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Kirk NM, Liang Y, Ly H. Pathogenesis and virulence of coronavirus disease: Comparative pathology of animal models for COVID-19. Virulence 2024; 15:2316438. [PMID: 38362881 PMCID: PMC10878030 DOI: 10.1080/21505594.2024.2316438] [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: 10/20/2023] [Accepted: 02/04/2024] [Indexed: 02/17/2024] Open
Abstract
Animal models that can replicate clinical and pathologic features of severe human coronavirus infections have been instrumental in the development of novel vaccines and therapeutics. The goal of this review is to summarize our current understanding of the pathogenesis of coronavirus disease 2019 (COVID-19) and the pathologic features that can be observed in several currently available animal models. Knowledge gained from studying these animal models of SARS-CoV-2 infection can help inform appropriate model selection for disease modelling as well as for vaccine and therapeutic developments.
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Affiliation(s)
- Natalie M. Kirk
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
| | - Yuying Liang
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
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2
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Martinez DR, Moreira FR, Catanzaro NJ, Diefenbacher MV, Zweigart MR, Gully KL, De la Cruz G, Brown AJ, Adams LE, Yount B, Baric TJ, Mallory ML, Conrad H, May SR, Dong S, Scobey DT, Nguyen C, Montgomery SA, Perry JK, Babusis D, Barrett KT, Nguyen AH, Nguyen AQ, Kalla R, Bannister R, Feng JY, Cihlar T, Baric RS, Mackman RL, Bilello JP, Schäfer A, Sheahan TP. The oral nucleoside prodrug GS-5245 is efficacious against SARS-CoV-2 and other endemic, epidemic, and enzootic coronaviruses. Sci Transl Med 2024; 16:eadj4504. [PMID: 38776389 DOI: 10.1126/scitranslmed.adj4504] [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: 06/27/2023] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Despite the wide availability of several safe and effective vaccines that prevent severe COVID-19, the persistent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) that can evade vaccine-elicited immunity remains a global health concern. In addition, the emergence of SARS-CoV-2 VOCs that can evade therapeutic monoclonal antibodies underscores the need for additional, variant-resistant treatment strategies. Here, we characterize the antiviral activity of GS-5245, obeldesivir (ODV), an oral prodrug of the parent nucleoside GS-441524, which targets the highly conserved viral RNA-dependent RNA polymerase (RdRp). We show that GS-5245 is broadly potent in vitro against alphacoronavirus HCoV-NL63, SARS-CoV, SARS-CoV-related bat-CoV RsSHC014, Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 WA/1, and the highly transmissible SARS-CoV-2 BA.1 Omicron variant. Moreover, in mouse models of SARS-CoV, SARS-CoV-2 (WA/1 and Omicron B1.1.529), MERS-CoV, and bat-CoV RsSHC014 pathogenesis, we observed a dose-dependent reduction in viral replication, body weight loss, acute lung injury, and pulmonary function with GS-5245 therapy. Last, we demonstrate that a combination of GS-5245 and main protease (Mpro) inhibitor nirmatrelvir improved outcomes in vivo against SARS-CoV-2 compared with the single agents. Together, our data support the clinical evaluation of GS-5245 against coronaviruses that cause or have the potential to cause human disease.
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Affiliation(s)
- David R Martinez
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Center for Infection and Immunity, Yale School of Medicine, New Haven, CT 06510, USA
| | - Fernando R Moreira
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Meghan V Diefenbacher
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark R Zweigart
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kendra L Gully
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gabriela De la Cruz
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Ariane J Brown
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lily E Adams
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thomas J Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Helen Conrad
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samantha R May
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie Dong
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - D Trevor Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cameron Nguyen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie A Montgomery
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | | | | | | | | | | | - Rao Kalla
- Gilead Sciences, Inc., Foster City, CA 94404, USA
| | | | - Joy Y Feng
- Gilead Sciences, Inc., Foster City, CA 94404, USA
| | - Tomas Cihlar
- Gilead Sciences, Inc., Foster City, CA 94404, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
- Rapidly Emerging Antiviral Drug Development Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Rapidly Emerging Antiviral Drug Development Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
- Rapidly Emerging Antiviral Drug Development Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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3
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Zhuang J, Yan Z, Zhou T, Li Y, Wang H. The role of receptors in the cross-species spread of coronaviruses infecting humans and pigs. Arch Virol 2024; 169:35. [PMID: 38265497 DOI: 10.1007/s00705-023-05956-7] [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: 07/14/2023] [Accepted: 11/19/2023] [Indexed: 01/25/2024]
Abstract
The pandemic caused by SARS-CoV-2, which has proven capable of infecting over 30 animal species, highlights the critical need for understanding the mechanisms of cross-species transmission and the emergence of novel coronavirus strains. The recent discovery of CCoV-HuPn-2018, a recombinant alphacoronavirus from canines and felines that can infect humans, along with evidence of SARS-CoV-2 infection in pig cells, underscores the potential for coronaviruses to overcome species barriers. This review investigates the origins and cross-species transmission of both human and porcine coronaviruses, with a specific emphasis on the instrumental role receptors play in this process.
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Affiliation(s)
- Jie Zhuang
- Department of Basic Veterinary Medicine, College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, 121000, China
| | - Zhiwei Yan
- Department of Basic Veterinary Medicine, College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, 121000, China
| | - Tiezhong Zhou
- Department of Basic Veterinary Medicine, College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, 121000, China
| | - Yonggang Li
- Department of Pathogenic Biology, School of Basic Medical Sciences, Jinzhou Medical University, Jinzhou, 121000, China.
| | - Huinuan Wang
- Department of Basic Veterinary Medicine, College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, 121000, China.
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4
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Wang Y, Ye M, Zhang F, Freeman ZT, Yu H, Ye X, He Y. Ontology-based taxonomical analysis of experimentally verified natural and laboratory human coronavirus hosts and its implication for COVID-19 virus origination and transmission. PLoS One 2024; 19:e0295541. [PMID: 38252647 PMCID: PMC10802970 DOI: 10.1371/journal.pone.0295541] [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: 04/25/2023] [Accepted: 11/26/2023] [Indexed: 01/24/2024] Open
Abstract
To fully understand COVID-19, it is critical to study all possible hosts of SARS-CoV-2 (the pathogen of COVID-19). In this work, we collected, annotated, and performed ontology-based taxonomical analysis of all the reported and verified hosts for all human coronaviruses including SARS-CoV, MERS-CoV, SARS-CoV-2, HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1. A total of 37 natural hosts and 19 laboratory animal hosts of human coronaviruses were identified based on experimental evidence. Our analysis found that all the verified susceptible natural and laboratory animals belong to therian mammals. Specifically, these 37 natural therian hosts include one wildlife marsupial mammal (i.e., Virginia opossum) and 36 Eutheria mammals (a.k.a. placental mammals). The 19 laboratory animal hosts are also classified as therian mammals. The mouse models with genetically modified human ACE2 or DPP4 were more susceptible to virulent human coronaviruses with clear symptoms, suggesting the critical role of ACE2 and DPP4 to coronavirus virulence. Coronaviruses became more virulent and adaptive in the mouse hosts after a series of viral passages in the mice, providing clue to the possible coronavirus origination. The Huanan Seafood Wholesale Market animals identified early in the COVID-19 outbreak were also systematically analyzed as possible COVID-19 hosts. To support knowledge standardization and query, the annotated host knowledge was modeled and represented in the Coronavirus Infectious Disease Ontology (CIDO). Based on our and others' findings, we further propose a MOVIE model (i.e., Multiple-Organism viral Variations and Immune Evasion) to address how viral variations in therian animal hosts and the host immune evasion might have led to dynamic COVID-19 pandemic outcomes.
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Affiliation(s)
- Yang Wang
- Guizhou University School of Medicine, Guiyang, Guizhou, China
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital and NHC Key Laboratory of Immunological Diseases, People’s Hospital of Guizhou University, Guiyang, Guizhou, China
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States of America
| | - Muhui Ye
- Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong, China
| | - Fengwei Zhang
- Guizhou University School of Medicine, Guiyang, Guizhou, China
| | - Zachary Thomas Freeman
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States of America
| | - Hong Yu
- Guizhou University School of Medicine, Guiyang, Guizhou, China
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital and NHC Key Laboratory of Immunological Diseases, People’s Hospital of Guizhou University, Guiyang, Guizhou, China
| | - Xianwei Ye
- Guizhou University School of Medicine, Guiyang, Guizhou, China
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital and NHC Key Laboratory of Immunological Diseases, People’s Hospital of Guizhou University, Guiyang, Guizhou, China
| | - Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States of America
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States of America
- Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, United States of America
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5
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Lu M, Wan W, Li Y, Li H, Sun B, Yu K, Zhao J, Franzo G, Su S. Codon usage bias analysis of the spike protein of human coronavirus 229E and its host adaptability. Int J Biol Macromol 2023; 253:127319. [PMID: 37820917 DOI: 10.1016/j.ijbiomac.2023.127319] [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: 08/24/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
Human coronavirus 229E (HCoV-229E) represents one of the known coronaviruses capable of infecting humans and causes mild respiratory symptoms. It is also considered to have a zoonotic source, originating from animals and being transmitted the humans. In this study, a comprehensive phylogenetic and codon usage analysis of the spike (S) gene of HCoV-229E was conducted. Utilizing phylogenetic analysis and principal component analysis, HCoV-229E was categorized into four distinct clusters, each demonstrating unique host affiliations. Furthermore, it was observed that the codon usage bias within the S gene of HCoV-229E is relatively low, primarily influenced by natural selection patterns, with contributions from mutation pressure and dinucleotide abundance. Comparative analysis involving Codon Adaptation Index (CAI) and Relative Codon Deoptimization Index (RCDI) revealed that the codon usage pattern of HCoV-229E mirrors more closely that of camels, as opposed to alpacas and humans. The elucidation of the codon usage pattern within HCoV-229E, which we have meticulously examined, offers valuable insights for a more comprehensive comprehension of viral features, history, and evolutionary trajectory.
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Affiliation(s)
- Meng Lu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Wenbo Wan
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Yuxing Li
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Haipeng Li
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Bowen Sun
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Kang Yu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Jin Zhao
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, Legnaro 35020, PD, Italy
| | - Shuo Su
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, 131 Dong'an Road, Shanghai 200032, People's Republic of China.
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6
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Liu W, Zhang M, Hu C, Song H, Mei Y, Liu Y, Zhang Q. Remdesivir Derivative VV116 Is a Potential Broad-Spectrum Inhibitor of Both Human and Animal Coronaviruses. Viruses 2023; 15:2295. [PMID: 38140536 PMCID: PMC10748125 DOI: 10.3390/v15122295] [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: 10/07/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Coronaviruses represent a significant threat to both human and animal health, encompassing a range of pathogenic strains responsible for illnesses, from the common cold to more severe diseases. VV116 is a deuterated derivative of Remdesivir with oral bioavailability that was found to potently inhibit SARS-CoV-2. In this work, we investigated the broad-spectrum antiviral activity of VV116 against a variety of human and animal coronaviruses. We examined the inhibitory effects of VV116 on the replication of the human coronaviruses HCoV-NL63, HCoV-229E, and HCoV-OC43, as well as the animal coronaviruses MHV, FIPV, FECV, and CCoV. The findings reveal that VV116 effectively inhibits viral replication across these strains without exhibiting cytotoxicity, indicating its potential for safe therapeutic use. Based on the results of a time-of-addition assay and an rNTP competitive inhibition assay, it is speculated that the inhibitory mechanism of VV116 against HCoV-NL63 is consistent with its inhibition of SARS-CoV-2. Our work presents VV116 as a promising candidate for broad-spectrum anti-coronavirus therapy, with implications for both human and animal health, and supports the expansion of its therapeutic applications as backed by detailed experimental data.
