ABSTRACTThe 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 < 0.05). A total of 9004 mutations were identified using QNome sequencing, with substitutions being the most prevalent, in contrast, 10 997 mutations were detected on MGI (p < 0.05). Furthermore, 23 large deletions (i.e., deletions≥ 10 bp) were identified by QNome while 19/23 were supported by evidence from short‐read sequencing. Phylogenetic analysis revealed that the Pango lineage of consensus genomes for SARS‐CoV‐2 sequenced by QNome concorded 83.04% with MGI. QNome nanopore sequencing, though challenged by read quality and accuracy compared to MGI, is overcoming these issues through bioinformatics and computational advances. The advantage of structure variation (SV) detection capabilities and real‐time data analysis renders it a promising alternative nanopore platform for the surveillance of the SARS‐CoV‐2.