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Li J, Zhou J, Zhang T, Wu H, Li F, Qi C, Fan L, Yuan X, Wang W, Guo R, Fan B, Tang X, Pang D, Ouyang H, Xie Z, Li B. Effective inhibition of PDCoV infection in chimeric APN gene-edited neonatal pigs. J Virol 2024; 98:e0061124. [PMID: 39078151 PMCID: PMC11334500 DOI: 10.1128/jvi.00611-24] [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: 04/03/2024] [Accepted: 05/23/2024] [Indexed: 07/31/2024] Open
Abstract
Porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus, is a serious threat to piglets and has zoonotic potential. Here, we aimed to further explore the role of aminopeptidase N (APN) as a receptor for PDCoV and test the inhibitory effect of a chimeric APN protein strategy on PDCoV infection. PK-15 cells and LLC-PK1 cells expressing chimeric APN were selected and infected with PDCoV. Viral replication was significantly decreased in these chimeric APN cells compared with that in control group cells. To further characterize the effect of the chimeric APN strategy on PDCoV infection in vitro, primary intestinal epithelial cells isolated from chimeric APN pigs were inoculated with PDCoV. Viral challenge of these cells led to decreased PDCoV infection. More importantly, virally challenged chimeric APN neonatal piglets displayed reduced viral load, significantly fewer microscopic lesions in the intestinal tissue, and no diarrhea. Taken together, these findings deepen our understanding of the mechanism of PDCoV infection and provide a valuable model for the production of disease-resistant animals. IMPORTANCE Porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus, causes diarrhea in piglets and possesses the potential to infect humans. However, there are currently no effective measures for the prevention or control of PDCoV infection. Here, we have developed PK-15 cells, LLC-PK1 cells, and primary intestinal epithelial cells expressing chimeric APN, and viral challenge of these cells led to decreased PDCoV infection. Furthermore, virally challenged chimeric APN neonatal piglets displayed reduced viral load, significantly fewer microscopic lesions in the intestinal tissue, and no diarrhea. These data show that chimeric APN is a promising strategy to combat PDCoV infection.
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Affiliation(s)
- Jizong Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- Institute of Life Sciences, School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
- Guotai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, China
| | - Jian Zhou
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Tianyi Zhang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Heyong Wu
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Feng Li
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Chunyun Qi
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Liyuan Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Xuesong Yuan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Wei Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- Guotai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, China
| | - Rongli Guo
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- Guotai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, China
| | - Baochao Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- Institute of Life Sciences, School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
- Guotai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, China
| | - Xiaochun Tang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Daxin Pang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Hongsheng Ouyang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Zicong Xie
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture, Nanjing, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- Institute of Life Sciences, School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
- Guotai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, China
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2
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Agusi ER, Schön J, Allendorf V, Eze EA, Asala O, Shittu I, Balkema-Buschmann A, Wernike K, Tekki I, Ofua M, Adefegha O, Olubade O, Ogunmolawa O, Dietze K, Globig A, Hoffmann D, Meseko CA. SARS-CoV and SARS-CoV -2 cross-reactive antibodies in domestic animals and wildlife in Nigeria suggest circulation of sarbecoviruses. One Health 2024; 18:100709. [PMID: 38533194 PMCID: PMC10963646 DOI: 10.1016/j.onehlt.2024.100709] [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: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Anthropogenic exposure of domestic animals, as well as wildlife, can result in zoonotic transmission events with known and unknown pathogens including sarbecoviruses. During the COVID-19 pandemic, SARS-CoV-2 infections in animals, most likely resulting from spill-over from humans, have been documented worldwide. However, only limited information is available for Africa. The anthropozoonotic transmission from humans to animals, followed by further inter- and intraspecies propagation may contribute to viral evolution, and thereby subsequently alter the epidemiological patterns of transmission. To shed light on the possible role of domestic animals and wildlife in the ecology and epidemiology of sarbecoviruses in Nigeria, and to analyze the possible circulation of other, undiscovered, but potentially zoonotic sarbecoviruses in animals, we tested 504 serum samples from dogs, rabbits, bats, and pangolins collected between December 2020 and April 2022. The samples were analyzed using an indirect multi-species enzyme-linked immunosorbent assay (ELISA) based on the receptor binding domain (RBD) of SARS-CoV and SARS-CoV -2, respectively. ELISA reactive sera were further analyzed by highly specific virus neutralization test and indirect immunofluorescence assay for confirmation of the presence of antibodies. In this study, we found SARS-CoV reactive antibodies in 16 (11.5%) dogs, 7 (2.97%) rabbits, 2 (7.7%) pangolins and SARS-CoV-2 reactive antibodies in 20 (13.4%) dogs, 6 (2.5%) rabbits and 2 (7.7%) pangolins, respectively. Interestingly, 2 (2.3%) bat samples were positive only for SARS-CoV RBD reactive antibodies. These serological findings of SARS-CoV and/or SARS-CoV-2 infections in both domestic animals and wildlife indicates exposure to sarbecoviruses and requires further One Health-oriented research on the potential reservoir role that different species might play in the ecology and epidemiology of coronaviruses at the human-animal interface.
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Affiliation(s)
- Ebere R Agusi
- National Veterinary Research Institute, Vom, Nigeria
- University of Nigeria, Nsukka, Nigeria
| | - Jacob Schön
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
| | - Valerie Allendorf
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
| | | | | | | | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
| | - Kerstin Wernike
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
| | - Ishaya Tekki
- National Veterinary Research Institute, Vom, Nigeria
| | - Mark Ofua
- SaintMarks-Lagos Urban Forest Sanctuary Initiative (LUFASI), Lagos, Nigeria
| | | | | | | | - Klaas Dietze
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
| | - Anja Globig
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
| | - Donata Hoffmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
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Wei X, Tan H, Lobb B, Zhen W, Wu Z, Parks DH, Neufeld JD, Moreno-Hagelsieb G, Doxey AC. AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods. Brief Bioinform 2024; 25:bbae229. [PMID: 38747283 PMCID: PMC11094555 DOI: 10.1093/bib/bbae229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/02/2024] [Accepted: 04/26/2024] [Indexed: 05/19/2024] Open
Abstract
The analysis and comparison of gene neighborhoods is a powerful approach for exploring microbial genome structure, function, and evolution. Although numerous tools exist for genome visualization and comparison, genome exploration across large genomic databases or user-generated datasets remains a challenge. Here, we introduce AnnoView, a web server designed for interactive exploration of gene neighborhoods across the bacterial and archaeal tree of life. Our server offers users the ability to identify, compare, and visualize gene neighborhoods of interest from 30 238 bacterial genomes and 1672 archaeal genomes, through integration with the comprehensive Genome Taxonomy Database and AnnoTree databases. Identified gene neighborhoods can be visualized using pre-computed functional annotations from different sources such as KEGG, Pfam and TIGRFAM, or clustered based on similarity. Alternatively, users can upload and explore their own custom genomic datasets in GBK, GFF or CSV format, or use AnnoView as a genome browser for relatively small genomes (e.g. viruses and plasmids). Ultimately, we anticipate that AnnoView will catalyze biological discovery by enabling user-friendly search, comparison, and visualization of genomic data. AnnoView is available at http://annoview.uwaterloo.ca.
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Affiliation(s)
- Xin Wei
- Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Huagang Tan
- Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Briallen Lobb
- Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - William Zhen
- Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Zijing Wu
- Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Brisbane, Australia
| | - Josh D Neufeld
- Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada
| | - Andrew C Doxey
- Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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4
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Goldstein SA, Feeley TM, Babler KM, Hilbert ZA, Downhour DM, Moshiri N, Elde NC. Hidden evolutionary constraints dictate the retention of coronavirus accessory genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.12.561935. [PMID: 37873270 PMCID: PMC10592793 DOI: 10.1101/2023.10.12.561935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Coronaviruses exhibit many mechanisms of genetic innovation (1-5), including the acquisition of accessory genes that originate by capture of cellular genes or through duplication of existing viral genes (6,7). Accessory genes influence viral host range and cellular tropism, but little is known about how selection acts on these variable regions of virus genomes. We used experimental evolution of mouse hepatitis virus (MHV) encoding a cellular AKAP7 phosphodiesterase and an inactive native phosphodiesterase, NS2 (ref 8) to simulate the capture of a host gene and analyze its evolution. After courses of serial infection, the gene encoding inactive NS2, ORF2, unexpectedly remained intact, suggesting it is under cryptic constraint uncoupled from the function of NS2. In contrast, AKAP7 was retained under strong selection but rapidly lost under relaxed selection. Guided by the retention of ORF2 and similar patterns in related betacoronaviruses, we analyzed ORF8 of SARS-CoV-2, which arose via gene duplication6 and contains premature stop codons in several globally successful lineages. As with MHV ORF2, the coding-defective SARS-CoV-2 ORF8 gene remains largely intact, mirroring patterns observed during MHV experimental evolution, challenging assumptions on the dynamics of gene loss in virus genomes and extending these findings to viruses currently adapting to humans.
