2003/04 Research Final Report Summaries

MAF Policy Information Paper 55
ISSN 1171-4654
ISBN 0-478-07844-7
December 2004

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Disclaimer

While every effort has been made to ensure that the information herein is accurate. The Ministry of Agriculture and Forestry (MAF) does not accept liability for error or fact or opinion which may be present, nor for the consequences of any financial decision based on this information. The reports and material submitted by the various research providers, which are contained within the publications, have been prepared in accordance with reasonable standards of scientific endeavour. The research providers also have no control over its use by third parties, and shall likewise have no liability to a third party arising from their use of this information.

Any views or opinions expressed do not represent the official view of the Ministry of Agriculture and Forestry.

Printing of material from this report is welcomed (except for commercial use or on advertising or promotional material), provided proper acknowledgement is made to the source.

For additional information

Comments and enquiries concerning the contents of this document can be directed to:

Science Policy
MAF Policy
P O Box 2526
WELLINGTON

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Manager
MAF Information Bureau
P O Box 2526
WELLINGTON
Telephone: (04) 894 0100
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Or alternatively we invite you to visit our site at:

www.maf.govt.nz/publications

1. Facilitating Market Access Category

1.1 FMA 110

Programme Title:

Prolapses in Pigs

Programme Leader:

David Lawton

Institution:

Massey University

GOAL

To identify an appropriate approach or approaches to manage grower pigs and sows with prolapses to maintain appropriate welfare standards.

BACKGROUND

The Animal Welfare Act 1999 states that it is an offence to transport an animal in a manner or position that causes the animal unreasonable or unnecessary pain or distress. The New Zealand Food Safety Authority (NZFSA) is responsible for defining the requirements for acceptability for animals for processing into food. These requirements include that animals are normal, uninjured and disease free unless certified as fit for transport by a veterinarian.

The New Zealand pork industry is supportive of these general requirements. However, its experience, supported by its veterinary advisers, considers that pigs with prolapse that meet certain criteria can be transported to slaughter and enter into the food processing chain without compromising the welfare of the animal. In some situations this approach may represent the best practical option for the pig’s welfare.

It was agreed that a review of the relevant science was a necessary basis from which to set regulatory requirements for managing pigs with prolapse. An indicative measure of the number of pigs likely to be affected would also be useful.

APPROACH & OUTCOMES

A literature review has evaluated the current literature on rectal/vaginal prolapse in the pig. The review considered the anatomy, pathogenesis and aetiology of prolapse development. A “best estimate” of pigs in the New Zealand pork industry likely to be affected by prolapse was established via a survey of a small selected group of New Zealand pork producers.

These inputs formed the basis for recommending appropriate practical management options to deal with pigs with prolapse in New Zealand.

Outcomes:

Recommended management practices were identified for both grower pigs with rectal prolapse and sows with rectal and/or vaginal prolapse.

A key finding was that transport to slaughter is an appropriate management option where the prolapse is fresh and the animal is bright and alert with no obvious signs of discomfort. Certain qualifying criteria were identified, including that “fresh” ideally means within 72 hours, and ideally the pig should be transported separately or with some similar status pigs. Both transporters and slaughter house personnel should be made aware of the delivery of pigs with prolapse.

Another management option is treatment that is recommended by a veterinarian. This option may be necessary for sows due to farrow or with unweaned piglets, to maintain net welfare of both the sow and her unborn and/or unweaned piglets.

The uncertainty associated with specifying exactly what constitutes a “fresh” prolapse and also the impact of transport were noted. A further recommendation is to develop a pictorial guide.

It is recognised that the final decision on the welfare of a pig with prolapse will be made by the slaughter house veterinarian. Copies of the report will be provided to all slaughter house veterinarians.

1.2 FMA 111

Programme Title:

Soil phytosanitary issues

Programme Leader:

Dr John Marshall

Institution:

Crop and Food CRI

RESEARCH PROGRAMME NOT YET COMPLETED AND REPORTED AT TIME OF THE PREPARATION OF THIS PUBLICATION. THIS WILL BE REPORTED IN NEXT RESEARCH RESULTS PUBLICATION.

1.3 FMA 113

Programme Title:

Transport and heat stress

Programme Leader:

Terry Reid

Institution:

Canesis

RESEARCH PROGRAMME NOT YET COMPLETED AND REPORTED AT TIME OF THE PREPARATION OF THIS PUBLICATION. THIS WILL BE REPORTED IN NEXT RESEARCH RESULTS PUBLICATION

1.4 FMA 114

Programme Title:

Economic costs and animal welfare

Programme Leader:

Kevin Stafford

Institution:

Massey University

RESEARCH PROGRAMME NOT YET COMPLETED AND REPORTED AT TIME OF THE PREPARATION OF THIS PUBLICATION. THIS WILL BE REPORTED IN NEXT RESEARCH RESULTS PUBLICATION

1.5 FMA 115

Programme Title:

Deer wintering systems

Programme Leader:

Gary Rae

Institution:

Canterbury Agriculture

RESEARCH PROGRAMME NOT YET COMPLETED AND REPORTED AT TIME OF THE PREPARATION OF THIS PUBLICATION. THIS WILL BE REPORTED IN NEXT RESEARCH RESULTS PUBLICATION.

1.6 FMA 116

Programme Title:

Shelter for lambing

Programme Leader:

Dr Jo Pollard

Institution:

AgResearch CRI

SUMMARY

To provide farmers and MAF with a review of information on the costs, benefits and risks of providing different forms of shelter for lambing.

Context of project: In New Zealand flocks, 10-25 % of lambs die during the first three days after birth. This loss and the apparent lack of care in lambing paddocks offering little in the way of shelter can be detrimental to New Zealand’s image as a responsible producer of animal products. It was considered likely that farmers had inadequate information on the costs, benefits and risks of providing shelter and this may be a factor underlying the lack of shelter on many farms. This review described and summarised this information for use by farmers and by MAF and the National Animal Advisory Committee in revising standards and recommendations in the sheep code of welfare required by the Animal Welfare Act (1999).

Approach: A literature review was carried out covering the following topics: the thermal physiology of lambs (including effects of weather conditions and animal factors); forms of shelter suitable for lambing in New Zealand (including their costs, management requirements and effects on pasture production and fertility); and the benefits and use of shelter by sheep at lambing. An economic model was applied using three case study farms based on physical data from the MWI Economic survey farms in Wairarapa, Canterbury and Southland representing 58% of New Zealand’s sheep flock. Lamb survival was predicted using the LambAlive lamb mortality model and NIWA climatic data from 1999 to 2003. Economic data from the MWI Economic service was used to value the lambs saved and extra pasture grown (through increasing stocking rate). The estimates of shelter belt production and values were taken from the literature.

BACKGROUND

Outcomes: Wind and wet coats create dangerous conditions for lambs even at moderate temperatures by exceeding their capacity for heat production in the short or long term. Lambs compromised by birth injury, small size, inexperienced dams, etc. are particularly at risk. Deaths from starvation and exposure are linked because cold conditions debilitate lambs and impair progress towards sucking, while lack of colostrum reduces the ability to produce heat. Wet, cold, windy weather increased mortality rates in Australian Merino and Corriedale lambs by 38-76 %, and in New Zealand lamb breeds by 10-20 % (more in snow conditions). Shelter decreased single lamb mortality by 3-13 %, and twin lamb mortality by 14-37 % in Australian Merino and Corriedale sheep. Reductions in lamb mortality rates due to shelter in New Zealand studies have generally been less than 10 %. The most effective shelter would protect lambs from wind and rain and possibly conductive heat losses to the ground. Sunshine is highly beneficial in reducing heat loss. There is little information on effects of shelter on lamb growth or health.

