Publication date: Dec 01, 2024

The genomic analysis of SARS-CoV-2 has served as a crucial tool for generating invaluable data that fulfils both epidemiological and clinical necessities. Long-read sequencing technology (e. g., ONT) has been widely used, providing a real-time and faster response when necessitated. A novel nanopore-based long-read sequencing platform named QNome nanopore has been successfully used for bacterial genome sequencing and assembly; however, its performance in the SARS-CoV-2 genomic surveillance is still lacking. Synthetic SARS-CoV-2 controls and 120 nasopharyngeal swab (NPS) samples that tested positive by real-time polymerase chain reaction were sequenced on both QNome and MGI platforms in parallel. The analytical performance of QNome was compared to the short-read sequencing on MGI. For the synthetic SARS-CoV-2 controls, despite the increased error rates observed in QNome nanopore sequencing reads, accurate consensus-level sequence determination was achieved with an average mapping quality score of approximately 60 (i. e., a mapping accuracy of 99. 9999%). For the NPS samples, the average genomic coverage was 89. 35% on the QNome nanopore platform compared with 90. 39% for MGI. In addition, fewer consensus genomes from QNome were determined to be good by Nextclade compare with MGI (p 

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