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5
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Bandyopadhyay SS, Halder AK, Saha S, Chatterjee P, Nasipuri M, Basu S. Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome. Vaccines (Basel) 2023; 11:vaccines11030549. [PMID: 36992133 DOI: 10.3390/vaccines11030549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
SARS-CoV-2 is a novel coronavirus that replicates itself via interacting with the host proteins. As a result, identifying virus and host protein-protein interactions could help researchers better understand the virus disease transmission behavior and identify possible COVID-19 drugs. The International Committee on Virus Taxonomy has determined that nCoV is genetically 89% compared to the SARS-CoV epidemic in 2003. This paper focuses on assessing the host–pathogen protein interaction affinity of the coronavirus family, having 44 different variants. In light of these considerations, a GO-semantic scoring function is provided based on Gene Ontology (GO) graphs for determining the binding affinity of any two proteins at the organism level. Based on the availability of the GO annotation of the proteins, 11 viral variants, viz., SARS-CoV-2, SARS, MERS, Bat coronavirus HKU3, Bat coronavirus Rp3/2004, Bat coronavirus HKU5, Murine coronavirus, Bovine coronavirus, Rat coronavirus, Bat coronavirus HKU4, Bat coronavirus 133/2005, are considered from 44 viral variants. The fuzzy scoring function of the entire host–pathogen network has been processed with ~180 million potential interactions generated from 19,281 host proteins and around 242 viral proteins. ~4.5 million potential level one host–pathogen interactions are computed based on the estimated interaction affinity threshold. The resulting host–pathogen interactome is also validated with state-of-the-art experimental networks. The study has also been extended further toward the drug-repurposing study by analyzing the FDA-listed COVID drugs.
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Affiliation(s)
- Soumyendu Sekhar Bandyopadhyay
- Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
- Department of Computer Science and Engineering, School of Engineering and Technology, Adamas University, Kolkata 700126, India
| | - Anup Kumar Halder
- Faculty of Mathematics and Information Sciences, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Sovan Saha
- Department of Computer Science and Engineering (Artificial Intelligence and Machine Learning), Techno Main Salt Lake, Sector V, Kolkata 700091, India
| | - Piyali Chatterjee
- Department of Computer Science and Engineering, Netaji Subhash Engineering College, Kolkata 700152, India
| | - Mita Nasipuri
- Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
| | - Subhadip Basu
- Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
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6
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Abstract
The existence of coronaviruses has been known for many years. These viruses cause significant disease that primarily seems to affect agricultural species. Human coronavirus disease due to the 2002 outbreak of Severe Acute Respiratory Syndrome and the 2012 outbreak of Middle East Respiratory Syndrome made headlines; however, these outbreaks were controlled, and public concern quickly faded. This complacency ended in late 2019 when alarms were raised about a mysterious virus responsible for numerous illnesses and deaths in China. As we now know, this novel disease called Coronavirus Disease 2019 (COVID-19) was caused by Severe acute respiratory syndrome-related-coronavirus-2 (SARS-CoV-2) and rapidly became a worldwide pandemic. Luckily, decades of research into animal coronaviruses hastened our understanding of the genetics, structure, transmission, and pathogenesis of these viruses. Coronaviruses infect a wide range of wild and domestic animals, with significant economic impact in several agricultural species. Their large genome, low dependency on host cellular proteins, and frequent recombination allow coronaviruses to successfully cross species barriers and adapt to different hosts including humans. The study of the animal diseases provides an understanding of the virus biology and pathogenesis and has assisted in the rapid development of the SARS-CoV-2 vaccines. Here, we briefly review the classification, origin, etiology, transmission mechanisms, pathogenesis, clinical signs, diagnosis, treatment, and prevention strategies, including available vaccines, for coronaviruses that affect domestic, farm, laboratory, and wild animal species. We also briefly describe the coronaviruses that affect humans. Expanding our knowledge of this complex group of viruses will better prepare us to design strategies to prevent and/or minimize the impact of future coronavirus outbreaks.
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Key Words
- bcov, bovine coronavirus
- ccov, canine coronavirus
- cov(s), coronavirus(es)
- covid-19, coronavirus disease 2019
- crcov, canine respiratory coronavirus
- e, coronaviral envelope protein
- ecov, equine coronavirus
- fcov, feline coronavirus
- fipv, feline infectious peritonitis virus
- gfcov, guinea fowl coronavirus
- hcov, human coronavirus
- ibv, infectious bronchitis virus
- m, coronaviral membrane protein
- mers, middle east respiratory syndrome-coronavirus
- mhv, mouse hepatitis virus
- pedv, porcine epidemic diarrhea virus
- pdcov, porcine deltacoronavirus
- phcov, pheasant coronavirus
- phev, porcine hemagglutinating encephalomyelitis virus
- prcov, porcine respiratory coronavirus
- rt-pcr, reverse transcriptase polymerase chain reaction
- s, coronaviral spike protein
- sads-cov, swine acute diarrhea syndrome-coronavirus
- sars-cov, severe acute respiratory syndrome-coronavirus
- sars-cov-2, severe acute respiratory syndrome–coronavirus–2
- tcov, turkey coronavirus
- tgev, transmissible gastroenteritis virus
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Affiliation(s)
- Alfonso S Gozalo
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland;,
| | - Tannia S Clark
- Office of Laboratory Animal Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - David M Kurtz
- Comparative Medicine Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina
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Evaluating the transmission feasibility of SARS-CoV-2 Omicron (B.1.1.529) variant to 143 mammalian hosts: insights from S protein RBD and host ACE2 interaction studies. Funct Integr Genomics 2023; 23:36. [PMID: 36631570 PMCID: PMC9838434 DOI: 10.1007/s10142-023-00962-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023]
Abstract
In comparison to previously known severe respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, the newly emerged Omicron (B.1.1.529) variant shows higher infectivity in humans. Exceptionally high infectivity of this variant raises concern of its possible transmission via other intermediate hosts. The SARS-CoV-2 infectivity is established via the association of spike (S) protein receptor binding domain (RBD) with host angiotensin I converting enzyme 2 (hACE2) receptor. In the course of this study, we investigated the interaction between Omicron S protein RBD with the ACE2 receptor of 143 mammalian hosts including human by protein-protein interaction analysis. The goal of this study was to forecast the likelihood that the virus may infect other mammalian species that coexist with or are close to humans in the household, rural, agricultural, or zoological environments. The Omicron RBD was found to interact with higher binding affinity with the ACE2 receptor of 122 mammalian hosts via different amino acid residues from the human ACE2 (hACE2). The rat (Rattus rattus) ACE2 was found to show the strongest interaction with Omicron RBD with a binding affinity of -1393.6 kcal/mol. These distinct strong binding affinity of RBD of Omicron with host ACE2 indicates a greater potential of new host transmissibility and infection via intermediate hosts. Though expected but the phylogenetic position of the mammalian species may not dictate the Omicron RBD binding to the host ACE2 receptor suggesting an involvement of multiple factors in guiding host divergence of the variant.
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Pourbagher-Shahri AM, Mohammadi G, Ghazavi H, Forouzanfar F. Susceptibility of domestic and companion animals to SARS-CoV-2: a comprehensive review. Trop Anim Health Prod 2023; 55:60. [PMID: 36725815 PMCID: PMC9891761 DOI: 10.1007/s11250-023-03470-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 01/17/2023] [Indexed: 02/03/2023]
Abstract
The ongoing coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a large global outbreak. The reports of domestic animals' infection with SARS-CoV-2 raise concerns about the virus's longer-lasting spread, the establishment of a new host reservoir, or even the evolution of a new virus, as seen with COVID-19. In this review, we focus on the susceptibility of domestic animals, especially companion animals, towards SARS-CoV-2 in light of existing studies of natural infection, experimental infection, and serological surveys. Susceptibility of domestic and companion animals to SARS-CoV-2 infection.
