- 5. Maintaining Biosecurity
- Investigating green-grafting as a technique for detecting viral infection in imported grapevine stock
- Distribution of saprophytic fungi in New Zealand
- Endogenous positive control PCR assays
- Generic detection of plant viruses
- “Differential diagnosis for mouth and feet lesions in NZ sheep caused by infectious diseases and Non-infectious causes”.
- Development of a synthetic pheromone for use in the gum leaf skeletoniser eradication programme
- Enhancement of national animal health surveillance through capture of veterinary technical data to define disease incidence in farm animals (2002 / 03)
- Interisland livestock movements and traceability
- Contact rates for livestock
5. Maintaining Biosecurity
This category provides information which will assist in developing and implementing policies which help to protect New Zealand’s agricultural, horticultural and forestry industries from the adverse effects of introduced pests and diseases.
5.1 MBS 320
Programme Title: |
Investigating green-grafting as a technique for detecting viral infection in imported grapevine stock |
Programme Leader: |
Marian McKenzie |
Institution: |
Crop & Food |
Programme Goal and Rationale: To develop the green-grafting technique for grapevine material in vivo, and using tissue culture in vitro, and assess the technique as a method for detecting viral infection.
Viral disease constitutes a permanent danger for the vineyard with a large variety of viruses specific to grapevines found throughout the world. Some of these are currently found in New Zealand, e.g. leaf roll, fan leaf, corky bark and stem pitting viruses. However, considering the current size and rate of growth of the wine industry in New Zealand, and the importation of new grape varieties to feed this demand, our vineyards are also threatened by previously unknown viruses present in imported grapevine stocks. The means to reduce losses caused by viral infection once stock is introduced are limited. Therefore, it is increasingly important that we have a robust, sensitive, rapid and reliable technique for assessing grape clones entering New Zealand for any viral cargo they carry.
Current viral testing techniques include graft-indexing of woody cuttings, where the incoming stock is grafted onto indicator rootstock. However, this method is time- and labour-intensive, with a 2-3 year incubation period of the grafted indicators in a nursery. A second method uses serological (e.g. ELISA) or molecular (e.g. PCR) techniques to detect the presence of virus particles. These are rapid and reliable techniques, but are limited to known viruses for which antibodies and genome sequences are available.
A relatively new technique, green-grafting, has recently been developed for vegetative propagation and has been successfully adopted in several grape-growing countries to rapidly diagnose viral disease. Furthermore, there is some evidence that a new tissue culture based grafting system may increase the speed of viral detection even further. We propose to investigate several green-grafting techniques to optimise these procedures for New Zealand conditions. Using our knowledge of, and contacts within the New Zealand grape growing industry we will choose root stock and material to be tested for viral infection. We will investigate various green-grafting regimes in vivo as well as in vitro (outlined in objectives 1 and 2 of this proposal), and assess the most successful techniques as methods for detecting viral infection using visual symptom analysis with serological detection for confirmation of viral contamination (objective 3). Using these techniques we aim to produce a green-grafting based technique which is rapid, sensitive and reliable for detecting the presence of viral infection in imported grape varieties.
Objective 1
Objective Title: |
Green-grafting of grapevine for virus detection |
Research Leader: |
Dr Ranjith Pathirana |
Description:
Grapevine viral diseases may be broadly classified into two major groups. In the first group, the viral pathogens have been identified and are detected by serological techniques such as ELISA. In the second group the causal agents are unknown but detected by graft-indexing on indicator grapevine varieties. In this part of the project we propose to standardise a protocol for green-grafting using greenhouse grown plants. We will test two green-grafting techniques to optimise the procedure for use in diagnosing viral diseases. Once tested on material known to carry particular viruses, the method would provide a rapid, reliable and sensitive technique for the quarantine assessment of new introductions. It will have the additional advantage of testing the quarantine material under controlled greenhouse environments, thus preventing escape of quarantine pests and diseases.
Objective 2
Objective Title: |
Micrografting of grapevine for virus detection |
Research Leader: |
Dr Ranjith Pathirana |
Description:
Micrografting under in vitro conditions utilises actively growing rootstock and scions and is an alternate procedure to standard green-grafting. Successful micrografting would enable the diagnosis of viral diseases more rapidly than conventional grafting methods or even green-grafting under greenhouse conditions. The possibility of using micrografting for early diagnosis of viral diseases has been previously demonstrated for corky bark virus (Tanne et al. 1993). The objective of this part of the project is to develop a reliable protocol for in vitro micrografting of grapevines. We propose to assess the possibility of visual identification of symptoms early in the in vitro culture system and also after exflasking in the greenhouse. The optimization of media for the in vitro culture of grapevine will enable not only the diagnosis of viral diseases of quarantine significance, as is the aim of this proposal, but could also be used for the rapid multiplication of new cultivars, virus elimination by meristem culture, overcoming graft incompatibility commonly observed among different Vitis species, and screening for virus resistance in potential root stocks.
