1
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Cool K, Gaudreault NN, Trujillo JD, Morozov I, McDowell CD, Bold D, Kwon T, Balaraman V, Assato P, Madden DW, Mantlo E, Souza-Neto J, Matias-Ferreyra F, Retallick J, Singh G, Schotsaert M, Carossino M, Balasuriya UBR, Wilson WC, Pogranichniy RM, García-Sastre A, Richt JA. Experimental co-infection of calves with SARS-CoV-2 Delta and Omicron variants of concern. Emerg Microbes Infect 2024; 13:2281356. [PMID: 37938158 PMCID: PMC10763854 DOI: 10.1080/22221751.2023.2281356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 11/04/2023] [Indexed: 11/09/2023]
Abstract
Since emerging in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has repeatedly crossed the species barrier with natural infections reported in various domestic and wild animal species. The emergence and global spread of SARS-CoV-2 variants of concern (VOCs) has expanded the range of susceptible host species. Previous experimental infection studies in cattle using Wuhan-like SARS-CoV-2 isolates suggested that cattle were not likely amplifying hosts for SARS-CoV-2. However, SARS-CoV-2 sero- and RNA-positive cattle have since been identified in Europe, India, and Africa. Here, we investigated the susceptibility and transmission of the Delta and Omicron SARS-CoV-2 VOCs in cattle. Eight Holstein calves were co-infected orally and intranasally with a mixed inoculum of SARS-CoV-2 VOCs Delta and Omicron BA.2. Twenty-four hours post-challenge, two sentinel calves were introduced to evaluate virus transmission. The co-infection resulted in a high proportion of calves shedding SARS-CoV-2 RNA at 1- and 2-days post-challenge (DPC). Extensive tissue distribution of SARS-CoV-2 RNA was observed at 3 and 7 DPC and infectious virus was recovered from two calves at 3 DPC. Next-generation sequencing revealed that only the SARS-CoV-2 Delta variant was detected in clinical samples and tissues. Similar to previous experimental infection studies in cattle, we observed only limited seroconversion and no clear evidence of transmission to sentinel calves. Together, our findings suggest that cattle are more permissive to infection with SARS-CoV-2 Delta than Omicron BA.2 and Wuhan-like isolates but, in the absence of horizontal transmission, are not likely to be reservoir hosts for currently circulating SARS-CoV-2 variants.
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Affiliation(s)
- Konner Cool
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Jessie D. Trujillo
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Igor Morozov
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Chester D. McDowell
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Dashzeveg Bold
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Taeyong Kwon
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Velmurugan Balaraman
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Patricia Assato
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Daniel W. Madden
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Emily Mantlo
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Jayme Souza-Neto
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Franco Matias-Ferreyra
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Jaime Retallick
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Udeni B. R. Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - William C. Wilson
- Foreign Arthropod-Borne Animal Diseases Research Unit, National Bio and Agro-Defense Facility, United States Department of Agriculture, Manhattan, KS, USA
| | - Roman M. Pogranichniy
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
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2
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McEachran MC, Harvey JA, Mummah RO, Bletz MC, Teitelbaum CS, Rosenblatt E, Rudolph FJ, Arce F, Yin S, Prosser DJ, Mosher BA, Mullinax JM, DiRenzo GV, Couret J, Runge MC, Grant EHC, Cook JD. Reframing wildlife disease management problems with decision analysis. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024:e14284. [PMID: 38785034 DOI: 10.1111/cobi.14284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 05/25/2024]
Abstract
Contemporary wildlife disease management is complex because managers need to respond to a wide range of stakeholders, multiple uncertainties, and difficult trade-offs that characterize the interconnected challenges of today. Despite general acknowledgment of these complexities, managing wildlife disease tends to be framed as a scientific problem, in which the major challenge is lack of knowledge. The complex and multifactorial process of decision-making is collapsed into a scientific endeavor to reduce uncertainty. As a result, contemporary decision-making may be oversimplified, rely on simple heuristics, and fail to account for the broader legal, social, and economic context in which the decisions are made. Concurrently, scientific research on wildlife disease may be distant from this decision context, resulting in information that may not be directly relevant to the pertinent management questions. We propose reframing wildlife disease management challenges as decision problems and addressing them with decision analytical tools to divide the complex problems into more cognitively manageable elements. In particular, structured decision-making has the potential to improve the quality, rigor, and transparency of decisions about wildlife disease in a variety of systems. Examples of management of severe acute respiratory syndrome coronavirus 2, white-nose syndrome, avian influenza, and chytridiomycosis illustrate the most common impediments to decision-making, including competing objectives, risks, prediction uncertainty, and limited resources.
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Affiliation(s)
- Margaret C McEachran
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts, USA
| | - Johanna A Harvey
- Department of Environmental Science and Technology, University of Maryland, College Park, Maryland, USA
| | - Riley O Mummah
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts, USA
| | - Molly C Bletz
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts, USA
| | - Claire S Teitelbaum
- Akima Systems Engineering, Herndon, Virginia, USA
- Contractor to Eastern Ecological Science Center at Patuxent Research Refuge, U.S. Geological Survey, Laurel, Maryland, USA
| | - Elias Rosenblatt
- Rubenstein School of Environment and Natural Resources, University of Vermont, Burlington, Vermont, USA
| | - F Javiera Rudolph
- Department of Ecosystem Sciences and Management, Pennsylvania State University, Center Valley, Pennsylvania, USA
| | - Fernando Arce
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts, USA
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State University, Starkville, Mississippi, USA
| | - Shenglai Yin
- School of Biological Sciences, Center for Earth Observation and Modeling, University of Oklahoma, Norman, Oklahoma, USA
| | - Diann J Prosser
- Eastern Ecological Science Center at Patuxent Research Refuge, U.S. Geological Survey, Laurel, Maryland, USA
| | - Brittany A Mosher
- Rubenstein School of Environment and Natural Resources, University of Vermont, Burlington, Vermont, USA
| | - Jennifer M Mullinax
- Department of Environmental Science and Technology, University of Maryland, College Park, Maryland, USA
| | - Graziella V DiRenzo
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts, USA
- Massachusetts Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jannelle Couret
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Michael C Runge
- Eastern Ecological Science Center at Patuxent Research Refuge, U.S. Geological Survey, Laurel, Maryland, USA
| | - Evan H Campbell Grant
- Eastern Ecological Science Center at the S.O. Conte Research Laboratory, U.S. Geological Survey, Turners Falls, Massachusetts, USA
| | - Jonathan D Cook
- Eastern Ecological Science Center at Patuxent Research Refuge, U.S. Geological Survey, Laurel, Maryland, USA
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3
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Chakraborty C, Bhattacharya M, Islam MA, Zayed H, Ohimain EI, Lee SS, Bhattacharya P, Dhama K. Reverse Zoonotic Transmission of SARS-CoV-2 and Monkeypox Virus: A Comprehensive Review. J Microbiol 2024:10.1007/s12275-024-00138-9. [PMID: 38777985 DOI: 10.1007/s12275-024-00138-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Reverse zoonosis reveals the process of transmission of a pathogen through the human-animal interface and the spillback of the zoonotic pathogen. In this article, we methodically demonstrate various aspects of reverse zoonosis, with a comprehensive discussion of SARS-CoV-2 and MPXV reverse zoonosis. First, different components of reverse zoonosis, such as humans, different pathogens, and numerous animals (poultry, livestock, pets, wild animals, and zoo animals), have been demonstrated. Second, it explains the present status of reverse zoonosis with different pathogens during previous occurrences of various outbreaks, epidemics, and pandemics. Here, we present 25 examples from literature. Third, using several examples, we comprehensively illustrate the present status of the reverse zoonosis of SARS-CoV-2 and MPXV. Here, we have provided 17 examples of SARS-CoV-2 reverse zoonosis and two examples of MPXV reverse zoonosis. Fourth, we have described two significant aspects of reverse zoonosis: understanding the fundamental aspects of spillback and awareness. These two aspects are required to prevent reverse zoonosis from the current infection with two significant viruses. Finally, the One Health approach was discussed vividly, where we urge scientists from different areas to work collaboratively to solve the issue of reverse zoonosis.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, VyasaVihar, Balasore, 756020, Odisha, India
| | - Md Aminul Islam
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, Bangladesh
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| | - Elijah Ige Ohimain
- Microbiology Department, Niger Delta University, Wilberforce Island, Bayelsa State, Nigeria
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 24252, Republic of Korea.
| | - Prosun Bhattacharya
- COVID-19 Research, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
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4
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Lieber CM, Kang HJ, Sobolik EB, Sticher ZM, Ngo VL, Gewirtz AT, Kolykhalov AA, Natchus MG, Greninger AL, Suthar MS, Plemper RK. Efficacy of late-onset antiviral treatment in immune-compromised hosts with persistent SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595478. [PMID: 38826222 PMCID: PMC11142196 DOI: 10.1101/2024.05.23.595478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The immunocompromised are at high risk of prolonged SARS-CoV-2 infection and progression to severe COVID-19. However, efficacy of late-onset direct-acting antiviral (DAA) therapy with therapeutics in clinical use and experimental drugs to mitigate persistent viral replication is unclear. In this study, we employed an immunocompromised mouse model, which supports prolonged replication of SARS-CoV-2 to explore late-onset treatment options. Tandem immuno-depletion of CD4 + and CD8 + T cells in C57BL/6 mice followed by infection with SARS-CoV-2 variant of concern (VOC) beta B.1.351 resulted in prolonged infection with virus replication for five weeks after inoculation. Early-onset treatment with nirmatrelvir/ritonavir (paxlovid) or molnupiravir was only moderately efficacious, whereas the experimental therapeutic 4'-fluorourdine (4'-FlU, EIDD-2749) significantly reduced virus load in upper and lower respiratory compartments four days post infection (dpi). All antivirals significantly lowered virus burden in a 7-day treatment regimen initiated 14 dpi, but paxlovid-treated animals experienced rebound virus replication in the upper respiratory tract seven days after treatment end. Viral RNA was detectable 28 dpi in paxlovid-treated animals, albeit not in the molnupiravir or 4'-FlU groups, when treatment was initiated 14 dpi and continued for 14 days. Low-level virus replication continued 35 dpi in animals receiving vehicle but had ceased in all treatment groups. These data indicate that late-onset DAA therapy significantly shortens the duration of persistent virus replication in an immunocompromised host, which may have implications for clinical use of antiviral therapeutics to alleviate the risk of progression to severe disease in highly vulnerable patients. Importance Four years after the onset of the global COVID-19 pandemic, the immunocompromised are at greatest risk of developing life-threatening severe disease. However, specific treatment plans for this most vulnerable patient group have not yet been developed. Employing a CD4 + and CD8 + T cell-depleted immunocompromised mouse model of SARS-CoV-2 infection, we explored therapeutic options of persistent infections with standard-of-care paxlovid, molnupiravir, and the experimental therapeutic 4'-FlU. Late-onset treatment initiated 14 days after infection was efficacious, but only 4'-FlU was rapidly sterilizing. No treatment-experienced viral variants with reduced susceptibility to the drugs emerged, albeit virus replication rebounded in animals of the paxlovid group after treatment end. This study supports the use of direct-acting antivirals for late-onset management of persistent SARS-CoV-2 infection in immunocompromised hosts. However, treatment courses likely require to be extended for maximal therapeutic benefit, calling for appropriately powered clinical trials to meet the specific needs of this patient group.
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5
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Iglesias-Caballero M, Mas V, Vázquez-Morón S, Vázquez M, Camarero-Serrano S, Cano O, Palomo C, Ruano MJ, Cano-Gómez C, Infantes-Lorenzo JA, Campoy A, Agüero M, Pozo F, Casas I. Genomic Context of SARS-CoV-2 Outbreaks in Farmed Mink in Spain during Pandemic: Unveiling Host Adaptation Mechanisms. Int J Mol Sci 2024; 25:5499. [PMID: 38791536 PMCID: PMC11122236 DOI: 10.3390/ijms25105499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects various mammalian species, with farmed minks experiencing the highest number of outbreaks. In Spain, we analyzed 67 whole genome sequences and eight spike sequences from 18 outbreaks, identifying four distinct lineages: B.1, B.1.177, B.1.1.7, and AY.98.1. The potential risk of transmission to humans raises crucial questions about mutation accumulation and its impact on viral fitness. Sequencing revealed numerous not-lineage-defining mutations, suggesting a cumulative mutation process during the outbreaks. We observed that the outbreaks were predominantly associated with different groups of mutations rather than specific lineages. This clustering pattern by the outbreaks could be attributed to the rapid accumulation of mutations, particularly in the ORF1a polyprotein and in the spike protein. Notably, the mutations G37E in NSP9, a potential host marker, and S486L in NSP13 were detected. Spike protein mutations may enhance SARS-CoV-2 adaptability by influencing trimer stability and binding to mink receptors. These findings provide valuable insights into mink coronavirus genetics, highlighting both host markers and viral transmission dynamics within communities.
