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

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 variablenumber 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.

Analysis of variable genomic loci in white spot ­syndrome virus to predict its origins in Procambarus clarkii crayfish farmed in China

“…The isolate 08JS also possessed sequences indicative of it being a close relative of the reference WSSV-TW isolate originating from shrimp farmed in Taiwan in the early 1990s, and isolate 09JS possessed sequences indicative of it being a close relative of the reference WSSV-CN isolate originating from shrimp farmed in China in the early 1990s. Moreover, the hypothesis proposed by Dieu et al (2010) that the WSSV type now common in shrimp farmed in central Vietnam originated from WSSV-CN was supported by sequences determined for the P. clarkii WSSV isolate 09JS. …”

Genotyping WSSV isolates from northwestern Mexican shrimp farms affected by white spot disease outbreaks in 2010-2012

“…Also, a 7-RU haplotype previously found in Vietnam by Dieu et al (2010) had 6 RUs of 45 bp and 1 of 102 bp. In contrast, this study reports a haplotype with 7 RUs, 5 of which are of 45 bp and 2 of which are of 102 bp.…”

“…Most of the epidemiological studies performed with WSSV and these 3 markers are based only on the size of the mini-satellite and are expressed as the number of RUs (Dieu et al 2004, Pradeep et al 2008, Dieu et al 2010, Tan & Shi 2011, Shekar et al 2012, and Mexico is no exception (Galaviz-Silva et al 2009, Gonzalez-Galaviz et al 2013. However, each RU may contain SNPs that are useful for differentiating haplotypes that have the same number of RUs.…”

Oyster mortality

“…Insertions and deletions at microsatellite loci are considered to be caused by replication slippage errors (Davis et al, 1999) and can occur reversibly at high frequency. Therefore, polymorphisms that result from these slippage errors can be valuable as epidemiological markers, keeping in mind that the usable spatiotemporal scale will depend on the frequency of changes (Dieu et al, 2010). The currently known variation of the OsHV-1 microsatellite locus covers a range of 2 to 17 repeats.…”