The Global Virome in One Network (VIRION): an atlas of vertebrate-virus associations
The Global Virome in One Network (VIRION): an atlas of vertebrate-virus associations
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全球病毒组一体化网络 (VIRION)：脊椎动物病毒关联图谱
DOI：
10.1101/2021.08.06.455442
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Carlson C
中科院分区：
文献类型：
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作者：
Carlson C
编目地球上病毒多样性的数据在来源、学科、格式和不同程度的开放共享方面已经支离破碎，给宏观生态学、进化和公共卫生研究带来了挑战。在这里，我们通过建立一个动态维护的脊椎动物-病毒关联数据库来解决这个问题，这个数据库被称为“全球病毒网络”（VIRION）。通过对静态数据集的协调和对动态更新数据库的集成，构建了VIRION数据库。这些数据源都针对一个分类学主干进行协调，包括关于宿主和病毒分类学有效性和更高分类的元数据；关于抽样方法和证据强度的其他元数据也以统一格式提供。总的来说，VIRION数据库是同类数据库中最大的开源开放访问数据库，拥有大约50万条独特记录，包括9521种已确定的病毒“物种”（其中1661种已获得ICTV批准），3692种已确定的脊椎动物宿主物种，以及23147种在分类上有效的生物之间独特的相互作用。总的来说，这些数据涵盖了大约四分之一的哺乳动物多样性，十分之一的鸟类多样性和估计的脊椎动物总多样性的6%，以及比以往任何数据库都大得多的病毒组比例。我们展示了如何使用这些数据来测试关于微生物学，生态学和进化的假设，并为解决这些数据中共存的独特证据组合的最佳实践提出建议。动物和它们的病毒是通过一个庞大的、错综复杂的物种相互作用的网络联系在一起的。主机-病毒网络上的数据可从多个来源获得，这些来源使用不同的命名约定，通常以不同的详细程度报告元数据。VIRION是一个新的数据库，它结合了这些现有的数据源，将分类法统一到一个统一的主干，并以病毒学家设计和为病毒学家设计的格式报告元数据。研究人员可以使用VIRION轻松回答诸如“任何鱼类病毒都能感染人类吗？”或“哪种蝙蝠携带冠状病毒？”之类的问题，或者建立更先进的预测模型，使其朝着全面了解全球病毒库迈出了前所未有的一步。
Data that catalogue viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open sharing, posing challenges for research on macroecology, evolution, and public health. Here, we solve this problem by establishing a dynamically maintained database of vertebrate-virus associations, called The Global Virome in One Network (VIRION). The VIRION database has been assembled through both reconciliation of static data sets and integration of dynamically updated databases. These data sources are all harmonized against one taxonomic backbone, including metadata on host and virus taxonomic validity and higher classification; additional metadata on sampling methodology and evidence strength are also available in a harmonized format. In total, the VIRION database is the largest open-source, open-access database of its kind, with roughly half a million unique records that include 9,521 resolved virus “species” (of which 1,661 are ICTV ratified), 3,692 resolved vertebrate host species, and 23,147 unique interactions between taxonomically valid organisms. Together, these data cover roughly a quarter of mammal diversity, a 10th of bird diversity, and ∼6% of the estimated total diversity of vertebrates, and a much larger proportion of their virome than any previous database. We show how these data can be used to test hypotheses about microbiology, ecology, and evolution and make suggestions for best practices that address the unique mix of evidence that coexists in these data.IMPORTANCEAnimals and their viruses are connected by a sprawling, tangled network of species interactions. Data on the host-virus network are available from several sources, which use different naming conventions and often report metadata in different levels of detail. VIRION is a new database that combines several of these existing data sources, reconciles taxonomy to a single consistent backbone, and reports metadata in a format designed by and for virologists. Researchers can use VIRION to easily answer questions like “Can any fish viruses infect humans?” or “Which bats host coronaviruses?” or to build more advanced predictive models, making it an unprecedented step toward a full inventory of the global virome.