Published online Aug 12, 2015. doi: 10.5501/wjv.v4.i3.265
Peer-review started: January 27, 2015
First decision: March 6, 2015
Revised: March 23, 2015
Accepted: May 7, 2015
Article in press: May 8, 2015
Published online: August 12, 2015
Viruses are a cause of significant health problem worldwide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of which emerge as outbreaks. In such situations, discovery of novel viruses is utmost important for deciding prevention and treatment strategies. Since last century, a number of different virus discovery methods, based on cell culture inoculation, sequence-independent PCR have been used for identification of a variety of viruses. However, the recent emergence and commercial availability of next-generation sequencers (NGS) has entirely changed the field of virus discovery. These massively parallel sequencing platforms can sequence a mixture of genetic materials from a very heterogeneous mix, with high sensitivity. Moreover, these platforms work in a sequence-independent manner, making them ideal tools for virus discovery. However, for their application in clinics, sample preparation or enrichment is necessary to detect low abundance virus populations. A number of techniques have also been developed for enrichment or viral nucleic acids. In this manuscript, we review the evolution of sequencing; NGS technologies available today as well as widely used virus enrichment technologies. We also discuss the challenges associated with their applications in the clinical virus discovery.
Core tip: Rapid development and commercial availability of next-generation sequencers (NGS) systems have dramatically changed almost every field of biological research, especially microbiology and metagenomics. Different NGS systems have been adapted and used for numerous applications in virology too. These systems are capable of rapidly sequencing and analyzing a complex mixture of nucleic acid templates, in a massively parallel fashion, making them ideal tools for viral metagenomics and discovery. This manuscript reviews the prevailing NGS technologies, their application in virus discovery to serve as a guide for the readers, working in the field of virology, public health and in biothreat mitigation programs.