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1. Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data

Author

Nadeau, Sarah A., primary, Vaughan, Timothy G., additional, Beckmann, Christiane, additional, Topolsky, Ivan, additional, Chen, Chaoran, additional, Hodcroft, Emma, additional, Schär, Tobias, additional, Nissen, Ina, additional, Santacroce, Natascha, additional, Burcklen, Elodie, additional, Ferreira, Pedro, additional, Jablonski, Kim Philipp, additional, Posada-Céspedes, Susana, additional, Capece, Vincenzo, additional, Seidel, Sophie, additional, Santamaria de Souza, Noemi, additional, Martinez-Gomez, Julia M., additional, Cheng, Phil, additional, Bosshard, Philipp P., additional, Levesque, Mitchell P., additional, Kufner, Verena, additional, Schmutz, Stefan, additional, Zaheri, Maryam, additional, Huber, Michael, additional, Trkola, Alexandra, additional, Cordey, Samuel, additional, Laubscher, Florian, additional, Gonçalves, Ana Rita, additional, Aeby, Sébastien, additional, Pillonel, Trestan, additional, Jacot, Damien, additional, Bertelli, Claire, additional, Greub, Gilbert, additional, Leuzinger, Karoline, additional, Stange, Madlen, additional, Mari, Alfredo, additional, Roloff, Tim, additional, Seth-Smith, Helena, additional, Hirsch, Hans H., additional, Egli, Adrian, additional, Redondo, Maurice, additional, Kobel, Olivier, additional, Noppen, Christoph, additional, du Plessis, Louis, additional, Beerenwinkel, Niko, additional, Neher, Richard A., additional, Beisel, Christian, additional, and Stadler, Tanja, additional

Published
2023
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2. Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data

Author

Nadeau, Sarah A., primary, Vaughan, Timothy G., additional, Beckmann, Christiane, additional, Topolsky, Ivan, additional, Chen, Chaoran, additional, Hodcroft, Emma, additional, Schär, Tobias, additional, Nissen, Ina, additional, Santacroce, Natascha, additional, Burcklen, Elodie, additional, Ferreira, Pedro, additional, Jablonski, Kim Philipp, additional, Posada-Céspedes, Susana, additional, Capece, Vincenzo, additional, Seidel, Sophie, additional, de Souza, Noemi Santamaria, additional, Martinez-Gomez, Julia M., additional, Cheng, Phil, additional, Bosshard, Philipp P., additional, Levesque, Mitchell P., additional, Kufner, Verena, additional, Schmutz, Stefan, additional, Zaheri, Maryam, additional, Huber, Michael, additional, Trkola, Alexandra, additional, Cordey, Samuel, additional, Laubscher, Florian, additional, Gonçalves, Ana Rita, additional, Aeby, Sébastien, additional, Pillonel, Trestan, additional, Jacot, Damien, additional, Bertelli, Claire, additional, Greub, Gilbert, additional, Leuzinger, Karoline, additional, Stange, Madlen, additional, Mari, Alfredo, additional, Roloff, Tim, additional, Seth-Smith, Helena, additional, Hirsch, Hans H., additional, Egli, Adrian, additional, Redondo, Maurice, additional, Kobel, Olivier, additional, Noppen, Christoph, additional, du Plessis, Louis, additional, Beerenwinkel, Niko, additional, Neher, Richard A., additional, Beisel, Christian, additional, and Stadler, Tanja, additional

Published
2021
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3. Within-patient genetic diversity of SARS-CoV-2

Author

Kuipers, Jack, Batavia, Aashil A., Jablonski, Kim Philipp, Bayer, Fritz, Borgsmüller, Nico, Dondi, Arthur, Drăgan, Monica-Andreea, Ferreira, Pedro, Jahn, Katharina, Lamberti, Lisa, Pirkl, Martin, Posada Cespedes, Susana, Topolsky, Ivan, Nissen, Ina, Santacroce, Natascha, Burcklen, Elodie, Schär, Tobias, Capece, Vincenzo, Beckmann, Christiane, Kobel, Olivier, Noppen, Christoph, Redondo, Maurice, Nadeau, Sarah Ann, Seidel, Sophie, Santamaria de Souza, Noemie, Beisel, Christian, Stadler, Tanja, and Beerenwinkel, Niko

