Fouret Julien, Brunet Frédéric G, Binet Martin, Aurine Noémie, Enchéry Francois, Croze Séverine, Guinier Marie, Goumaidi Abdelghafar, Preininger Doris, Volff Jean-Nicolas, Bailly-Bechet Marc, Lachuer Joël, Horvat Branka, Legras-Lachuer Catherine
CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France.
Viroscan3D, Trévoux, France.
Front Microbiol. 2020 Jul 29;11:1807. doi: 10.3389/fmicb.2020.01807. eCollection 2020.
Indian fruit bats, flying fox was identified as an asymptomatic natural host of recently emerged Nipah virus, which is known to induce a severe infectious disease in humans. The absence of genome sequence presents an important obstacle for further studies of virus-host interactions and better understanding of mechanisms of zoonotic viral emergence. Generation of the high-quality genome sequence is often linked to a considerable effort associated to elevated costs. Although secondary scaffolding methods have reduced sequencing expenses, they imply the development of new tools for the integration of different data sources to achieve more reliable sequencing results. We initially sequenced the genome using the combination of Illumina paired-end and Nanopore sequencing, with a depth of 57.4x and 6.1x, respectively. Then, we introduced the novel scaff2link software to integrate multiple sources of information for secondary scaffolding, allowing to remove the association with discordant information among two sources. Different quality metrics were next produced to validate the benefits from secondary scaffolding. The genome, assembled by this method, has a length of 1,985 Mb and consists of 33,613 contigs and 16,113 scaffolds with an NG50 of 19 Mb. At least 22.5% of the assembled sequences is covered by interspersed repeats already described in other species and 19,823 coding genes are annotated. Phylogenetic analysis demonstrated the clustering of genome with two other bat species, and , for which genome sequences are currently available. SARS-CoV entry receptor ACE2 sequence of was 82.7% identical with ACE2 of bats, thought to be the natural host of SARS-CoV. Altogether, our results confirm that a lower depth of sequencing is enough to obtain a valuable genome sequence, using secondary scaffolding approaches and demonstrate the benefits of the scaff2link application. The genome sequence is now available to the scientific community to (i) proceed with further genomic analysis of , (ii) to characterize the underlying mechanism allowing Nipah virus maintenance and perpetuation in its bat host, and (iii) to monitor their evolutionary pathways toward a better understanding of bats' ability to control viral infections.
印度果蝠，即狐蝠，被确定为新出现的尼帕病毒的无症状自然宿主，尼帕病毒已知会在人类中引发严重传染病。缺乏基因组序列是进一步研究病毒与宿主相互作用以及更好地理解人畜共患病毒出现机制的一个重要障碍。高质量基因组序列的生成通常与高昂成本相关的大量工作联系在一起。尽管二级支架搭建方法降低了测序成本，但这意味着要开发新工具来整合不同数据源，以获得更可靠的测序结果。我们最初使用Illumina双端测序和纳米孔测序相结合的方法对基因组进行测序，深度分别为57.4倍和6.1倍。然后，我们引入了新颖的scaff2link软件来整合多种信息源进行二级支架搭建，从而能够消除两个数据源之间不一致信息的关联。接下来生成了不同的质量指标来验证二级支架搭建的益处。通过这种方法组装的基因组长度为1985 Mb，由33613个重叠群和16113个支架组成，NG50为19 Mb。至少22.5%的组装序列被其他物种中已描述的散布重复序列覆盖，并且注释了19823个编码基因。系统发育分析表明，该基因组与另外两种目前已有基因组序列的蝙蝠物种聚类在一起。该蝙蝠的SARS-CoV进入受体ACE2序列与被认为是SARS-CoV自然宿主的蝙蝠的ACE2序列有82.7%的同一性。总之，我们的结果证实，使用二级支架搭建方法，较低深度的测序就足以获得有价值的基因组序列，并证明了scaff2link应用的益处。现在科学界可以获得该基因组序列，以便（i）对该蝙蝠进行进一步的基因组分析，（ii）表征尼帕病毒在其蝙蝠宿主中维持和延续的潜在机制，以及（iii）监测它们的进化途径，以便更好地理解蝙蝠控制病毒感染的能力。
