1887

Journal of General Virology header logo

Volume 91, Issue 5

Evaluation of white spot syndrome virus variable DNA loci as molecular markers of virus spread at intermediate spatiotemporal scales Free

Abstract

Variable genomic loci have been employed in a number of molecular epidemiology studies of white spot syndrome virus (WSSV), but it is unknown which loci are suitable molecular markers for determining WSSV spread on different spatiotemporal scales. Although previous work suggests that multiple introductions of WSSV occurred in central Vietnam, it is largely uncertain how WSSV was introduced and subsequently spread. Here, we evaluate five variable WSSV DNA loci as markers of virus spread on an intermediate (i.e. regional) scale, and develop a detailed and statistically supported model for the spread of WSSV. The genotypes of 17 WSSV isolates from along the coast of Vietnam – nine of which were newly characterized in this study – were analysed to obtain sufficient samples on an intermediate scale and to allow statistical analysis. Only the ORF23/24 variable region is an appropriate marker on this scale, as geographically proximate isolates show similar deletion sizes. The ORF14/15 variable region and variable-number tandem repeat (VNTR) loci are not useful as markers on this scale. ORF14/15 may be suitable for studying larger spatiotemporal scales, whereas VNTR loci are probably suitable for smaller scales. For ORF23/24, there is a clear pattern in the spatial distribution of WSSV: the smallest genomic deletions are found in central Vietnam, and larger deletions are found in the south and the north. WSSV genomic deletions tend to increase over time with virus spread in cultured shrimp, and our data are therefore congruent with the hypothesis that WSSV was introduced in central Vietnam and then radiated out.

  • Received:
  • Accepted:
  • Published Online:
© SGM
Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.018028-0
2010-05-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/jgv/91/5/1164.html?itemId=/content/journal/jgv/10.1099/vir.0.018028-0&mimeType=html&fmt=ahah