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Affiliation(s)
- Weiyong Liu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (W.L.); (C.H.); (H.S.)
| | - Min Zhang
- Department of Emergency Medicine, The Third People’s Hospital of Hubei Province, Wuhan 430033, China;
| | - Chengxiu Hu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (W.L.); (C.H.); (H.S.)
| | - Huijuan Song
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (W.L.); (C.H.); (H.S.)
| | - Yi Mei
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China;
| | - Yingle Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China;
| | - Qi Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China;
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Llanco L, Retamozo K, Oviedo N, Manchego A, Lázaro C, Navarro-Mamani DA, Santos N, Rojas M. Co-Circulation of Multiple Coronavirus Genera and Subgenera during an Epizootic of Lethal Respiratory Disease in Newborn Alpacas ( Vicugna pacos) in Peru: First Report of Bat-like Coronaviruses in Alpacas. Animals (Basel) 2023; 13:2983. [PMID: 37760383 PMCID: PMC10525639 DOI: 10.3390/ani13182983] [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: 08/16/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Coronaviruses (CoVs) infect a wide range of hosts, including humans, domestic animals, and wildlife, typically causing mild-to-severe respiratory or enteric disease. The main objective of this study was to identify CoV genera and subgenera detected in Peruvian alpacas. Lung lavage specimens were collected from 32 animals aged 1 to 6 weeks. CoVs were identified by using RT-PCR to amplify a pan-CoV conserved region of the RNA-dependent RNA polymerase-encoding gene. A nested PCR was performed to identify β-CoVs. Then, β-CoV-positive samples were subjected to RT-PCR using specific primers to identify the Embecovirus subgenus. Out of 32 analyzed samples, 30 (93.8%) tested positive for at least one CoV genus. β-, α-, or unclassified CoVs were identified in 24 (80%), 1 (3.3%), and 1 (3.3%) of the positive samples, respectively. A CoV genus could not be identified in two (6.7%) samples. A mixture of different CoV genera was detected in two (6.7%) samples: one was co-infected with β- and α-CoVs, and the other contained a β- and an unclassified CoV. A sequence analysis of the amplicons generated by the PCR identified 17 β-CoV strains belonging to the subgenus Embecovirus and two α-CoV strains belonging to Decacovirus. A phylogenetic analysis of two strains revealed a relationship with an unclassified Megaderma BatCoV strain. A subgenus could not be identified in nine β-CoV samples. Our data show a high prevalence and a high genetic diversity of CoV genera and subgenera that infect alpacas, in which the β-CoV subgenus Embecovirus predominated. Our data also suggest a new role for bats in the dissemination and transmission of uncommon CoVs to alpacas raised in rural Peru.
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Affiliation(s)
- Luis Llanco
- Escuela de Medicina Humana, Universidad Privada San Juan Bautista, Apartado, Chincha 15067, Peru;
| | - Karubya Retamozo
- Laboratório de Inmunología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru; (K.R.); (N.O.); (A.M.)
| | - Noriko Oviedo
- Laboratório de Inmunología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru; (K.R.); (N.O.); (A.M.)
| | - Alberto Manchego
- Laboratório de Inmunología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru; (K.R.); (N.O.); (A.M.)
| | - César Lázaro
- Laboratório de Farmacología y Toxicología Veterinaria, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru;
| | - Dennis A. Navarro-Mamani
- Laboratório de Virología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru;
| | - Norma Santos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil;
| | - Miguel Rojas
- Laboratório de Inmunología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru; (K.R.); (N.O.); (A.M.)
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8
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Das T, Sikdar S, Chowdhury MHU, Nyma KJ, Adnan M. SARS-CoV-2 prevalence in domestic and wildlife animals: A genomic and docking based structural comprehensive review. Heliyon 2023; 9:e19345. [PMID: 37662720 PMCID: PMC10474441 DOI: 10.1016/j.heliyon.2023.e19345] [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: 01/22/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 09/05/2023] Open
Abstract
The SARS-CoV-2 virus has been identified as the infectious agent that led to the COVID-19 pandemic, which the world has seen very recently. Researchers have linked the SARS-CoV-2 outbreak to bats for the zoonotic spread of the virus to humans. Coronaviruses have a crown-like shape and positive-sense RNA nucleic acid. It attaches its spike glycoprotein to the host angiotensin-converting enzyme 2 (ACE2) receptor. Coronavirus genome comprises 14 ORFs and 27 proteins, spike glycoprotein being one of the most critical proteins for viral pathogenesis. Many mammals and reptiles, including bats, pangolins, ferrets, snakes, and turtles, serve as the principal reservoirs for this virus. But many experimental investigations have shown that certain domestic animals, including pigs, chickens, dogs, cats, and others, may also be able to harbor this virus, whether they exhibit any symptoms. These animals act as reservoirs for SARS-CoV, facilitating its zoonotic cross-species transmission to other species, including humans. In this review, we performed a phylogenetic analysis with multiple sequence alignment and pairwise evolutionary distance analysis, which revealed the similarity of ACE2 receptors in humans, chimpanzees, domestic rabbits, house mice, and golden hamsters. Pairwise RMSD analysis of the spike protein from some commonly reported SARS-CoV revealed that bat and pangolin coronavirus shared the highest structural similarity with human coronavirus. In a further experiment, molecular docking confirmed a higher affinity of pig, bat, and pangolin coronavirus spike proteins' affinity to the human ACE2 receptor. Such comprehensive structural and genomic analysis can help us to forecast the next likely animal source of these coronaviruses that may infect humans. To combat these zoonotic illnesses, we need a one health strategy that considers the well-being of people and animals and the local ecosystem.
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Affiliation(s)
- Tuhin Das
- Department of Microbiology, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Suranjana Sikdar
- Department of Microbiology, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Md. Helal Uddin Chowdhury
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram, 4331, Bangladesh
| | | | - Md. Adnan
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, 84112, United States
- Department of Pharmacy, International Islamic University Chittagong, Chattogram, 4318, Bangladesh
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9
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Hakem A, Desmarets L, Sahli R, Malek RB, Camuzet C, François N, Lefèvre G, Samaillie J, Moureu S, Sahpaz S, Belouzard S, Ksouri R, Séron K, Rivière C. Luteolin Isolated from Juncus acutus L., a Potential Remedy for Human Coronavirus 229E. Molecules 2023; 28:molecules28114263. [PMID: 37298740 DOI: 10.3390/molecules28114263] [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: 05/06/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, addressed the lack of specific antiviral drugs against coronaviruses. In this study, bioguided fractionation performed on both ethyl acetate and aqueous sub-extracts of Juncus acutus stems led to identifying luteolin as a highly active antiviral molecule against human coronavirus HCoV-229E. The apolar sub-extract (CH2Cl2) containing phenanthrene derivatives did not show antiviral activity against this coronavirus. Infection tests on Huh-7 cells, expressing or not the cellular protease TMPRSS2, using luciferase reporter virus HCoV-229E-Luc showed that luteolin exhibited a dose-dependent inhibition of infection. Respective IC50 values of 1.77 µM and 1.95 µM were determined. Under its glycosylated form (luteolin-7-O-glucoside), luteolin was inactive against HCoV-229E. Time of addition assay showed that utmost anti-HCoV-229E activity of luteolin was achieved when added at the post-inoculation step, indicating that luteolin acts as an inhibitor of the replication step of HCoV-229E. Unfortunately, no obvious antiviral activity for luteolin was found against SARS-CoV-2 and MERS-CoV in this study. In conclusion, luteolin isolated from Juncus acutus is a new inhibitor of alphacoronavirus HCoV-229E.
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Affiliation(s)
- Asma Hakem
- Joint Research Unit 1158, BioEcoAgro, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 59650 Villeneuve-d'Ascq, France
- Laboratory of Aromatic and Medicinal Plants, Biotechnology Centre of Borj-Cedria (CBBC), Hammam-Lif 2050, Tunisia
| | - Lowiese Desmarets
- Center for Infection and Immunity of Lille (CIIL), Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017, 59000 Lille, France
| | - Ramla Sahli
- Joint Research Unit 1158, BioEcoAgro, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 59650 Villeneuve-d'Ascq, France
- Laboratory of Aromatic and Medicinal Plants, Biotechnology Centre of Borj-Cedria (CBBC), Hammam-Lif 2050, Tunisia
| | - Rawen Ben Malek
- Joint Research Unit 1158, BioEcoAgro, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 59650 Villeneuve-d'Ascq, France
| | - Charline Camuzet
- Center for Infection and Immunity of Lille (CIIL), Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017, 59000 Lille, France
| | - Nathan François
- Center for Infection and Immunity of Lille (CIIL), Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017, 59000 Lille, France
| | - Gabriel Lefèvre
- Joint Research Unit 1158, BioEcoAgro, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 59650 Villeneuve-d'Ascq, France
| | - Jennifer Samaillie
- Joint Research Unit 1158, BioEcoAgro, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 59650 Villeneuve-d'Ascq, France
| | - Sophie Moureu
- Joint Research Unit 1158, BioEcoAgro, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 59650 Villeneuve-d'Ascq, France
| | - Sevser Sahpaz
- Joint Research Unit 1158, BioEcoAgro, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 59650 Villeneuve-d'Ascq, France
| | - Sandrine Belouzard
- Center for Infection and Immunity of Lille (CIIL), Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017, 59000 Lille, France
| | - Riadh Ksouri
- Laboratory of Aromatic and Medicinal Plants, Biotechnology Centre of Borj-Cedria (CBBC), Hammam-Lif 2050, Tunisia
| | - Karin Séron
- Center for Infection and Immunity of Lille (CIIL), Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017, 59000 Lille, France
| | - Céline Rivière
- Joint Research Unit 1158, BioEcoAgro, Univ. Lille, INRAE, Univ. Liège, UPJV, JUNIA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV-Institut Charles Viollette, 59650 Villeneuve-d'Ascq, France
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10
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Cotten M, Phan MV. Evolution of increased positive charge on the SARS-CoV-2 spike protein may be adaptation to human transmission. iScience 2023; 26:106230. [PMID: 36845032 PMCID: PMC9937996 DOI: 10.1016/j.isci.2023.106230] [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: 10/07/2022] [Revised: 12/19/2022] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve and infect individuals. The exterior surface of the SARS-CoV-2 virion is dominated by the spike protein, and the current work examined spike protein biochemical features that have changed during the 3 years in which SARS-CoV-2 has infected humans. Our analysis identified a striking change in spike protein charge, from -8.3 in the original Lineage A and B viruses to -1.26 in most of the current Omicron viruses. We conclude that in addition to immune selection pressure, the evolution of SARS-CoV-2 has also altered viral spike protein biochemical properties, which may influence virion survival and promote transmission. Future vaccine and therapeutic development should also exploit and target these biochemical properties.
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Affiliation(s)
- Matthew Cotten
- Medical Research Council–University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
- UK Medical Research Council–Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Plot 51- 59 Nakiwogo Road, P.O Box 49, Entebbe, Uganda, UK
| | - My V.T. Phan
- UK Medical Research Council–Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Plot 51- 59 Nakiwogo Road, P.O Box 49, Entebbe, Uganda, UK
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11
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Kwon T, Gaudreault NN, Cool K, McDowell CD, Morozov I, Richt JA. Stability of SARS-CoV-2 in Biological Fluids of Animals. Viruses 2023; 15:v15030761. [PMID: 36992470 PMCID: PMC10058514 DOI: 10.3390/v15030761] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Since its first emergence in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to evolve genetically, jump species barriers, and expand its host range. There is growing evidence of interspecies transmission including infection of domestic animals and widespread circulation in wildlife. However, knowledge of SARS-CoV-2 stability in animal biological fluids and their role in transmission is still limited as previous studies focused on human biological fluids. Therefore, this study aimed to determine the SARS-CoV-2 stability in biological fluids from three animal species, cats, sheep and white-tailed deer (WTD). Saliva, feces, 10% fecal suspensions, and urine of cats, sheep, and WTD were mixed with a known concentration of virus and incubated under indoor and three different climatic conditions. Our results show that the virus was stable for up to 1 day in the saliva of cats, sheep, and WTD regardless of the environmental conditions. The virus remained infectious for up to 6 days in feces and 15 days in fecal suspension of WTD, whereas the virus was rather unstable in cat and sheep feces and fecal suspensions. We found the longest survival of SARS-CoV-2 in the urine of cats, sheep, and WTD. Furthermore, side-by-side comparison with different SARS-CoV-2 strains showed that the Alpha, Delta, and Omicron variants of concern were less stable than the ancestral Wuhan-like strain in WTD fecal suspension. The results of our study provide valuable information for assessing the potential role of various animal biological fluids in SARS-CoV-2 transmission.