Objective 3
Objective Title: |
Assessing green-grafting techniques for viral detection |
Research Leader: |
Dr Marian McKenzie |
Description:
Objectives 1 and 2 outline the methods we will use to produce green-grafted and micro-grafted grapevine material. In the third objective material from the most promising green grafting technique(s) will be assessed for its potential as a viral indexing tool. By targeting viruses whose symptoms have been well documented in grape plants, for example grapevine leaf roll virus and grapevine fanleaf virus, we will visually analyse our grafted material for viral infection symptoms. Alongside the visual analysis we will use ELISA or PCR for the detection of viral infection. This will allow us to confirm the presence of viral contamination and assess the reliability of visual symptom analysis as a cue of viral infection.
5.2 MBS 321
Programme Title: |
Distribution of saprophytic fungi in New Zealand |
Programme Leader: |
Dr S R Pennycook |
Institution: |
Landcare Research |
Programme Goal: To improve the efficiency and effectiveness of border biosecurity, by providing data that can be used to develop phytosanitary measures appropriate to the risk posed by individual fungal genera.
Rationale: New Zealand is free from many economically important fungal pathogens that infect agricultural crops overseas. Border inspections by MAF Quarantine Service frequently intercept fungi on imported plant material, fruit and vegetables. Following identification of the fungi by the National Plant Pest Reference Laboratory, a decision is made on what kind of treatment is required.
Many of the fungi isolated at the border are in genera such as Penicillium, Mucor and Aspergillus, in which most species are harmless, ubiquitous saprophytes. However, species in such genera are often difficult to identify accurately. Expertise in their identity is not available locally, and the scarcity of world experts in the diagnosis and taxonomy of these groups makes it costly and impractical to outsource their expertise. The lack of readily available information on the pathogenicity of these fungi and their distribution in New Zealand frequently results in MAF implementing a conservative course of treatment. Such treatment is expensive, causes potentially unnecessary delays, and can be inappropriate when the item is for human consumption. This problem could be minimised by better assessment of the risk posed to New Zealand biosecurity by species within these problematic genera. Providing MAF staff with accurate, New Zealand-relevant information on the potentially small numbers of species in these genera likely to pose a real risk will lead to more informed decisions on appropriate courses of action.
Landcare Research has developed extensive databases on the fungi recorded from New Zealand, and on the specimens and literature supporting these records. Our collaborating partners in MAF’s National Plant Pest Laboratory and Forest Research have complementary data from the PPIN database and the Forest Research diagnostics database respectively. Landcare Research owns one of the largest mycological libraries in the Southern Hemisphere, and has the staff with the necessary skills and experience to interpret accurately the data available, both at a New Zealand and a world scale. We will use this knowledge and data to provide the information required by MAF Policy to decide whether border security measures can be streamlined for certain fungal groups.
Objective 1
Objective Title: |
Distribution of saprophytic fungi in New Zealand |
Research Leader: |
Dr S R Pennycook |
Description:
This objective aims to provide a tool for use by MAF Quarantine Service staff to assess whether the risk to New Zealand’s biosecurity from fungi in genera that comprise mostly ubiquitous and cosmopolitan species can be managed more effectively.
National biosecurity will be enhanced by minimising unnecessary costs relating to treatment and delay, when dealing with fungi in genera likely to be of low risk to New Zealand.
5.3 MBS 322
Programme Title: |
Optimising nucleic acid extraction from plants for pathogen testing |
Programme Leader: |
Dr Gail M Timmerman-Vaughan |
Institution: |
Crop & Food |
Programme Goal and Rationale: Molecular diagnostic methods, particularly those based on sequence detection using polymerase chain reaction (PCR), have tremendous potential to determine the presence of plant pathogens. The goal of this programme is to develop nucleic acid extraction protocols and quality control assays to underpin the use of PCR and RT-PCR (reverse transcription PCR) assays to detect pathogens in the diverse plants that are imported into or grown in New Zealand. This will permit the increased use of nucleic acid-based diagnostic tests for plant pathogens to supplement and complement existing conventional methods.
The research proposed in this programme builds on research being conducted at Crop & Food Research on plant genomes, on development of PCR-based diagnostics, and on research on molecular detection of plant pathogens. Crop & Food Research operates a Level III Quarantine greenhouse facility.
