A serotype-specific and tiled amplicon multiplex PCR method for whole genome sequencing of dengue virus

IF 2.2 4区医学 Q3 BIOCHEMICAL RESEARCH METHODS

Journal of virological methods Pub Date : 2024-05-23 DOI:10.1016/j.jviromet.2024.114968

Tran Thuy Vi , Duong Thi Hue Kien , Vo Thi Long , Le Thi Dui , Vu Thi Tuyet Nhu , Nguyen Thi Giang , Huynh Thi Xuan Trang , Sophie Yacoub , Cameron P. Simmons

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引用次数: 0

Abstract

Dengue fever, a mosquito-borne viral disease of significant public health concern in tropical and subtropical regions, is caused by any of the four serotypes of the dengue virus (DENV1–4). Cutting-edge technologies like next-generation sequencing (NGS) are revolutionizing virology, enabling in-depth exploration of DENV's genetic diversity. Here, we present an optimized workflow for full-genome sequencing of DENV 1–4 utilizing tiled amplicon multiplex PCR and Illumina sequencing. Our assay, sequenced on the Illumina MiSeq platform, demonstrates its ability to recover the full-length dengue genome across various viral abundances in clinical specimens with high-quality base coverage. This high quality underscores its suitability for precise examination of intra-host diversity, enriching our understanding of viral evolution and holding potential for improved diagnostic and intervention strategies in regions facing dengue outbreaks.

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用于登革热病毒全基因组测序的血清型特异性叠加扩增片段多重 PCR 方法

登革热是一种由蚊子传播的病毒性疾病，在热带和亚热带地区引起严重的公共卫生问题，由登革热病毒（DENV1-4）的四种血清型中的任何一种引起。下一代测序（NGS）等尖端技术正在彻底改变病毒学，使深入探索 DENV 遗传多样性成为可能。在这里，我们介绍了一种优化的工作流程，利用平铺扩增片段多重 PCR 和 Illumina 测序对 DENV 1-4 进行全基因组测序。我们在Illumina MiSeq平台上进行测序的检测方法证明了它有能力以高质量的碱基覆盖率恢复临床样本中不同病毒丰度的全长登革热基因组。这种高质量突显了它在精确检测宿主内多样性方面的适用性，丰富了我们对病毒进化的了解，并为面临登革热疫情的地区改进诊断和干预策略提供了潜力。

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来源期刊

Journal of virological methods 医学-病毒学

CiteScore

5.80

自引率

0.00%

发文量

209

审稿时长

41 days

期刊介绍： The Journal of Virological Methods focuses on original, high quality research papers that describe novel and comprehensively tested methods which enhance human, animal, plant, bacterial or environmental virology and prions research and discovery. The methods may include, but not limited to, the study of: Viral components and morphology- Virus isolation, propagation and development of viral vectors- Viral pathogenesis, oncogenesis, vaccines and antivirals- Virus replication, host-pathogen interactions and responses- Virus transmission, prevention, control and treatment- Viral metagenomics and virome- Virus ecology, adaption and evolution- Applied virology such as nanotechnology- Viral diagnosis with novelty and comprehensive evaluation. We seek articles, systematic reviews, meta-analyses and laboratory protocols that include comprehensive technical details with statistical confirmations that provide validations against current best practice, international standards or quality assurance programs and which advance knowledge in virology leading to improved medical, veterinary or agricultural practices and management.

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