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Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples

  1. Xiao, Minfeng
  2. Liu, Xiaoqing
  3. Ji, Jingkai
  4. Li, Min
  5. Li, Jiandong
  6. Yang, Lin
  7. Sun, Wanying
  8. Ren, Peidi
  9. Yang, Guifang
  10. Zhao, Jincun
  11. Liang, Tianzhu
  12. Ren, Huahui
  13. Chen, Tian
  14. Zhong, Huanzi
  15. Song, Wenchen
  16. Wang, Yanqun
  17. Deng, Ziqing
  18. Zhao, Yanping
  19. Ou, Zhihua
  20. Wang, Daxi
  21. Cai, Jielun
  22. Cheng, Xinyi
  23. Feng, Taiqing
  24. Wu, Honglong
  25. Gong, Yanping
  26. Yang, Huanming
  27. Wang, Jian
  28. Xu, Xun
  29. Zhu, Shida
  30. Chen, Fang
  31. Zhang, Yanyan
  32. Chen, Weijun
  33. Li, Yimin
  34. Li, Junhua ORCID logo

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1000 Titel
  • Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples
1000 Autor/in
  1. Xiao, Minfeng |
  2. Liu, Xiaoqing |
  3. Ji, Jingkai |
  4. Li, Min |
  5. Li, Jiandong |
  6. Yang, Lin |
  7. Sun, Wanying |
  8. Ren, Peidi |
  9. Yang, Guifang |
  10. Zhao, Jincun |
  11. Liang, Tianzhu |
  12. Ren, Huahui |
  13. Chen, Tian |
  14. Zhong, Huanzi |
  15. Song, Wenchen |
  16. Wang, Yanqun |
  17. Deng, Ziqing |
  18. Zhao, Yanping |
  19. Ou, Zhihua |
  20. Wang, Daxi |
  21. Cai, Jielun |
  22. Cheng, Xinyi |
  23. Feng, Taiqing |
  24. Wu, Honglong |
  25. Gong, Yanping |
  26. Yang, Huanming |
  27. Wang, Jian |
  28. Xu, Xun |
  29. Zhu, Shida |
  30. Chen, Fang |
  31. Zhang, Yanyan |
  32. Chen, Weijun |
  33. Li, Yimin |
  34. Li, Junhua |
1000 Erscheinungsjahr 2020
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2020-06-30
1000 Erschienen in
1000 Quellenangabe
  • 12(1):57
1000 Copyrightjahr
  • 2020
1000 Lizenz
1000 Verlagsversion
  • https://doi.org/10.1186/s13073-020-00751-4 |
1000 Ergänzendes Material
  • https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00751-4#Sec21 |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • BACKGROUND: COVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genomes reported. One reason is that the challenges underneath sequencing SARS-CoV-2 directly from clinical samples have not been completely tackled, i.e., sequencing samples with low viral load often results in insufficient viral reads for analyses. METHODS: We applied a novel multiplex PCR amplicon (amplicon)-based and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of SARS-CoV-2 from serials dilutions of a cultured isolate, and eight clinical samples covering a range of sample types and viral loads. We also examined and compared the sensitivity, accuracy, and other characteristics of these approaches in a comprehensive manner. RESULTS: We demonstrated that both amplicon and capture methods efficiently enriched SARS-CoV-2 content from clinical samples, while the enrichment efficiency of amplicon outran that of capture in more challenging samples. We found that capture was not as accurate as meta and amplicon in identifying between-sample variations, whereas amplicon method was not as accurate as the other two in investigating within-sample variations, suggesting amplicon sequencing was not suitable for studying virus-host interactions and viral transmission that heavily rely on intra-host dynamics. We illustrated that meta uncovered rich genetic information in the clinical samples besides SARS-CoV-2, providing references for clinical diagnostics and therapeutics. Taken all factors above and cost-effectiveness into consideration, we proposed guidance for how to choose sequencing strategy for SARS-CoV-2 under different situations. CONCLUSIONS: This is, to the best of our knowledge, the first work systematically investigating inter- and intra-individual variations of SARS-CoV-2 using amplicon- and capture-based whole-genome sequencing, as well as the first comparative study among multiple approaches. Our work offers practical solutions for genome sequencing and analyses of SARS-CoV-2 and other emerging viruses.
1000 Sacherschließung
gnd 1206347392 COVID-19
lokal Virus evolution
lokal Emerging infectious diseases
lokal Hybrid capture
lokal iSNV
lokal Genomic surveillance
lokal Multiplex PCR
lokal Quasispecies
lokal Metatranscriptomic sequencing
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
