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Vandegrift KJ, Yon M, Surendran-Nair M, Gontu A, Amirthalingam S, Nissly RH, Levine N, Stuber T, DeNicola AJ, Boulanger JR, Kotschwar N, Aucoin SG, Simon R, Toal K, Olsen RJ, Davis JJ, Bold D, Gaudreault NN, Richt JA, Musser JM, Hudson PJ, Kapur V, Kuchipudi SV. Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.04.479189. [PMID: 35169802 PMCID: PMC8845426 DOI: 10.1101/2022.02.04.479189] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
White-tailed deer ( Odocoileus virginianus ) are highly susceptible to infection by SARS-CoV-2, with multiple reports of widespread spillover of virus from humans to free-living deer. While the recently emerged SARS-CoV-2 B.1.1.529 Omicron variant of concern (VoC) has been shown to be notably more transmissible amongst humans, its ability to cause infection and spillover to non-human animals remains a challenge of concern. We found that 19 of the 131 (14.5%; 95% CI: 0.10-0.22) white-tailed deer opportunistically sampled on Staten Island, New York, between December 12, 2021, and January 31, 2022, were positive for SARS-CoV-2 specific serum antibodies using a surrogate virus neutralization assay, indicating prior exposure. The results also revealed strong evidence of age-dependence in antibody prevalence. A significantly (χ 2 , p < 0.001) greater proportion of yearling deer possessed neutralizing antibodies as compared with fawns (OR=12.7; 95% CI 4-37.5). Importantly, SARS-CoV-2 nucleic acid was detected in nasal swabs from seven of 68 (10.29%; 95% CI: 0.0-0.20) of the sampled deer, and whole-genome sequencing identified the SARS-CoV-2 Omicron VoC (B.1.1.529) is circulating amongst the white-tailed deer on Staten Island. Phylogenetic analyses revealed the deer Omicron sequences clustered closely with other, recently reported Omicron sequences recovered from infected humans in New York City and elsewhere, consistent with human to deer spillover. Interestingly, one individual deer was positive for viral RNA and had a high level of neutralizing antibodies, suggesting either rapid serological conversion during an ongoing infection or a "breakthrough" infection in a previously exposed animal. Together, our findings show that the SARS-CoV-2 B.1.1.529 Omicron VoC can infect white-tailed deer and highlights an urgent need for comprehensive surveillance of susceptible animal species to identify ecological transmission networks and better assess the potential risks of spillback to humans. KEY FINDINGS These studies provide strong evidence of infection of free-living white-tailed deer with the SARS-CoV-2 B.1.1.529 Omicron variant of concern on Staten Island, New York, and highlight an urgent need for investigations on human-to-animal-to-human spillovers/spillbacks as well as on better defining the expanding host-range of SARS-CoV-2 in non-human animals and the environment.
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Affiliation(s)
- Kurt J. Vandegrift
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Michele Yon
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Meera Surendran-Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Abhinay Gontu
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Saranya Amirthalingam
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Nicole Levine
- Department of Animal Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, Iowa, USA
| | | | | | | | - Sarah Grimké Aucoin
- City of New York Parks & Recreation, 1234 5 Avenue, 5 Floor, New York, NY 10029, USA
| | - Richard Simon
- City of New York Parks & Recreation, 1234 5 Avenue, 5 Floor, New York, NY 10029, USA
| | - Katrina Toal
- City of New York Parks & Recreation, 1234 5 Avenue, 5 Floor, New York, NY 10029, USA
| | - Randall J. Olsen
- Laboratory 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
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
| | - James J. Davis
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago and Division of Data Science and Learning, Argonne National Laboratory, Argonne, Illinois, USA
| | - Dashzeveg Bold
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - James M. Musser
- Laboratory 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
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
| | - Peter J. Hudson
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Vivek Kapur
- Department of Animal Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Suresh V. Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
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Simmonds P. Pervasive RNA Secondary Structure in the Genomes of SARS-CoV-2 and Other Coronaviruses. mBio 2020; 11:e01661-20. [PMID: 33127861 PMCID: PMC7642675 DOI: 10.1128/mbio.01661-20] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/12/2020] [Indexed: 12/25/2022] Open
Abstract
The ultimate outcome of the coronavirus disease 2019 (COVID-19) pandemic is unknown and is dependent on a complex interplay of its pathogenicity, transmissibility, and population immunity. In the current study, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was investigated for the presence of large-scale internal RNA base pairing in its genome. This property, termed genome-scale ordered RNA structure (GORS) has been previously associated with host persistence in other positive-strand RNA viruses, potentially through its shielding effect on viral RNA recognition in the cell. Genomes of SARS-CoV-2 were remarkably structured, with minimum folding energy differences (MFEDs) of 15%, substantially greater than previously examined viruses such as hepatitis C virus (HCV) (MFED of 7 to 9%). High MFED values were shared with all coronavirus genomes analyzed and created by several hundred consecutive energetically favored stem-loops throughout the genome. In contrast to replication-associated RNA structure, GORS was poorly conserved in the positions and identities of base pairing with other sarbecoviruses-even similarly positioned stem-loops in SARS-CoV-2 and SARS-CoV rarely shared homologous pairings, indicative of more rapid evolutionary change in RNA structure than in the underlying coding sequences. Sites predicted to be base paired in SARS-CoV-2 showed less sequence diversity than unpaired sites, suggesting that disruption of RNA structure by mutation imposes a fitness cost on the virus that is potentially restrictive to its longer evolution. Although functionally uncharacterized, GORS in SARS-CoV-2 and other coronaviruses represents important elements in their cellular interactions that may contribute to their persistence and transmissibility.IMPORTANCE The detection and characterization of large-scale RNA secondary structure in the genome of SARS-CoV-2 indicate an extraordinary and unsuspected degree of genome structural organization; this could be effectively visualized through a newly developed contour plotting method that displays positions, structural features, and conservation of RNA secondary structure between related viruses. Such RNA structure imposes a substantial evolutionary cost; paired sites showed greater restriction in diversity and represent a substantial additional constraint in reconstructing its molecular epidemiology. Its biological relevance arises from previously documented associations between possession of structured genomes and persistence, as documented for HCV and several other RNA viruses infecting humans and mammals. Shared properties potentially conferred by large-scale structure in SARS-CoV-2 include increasing evidence for prolonged infections and induced immune dysfunction that prevents development of protective immunity. The findings provide an additional element to cellular interactions that potentially influences the natural history of SARS-CoV-2, its pathogenicity, and its transmission.
