A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples

• DOI: 10.1016/j.isci.2021.102892
• Publication Date: 2021-07-21T22:27:01Z
• Authors: Tiantian Liu; Zhong Chen; Wanqiu Chen; Xin Chen; Maryam Hosseini; Zhaowei Yang; Jing Li; Diana Ho; David Turay; Ciprian P. Gheorghe; Wendell Jones; Charles Wang
• Keywords: Benchmarking; Amplicon; Coronavirus; Amplicon sequencing

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging new type of that responsible for the COVID-19 pandemic and unprecedented global health emergency. Whole-genome sequencing (WGS) SARS-CoV-2 plays a critical role in understanding disease. Performance variation exists across viral WGS technologies, but there currently no benchmarking study comparing different protocols. We compared seven library protocols using RNA from patient nasopharyngeal swab samples under two storage conditions with low high inputs. found large differences mappability genome coverage, variations sensitivity, reproducibility, precision single-nucleotide variant calling For certain amplicon-based protocols, appropriate primer trimming step accurate calling. ranked performance based on six metrics. Our findings offer guidance choosing to characterize its evolution.