Ramamurthy Mageshbabu, Sankar Sathish, Kannangai Rajesh, Nandagopal Balaji, Sridharan Gopalan
Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, Tamil Nadu 632 055 India.
Department of Clinical Virology, Christian Medical College and Hospital, Vellore, Tamil Nadu 632 004 India.
Virusdisease. 2017 Dec;28(4):349-359. doi: 10.1007/s13337-017-0415-3. Epub 2017 Dec 5.
This review is focused at exploring the strengths of modern technology driven data compiled in the areas of virus gene sequencing, virus protein structures and their implication to viral diagnosis and therapy. The information for virome analysis (viromics) is generated by the study of viral genomes (entire nucleotide sequence) and viral genes (coding for protein). Presently, the study of viral infectious diseases in terms of etiopathogenesis and development of newer therapeutics is undergoing rapid changes. Currently, viromics relies on deep sequencing, next generation sequencing (NGS) data and public domain databases like GenBank and unique virus specific databases. Two commonly used NGS platforms: Illumina and Ion Torrent, recommend maximum fragment lengths of about 300 and 400 nucleotides for analysis respectively. Direct detection of viruses in clinical samples is now evolving using these methods. Presently, there are a considerable number of good treatment options for HBV/HIV/HCV. These viruses however show development of drug resistance. The drug susceptibility regions of the genomes are sequenced and the prediction of drug resistance is now possible from 3 public domains available on the web. This has been made possible through advances in the technology with the advent of high throughput sequencing and meta-analysis through sophisticated and easy to use software and the use of high speed computers for bioinformatics. More recently NGS technology has been improved with single-molecule real-time sequencing. Here complete long reads can be obtained with less error overcoming a limitation of the NGS which is inherently prone to software anomalies that arise in the hands of personnel without adequate training. The development in understanding the viruses in terms of their genome, pathobiology, transcriptomics and molecular epidemiology constitutes viromics. It could be stated that these developments will bring about radical changes and advancement especially in the field of antiviral therapy and diagnostic virology.
本综述聚焦于探索现代技术驱动的数据在病毒基因测序、病毒蛋白结构及其对病毒诊断和治疗的意义等领域的优势。病毒组分析（病毒组学）的信息是通过对病毒基因组（完整核苷酸序列）和病毒基因（编码蛋白质）的研究产生的。目前，在病毒感染性疾病的病因发病机制和新型治疗方法的开发方面正在经历快速变革。目前，病毒组学依赖于深度测序、下一代测序（NGS）数据以及诸如GenBank等公共领域数据库和独特的病毒特异性数据库。两种常用的NGS平台：Illumina和Ion Torrent，分别推荐用于分析的最大片段长度约为300和400个核苷酸。现在正在使用这些方法改进临床样本中病毒的直接检测。目前，对于乙肝病毒/艾滋病毒/丙肝病毒有相当多不错的治疗选择。然而，这些病毒显示出耐药性的发展。对基因组的药物敏感性区域进行测序，现在可以从网上可用的3个公共领域预测耐药性。随着高通量测序的出现以及通过复杂且易于使用的软件进行荟萃分析，并使用高速计算机进行生物信息学分析，技术的进步使这成为可能。最近，NGS技术通过单分子实时测序得到了改进。在这里，可以获得完整的长读段且错误较少，克服了NGS的一个局限性，即NGS在没有经过充分培训的人员手中固有地容易出现软件异常。在病毒的基因组、病理生物学、转录组学和分子流行病学方面的认识发展构成了病毒组学。可以说，这些发展将带来根本性的变化和进步，特别是在抗病毒治疗和诊断病毒学领域。