Objective 1
Objective Title: |
Plant nucleic acid extraction |
Research Leader: |
Dr Gail M Timmerman-Vaughan |
Description:
Molecular detection of nucleic acid sequences to determine the presence of pathogens in plant materials has the advantages of being sensitive, relatively quick, applicable to problems that may otherwise be intractable and is complementary to conventional pathogen detection methods. The extraction of RNA and/or DNA of adequate quality and quantity is a prerequisite for pathogen detection using nucleic acids. In this objective, we aim to assess and then optimise methods to extract DNA and RNA (total nucleic acids, T-NA) and RNA suitable for use in PCR (polymerase chain reaction) and RT-PCR (reverse transcription-PCR) for members of at least twenty important families that represent the wide range of flowering plants that are imported into or grown in New Zealand. We will produce a manual detailing protocols for nucleic acid extraction from members of the plant families being examined. The outcome of the research will be improved methods in support of maintaining and enforcing New Zealand’s biosecurity as a result of increased ability to detect the presence of pathogens in symptomatic and asymptomatic plant material.
Objective 2
Objective Title: |
Endogenous positive control PCR assays |
Research Leader: |
Dr Gail M Timmerman-Vaughan |
Description:
The aim of this objective is to develop positive control PCR assays based on endogenous plant sequences as a quality control step for PCR or RT-PCR-based pathogen detection. We propose in the first instance to develop assays based on sequences from the conserved plant chloroplast ndhB gene. We have chosen this nucleotide sequence because it is highly conserved and contains an intron, enabling processed transcripts indicative of successful RT-PCR to be detected and distinguised from PCR products amplified from DNA. The ndhB gene is one of a number of chloroplast genes containing introns (for example, the maize chloroplast genome contains 12 pre-mRNA introns). We will test the PCR reactions on the T-NA and RNA extractions from the range of plants listed above and will optimise the conditions to produce a reliable positive control assay that is widely applicable across diverse families of plants. In the event that the ndhB sequence is not suitable for use as a positive control assay, other conserved transcribed nucleotide sequences (18S rDNA or chloroplast cox1 sequences) will be used to develop endogenous control assays. The materials, methods and results will be detailed in a laboratory manual. The use of the ndhB sequence as a positive control assay for plant pathogen diagnostics is novel, therefore a brief manuscript will be submitted for publication. The outcome of this research will be maintaining or enhancing New Zealand’s biosecurity through enhanced ability to detect plant pathogens as a result of development of technical ability to extract nucleic acids from a wide range of plants.
5.4 MBS 323
Programme Title: |
Generic detection of plant viruses |
Programme Leaders: |
Dr Mike Pearson – Auckland University Dr Dan Cohen – HortResearch (Mt Albert) |
Institution: |
Auckland University |
Programme Goal: To develop a PCR detection system using broad-spectrum or “universal” primers for plant viruses of quarantine importance to NZ.
Rationale: Primers designed to sequences of conserved regions within a virus genome and are able to amplify all members of a group. Once amplified the product may be sequenced to identify the species of virus present. Generic primers have already been designed for a number of virus groups, e.g. Potyviridae (Gibbs & Mackenzie, 1997; J. Vir. Meth. 63: 9), Potexvirus and Tobamovirus (Gibbs et al., 1998; J. Vir. Meth. 74: 67-76), Closterovirus (Karasev et al, 1994 J. Gen. Virology 75: 1415 ;Tian et al , 1996. Phytopathology 86: 1167), Bymovirus (Monger et al, 2001. Eur. J. Pl. Path. 107: 661), Tospovirus (Chu et al 2001. Phytopathology. 91: 361), Cucumovirus (Choi et al, 1999. J. Vir. Meth. 83: 67), Vitivirus and Trichovirus (Saldarelli et al, 1998. Eu.J. Pl. Path. 104: 945) and Begomovirus (Brown-JK, 2000. Virus-Research. 71:233). In some cases these primers work well but in other cases they may not be reliable enough for routine diagnostic work.
Since primer design is improving and sequences are constantly being added to the databases we will first check for published primers for the virus groups of interest. Published primer sequences will be checked to determine whether they can be optimised and relevant viral sequences will be analysed to determine whether there are alternative conserved regions to design novel primers. Where the number of virus species within a genus is small, or only a few species have been sequenced, we will explore the possibility of designing species specific primers that can be combined in a multiplex PCR approach.