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Affiliation(s)
- Ali Mohammad Pourbagher-Shahri
- Neuroscience Research Center, Mashhad University of Medical Sciences, Mashhad, Iran ,Department of Neuroscience, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gholamreza Mohammadi
- Department of Clinical Science, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hamed Ghazavi
- Neuroscience Research Center, Mashhad University of Medical Sciences, Mashhad, Iran ,Department of Neuroscience, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Forouzanfar
- Neuroscience Research Center, Mashhad University of Medical Sciences, Mashhad, Iran ,Department of Neuroscience, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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9
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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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Zhao Q, Tian Y, Liu L, Jiang Y, Sun H, Tan S, Huang B. The Genomic and Genetic Evolution Analysis of Rabbit Astrovirus. Vet Sci 2022; 9:603. [PMID: 36356080 PMCID: PMC9697364 DOI: 10.3390/vetsci9110603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023] Open
Abstract
Rabbit astrovirus (RAstV) is a pathogen that causes diarrhea in rabbits, with high infection rate at various stages, which can often cause secondary or mixed infections with other pathogens, bringing great economic losses to the rabbit industry. In this study, 10 samples were collected from cases of rabbits with diarrhea on a rabbit meat farm in the Shandong area of China. The positive sample for astrovirus detected by RT-PCR was inoculated into an RK 13 cell line. A rabbit astrovirus strain named Z317 was successfully isolated, which produced an obvious cytopathic effect 48 h post-inoculation in the RK 13 cell line. The genome structure of this isolate was studied by high-throughput sequencing, showing that the Z317 strain had the highest similarity with the American strain TN/2208/2010, with 92.43% nucleotide homology, belonging to group MRAstV-23. The basic properties of the Z317 capsid (Cap) protein were analyzed, and 10 liner B cell epitopes were screened with the online biosoft Bepipred 2.0 and SVMTriP, including 445–464, 186–205, 655–674, 88–107, 792–811, 45–64, and 257–276 amino acids. This is the first contribution concerning RAstV genomes in China; more studies are needed to understand the diversity and impact of RAstV on rabbit health.
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11
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Bahoussi AN, Guo YY, Shi RZ, Wang PH, Li YQ, Wu CX, Xing L. Genetic Characteristics of Porcine Hemagglutinating Encephalomyelitis Coronavirus: Identification of Naturally Occurring Mutations Between 1970 and 2015. Front Microbiol 2022; 13:860851. [PMID: 35369458 PMCID: PMC8971845 DOI: 10.3389/fmicb.2022.860851] [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: 01/23/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Porcine hemagglutinating encephalomyelitis virus (PHEV) is a Betacoronavirus characterized by neurological symptoms and a worldwide prevalence. Although PHEV is one of the earliest discovered porcine coronaviruses, it remains poorly studied. The full-length genome of the earliest PHEV strain collected in 1970 in the United States (PHEV/67 N/US/1970) was determined in October 2020. Using this virus as a prototype, we comparatively analyzed all available PHEV full-length sequences during 1970–2015. In phylogenetic trees based on PHEV full-length or spike glycoprotein open reading frame genomic sequences, PHEV/67 N/US/1970 was sorted into a clade different from that of viruses isolated in the United States in 2015. Intriguingly, United States and Belgium viruses isolated in 2015 and 2005, respectively, revealed multiple deletion mutation patterns compared to the strain PHEV/67 N/US/1970, leading to a truncated or a non-functional NS2A coding region. In addition, the genomic similarity analysis showed a hypervariability of the spike glycoprotein coding region, which can affect at least eight potential linear B cell epitopes located in the spike glycoprotein. This report indicates that PHEVs in the United States underwent a significant genetic drift, which might influence PHEV surveillance in other countries.
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Affiliation(s)
| | - Yan-Yan Guo
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Rui-Zhu Shi
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Pei-Hua Wang
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Ya-Qian Li
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Chang-Xin Wu
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, China
| | - Li Xing
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, China
- *Correspondence: Li Xing,
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12
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Teng JLL, Wernery U, Lee HH, Fung J, Joseph S, Li KSM, Elizabeth SK, Fong JYH, Chan KH, Chen H, Lau SKP, Woo PCY. Co-circulation of a Novel Dromedary Camel Parainfluenza Virus 3 and Middle East Respiratory Syndrome Coronavirus in a Dromedary Herd With Respiratory Tract Infections. Front Microbiol 2021; 12:739779. [PMID: 34956112 PMCID: PMC8705932 DOI: 10.3389/fmicb.2021.739779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
Since the emergence of Middle East Respiratory Syndrome (MERS) in 2012, there have been a surge in the discovery and evolutionary studies of viruses in dromedaries. Here, we investigated a herd of nine dromedary calves from Umm Al Quwain, the United Arab Emirates that developed respiratory signs. Viral culture of the nasal swabs from the nine calves on Vero cells showed two different types of cytopathic effects (CPEs), suggesting the presence of two different viruses. Three samples showed typical CPEs of Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) in Vero cells, which was confirmed by partial RdRp gene sequencing. Complete genome sequencing of the three MERS-CoV strains showed that they belonged to clade B3, most closely related to another dromedary MERS-CoV isolate previously detected in Dubai. They also showed evidence of recombination between lineages B4 and B5 in ORF1ab. Another three samples showed non-typical CPEs of MERS-CoV with cell rounding, progressive degeneration, and detachment. Electron microscopy revealed spherical viral particles with peplomers and diameter of about 170nm. High-throughput sequencing and metagenomic analysis showed that the genome organization (3'-N-P-M-F-HN-L-5') was typical of paramyxovirus. They possessed typical genome features similar to other viruses of the genus Respirovirus, including a conserved motif 323FAPGNYALSYAM336 in the N protein, RNA editing sites 5'-717AAAAAAGGG725-3', and 5'-1038AGAAGAAAGAAAGG1051-3' (mRNA sense) in the P gene with multiple polypeptides coding capacity, a nuclear localization signal sequence 245KVGRMYSVEYCKQKIEK261 in the M protein, a conserved sialic acid binding motif 252NRKSCS257 in the HN protein, conserved lengths of the leader (55nt) and trailer (51nt) sequences, total coding percentages (92.6–93.4%), gene-start (AGGANNAAAG), gene-end (NANNANNAAAAA), and trinucleotide intergenic sequences (CTT, mRNA sense). Phylogenetic analysis of their complete genomes showed that they were most closely related to bovine parainfluenza virus 3 (PIV3) genotype C strains. In the phylogenetic tree constructed using the complete L protein, the branch length between dromedary camel PIV3 (DcPIV3) and the nearest node is 0.04, which is >0.03, the definition used for species demarcation in the family Paramyxoviridae. Therefore, we show that DcPIV3 is a novel species of the genus Respirovirus that co-circulated with MERS-CoV in a dromedary herd in the Middle East.
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Affiliation(s)
- Jade Lee Lee Teng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Hwei Huih Lee
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Joshua Fung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Sunitha Joseph
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Kenneth Sze Ming Li
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | | | - Jordan Yik Hei Fong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Kwok-Hung Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Honglin Chen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Susanna Kar Pui Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Patrick Chiu Yat Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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13
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Mei H, Kosakovsky Pond S, Nekrutenko A. Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses. Mol Biol Evol 2021; 38:5678-5684. [PMID: 34505896 PMCID: PMC8499926 DOI: 10.1093/molbev/msab265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The programmed frameshift element (PFE) rerouting translation from ORF1a to ORF1b is essential for the propagation of coronaviruses. The combination of genomic features that make up PFE-the overlap between the two reading frames, a slippery sequence, as well as an ensemble of complex secondary structure elements-places severe constraints on this region as most possible nucleotide substitution may disrupt one or more of these elements. The vast amount of SARS-CoV-2 sequencing data generated within the past year provides an opportunity to assess the evolutionary dynamics of PFE in great detail. Here, we performed a comparative analysis of all available coronaviral genomic data available to date. We show that the overlap between ORF1a and ORF1b evolved as a set of discrete 7, 16, 22, 25, and 31 nucleotide stretches with a well-defined phylogenetic specificity. We further examined sequencing data from over 1,500,000 complete genomes and 55,000 raw read data sets to demonstrate exceptional conservation and detect signatures of selection within the PFE region.
