Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia
作者: Samuel C. B. StubbsBarbara A. BlacklawsBenediktus YohanFrilasita A. YudhaputriRahma F. HayatiBrian SchwemEdsel M. SalvañaRaul V. DesturaJames S. LesterKhin S. MyintR. Tedjo SasmonoSimon D. W. Frost
作者单位: 1Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
2Eijkman Institute for Molecular Biology, Jakarta, Indonesia
3University of Philippines Manila, Manila, Philippines
4The Alan Turing Institution, London, UK
5Present address: London School of Hygiene and Tropical Medicine, London, UK
6Microsoft Healthcare, Redmond, USA
刊名: Virology Journal, 2020, Vol.17 (1), pp.17-27
来源数据库: Springer Nature Journal
DOI: 10.1186/s12985-020-1294-6
关键词: Dengue virusDisease surveillanceVirus sequencingNanopore sequencing
英文摘要: Abstract(#br)Background(#br)Dengue virus (DENV) infects hundreds of thousands of people annually in Indonesia. However, DENV sequence data from the country are limited, as samples from outbreaks must be shipped across long-distances to suitably equipped laboratories to be sequenced. This approach is time-consuming, expensive, and frequently results in failure due to low viral load or degradation of the RNA genome. Methods(#br)We evaluated a method designed to address this challenge, using the ‘Primal Scheme’ multiplex PCR tiling approach to rapidly generate short, overlapping amplicons covering the complete DENV coding-region, and sequencing the amplicons on the portable Nanopore MinION device. The resulting sequence data was assessed in terms of genome coverage, consensus sequence...
全文获取路径: Springer Nature  (合作)
影响因子:2.092 (2012)