Improved primers will significantly assist in detecting viruses of quarantine importance and discriminate from those from viruses already present in New Zealand. This, in turn, will greatly assist MAF Biosecurity in meeting its obligations under the Biosecurity Act, 1993 and Hazardous Substance and New Organism Act, 1996.
Objective 1
Objective Title: |
Primer design and evaluation |
Research Leader: |
Dr Mike Pearson |
Description:
Aims:
To design and/or optimise generic virus primers for the following virus families and genera :
1. Closteroviridae (to include Closterovirus, Crinivirus)
2. Comoviridae (to include Nepovirus)
3. Togaviridae (to include Furovirus, Pecluvirus, Pomovirus and Tobravirus)
4. Luteoviridae (to include Luteovirus)
5. Geminiviridae (to include Begomovirus)
6. Bunyaviridae (to include Tospovirus)
7. Unassigned (Potexvirus, Tobamovirus)
Basic requirements:
- Primers sequences designed for a virus genus must amplify the target sequence from all (or most) members of the genus, ideally at a single annealing temperature.
- PCR products should be preferably 300 to 700 bp and be suitable for direct sequencing. (N.B. it may be necessary to use primers for longer sequences in order to use highly conserved regions for primer attachment).
- The inclusion of a restriction sites within the PCR product might allow differentiation of species within the genus
Expected outcomes:
The development of PCR primers that will simplify and speed up the detection of certain plant viruses, thus improving the efficiency and quality of quarantine surveillance.
Objective 2
Objective Title: |
Preliminary testing of primers |
Research Leader: |
Dr Dan Cohen |
Description:
Aims:
To test generic virus primers designed in Objective 1 against a limited number of viruses and hosts to establish their ability to reliably amplify specified viral sequences.
Expected outcomes:
Selection of primers that work with specified virus/host combinations, to be passed on to NPRL for testing on a wider range of viruses and hosts.
Methodology:
The procedures to test primers will include:
- Screening against 1-2 representative species/strains of the genus.
- Screening will be against extracts from infected plants (where possible) or freeze dried, virus infected plant tissue.
- Tests will also be performed in parallel with primers for a common plant gene to ensure that the extract is PCR competent.
- A repeat PCR with individual primer pairs will be carried out if a multiplex PCR is used.
- The identity of PCR products will be verified by sequencing.
- The procedures to test primers will include optimisation of PCR conditions, e.g. annealing temperature, Mg2+ and primer concentrations.
5.5 MBS 324
Programme Title: |
“Differential diagnosis for mouth and feet lesions in NZ sheep caused by infectious diseases and Non-infectious causes”. |
Programme Leaders: |
Dr Hugh Black |
Institution: |
Agriquality |
Goal: |
Build a profile of the mouth and feet lesions that occur in New Zealand sheep that need to be considered within the differential diagnosis for foot and mouth disease. |
Significance: |
Diagnosing foot and mouth disease on clinical grounds in sheep has proven difficult during the British epidemic in 2001. Erosive lesions, labelled Ovine Mouth and Gum Obscure Disease (OMAGOD), reduce the specificity of clinical diagnosis, potentially raising costs associated with control on properties that are falsely described as positive. Patrol Veterinarians will require instruction on the likely range of lesions that they would encounter during surveillance during a foot and mouth disease response in New Zealand. |
Objective 1
Objective Title: |
Syndromes and endemic diseases that may be included in the differential diagnosis of foot and mouth disease in sheep. |
Objective Leader: |
Dr Hugh Black |
Description:
Collate information (photographic and descriptive pathology) relating to diseases in sheep that may be considered within the differential diagnosis of foot and mouth disease in sheep.
Methodology:
The proposed structure is divided into 3 parts:
Literature and resource review: Undertake a literature review that will include:
- Forman and Geering, Exotic Diseases of Animals, Australian Government Publishing Service, Canberra 1995
- R de la Rua, GH Watkins, P Watson, Idiopathic mouth ulcers in sheep, The Veterinary Record, 7 July, 2001, pp 30-31
- H Black, J Vujcich, R Sanson, Sheep Diseases Surveillance using Sentinel Practices & Sentinel Farms BAH/58/2, In progress.
- Review existing resources such as textbooks, published papers, photographs from the Pathology Registry, MAF and AgriQuality training material, Massey lecture slides, IIV callouts to suspect sheep lesions, etc.
