Copyright ©The Author(s) 2015. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Virology. Aug 12, 2015; 4(3): 265-276
Published online Aug 12, 2015. doi: 10.5501/wjv.v4.i3.265
Next-generation sequencing in clinical virology: Discovery of new viruses
Sibnarayan Datta, Raghvendra Budhauliya, Bidisha Das, Soumya Chatterjee, Vanlalhmuaka, Vijay Veer
Sibnarayan Datta, Raghvendra Budhauliya, Bidisha Das, Soumya Chatterjee, Vanlalhmuaka, Vijay Veer, Molecular Virology Laboratory, Defence Research Laboratory (DRDO), Tezpur, Assam, PIN-784001, India
Author contributions: Datta S conceptualized and designed the review; Datta S, Budhauliya R and Das B drafted the manuscript; Chatterjee S, Vanlalhmuaka and Veer V edited and critically revised the manuscript.
Supported by The author’s laboratory is supported by the Defence Research and Development Organization (DRDO), Ministry of Defence, Government of India.
Conflict-of-interest statement: The authors declare no conflict of interest related to the submitted manuscript.
Open-Access: This article is an open-access article which was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See:
Correspondence to: Sibnarayan Datta, PhD, Molecular Virology Laboratory, Defence Research Laboratory (DRDO), Post bag No. 2, Tezpur, Assam, PIN-784001, India.
Telephone: +91-3712-258508 Fax: +91-3712-258534
Received: January 24, 2015
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.

Keywords: PCR, Next-generation sequencers, Virus discovery, Sequence-independent single-primer amplification, Virus discovery based on cDNA-AFLP, Rolling circle amplification, Metagenomics

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.