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Mr. Christian Baumann
Institute for Infectious Diseases, University of Bern

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0 Cell Culture
0 Diagnostics
0 Molecular Biology
0 Nanoscience
0 Virology

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Journal article
Published: 25 March 2021 in Microorganisms
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The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological and microbiological definitions. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 13,387 VoCs have been identified since the detection of the first Swiss case in October 2020, with 4194 being B.1.1.7, 172 B.1.351, and 7 P.1. The remaining 9014 cases of VoCs have been described without further lineage specification. Overall, all diagnostic centers reported a rapid increase of the percentage of detected VOCs, with a range of 6 to 46% between 25 to 31 of January 2021 increasing towards 41 to 82% between 22 to 28 of February. A total of 739 N501Y positive genomes were analysed and show a broad range of introduction events to Switzerland. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.

ACS Style

Ana Goncalves Cabecinhas; Tim Roloff; Madlen Stange; Claire Bertelli; Michael Huber; Alban Ramette; Chaoran Chen; Sarah Nadeau; Yannick Gerth; Sabine Yerly; Onya Opota; Trestan Pillonel; Tobias Schuster; Cesar Metzger; Jonas Sieber; Michael Bel; Nadia Wohlwend; Christian Baumann; Michel Koch; Pascal Bittel; Karoline Leuzinger; Myrta Brunner; Franziska Suter-Riniker; Livia Berlinger; Kirstine Søgaard; Christiane Beckmann; Christoph Noppen; Maurice Redondo; Ingrid Steffen; Helena Seth-Smith; Alfredo Mari; Reto Lienhard; Martin Risch; Oliver Nolte; Isabella Eckerle; Gladys Martinetti Lucchini; Emma Hodcroft; Richard Neher; Tanja Stadler; Hans Hirsch; Stephen Leib; Lorenz Risch; Laurent Kaiser; Alexandra Trkola; Gilbert Greub; Adrian Egli. SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Microorganisms 2021, 9, 677 .

AMA Style

Ana Goncalves Cabecinhas, Tim Roloff, Madlen Stange, Claire Bertelli, Michael Huber, Alban Ramette, Chaoran Chen, Sarah Nadeau, Yannick Gerth, Sabine Yerly, Onya Opota, Trestan Pillonel, Tobias Schuster, Cesar Metzger, Jonas Sieber, Michael Bel, Nadia Wohlwend, Christian Baumann, Michel Koch, Pascal Bittel, Karoline Leuzinger, Myrta Brunner, Franziska Suter-Riniker, Livia Berlinger, Kirstine Søgaard, Christiane Beckmann, Christoph Noppen, Maurice Redondo, Ingrid Steffen, Helena Seth-Smith, Alfredo Mari, Reto Lienhard, Martin Risch, Oliver Nolte, Isabella Eckerle, Gladys Martinetti Lucchini, Emma Hodcroft, Richard Neher, Tanja Stadler, Hans Hirsch, Stephen Leib, Lorenz Risch, Laurent Kaiser, Alexandra Trkola, Gilbert Greub, Adrian Egli. SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Microorganisms. 2021; 9 (4):677.

Chicago/Turabian Style

Ana Goncalves Cabecinhas; Tim Roloff; Madlen Stange; Claire Bertelli; Michael Huber; Alban Ramette; Chaoran Chen; Sarah Nadeau; Yannick Gerth; Sabine Yerly; Onya Opota; Trestan Pillonel; Tobias Schuster; Cesar Metzger; Jonas Sieber; Michael Bel; Nadia Wohlwend; Christian Baumann; Michel Koch; Pascal Bittel; Karoline Leuzinger; Myrta Brunner; Franziska Suter-Riniker; Livia Berlinger; Kirstine Søgaard; Christiane Beckmann; Christoph Noppen; Maurice Redondo; Ingrid Steffen; Helena Seth-Smith; Alfredo Mari; Reto Lienhard; Martin Risch; Oliver Nolte; Isabella Eckerle; Gladys Martinetti Lucchini; Emma Hodcroft; Richard Neher; Tanja Stadler; Hans Hirsch; Stephen Leib; Lorenz Risch; Laurent Kaiser; Alexandra Trkola; Gilbert Greub; Adrian Egli. 2021. "SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing." Microorganisms 9, no. 4: 677.

Journal article
Published: 31 July 2020 in Viruses
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Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, enteroviruses are identified by PCR-based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. The approach was complemented by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% and 99.6% of the most similar reference genome sequences. The identification of the enterovirus sequences in the samples was confirmed by short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94% and 97%. Here, we show that nanopore DRS can be used to correctly identify enterovirus genotypes from patient stool samples with high viral load and that the approach also provides rich metatranscriptomic information on sample composition for all life domains.

ACS Style

Carole Grädel; Miguel A. Terrazos Miani; Christian Baumann; Maria Teresa Barbani; Stefan Neuenschwander; Stephen L. Leib; Franziska Suter-Riniker; Alban Ramette. Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing. Viruses 2020, 12, 841 .

AMA Style

Carole Grädel, Miguel A. Terrazos Miani, Christian Baumann, Maria Teresa Barbani, Stefan Neuenschwander, Stephen L. Leib, Franziska Suter-Riniker, Alban Ramette. Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing. Viruses. 2020; 12 (8):841.

Chicago/Turabian Style

Carole Grädel; Miguel A. Terrazos Miani; Christian Baumann; Maria Teresa Barbani; Stefan Neuenschwander; Stephen L. Leib; Franziska Suter-Riniker; Alban Ramette. 2020. "Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing." Viruses 12, no. 8: 841.

Other
Published: 09 June 2020
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Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, those viruses are identified by PCR based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. Results of the approach were complemented with those obtained by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% to 99.6 % of the best reference genomes. The identification of the enterovirus sequences in the sample was confirmed by the short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94-97%. Here we show that nanopore DRS can be used to correctly identify the genotypes of enteroviruses from patient stool samples with high viral load.

ACS Style

Carole Grädel; Miguel A Terrazos Miani; Christian Baumann; Maria Teresa Barbani; Stefan Neuenschwander; Stephen L Leib; Franziska Suter-Riniker; Alban Ramette. Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing. 2020, 1 .

AMA Style

Carole Grädel, Miguel A Terrazos Miani, Christian Baumann, Maria Teresa Barbani, Stefan Neuenschwander, Stephen L Leib, Franziska Suter-Riniker, Alban Ramette. Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing. . 2020; ():1.

Chicago/Turabian Style

Carole Grädel; Miguel A Terrazos Miani; Christian Baumann; Maria Teresa Barbani; Stefan Neuenschwander; Stephen L Leib; Franziska Suter-Riniker; Alban Ramette. 2020. "Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing." , no. : 1.