Slaughterhouse Survey: A pathologist (Dr H Black) to observe sheep sent for slaughter during the cull ewe season that peaks in February and March, at say 2 slaughter plants, one NI and one SI. Mouths and feet to be examined, remove heads and feet with lesions for subsequent photography at the end of processing runs. The number of sheep examined to the number of lesions observed will be recorded to establish prevalence. Daily kill rates should approximate 500 ewes and 1000 lambs. Thus 2 slaughter plants which worked two shifts in the peak Jan-April period may yield a population of the order of 10,000-20,000 ewes & an even higher number of lambs available for examination, per plant, per NI and SI.
Objective 2
Objective Title: |
Publicity information |
Objective Leader: |
Mr T Donaldson |
Description:
Prepare publicity information relating to syndromes and endemic diseases that may be included in the differential diagnosis of foot and mouth disease in sheep.
Methodology:
Information collected from work undertaken in Objective 1will be assessed. It would then be formatted and will be prepared to be suitable as an educational resource for IIV, Patrol Veterinarian and other veterinary educational awareness.
This may include: Information sheets; Power Point Presentations; PDF format (for use in websites/intranets); and CDs for computers.
5.6 MBS 325
Programme Title: |
Contingent valuation of urban tree condition and quantity |
Programme Leader: |
Prof. John Craig |
Institution: |
Auckland University |
Programme Goal: The programme is intended to use the technique of contingent valuation to elicit household WTP (willingness to pay) for the avoidance of a range of reductions in the condition and quantity of urban tree estate. The elicited value may be used to estimate the economic impacts of those factors that cause damage to urban trees and to conduct cost-benefit analysis of response options or preventive measures.
Objective 1
Objective Title: |
Identifying and Ranking Benefits |
Research Leader: |
Éva-Terézia Vesely |
Description:
As the urban tree estate has a series of benefits ranking from ecological (such as reduction of air and noise pollution, water protection, wind sheltering, climate improvement, erosion control and habitat for urban biodiversity) to socio-cultural ones (such as aesthetic, psychological and educational), it becomes important to identify which are the benefits that people perceive and value. By ranking these benefits it will become clear which ones are considered when expressing stated preference and which ones remain out from the contingent valuation exercise.
Objective 2
Objective Title: |
Eliciting Values |
Research Leader: |
Éva-Terézia Vesely |
Description:
By developing a contingent market (hypothetical), the stated preference of New Zealand’s urban population is going to be elicited for avoiding a range of quantitative and qualitative reductions in the condition of the urban tree estate (a non-market good).
Step1: Design the survey.
Step2: Implement the survey.
Step3: Analyse data.
Step4: Examine validity and indicate limitations.
Objective 3
Objective Title: |
Identifying Determinants |
Research Leader: |
Éva-Terézia Vesely |
Description:
Relationships between the demographic characteristics and perceptions of respondents regarding the condition of the urban tree estate and the indicated willingness to pay for the avoidance of qualitative and quantitative reductions are identified and examined. The results are interpreted in a framework defined by the ongoing international research in this field.
5.7 MBS 326
Programme Title: |
Development of a synthetic pheromone for use in the gum leaf skeletoniser eradication programme |
Programme Leader: |
Max Suckling |
Institution: |
Hort+Research |
Programme Goal: The goal of this programme is to develop a synthetic pheromone for the gum leaf skeletoniser (Uraba lugens), in order to help MAF to provide a more effective monitoring tool for detecting any residual (or future) population and indicating where to apply treatment measures to increase the probability of successful eradication.
Gum leaf skeletoniser is native to Australia and is considered a serious defoliator of eucalypt trees. Gum leaf skeletoniser was first detected on 13 June 1997 within the Tauranga District, and subsequent attempts to eradicate it appear to have been successful. However, the insect is still considered a significant biosecurity risk by MAF. In the absence of Australian natural enemies, the impact of this insect in New Zealand is potentially significant.
Moth sex pheromones have a proven track record in monitoring for many species, and over 1,500 moth pheromones are known (Suckling and Karg 2000). The identification of the pheromone of this Australian noctuid moth presents a technical challenge requiring close co-operation between Australian and New Zealand research teams. The identification will be achieved by pheromone extraction, identification, and synthesis (or purchase if available), followed by laboratory and field validation through trapping in Australia (or NZ if the insect reappears).
5.8 MBS 327
Programme Goal:
Goal: To develop and implement a working model of the Veterinary Practitioner Assisted Disease surveillance (VetPAD) system to collect detailed animal health data on cattle, sheep and deer populations. The system will include software installed on hand held PDAs to capture and download data to a database in each participating rural practice, and centralised analysis and reporting of disease events over time
Rationale: The 2000 pilot study “Use of veterinary practices to define baseline patterns of animal disease for national animal health surveillance” demonstrated the potential value of animal health data collected by private veterinary practices for animal disease surveillance in New Zealand. The study was limited to dairy cattle and to a small number of cooperating practices and farms, and data were collected manually. The next step to develop a functional and practical system for capturing veterinary clinical data is to implement and evaluate a working model for data collection and analysis leading to reporting of spatial and temporal trends in endemic diseases.
