Title: 5 challenges in understanding the role of the virome in health and disease
David Wang
March 26, 2020
在微生物組研究中，相比於細菌及真菌的相關研究，目前對病毒組的研究相對滯後。PLoS Pathogens上發表的一篇評論觀點，列舉了病毒組研究面臨的5大挑戰，並討論了潛在的應對策略，展望了病毒組研究的未來發展方向。
第一，不同於細菌的16S rRNA及真菌的ITS，病毒缺少通用序列，因此難以鑑定出所有的病毒；
第二，不適當的採樣方式可能導致分析結果更偏向於DNA病毒，而忽略了RNA病毒；
第三，雖然宏基因組分析促進了對病毒序列的檢測與鑑定，但因缺少培養系統，難以對病毒進行分離以研究其與疾病的因果關聯；
第四，缺少合適的實驗動物感染模型用於研究病毒感染；
第五，真菌病毒與噬菌體之間存在的差異使這兩個領域的研究相對分離而獨立。
與疾病的因果分析是最嚴峻的挑戰，還有一些病毒組學固有的挑戰。
As was the case then, the most critical challenge ahead is defining whether the virome plays a causal role in the associated diseases. In addition, there are additional, unique challenges inherent to virome analysis that render it less tractable than the bacterial microbiome.
Inability to identify all viruses due to the absence of a universal viral sequence: The challenge of viral “dark matter”
第一，不同於細菌的16S rRNA及真菌的ITS，病毒缺少通用序列，因此難以鑑定出所有的病毒；
機器學習方法可以用於計算暗物質
To computationally address the dark matter, new and improved data mining strategies are needed. One approach is to apply methods superior at detection of remote homologies, such as hidden Markov models customized for viral proteins [10]. Other machine learning strategies may include development of primary sequence-alignment–independent classification approaches [11] or development of artificial neural networks [12].
擴大可培養病毒的範圍
The dark matter clearly harbors hidden treasures because mining of the dark matter has led to discoveries such as crAssphage, the most abundant bacteriophage in human enteric viromes [9].
Inadequate sampling strategies bias towards DNA viruses and against RNA viruses
第二，不適當的採樣方式可能導致分析結果更偏向於DNA病毒，而忽略了RNA病毒；
僅對DNA測序的偏向已成爲一種自我增強的正反饋迴路。
the bias of sequencing exclusively DNA has served as a self-reinforcing positive feedback loop
最近的研究檢查了對RNA測序的樣本的研究表明，世界上RNA噬菌體的丰度和多樣性要高得多[13]。因此，爲了更全面地瞭解病毒，設計病毒研究以使RNA病毒保留在標本中以及將RNA片段納入測序和分析至關重要。
however, recent studies examining samples that have sequenced RNA have demonstrated that there is a much greater abundance and diversity of RNA phages in the world [13]. Thus, in order achieve a more complete view of the virome, it is critical that virome studies be designed such that RNA viruses are preserved in the specimens and that the RNA fraction is incorporated into the sequencing and analysis.
Lack of culture systems to propagate components of the virome
第三，雖然宏基因組分析促進了對病毒序列的檢測與鑑定，但因缺少培養系統，難以對病毒進行分離以研究其與疾病的因果關聯；
宏基因組學的出現大大增強了我們以無偏見的方式檢測已知和新型病毒序列以及建立這些序列與各種疾病的新型關聯的能力[1-7]。
The advent of metagenomics has greatly enhanced our ability to detect known and novel viral sequences in unbiased fashion and to establish novel associations of these sequences with various disease [1–7].
鑑於缺乏培養病毒的能力可能是該病毒研究進展的最根本障礙，因此絕對有必要爲開發培養系統而付出努力。
Nonetheless, given that the lack of ability to culture a virus is perhaps the most fundamental barrier to progress in the study of that virus, dedicated efforts to develop culture systems are absolutely necessary.
The need for experimental animal-infection models
第四，缺少合適的實驗動物感染模型用於研究病毒感染；
總體而言，必須花費大量的精力和資源來建立適合定義病毒作用的穩健的動物感染模型。爲了使病毒學研究超出單純的關聯研究領域，這是絕對必要的步驟。
Overall, significant effort and resources must be expended to establish robust animal-infection models suitable to define the role of the virome. This is a step that is absolutely necessary in order to move virome studies beyond the realm of mere association studies.
Dichotomy between eukaryotic virus and phage communities
第五，真菌病毒與噬菌體之間存在的差異使這兩個領域的研究相對分離而獨立。
需要多背景科學家聯合將噬菌體，細菌，真核病毒和真核細胞連接在一起
Thus, there is a great need to bring these disparate communities together in order to collectively attack questions associated with the virome, especially as more complex trans-kingdom interactions are identified linking phages, bacteria, eukaryotic viruses, and eukaryotic cells.
In conclusion, the coming years will undoubtedly be witness to many more studies demonstrating associations of the virome with various diseases. Hopefully, there will be commensurate development of new computational approaches that significantly decrease the fraction of viral dark matter and an increase in the fraction of studies that holistically evaluate the virome. With new cell-culture systems and animal models for novel viruses, there will ideally be studies that attribute causal roles for some of the associations. Finally, it may be that virome studies will serve as a catalyst to help integrate the eukaryotic viral and phage communities.