Lambing sheep tend to seek isolation and shelter. They prefer dense shelter that protects from many angles and will walk windward to reach familiar shelter. Scattered shelter allows isolation, increases sheltering opportunities for lambs and should reduce concentrations of sheep. Appropriate shelter is likely to reduce pain/discomfort from cold, reduce starvation deaths and allow normal behaviour patterns to occur.

Suitable boundary shelter is a double row with a dense hedge windward and taller, permeable trees leeward. The establishment cost is about $6.00/m (with electric fencing) and $9.50/m (standard fencing). Economic modeling predicted that the value of lambs kept alive by traditional shelter provided only a marginal return in Wairarapa and Canterbury, unless other benefits such as increased pasture growth, resource protection and timber were included. Shelter was most beneficial as ambient temperatures declined and provided a significant economic advantage in Southland. Careful selection of plant stock and species, planning (considering location, orientation, irrigation and shading), site preparation and management will maximize shelter effectiveness and minimize problems with pests, harsh climate and disease. Alternative shelter likely to be cost-effective includes lamb covers (wool, commercial plastic or bread bag) and within-paddock shelter (tussocks/marginally palatable shrubs, or fodder species). Research needs identified were the effects of shelter (including tussocks and lamb covers) from wind, rain and wet ground on lamb survival, growth and health.

DISCUSSION

The project aimed to provide farmers and MAF with a review of information on the costs, benefits and risks of providing different forms of shelter for lambing. A literature review was carried out covering the following topics: the thermal physiology of lambs (including effects of weather conditions and animal factors); forms of shelter suitable for lambing in New Zealand (including costs, management requirements and effects on pasture production and fertility); and the benefits and use of shelter by sheep at lambing. An economic model was applied using three case study farms based on physical data from the MWI Economic survey farms in Wairarapa, Canterbury and Southland representing 58% of New Zealand’s sheep flock. Lamb survival was predicted using the LambAlive lamb mortality model and NIWA climatic data from 1999 to 2003. Economic data from the MWI Economic service was used to value the lambs saved and extra pasture grown (through increasing stocking rate). The estimates of shelter belt production and values were taken from the literature.

PUBLICATIONS

Pollard, J.C., Wills, B.J., Stevens, D.R., Wass, J.A., Harris, M.J., 2004. Shelter for lambing. Client Report. MAFPolicy Project FMA 116. 58 pp.

1.7 FMA 118

Programme Title:

Lambs’ neural responses

Programme Leader:

Dr Craig Johnson

Institution:

Massey University

SUMMARY

To quantify the way in which the cerebro-cortical response of lambs to rubber ring castration changes in the first eight weeks of life.

BACKGROUND

The aim of this project was to characterize the way in which the electroencephalogram (EEG) of lambs changes in response to rubber ring castration during the first eight weeks of life. Last year we demonstrated that this response is greater in two-week old than four-week old lambs. This study extends our previous work and surveys the electroencephalographic response to castration over the first eight weeks after birth.

APPROACH & OUTCOMES

Lambs ranging in age from 3 hours to eight weeks (n=68) were used in this study. Anaesthesia was induced by mask and maintained with halothane in oxygen. End tidal carbon dioxide (PECO2), end tidal halothane (PEHal), blood oxygen saturation and body temperature were monitored. PEHal was titrated to 1.2% and PECO2 to between 40 and 60 mmHg. Data collection commenced 10 minutes after PEHal was stabilised at 1.2 %. Fifteen minutes after the start of data collection the lambs were castrated by application of rubber ring according to standard animal husbandry practice. Data were collected for a further 15 minutes.

Total power (ptot), median frequency (F50) and the 95% spectral edge frequency (F95) were calculated from the EEG for consecutive two-second epochs. Data from 5 spectra were averaged to give one data point every 10 seconds. Electroencephalographic variables for the 5 minute period immediately after the start of castration were compared with that immediately prior to castration. Data are described in terms of percentage increase from baseline and presented as standard error of the mean ( ± SEM). A curve of best fit was constructed for lambs aged between 3h and 10 days.

Outcomes:

Following castration the majority of lambs exhibited an increase in F50 (90 % of lambs) and F95 (70 % of lambs), and a decrease in ptot (90 % of lambs). These changes were statistically significant (Table 1). Furthermore, there appeared to be a trend in response with age. Over the first 10 days after birth there appeared to be an increase in F50 and F95 and decrease in the ptot (F50 illustrated in Fig 1a). These trends continued for all variables until about the fifth week, after which the magnitude of the change decreased (F50 illustrated in Fig 1b). In addition, F50 appeared to cross the y–axis near the origin. Data points plotted in Fig 1 represent the rolling mean of values for ten animals. For each group the final value is plotted as mean age against mean change in EEG variable.

Table 1

 

f50

f95

ptot

Mean difference (%)

16 ± 2

3 ± 1

-6 ± 1

Significance (p value)

0.0001

0.03

0.0001

Figure 1

a)b)

Summary:

This study aimed to quantify the way in which the cerebro-cortical response of lambs to rubber ring castration changes in the first eight weeks of life.

Lambs ranging in age from 3 hours to eight weeks were anaesthetised. Anaesthesia was induced by mask with halothane in oxygen. Once the lambs were anaesthetised tidal carbon dioxide (PECO2), end tidal halothane (PEHal), blood oxygen saturation (SpO2) and body temperature (T) were monitored. PEHal was titrated to 1.2% and PECO2 to between 40 and 60 mmHg. Fifteen minutes after the start of data collection the lambs were castrated by application of rubber ring according to standard animal husbandry practice. Data were collected for a further 15 minutes. Total power (ptot), median frequency (F50) and the 95% spectral edge frequency (F95) were calculated from the EEG. Electroencephalographic variables for the 5 minute period immediately after the start of castration were compared with that immediately prior to castration. Data are described in terms of percentage increase from baseline and presented as mean ± SEM. A curve of best fit was constructed for lambs aged between 3h and 10 days.

Following castration the majority of lambs exhibited an increase in F50 (90 % of lambs) and F95 (70 % of lambs), and a decrease in ptot (90 % of lambs). Furthermore, there appeared to be a trend in response with age. Over the first 10 days after birth there appeared to be an increase in F50 and F95 and decrease in the ptot. These trends continued for all variables until about the fifth week, after which the magnitude of the change decreased. In addition, F50 appeared to cross the y–axis near the origin.

PUBLICATIONS:

CB Johnson KJ Stafford SP Sylvester SL Mitchinson RN Ward and DJ Mellor (2004). The effect of age on the cerebro-cortical response of lambs to rubber-ring castration. Proceedings NZPS.

1.8 FMA 119

Programme Title:

Level 3 Post Entry Quarantine

Programme Leader:

Bruce Koller

Institution:

Nimmo-Bell Consultancy

SUMMARY

To ensure that New Zealand’s agricultural and horticultural sectors are based on the best genetic material available from anywhere in the world.

BACKGROUND

A partnership between the industry sectors and government would enable the restoration and continued provision, at least cost, of level 3 post-entry quarantine facilities, diagnostic capabilities and testing for imported plant material. This will facilitate the entry into quarantine of desirable propagative material, its maintenance, and its release to industry in the shortest time possible without compromising biosecurity.

APPROACH & OUTCOMES

For this business to operate effectively it will need to be a partnership between central government (represented by MAF, which we referred to in this document as “government”) and other interested parties (which we refer to as “private”). It is expected these will include industry sector associations and organisations, CRIs, universities and entrepreneurial companies, partnerships, and individuals from the private sector.