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12
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Harrison CM, Doster JM, Landwehr EH, Kumar NP, White EJ, Beachboard DC, Stobart CC. Evaluating the Virology and Evolution of Seasonal Human Coronaviruses Associated with the Common Cold in the COVID-19 Era. Microorganisms 2023; 11:microorganisms11020445. [PMID: 36838410 PMCID: PMC9961755 DOI: 10.3390/microorganisms11020445] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Approximately 15-30% of all cases of the common cold are due to human coronavirus infections. More recently, the emergence of the more severe respiratory coronaviruses, SARS-CoV and MERS-CoV, have highlighted the increased pathogenic potential of emergent coronaviruses. Lastly, the current emergence of SARS-CoV-2 has demonstrated not only the potential for significant disease caused by emerging coronaviruses, but also the capacity of novel coronaviruses to promote pandemic spread. Largely driven by the global response to the COVID-19 pandemic, significant research in coronavirus biology has led to advances in our understanding of these viruses. In this review, we evaluate the virology, emergence, and evolution of the four endemic coronaviruses associated with the common cold, their relationship to pandemic SARS-CoV-2, and discuss the potential for future emergent human coronaviruses.
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Affiliation(s)
- Cameron M. Harrison
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Jayden M. Doster
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Emily H. Landwehr
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Nidhi P. Kumar
- Department of Biology, DeSales University, Central Valley, PA 18034, USA
| | - Ethan J. White
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Dia C. Beachboard
- Department of Biology, DeSales University, Central Valley, PA 18034, USA
| | - Christopher C. Stobart
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
- Correspondence:
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13
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Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC. Extensive Recombination-driven Coronavirus Diversification Expands the Pool of Potential Pandemic Pathogens. Genome Biol Evol 2022; 14:6795266. [PMID: 36477201 PMCID: PMC9730504 DOI: 10.1093/gbe/evac161] [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] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last 20 years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare the dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) that bundles nucleotide identity, recombination, and phylogenetic analysis into a single pipeline. We analyzed recombination dynamics among three groups of coronaviruses with noteworthy impacts on human health and agriculture: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses from undersampled or unsampled lineages, including in typically highly conserved regions of the genome. In several cases, no parental origin of recombinant regions could be found in genetic databases, demonstrating our shallow characterization of coronavirus diversity and expanding the genetic pool that may contribute to future zoonotic events. Our results also illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health.
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Affiliation(s)
| | | | - Brent S Pedersen
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
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14
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Abstract
RNA viruses include respiratory viruses, such as coronaviruses and influenza viruses, as well as vector-borne viruses, like dengue and West Nile virus. RNA viruses like these encounter various environments when they copy themselves and spread from cell to cell or host to host. Ex vivo differences, such as geographical location and humidity, affect their stability and transmission, while in vivo differences, such as pH and host gene expression, impact viral receptor binding, viral replication, and the host immune response against the viral infection. A critical factor affecting RNA viruses both ex vivo and in vivo, and defining the outcome of viral infections and the direction of viral evolution, is temperature. In this minireview, we discuss the impact of temperature on viral replication, stability, transmission, and adaptation, as well as the host innate immune response. Improving our understanding of how RNA viruses function, survive, and spread at different temperatures will improve our models of viral replication and transmission risk analyses.
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Affiliation(s)
- Karishma Bisht
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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15
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McIntosh K, Perlman S, Monto A, Englund JA. A Proposal to Refer to Four Coronaviruses of Limited Human Virulence "Common Cold Coronaviruses". J Infect Dis 2022; 226:2047-2049. [PMID: 36052654 PMCID: PMC9494316 DOI: 10.1093/infdis/jiac355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 01/04/2023] Open
Abstract
We propose the term "common cold coronaviruses," or ccCoV, to describe the four human coronaviruses commonly associated with upper respiratory tract disease - coronaviruses 229E, OC43, NL63, and HKU1. This will differentiate these previously described coronaviruses from those causing more severe disease in humans - including the viruses severe acute respiraotry syndrome coronavirus (SARS-CoV), the Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV-2.
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Affiliation(s)
- Kenneth McIntosh
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA,Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Arnold Monto
- Department of Epidemiology and Global Public Health, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Janet A Englund
- Correspondence: Janet A. Englund, MD, Seattle Children’s Hospital, 4500 Sand Point Way NE, MA7.234, Seattle, WA 98105 ()
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16
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Li Y, Zheng P, Liu T, Shi C, Wang B, Xu Y, Jin T. Structural Requirements and Plasticity of Receptor-Binding Domain in Human Coronavirus Spike. Front Mol Biosci 2022; 9:930931. [PMID: 35903152 PMCID: PMC9315343 DOI: 10.3389/fmolb.2022.930931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/22/2022] Open
Abstract
The most recent human coronaviruses including severe acute respiratory syndrome coronavirus-2 causing severe respiratory tract infection and high pathogenicity bring significant global public health concerns. Infections are initiated by recognizing host cell receptors by coronavirus spike protein S1 subunit, and then S2 mediates membrane fusion. However, human coronavirus spikes undergo frequent mutation, which may result in diverse pathogenesis and infectivity. In this review, we summarize some of these recent structural and mutational characteristics of RBD of human coronavirus spike protein and their interaction with specific human cell receptors and analyze the structural requirements and plasticity of RBD. Stability of spike protein, affinity toward receptor, virus fitness, and infectivity are the factors controlling the viral tropisms. Thus, understanding the molecular details of RBDs and their mutations is critical in deciphering virus evolution. Structural information of spike and receptors of human coronaviruses not only reveals the molecular mechanism of host–microbe interaction and pathogenesis but also helps develop effective drug to control these infectious pathogens and cope with the future emerging coronavirus outbreaks.
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Affiliation(s)
- Yajuan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Peiyi Zheng
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tingting Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Cuixiao Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Bo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tengchuan Jin
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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17
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Otieno JR, Cherry JL, Spiro DJ, Nelson MI, Trovão NS. Origins and Evolution of Seasonal Human Coronaviruses. Viruses 2022; 14:1551. [PMID: 35891531 PMCID: PMC9320361 DOI: 10.3390/v14071551] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Four seasonal human coronaviruses (sHCoVs) are endemic globally (229E, NL63, OC43, and HKU1), accounting for 5-30% of human respiratory infections. However, the epidemiology and evolution of these CoVs remain understudied due to their association with mild symptomatology. Using a multigene and complete genome analysis approach, we find the evolutionary histories of sHCoVs to be highly complex, owing to frequent recombination of CoVs including within and between sHCoVs, and uncertain, due to the under sampling of non-human viruses. The recombination rate was highest for 229E and OC43 whereas substitutions per recombination event were highest in NL63 and HKU1. Depending on the gene studied, OC43 may have ungulate, canine, or rabbit CoV ancestors. 229E may have origins in a bat, camel, or an unsampled intermediate host. HKU1 had the earliest common ancestor (1809-1899) but fell into two distinct clades (genotypes A and B), possibly representing two independent transmission events from murine-origin CoVs that appear to be a single introduction due to large gaps in the sampling of CoVs in animals. In fact, genotype B was genetically more diverse than all the other sHCoVs. Finally, we found shared amino acid substitutions in multiple proteins along the non-human to sHCoV host-jump branches. The complex evolution of CoVs and their frequent host switches could benefit from continued surveillance of CoVs across non-human hosts.
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Affiliation(s)
- James R. Otieno
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Joshua L. Cherry
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - David J. Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
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18
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Mullin S, Wyk BV, Asher JL, Compton SR, Allore HG, Zeiss CJ. Modeling pandemic to endemic patterns of SARS-CoV-2 transmission using parameters estimated from animal model data. PNAS NEXUS 2022; 1:pgac096. [PMID: 35799833 PMCID: PMC9254158 DOI: 10.1093/pnasnexus/pgac096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/29/2022] [Indexed: 02/06/2023]
Abstract
The contours of endemic coronaviral disease in humans and other animals are shaped by the tendency of coronaviruses to generate new variants superimposed upon nonsterilizing immunity. Consequently, patterns of coronaviral reinfection in animals can inform the emerging endemic state of the SARS-CoV-2 pandemic. We generated controlled reinfection data after high and low risk natural exposure or heterologous vaccination to sialodacryoadenitis virus (SDAV) in rats. Using deterministic compartmental models, we utilized in vivo estimates from these experiments to model the combined effects of variable transmission rates, variable duration of immunity, successive waves of variants, and vaccination on patterns of viral transmission. Using rat experiment-derived estimates, an endemic state achieved by natural infection alone occurred after a median of 724 days with approximately 41.3% of the population susceptible to reinfection. After accounting for translationally altered parameters between rat-derived data and human SARS-CoV-2 transmission, and after introducing vaccination, we arrived at a median time to endemic stability of 1437 (IQR = 749.25) days with a median 15.4% of the population remaining susceptible. We extended the models to introduce successive variants with increasing transmissibility and included the effect of varying duration of immunity. As seen with endemic coronaviral infections in other animals, transmission states are altered by introduction of new variants, even with vaccination. However, vaccination combined with natural immunity maintains a lower prevalence of infection than natural infection alone and provides greater resilience against the effects of transmissible variants.
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Affiliation(s)
- Sarah Mullin
- Yale Center for Medical Informatics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Brent Vander Wyk
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jennifer L Asher
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Susan R Compton
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Heather G Allore
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA
| | - Caroline J Zeiss
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06520, USA
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19
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Mullin S, Wyk BV, Asher JL, Compton SR, Allore HG, Zeiss CJ. Modeling pandemic to endemic patterns of SARS-CoV-2 transmission using parameters estimated from animal model data. PNAS NEXUS 2022; 1:pgac096. [PMID: 35799833 PMCID: PMC9254158 DOI: 10.1093/pnasnexus/pgac096;] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The contours of endemic coronaviral disease in humans and other animals are shaped by the tendency of coronaviruses to generate new variants superimposed upon nonsterilizing immunity. Consequently, patterns of coronaviral reinfection in animals can inform the emerging endemic state of the SARS-CoV-2 pandemic. We generated controlled reinfection data after high and low risk natural exposure or heterologous vaccination to sialodacryoadenitis virus (SDAV) in rats. Using deterministic compartmental models, we utilized in vivo estimates from these experiments to model the combined effects of variable transmission rates, variable duration of immunity, successive waves of variants, and vaccination on patterns of viral transmission. Using rat experiment-derived estimates, an endemic state achieved by natural infection alone occurred after a median of 724 days with approximately 41.3% of the population susceptible to reinfection. After accounting for translationally altered parameters between rat-derived data and human SARS-CoV-2 transmission, and after introducing vaccination, we arrived at a median time to endemic stability of 1437 (IQR = 749.25) days with a median 15.4% of the population remaining susceptible. We extended the models to introduce successive variants with increasing transmissibility and included the effect of varying duration of immunity. As seen with endemic coronaviral infections in other animals, transmission states are altered by introduction of new variants, even with vaccination. However, vaccination combined with natural immunity maintains a lower prevalence of infection than natural infection alone and provides greater resilience against the effects of transmissible variants.
