level case-detection, and improved understanding of biosecurity management practices. The paper by Jordan et al. is available in the (opens in a new window)Irish Veterinary Journal 73, 18.
May 2020
COVID-19
Since mid-March, several CVERA colleagues have contributed to the work of the IEMAG (Irish Epidemiological Modelling Advisory Group), one of the 9 subgroups of the National Public Health Emergency Team (NPHET). Chaired by Philip Nolan, IEMAG provides advice and expertise in support of national decision-making in the area of epidemiological data and modelling. Areas of CVERA contribution have included estimating key epidemiological parameters (such as incubation period, proportion of infected people who are asymptomatic etc), providing biological input into model development, contributing to the design and assembly of national databases, spatial analysis and developing a COVID-19 early warning system. This latter work is adapted from an early warning system for bovine TB, currently under development. The following CVERA, UCD Veterinary Medicine and DAFM colleagues have each been involved: Ann Barber, Andrew Byrne (DAFM One Health), Miriam Casey, Áine Collins, John Griffin (DAFM retired), Liz Lane (DAFM), Jamie Madden, Conor McAloon (UCD Veterinary Medicine), Guy McGrath and Simon More. Peer reviewed papers resulting from this work will be added to the CVERA website as they are published.
Is moving from targeted culling to BCG-vaccination of badgers (Meles meles) associated with an unacceptable increased incidence of cattle herd tuberculosis in the Republic of Ireland? A practical non-inferiority wildlife intervention study in the Republic of Ireland (2011-2017)
Led by Prof Wayne Martin from the University of Guelph and DAFM colleagues, this work was undertaken to investigate, whether vaccination of badgers with Bacille Calmette-Guérin (BCG) is an alternative to badger culling within the national bTB eradication programme. Thus, in 2011, a five-year non-inferiority study was implemented in seven counties in the ROI. This study was designed to compare and contrast the bTB incidence in cattle herds in areas where intramuscular badger vaccination would be implemented versus remaining area of the same county where targeted badger culling was maintained as the standard treatment response to probable badger-sourced BTB breakdowns. Overall, our study results indicated that vaccination was not inferior to targeted badger-culling in four counties and badger vaccination was deemed to produce ambivalent results in one (County Cork North). A post-study investigation, in County Galway, where vaccination was deemed inferior to target culling, revealed that widespread purchases of cattle from a nearby cattle mart, by herd owners in the vaccination area, was associated with the increased herd and vaccination area risk of bTB. No single ‘biasing hypothesis’ was evident for the apparent vaccine inferiority in the second study site (County Monaghan) where vaccination was deemed inferior to targeted culling; hence no further investigations were conducted. This open access paper is available at (opens in a new window)Preventive Veterinary Medicine 179, 105004.
Herd-level factors associated with detection of calves persistently infected with bovine viral diarrhoea virus (BVDV) in Irish cattle herds with negative herd status (NHS) during 2017
This project was led by Dr Damien Barrett SVI in DAFM with staff from UCD, AHI and ICBF. Considerable progress has been made in the national BVD eradication programme, with the animal-level prevalence of calves born persistently infected (PI) falling from 0.67% in 2013 to 0.06% in 2018. Over the same period, the herd-level prevalence fell from 11.3% to 1.1%. In the programme, herds in which all animals have a known negative status and which have not contained any PI animals for 12 months or more are assigned a negative herd status (NHS). Of concern within the programme, PI calves have been identified in a small proportion of herds that had previously been assigned NHS. Given this context, a case-control study was conducted to investigate potential risk factors associated with loss of NHS in 2017. Trojan cattle and the density of BVD infection within 10 km of the herd emerged as significant factors in a multivariable logistic regression model. This work adds to the evidence base in support of the BVD eradication programme, particularly establishing why BVD re-emerged in herds which had been free of BVD for at least the previous 12 months prior to the identification of a BVD positive calf. This information will be especially important in the context of identifying herds which may be more likely to contain BVD positive animals once the programme moves to herd-based serology status for trading purposes in the post-eradication phase. This open access paper is available at (opens in a new window)Preventive Veterinary Medicine 179, 104990.