The charter: The business will, as an effective partnership:

Work with the interested private parties to identify and source new plant genetic material such that each of the industry groups has access to genetic material of the highest quality. This will ensure product of exceptional quality is available to consumers in New Zealand and internationally and that profitability is enhanced. A significant contribution will be made to the growth of these industries and to innovation that will benefit the contributors and citizens of New Zealand.

Respond to the needs of entrepreneurs so that new plant products can be introduced, developed and marketed successfully.

Facilitate and contribute to the review of existing Import Health Standards and the development of new standards for crops not presently specified.

Facilitate and contribute to the development of protocols and manuals for the operation of containment facilities and the provision of diagnostic services.

Facilitate and contribute to the organisation of plant importation requirements (Level 1 through Level 3) into one cost-effective seamless system.

Contract the supply of containment facilities and diagnostic services such that there is continuity of supply of these services and that plant genetic material is able to be imported, tested and released to the importers in the shortest possible time and at reasonable cost.

Operate a system such that the integrity of imports is preserved, the confidentiality of commercial information is maintained and that entrepreneurs taking the initiative have every opportunity to benefit from their investment.

Develop and implement appropriate systems for the auditing of the contracted services and the retention of appropriate information in computerised databases.

The functions of the Establishment Board of this business will include:

Building effective relationships with the horticultural industry sectors and ornamental importers to determine what assistance is needed to enable the accession and importation of plant genetic material that has not been able to be imported since 2001.

Developing the business plan and budget to implement the Charter and securing the necessary funding from the contributing partners.

Managing the interface between government and private participants and contributors to the partnership.

Resourcing and implementing the activities necessary to fulfil the requirements of the Charter.

Acquiring information on likely future demand and developing strategies to manage annual fluctuations in the demand such that the continued availability of the services are ensured.

1.9 FMA 120

Programme Title:

Benchmarking New Zealand forest competitiveness

Programme Leader:

German Ortiz

Institution:

Forest Research CRI

BACKGROUND

The purpose of this project was to update the report prepared by Forest Research for MAF in 2001 titled “The Forest Processing Investment Environment” (Brown & Ortiz), specifically Part II. Benchmarking New Zealand Competitiveness. MAF also wanted to extend the analysis to Brazil, China and India. As a further but related item, MAF wanted to source specific information on the tax regime in the evaluated countries for new investments in wood processing equipment and related capital investments (including information on depreciation rates if possible).

MAF wanted to have an update on the status of the competitiveness of the New Zealand wood processing industry taking into consideration changes in the forest processing investment environment in New Zealand and in the evaluated countries since the original report was produced.

APPROACH & OUTCOMES

In general terms the methodology used for the update was the same as for the original report. A country competitiveness evaluation was done using the IMD’s World Competitiveness Yearbook as source. Then a specific evaluation of wood processing factors was done, using quantitative and qualitative information, with multiple sources including a literature review and interviews with Forest Research staff and external experts. The evaluation of wood processing factors led to a scale classification of the wood processing factors of competitiveness from 1 to 10, with 1 indicating the least competitive and 10 indicating the most competitive. Finally, an index was built comparing New Zealand and 8 other competitor countries combining the country competitiveness with the wood processing factors competitiveness.

Outcomes:

The following table summarises the results of the Wood Processing Competitiveness Index update for 2004:

The results of the index show that the competitiveness of New Zealand’s wood processing industry did not change from its evaluation of 2001, remaining with the same score (7.0), and in the same relative position in relation to the countries evaluated in the original study. Furthermore, all the countries evaluated in the original study kept their relative position in the 2004 update. The reasons for this are mainly due to the relative lack of significant changes in the components of the index, or because changes in the general competitiveness component were balanced with changes in the wood processing component, as was the case for Australia, for example.

New Zealand’s wood processing industry’s major competitive strengths are its processing development and industry knowledge, its general competitiveness level, and its wood resources, while its weaknesses are its relative low market development and investment attractiveness. A brief summary of the competitiveness level for each selected country is also presented in the report.

Finally, on the specific topic of depreciation rules, the study concluded that these are not a significant factor for the competitiveness of the wood processing industry in any of the countries selected for this report including New Zealand.

This project updated the report prepared by Forest Research for MAF in 2001 titled “The Forest Processing Investment Environment” (Brown & Ortiz), specifically Part II: Benchmarking New Zealand Competitiveness.

MAF wanted to have an update on the status of the competitiveness of the New Zealand wood processing industry taking into consideration changes in the forest processing investment environment in New Zealand and in the evaluated countries since the original report was produced.

1.10 FMA 123

Programme Title:

Shade for sheep

Programme Leader:

Drs Jim Webster & Jo Pollard

Institution:

AgResearch CRI

BACKGROUND

To define the behavioural and physiological needs of sheep for shade in hot, dry and hot, or humid environments.

Context of project

In many regions of New Zealand sheep seek shade on sunny days during much of the year. Shade is likely to be needed most in hot, humid conditions where respiratory cooling is less effective but they may also experience an excessive heat load in areas with high solar radiation. This project assessed the needs of sheep for shade in dry and humid environments by quantifying effects of shade on behaviour and physiological indicators of thermal status. The project provided information on the degree to which welfare is compromised by lack of shade in these environments, to assist MAF Policy in preparing welfare guidelines for sheep husbandry.

APPROACH & OUTCOMES

This project aimed to define the behavioural and physiological needs of sheep for shade in dry and humid environments, by quantifying effects of shade on behaviour and physiological indicators of thermal status, to assist MAF Policy in preparing welfare guidelines for sheep husbandry.

Sheep were studied in February 2003 at Poolburn (mean daily temperature 18.5oC and humidity 49%), and in January 2004 at Hamilton (mean daily temperature 22.0oC and humidity 67%). At each site 24 Romney crossbred ewes, divided into two groups of 12, were observed on 10 consecutive fine days. The groups were studied in adjacent paddocks, one with shade provided by trees and one with no shade, for five days; then groups were swapped between paddocks. Records were made of daytime activities; respiration rate in the early morning, early afternoon and during handling; and intra-vaginal temperature and weather conditions every 10 minutes during the 10 days.

Activities (grazing, standing and lying down) differed between groups with and without shade, and differences were more pronounced at Hamilton than Poolburn. Sheep with shade used it in over 80% of observations in which they were lying down, when shade was visible. At Poolburn intra-vaginal temperatures were higher in the sheep without shade during the full 24 hour period and during daylight hours (P<0.001). At Hamilton the difference in intra-vaginal temperatures between no shade and shade treatments was greater than at Poolburn and persisted at night-time (P<0.001). Respiration rates in the early morning did not differ between sheep without shade and those with shade at either site. Respiration rates in the afternoon at both sites were higher in the sheep without shade than in those with shade (respective means at Poolburn were 121 compared to 93, standard error deviation (SED) 7.0 breaths/min, P<0.001; at Hamilton 226 compared to 130, SED 8.1 breaths/min, P<0.001). At Hamilton, open mouth panting was seen in resting sheep. The substantial use of shade and reductions in intra-vaginal temperature and respiration rate in the sheep with shade (especially at Hamilton) indicated that it was of significant benefit to the welfare of the sheep in the study.

PUBLICATIONS

Pollard, J.C.; Cox, N.; Hogan, N.; Huddart, F.; Chaya, W.; Paterson, R.; Wigbolus, L. 2004 Behavioural and physiological responses of sheep to shade. Client Report. MAFPolicy Project FMA 123. 36 pp.

