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Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses

By Ming Wang, Aisi Fu, Ben Hu, Yongqing Tong, Ran Liu, Jiashuang Gu, Jianghao Liu, Wen Jiang, Gaigai Shen, Wanxu Zhao, Dong Men, Zixin Deng, Lilei Yu, Yan Li, Tiangang Liu

Posted 06 Mar 2020
medRxiv DOI: 10.1101/2020.03.04.20029538

The ongoing novel coronavirus pneumonia COVID-19 outbreak in Wuhan, China, has engendered numerous cases of infection and death. COVID-19 diagnosis relies upon nucleic acid detection; however, current recommended methods exhibit high false-negative rates, low sensitivity, and cannot identify other respiratory virus infections, thereby resulting patient misdiagnosis and impeding epidemic containment. Combining the advantages of target amplification and long-read, real-time nanopore sequencing, we developed nanopore target sequencing (NTS) to detect SARS- CoV-2 and other respiratory viruses simultaneously within 6-10 h. Parallel testing with approved qPCR kits of SARS-CoV-2 and NTS using 61 nucleic acid samples from suspected COVID-19 cases confirmed that NTS identified more infected patients as positive, and could also monitor for mutated nucleic acid sequence or other respiratory virus infection in the test sample. NTS is thus suitable for contemporary COVID-19 diagnosis; moreover, this platform can be further extended for diagnosing other viruses or pathogens.

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