Fukuda Yuto, Suzuki Takako, Iwata Ken-Ichi, Haruta Kazunori, Yamaguchi Makoto, Torii Yuka, Narita Atsushi, Muramatsu Hideki, Takahashi Yoshiyuki, Kawada Jun-Ichi
Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
Vaccine. 2024 Apr 19;42(11):2927-2932. doi: 10.1016/j.vaccine.2024.03.046. Epub 2024 Mar 27.
The introduction of varicella vaccines into routine pediatric immunization programs has led to a considerable reduction in varicella incidence. However, there have been reports of varicella, herpes zoster, and meningitis caused by the vaccine strain of varicella-zoster virus (VZV), raising concerns. Establishing the relationship between the wild-type and vaccine strains in VZV infections among previously vaccinated individuals is crucial. Differences in the single nucleotide polymorphisms (SNPs) among vaccine strains can be utilized to identify the strain. In this study, we employed nanopore sequencing to identify VZV strains and analyzed clinical samples.
We retrospectively examined vesicle and cerebrospinal fluid samples from patients with VZV infections. One sample each of the wild-type and vaccine strains, previously identified using allelic discrimination real-time PCR and direct sequencing, served as controls. Ten samples with undetermined VZV strains were included. After DNA extraction, a long PCR targeting the VZV ORF62 region was executed. Nanopore sequencing identified SNPs, allowing discrimination between the vaccine and wild-type strains.
Nanopore sequencing confirmed SNPs at previously reported sites (105,705, 106,262, 107,136, and 107,252), aiding in distinguishing between wild-type and vaccine strains. Among the ten unknown samples, nine were characterized as wild strains and one as a vaccine strain. Even in samples with low VZV DNA levels, nanopore sequencing was effective in strain identification.
This study validates that nanopore sequencing is a reliable method for differentiating between the wild-type and vaccine strains of VZV. Its ability to produce long-read sequences is remarkable, allowing simultaneous confirmation of known SNPs and the detection of new mutations. Nanopore sequencing can serve as a valuable tool for the swift and precise identification of wild-type and vaccine strains and has potential applications in future VZV surveillance.
水痘疫苗引入常规儿童免疫计划后，水痘发病率显著降低。然而，有报告称水痘-带状疱疹病毒（VZV）疫苗株可引起水痘、带状疱疹和脑膜炎，引发了人们的担忧。确定既往接种疫苗个体中VZV感染的野生型和疫苗株之间的关系至关重要。疫苗株之间单核苷酸多态性（SNP）的差异可用于识别毒株。在本研究中，我们采用纳米孔测序来识别VZV毒株并分析临床样本。
我们回顾性检查了VZV感染患者的水疱和脑脊液样本。之前使用等位基因鉴别实时PCR和直接测序鉴定的野生型和疫苗株各一份样本作为对照。纳入了10份VZV毒株未确定的样本。DNA提取后，进行靶向VZV ORF62区域的长PCR。纳米孔测序确定SNP，从而区分疫苗株和野生型毒株。
纳米孔测序在先前报道的位点（105,705、106,262、107,136和107,252）确认了SNP，有助于区分野生型和疫苗株。在10份未知样本中，9份被鉴定为野生株，1份为疫苗株。即使在VZV DNA水平较低的样本中，纳米孔测序在毒株鉴定中也很有效。
本研究证实纳米孔测序是区分VZV野生型和疫苗株的可靠方法。其产生长读长序列的能力显著，能够同时确认已知SNP并检测新突变。纳米孔测序可作为快速准确鉴定野生型和疫苗株的有价值工具，并在未来VZV监测中具有潜在应用。