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Affiliation(s)
- Sarah Mullin
- Yale Center for Medical Informatics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Brent Vander Wyk
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jennifer L Asher
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Susan R Compton
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Heather G Allore
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA,Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA
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20
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Yuan L, Fung TS, He J, Chen RA, Liu DX. Modulation of Viral Replication, Apoptosis and Antiviral Response by Induction and Mutual Regulation of EGR and AP-1 Family Genes During Coronavirus Infection. Emerg Microbes Infect 2022; 11:1717-1729. [PMID: 35727266 PMCID: PMC9262369 DOI: 10.1080/22221751.2022.2093133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Coronaviruses have evolved a variety of strategies to exploit normal cellular processes and signalling pathways for their efficient reproduction in a generally hostile cellular environment. One immediate-early response gene (IEG) family, the AP-1 gene family, was previously shown to be activated by coronavirus infection. In this study, we report that another IEG family, the EGR family, is also activated in cells infected with four different coronaviruses in three genera, i.e. gammacoronavirus infectious bronchitis virus (IBV), alphacoronaviruses porcine epidemic diarrhoea virus (PEDV) and human coronavirus-229E (HCoV-229E), and betacoronavirus HCoV-OC43. Knockdown of EGR1 reduced the expression of cJUN and cFOS, and knockdown of cJUN and/or cFOS reduced the expression of EGR1, demonstrating that these two IEG families may be cross-activated and mutual regulated. Furthermore, ERK1/2 was identified as an upstream kinase, and JNK and p38 as inhibitors of EGR1 activation in coronavirus-infected cells. However, upregulation of EGR family genes, in particular EGR1, appears to play a differential role in regulating viral replication, apoptosis and antiviral response. EGR1 was shown to play a limited role in regulation of coronavirus replication, and an anti-apoptotic role in cells infected with IBV or PEDV, but not in cells infected with HCoV-229E. Upregulation of EGR1 may also play a differential role in the regulation of antiviral response against different coronaviruses. This study reveals a novel regulatory network shared by different coronaviruses in the immediate-early response of host cells to infection.
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Affiliation(s)
- Lixia Yuan
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526000, Guangdong, China
| | - To Sing Fung
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China
| | - Jiawen He
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526000, Guangdong, China
| | - Rui Ai Chen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526000, Guangdong, China
| | - Ding Xiang Liu
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526000, Guangdong, China
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21
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Balloux F, Tan C, Swadling L, Richard D, Jenner C, Maini M, van Dorp L. The past, current and future epidemiological dynamic of SARS-CoV-2. OXFORD OPEN IMMUNOLOGY 2022; 3:iqac003. [PMID: 35872966 PMCID: PMC9278178 DOI: 10.1093/oxfimm/iqac003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/11/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2, the agent of the COVID-19 pandemic, emerged in late 2019 in China, and rapidly spread throughout the world to reach all continents. As the virus expanded in its novel human host, viral lineages diversified through the accumulation of around two mutations a month on average. Different viral lineages have replaced each other since the start of the pandemic, with the most successful Alpha, Delta and Omicron variants of concern (VoCs) sequentially sweeping through the world to reach high global prevalence. Neither Alpha nor Delta was characterized by strong immune escape, with their success coming mainly from their higher transmissibility. Omicron is far more prone to immune evasion and spread primarily due to its increased ability to (re-)infect hosts with prior immunity. As host immunity reaches high levels globally through vaccination and prior infection, the epidemic is expected to transition from a pandemic regime to an endemic one where seasonality and waning host immunization are anticipated to become the primary forces shaping future SARS-CoV-2 lineage dynamics. In this review, we consider a body of evidence on the origins, host tropism, epidemiology, genomic and immunogenetic evolution of SARS-CoV-2 including an assessment of other coronaviruses infecting humans. Considering what is known so far, we conclude by delineating scenarios for the future dynamic of SARS-CoV-2, ranging from the good-circulation of a fifth endemic 'common cold' coronavirus of potentially low virulence, the bad-a situation roughly comparable with seasonal flu, and the ugly-extensive diversification into serotypes with long-term high-level endemicity.
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Affiliation(s)
- François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Cedric Tan
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 138672 Singapore, Singapore
| | - Leo Swadling
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Damien Richard
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Charlotte Jenner
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Mala Maini
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
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22
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Faustino R, Faria M, Teixeira M, Palavra F, Sargento P, do Céu Costa M. Systematic review and meta-analysis of the prevalence of coronavirus: One health approach for a global strategy. One Health 2022; 14:100383. [PMID: 35399617 PMCID: PMC8979611 DOI: 10.1016/j.onehlt.2022.100383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 01/02/2023] Open
Abstract
Coronaviruses have been responsible for major epidemic crises in 2003 with SARS-CoV-1, in 2012 with MERS-CoV and in 2019 with SARS-CoV-2 (COVID-19), causing serious atypical pneumonia in humans. We intend, with this systematic analysis and meta-analysis, to clarify the prevalence of the various strains of coronavirus in different animal species. For this purpose, we carried out an electronic survey using Pubmed's Veterinary Science search tool to conduct a systematic assessment of published studies reporting the prevalence of different strains of coronavirus in different animal species between 2015 and 2020. We conducted different analysis to assess sensitivity, publication bias, and heterogeneity, using random effect. The final meta-analysis included 42 studies for systematic review and 29 in the meta-analysis. For the geographic regions with a prevalence greater than or equal to 0.20 (Forest plot overall; prevalence = 0.20, p < 0.01, Q = 10,476.22 and I2 = 100%), the most commonly detected viruses were: enteric coronavirus (ECoV), pigeon-dominant coronavirus, (PdCoV), Avian coronavirus M41, Avian coronavirus C46, Avian coronavirus A99, Avian coronavirus JMK, MERS-CoV, Bovine coronavirus, Ro-BatCoV GCCDC1, Alphacoronavirus, Betacoronavirus, Deltacoronavirus, Gamacoronavirus and human coronaviruses (HCoVs). The wide presence of different strains of coronavirus in different animal species on all continents demonstrates the great biodiversity and ubiquity of these viruses. The most recent epidemiological crises caused by coronavirus demonstrates our unpreparedness to anticipate and mitigate emerging risks, as well as the need to implement new epidemiological surveillance programs for viruses. Combined with the need to create advanced training courses in One Health, this is paramount in order to ensure greater effectiveness in fighting the next pandemics.
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23
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Activation of the MKK3-p38-MK2-ZFP36 Axis by Coronavirus Infection Restricts the Upregulation of AU-Rich Element-Containing Transcripts in Proinflammatory Responses. J Virol 2022; 96:e0208621. [PMID: 34985993 DOI: 10.1128/jvi.02086-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Coronavirus infections induce the expression of multiple proinflammatory cytokines and chemokines. We have previously shown that in cells infected with gammacoronavirus infectious bronchitis virus (IBV), interleukin 6 (IL-6), and IL-8 were drastically upregulated, and the MAP kinase p38 and the integrated stress response pathways were implicated in this process. In this study, we report that coronavirus infection activates a negative regulatory loop that restricts the upregulation of a number of proinflammatory genes. As revealed by the initial transcriptomic and subsequent validation analyses, the anti-inflammatory adenine-uridine (AU)-rich element (ARE)-binding protein, zinc finger protein 36 (ZFP36), and its related family members were upregulated in cells infected with IBV and three other coronaviruses, alphacoronaviruses porcine epidemic diarrhea virus (PEDV), human coronavirus 229E (HCoV-229E), and betacoronavirus HCoV-OC43, respectively. Characterization of the functional roles of ZFP36 during IBV infection demonstrated that ZFP36 promoted the degradation of transcripts coding for IL-6, IL-8, dual-specificity phosphatase 1 (DUSP1), prostaglandin-endoperoxide synthase 2 (PTGS2) and TNF-α-induced protein 3 (TNFAIP3), through binding to AREs in these transcripts. Consistently, knockdown and inhibition of JNK and p38 kinase activities reduced the expression of ZFP36, as well as the expression of IL-6 and IL-8. On the contrary, overexpression of mitogen-activated protein kinase kinase 3 (MKK3) and MAPKAP kinase-2 (MK2), the upstream and downstream kinases of p38, respectively, increased the expression of ZFP36 and decreased the expression of IL-8. Taken together, this study reveals an important regulatory role of the MKK3-p38-MK2-ZFP36 axis in coronavirus infection-induced proinflammatory response. IMPORTANCE Excessive and uncontrolled induction and release of proinflammatory cytokines and chemokines, the so-called cytokine release syndrome (CRS), would cause life-threatening complications and multiple organ failure in severe coronavirus infections, including severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and COVID-19. This study reveals that coronavirus infection also induces the expression of ZFP36, an anti-inflammatory ARE-binding protein, promoting the degradation of ARE-containing transcripts coding for IL-6 and IL-8 as well as a number of other proteins related to inflammatory response. Furthermore, the p38 MAP kinase, its upstream kinase MKK3 and downstream kinase MK2 were shown to play a regulatory role in upregulation of ZFP36 during coronavirus infection cycles. This MKK3-p38-MK2-ZFP36 axis would constitute a potential therapeutic target for severe coronavirus infections.
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24
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Development of an in vitro model for animal species susceptibility to SARS-CoV-2 replication based on expression of ACE2 and TMPRSS2 in avian cells. Virology 2022; 569:1-12. [PMID: 35217403 PMCID: PMC8837912 DOI: 10.1016/j.virol.2022.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 01/06/2023]
Abstract
The SARS-CoV-2 (SARS-CoV-2) virus has caused a worldwide pandemic because of the virus's ability to transmit efficiently human-to-human. A key determinant of infection is the attachment of the viral spike protein to the host receptor angiotensin-converting enzyme 2 (ACE2). Because of the presumed zoonotic origin of SARS-CoV-2, there is no practical way to assess the susceptibility of every species to SARS-CoV-2 by direct challenge studies. In an effort to have a better predictive model of animal host susceptibility to SARS-CoV-2, we expressed the ACE2 and/or transmembrane serine protease 2 (TMPRSS2) genes from humans and other animal species in the avian fibroblast cell line, DF1, that is not permissive to infection. We demonstrated that expression of both human ACE2 and TMPRSS2 genes is necessary to support SARS-CoV-2 infection and replication in DF1 and a non-permissive sub-lineage of MDCK cells. Titers of SARS-CoV-2 in these cell lines were comparable to those observed in control Vero cells. To further test the model, we developed seven additional transgenic cell lines expressing the ACE2 and TMPRSS2 derived from Felis catus (cat), Equus caballus (horse), Sus domesticus (pig), Capra hircus (goat), Mesocricetus auratus (Golden hamster), Myotis lucifugus (Little Brown bat) and Hipposideros armiger (Great Roundleaf bat) in DF1 cells. Results demonstrate permissive replication of SARS-CoV-2 in cat, Golden hamster, and goat species, but not pig or horse, which correlated with the results of reported challenge studies. Cells expressing genes from either bat species tested demonstrated temporal replication of SARS-CoV-2 that peaked early and was not sustained. The development of this cell culture model allows for more efficient testing of the potential susceptibility of many different animal species for SARS-CoV-2 and emerging variant viruses.
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25
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The structure of a novel antibody against the spike protein inhibits Middle East respiratory syndrome coronavirus infections. Sci Rep 2022; 12:1260. [PMID: 35075213 PMCID: PMC8786824 DOI: 10.1038/s41598-022-05318-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 01/07/2022] [Indexed: 11/08/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus, responsible for outbreaks of a severe respiratory illness in humans with a fatality rate of 30%. Currently, there are no vaccines or United States food and drug administration (FDA)-approved therapeutics for humans. The spike protein displayed on the surface of MERS-CoV functions in the attachment and fusion of virions to host cellular membranes and is the target of the host antibody response. Here, we provide a molecular method for neutralizing MERS-CoV through potent antibody-mediated targeting of the receptor-binding subdomain (RBD) of the spike protein. The structural characterization of the neutralizing antibody (KNIH90-F1) complexed with RBD using X-ray crystallography revealed three critical epitopes (D509, R511, and E513) in the RBD region of the spike protein. Further investigation of MERS-CoV mutants that escaped neutralization by the antibody supported the identification of these epitopes in the RBD region. The neutralizing activity of this antibody is solely provided by these specific molecular structures. This work should contribute to the development of vaccines or therapeutic antibodies for MERS-CoV.
