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On the Epidemiology and Evolution of White Spot Syndrome Virus of Shrimp

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On the Epidemiology and Evolution of White Spot Syndrome Virus of Shrimp On the epidemiology and evolution of white spot syndrome virus of shrimp Bui Thi Minh Dieu Thesis committee Thesis supervisor Prof.dr. J.M. Vlak Personal Chair at the Laboratory of Virology Wageningen University Thesis co-supervisor Dr. M.P. Zwart Postdoctoral Fellow Laboratory of Quantitative Veterinary Ecology Wageningen University Other members Prof.dr. J.A.J. Verreth, Wageningen University Prof.dr. P. Sorgeloos, Ghent University, Belgium Prof.dr. H.J. Nauwinck, Ghent University, Belgium Dr. L. Hemerik, Wageningen University This research was conducted under the auspices of the Graduate School of Production Ecology and Resource Conservation. On the epidemiology and evolution of white spot syndrome virus of shrimp Bui Thi Minh Dieu Thesis submitted in fulfillment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof.dr. M.J. Kropff in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Tuesday 1 June 2010 at 1.30 pm in the Aula Bui Th.M.D. Whispovirus epidemiology and evolution 142 pages Thesis, Wageningen University, Wageningen, NL (2010) With references, with summaries in Dutch, English and Vietnamese ISBN 978-90-8570-564-2 Abstract White Spot Syndrome Virus (WSSV) causes a devastating disease in shrimp aquaculture that has spread worldwide and probably increased in virulence over time. Understanding WSSV epidemiology and evolution is therefore important for developing novel intervention and management strategies. Both of these goals require finding suitable molecular markers to identify and discriminate WSSV strains, and hereby help infer their origin and track their spread. Five major variable WSSV genomic loci were evaluated as markers for virus identification and virus spread on different spatiotemporal scales. In this thesis the genetic variation between WSSV isolates from the key shrimp production regions in Vietnam was analyzed. A statistically supported model of spread suggests that multiple introductions of WSSV occurred in central Vietnam, and that the virus radiated out over time to the south and the north. Spurious variation was generated during molecular cloning of WSSV VNTR sequences, while no variation occurred in multiple replicates of amplification of VNTRs by Polymerase Chain Reaction. Moreover, VNTR sequences were stable over two passages of infection in vivo , indicating that in vivo cloning can be applied to study heterogeneity within WSSV isolates originating from a single shrimp. Genetic deletion of variable region variants appear to be more stable in extensive farms compare to intensive farms over time, indicating that farm practices affect the evolutionary dynamics of WSSV. Genetic variation between Asian WSSV isolates provides support for evolution of genome size according to a geometric model of adaptation, where incrementally smaller genomic deletions are substituted over time. The relationship between the molecular data and the time of first disease occurrence implies that shrimp transportation played an important role in the quick, long range spread of WSSV. Overall, the thesis results show that WSSV variable loci can be effectively employed as molecular markers to study WSSV spread and evolution on different spatiotemporal scales. However, the markers have different properties and the choice of a suitable marker for a pertinent question is critical. Abstract White spot syndrome virus là y ếu t ố gây b ệnh v ới tác ñộ ng h ủy di ệt ñố i v ới ngh ề nuôi tôm, b ệnh ñã lan truy ền kh ắp th ế gi ới v ới ñộ c tính ngày càng t ăng. Hi ểu v ề d ịch t ễ h ọc và ti ến hóa c ủa WSSV vì v ậy r ất quan tr ọng ñể phát tri ển các chi ến l ược phòng ng ừa và qu ản lý b ệnh. M ục ñích n ầy yêu c ầu xác ñị nh các y ếu t ố