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Affiliation(s)
- Han Mei
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sergei Kosakovsky Pond
- Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Anton Nekrutenko
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
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14
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Yuan Y, Zu S, Zhang Y, Zhao F, Jin X, Hu H. Porcine Deltacoronavirus Utilizes Sialic Acid as an Attachment Receptor and Trypsin Can Influence the Binding Activity. Viruses 2021; 13:v13122442. [PMID: 34960711 PMCID: PMC8705999 DOI: 10.3390/v13122442] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 02/06/2023] Open
Abstract
Porcine deltacoronavirus (PDCoV) is a novel coronavirus that causes diarrhea in nursing piglets. Studies showed that PDCoV uses porcine aminopeptidase N (pAPN) as an entry receptor, but the infection of pAPN-knockout cells or pigs with PDCoV revealed that pAPN might be not a critical functional receptor, implying there exists an unidentified receptor involved in PDCoV infection. Herein, we report that sialic acid (SA) can act as an attachment receptor for PDCoV invasion and facilitate its infection. We first demonstrated that the carbohydrates destroyed on the cell membrane using NaIO4 can alleviate the susceptibility of cells to PDCoV. Further study showed that the removal of SA, a typical cell-surface carbohydrate, could influence the PDCoV infectivity to the cells significantly, suggesting that SA was involved in the infection. The results of plaque assay and Western blotting revealed that SA promoted PDCoV infection by increasing the number of viruses binding to SA on the cell surface during the adsorption phase, which was also confirmed by atomic force microscopy at the microscopic level. In in vivo experiments, we found that the distribution levels of PDCoV and SA were closely relevant in the swine intestine, which contains huge amount of trypsin. We further confirmed that SA-binding capacity to PDCoV is related to the pre-treatment of PDCoV with trypsin. In conclusion, SA is a novel attachment receptor for PDCoV infection to enhance its attachment to cells, which is dependent on the pre-treatment of trypsin on PDCoV. This study paves the way for dissecting the mechanisms of PDCoV–host interactions and provides new strategies to control PDCoV infection.
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Affiliation(s)
- Yixin Yuan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Y.Y.); (S.Z.); (Y.Z.); (F.Z.); (X.J.)
| | - Shaopo Zu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Y.Y.); (S.Z.); (Y.Z.); (F.Z.); (X.J.)
| | - Yunfei Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Y.Y.); (S.Z.); (Y.Z.); (F.Z.); (X.J.)
| | - Fujie Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Y.Y.); (S.Z.); (Y.Z.); (F.Z.); (X.J.)
| | - Xiaohui Jin
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Y.Y.); (S.Z.); (Y.Z.); (F.Z.); (X.J.)
| | - Hui Hu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; (Y.Y.); (S.Z.); (Y.Z.); (F.Z.); (X.J.)
- Key Laboratory for Animal-Derived Food Safety of Henan Province, Zhengzhou 450046, China
- Correspondence:
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15
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Chakravarty N, Senthilnathan T, Paiola S, Gyani P, Castillo Cario S, Urena E, Jeysankar A, Jeysankar P, Ignatius Irudayam J, Natesan Subramanian S, Lavretsky H, Joshi S, Garcia G, Ramaiah A, Arumugaswami V. Neurological pathophysiology of SARS-CoV-2 and pandemic potential RNA viruses: a comparative analysis. FEBS Lett 2021; 595:2854-2871. [PMID: 34757622 PMCID: PMC8652524 DOI: 10.1002/1873-3468.14227] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/15/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022]
Abstract
SARS‐CoV‐2 has infected hundreds of millions of people with over four million dead, resulting in one of the worst global pandemics in recent history. Neurological symptoms associated with COVID‐19 include anosmia, ageusia, headaches, confusion, delirium, and strokes. These may manifest due to viral entry into the central nervous system (CNS) through the blood–brain barrier (BBB) by means of ill‐defined mechanisms. Here, we summarize the abilities of SARS‐CoV‐2 and other neurotropic RNA viruses, including Zika virus and Nipah virus, to cross the BBB into the CNS, highlighting the role of magnetic resonance imaging (MRI) in assessing presence and severity of brain structural changes in COVID‐19 patients. We present new insight into key mutations in SARS‐CoV‐2 variants B.1.1.7 (P681H) and B.1.617.2 (P681R), which may impact on neuropilin 1 (NRP1) binding and CNS invasion. We postulate that SARS‐CoV‐2 may infect both peripheral cells capable of crossing the BBB and brain endothelial cells to traverse the BBB and spread into the brain. COVID‐19 patients can be followed up with MRI modalities to better understand the long‐term effects of COVID‐19 on the brain.
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Affiliation(s)
- Nikhil Chakravarty
- Department of Epidemiology, University of California, Los Angeles, CA, USA
| | - Thrisha Senthilnathan
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA
| | - Sophia Paiola
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA
| | - Priya Gyani
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA
| | - Sebastian Castillo Cario
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA
| | - Estrella Urena
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA
| | - Akash Jeysankar
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA
| | - Prakash Jeysankar
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA
| | - Joseph Ignatius Irudayam
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA
| | | | - Helen Lavretsky
- Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Shantanu Joshi
- Department of Neurology, University of California, Los Angeles, CA, USA
| | - Gustavo Garcia
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA
| | - Arunachalam Ramaiah
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.,Tata Institute for Genetics and Society, Center at inStem, Bangalore, KA, India
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA.,California NanoSystems Institute, University of California, Los Angeles, CA, USA
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16
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Zhu W, Yang J, Lu S, Jin D, Wu S, Pu J, Luo XL, Liu L, Li Z, Xu J. Discovery and Evolution of a Divergent Coronavirus in the Plateau Pika From China That Extends the Host Range of Alphacoronaviruses. Front Microbiol 2021; 12:755599. [PMID: 34691006 PMCID: PMC8529330 DOI: 10.3389/fmicb.2021.755599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/14/2021] [Indexed: 12/26/2022] Open
Abstract
Although plateau pikas are the keystone species in the plateau ecosystem of the Qinghai Province of China, little is known about their role in the evolution and transmission of viral pathogens, especially coronaviruses. Here, we describe the characterization and evolution of a novel alphacoronavirus, termed plateau pika coronavirus (PPCoV) P83, which has a prevalence of 4.5% in plateau pika fecal samples. In addition to classical gene order, the complete viral genome contains a unique nonstructural protein (NS2), several variable transcription regulatory sequences and a highly divergent spike protein. Phylogenetic analysis indicates that the newly discovered PPCoV falls into the genus Alphacoronavirus and is most closely related to rodent alphacoronaviruses. The co-speciation analysis shows that the phylogenetic trees of the alphacoronaviruses and their hosts are not always matched, suggesting inter-species transmission is common in alphacoronaviruses. And, PPCoV origin was estimated by molecular clock based on membrane and RNA-dependent RNA polymerase encoding genes, respectively, which revealed an apparent discrepancy with that of co-speciation analysis. PPCoV was detected mainly in intestinal samples, indicating a potential enteric tropism for the virus. Overall, this study extends the host range of alphacoronaviruses to a new order (Lagomorpha), indicating that plateau pikas may be the natural reservoir of PPCoV and play an important and long-term role in alphacoronavirus evolution.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xue-Lian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China.,Research Institute of Public Heath, Nankai University, Tianjin, China
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17
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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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18
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Pomorska-Mól M, Turlewicz-Podbielska H, Gogulski M, Ruszkowski JJ, Kubiak M, Kuriga A, Barket P, Postrzech M. A cross-sectional retrospective study of SARS-CoV-2 seroprevalence in domestic cats, dogs and rabbits in Poland. BMC Vet Res 2021; 17:322. [PMID: 34620166 PMCID: PMC8495444 DOI: 10.1186/s12917-021-03033-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/27/2021] [Indexed: 12/21/2022] Open
Abstract
Background Coronaviruses (CoVs) have long been known to cause infection in domestic and free-living birds and mammals including humans. The zoonotic origin of SARS-CoV-2 and the biological properties of CoVs, including ability to cross interspecies barriers, enable its emergence in populations of various animals, including companion animals (cats, dogs, rabbits) an area requiring further study. To date, several cases of cats and dogs positive for SARS-CoV-2 and/or specific antibodies have been described. The aim of our cross-sectional retrospective study is to determine seroprevalence of SARS-CoV-2 in domestic dog, cat and rabbit population during recent COVID-19 pandemic in Poland. Results In total, serum samples from 279 cats and 343 dogs and 29 rabbits were used in the study. The seroprevalence of SARS-CoV-2 in cats and dogs reached 1.79% (95% CI: 0.77 – 4.13) and 1.17% (95% CI 0.45 – 2.96), respectively (p ≥ 0.05). Anti- SARS-CoV-2 antibodies were detected in 5 cats (mean S/P% 106 ± 48.23) and 4 dogs (mean S/P% 78.5 ± 16.58). All 29 samples from rabbits were negative for SARS-CoV-2 antibodies. No significant gender or age differences in seroprevalence in dogs and cats (p ≥ 0.05) were found. None of the animals with anti-SARS-CoV-2 antibodies displayed respiratory or gastrointestinal signs at the time of sampling. Conclusions Our results confirmed previous findings that SARS-CoV-2 infections in companion animals occurs but are not frequent. Future serological testing of large pet population may provide a comprehensive picture of disease dynamics in companion animals.
