Performance of COVIDSeq and Swift Normalase Amplicon SARS-CoV-2 Panels for SARS-CoV-2 Genome Sequencing: Practical Guide and Combining FASTQ Strategy
Hosoon Choi, Munok Hwang, Dhammika H. Navarathna, Jing Xu, Janell Lukey, Chetan Jinadatha
Abstract
Along with real-time reverse transcriptase PCR (RT-PCR) diagnostic testing, whole-genomic sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been an irreplaceable tool for epidemiological evaluation, and genomic sequence analysis has provided essential information in the development of antiviral therapeutics and vaccines (1, 2). Good sequencing coverage needs to be obtained to get information: the default threshold for lineage call at Pangolin is at least 50% of non-N bases (3). Obtaining sufficient WGS coverage from low-viral-load samples is challenging and often not subject to WGS in many labs. However, WGS of low-viral-load patient samples will enable a more complete picture of viral transmission and viral evolution (4).