基因组学技术在病毒鉴定与宿主溯源中的应用

基因组学技术, 特别是宏基因组测序在未知病毒的鉴定与溯源中起到了重要作用。相较于传统的病毒分离培养方法, 宏基因组技术可以从混合样本中获得病毒的核酸序列, 极大加速了未知病毒的鉴定与溯源, 在针对高流行性、高致病性的病毒研究中发挥了重要作用。基于宏基因组技术对未知病毒进行鉴定和溯源, 其准确性很大程度上依赖于取样及已知宿主的病毒库的完整性。然而, 当前病毒多样性的基础研究相对薄弱, 病毒的宿主信息则更加匮乏。野生动物和畜禽是人畜共患病致病病毒的重要中间宿主, 构建广泛的动物-病毒关联数据库对于准确、快速地鉴定和预防致病性病毒具有重要意义。本综述以SARS-CoV-2为例, 总结了基因组学技术在病毒的鉴定与溯源上的应用, 并针对当前动物病毒库完整性低的现状, 对构建野生和家养动物携带病毒的关联数据库的可行性提出依据与建议。

Verification of virus identity and host association using genomics technology

Genomics technology, especially metagenomic sequencing, has played an important role in identifying and tracing unknown viruses. While classical methods in virus taxonomy rely on phenotypic traits, the metagenomics pipeline assembles new virus genomes from short nucleotide fragments without the need for any a priori reference sequences. This new technology increases the efficiency in identifying viruses and hosts associated with those viruses. This is particularly useful in identifying viruses that can cause epidemics. One current challenge in accomplishing this, is the ability to trace the original and intermediate viral hosts. To do this, a comprehensive virus sequence library characterized by definite host information is needed. Unfortunately, such information is still limited. As wild and stock animals are main sources for pathogenic viruses, an extensive survey of the global virome is vitally important to help identify and prevent zoonotic epidemics. This review summarizes the application of genomics technologies in the identification of viruses and the hosts associated with those viruses, using the outbreak of SARS-CoV-2 as an example. We also address intrinsic drawbacks of current methodologies as well as the incompleteness of available virus libraries. We propose the necessity and feasibility in constructing a comprehensive virus database with host association that emphasizes the diversity of viruses and their interactions with other organisms.