Bovine viral diarrhoea virus in New Zealand dairy cattle : a review of diagnostic methodologies and preliminary data on circulating genotypes : a thesis presented in fulfilment of the requirements for the degree of Master of Philosophy in Veterinary Science at Massey University, Manawatu Campus, New Zealand

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Bovine viral diarrhoea (BVD) is a well-established disease in New Zealand beef and dairy cattle that causes significant economic losses for the industries each year. The pathogenesis of the disease is well understood and there is a wide range of reliable diagnostic tools that have allowed many European countries to successfully eradicate BVD through coordinated national disease control programmes. However, it is difficult to directly apply many of these frameworks in New Zealand due to the unique characteries of the pastoral farming systems that create different logistical and epidemiological challenges. There is a strong need to identify the most cost-effective means of applying existing diagnostic tests to design a feasible national control programme for New Zealand. To support this goal, this thesis has focused on filling two existing knowledge gaps: one around the performance of BVD diagnostics tests in herd and industry level disease control programmes and the other around using molecular diagnostic test methods to characterise the circulating bovine viral diarrhoea virus (BVDV) strains in the cattle populations. The last formal literature review on BVD diagnostic tests was published more than 15 years ago and there have been significant advances in the availability and performance of the tests since then. In Chapter 2, a non-systematic review was conducted on the evolution of BVD diagnostic tests over the past 60 years and how they have been applied to different herd and industry level BVD control programmes. The review includes an in-depth overview of key feature in the pathogenesis of BVD that impact test performance followed by detailed descriptions of the different diagnostic methodologies, their performance and their current applications. The discussion section highlights the remaining limitations and technical gaps in the current BVD diagnostic tests along with suggestions for future research directions. In particular, molecular epidemiology has been successfully applied in some countries as a part of their BVD control to understand suspected transmission routes but has not yet been applied in New Zealand. As a preliminary investigation, Chapter 3 was designed to understand current circulating BVDV strains in dairy cattle across New Zealand using a convenience sample virus positive serum samples that were submitted to commercial diagnostic laboratories during the study time period. Both the 5'UTR and NPro genes were sequenced from each sample to identify the strain type and phylogenetic analyses were performed to explore the genetic relatedness of each sequence. Although BVDV 1-A was found as the only subtype circulating among dairy cattle, there was a high variation among the sequences within group 1-A. The phylogenetic analysis showed a fair homogeny of New Zealand dairy isolates with overseas isolates, particularly with BVDV strains previously identified in China. There was also 100% homogeny between the New Zealand dairy isolates and those from cattle that were recently sequenced for another study, which is most likely from the sales of dairy calves into the beef industry for fattening. Several farms were also found to have multiple different phylogenetically distinct BVDV strains, which suggests that they may have been infected from multiple different sources. Molecular sequencing may provide a valuable tool for helping farmers understand the origins of BVDV outbreaks. However, there were some limitations with the sampling and detection methods used. Future research directions were proposed in the discussion including broadening the study into a national survey with adequate representative samples. Finally, Chapter 4 provides a brief discussion of how the findings from this work can be used to assist New Zealand in designing a more cost-effective national BVD control programme.