2. Maintaining Biosecurity Category

2.0 MBS 329

Programme Title:

Contact Rates for livestock

Programme Leader:

Dr Robert Sanson

Institution:

AgriQuality

SUMMARY

Establish reliable estimates of movement patterns between farms, to provide background data to support epidemic spread modelling

BACKGROUND

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. A previous study (Sanson et al., NZVJ 41, 21-28, 1993) studied movement patterns onto and off 178 farms in Southland during a single two-week period. This study attempted to update those findings using a broader cross-section of pastoral livestock farms

APPROACH & OUTCOMES

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 were asked to complete movement diaries covering two 3-week periods of the year, representing a Quiet and Busy time of the year respectively. All movements off farms were recorded into a database. Farm movements were assessed in terms of risk of transmission of foot-and-mouth disease (FMD) should it have been present on the participating farm. Frequency of movements by risk and distances travelled were calculated for the different farm sectors.

In addition, two livestock sales occurring at a large South Island saleyard were analysed and traced, to provide estimates of the ratio of animal consignments (lots) ending up back on farms vs. presented for sale.

Outcomes:

Busy period diaries were completed by 193 farmers, recording a total of 12,052 movements off their farms, an average of 62.4 movements per 3-week period. Of these, 2.48 involved the transport of livestock, equating to 0.83 livestock consignments per week. In contrast, 186 Quiet period diaries were returned, with a total of 10,885 movements off recorded, representing an average of 58.5 movements off during the 3-week period. Of these, 1.22 involved livestock, equating to 0.41 livestock consignments per week. Tables 1 and 2 summarise the number of movements by risk rating per farm per day where the destination was another farm.

Table 1. Number of movements to another farm per farm per day by risk rating for the different livestock sectors occurring during a Busy period of the year.

 

RISK RATING

Farm Type

HIGH

MED

LOW

BEF

0.033

0.473

0.089

DAI

0.051

0.975

0.062

GRADRY

0.133

1.006

0.125

SHP

0.026

0.419

0.038

SNB

0.06

0.651

0.08

Table 2. Number of movements to another farm per farm per day by risk rating for the different livestock sectors occurring during a Quiet period of the year.

 

RISK RATING

Farm Type

HIGH

MED

LOW

BEF

0.021

0.42

0.034

DAI

0.033

0.782

0.139

GRADRY

0.092

0.812

0.144

SHP

0.018

0.442

0.039

SNB

0.024

0.453

0.024


Table 3 summarises the sales records based on two successive days at Canterbury Park saleyard, Christchurch.

Table 3. Saleyard data for two successive sales days at Canterbury Park saleyard.

Item

Sale A

Sale B

Lots presented

56

21

Lots purchased

26

27

Lots purchased by dealers

2

1

Lots returned to vendor

0

0

Lots purchased by meatworks

5

0

Saleyard multiplier ratio

0.5

1.33

Summary:

Goal: Quantify movement patterns between farms, to provide data to support epidemic spread simulation using the InterSpread model.

Method: Approach a random sample of farmers to record all movements onto and off their farms during two 3-week periods representing a busy and quiet time of the year respectively. Classify movements by risk of transmission of FMD and calculate distances travelled. Trace and analyse livestock sales records from at least one sale.

Results: 193 farmers completed a Busy period diary, recording a total of 12,052 movements off their farms, an average of 62.4 movements per 3-week period. Of these, 2.48 involved the transport of livestock, equating to 0.83 livestock consignments per week. In contrast, 186 Quiet period diaries were returned, with a total of 10,885 movements off recorded, representing an average of 58.5 movements off during the 3-week period. Of these, 1.22 involved livestock, equating to 0.41 livestock consignments per week. Saleyard multiplier ratios (lots purchasded / lots presented for sale) from the traced sales data ranged from 0.5 to 1.33.

PUBLICATIONS

To date (16 March 2004), the study was presented at the Xth International Symposium on Veterinary Epidemiology and Economics, Viňa del Mar, Chile, 17-21 Novemebr 2003, and published in the Proceedings.

The study will also be presented at the Food Safety & Biosecurity Branch (FSB) sessions of the 2004 NZVA Conference in June.

2.1 MBS 330

Programme Title:

Treatments for peat

Programme Leader:

Lian-Heng Cheah

Institution:

Crop and Food CRI

SUMMARY

To evaluate and develop effective and practical technique(s) for control of regulated pests and pathogens associated with pest products.

BACKGROUND

New Zealand imports a range of peat products including peat and sphagnum moss. Peat is extracted from the ground and may harbour soil-borne pests and pathogens. MAF needs to identify methods of disinfestation that will ensure that there is no possibility of contamination of peat, peat products and sphagnum moss by pests.

APPROACH & OUTCOMES

Methods and materials

Peat from four sources was treated:-

Source:

Biogreen Australia

Type of Peat:

Australian Peat

Rainbow Park Nurseries

Canadian Peat Moss (sphagnum moss)

Scotts Australia PTY

Shamrock Peat

Transplant Systems Ltd

Kekkila Oji Finnish peat

1. Dry hot air

A grain drier was modified for the purposes of this experiment. Air was blown over heated coils to produce the hot air. This heated air was chanelled through a chamber connected to three containers which contained peat samples. The air circulated around the containers and heated the peat. The temperature wass controlled by a thermostat and could operate from 0o to 120oC.

Peat samples were placed in the centre of metal mesh containers (150mm x 150mm x 150mm, approx 75gm per sample). One container was used and the experiment was repeated three times for each run. In the first experiment, peat was heated at 85oC for 12 hours. In the second experiment, peat was heated at 100oC for 6 hours. One untreated control was used for each dry hot air treatment.

2. Envirosol fumigation

A stainless steel container (92L) with inlet and outlet valves was used in this experiment. Peat samples in metal mesh containers, (150mm x 150mm x 150mm, approx 75g each) were placed in the centre of a container. Fumigas 300 was injected into the container through an inlet valve. Two rates and durations of fumigation were tested. In the first experiment 3 seconds @ 5.56gm/sec application of Fumigas 300 using a pressurised gun for 8 hours was used and in the second experiment 6 seconds @ 5.56gm/sec application for 8 hours was used. One untreated control was used for each fumigation treatment. The experiment was repeated three times for each rate.

3. Steam

A Thermaqua steam boiler was used to generate steam. Steam generated was connected to a 60 x 40 cm stainless steel container (approx 40 litres) with a high-temperature hose. Peat products were placed in the centre of the container. Steam temperature generated was about 75-850C and this could be maintained for up to 12 hours. Treatments of 4 hr and 6 hr were tested.

Plating of the treated peat:

Samples of the treated peat were taken, diluted (5x dilutions) in water and the dilutions were then plated onto nutrient agar plates to test for bacteria. For fungi, 2x dilutions were plated onto PDA. The colonies formed were counted after 3, 5 and 7 days of incubation at 22oC. Three plates (3 replications) were used for each peat sample.

Outcomes:

The three sterilisation treatments (Envirosol fumigation, steam and dry hot air) had significantly better killing of bacteria and fungi compared to the untreated control. In general, fumigation was the most effective treatment among the three sterilisation technologies tested. Steam treatment was the second most effective followed by the dry hot air treatment.

Summary:

Three sterilisation treatments (Envirosol fumigation, steam and dry hot air) were applied to four peat products (Biogreen, Canadian, Kekkila and Shamrock) to test their effect on micro-organisms and pests in the products. All three sterilisation treatments killed significantly more bacteria and fungi than the untreated control. In general, Envirosol fumigation with Fumigas 300 (3 sec injection for 8h) was the most effective treatment. Steam treatment (100oC for 6h) was the second most effective followed by the dry hot air (85oC for 12h) treatment. Considering the standard errors, the fumigation and steam treatments may have equal effectiveness. In general, fumigation and steam treatments were equally effective for sterilising fungi in the peat products. Dry hot air was not as effective, but it was better than the untreated control treatment. All three treatments tested killed all mites and nematodes.