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26
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Ntumvi NF, Ndze VN, Gillis A, Le Doux Diffo J, Tamoufe U, Takuo JM, Mouiche MMM, Nwobegahay J, LeBreton M, Rimoin AW, Schneider BS, Monagin C, McIver DJ, Roy S, Ayukekbong JA, Saylors KE, Joly DO, Wolfe ND, Rubin EM, Lange CE. Wildlife in Cameroon harbor diverse coronaviruses, including many closely related to human coronavirus 229E. Virus Evol 2022; 8:veab110. [PMID: 35233291 PMCID: PMC8867583 DOI: 10.1093/ve/veab110] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 12/05/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Zoonotic spillover of animal viruses into human populations is a continuous and increasing public health risk. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the global impact of emergence. Considering the history and diversity of coronaviruses (CoVs), especially in bats, SARS-CoV-2 will likely not be the last to spillover from animals into human populations. We sampled and tested wildlife in the Central African country Cameroon to determine which CoVs are circulating and how they relate to previously detected human and animal CoVs. We collected animal and ecological data at sampling locations and used family-level consensus PCR combined with amplicon sequencing for virus detection. Between 2003 and 2018, samples were collected from 6,580 animals of several different orders. CoV RNA was detected in 175 bats, a civet, and a shrew. The CoV RNAs detected in the bats represented 17 different genetic clusters, coinciding with alpha (n = 8) and beta (n = 9) CoVs. Sequences resembling human CoV-229E (HCoV-229E) were found in 40 Hipposideridae bats. Phylogenetic analyses place the human-derived HCoV-229E isolates closest to those from camels in terms of the S and N genes but closest to isolates from bats for the envelope, membrane, and RNA-dependent RNA polymerase genes. The CoV RNA positivity rate in bats varied significantly (P < 0.001) between the wet (8.2 per cent) and dry seasons (4.5 per cent). Most sampled species accordingly had a wet season high and dry season low, while for some the opposite was found. Eight of the suspected CoV species of which we detected RNA appear to be entirely novel CoV species, which suggests that CoV diversity in African wildlife is still rather poorly understood. The detection of multiple different variants of HCoV-229E-like viruses supports the bat reservoir hypothesis for this virus, with the phylogenetic results casting some doubt on camels as an intermediate host. The findings also support the previously proposed influence of ecological factors on CoV circulation, indicating a high level of underlying complexity to the viral ecology. These results indicate the importance of investing in surveillance activities among wild animals to detect all potential threats as well as sentinel surveillance among exposed humans to determine emerging threats.
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Affiliation(s)
- Nkom F Ntumvi
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | | | - Amethyst Gillis
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Centre Region Route de Kribi, Yaoundé, BP 1364, Cameroon
| | - Joseph Le Doux Diffo
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | - Ubald Tamoufe
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | - Jean-Michel Takuo
- Metabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939, Cameroon
| | | | - Julius Nwobegahay
- CRESAR, Yaoundé, Centre Region 7039 Carrefour Intendance, BP 15939, Cameroon
| | | | - Anne W Rimoin
- Department of Epidemiology, University of California, 71-254 Center for Health Sciences, 650 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Bradley S Schneider
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
- Mosaic, Yaoundé, Centre Region, BP 35353, Cameroon
| | | | - David J McIver
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- CRESAR, Yaoundé, Centre Region 7039 Carrefour Intendance, BP 15939, Cameroon
- One Health Institute, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Sanjit Roy
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
- University of Victoria, 3800 Finnerty Road, Victoria BC V8P 5C2, Canada
| | | | - Karen E Saylors
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
| | - Damien O Joly
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
| | | | - Edward M Rubin
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
| | - Christian E Lange
- Metabiota Inc, 7-1611 Bowen Road, Nanaimo BC V9S 1G5, Canada
- Labyrinth Global Health, 546 15TH Ave NE, St.Petersburg, FL 33704, USA
- Metabiota Inc, 425 California Street, Suite 1200, San Francisco, CA 94104, USA
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27
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Kong F, Wang Q, Kenney SP, Jung K, Vlasova AN, Saif LJ. Porcine Deltacoronaviruses: Origin, Evolution, Cross-Species Transmission and Zoonotic Potential. Pathogens 2022; 11:79. [PMID: 35056027 PMCID: PMC8778258 DOI: 10.3390/pathogens11010079] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 01/27/2023] Open
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus of swine that causes acute diarrhoea, vomiting, dehydration and mortality in seronegative neonatal piglets. PDCoV was first reported in Hong Kong in 2012 and its etiological features were first characterized in the United States in 2014. Currently, PDCoV is a concern due to its broad host range, including humans. Chickens, turkey poults, and gnotobiotic calves can be experimentally infected by PDCoV. Therefore, as discussed in this review, a comprehensive understanding of the origin, evolution, cross-species transmission and zoonotic potential of epidemic PDCoV strains is urgently needed.
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Affiliation(s)
- Fanzhi Kong
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China;
| | - Qiuhong Wang
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.P.K.); (K.J.); (A.N.V.); (L.J.S.)
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Scott P. Kenney
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.P.K.); (K.J.); (A.N.V.); (L.J.S.)
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Kwonil Jung
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.P.K.); (K.J.); (A.N.V.); (L.J.S.)
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Anastasia N. Vlasova
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.P.K.); (K.J.); (A.N.V.); (L.J.S.)
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Linda J. Saif
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (S.P.K.); (K.J.); (A.N.V.); (L.J.S.)
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
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28
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Brema J, Gautam S, Singh D. Global implications of biodiversity loss on pandemic disease: COVID-19. COVID-19 AND THE SUSTAINABLE DEVELOPMENT GOALS 2022. [PMCID: PMC9334989 DOI: 10.1016/b978-0-323-91307-2.00006-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Unpredictable climate changes and adverse effects on the planetary health due to environmental degradation have led to the rise of concerns regarding human wellness in the recent days. Coronavirus disease 2019 (COVID-19) is said to be originated from wildlife species and represents a significant threat to human health, social, food, and economic security. However, understanding the underlying factors behind the emergence is still rudimentary. This study has made efforts to understand the relationship between the drivers that causes the emergence of infectious diseases (EID). The recent biodiversity crisis that has a severe impact on planetary health is a new contributory factor for the emergence of COVID-19. The biodiversity crisis is an outcome of the land use and land cover (LULC) change, contributing to climate change. In the overall global LULC, 60% are associated with direct human activities and 40% indirect causes such as climate change. Climate change is one of the critical factors that induce landcover change, associated with increasing consumerism, environmental pollution, excessive livestock production, population explosion, and food production. Geospatial techniques provide a viable solution for monitoring the key drivers responsible for EID, such as climate characteristics, LULC, global land cover under food production, and locations affected by infectious diseases in the past. The study’s main objective is to discuss the possibilities of evolving novel solutions to approach the forecasting of emerging infectious disease spread and its mitigation, bridging the sectors and stakeholders, with due relevance to sustainable development goals (SDGs) and other dimensions from global to community levels.
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29
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Hui DS, Azhar EI, Memish ZA, Zumla A. Human Coronavirus Infections—Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), and SARS-CoV-2. ENCYCLOPEDIA OF RESPIRATORY MEDICINE 2022. [PMCID: PMC7241405 DOI: 10.1016/b978-0-12-801238-3.11634-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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30
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A genome-wide CRISPR screen identifies interactors of the autophagy pathway as conserved coronavirus targets. PLoS Biol 2021; 19:e3001490. [PMID: 34962926 PMCID: PMC8741300 DOI: 10.1371/journal.pbio.3001490] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 01/07/2022] [Accepted: 11/22/2021] [Indexed: 11/22/2022] Open
Abstract
Over the past 20 years, 3 highly pathogenic human coronaviruses (HCoVs) have emerged—Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and, most recently, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)—demonstrating that coronaviruses (CoVs) pose a serious threat to human health and highlighting the importance of developing effective therapies against them. Similar to other viruses, CoVs are dependent on host factors for their survival and replication. We hypothesized that evolutionarily distinct CoVs may exploit similar host factors and pathways to support their replication cycles. Herein, we conducted 2 independent genome-wide CRISPR/Cas-9 knockout (KO) screens to identify MERS-CoV and HCoV-229E host dependency factors (HDFs) required for HCoV replication in the human Huh7 cell line. Top scoring genes were further validated and assessed in the context of MERS-CoV and HCoV-229E infection as well as SARS-CoV and SARS-CoV-2 infection. Strikingly, we found that several autophagy-related genes, including TMEM41B, MINAR1, and the immunophilin FKBP8, were common host factors required for pan-CoV replication. Importantly, inhibition of the immunophilin protein family with the compounds cyclosporine A, and the nonimmunosuppressive derivative alisporivir, resulted in dose-dependent inhibition of CoV replication in primary human nasal epithelial cell cultures, which recapitulate the natural site of virus replication. Overall, we identified host factors that are crucial for CoV replication and demonstrated that these factors constitute potential targets for therapeutic intervention by clinically approved drugs. This study identifies essential host dependency factors for human coronavirus replication, showing that these can be directly targeted by clinically approved inhibitors and that treatment leads to effective inhibition of coronavirus replication in primary human nasal epithelial cell cultures.
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31
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Puhl AC, Gomes GF, Damasceno S, Fritch EJ, Levi JA, Johnson NJ, Scholle F, Premkumar L, Hurst BL, LeeMontiel F, Veras FP, Batah SS, Fabro AT, Moorman NJ, Yount BL, Dickmander R, Baric R, Pearce KH, Cunha FQ, Alves-Filho JC, Cunha TM, Ekins S. Vandetanib Reduces Inflammatory Cytokines and Ameliorates COVID-19 in Infected Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.16.472155. [PMID: 34981062 PMCID: PMC8722599 DOI: 10.1101/2021.12.16.472155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The portfolio of SARS-CoV-2 small molecule drugs is currently limited to a handful that are either approved (remdesivir), emergency approved (dexamethasone, baricitinib) or in advanced clinical trials. We have tested 45 FDA-approved kinase inhibitors in vitro against murine hepatitis virus (MHV) as a model of SARS-CoV-2 replication and identified 12 showing inhibition in the delayed brain tumor (DBT) cell line. Vandetanib, which targets the vascular endothelial growth factor receptor (VEGFR), the epidermal growth factor receptor (EGFR), and the RET-tyrosine kinase showed the most promising results on inhibition versus toxic effect on SARS-CoV-2-infected Caco-2 and A549-hACE2 cells (IC50 0.79 μM) while also showing a reduction of > 3 log TCID50/mL for HCoV-229E. The in vivo efficacy of vandetanib was assessed in a mouse model of SARS-CoV-2 infection and statistically significantly reduced the levels of IL-6, IL-10, TNF-α, and mitigated inflammatory cell infiltrates in the lungs of infected animals but did not reduce viral load. Vandetanib rescued the decreased IFN-1β caused by SARS-CoV-2 infection in mice to levels similar to that in uninfected animals. Our results indicate that the FDA-approved vandetanib is a potential therapeutic candidate for COVID-19 positioned for follow up in clinical trials either alone or in combination with other drugs to address the cytokine storm associated with this viral infection.
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Affiliation(s)
- Ana C. Puhl
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | - Giovanni F. Gomes
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto, 14049-900 ; Sao Paulo, Brazil
| | - Samara Damasceno
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto, 14049-900 ; Sao Paulo, Brazil
| | - Ethan J. Fritch
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - James A. Levi
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Nicole J. Johnson
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Frank Scholle
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
| | - Brett L. Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT, USA
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - Felipe LeeMontiel
- PhenoVista Biosciences, 6195 Cornerstone Ct E. #114 San Diego CA 92121
| | - Flavio P. Veras
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto, 14049-900 ; Sao Paulo, Brazil
| | - Sabrina S. Batah
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Alexandre T. Fabro
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Nathaniel J. Moorman
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
- Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Boyd L. Yount
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebekah Dickmander
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
- Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Ralph Baric
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA
- Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth H. Pearce
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, USA
| | - Fernando Q. Cunha
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto, 14049-900 ; Sao Paulo, Brazil
| | - José C. Alves-Filho
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto, 14049-900 ; Sao Paulo, Brazil
| | - Thiago M. Cunha
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Avenida Bandeirantes, 3900, Ribeirao Preto, 14049-900 ; Sao Paulo, Brazil
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
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Zhou Z, Qiu Y, Ge X. The taxonomy, host range and pathogenicity of coronaviruses and other viruses in the Nidovirales order. ANIMAL DISEASES 2021; 1:5. [PMID: 34778878 PMCID: PMC8062217 DOI: 10.1186/s44149-021-00005-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022] Open
Abstract
The frequent emergence of coronavirus (CoV) epidemics has seriously threatened public health and stock farming. The major hosts for CoVs are birds and mammals. Although most CoVs inhabit their specific natural hosts, some may occasionally cross the host barrier to infect livestock and even people, causing a variety of diseases. Since the beginning of the new century, increasing attention has been given to research on CoVs due to the emergence of highly pathogenic and genetically diverse CoVs that have caused several epidemics, including the recent COVID-19 pandemic. CoVs belong to the Coronaviridae family of the Nidovirales order. Recently, advanced techniques for viral detection and viral genome analyses have enabled characterization of many new nidoviruses than ever and have greatly expanded the Nidovirales order with new classification and nomenclature. Here, we first provide an overview of the latest research progress in the classification of the Nidovirales order and then introduce the host range, genetic variation, genomic pattern and pathogenic features of epidemic CoVs and other epidemic viruses. This information will promote understanding of the phylogenetic relationship and infectious transmission of various pathogenic nidoviruses, including epidemic CoVs, which will benefit virological research and viral disease control.