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Affiliation(s)
- María Iglesias-Caballero
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Vicente Mas
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Sonia Vázquez-Morón
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Mónica Vázquez
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Sara Camarero-Serrano
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Olga Cano
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Concepción Palomo
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - María José Ruano
- Central Laboratory of Veterinarian (LCV), Ministry of Agriculture, Fisheries and Food, 28110 Algete, Madrid, Spain; (M.J.R.); (C.C.-G.); (M.A.)
| | - Cristina Cano-Gómez
- Central Laboratory of Veterinarian (LCV), Ministry of Agriculture, Fisheries and Food, 28110 Algete, Madrid, Spain; (M.J.R.); (C.C.-G.); (M.A.)
| | - José Antonio Infantes-Lorenzo
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Albert Campoy
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Montserrat Agüero
- Central Laboratory of Veterinarian (LCV), Ministry of Agriculture, Fisheries and Food, 28110 Algete, Madrid, Spain; (M.J.R.); (C.C.-G.); (M.A.)
| | - Francisco Pozo
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Inmaculada Casas
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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6
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Yang R, Han P, Han P, Li D, Zhao R, Niu S, Liu K, Li S, Tian WX, Gao GF. Molecular basis of hippopotamus ACE2 binding to SARS-CoV-2. J Virol 2024; 98:e0045124. [PMID: 38591877 PMCID: PMC11092335 DOI: 10.1128/jvi.00451-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a wide range of hosts, including hippopotami, which are semi-aquatic mammals and phylogenetically closely related to Cetacea. In this study, we characterized the binding properties of hippopotamus angiotensin-converting enzyme 2 (hiACE2) to the spike (S) protein receptor binding domains (RBDs) of the SARS-CoV-2 prototype (PT) and variants of concern (VOCs). Furthermore, the cryo-electron microscopy (cryo-EM) structure of the SARS-CoV-2 PT S protein complexed with hiACE2 was resolved. Structural and mutational analyses revealed that L30 and F83, which are specific to hiACE2, played a crucial role in the hiACE2/SARS-CoV-2 RBD interaction. In addition, comparative and structural analysis of ACE2 orthologs suggested that the cetaceans may have the potential to be infected by SARS-CoV-2. These results provide crucial molecular insights into the susceptibility of hippopotami to SARS-CoV-2 and suggest the potential risk of SARS-CoV-2 VOCs spillover and the necessity for surveillance. IMPORTANCE The hippopotami are the first semi-aquatic artiodactyl mammals wherein SARS-CoV-2 infection has been reported. Exploration of the invasion mechanism of SARS-CoV-2 will provide important information for the surveillance of SARS-CoV-2 in hippopotami, as well as other semi-aquatic mammals and cetaceans. Here, we found that hippopotamus ACE2 (hiACE2) could efficiently bind to the RBDs of the SARS-CoV-2 prototype (PT) and variants of concern (VOCs) and facilitate the transduction of SARS-CoV-2 PT and VOCs pseudoviruses into hiACE2-expressing cells. The cryo-EM structure of the SARS-CoV-2 PT S protein complexed with hiACE2 elucidated a few critical residues in the RBD/hiACE2 interface, especially L30 and F83 of hiACE2 which are unique to hiACE2 and contributed to the decreased binding affinity to PT RBD compared to human ACE2. Our work provides insight into cross-species transmission and highlights the necessity for monitoring host jumps and spillover events on SARS-CoV-2 in semi-aquatic/aquatic mammals.
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Affiliation(s)
- Ruirui Yang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Pu Han
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Pengcheng Han
- School of Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Dedong Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Runchu Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China
| | - Sheng Niu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Shihua Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wen-Xia Tian
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - George Fu Gao
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
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7
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Silva PV, Nobre CN. Computational methods in the analysis of SARS-CoV-2 in mammals: A systematic review of the literature. Comput Biol Med 2024; 173:108264. [PMID: 38564853 DOI: 10.1016/j.compbiomed.2024.108264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 02/15/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
SARS-CoV-2 is an enveloped RNA virus that causes severe respiratory illness in humans and animals. It infects cells by binding the Spike protein to the host's angiotensin-converting enzyme 2 (ACE2). The bat is considered the natural host of the virus, and zoonotic transmission is a significant risk and can happen when humans come into close contact with infected animals. Therefore, understanding the interconnection between human, animal, and environmental health is important to prevent and control future coronavirus outbreaks. This work aimed to systematically review the literature to identify characteristics that make mammals suitable virus transmitters and raise the main computational methods used to evaluate SARS-CoV-2 in mammals. Based on this review, it was possible to identify the main factors related to transmissions mentioned in the literature, such as the expression of ACE2 and proximity to humans, in addition to identifying the computational methods used for its study, such as Machine Learning, Molecular Modeling, Computational Simulation, between others. The findings of the work contribute to the prevention and control of future outbreaks, provide information on transmission factors, and highlight the importance of advanced computational methods in the study of infectious diseases that allow a deeper understanding of transmission patterns and can help in the development of more effective control and intervention strategies.
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Affiliation(s)
- Paula Vitória Silva
- Pontifical Catholic University of Minas Gerais - PUC Minas, 500 Dom José Gaspar Street, Building 41, Coração Eucarístico, Belo Horizonte, MG 30535-901, Brazil.
| | - Cristiane N Nobre
- Pontifical Catholic University of Minas Gerais - PUC Minas, 500 Dom José Gaspar Street, Building 41, Coração Eucarístico, Belo Horizonte, MG 30535-901, Brazil.
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8
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Tan CCS, van Dorp L, Balloux F. The evolutionary drivers and correlates of viral host jumps. Nat Ecol Evol 2024; 8:960-971. [PMID: 38528191 DOI: 10.1038/s41559-024-02353-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 03/27/2024]
Abstract
Most emerging and re-emerging infectious diseases stem from viruses that naturally circulate in non-human vertebrates. When these viruses cross over into humans, they can cause disease outbreaks, epidemics and pandemics. While zoonotic host jumps have been extensively studied from an ecological perspective, little attention has gone into characterizing the evolutionary drivers and correlates underlying these events. To address this gap, we harnessed the entirety of publicly available viral genomic data, employing a comprehensive suite of network and phylogenetic analyses to investigate the evolutionary mechanisms underpinning recent viral host jumps. Surprisingly, we find that humans are as much a source as a sink for viral spillover events, insofar as we infer more viral host jumps from humans to other animals than from animals to humans. Moreover, we demonstrate heightened evolution in viral lineages that involve putative host jumps. We further observe that the extent of adaptation associated with a host jump is lower for viruses with broader host ranges. Finally, we show that the genomic targets of natural selection associated with host jumps vary across different viral families, with either structural or auxiliary genes being the prime targets of selection. Collectively, our results illuminate some of the evolutionary drivers underlying viral host jumps that may contribute to mitigating viral threats across species boundaries.
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Affiliation(s)
- Cedric C S Tan
- UCL Genetics Institute, University College London, London, UK.
- The Francis Crick Institute, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
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9
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Lina A, Keith H, Jenny H, Mariana M, Gregorio T, Laure WV, Paolo T. Facing SARS-CoV-2 emergence on the animal health perspective: The role of the World Organisation for Animal Health in preparedness and official reporting of disease occurrence. Zoonoses Public Health 2024. [PMID: 38584342 DOI: 10.1111/zph.13133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 03/17/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024]
Abstract
AIMS Current data suggest that SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged from an animal source. However, to date, there is insufficient scientific evidence to identify the source of SARS-CoV-2 or to explain the original route of transmission to humans. A wide range of mammalian species have been shown to be susceptible to the virus through experimental infection, and in natural environments when in contact with infected humans. The main objective of this work was to provide a summary of the official data shared by countries on SARS-CoV-2 in animals with the World Organisation for Animal Health (WOAH), to highlight the role of WOAH as an international organization in coordinating scientific information actions and to discuss the implications and impact of these activities. METHODS AND RESULTS Between January 2020 and December 2022, 36 countries in Europe, the Americas, Asia and Africa officially reported SARS-CoV-2 identification in 26 animal species. Affected countries were generally responsive in confirming the pathogen (median of 5 days after onset) and reporting to WOAH (median of 7 days after confirmation). CONCLUSIONS During the pandemic, WOAH, supported by its network of experts, played a crucial role in collecting, analysing and disseminating veterinary scientific information, acting as the reference organization on these issues, thus avoiding misinformation and disinformation. Future perspectives to avoid new emerging threats are discussed.
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Affiliation(s)
- Awada Lina
- World Organisation for Animal Health (WOAH), Paris, France
| | - Hamilton Keith
- World Organisation for Animal Health (WOAH), Paris, France
| | | | | | | | | | - Tizzani Paolo
- World Organisation for Animal Health (WOAH), Paris, France
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10
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González-Aravena M, Galbán-Malagón C, Castro-Nallar E, Barriga GP, Neira V, Krüger L, Adell AD, Olivares-Pacheco J. Detection of SARS-CoV-2 in Wastewater Associated with Scientific Stations in Antarctica and Possible Risk for Wildlife. Microorganisms 2024; 12:743. [PMID: 38674687 PMCID: PMC11051888 DOI: 10.3390/microorganisms12040743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/10/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
Before December 2020, Antarctica had remained free of COVID-19 cases. The main concern during the pandemic was the limited health facilities available at Antarctic stations to deal with the disease as well as the potential impact of SARS-CoV-2 on Antarctic wildlife through reverse zoonosis. In December 2020, 60 cases emerged in Chilean Antarctic stations, disrupting the summer campaign with ongoing isolation needs. The SARS-CoV-2 RNA was detected in the wastewater of several scientific stations. In Antarctica, treated wastewater is discharged directly into the seawater. No studies currently address the recovery of infectious virus particles from treated wastewater, but their presence raises the risk of infecting wildlife and initiating new replication cycles. This study highlights the initial virus detection in wastewater from Antarctic stations, identifying viral RNA via RT-qPCR targeting various genomic regions. The virus's RNA was found in effluent from two wastewater plants at Maxwell Bay and O'Higgins Station on King George Island and the Antarctic Peninsula, respectively. This study explores the potential for the reverse zoonotic transmission of SARS-CoV-2 from humans to Antarctic wildlife due to the direct release of viral particles into seawater. The implications of such transmission underscore the need for continued vigilance and research.
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Affiliation(s)
| | - Cristóbal Galbán-Malagón
- GEMA, Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago 8580745, Chile;
- Anillo en Ciencia y Tecnología Antártica POLARIX, Santiago 8370146, Chile;
- Institute for Environment, Florida International University, Miami, FL 33199, USA
| | - Eduardo Castro-Nallar
- Anillo en Ciencia y Tecnología Antártica POLARIX, Santiago 8370146, Chile;
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Talca, Talca 3481118, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Campus Talca, Talca 3460000, Chile
| | - Gonzalo P. Barriga
- Laboratorio de Virus Emergentes, Programa de Virología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile;
| | - Víctor Neira
- Medicina Preventiva Animal, Facultad de Ciencias Veterinarias, Universidad de Chile, Santiago 8820808, Chile;
| | - Lucas Krüger
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas 6200985, Chile;
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago 7750000, Chile
| | - Aiko D. Adell
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 9350841, Chile;
- Millennium Initiative for Collaborative Research on Bacterial Resistance, MICROB-R, Santiago 7550000, Chile
| | - Jorge Olivares-Pacheco
- Millennium Initiative for Collaborative Research on Bacterial Resistance, MICROB-R, Santiago 7550000, Chile
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales, GRABPA, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
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11
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Rudar J, Kruczkiewicz P, Vernygora O, Golding GB, Hajibabaei M, Lung O. Sequence signatures within the genome of SARS-CoV-2 can be used to predict host source. Microbiol Spectr 2024; 12:e0358423. [PMID: 38436242 PMCID: PMC10986507 DOI: 10.1128/spectrum.03584-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024] Open
Abstract
We conducted an in silico analysis to better understand the potential factors impacting host adaptation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in white-tailed deer, humans, and mink due to the strong evidence of sustained transmission within these hosts. Classification models trained on single nucleotide and amino acid differences between samples effectively identified white-tailed deer-, human-, and mink-derived SARS-CoV-2. For example, the balanced accuracy score of Extremely Randomized Trees classifiers was 0.984 ± 0.006. Eighty-eight commonly identified predictive mutations are found at sites under strong positive and negative selective pressure. A large fraction of sites under selection (86.9%) or identified by machine learning (87.1%) are found in genes other than the spike. Some locations encoded by these gene regions are predicted to be B- and T-cell epitopes or are implicated in modulating the immune response suggesting that host adaptation may involve the evasion of the host immune system, modulation of the class-I major-histocompatibility complex, and the diminished recognition of immune epitopes by CD8+ T cells. Our selection and machine learning analysis also identified that silent mutations, such as C7303T and C9430T, play an important role in discriminating deer-derived samples across multiple clades. Finally, our investigation into the origin of the B.1.641 lineage from white-tailed deer in Canada discovered an additional human sequence from Michigan related to the B.1.641 lineage sampled near the emergence of this lineage. These findings demonstrate that machine-learning approaches can be used in combination with evolutionary genomics to identify factors possibly involved in the cross-species transmission of viruses and the emergence of novel viral lineages.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible virus capable of infecting and establishing itself in human and wildlife populations, such as white-tailed deer. This fact highlights the importance of developing novel ways to identify genetic factors that contribute to its spread and adaptation to new host species. This is especially important since these populations can serve as reservoirs that potentially facilitate the re-introduction of new variants into human populations. In this study, we apply machine learning and phylogenetic methods to uncover biomarkers of SARS-CoV-2 adaptation in mink and white-tailed deer. We find evidence demonstrating that both non-synonymous and silent mutations can be used to differentiate animal-derived sequences from human-derived ones and each other. This evidence also suggests that host adaptation involves the evasion of the immune system and the suppression of antigen presentation. Finally, the methods developed here are general and can be used to investigate host adaptation in viruses other than SARS-CoV-2.