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Affiliation(s)
- Małgorzata Pomorska-Mól
- Department of Preclinical Sciences and Infectious Diseases, Poznan University of Life Sciences, Wołynska 35, 60-637, Poznan, Poland.
| | - Hanna Turlewicz-Podbielska
- Department of Preclinical Sciences and Infectious Diseases, Poznan University of Life Sciences, Wołynska 35, 60-637, Poznan, Poland
| | - Maciej Gogulski
- Department of Preclinical Sciences and Infectious Diseases, Poznan University of Life Sciences, Wołynska 35, 60-637, Poznan, Poland
| | - Jakub J Ruszkowski
- Department of Animal Anatomy, Faculty of Veterinary Medicine and Animals Sciences, Poznan University of Life Sciences, Wojska Polskiego 71C, 60-625, Poznan, Poland
| | - Magdalena Kubiak
- Department of Internal Medicine and Diagnostics, Faculty of Veterinary Medicine and Animal Sciences, Poznan University of Life Sciences, Wolynska 35, 60-637, Poznan, Poland
| | - Anna Kuriga
- Department of Preclinical Sciences and Infectious Diseases, Poznan University of Life Sciences, Wołynska 35, 60-637, Poznan, Poland
| | - Przemysław Barket
- Veterinary Clinic Centrum Małych Zwierząt S.C. M. i P. Barket, Przemysl, Poland
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19
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Seifi T, Reza Kamali A. Antiviral performance of graphene-based materials with emphasis on COVID-19: A review. MEDICINE IN DRUG DISCOVERY 2021; 11:100099. [PMID: 34056572 PMCID: PMC8151376 DOI: 10.1016/j.medidd.2021.100099] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/06/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease-2019 has been one of the most challenging global epidemics of modern times with a large number of casualties combined with economic hardships across the world. Considering that there is still no definitive cure for the recent viral crisis, this article provides a review of nanomaterials with antiviral activity, with an emphasis on graphene and its derivatives, including graphene oxide, reduced graphene oxide and graphene quantum dots. The possible interactions between surfaces of such nanostructured materials with coronaviruses are discussed. The antiviral mechanisms of graphene materials can be related to events such as the inactivation of virus and/or the host cell receptor, electrostatic trapping and physico-chemical destruction of viral species. These effects can be enhanced by functionalization and/or decoration of carbons with species that enhances graphene-virus interactions. The low-cost and large-scale preparation of graphene materials with enhanced antiviral performances is an interesting research direction to be explored.
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20
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Scarpa F, Sanna D, Azzena I, Cossu P, Giovanetti M, Benvenuto D, Coradduzza E, Alexiev I, Casu M, Fiori PL, Ciccozzi M. Update on the Phylodynamics of SADS-CoV. Life (Basel) 2021; 11:life11080820. [PMID: 34440564 PMCID: PMC8402179 DOI: 10.3390/life11080820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/28/2021] [Accepted: 08/10/2021] [Indexed: 11/30/2022] Open
Abstract
Coronaviruses are known to be harmful and heterogeneous viruses, able to infect a large number of hosts. Among them, SADS-CoV (Swine Acute Diarrhea Syndrome Coronavirus), also known as PEAV (Porcine Enteric Alphacoronavirus), or SeA-CoV (Swine Enteric Alphacoronavirus), is the most recent Alphacoronavirus discovered, and caused several outbreaks reported in Chinese swine herds between late 2016 and 2019. We performed an upgraded phylodinamic reconstruction of SADS-CoV based on all whole genomes available on 21 June 2021. Results showed a very close relationship between SADS-CoV and HKU2-like CoV, which may represent the evolutionary intermediate step towards the present SADS-CoV. The direct progenitor of SADS-CoV is so far unknown and, although it is well known that horseshoe bats are reservoirs for Rhinolophus bat coronavirus HKU2-like (HKU2-like CoVs), the transmission path from bats to pigs is still unclear. The discrepancies in the phylogenetic position of rodent CoV, when different molecular markers were considered, corroborate the recombination hypothesis, suggesting that wild rats, which are frequent in farms, may have played a key role. The failure of the attempt at molecular dating, due to the lack of a clock signal, also corroborates the occurrence of a recombination event hypothesis. Zoonotic infections originating in wildlife can easily become a significant threat for human health. In such a context, due to the high recombination and cross-species capabilities of Coronavirus, SADS-CoV represents a possible high-risk pathogen for humans which needs a constant molecular monitoring.
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Affiliation(s)
- Fabio Scarpa
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (I.A.); (P.C.); (M.C.)
- Correspondence:
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (D.S.); (P.L.F.)
| | - Ilenia Azzena
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (I.A.); (P.C.); (M.C.)
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (D.S.); (P.L.F.)
| | - Piero Cossu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (I.A.); (P.C.); (M.C.)
| | - Marta Giovanetti
- Flavivirus Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil;
| | - Domenico Benvenuto
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (D.B.); (M.C.)
| | | | - Ivailo Alexiev
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria;
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (I.A.); (P.C.); (M.C.)
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (D.S.); (P.L.F.)
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy; (D.B.); (M.C.)
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21
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Etienne EE, Nunna BB, Talukder N, Wang Y, Lee ES. COVID-19 Biomarkers and Advanced Sensing Technologies for Point-of-Care (POC) Diagnosis. Bioengineering (Basel) 2021; 8:98. [PMID: 34356205 PMCID: PMC8301167 DOI: 10.3390/bioengineering8070098] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
COVID-19, also known as SARS-CoV-2 is a novel, respiratory virus currently plaguing humanity. Genetically, at its core, it is a single-strand positive-sense RNA virus. It is a beta-type Coronavirus and is distinct in its structure and binding mechanism compared to other types of coronaviruses. Testing for the virus remains a challenge due to the small market available for at-home detection. Currently, there are three main types of tests for biomarker detection: viral, antigen and antibody. Reverse Transcription-Polymerase Chain Reaction (RT-PCR) remains the gold standard for viral testing. However, the lack of quantitative detection and turnaround time for results are drawbacks. This manuscript focuses on recent advances in COVID-19 detection that have lower limits of detection and faster response times than RT-PCR testing. The advancements in sensing platforms have amplified the detection levels and provided real-time results for SARS-CoV-2 spike protein detection with limits as low as 1 fg/mL in the Graphene Field Effect Transistor (FET) sensor. Additionally, using multiple biomarkers, detection levels can achieve a specificity and sensitivity level comparable to that of PCR testing. Proper biomarker selection coupled with nano sensing detection platforms are key in the widespread use of Point of Care (POC) diagnosis in COVID-19 detection.
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Affiliation(s)
- Ernst Emmanuel Etienne
- Advanced Energy Systems and Microdevices Laboratory, Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA; (E.E.E.); (B.B.N.); (N.T.); (Y.W.)
| | - Bharath Babu Nunna
- Advanced Energy Systems and Microdevices Laboratory, Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA; (E.E.E.); (B.B.N.); (N.T.); (Y.W.)
- Division of Engineering in Medicine, Department of Medicine, Brigham, and Women’s Hospital, Harvard Medical School, Harvard University, Cambridge, MA 02139, USA
| | - Niladri Talukder
- Advanced Energy Systems and Microdevices Laboratory, Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA; (E.E.E.); (B.B.N.); (N.T.); (Y.W.)
| | - Yudong Wang
- Advanced Energy Systems and Microdevices Laboratory, Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA; (E.E.E.); (B.B.N.); (N.T.); (Y.W.)
| | - Eon Soo Lee
- Advanced Energy Systems and Microdevices Laboratory, Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA; (E.E.E.); (B.B.N.); (N.T.); (Y.W.)