A description and qualitative comparison of the elements of heterogeneous bovine viral diarrhoea control programs that influence confidence of freedom
This project was led by Annika van Roon from Utrecht University in the Netherlands in conjunction with colleagues from France, Germany, Sweden, the United Kingdom and Ireland. For endemic diseases in cattle that are not regulated within the EU, such as bovine viral diarrhoea (BVD), it can be difficult to compare the ‘free status’ that is generated by different national (or regional) control (or eradication) programmes. This creates problems for the safe trade of cattle between territories. Safe trade would be facilitated with an output-based framework that enables a transparent and standardized comparison of confidence of freedom for control programmes across herds, regions, or countries. The current paper represents the first step toward development of such a framework by seeking to describe and qualitatively compare elements of programmes that contribute to confidence of freedom. Using BVD as a case study, we identified a number of differences (including testing protocols and definitions of freedom) in BVD control programmes in 6 European countries (Germany, France, Ireland, the Netherlands, Sweden, and Scotland). The observed heterogeneity will create difficulties when comparing confidence of freedom from infection. These results highlight the need for a standardized practical methodology to objectively and quantitatively determine confidence of freedom resulting from different control programmes around the world. This open access paper is available at (opens in a new window)Journal of Dairy Science 103, 4654–4671.
The Seventh International Conference on Mycobacterium bovis (M. bovis 2020)
As a result of the COVID-19 pandemic, the Organising and Scientific Committees of M. bovis 2020 made the early decision to postpone the Conference until Summer 2021. The decision has been communicated to all speakers, delegates, venues, sponsors, delegate staff and suppliers and was made with their safety in mind. Subject to any regulations that are in place in 2021, we plan to carry the 2020 programme forward as much as possible. Updates on the rescheduled Conference will be added to (opens in a new window)https://www.mbovis2022.com/ as they are made.
February 2020
African swine fever in the EU
EFSA has published its latest annual update on the presence of African swine fever (ASF) in the European Union. In 2019, there was progressive expansion of the area of the EU affected by ASF, and all phases of the epidemic are now represented in the EU. The situation varies substantially between Member States, due to multiple influences including the structure of domestic pig production (in particular, the proportion of backyard holdings), geographical conditions, and the characteristics of the wild boar population. Backyard (non-commercial) farms present particular challenges for an ASF eradication programme, such as uncontrolled movements of pigs and people, poor biosecurity and the identification of holdings. Simon More is a member of EFSA’s ASF working group. Further information is available at (opens in a new window)https://www.efsa.europa.eu/en/news/african-swine-fever-disease-spreading-slowly-eu.
European perspectives on efforts to reduce antimicrobial usage in food animal production
A review was recently published of efforts within the EU to reduce antimicrobial usage in food animal production. This is particularly pertinent noting that new regulations on veterinary medicines and medicated feed, in force from 28 January 2022, will substantially influence antimicrobial prescribing and usage throughout Europe into the future. The review outlines the considerable progress that is being made in a number of member states, and is published in the (opens in a new window)Irish Veterinary Journal (2020) 73, 2.
Reviewing age-structured epidemiological models of cattle diseases tailored to support management decisions: Guidance for the future
Mechanistic simulation models are being increasingly used as tools to assist with animal health decision-making in the cattle sector. In this paper, which was co-authored by colleagues from the Helmholtz Centre for Environmental Research GmbH - UFZ in Leipzig, Germany, Animal Health Ireland and CVERA, Jonas Brock et al. provide an overview of studies reporting the use of age-structured cattle management models for infectious diseases, including their theoretical foundations, design paradigms and incorporated processes. They propose a structure incorporating three main features: [1] biological processes, [2] farming-related processes and [3] pathogen-related processes, and recommend that this structure be followed in future cattle disease models to facilitate science communication and to allow increased model transparency. The paper is published in (opens in a new window)Preventive Veterinary Medicine 174, 104814.
NexusMAP - developing an expert system model to support national decision-making
An existing spatio-temporal transmission model for Johne’s disease is available, accounting for population and infection dynamics, and simulating transmission of infection within and between dairy farms in Brittany. The model was developed by colleagues at BIOEPAR, Nantes, France. In a collaboration between BIOEPAR, CVERA and Animal Health Ireland, Floor Biemans from INRAE is currently adapting the French model to Irish conditions, including the incorporation of Irish cattle movement data. Several intervention strategies are being investigated with the aim to support decision-making for the national voluntary Johne’s control programme.
The Seventh International Conference on Mycobacterium bovis (M. bovis 2020)
The Scientific Committee received in excess of 270 abstracts for either oral or poster presentations from authors based in more than 35 countries. This reflects the extent to which M. bovis is a global health issue which was highlighted by the WHO, the OIE, the FAO and The Union in their 2017 publication “(opens in a new window)Roadmap for Zoonotic Tuberculosis”. The Conference will take place in Galway from 8-11 June. Early registration for M. bovis 2020 closes on 1st March. For more information, please visit (opens in a new window)https://www.mbovis2022.com/.