DNA Sequencing for Clinical and Public Health Virology: Some Assembly Required

• Published in: Clinical Virology Manual pp. 173 - 199
• Main Author: Bartkus, Joanne
• Format: Book Chapter
• Language: English
• Published: Washington, DC, USA ASM Press 01.12.2016
• Subjects: clinical virology; data analysis; DNA sequencing technologies; next generation sequencing methodologies; public health virology; quality assurance; sequencing applications; storage strategies
• ISBN: 9781555819149; 1555819141
• DOI: 10.1128/9781555819156.ch15

Recent advances in sequencing technology, coupled with the relatively small genomes of viruses, make routine sequencing of entire genomes in clinical and public health settings increasingly feasible. The first two widely adopted DNA sequencing methodologies described, the chemical cleavage method of Maxam and Gilbert (1) and the chain termination method of Sanger et al., were both published in the 1970s (2, 3). Coincidental to the subject of this chapter, the first full genome to be sequenced by Sanger was that of a virus, albeit a bacteriophage, PhiX 174 (4). The Sanger method proved to be the more durable sequencing technology and, especially after the process was automated in 1996, was the most widely used method for DNA sequencing for more than a decade. Beginning in 2005, however, advances in sequencing technology, the so‐called next generation sequencing (NGS) methodologies, resulted in a dramatic increase in the amount of sequence that can be generated and a concomitant dramatic decrease in the cost of sequencing. These factors have led to the widespread implementation of NGS in place of the Sanger method for typical sequencing applications and also for some novel purposes, for example, replacing microarrays to study gene expression. The increased use of NGS technologies has, not surprisingly, resulted in a rapid increase in the number of sequences submitted to the National Center for Biotechnology Information's (NCBI) Genbank database. In particular, the number of viral sequences submitted since 2012 has increased 22.9% as measured in nucleotide base pairs (5), and the number of publications based on NGS is increasing at an impressively rapid pace (6).