Global distribution of white spot syndrome virus genotypes determined using a novel genotyping assay

J Oakey,K Beattie,M Afsharnasab,D Underwood,S Sivakumar,V Alday-Sanz,C Smith,A Crook,A S Sahul Hameed,A Dhar

doi:10.1007/s00705-019-04265-2

Abstract

White spot disease, caused by infection with white spot syndrome virus (WSSV), is a serious panzootic affecting prawn aquaculture. The disease has spread rapidly around the prawn-culturing regions of the world through a number of previously identified mechanisms. The ability to distinguish and trace strains of WSSV is of great benefit to identify, and then limit, the translocation routes of the disease. Here, we describe a novel genotyping method using 34 short tandem repeat regions of the viral genome concurrently. This technique is highly sensitive to strain differences when compared to previous methods. The efficacy of the described method is demonstrated by testing WSSV isolates from around the globe, showing regional genotypic differences. The differences in the genotypes were used to create a global minimum spanning network, and in most cases the observed relationships were substantiated with verification of transboundary movement. This novel panel of STR markers will provide a valuable epidemiological tool for white spot disease. We have applied this to an outbreak of the disease in Queensland, Australia, that occurred in 2016. While the results indicate that the source of this outbreak currently remains cryptic, the analyses have provided valuable insights with which to further study the origins of the strains involved.

Highlights

White spot disease (WSD) is a serious panzootic affecting prawn aquaculture
Notional size ranges for the loci were estimated up to a 30-base increase or decrease compared to the alleles observed in white spot syndrome virus (WSSV)-AU, and hypothetical fragments were analysed in Multiplex Manager [26] to design a 4-dye multiplexed analysis protocol with as few reactions as possible while avoiding primer cross-reactivity or overlapping of fragments labelled with same dye, and using common primer annealing temperatures
The sensitivity of the genotyping was determined to be equivalent to the diagnostic PCR; STR fragments were generated from samples that had diagnostic PCR Ct values as high as 38 when tested by Biosecurity Sciences Laboratory (BSL), the larger fragments were not always observed in samples with Cts above 35

Summary

Introduction

White spot disease (WSD) is a serious panzootic affecting prawn aquaculture. The disease is caused by white spot syndrome virus (WSSV), a large double-stranded circular DNAHandling Editor: Chan-Shing Lin.The first reports of white spot disease in penaeids were in mainland China and Taiwan in 1992 [2, 5, 6]. White spot disease (WSD) is a serious panzootic affecting prawn aquaculture. The disease is caused by white spot syndrome virus (WSSV), a large double-stranded circular DNA. By the end of the decade, the disease had spread to Korea [7], Japan [8, 9], and throughout South-East Asia (Vietnam, Thailand, Malaysia, Indonesia) and India [10, 11]. This rapid proliferation of the disease was most likely through transboundary movement of infected animals. WSSV was found in wild prawns in retrospective analysis by in situ hybridisation of histology samples from Ecuador from 1996, prior to disease reported in 1999 [13].

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Conclusion