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Affiliation(s)
- Josip Rudar
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
- Department of Integrative Biology & Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Peter Kruczkiewicz
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
| | - Oksana Vernygora
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
| | - G. Brian Golding
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Mehrdad Hajibabaei
- Department of Integrative Biology & Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Oliver Lung
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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12
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Carvajal M, Saenz C, Fuentes N, Guevara R, Muñoz E, Prado-Vivar B, Diaz E, Alfonso-Cortes F, Coloma J, Grunauer M, Rojas-Silva P, Cardenas PA, Barragan V. SARS-CoV-2 infection in brown-headed spider monkeys ( Ateles fusciceps) at a wildlife rescue center on the coast of Ecuador-South America. Microbiol Spectr 2024; 12:e0274123. [PMID: 38364080 PMCID: PMC10986564 DOI: 10.1128/spectrum.02741-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/18/2024] [Indexed: 02/18/2024] Open
Abstract
Human populations can be affected in unpredictable ways by the emergence and spread of zoonotic diseases. The COVID-19 (coronavirus disease of 2019) pandemic was a reminder of how devastating these events can be if left unchecked. However, once they have spread globally, the impact of these diseases when entering non-exposed wildlife populations is unknown. The current study reports the infection of brown-headed spider monkeys (Ateles fusciceps) at a wildlife rescue center in Ecuador. Four monkeys were hospitalized, and all tested positive for SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) by RT-qPCR (Quantitative Reverse Transcription PCR). Fecal samples (n = 12) from monkeys at the rescue center also tested positive; three zookeepers responsible for feeding and deworming the monkeys also tested positive, suggesting human-animal transmission. Whole genome sequencing identified most samples' omicron clade 22B BA.5 lineage. These findings highlight the threat posed by an emerging zoonotic disease in wildlife species and the importance of preventing spillover and spillback events during epidemic or pandemic events.IMPORTANCEAlthough COVID-19 (coronavirus disease of 2019) has been primarily contained in humans through widespread vaccination, the impact and incidence of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus) and its transmission and epidemiology in wildlife may need to be addressed. In some natural environments, the proximity of animals to humans is difficult to control, creating perfect scenarios where susceptible wildlife can acquire the virus from humans. In these places, it is essential to understand how transmission can occur and to develop protocols to prevent infection. This study reports the infection of brown-headed spider monkeys with SARS-CoV-2, a red-listed monkey species, at a wildlife recovery center in Ecuador. This study reports the infection of brown-headed spider monkeys with SARS-CoV-2, indicating the potential for transmission between humans and wildlife primates and the importance of preventing such events in the future.
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Affiliation(s)
- Mateo Carvajal
- Universidad San Francisco de Quito, Instituto de Microbiología, Quito, Ecuador
| | - Carolina Saenz
- Universidad San Francisco de Quito, Hospital de Fauna Silvestre TUERI-USFQ, Quito, Ecuador
| | | | - Rommel Guevara
- Universidad San Francisco de Quito, Instituto de Microbiología, Quito, Ecuador
| | - Erika Muñoz
- Universidad San Francisco de Quito, Instituto de Microbiología, Quito, Ecuador
| | - Belen Prado-Vivar
- Universidad San Francisco de Quito, Instituto de Microbiología, Quito, Ecuador
| | - Eduardo Diaz
- Universidad San Francisco de Quito, Escuela de Medicina Veterinaria, Quito, Ecuador
| | | | | | - Michelle Grunauer
- Universidad San Francisco de Quito, Escuela de Medicina, Quito, Ecuador
| | | | - Paul A. Cardenas
- Universidad San Francisco de Quito, Instituto de Microbiología, Quito, Ecuador
| | - Veronica Barragan
- Universidad San Francisco de Quito, Instituto de Microbiología, Quito, Ecuador
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13
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Yasobant S, Ali S, Saxena D, Figueroa DP, Khan MMT. Editorial: The One Health approach in the context of public health. Front Public Health 2024; 12:1353709. [PMID: 38590816 PMCID: PMC10999541 DOI: 10.3389/fpubh.2024.1353709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Affiliation(s)
- Sandul Yasobant
- Center for One Health Education, Research and Development, and Department of Public Health Sciences, India Institute of Public Health, Gandhinagar, India
- School of Epidemiology and Public Health, Datta Meghe Institute of Medical Sciences, Wardha, India
- Global Health, Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Shahzad Ali
- University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Deepak Saxena
- Center for One Health Education, Research and Development, and Department of Public Health Sciences, India Institute of Public Health, Gandhinagar, India
- School of Epidemiology and Public Health, Datta Meghe Institute of Medical Sciences, Wardha, India
| | | | - Mohiuddin Md. Taimur Khan
- Department of Civil and Environmental Engineering, Washington State University, Tri Cities, WA, United States
- Center for Molecular Discovery and Cancer Center, University of New Mexico, Albuquerque, NM, United States
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14
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Lv JX, Liu X, Pei YY, Song ZG, Chen X, Hu SJ, She JL, Liu Y, Chen YM, Zhang YZ. Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak. Virus Evol 2024; 10:veae020. [PMID: 38562953 PMCID: PMC10984623 DOI: 10.1093/ve/veae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/24/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Despite extensive scientific efforts directed toward the evolutionary trajectory of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans at the beginning of the COVID-19 epidemic, it remains unclear how the virus jumped into and evolved in humans so far. Herein, we recruited almost all adult coronavirus disease 2019 (COVID-19) cases appeared locally or imported from abroad during the first 8 months of the outbreak in Shanghai. From these patients, SARS-CoV-2 genomes occupying the important phylogenetic positions in the virus phylogeny were recovered. Phylogenetic and mutational landscape analyses of viral genomes recovered here and those collected in and outside of China revealed that all known SARS-CoV-2 variants exhibited the evolutionary continuity despite the co-circulation of multiple lineages during the early period of the epidemic. Various mutations have driven the rapid SARS-CoV-2 diversification, and some of them favor its better adaptation and circulation in humans, which may have determined the waxing and waning of various lineages.
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Affiliation(s)
- Jia-Xin Lv
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Xiang Liu
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yuan-Yuan Pei
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
- Shanghai Public Health Clinical Center, No. 2901 Canglang Road, Jinshan District, Shanghai 210508, China
| | - Zhi-Gang Song
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
- Shanghai Public Health Clinical Center, No. 2901 Canglang Road, Jinshan District, Shanghai 210508, China
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou, Guangdong 510642, China
| | - Shu-Jian Hu
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Jia-Lei She
- Shanghai Public Health Clinical Center, No. 2901 Canglang Road, Jinshan District, Shanghai 210508, China
| | - Yi Liu
- Shanghai Public Health Clinical Center, No. 2901 Canglang Road, Jinshan District, Shanghai 210508, China
| | - Yan-Mei Chen
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yong-Zhen Zhang
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Human Phenome Institute, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
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15
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Ren Y, Li C, Nanayakkara Sapugahawatte D, Zhu C, Spänig S, Jamrozy D, Rothen J, Daubenberger CA, Bentley SD, Ip M, Heider D. Predicting hosts and cross-species transmission of Streptococcus agalactiae by interpretable machine learning. Comput Biol Med 2024; 171:108185. [PMID: 38401454 DOI: 10.1016/j.compbiomed.2024.108185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND Streptococcus agalactiae, commonly known as Group B Streptococcus (GBS), exhibits a broad host range, manifesting as both a beneficial commensal and an opportunistic pathogen across various species. In humans, it poses significant risks, causing neonatal sepsis and meningitis, along with severe infections in adults. Additionally, it impacts livestock by inducing mastitis in bovines and contributing to epidemic mortality in fish populations. Despite its wide host spectrum, the mechanisms enabling GBS to adapt to specific hosts remain inadequately elucidated. Therefore, the development of a rapid and accurate method differentiates GBS strains associated with particular animal hosts based on genome-wide information holds immense potential. Such a tool would not only bolster the identification and containment efforts during GBS outbreaks but also deepen our comprehension of the bacteria's host adaptations spanning humans, livestock, and other natural animal reservoirs. METHODS AND RESULTS Here, we developed three machine learning models-random forest (RF), logistic regression (LR), and support vector machine (SVM) based on genome-wide mutation data. These models enabled precise prediction of the host origin of GBS, accurately distinguishing between human, bovine, fish, and pig hosts. Moreover, we conducted an interpretable machine learning using SHapley Additive exPlanations (SHAP) and variant annotation to uncover the most influential genomic features and associated genes for each host. Additionally, by meticulously examining misclassified samples, we gained valuable insights into the dynamics of host transmission and the potential for zoonotic infections. CONCLUSIONS Our study underscores the effectiveness of random forest (RF) and logistic regression (LR) models based on mutation data for accurately predicting GBS host origins. Additionally, we identify the key features associated with each GBS host, thereby enhancing our understanding of the bacteria's host-specific adaptations.
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Affiliation(s)
- Yunxiao Ren
- Department for Data Science in Biomedicine, Faculty of Mathematics and Computer Science, Philipps-University of Marburg, Marburg, Germany
| | - Carmen Li
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Chendi Zhu
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Sebastian Spänig
- Department for Data Science in Biomedicine, Faculty of Mathematics and Computer Science, Philipps-University of Marburg, Marburg, Germany
| | - Dorota Jamrozy
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Julian Rothen
- Swiss Tropical and Public Health Institute (Swiss TPH) Basel, Department of Medical Parasitology and Infection Biology, 4002, Basel, Switzerland; University of Basel, 4002, Basel, Switzerland
| | - Claudia A Daubenberger
- Swiss Tropical and Public Health Institute (Swiss TPH) Basel, Department of Medical Parasitology and Infection Biology, 4002, Basel, Switzerland; University of Basel, 4002, Basel, Switzerland
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Dominik Heider
- Department for Data Science in Biomedicine, Faculty of Mathematics and Computer Science, Philipps-University of Marburg, Marburg, Germany; Institute for Computer Science, University of Düsseldorf, 40211, Düsseldorf, Germany; Center for Digital Health, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany.
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16
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Tavera Gonzales A, Bazalar Gonzales J, Silvestre Espejo T, Leiva Galarza M, Rodríguez Cueva C, Carhuaricra Huamán D, Luna Espinoza L, Maturrano Hernández A. Possible Spreading of SARS-CoV-2 from Humans to Captive Non-Human Primates in the Peruvian Amazon. Animals (Basel) 2024; 14:732. [PMID: 38473117 DOI: 10.3390/ani14050732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 03/14/2024] Open
Abstract
Human-to-animal transmission events of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) have been reported in both domestic and wild species worldwide. Despite the high rates of contagion and mortality during the COVID-19 (Coronavirus Diseases 2019) pandemic in Peru, no instances of natural virus infection have been documented in wild animals, particularly in the Amazonian regions where human-wildlife interactions are prevalent. In this study, we conducted a surveillance investigation using viral RNA sequencing of fecal samples collected from 76 captive and semi-captive non-human primates (NHPs) in the Loreto, Ucayali, and Madre de Dios regions between August 2022 and February 2023. We detected a segment of the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2 by metagenomic sequencing in a pooled fecal sample from captive white-fronted capuchins (Cebus unicolor) at a rescue center in Bello Horizonte, Ucayali. Phylogenetic analysis further confirmed that the retrieved partial sequence of the RdRp gene matched the SARS-CoV-2 genome. This study represents the first documented instance of molecular SARS-CoV-2 detection in NHPs in the Peruvian Amazon, underscoring the adverse impact of anthropic activities on the human-NHP interface and emphasizing the importance of ongoing surveillance for early detection and prediction of future emergence of new SARS-CoV-2 variants in animals.
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Affiliation(s)
- Andrea Tavera Gonzales
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Jhonathan Bazalar Gonzales
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
- Asociación Equipo Primatológico del Perú, Iquitos 16008, Peru
| | - Thalía Silvestre Espejo
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Milagros Leiva Galarza
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Carmen Rodríguez Cueva
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Dennis Carhuaricra Huamán
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
- Programa de Pós-Graduação Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, Rua do Matão 1010, São Paulo 05508-090, Brazil
| | - Luis Luna Espinoza
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Abelardo Maturrano Hernández
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
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17
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Takemura T, Ankhanbaatar U, Settypalli TBK, Purevtseren D, Shura G, Damdinjav B, Ben Ali HOA, Dundon WG, Cattoli G, Lamien CE. SARS-CoV-2 Infection in Beaver Farm, Mongolia, 2021. Emerg Infect Dis 2024; 30:391-394. [PMID: 38270179 PMCID: PMC10826759 DOI: 10.3201/eid3002.231318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
We report an outbreak of COVID-19 in a beaver farm in Mongolia in 2021. Genomic characterization revealed a unique combination of mutations in the SARS-CoV-2 of the infected beavers. Based on these findings, increased surveillance of farmed beavers should be encouraged.
