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Long\u2010read sequencing technology (e.g., ONT) has been widely used, providing a real\u2010time and faster response when necessitated. A novel nanopore\u2010based long\u2010read sequencing platform named QNome nanopore has been successfully used for bacterial genome sequencing and assembly; however, its performance in the SARS\u2010CoV\u20102 genomic surveillance is still lacking. Synthetic SARS\u2010CoV\u20102 controls and 120 nasopharyngeal swab (NPS) samples that tested positive by real\u2010time polymerase chain reaction were sequenced on both QNome and MGI platforms in parallel. The analytical performance of QNome was compared to the short\u2010read sequencing on MGI. For the synthetic SARS\u2010CoV\u20102 controls, despite the increased error rates observed in QNome nanopore sequencing reads, accurate consensus\u2010level 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 (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05). A total of 9004 mutations were identified using QNome sequencing, with substitutions being the most prevalent, in contrast, 10\u2009997 mutations were detected on MGI (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05). Furthermore, 23 large deletions (i.e., deletions\u2265\u200910\u2009bp) were identified by QNome while 19\/23 were supported by evidence from short\u2010read sequencing. Phylogenetic analysis revealed that the Pango lineage of consensus genomes for SARS\u2010CoV\u20102 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\u2010time data analysis renders it a promising alternative nanopore platform for the surveillance of the SARS\u2010CoV\u20102.<\/jats:p>","DOI":"10.1002\/jmv.70108","type":"journal-article","created":{"date-parts":[[2024,12,6]],"date-time":"2024-12-06T09:20:13Z","timestamp":1733476813000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Analytical Performance of a Novel Nanopore Sequencing for SARS\u2010CoV\u20102 Genomic Surveillance"],"prefix":"10.1002","volume":"96","author":[{"given":"Mulatijiang","family":"Maimaiti","sequence":"first","affiliation":[{"name":"Department of Clinical Laboratory Peking Union Medical College Hospital Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lingjun","family":"Kong","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory Peking Union Medical College Hospital Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qi","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory Peking Union Medical College Hospital Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ziyi","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory Peking Union Medical College Hospital Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yiwei","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory Peking Union Medical College Hospital Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenglin","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory Peking Union Medical College Hospital Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenhu","family":"Guo","sequence":"additional","affiliation":[{"name":"R&amp;D center Fuzhou Agenmic Biotechnology Co. 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