PT  - JOURNAL ARTICLE
AU  - Chen Chen
AU  - Jizhou Li
AU  - Lin Di
AU  - Qiuyu Jing
AU  - Pengcheng Du
AU  - Chuan Song
AU  - Jiarui Li
AU  - Qiong Li
AU  - Yunlong Cao
AU  - X. Sunney Xie
AU  - Angela R. Wu
AU  - Hui Zeng
AU  - Yanyi Huang
AU  - Jianbin Wang
TI  - MINERVA: A facile strategy for SARS-CoV-2 whole genome deep sequencing of clinical samples
AID  - 10.1101/2020.04.25.060947
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.04.25.060947
4099  - http://biorxiv.org/content/early/2020/05/26/2020.04.25.060947.short
4100  - http://biorxiv.org/content/early/2020/05/26/2020.04.25.060947.full
AB  - The novel coronavirus disease 2019 (COVID-19) pandemic poses a serious public health risk. Analyzing the genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from clinical samples is crucial for the understanding of viral spread and viral evolution, as well as for vaccine development. Existing sample preparation methods for viral genome sequencing are demanding on user technique and time, and thus not ideal for time-sensitive clinical samples; these methods are also not optimized for high performance on viral genomes. We have developed MetagenomIc RNA EnRichment VirAl sequencing (MINERVA), a facile, practical, and robust approach for metagenomic and deep viral sequencing from clinical samples. This approach uses direct tagmentation of RNA/DNA hybrids using Tn5 transposase to greatly simplify the sequencing library construction process, while subsequent targeted enrichment can generate viral genomes with high sensitivity, coverage, and depth. We demonstrate the utility of MINERVA on pharyngeal, sputum and stool samples collected from COVID-19 patients, successfully obtaining both whole metatranscriptomes and complete high-depth high-coverage SARS-CoV-2 genomes from these clinical samples, with high yield and robustness. MINERVA is compatible with clinical nucleic extracts containing carrier RNA. With a shortened hands-on time from sample to virus-enriched sequencing-ready library, this rapid, versatile, and clinic-friendly approach will facilitate monitoring of viral genetic variations during outbreaks, both current and future.Competing Interest StatementThe authors have declared no competing interest.