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Affiliation(s)
- Zhijian Zhou
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan China
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan China
| | - Xingyi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan China
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Aminopeptidase N Is an Entry Co-factor Triggering Porcine Deltacoronavirus Entry via an Endocytotic Pathway. J Virol 2021; 95:e0094421. [PMID: 34406863 DOI: 10.1128/jvi.00944-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Porcine deltacoronavirus (PDCoV) is a recently discovered coronavirus that poses a potential threat to the global swine industry. Although we know that aminopeptidase N (APN) is important for PDCoV replication, it is unclear whether it is the primary functional receptor, and the mechanism by which it promotes viral replication is not fully understood. Here, we systematically investigated the roles of porcine APN (pAPN) during PDCoV infection of nonsusceptible cells, including in viral attachment and internalization. Using a viral entry assay, we found that PDCoV can enter nonsusceptible cells but then fails to initiate efficient replication. pAPN and PDCoV virions clearly colocalized with the endocytotic markers RAB5, RAB7, and LAMP1, suggesting that pAPN mediates PDCoV entry by an endocytotic pathway. Most importantly, our study shows that regardless of which receptor PDCoV engages, only entry by an endocytotic route ultimately leads to efficient viral replication. This knowledge should contribute to the development of efficient antiviral treatments, which are especially useful in preventing cross-species transmission. IMPORTANCE PDCoV is a pathogen with the potential for transmission across diverse species, although the mechanism of such host-switching events (from swine to other species) is poorly understood. Here, we show that PDCoV enters nonsusceptible cells but without efficient replication. We also investigated the key role played by aminopeptidase N in mediating PDCoV entry via an endocytotic pathway. Our results demonstrate that viral entry via endocytosis is a major determinant of efficient PDCoV replication. This knowledge provides a basis for future studies of the cross-species transmissibility of PDCoV and the development of appropriate antiviral drugs.
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Jacob Machado D, Scott R, Guirales S, Janies DA. Fundamental evolution of all Orthocoronavirinae including three deadly lineages descendent from Chiroptera-hosted coronaviruses: SARS-CoV, MERS-CoV and SARS-CoV-2. Cladistics 2021; 37:461-488. [PMID: 34570933 PMCID: PMC8239696 DOI: 10.1111/cla.12454] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2021] [Indexed: 12/14/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in humans in 2002. Despite reports showing Chiroptera as the original animal reservoir of SARS-CoV, many argue that Carnivora-hosted viruses are the most likely origin. The emergence of the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 also involves Chiroptera-hosted lineages. However, factors such as the lack of comprehensive phylogenies hamper our understanding of host shifts once MERS-CoV emerged in humans and Artiodactyla. Since 2019, the origin of SARS-CoV-2, causative agent of coronavirus disease 2019 (COVID-19), added to this episodic history of zoonotic transmission events. Here we introduce a phylogenetic analysis of 2006 unique and complete genomes of different lineages of Orthocoronavirinae. We used gene annotations to align orthologous sequences for total evidence analysis under the parsimony optimality criterion. Deltacoronavirus and Gammacoronavirus were set as outgroups to understand spillovers of Alphacoronavirus and Betacoronavirus among ten orders of animals. We corroborated that Chiroptera-hosted viruses are the sister group of SARS-CoV, SARS-CoV-2 and MERS-related viruses. Other zoonotic events were qualified and quantified to provide a comprehensive picture of the risk of coronavirus emergence among humans. Finally, we used a 250 SARS-CoV-2 genomes dataset to elucidate the phylogenetic relationship between SARS-CoV-2 and Chiroptera-hosted coronaviruses.
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Affiliation(s)
- Denis Jacob Machado
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Rachel Scott
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Sayal Guirales
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Daniel A. Janies
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
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35
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Sharma HN, Latimore COD, Matthews QL. Biology and Pathogenesis of SARS-CoV-2: Understandings for Therapeutic Developments against COVID-19. Pathogens 2021; 10:1218. [PMID: 34578250 PMCID: PMC8470303 DOI: 10.3390/pathogens10091218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 01/18/2023] Open
Abstract
Coronaviruses are positive sense, single-stranded, enveloped, and non-segmented RNA viruses that belong to the Coronaviridae family within the order Nidovirales and suborder Coronavirinae. Two Alphacoronavirus strains: HCoV-229E and HCoV-NL63 and five Betacoronaviruses: HCoV-HKU1, HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2 have so far been recognized as Human Coronaviruses (HCoVs). Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 is currently the greatest concern for humanity. Despite the overflow of research on SARS-CoV-2 and other HCoVs published every week, existing knowledge in this area is insufficient for the complete understanding of the viruses and the diseases caused by them. This review is based on the analysis of 210 published works, and it attempts to cover the basic biology of coronaviruses, including the genetic characteristics, life cycle, and host-pathogen interaction, pathogenesis, the antiviral drugs, and vaccines against HCoVs, especially focusing on SARS-CoV-2. Furthermore, we will briefly discuss the potential link between extracellular vesicles (EVs) and SARS-CoV-2/COVID-19 pathophysiology.
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Affiliation(s)
- Homa Nath Sharma
- Microbiology Program, Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA;
| | | | - Qiana L. Matthews
- Microbiology Program, Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA;
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA;
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36
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Forni D, Cagliani R, Arrigoni F, Benvenuti M, Mozzi A, Pozzoli U, Clerici M, De Gioia L, Sironi M. Adaptation of the endemic coronaviruses HCoV-OC43 and HCoV-229E to the human host. Virus Evol 2021; 7:veab061. [PMID: 34527284 PMCID: PMC8344746 DOI: 10.1093/ve/veab061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 12/29/2022] Open
Abstract
Four coronaviruses (HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E) are endemic in human populations. All these viruses are seasonal and generate short-term immunity. Like the highly pathogenic coronaviruses, the endemic coronaviruses have zoonotic origins. Thus, understanding the evolutionary dynamics of these human viruses might provide insight into the future trajectories of SARS-CoV-2 evolution. Because the zoonotic sources of HCoV-OC43 and HCoV-229E are known, we applied a population genetics-phylogenetic approach to investigate which selective events accompanied the divergence of these viruses from the animal ones. Results indicated that positive selection drove the evolution of some accessory proteins, as well as of the membrane proteins. However, the spike proteins of both viruses and the hemagglutinin-esterase (HE) of HCoV-OC43 represented the major selection targets. Specifically, for both viruses, most positively selected sites map to the receptor-binding domains (RBDs) and are polymorphic. Molecular dating for the HCoV-229E spike protein indicated that RBD Classes I, II, III, and IV emerged 3-9 years apart. However, since the appearance of Class V (with much higher binding affinity), around 25 years ago, limited genetic diversity accumulated in the RBD. These different time intervals are not fully consistent with the hypothesis that HCoV-229E spike evolution was driven by antigenic drift. An alternative, not mutually exclusive possibility is that strains with higher affinity for the cellular receptor have out-competed strains with lower affinity. The evolution of the HCoV-OC43 spike protein was also suggested to undergo antigenic drift. However, we also found abundant signals of positive selection in HE. Whereas such signals might result from antigenic drift, as well, previous data showing co-evolution of the spike protein with HE suggest that optimization for human cell infection also drove the evolution of this virus. These data provide insight into the possible trajectories of SARS-CoV-2 evolution, especially in case the virus should become endemic.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza, Milan 20126, Italy
| | - Martino Benvenuti
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza, Milan 20126, Italy
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, via Francesco Sforza, Milan 20122, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza, Milan 20126, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
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Brüssow H, Brüssow L. Clinical evidence that the pandemic from 1889 to 1891 commonly called the Russian flu might have been an earlier coronavirus pandemic. Microb Biotechnol 2021; 14:1860-1870. [PMID: 34254725 PMCID: PMC8441924 DOI: 10.1111/1751-7915.13889] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/27/2021] [Indexed: 01/10/2023] Open
Abstract
Contemporary medical reports from Britain and Germany on patients suffering from a pandemic infection between 1889 and 1891, which was historically referred to as the Russian flu, share a number of characteristics with COVID-19. Most notable are aspects of multisystem affections comprising respiratory, gastrointestinal and neurological symptoms including loss of taste and smell perception; a protracted recovery resembling long covid and pathology observations of thrombosis in multiple organs, inflammation and rheumatic affections. As in COVID-19 and unlike in influenza, mortality was seen in elderly subjects while children were only weakly affected. Contemporary reports noted trans-species infection between pet animals or horses and humans, which would concur with a cross-infection by a broad host range bovine coronavirus dated by molecular clock arguments to an about 1890 cross-species infection event.
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Affiliation(s)
- Harald Brüssow
- Department of BiosystemsLaboratory of Gene TechnologyKU LeuvenLeuvenBelgium
| | - Lutz Brüssow
- Internal Medicine, Angiology and Gastroenterology SpecialistNeussGermany
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Singh J, Pandit P, McArthur AG, Banerjee A, Mossman K. Evolutionary trajectory of SARS-CoV-2 and emerging variants. Virol J 2021; 18:166. [PMID: 34389034 PMCID: PMC8361246 DOI: 10.1186/s12985-021-01633-w] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.
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Affiliation(s)
- Jalen Singh
- School of Interdisciplinary Science, McMaster University, Hamilton, ON, Canada
| | - Pranav Pandit
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
| | - Karen Mossman
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.
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39
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Do TND, Donckers K, Vangeel L, Chatterjee AK, Gallay PA, Bobardt MD, Bilello JP, Cihlar T, De Jonghe S, Neyts J, Jochmans D. A robust SARS-CoV-2 replication model in primary human epithelial cells at the air liquid interface to assess antiviral agents. Antiviral Res 2021; 192:105122. [PMID: 34186107 PMCID: PMC8233549 DOI: 10.1016/j.antiviral.2021.105122] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/15/2021] [Accepted: 06/21/2021] [Indexed: 11/28/2022]
Abstract
There are, besides remdesivir, no approved antivirals for the treatment of SARS-CoV-2 infections. To aid in the search for antivirals against this virus, we explored the use of human tracheal airway epithelial cells (HtAEC) and human small airway epithelial cells (HsAEC) grown at the air-liquid interface (ALI). These cultures were infected at the apical side with one of two different SARS-CoV-2 isolates. Each virus was shown to replicate to high titers for extended periods of time (at least 8 days) and, in particular an isolate with the D614G in the spike (S) protein did so more efficiently at 35 °C than 37 °C. The effect of a selected panel of reference drugs that were added to the culture medium at the basolateral side of the system was explored. Remdesivir, GS-441524 (the parent nucleoside of remdesivir), EIDD-1931 (the parent nucleoside of molnupiravir) and IFN (β1 and λ1) all resulted in dose-dependent inhibition of viral RNA and infectious virus titers collected at the apical side. However, AT-511 (the free base form of AT-527 currently in clinical testing) failed to inhibit viral replication in these in vitro primary cell models. Together, these results provide a reference for further studies aimed at selecting SARS-CoV-2 inhibitors for further preclinical and clinical development.
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Affiliation(s)
- Thuc Nguyen Dan Do
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Kim Donckers
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Laura Vangeel
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Arnab K Chatterjee
- CALIBR - Department of Medicinal Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Philippe A Gallay
- CALIBR - Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA
| | - Michael D Bobardt
- CALIBR - Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA
| | | | | | - Steven De Jonghe
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Johan Neyts
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium.
| | - Dirk Jochmans
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium.