The option of validation of the pilot study, by repeating the project across a random selection of practices nationally is seen to have limited merit as it repeats the work of Black et al and will do little to progress the concept towards achieving a functional surveillance capability This study proposes to develop and evaluate an automated electronic data collection system at a regional level through implementation in a group of cooperating practices over a period of three years. The Otago / Southland region is preferred as it contains approximately 20 % of the country’s livestock population and is serviced by relatively few veterinary practices. The project would also involve practices that participated in the pilot project and are known to support the concept.
Objective 1
Objective Title: |
User needs assessment |
Research Leader: |
Lachlan McIntyre |
Determine the user requirements of a functional VetPAD surveillance system and the end user requirements of VetPAD software both for users of VetPAD software and users of the surveillance data (MAF BA).
Methodology: Three focus group sessions will be conducted to allow the respective user groups to specify the outcomes they would expect from using the VetPAD system and software. The first meeting would specify the needs of MAF BA with respect to data analysis and reporting outputs. Particular outcomes might be estimates of frequency of a particular disease, or incorporation of trading country requirements for data on specific diseases or syndromes into MAF quarterly disease reporting.
The second meeting would determine software user functionality by industry leaders (e.g., John Harrison, Scott McDougall) and practitioners that participated in the pilot project (i.e., Horowhenua(1), Pahiatua(1) and Southland (2)). We will use a grounded theory approach to establish the needs of these potential users of the technology.
The third meeting will be held in Southland and will involve representatives of all practices in the Otago Southland region who have a significant large animal work load, with a view to recruitment for the data collection project as well as consolidating the user needs assessment.
Objective 2
Objective Title: |
Refine and evaluate prototype data-capture technology |
Research Leader: |
Graydon Alexander |
Description:
Create a palmtop data-capture method for commercial use in one private veterinary practice, based on a prototype design, which has been worked out in consultation with veterinary practices.
Methodology : To be commercially applicable, the data capture method needs to be integrated with routine practice operations. Our objective is to enable vets to use palmtop computers to record all clinical and business information at the end of a call and to print out immediately information for farmers, such as call details and drug administration/withdrawal period instructions. This on-farm data entry should bring advantages to practice management through reduced data handling and errors, point of sale billing, and more timely provision of management information (e.g., products used). We have developed a visual prototype of the proposed data collection format that will include both clinical and business data. The software needs to be designed in detail, programmed, tested, and then trialed under commercial conditions to test is value and ensure compatibility with practice management.
For purposes of surveillance, selected data fields will be extracted from the purpose built database within the practice computer. Fields currently tagged in the prototype for surveillance purposes include date, farm ID (linked to Agribase), animal description (ID design of an appropriate software application for the use on a palm-top computer. Initially the data will be transferred from the palmtop into a purpose-designed database separate from the practice accounting system. Direct interfacing to these systems through a generic data exchange format will be investigated to determine its feasibility, cost and acceptance by practices.
Objective 3
Objective Title: |
Collection of disease data from veterinary practices. |
Research Leader: |
Dr. Lachlan McIntyre |
- Description:
Over 3 years in the Otago / Southland region and also in those practices from the earlier study which wish to continue their involvement, collect disease data from collaborating veterinary practices, using the software developed in objective 2. There will be detailed evaluation and refinement over the three-year period to build a robust and reliable clinical surveillance system based on the VetPAD concept.
Methodology: All the rural veterinary practices in the Otago / Southland region will be approached. Co-operating practices will use the PDA provided, running the VetPAD software. This will allow them to record all billing data in the field and capture epidemiological data about the population of sheep, cattle and deer in the region. Practitioners will be trained to achieve some standardization of data collection procedures. A supporting quality assurance system for disease diagnosis and data collection will be established. The QA system would recognise the needs of MAF BA within the system. Appropriate data of disease events on client properties will be obtained from practice records.
Data will be transferred from the palmtops to a database we will install on each practice’s computer system. At the end of each day the practitioners will synchronise their PDA with this database, uploading data to the practice computer. From here the data will be electronically transferred to a central database for processing and analysis.
Objective 4
Objective Title: |
Data analysis |
Research Leader: |
Dr. Lachlan McIntyre |
Description:
Compare patterns of disease events indicated by data from veterinary visits.