ñánh d ấu di truy ền phân t ử ñể xác ñị nh và phân bi ệt các ch ủng WSSV, nh ờ ñó giúp ph ỏng ñoán ñược ngu ồn g ốc và bi ết ñược ñường lan truy ền b ệnh c ủa chúng. Lu ận án n ầy ñã ñánh giá kh ả n ăng thích h ợp làm y ếu t ố ñánh d ấu di truy ền phân t ử cho s ự lan truy ền c ủa virus của năm vị trí bi ến ñổ i di truy ền ch ủ y ếu trong b ộ gen WSSV ở các ph ạm vi không gian và th ời gian khác nhau. Chúng tôi ñã phân tích s ự bi ến ñổ i di truy ền ở các v ị trí gen n ầy gi ữa các ch ủng WSSV t ừ nh ững vùng s ản xu ất tôm ch ủ y ếu c ủa Vi ệt Nam. S ố li ệu nghiên cứu v ới s ự h ổ tr ợ c ủa phân tích th ống kê ñã ñề ngh ị m ột mô hình lan truy ền c ủa virus với nhi ều ñường xâm nh ập ñầ u tiên vào Mi ền Trung Vi ệt Nam và lan truy ền ñế n mi ền Nam và mi ền B ắc. Các ñoạn gen ch ứa các ñơn v ị l ập l ại liên k ề th ể hi ện s ự bi ến ñổ i di truy ền thông qua qui trình t ạo dòng phân t ử nh ưng l ại không bi ến ñổ i trong quá trình nhi ễm qua hai th ế h ệ liên ti ếp của tôm c ũng nh ư qua nhi ều l ần l ập l ại v ới k ỹ thu ật PCR. K ết qu ả n ầy cho th ấy s ự t ạo dòng trên cá th ể s ống có th ể ñược ứng d ụng ñể nghiên c ứu s ự ña d ạng di truy ền trong qu ần th ể c ủa m ột ch ủng WSSV có ngu ồn g ốc t ừ một cá th ể tôm. S ự m ất ñoạn gen c ủa các ch ủng virus ở các ao theo mô hình nuôi qu ảng canh th ể hi ện s ự ổn ñị nh di truy ền qua th ời gian so v ới mô hình nuôi thâm canh. Điều n ầy cho th ấy mô hình nuôi v ới cách qu ản lý khác nhau ñã anh h ưởng ñế n ñộ ng năng ti ến hóa c ủa WSSV. S ự bi ến ñổ i di truy ền gi ữa các ch ủng WSSV t ừ các n ước khác nhau ở Châu Á h ổ tr ợ cho gi ả thi ết là s ự ti ến hóa c ủa kích th ước b ộ gen c ủa virus tuân theo m ột mô hình hình h ọc c ủa s ự thích nghi v ới nh ững s ự m ất ñoạn di truy ền có kích th ước t ăng d ần theo th ời gian. M ối quan h ệ gi ữa d ữ li ệu phân t ử và th ời ñiểm xu ất hi ện b ệnh l ần ñầ u tiên ở các n ước cho th ấy r ằng s ự v ận chuy ển tôm qua giao d ịch th ươ ng m ại ñóng vai trò quan tr ọng trong vi ệc lan truy ền r ộng rãi và nhanh chóng c ủa WSSV. Tóm l ại, k ết qu ả nghiên c ứu c ủa lu ận án cho th ấy r ằng các ñoạn gen bi ến ñổ i có th ể ñược ứng d ụng hi ệu qu ả nh ư nh ững y ếu t ố ñánh d ấu di truy ền ñể nghiên c ứu s ự lan truy ền và ti ến hóa c ủa WSSV. Tuy nhiên các ñoạn gen n ầy v ới các ñặ c ñiểm khác nhau có ñộ h ữu d ụng khác nhau theo các ph ạm vi không gian và th ời gian khác nhau. Vì v ậy s ự l ựa ch ọn y ếu t ố ñánh d ấu di truy ền thích h ợp cho t ừng ph ạm vi là r ất quan tr ọng. Contents Chapter 1 General Introduction 1 Chapter 2 Molecular epidemiology of white spot syndrome virus 19 within Vietnam Chapter 3 Valuation of white spot syndrome virus variable DNA 41 loci as molecular markers of virus spread at intermediate spatiotemporal scales Chapter 4 Can VNTRs be used to study genetic variation within 57 white spot syndrome virus isolates? Chapter 5 Effects of extensive and intensive shrimp farming on the 63 genetic composition of white spot syndrome virus populations Chapter 6 Adaptive trajectory of genome size evolution in an 75 emerging shrimp virus Chapter 7 General Discussion 93 References 101 Summary (English) 119 Samenvatting (Dutch) 122 Summary (Vietnamese) 125 Acknowledgments 128 Curriculum Vitae 131 Publication Account 132 PE&RC PhD Education Statement 133 Chapter 1 General Introduction Shrimp aquaculture Shrimp is one of the most traded seafood products worldwide, occupying about 14% of the total value of fishery products. Shrimp farming is one of the main forms of global shrimp production with an increase in contribution from 6% in 1970 to 69% in 2004 and has become a ‘booming’ business (Rosenberry, 2002; FAO 2006). Shrimp farming provides a major source of income for small farmers and plays a potential role in the poverty alleviation in developing countries including that in small coastal villages (Adger, 1998; Lewis et al ., 2003).
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