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Affiliation(s)
- P Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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4
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Tsitsilonis OE, Paraskevis D, Lianidou E, Pierros V, Akalestos A, Kastritis E, Moutsatsou P, Scorilas A, Sphicopoulos T, Terpos E, Thomaidis N, Tsakris A, Voulgaris N, Daskalaki CC, Evangelakou Z, Fouki C, Gianniou DD, Gumeni S, Kostaki EG, Kostopoulos IV, Manola MS, Orologas-Stavrou N, Panteli C, Papanagnou ED, Rousakis P, Sklirou AD, Smilkou S, Stergiopoulou D, Trougakos IP, Tsiodras S, Sfikakis PP, Dimopoulos MA. Seroprevalence of Antibodies against SARS-CoV-2 among the Personnel and Students of the National and Kapodistrian University of Athens, Greece: A Preliminary Report. Life (Basel) 2020; 10:E214. [PMID: 32967110 PMCID: PMC7555935 DOI: 10.3390/life10090214] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 01/19/2023] Open
Abstract
Due to early implementation of public health measures, Greece had low number of SARS-CoV-2 infections and COVID-19 severe incidents in hospitalized patients. The National and Kapodistrian University of Athens (ΝΚUA), especially its health-care/medical personnel, has been actively involved in the first line of state responses to COVID-19. To estimate the prevalence of antibodies (Igs) against SARS-CoV-2 among NKUA members, we designed a five consecutive monthly serosurvey among randomly selected NKUA consenting volunteers. Here, we present the results from the first 2500 plasma samples collected during June-July 2020. Twenty-five donors were tested positive for anti-SARS-CoV-2 Igs; thus, the overall seroprevalence was 1.00%. The weighted overall seroprevalence was 0.93% (95% CI: 0.27, 2.09) and varied between males [1.05% (95% CI: 0.18, 2.92)] and females [0.84% (95% CI: 0.13, 2.49)], age-groups and different categories (higher in participants from the School of Health Sciences and in scientific affiliates/faculty members/laboratory assistants), but no statistical differences were detected. Although focused on the specific population of NKUA members, our study shows that the prevalence of anti-SARS-CoV-2 Igs for the period June-July 2020 remained low and provides knowledge of public health importance for the NKUA members. Given that approximately one in three infections was asymptomatic, continuous monitoring of the progression of the pandemic by assessing Ig seroprevalence is needed.
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Affiliation(s)
- Ourania E Tsitsilonis
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, NKUA, 15772 Athens, Greece
| | - Evi Lianidou
- Department of Chemistry, NKUA, Athens 15771, Greece
| | - Vassilios Pierros
- Department of Informatics and Telecommunications, NKUA, 15784 Athens, Greece
| | | | - Efstathios Kastritis
- Department of Clinical Therapeutics, School of Medicine, Alexandra General Hospital, NKUA, 11528 Athens, Greece
| | - Paraskevi Moutsatsou
- Department of Clinical Biochemistry, School of Medicine, University General Hospital Attikon, NKUA, 12462 Haidari, Greece
| | - Andreas Scorilas
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Thomas Sphicopoulos
- Department of Informatics and Telecommunications, NKUA, 15784 Athens, Greece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, Alexandra General Hospital, NKUA, 11528 Athens, Greece
| | | | | | | | - Christina C Daskalaki
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Zoi Evangelakou
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Christina Fouki
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, NKUA, 15772 Athens, Greece
| | - Despoina D Gianniou
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Sentiljana Gumeni
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Evangelia-Georgia Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, NKUA, 15772 Athens, Greece
| | - Ioannis V Kostopoulos
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Maria S Manola
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | | | - Chrysanthi Panteli
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Eleni-Dimitra Papanagnou
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Pantelis Rousakis
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Aimilia D Sklirou
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | | | | | - Ioannis P Trougakos
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Soritios Tsiodras
- Fourth Department of Propedeutic Internal Medicine, School of Medicine, University General Hospital Attikon, NKUA, 12462 Haidari, Greece
| | - Petros P Sfikakis
- First Department of Propaedeutic Internal Medicine, School of Medicine, Laiko General Hospital, NKUA, 15772 Athens, Greece
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