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Affiliation(s)
| | | | - Tirumala Bharani K. Settypalli
- International Atomic Energy Agency, Seibersdorf, Austria (T. Takemura, T.B.K. Settypalli, H.O.A.B. Ali, W.G. Dundon, G. Cattoli, C.E. Lamien)
- State Central Veterinary Laboratory, Ulaanbaatar City, Mongolia (U. Ankhanbaatar, D. Purevtseren, G. Shura, B. Damdinjav)
| | - Dulam Purevtseren
- International Atomic Energy Agency, Seibersdorf, Austria (T. Takemura, T.B.K. Settypalli, H.O.A.B. Ali, W.G. Dundon, G. Cattoli, C.E. Lamien)
- State Central Veterinary Laboratory, Ulaanbaatar City, Mongolia (U. Ankhanbaatar, D. Purevtseren, G. Shura, B. Damdinjav)
| | - Gansukh Shura
- International Atomic Energy Agency, Seibersdorf, Austria (T. Takemura, T.B.K. Settypalli, H.O.A.B. Ali, W.G. Dundon, G. Cattoli, C.E. Lamien)
- State Central Veterinary Laboratory, Ulaanbaatar City, Mongolia (U. Ankhanbaatar, D. Purevtseren, G. Shura, B. Damdinjav)
| | - Batchuluun Damdinjav
- International Atomic Energy Agency, Seibersdorf, Austria (T. Takemura, T.B.K. Settypalli, H.O.A.B. Ali, W.G. Dundon, G. Cattoli, C.E. Lamien)
- State Central Veterinary Laboratory, Ulaanbaatar City, Mongolia (U. Ankhanbaatar, D. Purevtseren, G. Shura, B. Damdinjav)
| | - Hatem Ouled Ahmed Ben Ali
- International Atomic Energy Agency, Seibersdorf, Austria (T. Takemura, T.B.K. Settypalli, H.O.A.B. Ali, W.G. Dundon, G. Cattoli, C.E. Lamien)
- State Central Veterinary Laboratory, Ulaanbaatar City, Mongolia (U. Ankhanbaatar, D. Purevtseren, G. Shura, B. Damdinjav)
| | - William G Dundon
- International Atomic Energy Agency, Seibersdorf, Austria (T. Takemura, T.B.K. Settypalli, H.O.A.B. Ali, W.G. Dundon, G. Cattoli, C.E. Lamien)
- State Central Veterinary Laboratory, Ulaanbaatar City, Mongolia (U. Ankhanbaatar, D. Purevtseren, G. Shura, B. Damdinjav)
| | - Giovanni Cattoli
- International Atomic Energy Agency, Seibersdorf, Austria (T. Takemura, T.B.K. Settypalli, H.O.A.B. Ali, W.G. Dundon, G. Cattoli, C.E. Lamien)
- State Central Veterinary Laboratory, Ulaanbaatar City, Mongolia (U. Ankhanbaatar, D. Purevtseren, G. Shura, B. Damdinjav)
| | - Charles E. Lamien
- International Atomic Energy Agency, Seibersdorf, Austria (T. Takemura, T.B.K. Settypalli, H.O.A.B. Ali, W.G. Dundon, G. Cattoli, C.E. Lamien)
- State Central Veterinary Laboratory, Ulaanbaatar City, Mongolia (U. Ankhanbaatar, D. Purevtseren, G. Shura, B. Damdinjav)
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18
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Khalil AM, Martinez-Sobrido L, Mostafa A. Zoonosis and zooanthroponosis of emerging respiratory viruses. Front Cell Infect Microbiol 2024; 13:1232772. [PMID: 38249300 PMCID: PMC10796657 DOI: 10.3389/fcimb.2023.1232772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Lung infections in Influenza-Like Illness (ILI) are triggered by a variety of respiratory viruses. All human pandemics have been caused by the members of two major virus families, namely Orthomyxoviridae (influenza A viruses (IAVs); subtypes H1N1, H2N2, and H3N2) and Coronaviridae (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2). These viruses acquired some adaptive changes in a known intermediate host including domestic birds (IAVs) or unknown intermediate host (SARS-CoV-2) following transmission from their natural reservoirs (e.g. migratory birds or bats, respectively). Verily, these acquired adaptive substitutions facilitated crossing species barriers by these viruses to infect humans in a phenomenon that is known as zoonosis. Besides, these adaptive substitutions aided the variant strain to transmit horizontally to other contact non-human animal species including pets and wild animals (zooanthroponosis). Herein we discuss the main zoonotic and reverse-zoonosis events that occurred during the last two pandemics of influenza A/H1N1 and SARS-CoV-2. We also highlight the impact of interspecies transmission of these pandemic viruses on virus evolution and possible prophylactic and therapeutic interventions. Based on information available and presented in this review article, it is important to close monitoring viral zoonosis and viral reverse zoonosis of pandemic strains within a One-Health and One-World approach to mitigate their unforeseen risks, such as virus evolution and resistance to limited prophylactic and therapeutic interventions.
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Affiliation(s)
- Ahmed Magdy Khalil
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Luis Martinez-Sobrido
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ahmed Mostafa
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, Environment and Climate Change Research Institute, National Research Centre, Giza, Egypt
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19
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Castillo AP, Miranda JVO, Fonseca PLC, Silva SDO, Lopes REN, Spanhol VC, Moreira RG, Nicolino RR, Queiroz DC, de Araújo E Santos LCG, Dos Santos APS, Rivetti HAA, Martins-Duarte ES, de Almeida Vitor RW, Dos Reis JKP, Aguiar RS, da Silveira JAG. Evidence of SARS-CoV-2 infection and co-infections in stray cats in Brazil. Acta Trop 2024; 249:107056. [PMID: 37913970 DOI: 10.1016/j.actatropica.2023.107056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/20/2023] [Accepted: 10/29/2023] [Indexed: 11/03/2023]
Abstract
The zoonotic virus SARS-CoV-2, which causes severe acute respiratory syndrome in humans (COVID-19), has been identified in cats. Notably, most positive cases were in cats that had close contact with infected humans, suggesting a role for humans in animal transmission routes. Previous studies have suggested that animals with immune depletion are more susceptible to SARS-CoV-2 infection. To date, there is limited evidence of SARS-CoV-2 infections in stray and free-range cats affected by other pathogens. In this study, we investigated infections caused by SARS-CoV-2, Leishmania spp., Toxoplasma gondii, Mycoplasma spp., Bartonella spp., Feline leukemia virus (FeLV), and Feline immunodeficiency virus (FIV) in stray cats from an urban park in Brazil during the COVID-19 pandemic. From February to September 2021, 78 mixed-breed cats were tested for SARS-CoV-2 and hemopathogens using molecular analysis at Américo Renné Giannetti Municipal Park, Belo Horizonte, Minas Gerais, Brazil. An enzyme-linked immunosorbent assay (ELISA) was used to detect IgG in T. gondii. None of the animals in this study showed any clinical signs of infections. The SARS-CoV-2 virus RNA was detected in 7.7 % of cats, and a whole virus genome sequence analysis revealed the SARS-CoV-2 Delta lineage (B.1.617.2). Phylogenetic analysis showed that SARS-CoV-2 isolated from cats was grouped into the sublineage AY.99.2, which matches the epidemiological scenario of COVID-19 in the urban area of our study. Leishmania infantum was detected and sequenced in 9 % of cats. The seroprevalence of T. gondii was 23.1 %. Hemotropic Mycoplasma spp. was detected in 7.7 % of the cats, with Mycoplasma haemofelis and Candidatus Mycoplasma haemominutum being the most common. Bartonella henselae and Bartonella clarridgeiae were detected in 38.5 % of the cats, FeLV was detected in 17,9 %, and none of the cats studied tested positive for FIV. This study reports, for the first time, the SARS-CoV-2 infection with whole-genome sequencing in stray cats in southeastern Brazil and co-infection with other pathogens, including Bartonella spp. and Feline leukemia virus. Our study observed no correlation between SARS-CoV-2 and the other detected pathogens. Our results emphasize the importance of monitoring SARS-CoV-2 in stray cats to characterize their epidemiological role in SARS-CoV-2 infection and reinforce the importance of zoonotic disease surveillance.
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Affiliation(s)
- Anisleidy Pérez Castillo
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil; Laboratório de PROTOVET, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária da Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Joao Victor Oliveira Miranda
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Paula Luize Camargos Fonseca
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Soraia de Oliveira Silva
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Rosálida Estevam Nazar Lopes
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Viviane Campos Spanhol
- Laboratório de Retroviroses, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária da Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rennan Garcias Moreira
- Centro de Laboratórios Multiusuários, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Rafael Romero Nicolino
- Departamento de Epidemiologia e Defesa Sanitária Animal, Escola de Veterinária da Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Daniel Costa Queiroz
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Luiza Campos Guerra de Araújo E Santos
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Anna Pio Soares Dos Santos
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Hugo Adriano Araújo Rivetti
- Centro de Controle de Zoonoses, Prefeitura de Belo Horizonte, R. Édna Quintel, 173 - São Bernardo, Belo Horizonte, MG 31270-705, Brazil
| | - Erica S Martins-Duarte
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Ricardo Wagner de Almeida Vitor
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Jenner Karlisson Pimenta Dos Reis
- Laboratório de Retroviroses, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária da Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Júlia Angélica Gonçalves da Silveira
- Laboratório de PROTOVET, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária da Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG 31270-901, Brazil.
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20
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Zhao J, Kang M, Wu H, Sun B, Baele G, He WT, Lu M, Suchard MA, Ji X, He N, Su S, Veit M. Risk assessment of SARS-CoV-2 replicating and evolving in animals. Trends Microbiol 2024; 32:79-92. [PMID: 37541811 DOI: 10.1016/j.tim.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
The retransmissions of SARS-CoV-2 from several mammals - primarily mink and white-tailed deer - to humans have raised concerns for the emergence of a new animal-derived SARS-CoV-2 variant to worsen the pandemic. Here, we discuss animal species that are susceptible to natural or experimental infection with SARS-CoV-2 and can transmit the virus to mates or humans. We describe cutting-edge techniques to assess the impact of a mutation in the viral spike (S) protein on its receptor and on antibody binding. Our review of spike sequences of animal-derived viruses identified nine unique amino acid exchanges in the receptor-binding domain (RBD) that are not present in any variant of concern (VOC). These mutations are present in SARS-CoV-2 found in companion animals such as dogs and cats, and they exhibit a higher frequency in SARS-CoV-2 found in mink and white-tailed deer, suggesting that sustained transmissions may contribute to maintaining novel mutations. Four of these exchanges, such as Leu452Met, could undermine acquired immune protection in humans while maintaining high affinity for the human angiotensin-converting enzyme 2 (ACE2) receptor. Finally, we discuss important avenues of future research into animal-derived viruses with public health risks.
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Affiliation(s)
- Jin Zhao
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Mei Kang
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China; Clinical Research Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongyan Wu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Bowen Sun
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Guy Baele
- Department of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Wan-Ting He
- School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Meng Lu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA; Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Na He
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Shuo Su
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China.
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany.
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21
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Musoles-Cuenca B, Aguiló-Gisbert J, Lorenzo-Bermejo T, Canales R, Ballester B, Romani-Cremaschi U, Martínez-Valverde R, Maiques E, Marteles D, Rueda P, Rubio V, Villanueva-Saz S, Rubio-Guerri C. Molecular and Serological Studies on Potential SARS-CoV-2 Infection among 43 Lemurs under Human Care-Evidence for Past Infection in at Least One Individual. Animals (Basel) 2023; 14:140. [PMID: 38200871 PMCID: PMC10778278 DOI: 10.3390/ani14010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/24/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
In the setting of the recent COVID-19 pandemic, transmission of SARS-CoV-2 to animals has been reported in both domestic and wild animals and is a matter of concern. Given the genetic and functional similarities to humans, non-human primates merit particular attention. In the case of lemurs, generally considered endangered, they are believed to be susceptible to SARS-CoV-2 infection. We have conducted a study for evidence of SARS-CoV-2 infection among the 43 lemurs of Mundomar, a zoological park in Benidorm, Spain. They belong to two endangered lemur species, 23 black-and-white ruffed lemurs (Varecia variegata) and 20 ring-tailed lemurs (Lemur catta). Health assessments conducted in 2022 and 2023 included molecular analyses for SARS-CoV-2 RNA of oral and rectal swabs using two different RT-qPCR assays, always with negative results for SARS-CoV-2 in all animals. The assessment also included serological testing for antibodies against the receptor-binding domain (RBD) of the spike protein (S) of SARS-CoV-2, which again yielded negative results in all animals except one black-and-white ruffed lemur, supporting prior infection of that animal with SARS-CoV-2. Our data, while not indicating a high susceptibility of lemurs to SARS-CoV-2 infection, show that they can be infected, adding to the existing information body on potential ways for SARS-CoV-2 virus spreading in zoos, highlighting the need for animal surveillance for the virus.
