Nanopore sequencing in distinguishing between wild-type and vaccine strains of Varicella-Zoster virus
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....
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| Veröffentlicht in: | Vaccine 2024-04, Vol.42 (11), p.2927-2932 |
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| creator | Fukuda, Yuto Suzuki, Takako Iwata, Ken-ichi Haruta, Kazunori Yamaguchi, Makoto Torii, Yuka Narita, Atsushi Muramatsu, Hideki Takahashi, Yoshiyuki Kawada, Jun-ichi |
| description | 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. |
| doi_str_mv | 10.1016/j.vaccine.2024.03.046 |
| format | Article |
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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.</description><identifier>ISSN: 0264-410X</identifier><identifier>EISSN: 1873-2518</identifier><identifier>DOI: 10.1016/j.vaccine.2024.03.046</identifier><identifier>PMID: 38548526</identifier><language>eng</language><publisher>Netherlands: Elsevier Ltd</publisher><subject>Cerebrospinal fluid ; Chicken pox ; Chickenpox ; Chickenpox Vaccine - genetics ; Child ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; DNA, Viral - genetics ; Herpes viruses ; Herpes zoster ; Herpes Zoster - prevention & control ; Herpesvirus 3, Human - genetics ; Human alphaherpesvirus 3 ; Humans ; Immunization ; Meningitis ; monitoring ; Nanopore Sequencing ; nanopores ; Nucleotides ; Pediatrics ; Polymerase chain reaction ; Polymerase Chain Reaction - methods ; Polymorphism, Restriction Fragment Length ; quantitative polymerase chain reaction ; Retrospective Studies ; Single-nucleotide polymorphism ; Strains (organisms) ; Vaccine ; Vaccines ; Varicella ; Varicella-zoster virus ; Viruses</subject><ispartof>Vaccine, 2024-04, Vol.42 (11), p.2927-2932</ispartof><rights>2024 Elsevier Ltd</rights><rights>Copyright © 2024 Elsevier Ltd. All rights reserved.</rights><rights>2024. Elsevier Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c374t-ca9c123089297b95026f859541dd220a9c9105f9d34a37820b7017116ec2af403</cites><orcidid>0000-0003-1553-2539</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0264410X24003335$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65534</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38548526$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fukuda, Yuto</creatorcontrib><creatorcontrib>Suzuki, Takako</creatorcontrib><creatorcontrib>Iwata, Ken-ichi</creatorcontrib><creatorcontrib>Haruta, Kazunori</creatorcontrib><creatorcontrib>Yamaguchi, Makoto</creatorcontrib><creatorcontrib>Torii, Yuka</creatorcontrib><creatorcontrib>Narita, Atsushi</creatorcontrib><creatorcontrib>Muramatsu, Hideki</creatorcontrib><creatorcontrib>Takahashi, Yoshiyuki</creatorcontrib><creatorcontrib>Kawada, Jun-ichi</creatorcontrib><title>Nanopore sequencing in distinguishing between wild-type and vaccine strains of Varicella-Zoster virus</title><title>Vaccine</title><addtitle>Vaccine</addtitle><description>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.</description><subject>Cerebrospinal fluid</subject><subject>Chicken pox</subject><subject>Chickenpox</subject><subject>Chickenpox Vaccine - genetics</subject><subject>Child</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>DNA, Viral - genetics</subject><subject>Herpes viruses</subject><subject>Herpes zoster</subject><subject>Herpes Zoster - prevention & control</subject><subject>Herpesvirus 3, Human - genetics</subject><subject>Human alphaherpesvirus 3</subject><subject>Humans</subject><subject>Immunization</subject><subject>Meningitis</subject><subject>monitoring</subject><subject>Nanopore Sequencing</subject><subject>nanopores</subject><subject>Nucleotides</subject><subject>Pediatrics</subject><subject>Polymerase chain 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Academic</collection><jtitle>Vaccine</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fukuda, Yuto</au><au>Suzuki, Takako</au><au>Iwata, Ken-ichi</au><au>Haruta, Kazunori</au><au>Yamaguchi, Makoto</au><au>Torii, Yuka</au><au>Narita, Atsushi</au><au>Muramatsu, Hideki</au><au>Takahashi, Yoshiyuki</au><au>Kawada, Jun-ichi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Nanopore sequencing in distinguishing between wild-type and vaccine strains of Varicella-Zoster virus</atitle><jtitle>Vaccine</jtitle><addtitle>Vaccine</addtitle><date>2024-04-19</date><risdate>2024</risdate><volume>42</volume><issue>11</issue><spage>2927</spage><epage>2932</epage><pages>2927-2932</pages><issn>0264-410X</issn><eissn>1873-2518</eissn><abstract>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.</abstract><cop>Netherlands</cop><pub>Elsevier Ltd</pub><pmid>38548526</pmid><doi>10.1016/j.vaccine.2024.03.046</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0003-1553-2539</orcidid></addata></record> |
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| subjects | Cerebrospinal fluid Chicken pox Chickenpox Chickenpox Vaccine - genetics Child Deoxyribonucleic acid DNA DNA sequencing DNA, Viral - genetics Herpes viruses Herpes zoster Herpes Zoster - prevention & control Herpesvirus 3, Human - genetics Human alphaherpesvirus 3 Humans Immunization Meningitis monitoring Nanopore Sequencing nanopores Nucleotides Pediatrics Polymerase chain reaction Polymerase Chain Reaction - methods Polymorphism, Restriction Fragment Length quantitative polymerase chain reaction Retrospective Studies Single-nucleotide polymorphism Strains (organisms) Vaccine Vaccines Varicella Varicella-zoster virus Viruses |
| title | Nanopore sequencing in distinguishing between wild-type and vaccine strains of Varicella-Zoster virus |
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