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40
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Chazal N. Coronavirus, the King Who Wanted More Than a Crown: From Common to the Highly Pathogenic SARS-CoV-2, Is the Key in the Accessory Genes? Front Microbiol 2021; 12:682603. [PMID: 34335504 PMCID: PMC8317507 DOI: 10.3389/fmicb.2021.682603] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that emerged in late 2019, is the etiologic agent of the current "coronavirus disease 2019" (COVID-19) pandemic, which has serious health implications and a significant global economic impact. Of the seven human coronaviruses, all of which have a zoonotic origin, the pandemic SARS-CoV-2, is the third emerging coronavirus, in the 21st century, highly pathogenic to the human population. Previous human coronavirus outbreaks (SARS-CoV-1 and MERS-CoV) have already provided several valuable information on some of the common molecular and cellular mechanisms of coronavirus infections as well as their origin. However, to meet the new challenge caused by the SARS-CoV-2, a detailed understanding of the biological specificities, as well as knowledge of the origin are crucial to provide information on viral pathogenicity, transmission and epidemiology, and to enable strategies for therapeutic interventions and drug discovery. Therefore, in this review, we summarize the current advances in SARS-CoV-2 knowledges, in light of pre-existing information of other recently emerging coronaviruses. We depict the specificity of the immune response of wild bats and discuss current knowledge of the genetic diversity of bat-hosted coronaviruses that promotes viral genome expansion (accessory gene acquisition). In addition, we describe the basic virology of coronaviruses with a special focus SARS-CoV-2. Finally, we highlight, in detail, the current knowledge of genes and accessory proteins which we postulate to be the major keys to promote virus adaptation to specific hosts (bat and human), to contribute to the suppression of immune responses, as well as to pathogenicity.
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Affiliation(s)
- Nathalie Chazal
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
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41
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Corman VM, Haage VC, Bleicker T, Schmidt ML, Mühlemann B, Zuchowski M, Jo WK, Tscheak P, Möncke-Buchner E, Müller MA, Krumbholz A, Drexler JF, Drosten C. Comparison of seven commercial SARS-CoV-2 rapid point-of-care antigen tests: a single-centre laboratory evaluation study. THE LANCET. MICROBE 2021; 2:e311-e319. [PMID: 33846704 PMCID: PMC8026170 DOI: 10.1016/s2666-5247(21)00056-2] [Citation(s) in RCA: 211] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND Antigen point-of-care tests (AgPOCTs) can accelerate SARS-CoV-2 testing. As some AgPOCTs have become available, interest is growing in their utility and performance. Here we aimed to compare the analytical sensitivity and specificity of seven commercially available AgPOCT devices. METHODS In a single-centre, laboratory evaluation study, we compared AgPOCT products from seven suppliers: the Abbott Panbio COVID-19 Ag Rapid Test, the RapiGEN BIOCREDIT COVID-19 Ag, the Healgen Coronavirus Ag Rapid Test Cassette (Swab), the Coris BioConcept COVID-19 Ag Respi-Strip, the R-Biopharm RIDA QUICK SARS-CoV-2 Antigen, the nal von minden NADAL COVID-19 Ag Test, and the Roche-SD Biosensor SARS-CoV Rapid Antigen Test. Tests were evaluated on recombinant SARS-CoV-2 nucleoprotein, cultured endemic and emerging coronaviruses, stored respiratory samples with known SARS-CoV-2 viral loads, stored samples from patients with respiratory pathogens other than SARS-CoV-2, and self-sampled swabs from healthy volunteers. We estimated analytical sensitivity in terms of approximate viral concentrations (quantified by real-time RT-PCR) that yielded positive AgPOCT results, and specificity in terms of propensity to generate false-positive results. FINDINGS In 138 clinical samples with quantified SARS-CoV-2 viral load, the 95% limit of detection (concentration at which 95% of test results were positive) in six of seven AgPOCT products ranged between 2·07 × 106 and 2·86 × 107 copies per swab, with an outlier (RapiGEN) at 1·57 × 1010 copies per swab. The assays showed no cross-reactivity towards cell culture or tissue culture supernatants containing any of the four endemic human coronaviruses (HCoV‑229E, HCoV‑NL63, HCoV‑OC43, or HCoV‑HKU1) or MERS-CoV, with the exception of the Healgen assay in one repeat test on HCoV-HKU1 supernatant. SARS-CoV was cross-detected by all assays. Cumulative specificities among stored clinical samples with non-SARS-CoV-2 infections (n=100) and self-samples from healthy volunteers (n=35; cumulative sample n=135) ranged between 98·5% (95% CI 94·2-99·7) and 100·0% (97·2-100·0) in five products, with two outliers at 94·8% (89·2-97·7; R-Biopharm) and 88·9% (82·1-93·4; Healgen). False-positive results did not appear to be associated with any specific respiratory pathogen. INTERPRETATION The sensitivity range of most AgPOCTs overlaps with SARS-CoV-2 viral loads typically observed in the first week of symptoms, which marks the infectious period in most patients. The AgPOCTs with limit of detections that approximate virus concentrations at which patients are infectious might enable shortcuts in decision making in various areas of health care and public health. FUNDING EU's Horizon 2020 research and innovation programme, German Ministry of Research, German Federal Ministry for Economic Affairs and Energy, German Ministry of Health, and Bill & Melinda Gates Foundation.
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Affiliation(s)
- Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; German Centre for Infection Research, Berlin, Germany
| | - Verena Claudia Haage
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Tobias Bleicker
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marie Luisa Schmidt
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Barbara Mühlemann
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | - Wendy K Jo
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Patricia Tscheak
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Elisabeth Möncke-Buchner
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marcel A Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; German Centre for Infection Research, Berlin, Germany
| | - Andi Krumbholz
- Institute for Infection Medicine, Christian-Albrecht University and University Medical Center Schleswig-Holstein, Kiel, Germany; Labor Dr Krause und Kollegen MVZ, Kiel, Germany
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; German Centre for Infection Research, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; German Centre for Infection Research, Berlin, Germany.
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42
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Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC. Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.03.429646. [PMID: 33564759 PMCID: PMC7872347 DOI: 10.1101/2021.02.03.429646] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last twenty years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) to measure nucleotide identity, locate recombination breakpoints, and infer phylogenetic relationships. We analyzed recombination dynamics among three groups of coronaviruses with noteworthy impacts on human health and agriculture: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses from sparsely sampled or undescribed lineages, which can disrupt the inference of phylogenetic relationships. In most cases, no parental origin of recombinant regions could be found in genetic databases, suggesting that much coronavirus diversity remains unknown. These patterns of recombination expand the genetic pool that may contribute to future zoonotic events. Our results also illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health.
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Affiliation(s)
- Stephen A. Goldstein
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.,Corresponding authors. (S.A.G), (N.C.E)
| | - Joe Brown
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Brent S. Pedersen
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Aaron R. Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.,Corresponding authors. (S.A.G), (N.C.E)
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43
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Phenotypic and genetic characterization of MERS coronaviruses from Africa to understand their zoonotic potential. Proc Natl Acad Sci U S A 2021; 118:2103984118. [PMID: 34099577 PMCID: PMC8237650 DOI: 10.1073/pnas.2103984118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The absence of zoonotic MERS-CoV in Africa in spite of an abundance of MERS-CoV–infected dromedaries has remained an enigma. We demonstrate that geographically and genetically distinct viruses from Africa have low replication competence in the human lung, providing a possible explanation for the absence of severe MERS disease in Africa. The findings suggest that MERS-CoV now entrenched in the Arabian Peninsula has acquired increased pathogenic potential for humans. We demonstrate that the spike protein contributes to this phenotypic difference. If pathogenic clade B viruses from the Arabian Peninsula are introduced into Africa, they are likely to become dominant, as they have in the Arabian Peninsula, and to be associated with adverse health impacts in Africa and increased pandemic threat. Coronaviruses are pathogens of pandemic potential. Middle East respiratory syndrome coronavirus (MERS-CoV) causes a zoonotic respiratory disease of global public health concern, and dromedary camels are the only proven source of zoonotic infection. More than 70% of MERS-CoV–infected dromedaries are found in East, North, and West Africa, but zoonotic MERS disease is only reported from the Arabian Peninsula. We compared viral replication competence of clade A and B viruses from the Arabian Peninsula with genetically diverse clade C viruses found in East (Egypt, Kenya, and Ethiopia), North (Morocco), and West (Nigeria and Burkina Faso) Africa. Viruses from Africa had lower replication competence in ex vivo cultures of the human lung and in lungs of experimentally infected human-DPP4 (hDPP4) knockin mice. We used lentivirus pseudotypes expressing MERS-CoV spike from Saudi Arabian clade A prototype strain (EMC) or African clade C1.1 viruses and demonstrated that clade C1.1 spike was associated with reduced virus entry into the respiratory epithelial cell line Calu-3. Isogenic EMC viruses with spike protein from EMC or clade C1.1 generated by reverse genetics showed that the clade C1.1 spike was associated with reduced virus replication competence in Calu-3 cells in vitro, in ex vivo human bronchus, and in lungs of hDPP4 knockin mice in vivo. These findings may explain why zoonotic MERS disease has not been reported from Africa so far, despite exposure to and infection with MERS-CoV.
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44
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[Basic information of Coronavirus]. Uirusu 2021; 70:29-36. [PMID: 33967109 DOI: 10.2222/jsv.70.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Coronaviruses are pathogens that infect many of animals, resulting in respiratory or enteric diseases. Coronaviruses constitute Nidovirales together with Arteriviridae. Most of human coronaviruses are known to cause mild illness and common cold. However, an epidemic of severe acute respiratory syndrome (SARS) occurred in 2002, ten years after SARS epidemic Middle East respiratory syndrome (MERS) emerged in 2012. Now, we face on a novel coronavirus which emerges in end of 2019. This novel coronavirus is named as SARS-CoV-2. SARS-CoV-2 is spread to worldwide within one to two months and causes coronavirus disease 2019 (COVID-19), respiratory illness. Coronaviruses are enveloped viruses possessing a positive-sense and large single stranded RNA genomes. The 5' two-thirds of the CoV genome consists of two overlapping open reading frames (ORFs 1a and 1b) that encode non-structural proteins (nsps). The other one-third of the genome consists of ORFs encoding structural proteins, including spike (S), membrane (M), envelope (E) and nucleocapsid (N) proteins, and accessory proteins. Upon infection of CoV into host cells, the translation of two precursor polyproteins, pp1a and pp1ab, occurs and these polyproteins are cleaved into 16 nsps by viral proteases. Structural proteins assemble to the vesicles located from ER to Golgi (ER Golgiintermediate compartment) and virions bud into the vesicles. Virions are released from infectedcells via exocytosis.
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45
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Ecology and Evolution of Betacoronaviruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1318:41-60. [PMID: 33973171 DOI: 10.1007/978-3-030-63761-3_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The crown-like outline of the virions of coronaviruses will long endure as the iconic image of 2020 - the year of the COVID-19 pandemic. This major human health emergency has been caused by a betacoronavirus, as have others in the past. In this chapter, we outline the taxonomy of betacoronaviruses and their properties, both genetic and biological. We discuss their recombinational and mutational histories separately to show that the sequence of the RaTG13 bat virus isolate is the closest currently known full-length genetic homolog of that of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). However, the RaTG13 bat virus and SARS-CoV-2 have probably diverged over 20 years. We discuss the ecology of their pangolin and bat hosts and conclude that, like other recent viral pandemics, the underlying cause of the SARS-CoV-2 emergence is probably the relentless growth of the world's human population and the overexploitation and disturbance of the environment.
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46
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Khan FM, Ahmad T, Gulistan M, Chammam W, Khan M, Hui J. Epidemiology of coronaviruses, genetics, vaccines, and scenario of current pandemic of coronavirus diseases 2019 (COVID-19): a fuzzy set approach. Hum Vaccin Immunother 2021; 17:1296-1303. [PMID: 33720797 DOI: 10.1080/21645515.2020.1798697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Human coronaviruses (HCoVs) are associated with a range of respiratory complications. In the last two decades, three major outbreaks have been reported due to HCoVs including the current pandemic. In December 2019, a newly emerged virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan city, China. This paper presents a detailed review of the literature and discusses the uncertain spread of coronavirus disease 2019 (COVID-19) using fuzzy set as classical set theory logic to measure uncertainty and vagueness of COVID-19 in China. Our findings show that both infection and death rate touched the peak (normal fuzzy sets) and have shown a decline. The graphs are not convex, which shows that there remains much uncertainty in the spread of COVID-19. Effective vaccines are clearly needed to control and prevent the COVID-19 pandemic.