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Affiliation(s)
- Beatriz Musoles-Cuenca
- Department of Biomedical Sciences, Faculty of Health Sciences, Universidad Cardenal Herrera-CEU, 46113 Valencia, Spain; (B.M.-C.); (T.L.-B.); (B.B.); (E.M.)
| | - Jordi Aguiló-Gisbert
- Servicio de Análisis, Investigación, Gestión de Animales Silvestres (SAIGAS), Veterinary Faculty, Universidad Cardenal Herrera-CEU, 46113 Valencia, Spain;
| | - Teresa Lorenzo-Bermejo
- Department of Biomedical Sciences, Faculty of Health Sciences, Universidad Cardenal Herrera-CEU, 46113 Valencia, Spain; (B.M.-C.); (T.L.-B.); (B.B.); (E.M.)
| | - Rocío Canales
- Veterinary Department, Mundomar Benidorm, 03503 Alicante, Spain; (R.C.); (U.R.-C.)
| | - Beatriz Ballester
- Department of Biomedical Sciences, Faculty of Health Sciences, Universidad Cardenal Herrera-CEU, 46113 Valencia, Spain; (B.M.-C.); (T.L.-B.); (B.B.); (E.M.)
| | | | | | - Elisa Maiques
- Department of Biomedical Sciences, Faculty of Health Sciences, Universidad Cardenal Herrera-CEU, 46113 Valencia, Spain; (B.M.-C.); (T.L.-B.); (B.B.); (E.M.)
| | - Diana Marteles
- Clinical Immunology Laboratory, Veterinary Faculty, University of Zaragoza, 50013 Zaragoza, Spain; (D.M.); (P.R.)
| | - Pablo Rueda
- Clinical Immunology Laboratory, Veterinary Faculty, University of Zaragoza, 50013 Zaragoza, Spain; (D.M.); (P.R.)
| | - Vicente Rubio
- Department of Genomics and Proteomics, Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas (IBV-CSIC), 46010 Valencia, Spain
- Group 739, IBV-CSIC, Centre for Biomedical Network Research, Instituto de Salud Carlos III (CIBERER-ISCIII), 46010 Valencia, Spain
| | - Sergio Villanueva-Saz
- Clinical Immunology Laboratory, Veterinary Faculty, University of Zaragoza, 50013 Zaragoza, Spain; (D.M.); (P.R.)
| | - Consuelo Rubio-Guerri
- Department of Pharmacy, Faculty of Health Sciences, Universidad Cardenal Herrera-CEU, 46113 Valencia, Spain
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22
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Ghai RR, Straily A, Wineland N, Calogero J, Stobierski MG, Signs K, Blievernicht M, Torres-Mendoza Y, Waltenburg MA, Condrey JA, Blankenship HM, Riner D, Barr N, Schalow M, Goodrich J, Collins C, Ahmad A, Metz JM, Herzegh O, Straka K, Arsnoe DM, Duffiney AG, Shriner SA, Kainulainen MH, Carpenter A, Whitehill F, Wendling NM, Stoddard RA, Retchless AC, Uehara A, Tao Y, Li Y, Zhang J, Tong S, Barton Behravesh C. Epidemiologic and Genomic Evidence for Zoonotic Transmission of SARS-CoV-2 among People and Animals on a Michigan Mink Farm, United States, 2020. Viruses 2023; 15:2436. [PMID: 38140677 PMCID: PMC10747742 DOI: 10.3390/v15122436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Farmed mink are one of few animals in which infection with SARS-CoV-2 has resulted in sustained transmission among a population and spillback from mink to people. In September 2020, mink on a Michigan farm exhibited increased morbidity and mortality rates due to confirmed SARS-CoV-2 infection. We conducted an epidemiologic investigation to identify the source of initial mink exposure, assess the degree of spread within the facility's overall mink population, and evaluate the risk of further viral spread on the farm and in surrounding wildlife habitats. Three farm employees reported symptoms consistent with COVID-19 the same day that increased mortality rates were observed among the mink herd. One of these individuals, and another asymptomatic employee, tested positive for SARS-CoV-2 by real-time reverse transcription PCR (RT-qPCR) 9 days later. All but one mink sampled on the farm were positive for SARS-CoV-2 based on nucleic acid detection from at least one oral, nasal, or rectal swab tested by RT-qPCR (99%). Sequence analysis showed high degrees of similarity between sequences from mink and the two positive farm employees. Epidemiologic and genomic data, including the presence of F486L and N501T mutations believed to arise through mink adaptation, support the hypothesis that the two employees with SARS-CoV-2 nucleic acid detection contracted COVID-19 from mink. However, the specific source of virus introduction onto the farm was not identified. Three companion animals living with mink farm employees and 31 wild animals of six species sampled in the surrounding area were negative for SARS-CoV-2 by RT-qPCR. Results from this investigation support the necessity of a One Health approach to manage the zoonotic spread of SARS-CoV-2 and underscores the critical need for multifaceted public health approaches to prevent the introduction and spread of respiratory viruses on mink farms.
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Affiliation(s)
- Ria R. Ghai
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Anne Straily
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Nora Wineland
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | - Jennifer Calogero
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | | | - Kimberly Signs
- Michigan Department of Health and Human Services, Lansing, MI 48909, USA
| | - Melissa Blievernicht
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | | | | | - Jillian A. Condrey
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | | | - Diana Riner
- Michigan Department of Health and Human Services, Lansing, MI 48909, USA
| | - Nancy Barr
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | - Michele Schalow
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | - Jarold Goodrich
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | - Cheryl Collins
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | - Ausaf Ahmad
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - John Michael Metz
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Owen Herzegh
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Kelly Straka
- Michigan Department of Natural Resources, Lansing, MI 48909, USA
| | - Dustin M. Arsnoe
- U.S. Department of Agriculture Animal and Plant Health Inspection Service, Washington, DC 20250, USA
| | - Anthony G. Duffiney
- U.S. Department of Agriculture Animal and Plant Health Inspection Service, Washington, DC 20250, USA
| | - Susan A. Shriner
- U.S. Department of Agriculture Animal and Plant Health Inspection Service, Washington, DC 20250, USA
| | | | - Ann Carpenter
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Florence Whitehill
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Natalie M. Wendling
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Robyn A. Stoddard
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Adam C. Retchless
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Anna Uehara
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Ying Tao
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Yan Li
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Jing Zhang
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Suxiang Tong
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
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23
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Ip YCA, Tan A, Ong J, Fernandez CJ, Lau C, Wong WK, Chang SF, Yap HH, Er KBH. Anthropogenic Transmission of SARS-CoV-2 from Humans to Lions, Singapore, 2021. Emerg Infect Dis 2023; 29:2550-2553. [PMID: 37885046 PMCID: PMC10683833 DOI: 10.3201/eid2912.221916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
In Singapore, 10 captive lions tested positive for SARS-CoV-2 by real-time PCR. Genomic analyses of nanopore sequencing confirmed human-to-animal transmission of the SARS-CoV-2 Delta variant. Viral genomes from the lions and zookeeper shared a unique spike protein substitution, S:A1016V. Widespread SARS-CoV-2 transmission among humans can increase the likelihood of anthroponosis.
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Nerpel A, Käsbohrer A, Walzer C, Desvars-Larrive A. Data on SARS-CoV-2 events in animals: Mind the gap! One Health 2023; 17:100653. [PMID: 38024278 PMCID: PMC10665207 DOI: 10.1016/j.onehlt.2023.100653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
Current research on SARS-CoV-2 has largely focused on the pandemic's impact on humans, with insufficient attention paid to monitoring, sharing, and communicating information about viral circulation and evolution in animal hosts. The objective of this study was to estimate and characterise the data gap between the number of SARS-CoV-2 cases and related deaths in animals officially notified to the World Organisation for Animal Health (WOAH) via its World Animal Health Information System (WAHIS) and known cases reported through two other data sources: ProMED-mail and scientific papers. We used the previously published dataset SARS-ANI to retrieve SARS-CoV-2 events in animals published through WAHIS and ProMED-mail. Additionally, we generated SARS-ANI SciLit v1.0, a novel structured dataset of SARS-CoV-2 events in animals published through scientific literature retrieved from PubMed. We evidenced that at least 52.8% of the SARS-CoV-2 animal cases and 65.8% of the deaths were not reported to WAHIS during 29/02/2020-16/08/2022. Combining information from three different data sources, we compiled a new comprehensive list of 35 animal species reported as susceptible to SARS-CoV-2 under natural conditions, representing a significant advance from the figures reported by the WOAH and the Food and Agriculture Organization of the United Nations. Furthermore, we identified animal species that were underreported to the WAHIS and found that dogs and cats garnered the most attention in research studies. We also showed that, compared to the official WAHIS reports, scientific papers generally experienced longer publication lags and demonstrated that national strategies regarding reporting/publishing of SARS-CoV-2 events in animals greatly differed among countries. This analysis provides valuable insights into the patterns of reporting animal infections with SARS-CoV-2. The study emphasises the need for improvements in data sharing regarding SARS-CoV-2 events in animals, as this is crucial for effective One Health surveillance, prevention, and control of emerging diseases of zoonotic origin.
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Affiliation(s)
- Afra Nerpel
- Unit of Veterinary Public Health and Epidemiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Annemarie Käsbohrer
- Unit of Veterinary Public Health and Epidemiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Chris Walzer
- Wildlife Conservation Society, 2300 Southern Blvd, Bronx, NY 10460, USA
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160 Vienna, Austria
| | - Amélie Desvars-Larrive
- Unit of Veterinary Public Health and Epidemiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
- Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080 Vienna, Austria
- VetFarm, University of Veterinary Medicine Vienna, Kremesberg 13, 2563 Pottenstein, Austria
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25
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Fernández-Bastit L, Vergara-Alert J, Segalés J. Transmission of severe acute respiratory syndrome coronavirus 2 from humans to animals: is there a risk of novel reservoirs? Curr Opin Virol 2023; 63:101365. [PMID: 37793299 DOI: 10.1016/j.coviro.2023.101365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoonotic virus able to infect humans and multiple nonhuman animal species. Most natural infections in companion, captive zoo, livestock, and wildlife species have been related to a reverse transmission, raising concern about potential generation of animal reservoirs due to human-animal interactions. To date, American mink and white-tailed deer are the only species that led to extensive intraspecies transmission of SARS-CoV-2 after reverse zoonosis, leading to an efficient spread of the virus and subsequent animal-to-human transmission. Viral host adaptations increase the probability of new SARS-CoV-2 variants' emergence that could cause a major global health impact. Therefore, applying the One Health approach is crucial to prevent and overcome future threats for human, animal, and environmental fields.
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Affiliation(s)
- Leira Fernández-Bastit
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Catalonia, Spain
| | - Júlia Vergara-Alert
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Catalonia, Spain
| | - Joaquim Segalés
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Catalonia, Spain; Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain.
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26
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Kotwa JD, Lobb B, Massé A, Gagnier M, Aftanas P, Banerjee A, Banete A, Blais-Savoie J, Bowman J, Buchanan T, Chee HY, Kruczkiewicz P, Nirmalarajah K, Soos C, Vernygora O, Yip L, Lindsay LR, McGeer AJ, Maguire F, Lung O, Doxey AC, Pickering B, Mubareka S. Genomic and transcriptomic characterization of delta SARS-CoV-2 infection in free-ranging white-tailed deer ( Odocoileus virginianus). iScience 2023; 26:108319. [PMID: 38026171 PMCID: PMC10665813 DOI: 10.1016/j.isci.2023.108319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/12/2023] [Accepted: 10/20/2023] [Indexed: 11/29/2023] Open
Abstract
White-tailed deer (WTD) are susceptible to SARS-CoV-2 and represent an important species for surveillance. Samples from WTD (n = 258) collected in November 2021 from Québec, Canada were analyzed for SARS-CoV-2 RNA. We employed viral genomics and host transcriptomics to further characterize infection and investigate host response. We detected Delta SARS-CoV-2 (B.1.617.2) in WTD from the Estrie region; sequences clustered with human sequences from October 2021 from Vermont, USA, which borders this region. Mutations in the S-gene and a deletion in ORF8 were detected. Host expression patterns in SARS-CoV-2 infected WTD were associated with the innate immune response, including signaling pathways related to anti-viral, pro- and anti-inflammatory signaling, and host damage. We found limited correlation between genes associated with innate immune response from human and WTD nasal samples, suggesting differences in responses to SARS-CoV-2 infection. Our findings provide preliminary insights into host response to SARS-CoV-2 infection in naturally infected WTD.
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Affiliation(s)
| | - Briallen Lobb
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Ariane Massé
- Ministère de l’Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs, Québec City, QC G1S 4X4, Canada
| | - Marianne Gagnier
- Ministère de l’Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs, Québec City, QC G1S 4X4, Canada
| | | | - Arinjay Banerjee
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andra Banete
- Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
| | | | - Jeff Bowman
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, ON K9J 8M5, Canada
| | - Tore Buchanan
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, ON K9J 8M5, Canada
| | - Hsien-Yao Chee
- Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
- Global Health Research Center and Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu 215316, China
| | - Peter Kruczkiewicz
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | | | - Catherine Soos
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, Saskatoon, SK S7N 3H5, Canada
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Oksana Vernygora
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Lily Yip
- Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
| | - L. Robbin Lindsay
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada
| | - Allison J. McGeer
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
- Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Department of Community Health & Epidemiology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Shared Hospital Laboratory, Toronto, ON M4N 3M5, Canada
| | - Oliver Lung
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Andrew C. Doxey
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Bradley Pickering
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
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27
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Tewari D, Miller R, Livengood J, Wang L, Killian ML, Bustamante F, Kessler C, Thirumalapura N, Terio K, Torchetti M, Lantz K, Rosenberg J. SARS-CoV-2 Infection Dynamics in the Pittsburgh Zoo Wild Felids with Two Viral Variants (Delta and Alpha) during the 2021-2022 Pandemic in the United States. Animals (Basel) 2023; 13:3094. [PMID: 37835700 PMCID: PMC10571823 DOI: 10.3390/ani13193094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/17/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been reported in multiple animal species besides humans. The goal of this study was to report clinical signs, infection progression, virus detection and antibody response in a group of wild felids housed in adjacent but neighboring areas at the Pittsburgh Zoo. Initially, five African lions (Panthera leo krugeri) housed together exhibited respiratory clinical signs with viral shedding in their feces in March of 2021 coinciding with infection of an animal keeper. During the second infection wave in December 2021, four Amur tigers (Panthera tigris altaica) and a Canadian lynx (Lynx canadensis) showed clinical signs and tested positive for viral RNA in feces. In infected animals, viral shedding in feces was variable lasting up to 5 weeks and clinical signs were observed for up to 4 weeks. Despite mounting an antibody response to initial exposure, lions exhibited respiratory clinical signs during the second infection wave, but none shed the virus in their feces. The lions were positive for alpha variant (B.1.1.7 lineage) during the first wave and the tiger and lynx were positive for delta variant (AY.25.1. lineage) during the second wave. The viruses recovered from felids were closely related to variants circulating in human populations at the time of the infection. Cheetahs (Acinonyx jubatus) in the park did not show either the clinical signs or the antibody response.