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22
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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)
| | - 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
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23
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Chen SC, Olsthoorn RCL, Yu CH. Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. Virus Evol 2021; 7:veab021. [PMID: 34141447 PMCID: PMC8206606 DOI: 10.1093/ve/veab021] [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] [Indexed: 12/23/2022] Open
Abstract
In many single-stranded (ss) RNA viruses, the cis-acting packaging signal that confers selectivity genome packaging usually encompasses short structured RNA repeats. These structural units, termed repetitive structural motifs (RSMs), potentially mediate capsid assembly by specific RNA–protein interactions. However, general knowledge of the conservation and/or the diversity of RSMs in the positive-sense ssRNA coronaviruses (CoVs) is limited. By performing structural phylogenetic analysis, we identified a variety of RSMs in nearly all CoV genomic RNAs, which are exclusively located in the 5′-untranslated regions (UTRs) and/or in the inter-domain regions of poly-protein 1ab coding sequences in a lineage-specific manner. In all alpha- and beta-CoVs, except for Embecovirus spp, two to four copies of 5′-gUUYCGUc-3′ RSMs displaying conserved hexa-loop sequences were generally identified in Stem-loop 5 (SL5) located in the 5′-UTRs of genomic RNAs. In Embecovirus spp., however, two to eight copies of 5′-agc-3′/guAAu RSMs were found in the coding regions of non-structural protein (NSP) 3 and/or NSP15 in open reading frame (ORF) 1ab. In gamma- and delta-CoVs, other types of RSMs were found in several clustered structural elements in 5′-UTRs and/or ORF1ab. The identification of RSM-encompassing structural elements in all CoVs suggests that these RNA elements play fundamental roles in the life cycle of CoVs. In the recently emerged SARS-CoV-2, beta-CoV-specific RSMs are also found in its SL5, displaying two copies of 5′-gUUUCGUc-3′ motifs. However, multiple sequence alignment reveals that the majority of SARS-CoV-2 possesses a variant RSM harboring SL5b C241U, and intriguingly, several variations in the coding sequences of viral proteins, such as Nsp12 P323L, S protein D614G, and N protein R203K-G204R, are concurrently found with such variant RSM. In conclusion, the comprehensive exploration for RSMs reveals phylogenetic insights into the RNA structural elements in CoVs as a whole and provides a new perspective on variations currently found in SARS-CoV-2.
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Affiliation(s)
- Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng-Kung University, No.1, University Road, Tainan City 701, Taiwan
| | - René C L Olsthoorn
- Department of Supramolecular Biomaterials Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden,The Netherlands
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng-Kung University, No.1, University Road, Tainan City 701, Taiwan
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24
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Mei H, Nekrutenko A. Stepwise evolution and exceptional conservation of ORF1a/b overlap in coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.06.14.448413. [PMID: 34159333 PMCID: PMC8219097 DOI: 10.1101/2021.06.14.448413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The programmed frameshift element (PFE) rerouting translation from ORF1a to ORF1b is essential for propagation of coronaviruses. A combination of genomic features that make up PFE-the overlap between the two reading frames, a slippery sequence, as well as an ensemble of complex secondary structure elements-puts severe constraints on this region as most possible nucleotide substitution may disrupt one or more of these elements. The vast amount of SARS-CoV-2 sequencing data generated within the past year provides an opportunity to assess evolutionary dynamics of PFE in great detail. Here we performed a comparative analysis of all available coronaviral genomic data available to date. We show that the overlap between ORF1a and b evolved as a set of discrete 7, 16, 22, 25, and 31 nucleotide stretches with a well defined phylogenetic specificity. We further examined sequencing data from over 350,000 complete genomes and 55,000 raw read datasets to demonstrate exceptional conservation of the PFE region.
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Affiliation(s)
- Han Mei
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Anton Nekrutenko
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
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25
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Clinical Management of COVID-19: A Review of Pharmacological Treatment Options. Pharmaceuticals (Basel) 2021; 14:ph14060520. [PMID: 34071185 PMCID: PMC8229327 DOI: 10.3390/ph14060520] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Since the outbreak and subsequent declaration of COVID-19 as a global pandemic in March 2020, concerted efforts have been applied by the scientific community to curtail the spread of the disease and find a cure. While vaccines constitute a vital part of the public health strategy to reduce the burden of COVID-19, the management of this disease will continue to rely heavily on pharmacotherapy. This study aims to provide an updated review of pharmacological agents that have been developed and/or repurposed for the treatment of COVID-19. To this end, a comprehensive literature search was conducted using the PubMed, Google Scholar, and LitCovid databases. Relevant clinical studies on drugs used in the management of COVID-19 were identified and evaluated in terms of evidence of efficacy and safety. To date, the FDA has approved three therapies for the treatment of COVID-19 Emergency Use Authorization: convalescent plasma, remdesivir, and casirivimab/imdevimab (REGN-COV2). Drugs such as lopinavir/ritonavir, umifenovir, favipiravir, anakinra, chloroquine, hydroxychloroquine, tocilizumab, interferons, tissue plasminogen activator, intravenous immunoglobulins, and nafamosat have been used off-label with mixed therapeutic results. Adjunctive administration of corticosteroids is also very common. The clinical experience with these approved and repurposed drugs is limited, and data on efficacy for the new indication are not strong. Overall, the response of the global scientific community to the COVID-19 pandemic has been impressive, as evident from the volume of scientific literature elucidating the molecular biology and pathophysiology of SARS-CoV-2 and the approval of three new drugs for clinical management. Reviewed studies have shown mixed data on efficacy and safety of the currently utilized drugs. The lack of standard treatment for COVID-19 has made it difficult to interpret results from most of the published studies due to the risk of attribution error. The long-term effects of drugs can only be assessed after several years of clinical experience; therefore, the efficacy and safety of current COVID-19 therapeutics should continue to be rigorously monitored as part of post-marketing studies.
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26
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Jelinek HF, Mousa M, Alefishat E, Osman W, Spence I, Bu D, Feng SF, Byrd J, Magni PA, Sahibzada S, Tay GK, Alsafar HS. Evolution, Ecology, and Zoonotic Transmission of Betacoronaviruses: A Review. Front Vet Sci 2021; 8:644414. [PMID: 34095271 PMCID: PMC8173069 DOI: 10.3389/fvets.2021.644414] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/25/2021] [Indexed: 12/18/2022] Open
Abstract
Coronavirus infections have been a part of the animal kingdom for millennia. The difference emerging in the twenty-first century is that a greater number of novel coronaviruses are being discovered primarily due to more advanced technology and that a greater number can be transmitted to humans, either directly or via an intermediate host. This has a range of effects from annual infections that are mild to full-blown pandemics. This review compares the zoonotic potential and relationship between MERS, SARS-CoV, and SARS-CoV-2. The role of bats as possible host species and possible intermediate hosts including pangolins, civets, mink, birds, and other mammals are discussed with reference to mutations of the viral genome affecting zoonosis. Ecological, social, cultural, and environmental factors that may play a role in zoonotic transmission are considered with reference to SARS-CoV, MERS, and SARS-CoV-2 and possible future zoonotic events.
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Affiliation(s)
- Herbert F. Jelinek
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center of Heath Engineering Innovation, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Nuffield Department of Women's and Reproduction Health, Oxford University, Oxford, United Kingdom
| | - Eman Alefishat
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Wael Osman
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ian Spence
- Discipline of Pharmacology, University of Sydney, Sydney, NSW, Australia
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Samuel F. Feng
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Mathematics, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Jason Byrd
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Paola A. Magni
- Discipline of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia
- Murdoch University Singapore, King's Centre, Singapore, Singapore
| | - Shafi Sahibzada
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Guan K. Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Division of Psychiatry, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba S. Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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27
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Lau SKP, He Z, Tsang CC, Chan TTY, Luk HKH, Chan E, Li KSM, Fung J, Chow FWN, Tam AR, Chung TWH, Wong SCY, Que TL, Fung KSC, Lung DC, Wu AKL, Hung IFN, Teng JLL, Wernery U, Hui SW, Martelli P, Woo PCY. A Sensitive and Specific Competitive Enzyme-Linked Immunosorbent Assay for Serodiagnosis of COVID-19 in Animals. Microorganisms 2021; 9:1019. [PMID: 34068581 PMCID: PMC8150753 DOI: 10.3390/microorganisms9051019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/12/2022] Open
Abstract
In addition to human cases, cases of COVID-19 in captive animals and pets are increasingly reported. This raises the concern for two-way COVID-19 transmission between humans and animals. Here, we developed a SARS-CoV-2 nucleocapsid protein-based competitive enzyme-linked immunosorbent assay (cELISA) for serodiagnosis of COVID-19 which can theoretically be used in virtually all kinds of animals. We used 187 serum samples from patients with/without COVID-19, laboratory animals immunized with inactive SARS-CoV-2 virions, COVID-19-negative animals, and animals seropositive to other betacoronaviruses. A cut-off percent inhibition value of 22.345% was determined and the analytical sensitivity and specificity were found to be 1:64-1:256 and 93.9%, respectively. Evaluation on its diagnostic performance using 155 serum samples from COVID-19-negative animals and COVID-19 human patients showed a diagnostic sensitivity and specificity of 80.8% and 100%, respectively. The cELISA can be incorporated into routine blood testing of farmed/captive animals for COVID-19 surveillance.