Subjects
respiratory system, human activities
Abstract

SARS-CoV-2, the virus responsible for the current COVID-19 pandemic, is evolving into different genetic variants by accumulating mutations as it spreads globally. In addition to this diversity of consensus genomes across patients, RNA viruses can also display genetic diversity within individual hosts, and co-existing viral variants may affect disease progression and the success of medical interventions. To systematically examine the intra-patient genetic diversity of SARS-CoV-2, we processed a large cohort of 3939 publicly-available deeply sequenced genomes with specialised bioinformatics software, along with 749 recently sequenced samples from Switzerland. We found that the distribution of diversity across patients and across genomic loci is very unbalanced with a minority of hosts and positions accounting for much of the diversity. For example, the D614G variant in the Spike gene, which is present in the consensus sequences of 67.4% of patients, is also highly diverse within hosts, with 29.7% of the public cohort being affected by this coexistence and exhibiting different variants. We also investigated the impact of several technical and epidemiological parameters on genetic heterogeneity and found that age, which is known to be correlated with poor disease outcomes, is a significant predictor of viral genetic diversity., bioRxiv

Published
2020

4. Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data

Author

Nadeau, Sarah, primary, Beckmann, Christiane, additional, Topolsky, Ivan, additional, Vaughan, Timothy, additional, Hodcroft, Emma, additional, Schär, Tobias, additional, Nissen, Ina, additional, Santacroce, Natascha, additional, Burcklen, Elodie, additional, Ferreira, Pedro, additional, Jablonski, Kim Philipp, additional, Posada-Céspedes, Susana, additional, Capece, Vincenzo, additional, Seidel, Sophie, additional, de Souza, Noemi Santamaria, additional, Martinez-Gomez, Julia M., additional, Cheng, Phil, additional, Bosshard, Philipp P., additional, Levesque, Mitchell P., additional, Kufner, Verena, additional, Schmutz, Stefan, additional, Zaheri, Maryam, additional, Huber, Michael, additional, Trkola, Alexandra, additional, Cordey, Samuel, additional, Laubscher, Florian, additional, Gonçalves, Ana Rita, additional, Leuzinger, Karoline, additional, Stange, Madlen, additional, Mari, Alfredo, additional, Roloff, Tim, additional, Seth-Smith, Helena, additional, Hirsch, Hans H., additional, Egli, Adrian, additional, Redondo, Maurice, additional, Kobel, Olivier, additional, Noppen, Christoph, additional, Beerenwinkel, Niko, additional, Neher, Richard A., additional, Beisel, Christian, additional, and Stadler, Tanja, additional

Published
2020
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5. Within-patient genetic diversity of SARS-CoV-2

Author

Kuipers, Jack, primary, Batavia, Aashil A, additional, Jablonski, Kim Philipp, additional, Bayer, Fritz, additional, Borgsmüller, Nico, additional, Dondi, Arthur, additional, Drăgan, Monica-Andreea, additional, Ferreira, Pedro, additional, Jahn, Katharina, additional, Lamberti, Lisa, additional, Pirkl, Martin, additional, Posada-Céspedes, Susana, additional, Topolsky, Ivan, additional, Nissen, Ina, additional, Santacroce, Natascha, additional, Burcklen, Elodie, additional, Schär, Tobias, additional, Capece, Vincenzo, additional, Beckmann, Christiane, additional, Kobel, Olivier, additional, Noppen, Christoph, additional, Redondo, Maurice, additional, Nadeau, Sarah, additional, Seidel, Sophie, additional, Santamaria de Souza, Noemie, additional, Beisel, Christian, additional, Stadler, Tanja, additional, and Beerenwinkel, Niko, additional

Published
2020
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