References

  1. Bewick, V., Cheek, L. & Ball, J.(2004). Statistics review 10: further nonparametric methods. Crit Care 8, 196–199.[CrossRef] [Google Scholar]
  2. Corsin, F., Turnbull, J. F., Hao, N. V., Mohan, C. V., Phi, T. T., Phuoc, L. H., Tinh, N. T. N. & Morgan, K. L.(2001). Risk factors associated with white spot syndrome virus infection in a Vietnamese rice-shrimp farming system. Dis Aquat Organ 47, 1–12.[CrossRef] [Google Scholar]
  3. Corsin, F., Phi, T. T., Phuoc, L. H., Tinh, N. T. N., Hao, N. V., Mohan, C. V., Turnbull, J. F. & Morgan, K. L.(2002). Problems and solutions with the design and execution of an epidemiological study of white spot disease in black tiger shrimp (Penaeus monodon) in Vietnam. Prev Vet Med 53, 117–132.[CrossRef] [Google Scholar]
  4. Davis, C. L., Field, D., Metzgar, D., Saiz, R., Morin, P. A., Smith, I. L., Spector, S. A. & Wills, C.(1999). Numerous length polymorphisms at short tandem repeats in human cytomegalovirus. J Virol 73, 6265–6270. [Google Scholar]
  5. Dieu, B. T. M., Marks, H., Siebenga, J., Goldbach, R., Zuidema, D., Duong, T. P. & Vlak, J. M.(2004). Molecular epidemiology of white spot syndrome virus within Vietnam. J Gen Virol 85, 3607–3618.[CrossRef] [Google Scholar]
  6. Eda, H. & Ozawa, S., The Cooperation Group for HSV-1 RFLP Variant StudyYoshino, K. & Yanagi, K.(2007). Contrasting geographic distribution profiles of the herpes simplex virus type 1 BgOL and BgKL variants in Japan suggest dispersion and replacement. J Clin Microbiol 45, 771–782.[CrossRef] [Google Scholar]
  7. Eyer-Silva, W. A. & Morgado, M. G.(2006). Molecular epidemiology of HIV-1 infection in a small Brazilian county. Usefulness of envelope and polymerase sequences to epidemiologic studies. J Acquir Immune Defic Syndr 41, 664–670.[CrossRef] [Google Scholar]
  8. Flegel, T. W.(1997). Major viral disease of the black tiger prawn (Penaeus monodon) in Thailand. World J Microbiol Biotechnol 13, 433–442.[CrossRef] [Google Scholar]
  9. Gouvea, V., Hoke, C., Jr & Innis, B. L.(1998). Genotyping of hepatitis E virus in clinical specimens by restriction endonuclease analysis. J Virol Methods 70, 71–78.[CrossRef] [Google Scholar]
  10. Greiser-Wilke, I., Fritzemeier, J., Koenen, F., Vanderhallen, H., Rutili, D., Mia, G. M. D., Romero, L., Rosell, R., Sanchez-Vizcaino, J. M. & Gabrie, A. S.(2000). Molecular epidemiology of a large classical swine fever epidemic in the European Union in 1997–1998. Vet Microbiol 77, 17–27.[CrossRef] [Google Scholar]
  11. Hamano, M., Maeda, K., Kai, K., Mochizuki, M., Tohya, Y. & Akashi, H.(2005). A novel genetic marker to differentiate feline herpesvirus type 1 field isolates. Vet Microbiol 106, 195–200.[CrossRef] [Google Scholar]
  12. Hoa, T. T. T., Hodgson, R. A. J., Oanh, D. T. H., Phuong, N. T., Preston, N. J. & Walker, P. J.(2005). Genotypic variations in tandem repeat DNA segments between ribonucleotide reductase subunit genes of white spot syndrome virus (WSSV) isolates from Vietnam. In Diseases in Asian Aquaculture V, pp. 339–351. Edited by P. J. Walker, R. G. Lester & M. G. Bondad-Reantaso. Manila, the Philippines: Fish Health Section, Asian Fisheries Society.
  13. Kang, H. H. & Lu, C. P.(2007). Comparison of variable region genes of shrimp white spot syndrome virus (WSSV) in different areas in China. Bing Du Xue Bao 23, 490–493 (in Chinese). [Google Scholar]
  14. Kiatpathomchai, W., Taweetungtragoon, A., Jittivadhana, K., Wongteerasupaya, C., Boonsaeng, V. & Flegel, T. W.(2005). Target for standard Thai PCR assay identical in 12 white spot syndrome virus (WSSV) types that differ in DNA multiple repeat length. J Virol Methods 130, 79–82.[CrossRef] [Google Scholar]
  15. Lan, Y., Lu, W. & Xu, X.(2002). Genomic instability of prawn white spot bacilliform virus (WSBV) and its association to virus virulence. Virus Res 90, 269–274.[CrossRef] [Google Scholar]
  16. Lo, C.-F., Ho, C.-H., Peng, S.-E., Chen, C.-H., Hsu, H.-C., Chiu, Y.-L., Chang, C.-F., Liu, K.-F., Su, M.-S. & other authors(1996a). White spot syndrome baculovirus (WSBV) detected in cultured and captured shrimp, crabs and other arthropods. Dis Aquat Organ 27, 215–225.[CrossRef] [Google Scholar]
  17. Lo, C.-F., Leu, J.-H., Ho, C.-H., Chen, C.-H., Peng, S.-E., Chen, Y.-T., Chou, C.-M., Yeh, P.-Y., Huang, C.-J. & other authors(1996b). Detection of baculovirus associated with white spot syndrome (WSBV) in penaeid shrimps using polymerase chain reaction. Dis Aquat Organ 25, 133–141.[CrossRef] [Google Scholar]
  18. Lo, C.-F., Hsu, H.-C., Tsai, M.-F., Ho, C.-H., Peng, S.-E., Kou, G.-H. & Lightner, D.-V.(1999). Specific genomic DNA fragment analysis of different geographical clinical samples of shrimp white spot syndrome virus. Dis Aquat Organ 35, 175–185.[CrossRef] [Google Scholar]
  19. Marks, H., Goldbach, R. W., Vlak, J. M. & van Hulten, M. C. W.(2004). Genetic variation among isolates of White spot syndrome virus. Arch Virol 149, 673–697.[CrossRef] [Google Scholar]
