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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 < 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.
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http://dx.doi.org/10.1002/jmv.70108 | DOI Listing |
J Med Virol
December 2024
Department of Clinical Laboratory, Peking Union Medical College Hospital, Beijing, China.
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.
View Article and Find Full Text PDFViruses
June 2024
Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Hepatitis A virus (HAV), a member of the genus ( HepV), remains a significant viral pathogen, frequently causing enterically transmitted hepatitis worldwide. In this study, we conducted an epidemiological survey of HepVs carried by small terrestrial mammals in the wild in Yunnan Province, China. Utilizing HepV-specific broad-spectrum RT-PCR, next-generation sequencing (NGS), and QNome nanopore sequencing (QNS) techniques, we identified and characterized two novel HepVs provisionally named EpMa-HAV and EpLe-HAV, discovered in the long-tailed mountain shrew () and long-tailed brown-toothed shrew (), respectively.
View Article and Find Full Text PDFElectrophoresis
September 2024
Institute of Health Service and Transfusion Medicine, Beijing, P. R. China.
Devices of nanopore sequencing can be highly portable and of low cost. Thus, nanopore sequencing is promising in in-field forensic applications. Previous investigations have demonstrated that nanopore sequencing is feasible for genotyping forensic short tandem repeats (STRs) by using sequencers of Oxford Nanopore Technologies.
View Article and Find Full Text PDFForensic Sci Int Genet
January 2024
Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China. Electronic address:
Forensic Sci Int Genet
November 2023
Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China. Electronic address:
Genetic associations between human mitochondrial DNA (mtDNA) heteroplasmy and mitochondrial diseases, aging, and cancer have been elaborated, contributing a lot to the further understanding of mtDNA polymorphic spectrum in anthropology, population, and forensic genetics. In the past decade, heteroplasmy detection using Sanger sequencing and next generation sequencing (NGS) was hampered by the former's inefficiency and the latter's inherent bias due to amplification and mapping of short reads, respectively. Nanopore sequencing stands out for its ability to yield long contiguous segments of DNA, providing a new insight into heterogeneity authentication.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!