Methodology: Data captured in the VetPAD database established in the practice computer will be e-mailed on a regular basis to the central database managed by the EpiCentre through Lachlan McIntyre (for security). Here the data will be cleaned and added to a larger database where data on the at-risk population are held (ie herd and flock sizes, location, etc), with appropriate privacy protection. Using this data, descriptive spatial and temporal statistics of disease events will be calculated and evaluated epidemiologically.
Future Intentions
In the first year of the study practice data will be collected by existing methods, without intervention by project personnel, although practice staff will know that they are taking part in the study.
It is intended that in year 2 practices will progressively change to the VetPAD system, and data collected in this standardized format during part of year 2 and all of year 3 will be compared for surveillance value with data collected from practice accounting software in a non-standardised format, prior to the changeover in that practice.
The study is planned to run over a three-year period and if that can be arranged, approved and funded it would be possible to begin developing indices of the normal patterns of disease incidence for broad categories of diseases and for certain particular diseases nominated by MAF BA. This can subsequently be used to determine whether a given disease is occurring with greater frequency than expected. The collection of detailed animal health data of this type also opens up the possibility of using weather data from the region to develop models that may predict the incidence of some diseases. With several practices from the region providing data, the between-practice variation in disease detection will become evident. Diseases of particular interest to MAF BA can be examined in more detail.
5.9 MBS 328
Programme Title: |
Interisland livestock movements and traceability |
Programme Leader: |
Bruce Binnie |
Institution: |
Agresearch |
Programme Goal:
The goal of the study is “Understand the changing patterns of livestock movements across Cook Strait and the mechanisms of traceability”.
The significance of the study is that “Cook Strait forms an important geographical barrier that would be potentially important for regionalisation during an exotic disease outbreak. Regionalisation requires effective movement control to be established, including tracing of recent movements”.
AgResearch will assemble a small team of Quality Assurance auditors and a biometrician to conduct this study. The QA auditors are qualified and accredited by the Joint Accreditation System of Australia and New Zealand. They have considerable experience auditing on-farm QA programmes for major NZ meat processing companies as well as designing QA programmes and standard operating procedures.
Our approach would be to obtain data of inter-island livestock movements for the last 5 years from Tranz Rail and Strait Shipping. These are the only two companies transferring livestock across the strait, and both have agreed to provide us with these data. We would analyse these data to define patterns of livestock movement within years, and changes to the patterns over the years. Where possible, factors influencing seasonality of movements and changes between years would be identified. (eg. Drought, building up the South Island dairy herd during May and June, procurement of North Island lambs for slaughter at the Alliance plant in Nelson)
The data would also reveal the major road transport operators engaged in inter-island livestock transfers. We would work with the major transport companies to:
further elucidate the patterns of movements (particularly the species composition by season) and possible causative factors
examine their methods of data recording, archiving and retrieval
develop recommended Standard Operating Procedures to ensure rapid notification to all road transport operators of an exotic disease outbreak, rapid and accurate identification of stock movements immediately prior to the outbreak including the current location of the livestock.
These SOPs will be compatible with the systems in place for Animal Status Declarations and national identification of cattle and deer.
Objective 1
Objective Title: |
Assemble and analyse data |
Objective Leader: |
Dr Martin Upsdell |
Description:
Establish the pattern of livestock movements, the trends over the last five years and the major transport operators engaged in inter-island livestock transfers.
Methodology:
Data of livestock movements will be obtained from Tranz Rail and Strait Shipping – the only two significant operators in this area. The Biometrics section at Ruakura will analyse the data to determine seasonal patterns of livestock movement by month, whether for immediate slaughter or not, and direction of movement. Trends between years will be examined. Factors affecting the seasonal patterns and trends between years will be sought and possible cause and effect relationships will be presented. (This analysis will also incorporate data coming from objective 2).
Objective 2
Objective Title: |
Describe transport operators’ traceability records |
Objective Leader: |
Bruce Binnie |
Description:
Describe the recording and archiving systems used by the transport operators. Identify strengths and weaknesses in the current systems.
Methodology:
Identify the transport operators responsible for 80% of the livestock movement of each species across Cook Strait while carrying out Objective 1. Interview these operators to determine their systems of recording, archiving and retrieving relevant data (livestock type, number, source, destination, date of pick-up, date of delivery, animal status declaration).
Describe how (if) these systems interface with the Animal Status Declarations and national identification of cattle and deer. Identify farmers who are already known to AgResearch who will supply details of inter-island movements of their stock, and use their details to assess the accuracy and ease of retrieval of livestock movement records held by road transport operators.