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Affiliation(s)
- Deepanker Tewari
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Ryan Miller
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Julia Livengood
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Leyi Wang
- Illinois Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA;
| | - Mary Lea Killian
- National Veterinary Services Laboratory, United States Department of Agriculture, Ames, IA 50010, USA; (M.L.K.); (M.T.); (K.L.)
| | - Felipe Bustamante
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Candy Kessler
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Nagaraja Thirumalapura
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Karen Terio
- Zoological Pathology Program, University of Illinois, Brookfield, IL 60513, USA;
| | - Mia Torchetti
- National Veterinary Services Laboratory, United States Department of Agriculture, Ames, IA 50010, USA; (M.L.K.); (M.T.); (K.L.)
| | - Kristina Lantz
- National Veterinary Services Laboratory, United States Department of Agriculture, Ames, IA 50010, USA; (M.L.K.); (M.T.); (K.L.)
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28
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Thieulent CJ, Carossino M, Peak L, Wolfson W, Balasuriya UBR. Multiplex One-Step RT-qPCR Assays for Simultaneous Detection of SARS-CoV-2 and Other Enteric Viruses of Dogs and Cats. Viruses 2023; 15:1890. [PMID: 37766296 PMCID: PMC10534472 DOI: 10.3390/v15091890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was transmitted from humans to dogs and cats (reverse zoonosis) during the COVID-19 pandemic. SARS-CoV-2 has been detected in fecal samples of infected dogs and cats, indicating potential fecal-oral transmission, environmental contamination, and zoonotic transmission (i.e., spillback). Additionally, gastrointestinal viral infections are prevalent in dogs and cats. In this study, we developed and validated a panel of multiplex one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays for the simultaneous detection of SARS-CoV-2 and common canine enteric viruses: Canine Enteric Assay_1 (CEA_1) for the detection of canine adenovirus-1, canine enteric coronavirus, canine distemper virus, and canine parvovirus, and CEA_2 for the detection of rotavirus A (RVA), and SARS-CoV-2); or common feline enteric viruses (Feline Enteric Assay_1 (FEA_1) for the detection of feline enteric coronavirus, feline panleukopenia virus, RVA, and SARS-CoV-2). All assays demonstrated high analytical sensitivity, detecting as few as 5-35 genome copies/µL in multiplex format. The repeatability and reproducibility of the multiplex assays were excellent, with coefficient of variation <4%. Among the 58 clinical samples tested, 34.5% were positive for at least one of these viruses, and SARS-CoV-2 was detected in two samples collected from one dog and one cat, respectively. In conclusion, these newly developed one-step multiplex RT-qPCR assays allow for rapid diagnosis of enteric viral infections, including SARS-CoV-2, in dogs and cats.
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Affiliation(s)
- Côme J. Thieulent
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; (C.J.T.); (M.C.); (L.P.)
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; (C.J.T.); (M.C.); (L.P.)
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Laura Peak
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; (C.J.T.); (M.C.); (L.P.)
| | - Wendy Wolfson
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Udeni B. R. Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; (C.J.T.); (M.C.); (L.P.)
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
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29
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Peka M, Balatsky V. Analysis of RBD-ACE2 interactions in livestock species as a factor in the spread of SARS-CoV-2 among animals. Vet Anim Sci 2023; 21:100303. [PMID: 37521409 PMCID: PMC10372456 DOI: 10.1016/j.vas.2023.100303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
The high mutation rate of SARS-CoV-2, which has led to the emergence of a number of virus variants, creates risks of transmission from humans to animal species and the emergence of new animal reservoirs of COVID-19. This study aimed to identify animal species among livestock susceptible to infection and develop an approach that would be possible to use for assessing the hazards caused by new SARS-CoV-2 variants for animals. Bioinformatic analysis was used to evaluate the ability of receptor-binding domains (RBDs) of different SARS-CoV-2 variants to interact with ACE2 receptors of livestock species. The results indicated that the stability of RBD-ACE2 complexes depends on both amino acid residues in the ACE2 sequences of animal species and on mutations in the RBDs of SARS-CoV-2 variants, with the residues in the interface of the RBD-ACE2 complex being the most important. All studied SARS-CoV-2 variants had high affinity for ferret and American mink receptors, while the affinity for horse, donkey, and bird species' receptors significantly increased in the highly mutated Omicron variant. Hazards that future SARS-CoV-2 variants may acquire specificity to new animal species remain high given the mutability of the virus. The continued use and expansion of the bioinformatic approach presented in this study may be relevant for monitoring transmission risks and preventing the emergence of new reservoirs of COVID-19 among animals.
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Affiliation(s)
- Mykyta Peka
- V. N. Karazin Kharkiv National University, 4 Svobody Sq, Kharkiv, 61022, Ukraine
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013, Ukraine
| | - Viktor Balatsky
- V. N. Karazin Kharkiv National University, 4 Svobody Sq, Kharkiv, 61022, Ukraine
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013, Ukraine
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30
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Flies AS, Flies EJ, Fountain-Jones NM, Musgrove RE, Hamede RK, Philips A, Perrott MRF, Dunowska M. Wildlife nidoviruses: biology, epidemiology, and disease associations of selected nidoviruses of mammals and reptiles. mBio 2023; 14:e0071523. [PMID: 37439571 PMCID: PMC10470586 DOI: 10.1128/mbio.00715-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023] Open
Abstract
Wildlife is the source of many emerging infectious diseases. Several viruses from the order Nidovirales have recently emerged in wildlife, sometimes with severe consequences for endangered species. The order Nidovirales is currently classified into eight suborders, three of which contain viruses of vertebrates. Vertebrate coronaviruses (suborder Cornidovirineae) have been extensively studied, yet the other major suborders have received less attention. The aim of this minireview was to summarize the key findings from the published literature on nidoviruses of vertebrate wildlife from two suborders: Arnidovirineae and Tornidovirineae. These viruses were identified either during investigations of disease outbreaks or through molecular surveys of wildlife viromes, and include pathogens of reptiles and mammals. The available data on key biological features, disease associations, and pathology are presented, in addition to data on the frequency of infections among various host populations, and putative routes of transmission. While nidoviruses discussed here appear to have a restricted in vivo host range, little is known about their natural life cycle. Observational field-based studies outside of the mortality events are needed to facilitate an understanding of the virus-host-environment interactions that lead to the outbreaks. Laboratory-based studies are needed to understand the pathogenesis of diseases caused by novel nidoviruses and their evolutionary histories. Barriers preventing research progress include limited funding and the unavailability of virus- and host-specific reagents. To reduce mortalities in wildlife and further population declines, proactive development of expertise, technologies, and networks should be developed. These steps would enable effective management of future outbreaks and support wildlife conservation.
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Affiliation(s)
- Andrew S. Flies
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Emily J. Flies
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- Healthy Landscapes Research Group, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Ruth E. Musgrove
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo K. Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Annie Philips
- Natural Resources and Environment Tasmania, Hobart, Tasmania, Australia
| | | | - Magdalena Dunowska
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
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31
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Barroso-Arévalo S, Díaz-Frutos M, Domínguez L, Sánchez-Vizcaíno JM. Importance of genomic surveillance of SARS-CoV-2 in cats during reverse zoonosis events: potential viral evolution may occur. Microbiol Spectr 2023; 11:e0068023. [PMID: 37565759 PMCID: PMC10581217 DOI: 10.1128/spectrum.00680-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/29/2023] [Indexed: 08/12/2023] Open
Abstract
The apparition of new variants of severe acute respiratory syndrome coronavirus 2 and lineages is constantly happening because of the high viral mutation rate. Since numerous reverse zoonosis events have been reported so far, genomic surveillance should be conducted in susceptible species to evaluate potential adaptations that may trigger the apparition of new variants. Here, we evaluate the evolution of the infection in a cat naturally infected in parallel with its owner, performing a comparative phylogenetic analysis. Sequencing analysis showed that both were infected with the Omicron BA.5/BF.1 lineage and revealed the presence of nucleotide substitution in the viral genome recovered from the cat with respect to the viral genome from the human sample. This nucleotide substitution (C11897A) produced the amino acid change Orf1a: Q3878K. Therefore, genomic surveillance in the case of reverse zoonosis events is still necessary in order to control possible adaptations of the virus to other susceptible species. IMPORTANCE Genomic surveillance of pets for severe acute respiratory syndrome coronavirus 2 is important to monitor the emergence of new variants of the virus associated with these animals. Pets can serve as a potential reservoir for the virus, and their close contact with humans increases the risk of transmission. By conducting genomic surveillance in pets, it is possible to detect and track new variants early on, allowing for more effective control measures to be put in place. This can help prevent the spread of these variants to human populations and potentially mitigate the impact of the pandemic. Furthermore, it may also provide insight into the evolution and spread of the virus within the animal population.
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Affiliation(s)
- Sandra Barroso-Arévalo
- VISAVET Health Surveillance Center, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - Marta Díaz-Frutos
- VISAVET Health Surveillance Center, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Center, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - José M. Sánchez-Vizcaíno
- VISAVET Health Surveillance Center, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
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32
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Ibrahim MA, Dénes A. Mathematical Modeling of SARS-CoV-2 Transmission between Minks and Humans Considering New Variants and Mink Culling. Trop Med Infect Dis 2023; 8:398. [PMID: 37624336 PMCID: PMC10459927 DOI: 10.3390/tropicalmed8080398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/19/2023] [Accepted: 07/30/2023] [Indexed: 08/26/2023] Open
Abstract
We formulated and studied mathematical models to investigate control strategies for the outbreak of the disease caused by SARS-CoV-2, considering the transmission between humans and minks. Two novel models, namely SEIR and SVEIR, are proposed to incorporate human-to-human, human-to-mink, and mink-to-human transmission. We derive formulas for the reproduction number R0 for both models using the next-generation matrix technique. We fitted our model to the daily number of COVID-19-infected cases among humans in Denmark as an example, and using the best-fit parameters, we calculated the values of R0 to be 1.58432 and 1.71852 for the two-strain and single-strain models, respectively. Numerical simulations are conducted to investigate the impact of control measures, such as mink culling or vaccination strategies, on the number of infected cases in both humans and minks. Additionally, we investigated the possibility of the mutated virus in minks being transmitted to humans. Our results indicate that to control the disease and spread of SARS-CoV-2 mutant strains among humans and minks, we must minimize the transmission and contact rates between mink farmers and other humans by quarantining such individuals. In order to reduce the virus mutation rate in minks, culling or vaccination strategies for infected mink farms must also be implemented. These measures are essential in managing the spread of SARS-CoV-2 and its variants, protecting public health, and mitigating the potential risks associated with human-to-mink transmission.
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Affiliation(s)
- Mahmoud A. Ibrahim
- Bolyai Institute, University of Szeged, Aradi Vértanúk Tere 1., 6720 Szeged, Hungary
- Department of Mathematics, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Attila Dénes
- National Laboratory for Health Security, Bolyai Institute, University of Szeged, Aradi Vértanúk Tere 1., 6720 Szeged, Hungary
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Feng A, Bevins S, Chandler J, DeLiberto TJ, Ghai R, Lantz K, Lenoch J, Retchless A, Shriner S, Tang CY, Tong SS, Torchetti M, Uehara A, Wan XF. Transmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States. Nat Commun 2023; 14:4078. [PMID: 37429851 DOI: 10.1038/s41467-023-39782-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023] Open
Abstract
SARS-CoV-2 is a zoonotic virus with documented bi-directional transmission between people and animals. Transmission of SARS-CoV-2 from humans to free-ranging white-tailed deer (Odocoileus virginianus) poses a unique public health risk due to the potential for reservoir establishment where variants may persist and evolve. We collected 8,830 respiratory samples from free-ranging white-tailed deer across Washington, D.C. and 26 states in the United States between November 2021 and April 2022. We obtained 391 sequences and identified 34 Pango lineages including the Alpha, Gamma, Delta, and Omicron variants. Evolutionary analyses showed these white-tailed deer viruses originated from at least 109 independent spillovers from humans, which resulted in 39 cases of subsequent local deer-to-deer transmission and three cases of potential spillover from white-tailed deer back to humans. Viruses repeatedly adapted to white-tailed deer with recurring amino acid substitutions across spike and other proteins. Overall, our findings suggest that multiple SARS-CoV-2 lineages were introduced, became enzootic, and co-circulated in white-tailed deer.
