Scale drop disease virus (SDDV) is a novel viral pathogen considered to be distributed in farmed barramundi (Lates calcarifer) in South‐East Asia. Despite the severity of the disease, only limited genomic information related to SDDV is available. In this study, samples of SDDV‐infected fish collected in 2019 were used. The microbiome of brain tissue was investigated using Illumina HiSeq DNA sequencing. Taxonomic analysis showed that SDDV was the main pathogen contained in the affected barramundi. De novo metagenome assembly recovered the SDDV genome, named isolate TH2019, 131 kb in length, and comprised of 135 ORFs. Comparison between this genome and the Singaporean SDDV reference genome revealed that the nucleotide identity within the aligned region was 99.97%. Missense, frameshift, insertion and deletion mutations were identified in 26 ORFs. Deletion of four deduced amino acid sequence in ORF_030L, identical to the SDDV isolate previously identified in Thailand, would be a potential biomarker for future strain classification. Interestingly, the genome of SDDV TH2019 harboured a unique 7,695‐bp‐long genomic region containing six hypothetical protein‐encoded genes. Collectively, this study demonstrated that the SDDV genome can be sequenced directly, although with limited coverage depth, using metagenomic analysis of barramundi sample with severe infection.

中文翻译：

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从感染的金枪鱼，Lates calcarifer（Bloch，1790）的巨基因组研究中检索到的鳞屑病病毒（SDDV）基因组序列草案。

鳞滴病病毒（SDDV）是一种新型病毒病原体，被认为可在养殖的澳洲肺鱼中传播（Lates calcarifer）。尽管疾病严重，但仅可获得与SDDV相关的有限基因组信息。在这项研究中，使用了2019年收集的SDDV感染鱼的样本。使用Illumina HiSeq DNA测序研究了脑组织的微生物组。分类学分析表明，SDDV是受影响的金枪鱼中的主要病原体。从头基因组大会从SDDV基因组中回收了命名为TH2019的分离株，全长131 kb，由135个ORF组成。该基因组与新加坡SDDV参考基因组之间的比较显示，比对区域内的核苷酸同一性为99.97％。在26个ORF中鉴定出错义，移码，插入和缺失突变。删除ORF_030L中的四个推导氨基酸序列，与先前在泰国鉴定出的SDDV分离物相同，将成为未来菌株分类的潜在生物标记。有趣的是，SDDV TH2019的基因组具有一个独特的7695 bp长的基因组区域，其中包含6个假设的蛋白质编码基因。总体而言，该研究表明，使用重度感染的肺鱼样本的宏基因组分析，尽管覆盖深度有限，但SDDV基因组可以直接测序。