2.2 MBS 331

Programme Title:

Fungi heat tolerances

Programme Leader:

Dr Geoff Ridley

Institution:

Forest Research CRI

SUMMARY

To provide data on the heat tolerance and lethality of fungi in wood to establish effective heat treatment regimes for fungi on wood products imported into New Zealand.

BACKGROUND

Currently MAF treats imported wood products contaminated by fungi by heating to 70oC for 4 hours (core temperature; MAF 2003). However, a new international standard for solid wood products suggests using 56oC for 30 minutes as an alternative treatment (FAO 2002). This is a pragmatic choice "chosen in consideration of the wide range of pests for which this combination is documented to be lethal and a commercially feasible treatment". In actuality this treatment is derived from a study to eradicate pine wood nematode, Bursaphelenchus xylophilus, from pine wood. Surprisingly, there is little in the way of published results on temperatures that kill individual fungal species.Where data do exist they are almost exclusively involved in sterilising materials; that is, the total destruction of all living microorganisms within the material being treated. Such treatment of wood products has the potential to be very destructive to them and unnecessary if the target microorganisms can be eliminated at a low temperature.

APPROACH & OUTCOMES

Wood blocks were infested with selected fungi and subjected to a range of temperatures and exposure times. The fungi tested were: Armillaria novae-zealandia, Botryodiplodia theobromae, Cladosporium herbarum, Fusarium circinatum, Ophiostoma novo-ulmi, Phellinus weirii, Phlebiopsis gigantea, Phytophthora cinnamomi, Schizophyllum commune and Sphaeropsis sapinea.

Summary:

The temperatures and exposure times necessary to eliminate fungi in wood were determined for Cladosporium herbarum, Phytophthora cinnamomi, Phellinus weirii, Phlebiopsis gigantea, Sphaeropsis sapinea, Botryodiplodia theobromae, Armillaria novae-zelandiae, Ophiostoma novo-ulmi, Fusarium circinatum, and Schizophyllum commune. In comparing in vitro and in vivo treatments, heat tolerance increase when Phlebiopsis gigantean, Sphaeropsis sapinea, Botryodiplodia theobromae, Ophiostoma novo-ulmi, and Fusarium circinatum are grown in wood. Tolerance to heat exposure declined for Phellinus weirii and Armillaria novae-zelandiae, and remained constant for Cladosporium herbarum and Phytophthora cinnamomi. Over time and subject to desiccation, heat tolerance declined for Phytophthora cinnamomi and Ophiostoma novo-ulmi, but increased for Cladosporium herbarum. Given the variation in temperatures and times necessary to kill this small subset of species tested, 40-70ºC for 10-40 minutes, a broad treatment standard is recommended. In most cases where imported products require treatment the infesting fungi will be unknown, tentatively identified or even misidentified, and likely to be in an unknown physiological state. In such cases a broad approach to treatment is recommended. MAF's current approach to treatment of moderately high temperature and long exposure time is therefore recommended.

2.3 MBS 332

Programme Title:

Modeling forest health

Programme Leader:

Tod Ramsfield

Institution:

Forest Research CRI

SUMMARY

The overall goal of the programme is to determine how well the Carter Model allocates pest detection survey effort in creating an effective forest health surveillance scheme, and to identify improvements to the model or possible alternative models. Existing costs and probabilities, factors that determine regional risk, and the marginal costing approach will be critically examined. The potential to include different survey methods will be explored.

BACKGROUND

Context of the project: Because of the threat posed by exotic organisms (i.e., insects and pathogens) to New Zealand’s forests, surveys are conducted to detect such organisms. The primary aim of these surveys is early detection as this allows a wider suite of eradication or management options to be considered. Surveys are conducted in indigenous forests, at hazard sites (see Hosking et al. 1999) and in commercial forests. Commercial forestry in New Zealand is dominated by exotic species, mainly radiata pine (Pinus radiata D. Don), which have been introduced to the country without most of their naturally associated pests and diseases. Survey effort to detect new pests and diseases in exotic forests is allocated using the Carter Model (Carter, 1989). This model determines the most cost-efficient combination of survey methods (aerial survey, drive-through survey and random-point plotting) for each of the 29 biological regions of New Zealand defined by Crosby et al. (1975). The aim of the Carter Model is to achieve the highest probability of detecting a new introduction for a given cost.

APPROACH & OUTCOMES

This report reviews the existing forest surveillance model as the first stage of the development of a model that will ultimately enable those responsible for biosecurity in New Zealand to make informed decisions on where surveillance effort should be placed. This critical review is comprised of three parts:

1. The existing costs and detection probabilities are thoroughly reviewed, along with the factors used to estimate regional risk.

2. The model is examined in detail to determine if the marginal costing approach is appropriate.

3. The potential for other surveillance methods – for example risk site surveys, beetle trapping, and small-block surveys – to be included in a surveillance model framework is examined.

Outcomes:

Detection probabilities were investigated by updating the records of new-to-New Zealand introductions that were originally presented in Carter (1989). The average annual number of new insects and fungi detected increased from 4.471 between 1950 and 1987 to 6.126 between 1988 and 2003. However, the number of new insect detections decreased from 2.158 per annum between 1950 and 1987 to 1.688 per annum between 1988 and 2003. At the same time the number of new fungus detections increased from 2.313 per annum between 1956 and 1987 to 4.438 per annum between 1988 and 2003. Records of 84 pest species detected between 1988 and 2003 indicate that 54 were found in at least two bioregions. A significant number of organisms were found in bioregions that had a low number of first detections. This indicates the importance of maintaining some level of surveillance in regions that have low numbers of first detections of new-to-New Zealand organisms.

The theoretical and empirical results upon which the probabilities of detecting a new organism using the three different survey methods (aerial, drive-through and walk-though) are based were reviewed. While some minor discrepancies were noted, the relative probabilities of detection across the three survey methods appear reasonable. A hierarchical Bayesian model was used to model the observed rates of first and subsequent detections of new introductions. Rather than using a point estimate of the number of new introductions detected in a bioregion, the Bayesian model optimally combines information from the population of bioregions with information on each individual bioregion. The Bayesian model shows that there is considerable uncertainty in the estimated rates, particularly when these rates are low. Where the detections are low, possibly by chance and a low sampling effort, the Carter model allocates an excessively low sampling effort, hence perpetuating a low number of detections for that region. Further investigation and development of the Bayesian model as a replacement for the Carter model is recommended.

PUBLICATIONS

None to date, but it is envisaged that a manuscript will be submitted to New Zealand Journal of Forestry Science presenting some of the results of this review.

2.4 MBS 333

Programme Title:

Fusarium circinatum

Programme Leader:

Tod Ramsfield

Institution:

Forest Research CRI

SUMMARY

The DNA based diagnostic for F. circinatum that has been developed at Forest Research was initially based on 61 Fusarium isolates that represented 15 different species and was also tested on a further 10 Fusarium species by collaborators within CSIRO. In order to further screen the test, a further 17 Fusarium isolates from 12 different species were ordered from the Landcare Research culture collection. DNA was extracted from these species and subjected to the diagnostic test, and none of the additional cultures gave positive results, further strengthening the robustness of the diagnostic test.

BACKGROUND

Pitch canker, caused by the fungus Fusarium circinatum, is an extremely serious disease of Pinus radiata that is not present in New Zealand but has caused large economic losses in California, Chile, South Africa and Spain, where it has been introduced. In order to maintain the F. circinatu- free status of New Zealand, a DNA based identification tool was developed at Forest Research to enable rapid detection of the pathogen in both culture and infected tissue.

