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SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms

View ORCID ProfilePaola Cristina Resende, Fernando Couto Motta, View ORCID ProfileSunando Roy, View ORCID ProfileLuciana Appolinario, View ORCID ProfileAllison Fabri, View ORCID ProfileJoilson Xavier, View ORCID ProfileKathryn Harris, View ORCID ProfileAline Rocha Matos, Braulia Caetano, View ORCID ProfileMaria Orgeswalska, View ORCID ProfileMilene Miranda, View ORCID ProfileCristiana Garcia, View ORCID ProfileAndré Abreu, Rachel Williams, View ORCID ProfileJudith Breuer, View ORCID ProfileMarilda M Siqueira
doi: https://doi.org/10.1101/2020.04.30.069039
Paola Cristina Resende
1Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Brazil
2University College London, United Kingdom
5Great Ormond Street Hospital, United Kingdom
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  • ORCID record for Paola Cristina Resende
  • For correspondence: paola@ioc.fiocruz.br
Fernando Couto Motta
1Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Brazil
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Sunando Roy
2University College London, United Kingdom
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Luciana Appolinario
1Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Brazil
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  • ORCID record for Luciana Appolinario
Allison Fabri
3Laboratory of Flaviviruses, Oswaldo Cruz Institute, FIOCRUZ, Brazil
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  • ORCID record for Allison Fabri
Joilson Xavier
4Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Kathryn Harris
5Great Ormond Street Hospital, United Kingdom
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  • ORCID record for Kathryn Harris
Aline Rocha Matos
1Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Brazil
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  • ORCID record for Aline Rocha Matos
Braulia Caetano
1Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Brazil
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Maria Orgeswalska
1Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Brazil
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  • ORCID record for Maria Orgeswalska
Milene Miranda
1Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Brazil
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  • ORCID record for Milene Miranda
Cristiana Garcia
1Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Brazil
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  • ORCID record for Cristiana Garcia
André Abreu
6National Coordination of Laboratories, Brazilian Ministry of Health, Brasília, Brazil
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Rachel Williams
2University College London, United Kingdom
7Pathogen Genomics Unit, University College London, United Kingdom
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Judith Breuer
2University College London, United Kingdom
5Great Ormond Street Hospital, United Kingdom
7Pathogen Genomics Unit, University College London, United Kingdom
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  • ORCID record for Judith Breuer
Marilda M Siqueira
1Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Brazil
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  • ORCID record for Marilda M Siqueira
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Summary

Genomic surveillance has become a useful tool for better understanding virus pathogenicity, origin and spread. Obtaining accurately assembled, complete viral genomes directly from clinical samples is still a challenging. Here, we describe three protocols using a unique primer set designed to recover long reads of SARS-CoV-2 directly from total RNA extracted from clinical samples. This protocol is useful, accessible and adaptable to laboratories with varying resources and access to distinct sequencing methods: Nanopore, Illumina and/or Sanger.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵* These authors share senior authorship

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted May 01, 2020.
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SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms
Paola Cristina Resende, Fernando Couto Motta, Sunando Roy, Luciana Appolinario, Allison Fabri, Joilson Xavier, Kathryn Harris, Aline Rocha Matos, Braulia Caetano, Maria Orgeswalska, Milene Miranda, Cristiana Garcia, André Abreu, Rachel Williams, Judith Breuer, Marilda M Siqueira
bioRxiv 2020.04.30.069039; doi: https://doi.org/10.1101/2020.04.30.069039
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SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms
Paola Cristina Resende, Fernando Couto Motta, Sunando Roy, Luciana Appolinario, Allison Fabri, Joilson Xavier, Kathryn Harris, Aline Rocha Matos, Braulia Caetano, Maria Orgeswalska, Milene Miranda, Cristiana Garcia, André Abreu, Rachel Williams, Judith Breuer, Marilda M Siqueira
bioRxiv 2020.04.30.069039; doi: https://doi.org/10.1101/2020.04.30.069039

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