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Letko M. Functional assessment of cell entry and receptor use for merbecoviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584892. [PMID: 38559009 PMCID: PMC10980018 DOI: 10.1101/2024.03.13.584892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The merbecovirus subgenus of coronaviruses includes Middle East Respiratory Syndrome Coronavirus (MERS-CoV), which is a zoonotic respiratory pathogen that transmits from dromedary camels to humans and causes severe respiratory disease. Viral discovery efforts have uncovered hundreds of merbecoviruses in different species across multiple continents, but few of these viruses have been isolated or studied under laboratory conditions, leaving basic questions regarding their threat to humans unresolved. Viral entry into host cells is considered an early and critical step for transmission between hosts. In this study, a scalable approach to assessing novel merbecovirus cell entry was developed and used to measure receptor use across the entire merbecovirus subgenus. Merbecoviruses are sorted into four clades based on the receptor binding domain of the spike glycoprotein. Receptor tropism is clade-specific, with only one clade using DPP4 and multiple clades using ACE2, including the entire HKU5 cluster of bat coronaviruses.
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Affiliation(s)
- Michael Letko
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, 99163
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De Sabato L, Ianiro G, Manzia F, Monini M, Chiappini B, Di Bartolo I, Vaccari G. Erinaceus coronavirus persistence in hedgehogs ( Erinaceus europaeus) in a non-invasive, in vivo, experimental setting. Front Vet Sci 2023; 10:1213990. [PMID: 37795019 PMCID: PMC10545950 DOI: 10.3389/fvets.2023.1213990] [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: 04/28/2023] [Accepted: 08/09/2023] [Indexed: 10/06/2023] Open
Abstract
In the last 20 years, new zoonotic CoV strains have emerged (SARS-CoV, MERS-CoV, and SARS-CoV-2), and new species have also been reported in animals. In Europe, the Erinaceus coronavirus (EriCoV) was recently described in Erinaceus europaeus. However, information on the prevalence and duration of viral shedding is unknown. In this study, feces samples were collected from 102 European hedgehogs hosted in the Center for the Recovery of Wild Fauna in Rome and analyzed for the presence of EriCoV RNA by Reverse Transcription-PCR. In total, 45 animals (44.1%) resulted positive for EriCoV at the first sampling and 63 (61.7%) animals were positive at the follow-up, which was performed from the 3rd to the 86th day. The duration of fecal virus shedding showed a mean duration of 22.8 days and lasted up to 62 days. Eighteen hedgehogs showed intermittent viral shedding. Phylogenetic analysis showed a correlation with EriCoV strains reported in Germany, the United Kingdom, and northern Italy. None of the EriCoV sequences showed the CD200 ortholog insertion, previously observed in strains isolated in animals from northern Italy. Interestingly, all but one animal revealed the presence in their feces of the same EriCoV sequences, analyzing the short genomic region at 3' spike gene and 5' ORF3a 500bp fragment (100% nt.id.) in both first and follow-up samples. This result suggests that animals were infected with the same strain during their stay at the center. Our results confirm that EriCoV can persist in hedgehogs for a long period, underlining that hedgehogs are an important commensal reservoir for Merbecovirus. A long duration of viral shedding increases the likelihood that the virus will spread in the environment.
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Affiliation(s)
- Luca De Sabato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Giovanni Ianiro
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Francesca Manzia
- Centre for the Recovery of Wild Fauna in Rome, LIPU, Rome, Italy
| | - Marina Monini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Barbara Chiappini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Ilaria Di Bartolo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Gabriele Vaccari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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Jota Baptista C, Oliveira PA, Gonzalo-Orden JM, Seixas F. Do Urban Hedgehogs ( Erinaceus europaeus) Represent a Relevant Source of Zoonotic Diseases? Pathogens 2023; 12:pathogens12020268. [PMID: 36839540 PMCID: PMC9961789 DOI: 10.3390/pathogens12020268] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 01/30/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
Urban fauna is defined as animal species that can live in urban environments. Several species, including the western-European hedgehog (Erinaceus europaeus), have now been identified as part of this urban fauna, becoming permanent residents of parks and gardens in different cities across Europe. Due to the importance that this phenomenon represents for zoonotic disease surveillance, several authors have been conducting zoonotic agents' surveys on hedgehog. The aim of this study is to compare zoonotic diseases' prevalence in hedgehogs in urban environments with those from more rural areas. A systematic review with meta-analysis of twelve studied of zoonotic diseases' (in urban and rural areas of Europe) was therefore conducted for this purpose. Fifteen different zoonoses have been assessed in urban environments and six in rural areas. Anaplasma phagocytophilum was the most prevalent zoonotic agent found in urban habitats (96%). Dermatophytosis shows statistically significant differences between locations (p-value < 0.001), with a higher prevalence in urban Poland (55%; n = 182). Our results suggest further research and a standardized monitoring of different hedgehog populations are essential to understanding the epidemiology of several zoonotic pathogens in different habitat types (urban, rural, natural, industrial, etc.) and preventing possible disease outbreaks.