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Affiliation(s)
- Aijing Feng
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Sarah Bevins
- USDA APHIS Wildlife Services National Wildlife Disease Program, Fort Collins, CO, USA
| | - Jeff Chandler
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Fort Collins, CO, USA
| | | | - Ria Ghai
- One Health Office, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kristina Lantz
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Julianna Lenoch
- USDA APHIS Wildlife Services National Wildlife Disease Program, Fort Collins, CO, USA
| | - Adam Retchless
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Susan Shriner
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Fort Collins, CO, USA
| | - Cynthia Y Tang
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Suxiang Sue Tong
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mia Torchetti
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Anna Uehara
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
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34
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Hamdy ME, El Deeb AH, Hagag NM, Shahein MA, Alaidi O, Hussein HA. Interspecies transmission of SARS CoV-2 with special emphasis on viral mutations and ACE-2 receptor homology roles. Int J Vet Sci Med 2023; 11:55-86. [PMID: 37441062 PMCID: PMC10334861 DOI: 10.1080/23144599.2023.2222981] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 05/11/2023] [Accepted: 05/19/2023] [Indexed: 07/15/2023] Open
Abstract
COVID-19 outbreak was first reported in 2019, Wuhan, China. The spillover of the disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), to a wide range of pet, zoo, wild, and farm animals has emphasized potential zoonotic and reverse zoonotic viral transmission. Furthermore, it has evoked inquiries about susceptibility of different animal species to SARS-CoV-2 infection and role of these animals as viral reservoirs. Therefore, studying susceptible and non-susceptible hosts for SARS-CoV-2 infection could give a better understanding for the virus and will help in preventing further outbreaks. Here, we review structural aspects of SARS-CoV-2 spike protein, the effect of the different mutations observed in the spike protein, and the impact of ACE2 receptor variations in different animal hosts on inter-species transmission. Moreover, the SARS-CoV-2 spillover chain was reviewed. Combination of SARS-CoV-2 high mutation rate and homology of cellular ACE2 receptors enable the virus to transcend species barriers and facilitate its transmission between humans and animals.
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Affiliation(s)
- Mervat E. Hamdy
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Ayman H. El Deeb
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
- Department of Virology, Faculty of Veterinary Medicine, King Salman International University, South Sinai, Egypt
| | - Naglaa M. Hagag
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Momtaz A. Shahein
- Department of Virology, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Osama Alaidi
- Biocomplexity for Research and Consulting Co., Cairo, Egypt
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Hussein A. Hussein
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
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Kuchipudi SV, Tan C, van Dorp L, Lichtveld M, Pickering B, Bowman J, Mubareka S, Balloux F. Coordinated surveillance is essential to monitor and mitigate the evolutionary impacts of SARS-CoV-2 spillover and circulation in animal hosts. Nat Ecol Evol 2023; 7:956-959. [PMID: 37231305 DOI: 10.1038/s41559-023-02082-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Suresh V Kuchipudi
- Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA.
| | - Cedric Tan
- UCL Genetics Institute, University College London, London, UK
- Francis Crick Institute, London, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Maureen Lichtveld
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bradley Pickering
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jeff Bowman
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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Brüssow H. Viral infections at the animal-human interface-Learning lessons from the SARS-CoV-2 pandemic. Microb Biotechnol 2023; 16:1397-1411. [PMID: 37338856 DOI: 10.1111/1751-7915.14269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 06/21/2023] Open
Abstract
This Lilliput explores the current epidemiological and virological arguments for a zoonotic origin of the COVID-19 pandemic. While the role of bats, pangolins and racoon dogs as viral reservoirs has not yet been proven, a spill-over of a coronavirus infection from animals into humans at the Huanan food market in Wuhan has a much greater plausibility than alternative hypotheses such as a laboratory virus escape, deliberate genetic engineering or introduction by cold chain food products. This Lilliput highlights the dynamic nature of the animal-human interface for viral cross-infections from humans into feral white tail deer or farmed minks (reverse zoonosis). Surveillance of viral infections at the animal-human interface is an urgent task since live animal markets are not the only risks for future viral spill-overs. Climate change will induce animal migration which leads to viral exchanges between animal species that have not met in the past. Environmental change and deforestation will also increase contact between animals and humans. Developing an early warning system for emerging viral infections becomes thus a societal necessity not only for human but also for animal and environmental health (One Health concept). Microbiologists have developed tools ranging from virome analysis in key suspects such as viral reservoirs (bats, wild game animals, bushmeat) and in humans exposed to wild animals, to wastewater analysis to detect known and unknown viruses circulating in the human population and sentinel studies in animal-exposed patients with fever. Criteria need to be developed to assess the virulence and transmissibility of zoonotic viruses. An early virus warning system is costly and will need political lobbying. The accelerating number of viral infections with pandemic potential over the last decades should provide the public pressure to extend pandemic preparedness for the inclusion of early viral alert systems.
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Affiliation(s)
- Harald Brüssow
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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37
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Picó Y, Barceló D. Microplastics and other emerging contaminants in the environment after COVID-19 pandemic: The need of global reconnaissance studies. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2023; 33:100468. [PMID: 37139099 PMCID: PMC10085870 DOI: 10.1016/j.coesh.2023.100468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Evidence of the increase of emerging contaminants in the environment due to the COVID-19 pandemic, such as personal protective equipment (PPE), disinfectants, pharmaceuticals, etc., has enlarged. Here we explain the variety of pathways of these emerging contaminants to enter the environment, including wastewater treatment plants, improper disposal of PPE, and runoff from surfaces treated with disinfectants. We also discuss the current state-of-art of the toxicological implications of these emerging contaminants. Initial research suggests that they may have harmful effects on aquatic organisms and human health. Future directions are suggested as further research is needed to fully understand the impacts of these contaminants on the environment and humans, as well as to develop effective approaches to mitigate their potential negative effects.
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Affiliation(s)
- Yolanda Picó
- Food and Environmental Research Group (SAMA-UV), Research Desertification Centre (CIDE) (CSIC-University of Valencia-GV), Moncada-Naquera Road, Km 4.5, 46113 Moncada, Valencia, Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP), Institute of Health Carlos III, Madrid, Spain
| | - Damià Barceló
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Jordi Girona, 18-26, 08034, Barcelona, Spain
- Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, C/Emili Grahit, 101, Edifici H2O, 17003, Girona, Spain
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38
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Italiya J, Bhavsar T, Černý J. Assessment and strategy development for SARS-CoV-2 screening in wildlife: A review. Vet World 2023; 16:1193-1200. [PMID: 37577208 PMCID: PMC10421538 DOI: 10.14202/vetworld.2023.1193-1200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/04/2023] [Indexed: 08/15/2023] Open
Abstract
Coronaviruses (members of the Coronaviridae family) are prominent in veterinary medicine, with several known infectious agents commonly reported. In contrast, human medicine has disregarded coronaviruses for an extended period. Within the past two decades, coronaviruses have caused three major outbreaks. One such outbreak was the coronavirus disease 2019 (COVID-19) caused by the coronavirus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Over the 3-year COVID-19 outbreak, several instances of zooanthroponosis have been documented, which pose risks for virus modifications and possible re-emergence of the virus into the human population, causing a new epidemic and possible threats for vaccination or treatment failure. Therefore, widespread screening of animals is an essential technique for mitigating future risks and repercussions. However, mass detection of SARS-CoV-2 in wild animals might be challenging. In silico prediction modeling, experimental studies conducted on various animal species, and natural infection episodes recorded in various species might provide information on the potential threats to wildlife. They may be useful for diagnostic and mass screening purposes. In this review, the possible methods of wildlife screening, based on experimental data and environmental elements that might play a crucial role in its effective implementation, are reviewed.
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Affiliation(s)
- Jignesh Italiya
- Centre for Infectious Animal Diseases, Faculty of Tropical Agrisciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague – Suchdol, Czechia
| | - Tanvi Bhavsar
- Animal Physiology Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Jiří Černý
- Centre for Infectious Animal Diseases, Faculty of Tropical Agrisciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague – Suchdol, Czechia
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Hecht G, Sarbo N, Svoboda W, Mead HL, Ruberto I, Altin JA, Engelthaler DM, Venkat H, Yaglom HD. "Sniffing" out SARS-CoV-2 in Arizona working dogs: an exploratory serosurvey. Front Vet Sci 2023; 10:1166101. [PMID: 37215472 PMCID: PMC10196159 DOI: 10.3389/fvets.2023.1166101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
Susceptibility to and infection with SARS-CoV-2 in companion animals has been well-documented throughout the COVID-19 pandemic. Surveillance for the virus in dogs has largely been focused on household pets; however, other canine populations may also be impacted. We partnered with a local veterinary hospital with a high working dog patient volume to conduct viral and neutralizing antibody testing in working dogs and identify potential risk factors in the dog's work and home environments. Surveillance of SARS-CoV-2 in law enforcement and security working dogs in Arizona found 24.81% (32/129) of dogs to be seropositive. Thirteen dogs presenting with clinical signs or with reported exposure to COVID-19 in the 30 days prior to sample collection were also tested by PCR; all samples were negative. 90.7% (n = 117) of dogs were reported to be asymptomatic or have no change in performance at the time of sampling. Two dogs (1.6%) had suspected anosmia as reported by their handlers; one of which was seropositive. Known exposure to the dog's COVID-19 positive handler or household member was identified as a significant risk factor. Demographics factors including sex, altered status, and type of work were not associated with canine seropositivity. Further work is warranted to understand the impact of SARS-CoV-2 and other infectious diseases in working dogs.
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Affiliation(s)
- Gavriella Hecht
- Arizona Department of Health Services, Phoenix, AZ, United States
| | - Nathan Sarbo
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Wayne Svoboda
- Hayden Road Animal Hospital, Scottsdale, AZ, United States
| | - Heather L. Mead
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Irene Ruberto
- Arizona Department of Health Services, Phoenix, AZ, United States
| | - John A. Altin
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | | | - Heather Venkat
- Arizona Department of Health Services, Phoenix, AZ, United States
- Centers for Disease Control and Prevention, Center for Preparedness and Response, Career Epidemiology Field Officer Program, Atlanta, GA, United States
| | - Hayley D. Yaglom
- Translational Genomics Research Institute, Flagstaff, AZ, United States
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Luo Y, Liu S, Xue J, Yang Y, Zhao J, Sun Y, Wang B, Yin S, Li J, Xia Y, Ge F, Dong J, Guo L, Ye B, Huang W, Wang Y, Xi JJ. High-throughput screening of spike variants uncovers the key residues that alter the affinity and antigenicity of SARS-CoV-2. Cell Discov 2023; 9:40. [PMID: 37041132 PMCID: PMC10088716 DOI: 10.1038/s41421-023-00534-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/03/2023] [Indexed: 04/13/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has elicited a worldwide pandemic since late 2019. There has been ~675 million confirmed coronavirus disease 2019 (COVID-19) cases, leading to more than 6.8 million deaths as of March 1, 2023. Five SARS-CoV-2 variants of concern (VOCs) were tracked as they emerged and were subsequently characterized. However, it is still difficult to predict the next dominant variant due to the rapid evolution of its spike (S) glycoprotein, which affects the binding activity between cellular receptor angiotensin-converting enzyme 2 (ACE2) and blocks the presenting epitope from humoral monoclonal antibody (mAb) recognition. Here, we established a robust mammalian cell-surface-display platform to study the interactions of S-ACE2 and S-mAb on a large scale. A lentivirus library of S variants was generated via in silico chip synthesis followed by site-directed saturation mutagenesis, after which the enriched candidates were acquired through single-cell fluorescence sorting and analyzed by third-generation DNA sequencing technologies. The mutational landscape provides a blueprint for understanding the key residues of the S protein binding affinity to ACE2 and mAb evasion. It was found that S205F, Y453F, Q493A, Q493M, Q498H, Q498Y, N501F, and N501T showed a 3-12-fold increase in infectivity, of which Y453F, Q493A, and Q498Y exhibited at least a 10-fold resistance to mAbs REGN10933, LY-CoV555, and REGN10987, respectively. These methods for mammalian cells may assist in the precise control of SARS-CoV-2 in the future.
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Affiliation(s)
- Yufeng Luo
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Shuo Liu
- Graduate School of Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Jiguo Xue
- Institute of Health Service and Transfusion Medicine, Beijing, China
| | - Ye Yang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Junxuan Zhao
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Ying Sun
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bolun Wang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Shenyi Yin
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Juan Li
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Yuchao Xia
- GeneX Health Co. Ltd, Beijing, China
- College of Science, Beijing Information Science and Technology University, Beijing, China
| | - Feixiang Ge
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | | | - Lvze Guo
- GeneX Health Co. Ltd, Beijing, China
| | - Buqing Ye
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Youchun Wang
- Graduate School of Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China.
| | - Jianzhong Jeff Xi
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China.
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Bacterial and viral rodent-borne infections on poultry farms. An attempt at a systematic review. J Vet Res 2023; 67:1-10. [PMID: 37008769 PMCID: PMC10062035 DOI: 10.2478/jvetres-2023-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/01/2023] [Indexed: 03/17/2023] Open
Abstract
Abstract
Introduction
Rodents are quite common at livestock production sites. Their adaptability, high reproductive capacity and omnivorousness make them apt to become a source of disease transmission to humans and animals. Rodents can serve as mechanical vectors or active shedders of many bacteria and viruses, and their transmission can occur through direct contact, or indirectly through contaminated food and water or by the arthropods which parasitise infected rodents. This review paper summarises how rodents spread infectious diseases in poultry production.
