White spot syndrome virus (WSSV) has been one of the most devastating pathogens affecting the global shrimp industry since its initial outbreaks in Asia in the early 1990s. In this study, we recovered 13 complete metagenome-assembled genomes (MAGs) of Japanese WSSV isolates and 30 draft WSSV MAGs recovered from publicly available sequencing data, to investigate the genomic evolution of WSSV. Phylogenetic analysis revealed two major phylotypes, designated phylotypes I and II. Bayesian divergence time estimates placed the divergence time of the two phylotypes between 1970 and the early 1980s, with an estimated substitution rate of 1.1 × 10^–5 substitutions per site per year, implying the existence of pre-pandemic genetic diversity of WSSV in Asia. Based on this scenario, phylotype I was responsible for the 1990s pandemic and spread worldwide, whereas phylotype II was localized in Asia and infiltrated Australia. Two cross-phylotype recombinant lineages were identified, which demonstrate the role of genomic recombination in generating the genetic diversity of WSSV. These results provide important insights into the evolution of WSSV and may help uncover the ultimate origins of this devastating pathogen.

自 20 世纪 90 年代初在亚洲首次爆发以来，白斑综合症病毒 (WSSV) 一直是影响全球虾业最具破坏性的病原体之一。在这项研究中，我们恢复了 13 个日本 WSSV 分离株的完整宏基因组组装基因组 (MAG) 和从公开测序数据中恢复的 30 个 WSSV MAG 草案，以研究 WSSV 的基因组进化。系统发育分析揭示了两种主要的系统发育型，称为系统发育型 I 和 II。贝叶斯分歧时间估计将两种系统型的分歧时间置于1970年至1980年代初之间，估计替代率为1.1 × 10 ^–5每年每个地点的替换次数，表明亚洲存在 WSSV 大流行前的遗传多样性。根据这种情况，系统发育型 I 导致了 20 世纪 90 年代的大流行并在全球范围内传播，而系统发育型 II 则局限于亚洲并渗透到澳大利亚。鉴定出两个跨系统发育型重组谱系，证明了基因组重组在产生 WSSV 遗传多样性中的作用。这些结果为 WSSV 的进化提供了重要的见解，并可能有助于揭示这种毁灭性病原体的最终起源。