BII-Design: Exploring the ecology and evolution of the global virome with big data and machine learning

这一设计活动将产生一个创建生物整合研究所的提案，该研究所将综合野生动物病毒学的最新进展，并寻求关于全球病毒组生态学和进化的新见解。SARS-CoV-2的大流行只是野生动物中危险病毒加速出现趋势的最新进展。全球旅行、城市化以及人类与野生动物接触的增加都使这些病毒更容易出现。未来，气候变化和土地利用变化将进一步重组全球病毒群，迫使哺乳动物跨越大陆，在新的生态系统中相遇，并以数千倍的频率交换病毒，这可能会对全球健康造成更多威胁。这些哺乳动物病毒中至少有10,000种可能感染人类，但全球大多数病毒组仍未被描述：仅发现了约1%的哺乳动物病毒，而其他脊椎动物病毒的比例要小得多。由于数据如此之少，很难预测哪些病毒将在未来构成威胁，或者它们将在何时、何地以及如何出现。预测下一次大流行威胁将需要跨越生物尺度的新数据，从单基因到深度进化时间，以及来自计算机科学和数学前沿的新统计方法。此外，该项目将为受训者举办暑期实习，并开发新的课程，将生物学与动手计算机科学实验室结合起来。该项目汇集了一群病毒学家、计算机科学家、统计学家和生态学家，探讨有关方法、推论和影响的前沿科学问题。该项目有三个目标：(1)综合所有脊椎动物分支的宿主-病毒关联的现有数据；(2)开发新的方法来预测宿主-病毒相互作用网络，使用新的数据流，如基因组特征的病毒株多样性，或来自免疫学研究的受体数据；(3)制定可操作的科学框架，将病毒生态学用于全球卫生科学和安全。这些目标将通过合作讲习班来实现。这样做将为全面执行关于建立新发病毒研究所的建议奠定基础。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This Design activity will result in a proposal to create a Biology Integration Institute that will synthesize recent advances in wildlife virology and pursue new insights about the ecology and evolution of the global virome. The pandemic emergence of SARS-CoV-2 is only the latest development in an accelerating trend of dangerous viruses emerging from wildlife. Global travel, urbanization, and increasing human-wildlife contact have all made it easier for these viruses to emerge. In the future, climate change and land use change will reassemble the global virome even further, forcing mammals to cross continents, meet in new ecosystems, and exchange viruses thousands of times more, potentially unleashing even more threats to global health. At least 10,000 of these mammal viruses might have the potential to infect humans, but most of the global virome is still undescribed: only about 1% of mammal viruses have been discovered, and a much smaller fraction in other vertebrates. With so little data, it is difficult to predict which viruses will pose a future threat, or where, when, and how they could emerge. Predicting the next pandemic threat will require new data spanning biological scales, from single genes up to deep evolutionary time, and new statistical methods from the cutting edge of computer science and mathematics. In addition, the project will host summer residencies for trainees and develope new coursework that combines biology with hands-on computer science labs.The project assembles a group of virologists, computer scientists, statisticians, and ecologists to explore cutting edge scientific questions about methodology, inference, and impact. The project has three aims: (1) synthesizing existing data about host-virus associations for all vertebrate clades; (2) developing novel approaches to predict host-virus interaction networks, using novel data streams like viral strain diversity characterized from genomes, or receptor data from immunological studies; and (3) developing frameworks for actionable science that will put viral ecology to use for global health science and security. These aims will be accomplished through collaborative workshops. In doing so it will establish a foundation for a full Implementation proposal to develop an Emerging Virus Institute.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.