Evolutionary Trajectory of White Spot Syndrome Virus (WSSV) Genome Shrinkage during Spread in Asia

Abstract

BackgroundWhite spot syndrome virus (WSSV) is the sole member of the novel Nimaviridae family, and the source of major economic problems in shrimp aquaculture. WSSV appears to have rapidly spread worldwide after the first reported outbreak in the early 1990s. Genomic deletions of various sizes occur at two loci in the WSSV genome, the ORF14/15 and ORF23/24 variable regions, and these have been used as molecular markers to study patterns of viral spread over space and time. We describe the dynamics underlying the process of WSSV genome shrinkage using empirical data and a simple mathematical model.Methodology/Principal FindingsWe genotyped new WSSV isolates from five Asian countries, and analyzed this information together with published data. Genome size appears to stabilize over time, and deletion size in the ORF23/24 variable region was significantly related to the time of the first WSSV outbreak in a particular country. Parameter estimates derived from fitting a simple mathematical model of genome shrinkage to the data support a geometric progression (k<1) of the genomic deletions, with k = 0.371±0.150.Conclusions/SignificanceThe data suggest that the rate of genome shrinkage decreases over time before attenuating. Bioassay data provided support for a link between genome size and WSSV fitness in an aquaculture setting. Differences in genomic deletions between geographic WSSV isolates suggest that WSSV spread did not follow a smooth pattern of geographic radiation, suggesting spread of WSSV over long distances by commercial activities. We discuss two hypotheses for genome shrinkage, an adaptive and a neutral one. We argue in favor of the adaptive hypothesis, given that there is support for a link between WSSV genome size and fitness.

Establishment of Shrimp Cell Lines: Perception and Orientation

“…The major fall out of the situation is the impediment which it imposes on the isolation of crustacean viruses [15,16,43]. The fact is that the requirement of continuous cell lines is so high to investigate the radiating viral threats to shrimp aquaculture [21,88,93].…”

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

“…By quantifying evolutionary divergence using a simple mathematical model, Zwart et al (2010) deduced that ORF23/24, but not ORF14/15, sequence variation correlates well with when a WSSV isolate was obtained compared to when WSD first emerged in shrimp in Taiwan, and not with geographical distance from Taiwan. The analysis suggested that the WSSV type that emerged in crayfish being farmed in China in 2006 was a descendent or relative of the virus type that emerged in penaeid shrimp farmed in East Asia in the early to mid-1990s.…”

Indel-II region deletion sizes in the white spot syndrome virus genome correlate with shrimp disease outbreaks in southern Vietnam

“…Sequence analyses of these 2 indel regions in other Asian WSSV strains have identified intermediatelength deletions (Dieu et al 2004, Zwart et al 2010. For example, WSSV strains from China contain shorter Indel-II deletions (1168 to 5928 bp) compared with WSSV-TW, while strains from Vietnam contain a medium-length Indel-II deletion (~8539 bp) not yet found in strains examined from other geographic regions (Dieu et al 2004; see also Yang et al 2001, Lan et al 2002, Tan & Shi 2011.Indel-I and Indel-II regions are now being used as molecular markers to study WSSV epidemiology (Dieu et al 2004, Zwart et al 2010, and Indel-II is proving to be particularly useful for examining the spatiotemporal spread of WSSV at regional (Dieu et al 2010) and intercontinental levels (Zwart et al 2010). Data on Indel-II support a hypothesis that all WSSV strains affecting farmed shrimp have a recent common ancestor.…”

“…2011). WSSV genome lengths estimated from analyses of Indel-I and Indel-II lengths suggest that genome shrinkage rates since 1992 are decreasing over time (Zwart et al 2010). While increased Indel-I and Indel-II deletion lengths have been associated with increased WSSV virulence (Marks et al 2005, Zwart et al 2010, an early study reported reduced virulence with increased Indel-II deletion lengths (Lan et al 2002).…”

“…WSSV genome lengths estimated from analyses of Indel-I and Indel-II lengths suggest that genome shrinkage rates since 1992 are decreasing over time (Zwart et al 2010). While increased Indel-I and Indel-II deletion lengths have been associated with increased WSSV virulence (Marks et al 2005, Zwart et al 2010, an early study reported reduced virulence with increased Indel-II deletion lengths (Lan et al 2002).Here we report on a spatiotemporal study examining Indel-I and Indel-II deletion lengths in WSSV strains detected in Penaeus monodon shrimp collected between 2006 and 2009 from different farm types in 2 regions of the Mekong Delta in Vietnam. The data associated increased Indel-II deletion lengths with WSSV disease and thus with higher intensity farming systems from which most diseased shrimp were collected over the study period.…”