دورية أكاديمية
DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus.
| العنوان: | DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. |
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| المؤلفون: | Vogels CBF; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA. chantal.vogels@yale.edu.; Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA. chantal.vogels@yale.edu., Hill V; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA., Breban MI; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA., Chaguza C; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.; Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA., Paul LM; Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA., Sodeinde A; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA., Taylor-Salmon E; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.; Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, USA., Ott IM; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA., Petrone ME; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.; Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia., Dijk D; Department of Medical Microbiology & Infection Prevention, Amsterdam UMC Location AMC, Amsterdam, The Netherlands., Jonges M; Department of Medical Microbiology & Infection Prevention, Amsterdam UMC Location AMC, Amsterdam, The Netherlands., Welkers MRA; Department of Medical Microbiology & Infection Prevention, Amsterdam UMC Location AMC, Amsterdam, The Netherlands.; Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands., Locksmith T; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA., Dong Y; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA., Tarigopula N; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA., Tekin O; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA., Schmedes S; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA., Bunch S; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA., Cano N; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA., Jaber R; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA., Panzera C; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA., Stryker I; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA., Vergara J; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA., Zimler R; Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA., Kopp E; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA., Heberlein L; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA., Herzog KS; Department of Epidemiology, University of Nebraska Medical Center, Omaha, Nebraska, USA., Fauver JR; Department of Epidemiology, University of Nebraska Medical Center, Omaha, Nebraska, USA., Morrison AM; Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA., Michael SF; Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA., Grubaugh ND; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA. nathan.grubaugh@yale.edu.; Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA. nathan.grubaugh@yale.edu.; Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA. nathan.grubaugh@yale.edu.; Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, USA. nathan.grubaugh@yale.edu. |
| المصدر: | BMC genomics [BMC Genomics] 2024 May 01; Vol. 25 (1), pp. 433. Date of Electronic Publication: 2024 May 01. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: London : BioMed Central, [2000- |
| مواضيع طبية MeSH: | Dengue Virus*/genetics , Dengue Virus*/isolation & purification , Dengue Virus*/classification , Whole Genome Sequencing*/methods , Genome, Viral* , Serogroup*, Humans ; Genotype ; Dengue/virology ; Dengue/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; RNA, Viral/genetics |
| مستخلص: | Background: The increasing burden of dengue virus on public health due to more explosive and frequent outbreaks highlights the need for improved surveillance and control. Genomic surveillance of dengue virus not only provides important insights into the emergence and spread of genetically diverse serotypes and genotypes, but it is also critical to monitor the effectiveness of newly implemented control strategies. Here, we present DengueSeq, an amplicon sequencing protocol, which enables whole-genome sequencing of all four dengue virus serotypes. Results: We developed primer schemes for the four dengue virus serotypes, which can be combined into a pan-serotype approach. We validated both approaches using genetically diverse virus stocks and clinical specimens that contained a range of virus copies. High genome coverage (>95%) was achieved for all genotypes, except DENV2 (genotype VI) and DENV 4 (genotype IV) sylvatics, with similar performance of the serotype-specific and pan-serotype approaches. The limit of detection to reach 70% coverage was 10-100 RNA copies/μL for all four serotypes, which is similar to other commonly used primer schemes. DengueSeq facilitates the sequencing of samples without known serotypes, allows the detection of multiple serotypes in the same sample, and can be used with a variety of library prep kits and sequencing instruments. Conclusions: DengueSeq was systematically evaluated with virus stocks and clinical specimens spanning the genetic diversity within each of the four dengue virus serotypes. The primer schemes can be plugged into existing amplicon sequencing workflows to facilitate the global need for expanded dengue virus genomic surveillance. (© 2024. The Author(s).) |
| التعليقات: | Update of: medRxiv. 2023 Oct 13;:. (PMID: 37873191) |
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| معلومات مُعتمدة: | R21GM142011 United States GM NIGMS NIH HHS; T32 AI055403 United States AI NIAID NIH HHS; R21 GM142011 United States GM NIGMS NIH HHS; UL1 TR001863 United States TR NCATS NIH HHS; DP2 AI176740 United States AI NIAID NIH HHS; T32AI055403 United States NH NIH HHS |
| فهرسة مساهمة: | Keywords: Amplicon sequencing; Dengue virus; Genomic surveillance; Next-generation sequencing; Whole-genome sequencing |
| المشرفين على المادة: | 0 (RNA, Viral) |
| تواريخ الأحداث: | Date Created: 20240501 Date Completed: 20240501 Latest Revision: 20240513 |
| رمز التحديث: | 20240513 |
| مُعرف محوري في PubMed: | PMC11062901 |
| DOI: | 10.1186/s12864-024-10350-x |
| PMID: | 38693476 |
| قاعدة البيانات: | MEDLINE |
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Full Text Finder | تدمد: | 1471-2164 |
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| DOI: | 10.1186/s12864-024-10350-x |