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Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania

View ORCID ProfileAhmed M. Moustafa, Colleen Bianco, Lidiya Denu, Azad Ahmed, Brandy Neide, John Everett, Shantan Reddy, Emilie Rabut, Jasmine Deseignora, Michael D. Feldman, Kyle G. Rodino, View ORCID ProfileFrederic Bushman, Rebecca M. Harris, Josh Chang Mell, Paul J. Planet
doi: https://doi.org/10.1101/2021.04.21.440801
Ahmed M. Moustafa
1Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
2Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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  • ORCID record for Ahmed M. Moustafa
  • For correspondence: moustafaam@chop.edu planetp@chop.edu
Colleen Bianco
1Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Lidiya Denu
1Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Azad Ahmed
3Department of Microbiology and Immunology, Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, PA 19129, USA
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Brandy Neide
1Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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John Everett
4Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Shantan Reddy
4Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Emilie Rabut
5Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
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Jasmine Deseignora
5Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
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Michael D. Feldman
6Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Kyle G. Rodino
6Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Frederic Bushman
4Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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  • ORCID record for Frederic Bushman
Rebecca M. Harris
6Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
7Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Josh Chang Mell
3Department of Microbiology and Immunology, Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, PA 19129, USA
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Paul J. Planet
1Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
7Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
8Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
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  • For correspondence: moustafaam@chop.edu planetp@chop.edu
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Abstract

Rapid whole genome sequencing of SARS-CoV-2 has presented the ability to detect new emerging variants of concern in near real time. Here we report the genome of a virus isolated in Pennsylvania in March 2021 that was identified as lineage B.1.1.7 (VOC-202012/01) that also harbors the E484K spike mutation, which has been shown to promote “escape” from neutralizing antibodies in vitro. We compare this sequence to the only 5 other B.1.1.7+E484K genomes from Pennsylvania, all of which were isolated in mid March. Beginning in February 2021, only a small number (n=60) of isolates with this profile have been detected in the US, and only a total of 253 have been reported globally (first in the UK in December 2020). Comparative genomics of all currently available high coverage B.1.1.7+E484K genomes (n=235) available on GISAID suggested the existence of 7 distinct groups or clonal complexes (CC; as defined by GNUVID) bearing the E484K mutation raising the possibility of 7 independent acquisitions of the E484K spike mutation in each background. Phylogenetic analysis suggested the presence of at least 3 distinct clades of B.1.1.7+E484K circulating in the US, with the Pennsylvanian isolates belonging to two distinct clades. Increased genomic surveillance will be crucial for detection of emerging variants of concern that can escape natural and vaccine induced immunity.

Competing Interest Statement

The authors have declared no competing interest.

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Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania
Ahmed M. Moustafa, Colleen Bianco, Lidiya Denu, Azad Ahmed, Brandy Neide, John Everett, Shantan Reddy, Emilie Rabut, Jasmine Deseignora, Michael D. Feldman, Kyle G. Rodino, Frederic Bushman, Rebecca M. Harris, Josh Chang Mell, Paul J. Planet
bioRxiv 2021.04.21.440801; doi: https://doi.org/10.1101/2021.04.21.440801
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Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania
Ahmed M. Moustafa, Colleen Bianco, Lidiya Denu, Azad Ahmed, Brandy Neide, John Everett, Shantan Reddy, Emilie Rabut, Jasmine Deseignora, Michael D. Feldman, Kyle G. Rodino, Frederic Bushman, Rebecca M. Harris, Josh Chang Mell, Paul J. Planet
bioRxiv 2021.04.21.440801; doi: https://doi.org/10.1101/2021.04.21.440801

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