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Multiple spillovers and onward transmission of SARS-Cov-2 in free-living and captive White-tailed deer (Odocoileus virginianus)

View ORCID ProfileSuresh V. Kuchipudi, Meera Surendran-Nair, Rachel M. Ruden, Michelle Yon, Ruth H. Nissly, Rahul K. Nelli, Lingling Li, Bhushan M. Jayarao, Kurt J. Vandegrift, Costas D. Maranas, Nicole Levine, Katriina Willgert, View ORCID ProfileAndrew J. K. Conlan, Randall J. Olsen, James J. Davis, James M. Musser, Peter J. Hudson, Vivek Kapur
doi: https://doi.org/10.1101/2021.10.31.466677
Suresh V. Kuchipudi
1Animal Diagnostic Laboratory and Huck Institutes of Life Sciences, Penn State, University Park, PA 16802, USA
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  • ORCID record for Suresh V. Kuchipudi
  • For correspondence: skuchipudi@psu.edu vkapur@psu.edu
Meera Surendran-Nair
1Animal Diagnostic Laboratory and Huck Institutes of Life Sciences, Penn State, University Park, PA 16802, USA
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Rachel M. Ruden
2Wildlife Bureau, Iowa Department of Natural Resources, Des Moines, Iowa, USA
3Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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Michelle Yon
4Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, PA,16802, USA
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Ruth H. Nissly
1Animal Diagnostic Laboratory and Huck Institutes of Life Sciences, Penn State, University Park, PA 16802, USA
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Rahul K. Nelli
3Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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Lingling Li
4Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, PA,16802, USA
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Bhushan M. Jayarao
4Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, PA,16802, USA
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Kurt J. Vandegrift
5The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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Costas D. Maranas
6Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
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Nicole Levine
7Department of Animal Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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Katriina Willgert
8Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, UK
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Andrew J. K. Conlan
8Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, UK
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Randall J. Olsen
9Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
10Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
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James J. Davis
11University of Chicago Consortium for Advanced Science and Engineering, University of Chicago and Division of Data Science and Learning, Argonne National Laboratory, Argonne, Illinois, USA
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James M. Musser
9Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
10Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
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Peter J. Hudson
5The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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Vivek Kapur
7Department of Animal Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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  • For correspondence: skuchipudi@psu.edu vkapur@psu.edu
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Abstract

Many animal species are susceptible to SARS-CoV-2 and could potentially act as reservoirs, yet transmission in non-human free-living animals has not been documented. White-tailed deer (Odocoileus virginianus), the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns transmit the virus to other captive deer. To test the hypothesis that SARS-CoV-2 may be circulating in deer, we evaluated 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through December of 2020 for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 deer (33.2%; 95% CI: 28, 38.9) samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, between Nov 23, 2020 and January 10, 2021, 80 of 97 (82.5%; 95% CI 73.7, 88.8) RPLN samples had detectable SARS-CoV-2 RNA by RT-PCR. Whole genome sequencing of the 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%), and B.1.311 (n = 19; 20%) accounting for ~75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple zooanthroponotic spillover events and deer-to-deer transmission. The discovery of sylvatic and enzootic SARS-CoV-2 transmission in deer has important implications for the ecology and long-term persistence, as well as the potential for spillover to other animals and spillback into humans. These findings highlight an urgent need for a robust and proactive “One Health” approach to obtaining a better understanding of the ecology and evolution of SARS-CoV-2.

One-Sentence Summary SARS-CoV-2 was detected in one-third of sampled White-tailed deer in Iowa between September 2020 and January of 2021 that likely resulted from multiple human-to-deer spillover events and deer-to-deer transmission.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Multiple spillovers and onward transmission of SARS-Cov-2 in free-living and captive White-tailed deer (Odocoileus virginianus)
Suresh V. Kuchipudi, Meera Surendran-Nair, Rachel M. Ruden, Michelle Yon, Ruth H. Nissly, Rahul K. Nelli, Lingling Li, Bhushan M. Jayarao, Kurt J. Vandegrift, Costas D. Maranas, Nicole Levine, Katriina Willgert, Andrew J. K. Conlan, Randall J. Olsen, James J. Davis, James M. Musser, Peter J. Hudson, Vivek Kapur
bioRxiv 2021.10.31.466677; doi: https://doi.org/10.1101/2021.10.31.466677
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Multiple spillovers and onward transmission of SARS-Cov-2 in free-living and captive White-tailed deer (Odocoileus virginianus)
Suresh V. Kuchipudi, Meera Surendran-Nair, Rachel M. Ruden, Michelle Yon, Ruth H. Nissly, Rahul K. Nelli, Lingling Li, Bhushan M. Jayarao, Kurt J. Vandegrift, Costas D. Maranas, Nicole Levine, Katriina Willgert, Andrew J. K. Conlan, Randall J. Olsen, James J. Davis, James M. Musser, Peter J. Hudson, Vivek Kapur
bioRxiv 2021.10.31.466677; doi: https://doi.org/10.1101/2021.10.31.466677

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