TY - JOUR T1 - Multiple approaches for massively parallel sequencing of HCoV-19 (SARS-CoV-2) genomes directly from clinical samples JF - bioRxiv DO - 10.1101/2020.03.16.993584 SP - 2020.03.16.993584 AU - Minfeng Xiao AU - Xiaoqing Liu AU - Jingkai Ji AU - Min Li AU - Jiandong Li AU - Lin Yang AU - Wanying Sun AU - Peidi Ren AU - Guifang Yang AU - Jincun Zhao AU - Tianzhu Liang AU - Huahui Ren AU - Tian Chen AU - Huanzi Zhong AU - Wenchen Song AU - Yanqun Wang AU - Ziqing Deng AU - Yanping Zhao AU - Zhihua Ou AU - Daxi Wang AU - Jielun Cai AU - Xinyi Cheng AU - Taiqing Feng AU - Honglong Wu AU - Yanping Gong AU - Huanming Yang AU - Jian Wang AU - Xun Xu AU - Shida Zhu AU - Fang Chen AU - Yanyan Zhang AU - Weijun Chen AU - Yimin Li AU - Junhua Li Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/03/19/2020.03.16.993584.abstract N2 - COVID-19 has caused a major epidemic worldwide, however, much is yet to be known about the epidemiology and evolution of the virus. One reason is that the challenges underneath sequencing HCoV-19 directly from clinical samples have not been completely tackled. Here we illustrate the application of amplicon and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of HCoV-19 from clinical samples covering a range of sample types and viral load. We also examine and compare the bias, sensitivity, accuracy, and other characteristics of these approaches in a comprehensive manner. This is, to date, the first work systematically implements amplicon and capture approaches in sequencing HCoV-19, as well as the first comparative study across methods. Our work offers practical solutions for genome sequencing and analyses of HCoV-19 and other emerging viruses. ER -