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Affiliation(s)
- Fazal Mehmood Khan
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China
| | - Tauseef Ahmad
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China.,Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Muhammad Gulistan
- Department of Mathematics and Statistics, Hazara University, Mansehra, Khyber Pakhtunkhwa, Islamic Republic of Pakistan
| | - Wathek Chammam
- Department of Mathematics, College of Science Al-Zulfi, Majmaah University, Al-Majmaah, Saudi Arabia
| | - Muhammad Khan
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Khyber Pakhtunkhwa, Islamic Republic of Pakistan
| | - Jin Hui
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China.,Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
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47
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Kang D, Ellgen C, Kulstad E. Possible effects of air temperature on COVID-19 disease severity and transmission rates. J Med Virol 2021; 93:5358-5366. [PMID: 33913555 PMCID: PMC8242372 DOI: 10.1002/jmv.27042] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/05/2021] [Accepted: 04/21/2021] [Indexed: 01/12/2023]
Abstract
Currently available data are consistent with increased severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication at temperatures encountered in the upper airways (25-33°C when breathing room temperature air, 25°C) compared to those in the lower airways (37°C). One factor that may contribute to more rapid viral growth in the upper airways is the exponential increase in SARS-CoV-2 stability that occurs with reductions in temperature, as measured in vitro. Because SARS-CoV-2 frequently initiates infection in the upper airways before spreading through the body, increased upper airway viral growth early in the disease course may result in more rapid progression of disease and potentially contribute to more severe outcomes. Similarly, higher SARS-CoV-2 viral titer in the upper airways likely supports more efficient transmission. Conversely, the possible significance of air temperature to upper airway viral growth suggests that prolonged delivery of heated air might represent a preventative measure and prophylactic treatment for coronavirus disease 2019.
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Affiliation(s)
- Dominique Kang
- Department of Theoretical Physics, Pacific Theoretical Physics and Mathematics Research, Pasadena, California, USA
| | - Clifford Ellgen
- Department of Theoretical Physics, Pacific Theoretical Physics and Mathematics Research, Pasadena, California, USA
| | - Erik Kulstad
- Department of Emergency Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
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48
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Maurin M, Fenollar F, Mediannikov O, Davoust B, Devaux C, Raoult D. Current Status of Putative Animal Sources of SARS-CoV-2 Infection in Humans: Wildlife, Domestic Animals and Pets. Microorganisms 2021; 9:868. [PMID: 33920724 PMCID: PMC8072559 DOI: 10.3390/microorganisms9040868] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 is currently considered to have emerged from a bat coronavirus reservoir. However, the real natural cycle of this virus remains to be elucidated. Moreover, the COVID-19 pandemic has led to novel opportunities for SARS-CoV-2 transmission between humans and susceptible animal species. In silico and in vitro evaluation of the interactions between the SARS-CoV-2 spike protein and eucaryotic angiotensin-converting enzyme 2 (ACE2) receptor have tentatively predicted susceptibility to SARS-CoV-2 infection of several animal species. Although useful, these data do not always correlate with in vivo data obtained in experimental models or during natural infections. Other host biological properties may intervene such as the body temperature, level of receptor expression, co-receptor, restriction factors, and genetic background. The spread of SARS-CoV-2 also depends on the extent and duration of viral shedding in the infected host as well as population density and behaviour (group living and grooming). Overall, current data indicate that the most at-risk interactions between humans and animals for COVID-19 infection are those involving certain mustelids (such as minks and ferrets), rodents (such as hamsters), lagomorphs (especially rabbits), and felines (including cats). Therefore, special attention should be paid to the risk of SARS-CoV-2 infection associated with pets.
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Affiliation(s)
- Max Maurin
- University Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, 38000 Grenoble, France;
| | - Florence Fenollar
- IHU-Méditerranée Infection, 13005 Marseille, France; (F.F.); (O.M.); (B.D.); (C.D.)
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France
| | - Oleg Mediannikov
- IHU-Méditerranée Infection, 13005 Marseille, France; (F.F.); (O.M.); (B.D.); (C.D.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Bernard Davoust
- IHU-Méditerranée Infection, 13005 Marseille, France; (F.F.); (O.M.); (B.D.); (C.D.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Christian Devaux
- IHU-Méditerranée Infection, 13005 Marseille, France; (F.F.); (O.M.); (B.D.); (C.D.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
- Centre National de la Recherche Scientifique, 13005 Marseille, France
| | - Didier Raoult
- IHU-Méditerranée Infection, 13005 Marseille, France; (F.F.); (O.M.); (B.D.); (C.D.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
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49
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Godoy MG, Kibenge MJT, Kibenge FSB. SARS-CoV-2 transmission via aquatic food animal species or their products: A review. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2021; 536:736460. [PMID: 33564203 PMCID: PMC7860939 DOI: 10.1016/j.aquaculture.2021.736460] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/28/2021] [Accepted: 01/30/2021] [Indexed: 05/06/2023]
Abstract
Outbreaks of COVID-19 (coronavirus disease 2019) have been reported in workers in fish farms and fish processing plants arising from person-to-person transmission, raising concerns about aquatic animal food products' safety. A better understanding of such incidents is important for the aquaculture industry's sustainability, particularly with the global trade in fresh and frozen aquatic animal food products where contaminating virus could survive for some time. Despite a plethora of COVID-19-related scientific publications, there is a lack of reports on the risk of contact with aquatic food animal species or their products. This review aimed to examine the potential for Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) contamination and the potential transmission via aquatic food animals or their products and wastewater effluents. The extracellular viability of SARS-CoV-2 and how the virus is spread are reviewed, supporting the understanding that contaminated cold-chain food sources may introduce SAR-CoV-2 via food imports although the virus is unlikely to infect humans through consumption of aquatic food animals or their products or drinking water; i.e., SARS-CoV-2 is not a foodborne virus and should not be managed as such but instead through strong, multifaceted public health interventions including physical distancing, rapid contact tracing, and testing, enhanced hand and respiratory hygiene, frequent disinfection of high-touch surfaces, isolation of infected workers and their contacts, as well as enhanced screening protocols for international seafood trade.
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Affiliation(s)
- Marcos G Godoy
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Lago Panguipulli 1390, Puerto Montt, Chile
- Laboratorio de Biotecnología Aplicada, Facultad de Medicina Veterinaria, Sede De La Patagonia, Lago Panguipulli 1390, Puerto Montt, 5480000, Chile
- Doctorado en Acuicultura. Programa Cooperativo Universidad de Chile, Universidad Católica del Norte, Pontificia Universidad Católica de Valparaíso, Chile
| | - Molly J T Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada
| | - Frederick S B Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada
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50
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Puhl AC, Fritch EJ, Lane TR, Tse LV, Yount BL, Sacramento CQ, Fintelman-Rodrigues N, Tavella TA, Maranhão Costa FT, Weston S, Logue J, Frieman M, Premkumar L, Pearce KH, Hurst BL, Andrade CH, Levi JA, Johnson NJ, Kisthardt SC, Scholle F, Souza TML, Moorman NJ, Baric RS, Madrid PB, Ekins S. Repurposing the Ebola and Marburg Virus Inhibitors Tilorone, Quinacrine, and Pyronaridine: In Vitro Activity against SARS-CoV-2 and Potential Mechanisms. ACS OMEGA 2021; 6:7454-7468. [PMID: 33778258 PMCID: PMC7992063 DOI: 10.1021/acsomega.0c05996] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/02/2021] [Indexed: 05/11/2023]
Abstract
Severe acute respiratory coronavirus 2 (SARS-CoV-2) is a newly identified virus that has resulted in over 2.5 million deaths globally and over 116 million cases globally in March, 2021. Small-molecule inhibitors that reverse disease severity have proven difficult to discover. One of the key approaches that has been widely applied in an effort to speed up the translation of drugs is drug repurposing. A few drugs have shown in vitro activity against Ebola viruses and demonstrated activity against SARS-CoV-2 in vivo. Most notably, the RNA polymerase targeting remdesivir demonstrated activity in vitro and efficacy in the early stage of the disease in humans. Testing other small-molecule drugs that are active against Ebola viruses (EBOVs) would appear a reasonable strategy to evaluate their potential for SARS-CoV-2. We have previously repurposed pyronaridine, tilorone, and quinacrine (from malaria, influenza, and antiprotozoal uses, respectively) as inhibitors of Ebola and Marburg viruses in vitro in HeLa cells and mouse-adapted EBOV in mice in vivo. We have now tested these three drugs in various cell lines (VeroE6, Vero76, Caco-2, Calu-3, A549-ACE2, HUH-7, and monocytes) infected with SARS-CoV-2 as well as other viruses (including MHV and HCoV 229E). The compilation of these results indicated considerable variability in antiviral activity observed across cell lines. We found that tilorone and pyronaridine inhibited the virus replication in A549-ACE2 cells with IC50 values of 180 nM and IC50 198 nM, respectively. We used microscale thermophoresis to test the binding of these molecules to the spike protein, and tilorone and pyronaridine bind to the spike receptor binding domain protein with K d values of 339 and 647 nM, respectively. Human Cmax for pyronaridine and quinacrine is greater than the IC50 observed in A549-ACE2 cells. We also provide novel insights into the mechanism of these compounds which is likely lysosomotropic.
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Affiliation(s)
- Ana C. Puhl
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Ethan J. Fritch
- Department
of Microbiology and Immunology, University
of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Thomas R. Lane
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Longping V. Tse
- Department
of Epidemiology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Boyd L. Yount
- Department
of Epidemiology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Carolina Q. Sacramento
- Laboratório
de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ 21040-900, Brazil
- Centro
De Desenvolvimento Tecnológico Em Saúde (CDTS), Fiocruz, Rio de
Janeiro 21040-900, Brazil
| | - Natalia Fintelman-Rodrigues
- Laboratório
de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ 21040-900, Brazil
- Centro
De Desenvolvimento Tecnológico Em Saúde (CDTS), Fiocruz, Rio de
Janeiro 21040-900, Brazil
| | - Tatyana Almeida Tavella
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacinto da Silva, Department
of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Fabio Trindade Maranhão Costa
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacinto da Silva, Department
of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Stuart Weston
- Department
of Microbiology and Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - James Logue
- Department
of Microbiology and Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Matthew Frieman
- Department
of Microbiology and Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Lakshmanane Premkumar
- Department
of Microbiology and Immunology, University
of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H. Pearce
- Center
for Integrative Chemical Biology and Drug Discovery, Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- UNC
Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, United States
| | - Brett L. Hurst
- Institute
for Antiviral Research, Utah State University, Logan, Utah 84322, United States
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah 84322, United States
| | - Carolina Horta Andrade
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacinto da Silva, Department
of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo 13083-970, Brazil
- LabMol—Laboratory of Molecular Modeling
and Drug Design, Faculdade
de Farmácia, Universidade Federal
de Goiás, Goiânia,
GO 74605-170, Brazil
| | - James A. Levi
- Department of Biological Sciences, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Nicole J. Johnson
- Department of Biological Sciences, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Samantha C. Kisthardt
- Department of Biological Sciences, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Frank Scholle
- Department of Biological Sciences, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thiago Moreno L. Souza
- Laboratório
de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ 21040-900, Brazil
- Centro
De Desenvolvimento Tecnológico Em Saúde (CDTS), Fiocruz, Rio de
Janeiro 21040-900, Brazil
| | - Nathaniel John Moorman
- Department
of Microbiology and Immunology, University
of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
- Center
for Integrative Chemical Biology and Drug Discovery, Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Rapidly Emerging Antiviral Drug Discovery
Initiative, University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Ralph S. Baric
- Department
of Microbiology and Immunology, University
of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department
of Epidemiology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
- Rapidly Emerging Antiviral Drug Discovery
Initiative, University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Peter B. Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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