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Affiliation(s)
- Catarina Jota Baptista
- Department of Veterinary Sciences, School of Agrarian and Veterinary Sciences (ECAV), University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Inov4Agro, University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
- Institute of Biomedicine (IBIOMED), University of León, 24071 León, Spain
- Correspondence: (C.J.B.); (F.S.)
| | - Paula A. Oliveira
- Department of Veterinary Sciences, School of Agrarian and Veterinary Sciences (ECAV), University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Inov4Agro, University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
| | | | - Fernanda Seixas
- Department of Veterinary Sciences, School of Agrarian and Veterinary Sciences (ECAV), University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5001-801 Vila Real, Portugal
- Veterinary and Animal Research Center (CECAV), AL4Animals, University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
- Correspondence: (C.J.B.); (F.S.)
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Machine-learning prediction of hosts of novel coronaviruses requires caution as it may affect wildlife conservation. Nat Commun 2022; 13:5101. [PMID: 36096892 PMCID: PMC9468137 DOI: 10.1038/s41467-022-32746-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/15/2022] [Indexed: 11/08/2022] Open
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Forni D, Cagliani R, Molteni C, Arrigoni F, Mozzi A, Clerici M, De Gioia L, Sironi M. Homology-based classification of accessory proteins in coronavirus genomes uncovers extremely dynamic evolution of gene content. Mol Ecol 2022; 31:3672-3692. [PMID: 35575901 PMCID: PMC9328142 DOI: 10.1111/mec.16531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/21/2022] [Accepted: 05/12/2022] [Indexed: 11/30/2022]
Abstract
Coronaviruses (CoVs) have complex genomes that encode a fixed array of structural and nonstructural components, as well as a variety of accessory proteins that differ even among closely related viruses. Accessory proteins often play a role in the suppression of immune responses and may represent virulence factors. Despite their relevance for CoV phenotypic variability, information on accessory proteins is fragmentary. We applied a systematic approach based on homology detection to create a comprehensive catalogue of accessory proteins encoded by CoVs. Our analyses grouped accessory proteins into 379 orthogroups and 12 super‐groups. No orthogroup was shared by the four CoV genera and very few were present in all or most viruses in the same genus, reflecting the dynamic evolution of CoV genomes. We observed differences in the distribution of accessory proteins in CoV genera. Alphacoronaviruses harboured the largest diversity of accessory open reading frames (ORFs), deltacoronaviruses the smallest. However, the average number of accessory proteins per genome was highest in betacoronaviruses. Analysis of the evolutionary history of some orthogroups indicated that the different CoV genera adopted similar evolutionary strategies. Thus, alphacoronaviruses and betacoronaviruses acquired phosphodiesterases and spike‐like accessory proteins independently, whereas horizontal gene transfer from reoviruses endowed betacoronaviruses and deltacoronaviruses with fusion‐associated small transmembrane (FAST) proteins. Finally, analysis of accessory ORFs in annotated CoV genomes indicated ambiguity in their naming. This complicates cross‐communication among researchers and hinders automated searches of large data sets (e.g., PubMed, GenBank). We suggest that orthogroup membership is used together with a naming system to provide information on protein function.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Cristian Molteni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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Abstract
Erinaceus europaeus is a cosmopolitan mammalian species broadly distributed in Europe, from natural to suburban areas. Due to its ecological role and susceptibility to distinct zoonotic agents, E. europaeus could be a suitable sentinel candidate for many global problems that negatively affect human and animal health. Hedgehogs can work as bioindicators to environmental contamination and can be hosts for multiple tickborne zoonotic agents. Thus, people who directly or indirectly make physical contact with this species are exposed to a variety of threats. Moreover, it has also been studied as an indicator for antibiotic resistance, which was already confirmed for tetracyclines. Additionally, it was also reported as a reservoir for methicillin-resistant Staphylococcus aureus (MRSA). More recently, hedgehogs have been recently recognised as potential reservoirs of MERS-CoV-like strains. Among other animals, this species can possibly represent an intermediate reservoir for SARS-CoV-2. The aim of this review is to briefly expose the scientific attainments about hedgehog health, namely agents, diseases, and threats that significantly affect general health concerns and that contribute to achieve One Health principles.
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