Material and Methods
The aim of this review was to use PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) principles to meta-analyse the available data on this topic. Three databases – PubMed, Web of Science and Scopus – and grey literature were searched for papers published from inception to July 2022 using the established keywords.
Results
An initial search identified 2,999 articles that met the criteria established by the keywords. This number remained after removing 597 articles that were repeated in some databases. The articles were searched for any mention of specific bacterial and viral pathogens.
Conclusion
The importance of rodents in the spread of bacterial diseases in poultry has been established, and the vast majority of such diseases involved Salmonella, Campylobacter, Escherichia coli, Staphylococcus (MRSA), Pasteurella, Erysipelothrix or Yersinia infections. Rodents also play a role in the transmission of viruses such as avian influenza virus, avian paramyxovirus 1, avian gammacoronavirus or infectious bursal disease virus, but knowledge of these pathogens is very limited and requires further research to expand it.
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A linear DNA encoding the SARS-CoV-2 receptor binding domain elicits potent immune response and neutralizing antibodies in domestic cats. Mol Ther Methods Clin Dev 2023; 28:238-248. [PMID: 36618106 PMCID: PMC9806924 DOI: 10.1016/j.omtm.2022.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of the COVID-19 pandemic, has been shown to infect a wide range of animal species, especially mammals, and besides human-to-human transmission, human-to-animal transmission has also been observed in some wild animals and pets, especially in cats. It has been demonstrated that cats are permissive to COVID-19 and are susceptible to airborne infections. Given the high transmissibility potential of SARS-CoV-2 to different host species and the close contact between humans and animals, it is crucial to find mechanisms to prevent the transmission chain and reduce the risk of spillover to susceptible species. Here, we show results from a clinical trial conducted in domestic cats to assess safety and immunogenicity of a linear DNA (linDNA) vaccine encoding the receptor-binding domain (RBD) from SARS-CoV-2 (Lin-COVID-eVax). Lin-COVID-eVax proved to be safe, with no significant adverse events, and was able to elicit both RBD-specific antibodies and T cells. Also, the linDNA vaccine induced neutralizing antibody titers against ancestral SARS-CoV-2 virus and its variants. These findings demonstrate the safety and immunogenicity of a genetic vaccine against COVID-19 administered to cats and strongly support the development of vaccines for preventing viral spread in susceptible species, especially those in close contact with humans.
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Affiliation(s)
- Jodie McVernon
- Department of Infectious Diseases, University of Melbourne at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- University of Melbourne, Parkville, Australia
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Nielsen SS, Alvarez J, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar C, Herskin M, Michel V, Miranda Chueca MÁ, Padalino B, Pasquali P, Roberts HC, Spoolder H, Velarde A, Viltrop A, Winckler C, Adlhoch C, Aznar I, Baldinelli F, Boklund A, Broglia A, Gerhards N, Mur L, Nannapaneni P, Ståhl K. SARS-CoV-2 in animals: susceptibility of animal species, risk for animal and public health, monitoring, prevention and control. EFSA J 2023; 21:e07822. [PMID: 36860662 PMCID: PMC9968901 DOI: 10.2903/j.efsa.2023.7822] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
The epidemiological situation of SARS-CoV-2 in humans and animals is continually evolving. To date, animal species known to transmit SARS-CoV-2 are American mink, raccoon dog, cat, ferret, hamster, house mouse, Egyptian fruit bat, deer mouse and white-tailed deer. Among farmed animals, American mink have the highest likelihood to become infected from humans or animals and further transmit SARS-CoV-2. In the EU, 44 outbreaks were reported in 2021 in mink farms in seven MSs, while only six in 2022 in two MSs, thus representing a decreasing trend. The introduction of SARS-CoV-2 into mink farms is usually via infected humans; this can be controlled by systematically testing people entering farms and adequate biosecurity. The current most appropriate monitoring approach for mink is the outbreak confirmation based on suspicion, testing dead or clinically sick animals in case of increased mortality or positive farm personnel and the genomic surveillance of virus variants. The genomic analysis of SARS-CoV-2 showed mink-specific clusters with a potential to spill back into the human population. Among companion animals, cats, ferrets and hamsters are those at highest risk of SARS-CoV-2 infection, which most likely originates from an infected human, and which has no or very low impact on virus circulation in the human population. Among wild animals (including zoo animals), mostly carnivores, great apes and white-tailed deer have been reported to be naturally infected by SARS-CoV-2. In the EU, no cases of infected wildlife have been reported so far. Proper disposal of human waste is advised to reduce the risks of spill-over of SARS-CoV-2 to wildlife. Furthermore, contact with wildlife, especially if sick or dead, should be minimised. No specific monitoring for wildlife is recommended apart from testing hunter-harvested animals with clinical signs or found-dead. Bats should be monitored as a natural host of many coronaviruses.
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Gabrielson K, Myers S, Yi J, Gabrielson E, Jimenez IA. Comparison of Cardiovascular Pathology In Animal Models of SARS-CoV-2 Infection: Recommendations Regarding Standardization of Research Methods. Comp Med 2023; 73:58-71. [PMID: 36731878 PMCID: PMC9948900 DOI: 10.30802/aalas-cm-22-000095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/04/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as the viral pathogen that led to the global COVID-19 pandemic that began in late 2019. Because SARS-CoV-2 primarily causes a respiratory disease, much research conducted to date has focused on the respiratory system. However, SARS-CoV-2 infection also affects other organ systems, including the cardiovascular system. In this critical analysis of published data, we evaluate the evidence of cardiovascular pathology in human patients and animals. Overall, we find that the presence or absence of cardiovascular pathology is reported infrequently in both human autopsy studies and animal models of SARS-CoV-2 infection. Moreover, in those studies that have reported cardiovascular pathology, we identified issues in their design and execution that reduce confidence in the conclusions regarding SARS-CoV-2 infection as a cause of significant cardiovascular pathology. Throughout this overview, we expand on these limitations and provide recommendations to ensure a high level of scientific rigor and reproducibility.
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Affiliation(s)
- Kathleen Gabrielson
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stephanie Myers
- School of Veterinary Medicine, Texas Tech University, Amarillo, Texas; and
| | - Jena Yi
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Edward Gabrielson
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Isabel A Jimenez
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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Shiraz R, Tripathi S. Enhanced recombination among Omicron subvariants of SARS-CoV-2 contributes to viral immune escape. J Med Virol 2023; 95:e28519. [PMID: 36691935 DOI: 10.1002/jmv.28519] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/14/2022] [Accepted: 01/19/2023] [Indexed: 01/25/2023]
Abstract
Genetic recombination is an important driver of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution, which requires the coinfection of a single host cell with different SARS-CoV-2 strains. To understand the emergence and prevalence of recombinant SARS-CoV-2 lineages through time and space, we analyzed SARS-CoV-2 genome sequences collected from November 2019 to July 2022. We observed an extraordinary increase in the emergence of SARS-CoV-2 recombinant lineages during the Omicron wave, particularly in Northern America and Europe. This phenomenon was independent of the sequencing frequency or genetic diversity of circulating SARS-CoV-2 strains. The recombination breakpoints were more prevalent in the 3'-untranslated region of the viral genome. Importantly, we noted the enrichment of certain amino acids in the Spike protein of recombinant lineages, which have been reported to confer immune escape from neutralizing antibodies and increase angiotensin-converting enzyme 2 receptor binding in some cases. We also observed I42V amino acid change genetically fixated in the NSP14 of the Omicron lineage, which needs further characterization for its potential role in enhanced recombination. Overall, we report the important and timely observation of accelerated recombination in the currently circulating SARS-CoV-2 Omicron variants and explore their potential contribution to viral fitness, particularly immune escape.
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Affiliation(s)
- Rishad Shiraz
- Microbiology and Cell Biology Department, Indian Institute of Science, Bengaluru, India.,Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Shashank Tripathi
- Microbiology and Cell Biology Department, Indian Institute of Science, Bengaluru, India.,Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
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SARS-CoV-2 Infection in Captive Hippos ( Hippopotamus amphibius), Belgium. Animals (Basel) 2023; 13:ani13020316. [PMID: 36670856 PMCID: PMC9855072 DOI: 10.3390/ani13020316] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/06/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
Two adult female hippos in Zoo Antwerp who were naturally infected with SARS-CoV-2 showed nasal discharge for a few days. Virus was detected by immunocytochemistry and PCR in nasal swab samples and by PCR in faeces and pool water. Serology was also positive. No treatment was necessary.
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Porter AF, Purcell DFJ, Howden BP, Duchene S. Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink. Virus Evol 2023; 9:vead002. [PMID: 36751428 PMCID: PMC9896948 DOI: 10.1093/ve/vead002] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 10/11/2022] [Accepted: 01/08/2023] [Indexed: 01/12/2023] Open
Abstract
To investigate genetic signatures of adaptation to the mink host, we characterised the evolutionary rate heterogeneity in mink-associated severe acute respiratory syndrome coronaviruses (SARS-CoV-2). In 2020, the first detected anthropozoonotic spillover event of SARS-CoV-2 occurred in mink farms throughout Europe and North America. Both spill-back of mink-associated lineages into the human population and the spread into the surrounding wildlife were reported, highlighting the potential formation of a zoonotic reservoir. Our findings suggest that the evolutionary rate of SARS-CoV-2 underwent an episodic increase upon introduction into the mink host before returning to the normal range observed in humans. Furthermore, SARS-CoV-2 lineages could have circulated in the mink population for a month before detection, and during this period, evolutionary rate estimates were between 3 × 10-3 and 1.05 × 10-2 (95 per cent HPD, with a mean rate of 6.59 × 10-3) a four- to thirteen-fold increase compared to that in humans. As there is evidence for unique mutational patterns within mink-associated lineages, we explored the emergence of four mink-specific Spike protein amino acid substitutions Y453F, S1147L, F486L, and Q314K. We found that mutation Y453F emerged early in multiple mink outbreaks and that mutations F486L and Q314K may co-occur. We suggest that SARS-CoV-2 undergoes a brief, but considerable, increase in evolutionary rate in response to greater selective pressures during species jumps, which may lead to the occurrence of mink-specific mutations. These findings emphasise the necessity of ongoing surveillance of zoonotic SARS-CoV-2 infections in the future.
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Affiliation(s)
| | | | | | - Sebastian Duchene
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC 3010, Australia
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Zhao X, Qin L, Ding X, Zhang Y, Niu X, Gao F, Jiang T, Chen L. Origin and Reversion of Omicron Core Mutations in the Evolution of SARS-CoV-2 Genomes. Viruses 2022; 15:30. [PMID: 36680069 PMCID: PMC9865174 DOI: 10.3390/v15010030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/01/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Genetic analyses showed nearly 30 amino acid mutations occurred in the spike protein of the Omicron variant of SARS-CoV-2. However, how these mutations occurred and changed during the generation and development of Omicron remains unclear. In this study, 6.7 million (all publicly available data from 2020/04/01 to 2022/04/01) SARS-CoV-2 genomes were analyzed to track the origin and evolution of Omicron variants and to reveal the genetic pathways of the generation of core mutations in Omicron. The haplotype network visualized the pre-Omicron, intact-Omicron, and post-Omicron variants and revealed their evolutionary direction. The correlation analysis showed the correlation feature of the core mutations in Omicron. Moreover, we found some core mutations, such as 142D, 417N, 440K, and 764K, reversed to ancestral residues (142G, 417K, 440N, and 764N) in the post-Omicron variant, suggesting the reverse mutations provided sources for the emergence of new variants. In summary, our analysis probed the origin and further evolution of Omicron sub-variants, which may add to our understanding of new variants and facilitate the control of the pandemic.
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Affiliation(s)
- Xinwei Zhao
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Luyao Qin
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Xiao Ding
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Feng Gao
- Institute of Molecular and Medical Virology, Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Taijiao Jiang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
- Guangzhou Laboratory, Guangzhou 510005, China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
- Guangzhou Laboratory, Guangzhou 510005, China
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Reggiani A, Rugna G, Bonilauri P. SARS-CoV-2 and animals, a long story that doesn't have to end now: What we need to learn from the emergence of the Omicron variant. Front Vet Sci 2022; 9:1085613. [PMID: 36590812 PMCID: PMC9798331 DOI: 10.3389/fvets.2022.1085613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
OIE, the world organization for animal health, recently released an update on the state of the art of knowledge regarding SARS-CoV-2 in animals. For farmed animals, ferrets and minks were found to be highly susceptible to the virus and develop symptomatic disease both in natural conditions and in experimental infections. Lagomorphs of the species Oryctolagus cuniculus are indicated as highly susceptible to the virus under experimental conditions, but show no symptoms of the disease and do not transmit the virus between conspecifics, unlike raccoon dogs (Nyctereutes procyonoides), which in addition to being highly susceptible to the virus under experimental conditions, can also transmit the virus between conspecifics. Among felines, the circulation of the virus has reached a level of cases such as sometimes suggests the experimental use of vaccines for human use or treatments with monoclonal antibodies. But even among wild animals, several species (White-tailed deer, Egyptian rousettes, and minks) have now been described as potential natural reservoirs of the virus. This proven circulation of SARS-CoV-2 among animals has not been accompanied by the development of an adequate surveillance system that allows following the evolution of the virus among its natural hosts. This will be all the more relevant as the surveillance system in humans inevitably drops and we move to surveillance by sentinels similar to the human flu virus. The lesson that we can draw from the emergence of Omicron and, more than likely, its animal origin must not be lost, and in this mini-review, we explain why.
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