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Affiliation(s)
- Susanna K. P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; (Z.H.); (C.-C.T.); (T.T.Y.C.); (H.K.H.L.); (E.C.); (K.S.M.L.); (J.F.); (F.W.N.C.); (T.W.H.C.); (J.L.L.T.)
| | - Zirong He
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; (Z.H.); (C.-C.T.); (T.T.Y.C.); (H.K.H.L.); (E.C.); (K.S.M.L.); (J.F.); (F.W.N.C.); (T.W.H.C.); (J.L.L.T.)
| | - Chi-Ching Tsang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; (Z.H.); (C.-C.T.); (T.T.Y.C.); (H.K.H.L.); (E.C.); (K.S.M.L.); (J.F.); (F.W.N.C.); (T.W.H.C.); (J.L.L.T.)
| | - Tony T. Y. Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; (Z.H.); (C.-C.T.); (T.T.Y.C.); (H.K.H.L.); (E.C.); (K.S.M.L.); (J.F.); (F.W.N.C.); (T.W.H.C.); (J.L.L.T.)
| | - Hayes K. H. Luk
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; (Z.H.); (C.-C.T.); (T.T.Y.C.); (H.K.H.L.); (E.C.); (K.S.M.L.); (J.F.); (F.W.N.C.); (T.W.H.C.); (J.L.L.T.)
| | - Elaine Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; (Z.H.); (C.-C.T.); (T.T.Y.C.); (H.K.H.L.); (E.C.); (K.S.M.L.); (J.F.); (F.W.N.C.); (T.W.H.C.); (J.L.L.T.)
| | - Kenneth S. M. Li
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; (Z.H.); (C.-C.T.); (T.T.Y.C.); (H.K.H.L.); (E.C.); (K.S.M.L.); (J.F.); (F.W.N.C.); (T.W.H.C.); (J.L.L.T.)
| | - Joshua Fung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; (Z.H.); (C.-C.T.); (T.T.Y.C.); (H.K.H.L.); (E.C.); (K.S.M.L.); (J.F.); (F.W.N.C.); (T.W.H.C.); (J.L.L.T.)
| | - Franklin W. N. Chow
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; (Z.H.); (C.-C.T.); (T.T.Y.C.); (H.K.H.L.); (E.C.); (K.S.M.L.); (J.F.); (F.W.N.C.); (T.W.H.C.); (J.L.L.T.)
| | - Anthony R. Tam
- Department of Medicine, Queen Mary Hospital, Pokfulam, Hong Kong;
| | - Tom W. H. Chung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; (Z.H.); (C.-C.T.); (T.T.Y.C.); (H.K.H.L.); (E.C.); (K.S.M.L.); (J.F.); (F.W.N.C.); (T.W.H.C.); (J.L.L.T.)
| | - Sally C. Y. Wong
- Department of Pathology, Queen Elizabeth Hospital, King’s Park, Hong Kong; (S.C.Y.W.); (D.C.L.)
| | - Tak-Lun Que
- Department of Pathology, Tuen Mun Hospital, Tuen Mun, Hong Kong;
| | - Kitty S. C. Fung
- Department of Pathology, United Christian Hospital, Kwun Tong, Hong Kong;
| | - David C. Lung
- Department of Pathology, Queen Elizabeth Hospital, King’s Park, Hong Kong; (S.C.Y.W.); (D.C.L.)
| | - Alan K. L. Wu
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong;
| | - Ivan F. N. Hung
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong;
| | - Jade L. L. Teng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; (Z.H.); (C.-C.T.); (T.T.Y.C.); (H.K.H.L.); (E.C.); (K.S.M.L.); (J.F.); (F.W.N.C.); (T.W.H.C.); (J.L.L.T.)
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, P.O. Box 597, Dubai, United Arab Emirates;
| | - Suk-Wai Hui
- Ocean Park Corporation, Aberdeen, Hong Kong; (S.-W.H.); (P.M.)
| | - Paolo Martelli
- Ocean Park Corporation, Aberdeen, Hong Kong; (S.-W.H.); (P.M.)
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong; (Z.H.); (C.-C.T.); (T.T.Y.C.); (H.K.H.L.); (E.C.); (K.S.M.L.); (J.F.); (F.W.N.C.); (T.W.H.C.); (J.L.L.T.)
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28
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Vlasova AN, Saif LJ. Bovine Coronavirus and the Associated Diseases. Front Vet Sci 2021; 8:643220. [PMID: 33869323 PMCID: PMC8044316 DOI: 10.3389/fvets.2021.643220] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/08/2021] [Indexed: 12/17/2022] Open
Abstract
Coronaviruses (CoVs) possess the largest and most complex RNA genome (up to 32 kb) that encodes for 16 non-structural proteins regulating RNA synthesis and modification. Coronaviruses are known to infect a wide range of mammalian and avian species causing remarkably diverse disease syndromes. Variable tissue tropism and the ability to easily cross interspecies barriers are the well-known characteristics of certain CoVs. The 21st century epidemics of severe acute respiratory CoV (SARS-CoV), Middle East respiratory CoV and the ongoing SARS-CoV-2 pandemic further highlight these characteristics and emphasize the relevance of CoVs to the global public health. Bovine CoVs (BCoVs) are betacoronaviruses associated with neonatal calf diarrhea, and with winter dysentery and shipping fever in older cattle. Of interest, no distinct genetic or antigenic markers have been identified in BCoVs associated with these distinct clinical syndromes. In contrast, like other CoVs, BCoVs exist as quasispecies. Besides cattle, BCoVs and bovine-like CoVs were identified in various domestic and wild ruminant species (water buffalo, sheep, goat, dromedary camel, llama, alpaca, deer, wild cattle, antelopes, giraffes, and wild goats), dogs and humans. Surprisingly, bovine-like CoVs also cannot be reliably distinguished from BCoVs using comparative genomics. Additionally, there are historical examples of zoonotic transmission of BCoVs. This article will discuss BCoV pathogenesis, epidemiology, interspecies transmission, immune responses, vaccines, and diagnostics.
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Affiliation(s)
- Anastasia N Vlasova
- Center for Food Animal Health Research, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH, United States
| | - Linda J Saif
- Center for Food Animal Health Research, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH, United States
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29
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Chathappady House NN, Palissery S, Sebastian H. Corona Viruses: A Review on SARS, MERS and COVID-19. Microbiol Insights 2021; 14:11786361211002481. [PMID: 33795938 PMCID: PMC7983408 DOI: 10.1177/11786361211002481] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 02/18/2021] [Indexed: 01/08/2023] Open
Abstract
After the outbreak of SARS and MERS, the world is now in the grip of another viral disease named COVID-19 caused by a beta Coronavirus - SARS COV-2 which appears to be the only one with a pandemic potential. The case of COVID-19 was reported in the Hubei province of Wuhan city in Central China at the end of December 2019 and it is suspected that the sea food market played a role in this outbreak which was closed abruptly. Subsequently, a Public Health Emergency of International Concern was declared on 30 January 2020 by the World Health Organization. Both SARS and MERS corona viruses had its reservoir in bats and were transferred to humans from palm civets and camels respectively. This virus can be transmitted through airborne droplets. Natural reservoir and intermediate host of COVID-19 is yet to be identified. This paper reviews the occurrences of viral diseases in the recent times including SARS and MERS. As an addition to this, the paper will contain a detailed examination of the COVID-19 Pandemic.
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Khamassi Khbou M, Daaloul Jedidi M, Bouaicha Zaafouri F, Benzarti M. Coronaviruses in farm animals: Epidemiology and public health implications. Vet Med Sci 2021; 7:322-347. [PMID: 32976707 PMCID: PMC7537542 DOI: 10.1002/vms3.359] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/27/2020] [Accepted: 08/29/2020] [Indexed: 12/12/2022] Open
Abstract
Coronaviruses (CoVs) are documented in a wide range of animal species, including terrestrial and aquatic, domestic and wild. The geographic distribution of animal CoVs is worldwide and prevalences were reported in several countries across the five continents. The viruses are known to cause mainly gastrointestinal and respiratory diseases with different severity levels. In certain cases, CoV infections are responsible of huge economic losses associated or not to highly public health impact. Despite being enveloped, CoVs are relatively resistant pathogens in the environment. Coronaviruses are characterized by a high mutation and recombination rate, which makes host jumping and cross-species transmission easy. In fact, increasing contact between different animal species fosters cross-species transmission, while agriculture intensification, animal trade and herd management are key drivers at the human-animal interface. If contacts with wild animals are still limited, humans have much more contact with farm animals, during breeding, transport, slaughter and food process, making CoVs a persistent threat to both humans and animals. A global network should be established for the surveillance and monitoring of animal CoVs.
