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Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function
Darren P Martin, Spyros Lytras, Alexander G Lucaci, Wolfgang Maier, Björn Grüning, Stephen D Shank, Steven Weaver, Oscar A MacLean, Richard J Orton, Philippe Lemey, Maciej F Boni, Houriiyah Tegally, Gordon Harkins, Cathrine Scheepers, Jinal N Bhiman, Josie Everatt, Daniel G Amoako, James Emmanuel San, Jennifer Giandhari, Alex Sigal, NGS-SA, Carolyn Williamson, Nei-yuan Hsiao, Anne von Gottberg, Arne De Klerk, Robert W Shafer, David L Robertson, Robert J Wilkinson, B Trevor Sewell, Richard Lessells, Anton Nekrutenko, Allison J. Greaney, Tyler N. Starr, Jesse D. Bloom, Ben Murrell, Eduan Wilkinson, Ravindra K Gupta, Tulio de Oliveira, Sergei L Kosakovsky Pond
doi: https://doi.org/10.1101/2022.01.14.476382
Darren P Martin
1Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa
Spyros Lytras
2MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
Alexander G Lucaci
3Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
Wolfgang Maier
4Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany,
Björn Grüning
4Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany,
Stephen D Shank
3Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
Steven Weaver
3Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
Oscar A MacLean
2MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
Richard J Orton
2MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
Philippe Lemey
5Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Maciej F Boni
6Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
Houriiyah Tegally
7KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
Gordon Harkins
8South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
Cathrine Scheepers
9National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
10SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
Jinal N Bhiman
9National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
10SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
Josie Everatt
9National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
Daniel G Amoako
9National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
James Emmanuel San
7KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
Jennifer Giandhari
7KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
Alex Sigal
11Africa Health Research Institute, Durban, South Africa
12
Carolyn Williamson
13Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
14Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town South Africa
17Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, South Africa
Nei-yuan Hsiao
14Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town South Africa
Anne von Gottberg
9National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
15School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
Arne De Klerk
1Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa
Robert W Shafer
16Division of Infectious Diseases, Department of medicine, Stanford university, Stanford, CA, USA
David L Robertson
2MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
Robert J Wilkinson
17Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, South Africa
18Francis Crick Institute, Midland Road, London NW1 1AT, UK
19Department of Infectious Diseases, Imperial College London, W12 0NN, UK
B Trevor Sewell
20Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa
Richard Lessells
7KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
Anton Nekrutenko
21Department Of Biochemistry and Molecular Biology, The Pennsylvania State University,
Allison J. Greaney
22Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
23Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA3
Tyler N. Starr
22Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
24Howard Hughes Medical Institute, Seattle, WA 98109, USA
Jesse D. Bloom
22Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
24Howard Hughes Medical Institute, Seattle, WA 98109, USA
Ben Murrell
25Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
Eduan Wilkinson
7KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
26Centre for Epidemic Response and Innovation (CERI), School of Data Science, Stellenbosch University
Ravindra K Gupta
11Africa Health Research Institute, Durban, South Africa
27Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge
Tulio de Oliveira
7KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
26Centre for Epidemic Response and Innovation (CERI), School of Data Science, Stellenbosch University
Sergei L Kosakovsky Pond
3Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
Article usage
Posted January 18, 2022.
Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function
Darren P Martin, Spyros Lytras, Alexander G Lucaci, Wolfgang Maier, Björn Grüning, Stephen D Shank, Steven Weaver, Oscar A MacLean, Richard J Orton, Philippe Lemey, Maciej F Boni, Houriiyah Tegally, Gordon Harkins, Cathrine Scheepers, Jinal N Bhiman, Josie Everatt, Daniel G Amoako, James Emmanuel San, Jennifer Giandhari, Alex Sigal, NGS-SA, Carolyn Williamson, Nei-yuan Hsiao, Anne von Gottberg, Arne De Klerk, Robert W Shafer, David L Robertson, Robert J Wilkinson, B Trevor Sewell, Richard Lessells, Anton Nekrutenko, Allison J. Greaney, Tyler N. Starr, Jesse D. Bloom, Ben Murrell, Eduan Wilkinson, Ravindra K Gupta, Tulio de Oliveira, Sergei L Kosakovsky Pond
bioRxiv 2022.01.14.476382; doi: https://doi.org/10.1101/2022.01.14.476382
Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function
Darren P Martin, Spyros Lytras, Alexander G Lucaci, Wolfgang Maier, Björn Grüning, Stephen D Shank, Steven Weaver, Oscar A MacLean, Richard J Orton, Philippe Lemey, Maciej F Boni, Houriiyah Tegally, Gordon Harkins, Cathrine Scheepers, Jinal N Bhiman, Josie Everatt, Daniel G Amoako, James Emmanuel San, Jennifer Giandhari, Alex Sigal, NGS-SA, Carolyn Williamson, Nei-yuan Hsiao, Anne von Gottberg, Arne De Klerk, Robert W Shafer, David L Robertson, Robert J Wilkinson, B Trevor Sewell, Richard Lessells, Anton Nekrutenko, Allison J. Greaney, Tyler N. Starr, Jesse D. Bloom, Ben Murrell, Eduan Wilkinson, Ravindra K Gupta, Tulio de Oliveira, Sergei L Kosakovsky Pond
bioRxiv 2022.01.14.476382; doi: https://doi.org/10.1101/2022.01.14.476382
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