The work conducted with MAF funding was a continuation of work that was initiated at Forest Research under FRST funding.

The detection method utilizes the polymerase chain reaction (PCR) to amplify target DNA that is specific to F. circinatum. The generation of two DNA bands of the correct size represents a positive reaction. The test was initially developed with a population of 167 isolates that represented 35 different Fusarium species and included 30 isolates of F. circinatum. To further screen the specificity of the test, DNA was extracted from 19 isolates of F. circinatum in California and a further 6 isolates of F. circinatum in South Africa. While in South Africa, DNA was also extracted from 10 other isolates that represented the species that are most closely related to F. circinatum. To date testing has revealed 3 isolates of F. circinatum, all from the same vegetative compatibility group (VCG), which were not detected by the test. One isolate out of 127 isolates of species other than F. circinatum gave a positive result. Statistical analysis of the results to date using Bayesian methods indicated that 93.6% of the time the test will correctly identify F. circinatum, isolates, and that 98.8% of the time the test will correctly identify isolates as not F. circinatum.

The test proved its utility in November 2003 when it was used to initially identify F.

circinatum within Douglas fir scion material held in a quarantine greenhouse in Christchurch. After detection, the pathogen was confirmed as F. circinatum by researchers in California and the National Plant Pest Reference Laboratory. Currently, experiments are being conducted to determine if it is possible to utilize the technique to detect the fungus within infected soil. Detection in soil would be a great advantage because it is possible that if the pathogen does arrive in New Zealand, it may be detected first in the nursery, as it was in South Africa and Chile.

APPROACH & OUTCOMES

When the Fusarium DNA was amplified using the multiplex PCR reaction developed previously (Ramsfield, 2004), some isolates produced the 234 base pair (bp) amplification product, but none of the isolates produced the combination of bands that would be classified as a positive reaction (Figure 1, Table 2). The only isolates that resulted in amplification of the 234 bp band were three isolates of F. anthophilum and one isolate of F. sacchari. Both of these species are members of section Liseola and are close relatives of F. circinatum and in a prior study, F. anthophilum was found to cross react with the primer pair that generates the 234 bp band. When the test was being developed, it was found that some of the primer sets that had been designed for F. circinatum also amplified DNA from close relatives, but when the two most specific PCR primer sets were combined, an F. circinatum specific reaction was identified. Only the presence of the 422 bp and 234 bp bands is considered to be a positive reaction and to date; only F. circinatum has produced these results. Other bands produced do not represent the target PCR products and are the result of amplification of non-target DNA by either primer pair or a combination of the PCR primers present in the reaction.

DNA extracted from every test isolate was also subjected to PCR amplification using the RAPD DNA primer UBC123 and PCR products were generated from all samples; therefore, the “negative” reactions that had no PCR products present represented individuals in which the PCR priming sites were absent, not failed reactions due to PCR inhibition or poor quality DNA.

2.5 MBS 336

Programme Title:

Phytoplasmas, viruses & viroids

Programme Leader:

Dr Mike Pearson

Institution:

Auckland Uniservices (Auckland University)

SUMMARY

To review and update records of phytoplasmas, plant viruses and viroids in New Zealand.

BACKGROUND

The species of phytoplasmas, plant viruses and viroids present in New Zealand and their associated host records were last thoroughly reviewed by Pennycook (1989). Although Pennycook (1989) is an important reference for MAF when assessing whether plant pathogens associated with imported commodities should be regulated there are a number of problems associated with using this reference in this way:

1. Pennycook (1989) lists not only well characterized phytoplasmas, viruses and viroids but also entries of less certain status (based on symptomology) and diseases of unknown aetiology. Therefore the validity of each record has to be assessed each time the reference is consulted.

2. There has been no update of Pennycook’s review since it was published. MAF records new phytoplasma, virus and viroid interceptions in its own database (PPIN). However, PPIN is not comprehensive and includes neither the records of Pennycook (1989) nor reports made by other organizations.

3. Changes in taxonomy mean that the status of some species must be reviewed.

MAF is currently forced to consult a wide range of references when determining the status of pathogens in New Zealand. Consequently there is a need for the records reported by Pennycook (1989) and those reported by MAF (PPIN) and in the scientific literature to be reviewed and combined into a definitive database. An accurate knowledge of the plant pathogens in New Zealand is critical to:

1. Plant Imports when determining which species should be regulated

2. Plant Exports when negotiating access for exports of plant commodities

3. Plant Pest Management when deciding responses during incursions of pathogens

Such knowledge is also a fundamental requirement supporting MAF’s obligations under the IPPC and will assist MAF in meeting its obligations under the Biosecurity Act 1993 and Hazardous Substances and New Organisms Act 1996.

APPROACH & OUTCOMES

MAF provided electronic spreadsheets of currently available lists of viruses, viroids, phytoplasmas (Pennycook, PPIN, etc.) plus electronic or hard copies of supporting documentation (journal articles, official reports, etc.).

In consultation with MAF, criteria were determined for inclusion of records in the updated list.

Existing lists were checked to determine whether records meet the agreed criteria, for errors, and for correct taxonomic names.

Additional distribution data and symptoms were added from the supporting literature, where available.

Bioabstracts, CABI, and Web of Science electronic databases, plus additional sources (including CABI Crop Protection Compendium and PPIN) were searched for records published since 1988 and these data were added to the spreadsheet.

The completed list of viruses, viroids, phytoplasmas and spirolplasmas, and their hosts, has been checked by all the main contributors (Mike Pearson, Gerard Clover, John Fletcher, and Paul Guy) and appropriate additions/corrections made.

Outcomes:

An updated and corrected list of viruses, viroids, phytoplasmas and spirolplasmas (see summary for additional details).

Provide an updated reference list collection of references (hard copies).

Summary:

As a result of this project the following the changes have been made to the list originally provided by MAF:

• 35 new virus species or disease records added;

• 21 virus species or viral-like diseases (plus some host records of other viruses) placed in the “unconfirmed” category;

• 1 new viroid species added;

• 3 existing and 2 new viroid records placed in the “unconfirmed” category;

• 5 new mollicute species added;

• 1 mollicute species has been placed in the “unconfirmed” category;

• the number of references has increased from 229 to 441.

For some of the species currently placed in the “unconfirmed” category there is reasonable suspicion that they may present in New Zealand (e.g. Citrus psorosis virus). We recommend that MAF consider which, if any, of these are of particular importance and whether further investigation (e.g. a field survey) is justified.

An edited version of the virus list (containing only virus name, host name, summary of evidence, distribution, and references) has been sent to several other people who work with viruses in New Zealand. They have been asked to look at the viruses they work with and provide comment if they are aware of any omissions. If any further information is obtained from the circulation of this list I will forward it to Gerard Clover.

PUBLICATIONS

A summary of the updated list will be published in a peer-reviewed scientific journal in the near future.

2.6 MBS 337

Programme Title:

Surface decontamination

Programme Leader:

John Fletcher

Institution:

Crop and Food CRI

RESEARCH PROGRAMME NOT YET COMPLETED AND REPORTED AT TIME OF THE PREPARATION OF THIS PUBLICATION. THIS WILL BE REPORTED IN NEXT RESEARCH RESULTS PUBLICATION.

2.7 MBS 339

Programme Title:

Hitchhiker pests

Programme Leader:

Susan Worner

Institution:

Lincoln University

SUMMARY

Goal:

Examine the use of exotic invertebrate interceptions and post-border reports to identify invertebrate hitchhikers of potential concern to indigenous flora and fauna.

