Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing
Whole genome sequencing provides rapid insight into key information about the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), such as virus typing and key mutation site, and this information is important for precise prevention, control and tracing of coronavirus disease 2019 (COVID-19)...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.973367/full |
| _version_ | 1811177497469911040 |
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| author | Junhong Luo Zixinrong Meng Xingyu Xu Lei Wang Kangchen Zhao Xiaojuan Zhu Qiao Qiao Yiyue Ge Lingfeng Mao Lunbiao Cui Lunbiao Cui |
| author_facet | Junhong Luo Zixinrong Meng Xingyu Xu Lei Wang Kangchen Zhao Xiaojuan Zhu Qiao Qiao Yiyue Ge Lingfeng Mao Lunbiao Cui Lunbiao Cui |
| author_sort | Junhong Luo |
| collection | DOAJ |
| description | Whole genome sequencing provides rapid insight into key information about the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), such as virus typing and key mutation site, and this information is important for precise prevention, control and tracing of coronavirus disease 2019 (COVID-19) outbreak in conjunction with the epidemiological information of the case. Nanopore sequencing is widely used around the world for its short sample-to-result time, simple experimental operation and long sequencing reads. However, because nanopore sequencing is a relatively new sequencing technology, many researchers still have doubts about its accuracy. The combination of the newly launched nanopore sequencing Q20+ kit (LSK112) and flow cell R10.4 is a qualitative improvement over the accuracy of the previous kits. In this study, we firstly used LSK112 kit with flow cell R10.4 to sequence the SARS-CoV-2 whole genome, and summarized the sequencing results of the combination of LSK112 kit and flow cell R10.4 for the 1200bp amplicons of SARS-CoV-2. We found that the proportion of sequences with an accuracy of more than 99% reached 30.1%, and the average sequence accuracy reached 98.34%, while the results of the original combination of LSK109 kit and flow cell R9.4.1 were 0.61% and 96.52%, respectively. The mutation site analysis showed that it was completely consistent with the final consensus sequence of next generation sequencing (NGS). The results showed that the combination of LSK112 kit and flow cell R10.4 allowed rapid whole-genome sequencing of SARS-CoV-2 without the need for verification of NGS. |
| first_indexed | 2024-04-11T06:02:48Z |
| format | Article |
| id | doaj.art-29d82e59975f4e6fb50a47c2e2412732 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-11T06:02:48Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-29d82e59975f4e6fb50a47c2e24127322022-12-22T04:41:35ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-10-011310.3389/fmicb.2022.973367973367Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencingJunhong Luo0Zixinrong Meng1Xingyu Xu2Lei Wang3Kangchen Zhao4Xiaojuan Zhu5Qiao Qiao6Yiyue Ge7Lingfeng Mao8Lunbiao Cui9Lunbiao Cui10School of Public Health, Nanjing Medical University, Nanjing, ChinaSchool of Public Health, Nanjing Medical University, Nanjing, ChinaHangzhou Baiyi Technology Co., Ltd., Hangzhou, ChinaHangzhou Baiyi Technology Co., Ltd., Hangzhou, ChinaNHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, ChinaNHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, ChinaNHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, ChinaNHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, ChinaHangzhou Baiyi Technology Co., Ltd., Hangzhou, ChinaSchool of Public Health, Nanjing Medical University, Nanjing, ChinaNHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, ChinaWhole genome sequencing provides rapid insight into key information about the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), such as virus typing and key mutation site, and this information is important for precise prevention, control and tracing of coronavirus disease 2019 (COVID-19) outbreak in conjunction with the epidemiological information of the case. Nanopore sequencing is widely used around the world for its short sample-to-result time, simple experimental operation and long sequencing reads. However, because nanopore sequencing is a relatively new sequencing technology, many researchers still have doubts about its accuracy. The combination of the newly launched nanopore sequencing Q20+ kit (LSK112) and flow cell R10.4 is a qualitative improvement over the accuracy of the previous kits. In this study, we firstly used LSK112 kit with flow cell R10.4 to sequence the SARS-CoV-2 whole genome, and summarized the sequencing results of the combination of LSK112 kit and flow cell R10.4 for the 1200bp amplicons of SARS-CoV-2. We found that the proportion of sequences with an accuracy of more than 99% reached 30.1%, and the average sequence accuracy reached 98.34%, while the results of the original combination of LSK109 kit and flow cell R9.4.1 were 0.61% and 96.52%, respectively. The mutation site analysis showed that it was completely consistent with the final consensus sequence of next generation sequencing (NGS). The results showed that the combination of LSK112 kit and flow cell R10.4 allowed rapid whole-genome sequencing of SARS-CoV-2 without the need for verification of NGS.https://www.frontiersin.org/articles/10.3389/fmicb.2022.973367/fullnanopore sequencingQ20+ kitSARS-CoV-2coronavirusaccuracy |
| spellingShingle | Junhong Luo Zixinrong Meng Xingyu Xu Lei Wang Kangchen Zhao Xiaojuan Zhu Qiao Qiao Yiyue Ge Lingfeng Mao Lunbiao Cui Lunbiao Cui Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing Frontiers in Microbiology nanopore sequencing Q20+ kit SARS-CoV-2 coronavirus accuracy |
| title | Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing |
| title_full | Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing |
| title_fullStr | Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing |
| title_full_unstemmed | Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing |
| title_short | Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing |
| title_sort | systematic benchmarking of nanopore q20 kit in sars cov 2 whole genome sequencing |
| topic | nanopore sequencing Q20+ kit SARS-CoV-2 coronavirus accuracy |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.973367/full |
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