  20. Marks, H., van Duijse, J. J. A., Zuidema, D., van Hulten, M. C. W. & Vlak, J. M.(2005). Fitness and virulence of an ancestral white spot syndrome virus isolate from shrimp. Virus Res 110, 9–20.[CrossRef] [Google Scholar]
  21. MOFI(2001).Annual Report of Fisheries Production in 2000 and Action Plan for the Year 2001 (in Vietnamese). Hanoi, Vietnam: Ministry of Fisheries.
  22. Moon, C. H., Do, J. W., Cha, S. J., Yoon, W. J., Kim, S. B., Ko, M. S., Park, M. A., Kim, J. W., Sohn, S. K. & other authors(2003). Highly conserved sequences of three major virion proteins of a Korean isolate of white spot syndrome virus (WSSV). Dis Aquat Organ 53, 11–13.[CrossRef] [Google Scholar]
  23. Musthaq, S. S., Sudhakaran, R., Ahmed, V. P. I., Balasubramanian, G. & Sahul Hameed, A. S.(2006). Variability in the tandem repetitive DNA sequences of white spot syndrome virus (WSSV) genome and suitability of VP28 gene to detect different isolates of WSSV from India. Aquaculture 256, 34–41.[CrossRef] [Google Scholar]
  24. Nadala, E. C. B. & Loh, P. C.(1998). A comparative study of three different isolates of white spot virus. Dis Aquat Organ 33, 231–234.[CrossRef] [Google Scholar]
  25. Nguyen, V. H.(2008). Vietnam's catfish and marine shrimp production: an example of growth and sustainability issues. Panorama Acuicola Magazine 13, 46–55. http://www.panoramaacuicola.com/ediciones/pam_13-3/46-55.pdf. [Google Scholar]
  26. Pradeep, B., Shekar, M., Gudkovs, N., Karunasagar, I. & Karunasagar, I.(2008a). Genotyping of white spot syndrome virus prevalent in shrimp farms of India. Dis Aquat Organ 78, 189–198.[CrossRef] [Google Scholar]
  27. Pradeep, B., Shekar, M., Karunasagar, I. & Karunasagar, I.(2008b). Characterization of variable genomic regions of Indian white spot syndrome virus. Virology 376, 24–30.[CrossRef] [Google Scholar]
  28. Pradeep, B., Karunasagar, I. & Karunasagar, I.(2009). Fitness and virulence of different strains of white spot syndrome virus. J Fish Dis 32, 801–805.[CrossRef] [Google Scholar]
  29. Sammels, L. M., Lindsay, M. D., Poidinger, M., Coelen, R. J. & Mackenzie, J. S.(1999). Geographic distribution and evolution of Sindbis virus in Australia. J Gen Virol 80, 739–748. [Google Scholar]
  30. Sokal, R. R. & Rohlf, F. J.(1995).Biometry: the Principles and Practice of Statistics in Biological Research. New York: W. H. Freeman.
  31. Tan, Y., Xing, Y., Zhang, H., Feng, Y., Zhou, Y. & Shi, Z. L.(2009). Molecular detection of three shrimp viruses and genetic variation of white spot syndrome virus in Hainan Province, China, in 2007. J Fish Dis 32, 777–784.[CrossRef] [Google Scholar]
  32. Uzcategui, N. Y., Camacho, D., Comach, G., Cuello de Uzcategui, R., Holmes, E. C. & Gould, E. A.(2001). Molecular epidemiology of dengue type 2 virus in Venezuela: evidence for in situ virus evolution and recombination. J Gen Virol 82, 2945–2953. [Google Scholar]
  33. van Hulten, M. C. W., Witteveldt, J., Peters, S., Kloosterboer, N., Tarchini, R., Fiers, M., Sandbrink, H., Lankhorst, R. K. & Vlak, J. M.(2001). The white spot syndrome virus DNA genome sequence. Virology 286, 7–22.[CrossRef] [Google Scholar]
  34. Vlak, J. M., Bonami, J. R., Flegel, T. W., Kou, G. H., Lightner, D. V., Lo, C. F., Loh, P. C. & Walker, P. W.(2005). Family Nimaviridae. In Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses, pp. 187–192. Edited by C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger & L. A. Ball. San Diego, CA:Elsevier Academic Press.
  35. Waikhom, G., John, K. R., George, M. R. & Jeyaseelan, M. J. P.(2006). Differential host passaging alters pathogenicity and induces genomic variation in white spot syndrome virus. Aquaculture 261, 54–63.[CrossRef] [Google Scholar]
  36. Wald, A. & Wolfowitz, J.(1940). On a test whether two samples are from the same population. Ann Math Stat 11, 147–162.[CrossRef] [Google Scholar]
  37. Wang, C.-H., Lo, C.-F., Leu, J.-H., Chou, C.-M., Yeh, P.-Y., Chou, H.-Y., Tung, M.-C., Chang, C.-F., Su, M.-S. & Kou, G.-H.(1995). Purification and genomic analysis of baculovirus associated with white spot syndrome (WSBV) of Penaeus monodon. Dis Aquat Organ 23, 239–242.[CrossRef] [Google Scholar]
  38. Wang, Y. T., Liu, W., Seah, J. N., Lam, C. S., Xiang, J. H., Korzh, V. & Kwang, J.(2002). White spot syndrome virus (WSSV) infects specific hemocytes of the shrimp Penaeus merguiensis. Dis Aquat Organ 52, 249–259.[CrossRef] [Google Scholar]
  39. Yang, F., He, J., Lin, X., Li, Q., Pan, D., Zhang, X. & Xu, X.(2001). Complete genome sequence of the shrimp white spot bacilliform virus. J Virol 75, 11811–11820.[CrossRef] [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.018028-0
Loading
Evaluation of white spot syndrome virus variable DNA loci as molecular markers of virus spread at intermediate spatiotemporal scales
J. Gen. Virol. 91, 1164 (2010); https://doi.org/10.1099/vir.0.018028-0
/content/journal/jgv/10.1099/vir.0.018028-0
/content/journal/jgv/10.1099/vir.0.018028-0
Loading

Data & Media loading...

Supplements

vol. , part 5, pp. 1164–1172

Primers used in PCR analysis for the variable loci of WSSV [ PDF] (70 KB)

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error