Laboratory of Virology, Wageningen University, Wageningen, The Netherlands.
PLoS One. 2010 Oct 14;5(10):e13400. doi: 10.1371/journal.pone.0013400.
White 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 FINDINGS: We 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/SIGNIFICANCE: The 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.
白斑综合征病毒（WSSV）是新型尼马病毒科的唯一成员，也是虾类养殖中主要经济问题的根源。自 20 世纪 90 年代初首次报告爆发以来，WSSV 似乎已在全球范围内迅速传播。WSSV 基因组中的两个位点（ORF14/15 和 ORF23/24 可变区）发生了各种大小的基因组缺失，这些缺失已被用作研究病毒在空间和时间上传播模式的分子标记。我们使用经验数据和简单的数学模型描述了 WSSV 基因组缩小的过程。
方法/主要发现：我们对来自五个亚洲国家的新 WSSV 分离株进行了基因分型，并结合已发表的数据对此进行了分析。基因组大小似乎随着时间的推移而稳定，ORF23/24 可变区的缺失大小与特定国家首次 WSSV 爆发的时间显著相关。从拟合基因组缩小的简单数学模型到数据中得出的参数估计值支持基因组缺失的几何级数（k<1），其中 k = 0.371 ± 0.150。
结论/意义：数据表明，在衰减之前，基因组缩小的速度随时间降低。生物测定数据为在水产养殖环境中基因组大小与 WSSV 适应性之间的联系提供了支持。地理 WSSV 分离株之间的基因组缺失差异表明，WSSV 的传播并没有遵循地理辐射的平滑模式，这表明 WSSV 通过商业活动在长距离上传播。我们讨论了基因组缩小的两种假说，适应性和中性假说。鉴于有证据表明 WSSV 基因组大小与适应性之间存在联系，我们支持适应性假说。
