Implementation of Next-Generation Sequencing for Hepatitis B Virus Resistance Testing and Genotyping in a Clinical Microbiology Laboratory

• Published in: Journal of clinical microbiology Vol. 54; no. 1; pp. 127 - 133
• Main Authors: Lowe, Christopher F, Merrick, Linda, Harrigan, P Richard, Mazzulli, Tony, Sherlock, Christopher H, Ritchie, Gordon
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 01.01.2016
• Subjects: Costs and Cost Analysis; DNA, Viral - chemistry; DNA, Viral - genetics; Genotyping Techniques - methods; Hepatitis B virus; Hepatitis B virus - drug effects; Hepatitis B virus - genetics; Hepatitis B virus - isolation & purification; Hepatitis B, Chronic - virology; High-Throughput Nucleotide Sequencing - methods; Humans; Microbial Sensitivity Tests - methods; Mutation; Polymerase Chain Reaction; Reproducibility of Results; Virology
• ISSN: 0095-1137; 1098-660X
• DOI: 10.1128/jcm.02229-15

Sanger sequencing or DNA hybridization have been the primary modalities for hepatitis B (HBV) resistance testing and genotyping; however, there are limitations, such as low sensitivity and the inability to detect novel mutations. Next-generation sequencing (NGS) for HBV can overcome these limitations, but there is limited guidance for clinical microbiology laboratories to validate this novel technology. In this study, we describe an approach to implementing deep pyrosequencing for HBV resistance testing and genotyping in a clinical virology laboratory. A nested PCR targeting the pol region of HBV (codons 143 to 281) was developed, and the PCR product was sequenced by the 454 Junior (Roche). Interpretation was performed by ABL TherapyEdge based on European Association for the Study of the Liver (EASL) guidelines. Previously characterized HBV samples by INNO-LiPA (LiPA) were compared to NGS with discordant results arbitrated by Sanger sequencing. Genotyping of 105 distinct samples revealed a concordance of 95.2% (100/105), with Sanger sequencing confirming the NGS result. Resistance testing by NGS was concordant with LiPA in 85% (68/80) of previously characterized samples. Additional mutations were found in 8 samples, which related to the identification of low-level mutant subpopulations present at <10% (6/8). To balance the costs of testing for the validation study, reproducibility of the NGS was investigated through an analysis of sequence variants at loci not associated with resistance in a single patient sample. Our validation approach attempts to balance costs with efficient data acquisition.