Objective 3
Objective Title: |
Notification, tracing and information retrieval procedures |
Objective Leader: |
Bruce Binnie |
Description:
Develop procedures for notification to transport operators of a disease outbreak, for tracing livestock that have recently crossed the Strait to their current location and for retrieving information rapidly.
Methodology:
Verify our understanding of the key requirements with MAF Biosecurity personnel. In liaison with the Road Transport Federation, design systems for the procedures that are both effective and practical. Report these systems as SOPs.
Note:
MAF Biosecurity's intention will be to integrate the SOP developed into existing delivery mechanisms providing tracing capability during exotic disease responses. Tracing capability is a requirement under MAF Biosecurity's 153 Standard for the supplier of services to the Exotic Disease Response Centre and Field Operations Response Teams. These services under the 153 Standard are presently contracted to AgriQuality NZ Ltd as service supplier.
5.10 MBS 329
Programme Title: |
Contact rates for livestock |
Programme Leader: |
Dr Robert Sanson |
Institution: |
Agriquality |
Programme Goal:
Establish reliable estimates of movement patterns between farms, to provide background data to support epidemic spread modelling.
Rationale:
Modelling using InterSpread is an important tool to understand spread, resource requirements and control mechanisms for exotic disease responses. Models require accurate estimates of contact rates and the spatial patterns of contact.
Previous research:
The movement study published by Sanson and co-workers (1993) has been used to provide the default inter-farm movement parameters used by the InterSpread simulation model. That study analysed movement data collected from 178 farmers in four sub-areas of Southland. Each farmer recorded all movements onto and off the farm during a single 2-week period. The basic study design, using farmer-completed diaries, has been considered a useful technique, and has since been or is being replicated in countries such as the Netherlands and Denmark.
Deficiencies of the study were:
- Only covered two weeks, without reference to “quiet” or “busy” times of the year
- Only included farmers in Southland
- Did not specifically measure the multiplier ratio of animal lots leaving sale yards for farms over the number of animal lots being presented for sale. This multiplier factor proved to be a major exacerbator during the UK 2001 FMD epidemic and needs to be quantified in New Zealand.
Further, the study is now approximately 10 years old.
The proposed study design will address the above issues.
Objective 1
Objective Title: |
Farm to farm movements |
Research Leader: |
Dr Robert Sanson |
Description:
Quantify the frequency and distance of movements off New Zealand livestock farms. Establish reliable estimates of direct farm-to-farm movement rates and spatial patterns to assist response modelling.
Methodology:
Five hundred farmers, comprising 100 randomly selected from each of the dairy, dairy dry stock and grazing, beef, sheep and mixed sheep and beef farm types recorded in AgriBase (AgriQuality’s nationwide database detailing farm data which is geo-spatially referenced), will be asked to complete movement diaries covering two 3-week periods during the year. These periods will target each farmer’s “busy” and “quiet” times of their farming operations, defined according to the likelihood of animal movements, and will be agreed upon during an initial interview conducted by AgriQuality Livestock Consultants. In effect, this will provide upper and lower estimates of movement rates. All movements will be entered into a database, and assessed according to likelihood of transmission of foot-and-mouth disease (FMD) into high, medium, low or nil risk. Movement risk will be assessed according to EpiMAN tracing expert system rules for FMD. All sources and destinations will be geo-coded in a geographic information system (GIS), and distances calculated. The data will be used to derive the inter-farm movement parameters required for the epidemic modelling program InterSpread, specifically:
- Numbers of high, medium and low risk movements per day for each of the Dairy, Beef, Sheep, Mixed Sheep and Beef, and Dairy Dry / Grazing sectors
Histograms of movement distances by sector and risk
The study’s goal and the usefulness of the material for the proposed MAF basis of assessments is critically dependant on accurate record keeping and a high level of farmer return for this detailed information.
Objective 2
Objective Title: |
Sale yard “multiplier” factor |
Research Leader: |
Dr Robert Sanson |
Description
Quantify the mean ratio of the number of animal lots moving from saleyards to farms divided by the number of animal lots presented for sale (the so called “sale yard multiplier” factor).
Methodology: Sale yard records extracted from a number of actual sales conducted by Wrightson Limited over the past twelve months will be analysed to estimate the mean ratio of farmer purchased lots to incoming animal lots.
Contact for Enquiries
Farm Monitoring Programme Manager
Monitoring and Evaluation
MAF Policy
PO Box 2526
Wellington
NEW ZEALAND
Phone: +64 4 894 0623
Fax: +64 4 894 0741
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