BACKGROUND

While there are established methods to characterise biosecurity threats to productive sectors, assessing the risks of organisms such as hitchhiker species, to indigenous flora and fauna is difficult. Hitchhikers are species that are carried by or with a commodity, but are not pests of that commodity. Such species may pose threats to indigenous terrestrial ecosystems and as such their potential impacts should be assessed. The objective of this study was to address this knowledge deficiency and examine existing data to identify invertebrate hitchhikers of potential concern to indigenous flora and fauna.

APPROACH & OUTCOMES

Over 45 international databases were reviewed and species that have demonstrated impacts on indigenous terrestrial ecosystems were identified. Those species were cross referenced with a synthesised MAF database that records interceptions of exotic invertebrate species at the New Zealand border. The cross referencing was carried out to identify highly invasive invertebrates that threaten New Zealand. Impact assessments of selected species on New Zealand’s indigenous flora and fauna were undertaken.

Outcomes:

From the review of relevant listings of internationally known invasive invertebrates, approximately 130 invertebrate species were found to be of significance in this study.

On cross referencing with the MAF interception database, some 40 species and about 30 genera (covering almost 80 species) were found to have been intercepted by MAF inspectors. Approximately 120 of the original 130 species have not been intercepted at New Zealand’s border. The database was also sorted to create a list of the most intercepted species. In consultation with MAF, 12 invasive invertebrate species were selected for further assessment. Detailed analysis was carried out on each of these 12 species to assess their potential impacts on New Zealand’s indigenous flora and fauna.

Information gaps in MAF’s interception database were determined and recommendations were made to improve data quality. The species identified for detailed impact assessments were:

1. Asian gypsy moth (Lymantria dispar)

2. Cotton or melon aphid (Aphis gossypii)

3. Cockerell scale (Pseudaulacaspis cockerelli)

4. Fijian cane root grub (Adoretus versutus)

5. Cape honeybee (Apis mellifera capensis)

6. Fall webworm (Hyphantria cunea)

7. Red imported fire ant (Solenopsis invicta)

8. Japanese beetle (Popillia japonica)

9. Giant African snail (Achatina fulica)

10. Western yellow jacket (Vespula pennsylvanica)

11. Badge huntsman spiders (Neosparassus spp).

12. Parasitic wasp (Cirrospilus vittatus)

Summary:

The goal of this project was to examine the use of exotic invertebrate interceptions and post-border reports to identify invertebrate hitchhiker species of potential concern to indigenous flora and fauna. While the impacts of exotic species on productive systems are straightforward to assess, this study was carried out to develop methodology that would help identify exotic hitchhiker species of most threat to New Zealand’s native terrestrial ecosystems.

Over 45 international databases were reviewed and species with demonstrated impacts on indigenous terrestrial ecosystems elsewhere in the world were identified. Those species were cross referenced with a MAF database that records exotic invertebrate interceptions at the New Zealand border to identify highly invasive invertebrates that threaten New Zealand. Detailed assessments of the impact of a number of selected species on New Zealand’s indigenous flora and fauna were then carried out.

Approximately 130 invertebrate species were identified as highly invasive from a review of relevant listings of internationally known invasive species. When these species were cross referenced with the MAF interception database, 40 species and about 30 genera (covering almost 80 species) were found to have been intercepted at New Zealand’s borders. In consultation with MAF, 12 invasive invertebrate species were selected for further assessment and analysis to assess their potential impacts on New Zealand’s indigenous flora and fauna. Information gaps in MAF’s interception database data were determined and recommendations were made to improve data quality to assist future analyses.

2.8 MBS 340

Programme Title:

Bird haemoparasites

Programme Leader:

Richard Jakob-Hoff

Institution:

Auckland Zoo

SUMMARY

This is the final of three reports to determine New Zealand’s capacity to identify and respond to haemoparasites in native and introduced birds. Building on our previous reports – “Status of Avian Haemoparasites in New Zealand” and a “Review of Avian Haemoparasite Diagnostic Techniques”, this report details the findings of two surveys:

1) a national survey of wildlife veterinarians and medical and veterinary laboratories designed to establish New Zealand’s current diagnostic capability and capacity gaps;and

2) an international survey aimed at locating the diagnostic expertise and techniques currently missing in this country.

BACKGROUND

Of 112 people surveyed nationally, 60 (54%) returned their questionnaires: 30 from the medical diagnostic community, 18 from veterinary pathology and laboratory diagnosticians and 12 from wildlife veterinarians. Key findings were:

• Only 9 people had direct personal experience in the identification of avian haemoparasites - and the type and extent of experience varied considerably.

• All laboratories involved in screening avian blood reported a low case load and a very low number of positive diagnoses.

• Human medical laboratory personnel also reported a generally low case load but compensated by establishing a number of diagnostic reference centres and maintaining active quality control and continuing education programs targeted at haemoparasite identification.

• There was some overlap in the haemoparasites of interest to both veterinary and medical diagnosticians and a desire by several of the latter to increase their knowledge of animal parasites.

• Blood smear examination under the light microscope was still the primary method of diagnosis although some serology and PCR was also used for human malaria.

• Twenty six respondents from around the country agreed to have their names, contact details and experience included in a Register of Haemoparasite Diagnostic Expertise for access by biosecurity authorities.

The seven overseas people surveyed revealed that, between them, they covered the expertise and diagnostic techniques currently lacking in New Zealand. Services offered included assistance with diagnosis, training to up-skill New Zealand diagnosticians and access to libraries of avian haemoparasite slides and other reference materials. This included access to the International Reference Centre for Avian Haematozoa held at Queensland Museum in Brisbane.

APPROACH & OUTCOMES

Based on their research, the authors suggest baseline requirements for the maintenance of a national avian haemoparasite diagnostic capability that will enable rapid, accurate identification of any such parasite of concern to New Zealand. Key recommendations, provided under the four headings of Diagnostic Expertise, Diagnostic Laboratories, Information Storage and Retrieval and Organisational Support, are:

• Initially import overseas expertise to up-skill local diagnosticians in a training workshop

• Establish one or two centres of avian haematology expertise

• Establish one or two reference laboratories to develop the biotechnological tests required to avoid delays from shipping biological samples overseas

• Obtain the biological specimens required to validate the serological and molecular diagnostic tests

• Develop the existing “Parabase” and “Takahe” wildlife disease surveillance databases as web-based resources with linkages to other related or relevant databases

• Establish a New Zealand Reference Centre for Avian Haematozoa

• Harness the interest and existing organisational infra-structure of the human diagnostic community by suggesting to the New Zealand Institute of Medical Laboratory Science the establishment of a Comparative Haematology Special Interest Group. This could draw on the individuals on the Register of Haemoparasites Diagnostic Expertise for initial membership

• Ensure adequate long-term fiscal commitment by central government to establish and maintain the diagnostic and organisational infrastructure described above

Noting that no systematic surveillance of avian haemoparasites has occurred in New Zealand for over 50 years, the authors also recommend that a nationally co-ordinated, systematic surveillance program should be implemented as soon as possible and should target both host and vector species.

2.9 MBS 343

Programme Title:

Nucleic acid extraction

Programme Leader:

Dr Gail Timmerman-Vaughan

Institution:

Crop & Food Research

GOAL:

The goal of this programme is to develop nucleic acid extraction protocols and quality control assays to underpin the use of polymerase chain reaction (PCR) and RT-PCR (reverse transcription PCR) assays to detect pathogens in the diverse plants that are imported into or grown in New Zealand.