  1. https://frl.publisso.de/adhoc/uri/WGlhbywgTWluZmVuZw==|https://frl.publisso.de/adhoc/uri/TGl1LCBYaWFvcWluZw==|https://frl.publisso.de/adhoc/uri/SmksIEppbmdrYWk=|https://frl.publisso.de/adhoc/uri/TGksIE1pbg==|https://frl.publisso.de/adhoc/uri/TGksIEppYW5kb25n|https://frl.publisso.de/adhoc/uri/WWFuZywgTGlu|https://frl.publisso.de/adhoc/uri/U3VuLCBXYW55aW5n|https://frl.publisso.de/adhoc/uri/UmVuLCBQZWlkaQ==|https://frl.publisso.de/adhoc/uri/WWFuZywgR3VpZmFuZw==|https://frl.publisso.de/adhoc/uri/WmhhbywgSmluY3Vu|https://frl.publisso.de/adhoc/uri/TGlhbmcsIFRpYW56aHU=|https://frl.publisso.de/adhoc/uri/UmVuLCBIdWFodWk=|https://frl.publisso.de/adhoc/uri/Q2hlbiwgVGlhbg==|https://frl.publisso.de/adhoc/uri/WmhvbmcsIEh1YW56aQ==|https://frl.publisso.de/adhoc/uri/U29uZywgV2VuY2hlbg==|https://frl.publisso.de/adhoc/uri/V2FuZywgWWFucXVu|https://frl.publisso.de/adhoc/uri/RGVuZywgWmlxaW5n|https://frl.publisso.de/adhoc/uri/WmhhbywgWWFucGluZw==|https://frl.publisso.de/adhoc/uri/T3UsIFpoaWh1YQ==|https://frl.publisso.de/adhoc/uri/V2FuZywgRGF4aQ==|https://frl.publisso.de/adhoc/uri/Q2FpLCBKaWVsdW4=|https://frl.publisso.de/adhoc/uri/Q2hlbmcsIFhpbnlp|https://frl.publisso.de/adhoc/uri/RmVuZywgVGFpcWluZw==|https://frl.publisso.de/adhoc/uri/V3UsIEhvbmdsb25n|https://frl.publisso.de/adhoc/uri/R29uZywgWWFucGluZw==|https://frl.publisso.de/adhoc/uri/WWFuZywgSHVhbm1pbmc=|https://frl.publisso.de/adhoc/uri/V2FuZywgSmlhbg==|https://frl.publisso.de/adhoc/uri/WHUsIFh1bg==|https://frl.publisso.de/adhoc/uri/Wmh1LCBTaGlkYQ==|https://frl.publisso.de/adhoc/uri/Q2hlbiwgRmFuZw==|https://frl.publisso.de/adhoc/uri/WmhhbmcsIFlhbnlhbg==|https://frl.publisso.de/adhoc/uri/Q2hlbiwgV2VpanVu|https://frl.publisso.de/adhoc/uri/TGksIFlpbWlu|https://orcid.org/0000-0001-6784-1873
1000 Label
1000 Förderer
  1. National Major Science and Technology Projects of China |
  2. Chinese Center for Disease Control and Prevention |
  3. Ministry of Science and Technology of the People's Republic of China |
  4. Government of Guangdong Province |
  5. Guangdong Provincial Key Laboratory of Genome Read and Write |
  6. Guangdong Provincial Academician Workstation of BGI Synthetic Genomics |
  7. Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics |
1000 Fördernummer
  1. 2017ZX10303406
  2. 2018ZX10301101-004
  3. 2020YFC0841400
  4. 2020B111107001; 2020B111108001; 2018B020207013
  5. 2017B030301011
  6. 2017B090904014
  7. DRC-SZ [2016]884
1000 Förderprogramm
  1. -
  2. National Major Project for Control and Prevention of Infectious Disease in China
  3. emergency grants for prevention and control
  4. emergency grants for prevention and control
  5. -
  6. -
  7. -
1000 Dateien
1000 Förderung
  1. 1000 joinedFunding-child
    1000 Förderer National Major Science and Technology Projects of China |
    1000 Förderprogramm -
    1000 Fördernummer 2017ZX10303406
  2. 1000 joinedFunding-child
    1000 Förderer Chinese Center for Disease Control and Prevention |
    1000 Förderprogramm National Major Project for Control and Prevention of Infectious Disease in China
    1000 Fördernummer 2018ZX10301101-004
  3. 1000 joinedFunding-child
    1000 Förderer Ministry of Science and Technology of the People's Republic of China |
    1000 Förderprogramm emergency grants for prevention and control
    1000 Fördernummer 2020YFC0841400
  4. 1000 joinedFunding-child
    1000 Förderer Government of Guangdong Province |
    1000 Förderprogramm emergency grants for prevention and control
    1000 Fördernummer 2020B111107001; 2020B111108001; 2018B020207013
  5. 1000 joinedFunding-child
    1000 Förderer Guangdong Provincial Key Laboratory of Genome Read and Write |
    1000 Förderprogramm -
    1000 Fördernummer 2017B030301011
  6. 1000 joinedFunding-child
    1000 Förderer Guangdong Provincial Academician Workstation of BGI Synthetic Genomics |
    1000 Förderprogramm -
    1000 Fördernummer 2017B090904014
  7. 1000 joinedFunding-child
    1000 Förderer Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics |
    1000 Förderprogramm -
    1000 Fördernummer DRC-SZ [2016]884
1000 Objektart article
1000 Beschrieben durch
1000 @id frl:6421636.rdf
1000 Erstellt am 2020-07-01T11:50:15.601+0200
1000 Erstellt von 122
1000 beschreibt frl:6421636
1000 Bearbeitet von 122
1000 Zuletzt bearbeitet Wed Jul 01 11:53:19 CEST 2020
1000 Objekt bearb. Wed Jul 01 11:52:58 CEST 2020
1000 Vgl. frl:6421636
1000 Oai Id
  1. oai:frl.publisso.de:frl:6421636 |
1000 Sichtbarkeit Metadaten public
1000 Sichtbarkeit Daten public
1000 Gegenstand von

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