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Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas

S. Wesley Long, Randall J. Olsen, Paul A. Christensen, David W. Bernard, James R. Davis, Maulik Shukla, Marcus Nguyen, Matthew Ojeda Saavedra, Concepcion C. Cantu, Prasanti Yerramilli, Layne Pruitt, Sishir Subedi, Heather Hendrickson, Ghazaleh Eskandari, Muthiah Kumaraswami, Jason S. McLellan, James M. Musser
doi: https://doi.org/10.1101/2020.05.01.072652
S. Wesley Long
aCenter for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
bDepartments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
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Randall J. Olsen
aCenter for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
bDepartments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
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Paul A. Christensen
aCenter for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
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David W. Bernard
aCenter for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
bDepartments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
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James R. Davis
cConsortium for Advanced Science and Engineering, University of Chicago, 5801 South Ellis Avenue, Chicago, Illinois, 60637
dComputing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439
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Maulik Shukla
cConsortium for Advanced Science and Engineering, University of Chicago, 5801 South Ellis Avenue, Chicago, Illinois, 60637
dComputing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439
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Marcus Nguyen
cConsortium for Advanced Science and Engineering, University of Chicago, 5801 South Ellis Avenue, Chicago, Illinois, 60637
dComputing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439
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Matthew Ojeda Saavedra
aCenter for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
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Concepcion C. Cantu
aCenter for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
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Prasanti Yerramilli
aCenter for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
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Layne Pruitt
aCenter for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
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Sishir Subedi
aCenter for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
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Heather Hendrickson
aCenter for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
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Ghazaleh Eskandari
aCenter for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
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Muthiah Kumaraswami
aCenter for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
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Jason S. McLellan
eDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
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James M. Musser
aCenter for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
bDepartments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
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  • For correspondence: jmmusser@houstonmethodist.org
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Abstract

We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. These genomes were from the viruses causing infections in the earliest recognized phase of the pandemic affecting Houston. Substantial viral genomic diversity was identified, which we interpret to mean that the virus was introduced into Houston many times independently by individuals who had traveled from different parts of the country and the world. The majority of viruses are apparent progeny of strains derived from Europe and Asia. We found no significant evidence of more virulent viral types, stressing the linkage between severe disease, underlying medical conditions, and perhaps host genetics. We discovered a signal of selection acting on the spike protein, the primary target of massive vaccine efforts worldwide. The data provide a critical resource for assessing virus evolution, the origin of new outbreaks, and the effect of host immune response.

Significance COVID-19, the disease caused by the SARS-CoV-2 virus, is a global pandemic. To better understand the first phase of virus spread in metropolitan Houston, Texas, we sequenced the genomes of 320 SARS-CoV-2 strains recovered from COVID-19 patients early in the Houston viral arc. We identified no evidence that a particular strain or its progeny causes more severe disease, underscoring the connection between severe disease, underlying health conditions, and host genetics. Some amino acid replacements in the spike protein suggest positive immune selection is at work in shaping variation in this protein. Our analysis traces the early molecular architecture of SARS-CoV-2 in Houston, and will help us to understand the origin and trajectory of future infection spikes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Addition of GISAID deposition statement in methods.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas
S. Wesley Long, Randall J. Olsen, Paul A. Christensen, David W. Bernard, James R. Davis, Maulik Shukla, Marcus Nguyen, Matthew Ojeda Saavedra, Concepcion C. Cantu, Prasanti Yerramilli, Layne Pruitt, Sishir Subedi, Heather Hendrickson, Ghazaleh Eskandari, Muthiah Kumaraswami, Jason S. McLellan, James M. Musser
bioRxiv 2020.05.01.072652; doi: https://doi.org/10.1101/2020.05.01.072652
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Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas
S. Wesley Long, Randall J. Olsen, Paul A. Christensen, David W. Bernard, James R. Davis, Maulik Shukla, Marcus Nguyen, Matthew Ojeda Saavedra, Concepcion C. Cantu, Prasanti Yerramilli, Layne Pruitt, Sishir Subedi, Heather Hendrickson, Ghazaleh Eskandari, Muthiah Kumaraswami, Jason S. McLellan, James M. Musser
bioRxiv 2020.05.01.072652; doi: https://doi.org/10.1101/2020.05.01.072652

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