Molecular epidemiology of Kyasanur forest disease employing ONT-NGS a field forward sequencing

IF 4 3区 医学 Q2 VIROLOGY
Shashi Sharma , Pooja Yadav , Paban Kumar Dash, Suman Dhankher
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引用次数: 0

Abstract

The future of infectious agent detection and molecular characterization lies in field-forward, on-site strategies. The lack of genomic information for recently circulating Kyasanur Forest Disease virus strains is critical. Kyasanur Forest Virus Disease virus PCR-positive samples from 2018 to 2020 were selected for sequencing. Detailed molecular phylogenetic analyses were performed. In this study, we deciphered KFDV whole genomes using the ONT-NGS technique to analyze targeted KFD surveillance from 2018–2020. This study is the first to report recently circulating KFDV strains employing a simple on-site field-forward approach for viral surveillance. Altogether, 19 KFDV genomes were sequenced, and 28 non-synonymous variants were detected in the viral strains circulating from 2018–2020 in the Shivamogga district of Karnataka state in India. The prevailing Variant was detected in more than 10 changes in 80 % of the samples in the viral envelope protein. Recently, circulating KFDV has been the predominant lineage over the past years. India reports seasonal outbreaks almost every year from the Karnataka state of the KFD. The genomic sequences deciphered here belong to the period (2018–2020) that covers the KFDV sequences as the first information. This will contribute to the development and revisiting of diagnostic and vaccine strategies.
利用ONT-NGS进行野地正向测序的Kyasanur森林病害分子流行病学研究
感染因子检测和分子表征的未来在于现场前进,现场策略。缺乏最近流行的恰萨努尔森林病病毒株的基因组信息是至关重要的。选取2018 ~ 2020年恰萨努尔森林病毒病病毒pcr阳性样本进行测序。进行了详细的分子系统发育分析。在这项研究中,我们使用ONT-NGS技术破译了KFDV的全基因组,分析了2018-2020年KFD的靶向监测。这项研究首次报道了最近流行的KFDV菌株采用简单的现场现场前向方法进行病毒监测。总共对19个KFDV基因组进行了测序,并在印度卡纳塔克邦Shivamogga地区2018-2020年流行的病毒株中检测到28个非同义变体。在80%的病毒包膜蛋白样品中,在超过10个变化中检测到流行的变体。最近,在过去的几年中,流行KFDV已成为主要的谱系。印度几乎每年都报告卡纳塔克邦的季节性疫情。这里破译的基因组序列属于覆盖KFDV序列作为第一信息的时期(2018-2020)。这将有助于制定和重新审视诊断和疫苗战略。
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来源期刊
Journal of Clinical Virology
Journal of Clinical Virology 医学-病毒学
CiteScore
22.70
自引率
1.10%
发文量
149
审稿时长
24 days
期刊介绍: The Journal of Clinical Virology, an esteemed international publication, serves as the official journal for both the Pan American Society for Clinical Virology and The European Society for Clinical Virology. Dedicated to advancing the understanding of human virology in clinical settings, the Journal of Clinical Virology focuses on disseminating research papers and reviews pertaining to the clinical aspects of virology. Its scope encompasses articles discussing diagnostic methodologies and virus-induced clinical conditions, with an emphasis on practicality and relevance to clinical practice. The journal publishes on topics that include: • new diagnostic technologies • nucleic acid amplification and serologic testing • targeted and metagenomic next-generation sequencing • emerging pandemic viral threats • respiratory viruses • transplant viruses • chronic viral infections • cancer-associated viruses • gastrointestinal viruses • central nervous system viruses • one health (excludes animal health)
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