BACKGROUND

Molecular diagnostic methods, particularly those based on sequence detection using PCR, have tremendous potential to determine the presence of plant pathogens. The research in this programme will permit the increased use of nucleic acid-based diagnostic tests for plant pathogens to supplement and complement existing conventional methods. This programme builds on research conducted at Crop & Food Research on genomes of a wide variety of plants, on development of PCR-based diagnostics and on research on the molecular detection of plant pathogens.

APPROACH & OUTCOMES

Plant pathogens have genetic material that consists of either DNA (e.g. fungi, bacteria and some viruses) or RNA (RNA plant viruses, viroids). Therefore, the extraction of RNA and/or DNA of adequate quality and quantity for PCR-based detection systems is a prerequisite for their detection. The range of plant species that is of interest for pathogen detection is very broad, and technical challenges to nucleic acid extraction can arise as a result of the composition of plant tissues, particularly for polysaccharides, phenolics and other secondary metabolites. We have assessed methods for extracting total nucleic acids (T-NA) that contain both DNA and RNA, and for extracting RNA, for members of 32 diverse flowering plant families, represented by more than 57 genera. We have also developed a positive control assay for PCR and RT-PCR based on a conserved chloroplast sequence. The utility of this positive control assay has been demonstrated for both T-NA and RNA extractions derived from this list of diverse plant genera.

Outcomes:

The research in this programme has been successful in developing methods for extracting T-NA and RNA from a diverse range of plant species. T-NA has been extracted from members of 32 diverse botanical families using one of three different methods, and the suitability of these T-NA extractions for use in PCR-based diagnostics has been demonstrated with a number of quality control assessments. RNA has been extracted from the same diverse range of plants using one of two methods, and the quality and quantity of the RNA extracted has been characterised.

Difficulties in obtaining good quality nucleic acid extractions were encountered for some plant genera within the Proteaceae, Rosaceae, Ericaceae, Onagraceae, Theaceae, Myrtaceae, Labiatae, Pittosporaceae and Geraniaceae. These difficulties were largely overcome by applying other extraction methods that operate on different principles. In some cases, however, suitable quality extractions were never obtained (e.g. for vireya Rhododendron, while azalea type Rhododendron was extracted successfully). A positive control assay that is universally applicable across the angiosperms (and possibly across wider botanical groupings) was developed, and applied in both PCR and RT-PCR to characterise the quality of the nucleic acid extraction methods. While development of PCR assays for T-NA and RT-PCR assays for RNA extractions was straightforward, considerable optimisation was undertaken to attempt to develop RT-PCR assays that reliably amplify the processed RNA transcript sequences from T-NA. A particularly valuable characteristic of the quality control assay we have developed is that different sized products are produced from genomic DNA versus processed RNA transcripts, enabling T-NA and RNA extracts to be assessed in order to determine whether they contain RNA and/or DNA.

Summary:

Molecular detection of nucleic acid sequences to determine the presence of pathogens in plant materials has the advantage of being quick, sensitive, and applicable to difficult problems. It also complements conventional pathogen detection methods. The research in this programme has developed nucleic acid extraction protocols and a positive control PCR assay that can underpin DNA and RNA sequence-based pathogen detection in the wide range of plants that are imported into or grown in New Zealand. A number of methods to isolate T-NA and RNA have been applied in order to overcome the technical barriers to nucleic acid extraction that can be encountered in plant species, such as the presence of polysaccharides, phenolics and other secondary metabolites. The positive control PCR assay has been developed and optimal conditions established for amplifying PCR products from T-NA and RT-PCR products from RNA. A Laboratory Manual for the use of molecular diagnostic laboratories has been produced.

PUBLICATIONS

Timmerman-Vaughan, G.M., Pither-Joyce, M. and Clover, G.R.G. (2004). A positive-control PCR assay based on chloroplast ndhB sequences that is applicable to nucleic acid extractions from diverse plant taxa. Plant Molecular Biology Reporter (accepted for publication).

2.10 MBS 344

Programme Title:

Generic detection of Viruses – part 2

Programme Leader:

Dr Mike Pearson

Institution:

Auckland University

SUMMARY

To develop a PCR detection system using broad-spectrum or “universal” primers for plant viruses of quarantine importance to NZ.

BACKGROUND

Primers designed to sequences of conserved regions within a virus genome 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. In some cases these primers work well but in other cases they may not be reliable enough for routine diagnostic work.

Improved primers will assist in detecting viruses of quarantine importance and discriminating between those and 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 Substances and New Organisms Act 1996.

APPROACH & OUTCOMES

Literature was checked for published primers for the virus groups of interest.

All relevant sequences were downloaded from GenBank and alignments were made for individual genes. Published primer sequences were checked to determine whether they could be optimized. Relevant viral sequences were analysed to determine whether there were alternative conserved regions and if so new primers were designed. Where consensus sequences could not be identified for all sequences within a genus the possibility of using several primer sets combined in a multiplex PCR was considered. Existing and new primers were tested against representative viruses from the genus of interest.

Outcomes:

Potential primers have been designed for the following virus genera: Closterovirus, Crinivirus, Ampelovirus, Nepovirus, Fabavirus, Luteovirus, Polerivirus, Enamovirus, Tospovirus, Tobamovirus Tobravirus.

Following preliminary testing the following primers show the greatest promise and should be further evaluated: Luteovirus, Polerivirus, Enamovirus, Tospovirus, Tobravirus

Summary:

Table 1. Summary of plant virus primer work 2002-2004

Virus Genus

1o Lit search

Lit eval

Sequ align

Primer design

Primer test

Comments

Closterovirus

X

X

X

X

X

Initial evaluation not promising but primers retested in phase 2 using modifications suggested by Dovas et al., 2003

Crinivirus

X

X

X

X

X

Ampelovirus

X

X

X

X

X

Nepovirus

X

X

X

X

X

1st design priority for phase 2

Fabavirus

X

X

X

X

X

1st design priority for phase 2

Luteovirus

X

X

X

X

X

 

Polerovirus

X

X

X

X

X

 

Enamovirus

X

X

X

X

X

 

Begomovirus

X

       

3rd design priority for phase 2

Tospovirus

X

X

X

X

X

To be completed in phase 2

Furovirus

X

X

X

     

Pecluvirus

X

X

X

     

Pomovirus

X

X

X

     

Potexvirus

X

         

Tobamovirus

X

X

X

X

X

2nd design priority for phase 2

Tobravirus

X

X

X

X

X

To be completed in phase 2

X = completed IP = in progress X highlight = phase 2 of project

PUBLICATIONS

The results of the work on tobraviruses, tospoviruses and luteoviriuses will be published in a peer-reviewed scientific journal, but some additional optimization work will be required before this can be done. Preliminary discussions with Gerard Clover (MAF BA) have been held regarding this and we have agreed to start with the tobraviruses.

2.11 MBS 345

Programme Title:

Veterinary sentinel project (03/04)

Programme Leader:

Dr Lachlan McIntyre

Institution:

Massey University

SUMMARY

VetPAD is a term coined for both Veterinary Practitioner Animal Disease surveillance, and software developed to make this surveillance workable in practice. This report discusses the progress made in developing the VetPAD software, adjusting it to ensure it is suitable for use in a veterinary practitioner disease surveillance network, and trialling it in a number of practices. In MAF project MBS-327 (Use of veterinary practices to define baseline patterns of animal disease for national animal health surveillance), it was shown that when compared with either farmer or laboratory-based surveillance systems

• veterinary practitioners have very high rates of on-farm contact with dairy clients;

• the range of disease syndromes seen provides a suitable spectrum for a clinical surveillance strategy; and

• veterinary practitioners had the best opportunity for rec