ViruSurf

ViruSurf is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database offers a subset of these functionalities. Given the current pandemic outbreak, SARS-CoV-2 data are collected from the four sources; but ViruSurf contains other virus species harmful to humans, including SARS-CoV, MERS-CoV, Ebola, and Dengue. The database is centered on sequences, described from their biological, technological, and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences. Several example queries on the database confirm and possibly improve results from recent research papers; results can be recomputed over time and upon selected populations. Effective search over large and curated sequence data may enable faster responses to future threats that could arise from new viruses.ViruSurf是一款大型公开病毒序列数据库，整合了来自多源异构数据源（RefSeq、GenBank、COG-UK及NMDC）的元数据并完成了整理（curated）；该数据库还提供基于原始序列调用得到的经计算核苷酸与氨基酸变异数据。针对GISAID的专属ViruSurf数据库仅提供上述部分功能。鉴于当前新冠疫情大流行，研究人员从上述四大数据源收集了SARS-CoV-2相关数据；但ViruSurf数据库同时收录了其他多种对人类致病的病毒，包括SARS-CoV、MERS-CoV、埃博拉（Ebola）及登革病毒（Dengue）。该数据库以病毒序列为核心，从生物学、技术与组织三个维度对序列进行描述；此外，分析维度则通过注释信息与变异特征对序列进行刻画。其网页界面支持以简洁方式构建复杂搜索查询，用户可自由组合来自上述四个维度的属性条件来搭建任意查询，从而提取目标序列。数据库内置的若干示例查询可验证并可能优化近期学术论文的研究结果；同时支持基于选定的种群与时间维度重新计算查询结果。对大规模经整理（curated）的序列数据开展高效检索，或可帮助人类更快应对未来新型病毒可能引发的公共卫生威胁。

搜集汇总

背景与挑战

背景概述

ViruSurf是一个大型公共数据库，整合了来自RefSeq、GenBank等多个来源的病毒序列及其经过整理的元数据，并计算了核苷酸和氨基酸变异。该数据库不仅包含SARS-CoV-2数据，还涵盖SARS-CoV、MERS-CoV等多种对人类有害的病毒物种。其核心围绕序列的四个维度（生物、技术、组织、分析）进行描述，并通过网页界面支持复杂查询，以促进对病毒威胁的快速响应研究。