Application of next-generation sequencing to detect acyclovir-resistant herpes simplex virus type 1 variants at low frequency in thymidine kinase gene of the isolates recovered from patients with hematopoietic stem cell transplantation

Hikaru Fujii; Satsuki Kakiuchi; Masanori Tsuji; Hidekazu Nishimura; Tomoki Yoshikawa; Souichi Yamada; Natsumi Omura; Takuya Inagaki; Miho Shibamura; Shizuko Harada; Shuichi Taniguchi; Masayuki Saijo

doi:10.1016/j.jviromet.2017.10.019

Application of next-generation sequencing to detect acyclovir-resistant herpes simplex virus type 1 variants at low frequency in thymidine kinase gene of the isolates recovered from patients with hematopoietic stem cell transplantation

J Virol Methods. 2018 Jan:251:123-128. doi: 10.1016/j.jviromet.2017.10.019. Epub 2017 Oct 23.

Authors

Affiliations

¹ Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.
² Department of Pediatrics, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
³ Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-8470, Japan.
⁴ Virus Research Center, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Sendai-shi, Miyagi, 983-8520, Japan.
⁵ Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan; Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan.
⁶ Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan; Department of Pediatrics, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
⁷ Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan. Electronic address: msaijo@nih.go.jp.

PMID: 29074089
DOI: 10.1016/j.jviromet.2017.10.019

Abstract

Ion Torrent next-generation sequencing (NGS) technology was applied to study the mode of emergence of acyclovir (ACV)-resistant (ACVr) herpes simplex virus type 1 (HSV-1) in patients with hematopoietic stem cell transplantation (HSCT) by quantitatively detecting mutations in the viral thymidine kinase (vTK) gene in the HSV-1 isolates recovered from HSCT patients. All of the mutations detected with the Sanger sequencing method in the vTK genes of HSV-1 isolates were also detected with the NGS assay. Furthermore, different mutations, which conferred ACV resistance and were not detected with the Sanger sequencing method, were also detected in a quantitative manner by using the NGS assay. The approach described here is applicable to studying the emergence process of vTK gene mutation-associated ACVr HSV-1 more in detail than the Sanger method. The NGS assay makes it possible to make a diagnosis of vTK gene mutation-associated ACVr HSV-1 infections at the early stage, which the ratio of ACVr HSV-1 is much lower than that of ACV-sensitive (ACVs) HSV-1.

Keywords: Acyclovir-resistant; HSV-1; Hematopoietic stem cell transplantation; Ion torrent.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Acyclovir / pharmacology*
Antiviral Agents / pharmacology*
Drug Resistance, Viral*
Genotyping Techniques / methods*
Hematopoietic Stem Cell Transplantation
Herpes Simplex / virology
Herpesvirus 1, Human / drug effects*
Herpesvirus 1, Human / enzymology
Herpesvirus 1, Human / genetics
High-Throughput Nucleotide Sequencing / methods*
Humans
Microbial Sensitivity Tests / methods*
Mutation
Thymidine Kinase / genetics

Substances

Antiviral Agents
Thymidine Kinase
Acyclovir