Microbial Metagenomic Approach Uncovers the First Rabbit Haemorrhagic Disease Virus genome in Sub-Saharan Africa
Microbial Metagenomic Approach Uncovers the First Rabbit Haemorrhagic Disease Virus genome in Sub-Saharan Africa
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微生物宏基因组学方法揭示了撒哈拉以南非洲地区第一个兔出血性疾病病毒基因组
DOI：
10.1101/2020.11.19.390559
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Happi A
中科院分区：
文献类型：
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作者：
Happi A
兔出血性疾病（RHD）导致家兔和野兔的高发病率和死亡率。在这里，我们首次报告了来自撒哈拉以南非洲的家兔体内 Lagovirus GI.2 病毒的基因组特征。我们使用无偏见的微生物宏基因组下一代测序 (mNGS) 方法来诊断导致尼日利亚伊巴丹疑似 RHD 暴发的病原体。对 2 个农场爆发疫情的 5 只兔子的肝脏、脾脏和肺样本进行了分析。 mNGS 揭示了两个农场的一个完整的 RHDV2 基因组和两个部分的 RHDV2 基因组。系统发育分析显示与欧洲的 RHDV2 谱系紧密聚类（与荷兰的 RHDV2 相似性为 98.6%，与德国的 RHDV2 相似性为 99.1% 至 100%），表明潜在的输入。随后，所有样本均通过针对 VP60 基因的 RHDV 病毒特异性 RT-PCR 进行确认，五只兔子样本的预期条带大小为 398 bp。我们的研究结果强调需要加强 RHDV2 的基因组监测，以追踪其起源、了解其多样性并为尼日利亚和撒哈拉以南非洲地区的公共卫生政策提供信息。
Rabbit Haemorrhagic Disease (RHD) causes high morbidity and mortality in rabbits and hares. Here, we report the first genomic characterization of lagovirus GI.2 virus in domestic rabbits from sub-Saharan Africa. We used an unbiased microbial metagenomic Next Generation Sequencing (mNGS) approach to diagnose the pathogen causing the suspected outbreak of RHD in Ibadan, Nigeria. The liver, spleen, and lung samples of five rabbits from an outbreak in 2 farms were analyzed. The mNGS revealed one full and two partial RHDV2 genomes on both farms. Phylogenetic analysis showed close clustering with RHDV2 lineages from Europe (98.6% similarity with RHDV2 in the Netherlands, and 99.1 to 100% identity with RHDV2 in Germany), suggesting potential importation. Subsequently, all the samples were confirmed by RHDV virus-specific RT-PCR targeting the VP60 gene with the expected band size of 398 bp for the five rabbits sampled. Our findings highlight the need for increased genomic surveillance of RHDV2 to track its origin, understand its diversity and to inform public health policy in Nigeria, and Sub-Saharan Africa.