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Affiliation(s)
- Médiha Khamassi Khbou
- Laboratory of Infectious Animal Diseases, Zoonoses, and Sanitary RegulationUniv. Manouba. Ecole Nationale de Médecine Vétérinaire de Sidi ThabetSidi ThabetTunisia
| | - Monia Daaloul Jedidi
- Laboratory of Microbiology and ImmunologyUniv. ManoubaEcole Nationale de Médecine Vétérinaire de Sidi ThabetSidi ThabetTunisia
| | - Faten Bouaicha Zaafouri
- Department of Livestock Semiology and MedicineUniv. ManoubaEcole Nationale de Médecine Vétérinaire de Sidi ThabetSidi ThabetTunisia
| | - M’hammed Benzarti
- Laboratory of Infectious Animal Diseases, Zoonoses, and Sanitary RegulationUniv. Manouba. Ecole Nationale de Médecine Vétérinaire de Sidi ThabetSidi ThabetTunisia
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Predicting mammalian hosts in which novel coronaviruses can be generated. Nat Commun 2021; 12:780. [PMID: 33594041 PMCID: PMC7887240 DOI: 10.1038/s41467-021-21034-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/08/2021] [Indexed: 12/23/2022] Open
Abstract
Novel pathogenic coronaviruses – such as SARS-CoV and probably SARS-CoV-2 – arise by homologous recombination between co-infecting viruses in a single cell. Identifying possible sources of novel coronaviruses therefore requires identifying hosts of multiple coronaviruses; however, most coronavirus-host interactions remain unknown. Here, by deploying a meta-ensemble of similarity learners from three complementary perspectives (viral, mammalian and network), we predict which mammals are hosts of multiple coronaviruses. We predict that there are 11.5-fold more coronavirus-host associations, over 30-fold more potential SARS-CoV-2 recombination hosts, and over 40-fold more host species with four or more different subgenera of coronaviruses than have been observed to date at >0.5 mean probability cut-off (2.4-, 4.25- and 9-fold, respectively, at >0.9821). Our results demonstrate the large underappreciation of the potential scale of novel coronavirus generation in wild and domesticated animals. We identify high-risk species for coronavirus surveillance. Homologous recombination between co-infecting coronaviruses can produce novel pathogens. Here, Wardeh et al. develop a machine learning approach to predict associations between mammals and multiple coronaviruses and hence estimate the potential for generation of novel coronaviruses by recombination.
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Mulabbi EN, Tweyongyere R, Byarugaba DK. The history of the emergence and transmission of human coronaviruses. Onderstepoort J Vet Res 2021; 88:e1-e8. [PMID: 33567843 PMCID: PMC7876959 DOI: 10.4102/ojvr.v88i1.1872] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022] Open
Abstract
Human coronaviruses are known respiratory pathogens associated with a range of respiratory illnesses, and there are considerable morbidity and hospitalisation amongst immune-compromised individuals of all age groups. The emergence of a highly pathogenic human coronavirus in China in 2019 has confirmed the long-held opinion that these viruses are important emerging and re-emerging pathogens. In this review article, we trace the discovery and emergence of coronaviruses (CoVs) over time since they were first reported. The review article will enrich our understanding on the host range, diversity and evolution, transmission of human CoVs and the threat posed by these viruses circulating in animal populations but overtime have spilled over to humans because of the increased proximity between humans and animals.
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Affiliation(s)
- Elijah N Mulabbi
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala.
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Hedman HD, Krawczyk E, Helmy YA, Zhang L, Varga C. Host Diversity and Potential Transmission Pathways of SARS-CoV-2 at the Human-Animal Interface. Pathogens 2021; 10:180. [PMID: 33567598 PMCID: PMC7915269 DOI: 10.3390/pathogens10020180] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
Emerging infectious diseases present great risks to public health. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19), has become an urgent public health issue of global concern. It is speculated that the virus first emerged through a zoonotic spillover. Basic research studies have suggested that bats are likely the ancestral reservoir host. Nonetheless, the evolutionary history and host susceptibility of SARS-CoV-2 remains unclear as a multitude of animals has been proposed as potential intermediate or dead-end hosts. SARS-CoV-2 has been isolated from domestic animals, both companion and livestock, as well as in captive wildlife that were in close contact with human COVID-19 cases. Currently, domestic mink is the only known animal that is susceptible to a natural infection, develop severe illness, and can also transmit SARS-CoV-2 to other minks and humans. To improve foundational knowledge of SARS-CoV-2, we are conducting a synthesis review of its host diversity and transmission pathways. To mitigate this COVID-19 pandemic, we strongly advocate for a systems-oriented scientific approach that comprehensively evaluates the transmission of SARS-CoV-2 at the human and animal interface.
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Affiliation(s)
- Hayden D. Hedman
- Summit County Local Public Health Agency, Summit County, Frisco, CO 80443, USA;
| | - Eric Krawczyk
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL 60612, USA;
| | - Yosra A. Helmy
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA;
| | - Lixin Zhang
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA;
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Csaba Varga
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA
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Rabaan AA, Al-Ahmed SH, Sah R, Alqumber MA, Haque S, Patel SK, Pathak M, Tiwari R, Yatoo MI, Haq AU, Bilal M, Dhama K, Rodriguez-Morales AJ. MERS-CoV: epidemiology, molecular dynamics, therapeutics, and future challenges. Ann Clin Microbiol Antimicrob 2021; 20:8. [PMID: 33461573 PMCID: PMC7812981 DOI: 10.1186/s12941-020-00414-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023] Open
Abstract
The Severe Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has gained research attention worldwide, given the current pandemic. Nevertheless, a previous zoonotic and highly pathogenic coronavirus, the Middle East Respiratory Syndrome coronavirus (MERS-CoV), is still causing concern, especially in Saudi Arabia and neighbour countries. The MERS-CoV has been reported from respiratory samples in more than 27 countries, and around 2500 cases have been reported with an approximate fatality rate of 35%. After its emergence in 2012 intermittent, sporadic cases, nosocomial infections and many community clusters of MERS continued to occur in many countries. Human-to-human transmission resulted in the large outbreaks in Saudi Arabia. The inherent genetic variability among various clads of the MERS-CoV might have probably paved the events of cross-species transmission along with changes in the inter-species and intra-species tropism. The current review is drafted using an extensive review of literature on various databases, selecting of publications irrespective of favouring or opposing, assessing the merit of study, the abstraction of data and analysing data. The genome of MERS-CoV contains around thirty thousand nucleotides having seven predicted open reading frames. Spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins are the four main structural proteins. The surface located spike protein (S) of betacoronaviruses has been established to be one of the significant factors in their zoonotic transmission through virus-receptor recognition mediation and subsequent initiation of viral infection. Three regions in Saudi Arabia (KSA), Eastern Province, Riyadh and Makkah were affected severely. The epidemic progression had been the highest in 2014 in Makkah and Riyadh and Eastern Province in 2013. With a lurking epidemic scare, there is a crucial need for effective therapeutic and immunological remedies constructed on sound molecular investigations.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Shamsah H Al-Ahmed
- Specialty Paediatric Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Ranjit Sah
- Tribhuvan University Institute of Medicine, Kathmandu, Nepal
| | - Mohammed A Alqumber
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Shailesh Kumar Patel
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India
| | - Mamta Pathak
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, 281001, India
| | - Mohd Iqbal Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shuhama, Alusteng Srinagar, Shalimar, Srinagar, Jammu and Kashmir, 190006, India
| | - Abrar Ul Haq
- Division of Clinical Veterinary Medicine Ethics & Jurisprudence, Faculty of Veterinary Sciences and Animal Husbandry, Sher E Kashmir University of Agricultural Sciences and Technology, Kashmir, Shuhama, Srinagar, 190006, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India.
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia. .,Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Americas, Pereira, Risaralda, Colombia. .,School of Medicine, Universidad Privada Franz Tamayo (UNIFRANZ), Cochabamba, Bolivia.
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35
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Isolation of MERS-related coronavirus from lesser bamboo bats that uses DPP4 and infects human-DPP4-transgenic mice. Nat Commun 2021; 12:216. [PMID: 33431849 PMCID: PMC7801609 DOI: 10.1038/s41467-020-20458-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/27/2020] [Indexed: 12/26/2022] Open
Abstract
While a number of human coronaviruses are believed to be originated from ancestral viruses in bats, it remains unclear if bat coronaviruses are ready to cause direct bat-to-human transmission. Here, we report the isolation of a MERS-related coronavirus, Tylonycteris-bat-CoV-HKU4, from lesser bamboo bats. Tylonycteris-bat-CoV-HKU4 replicates efficiently in human colorectal adenocarcinoma and hepatocarcinoma cells with cytopathic effects, and can utilize human-dipeptidyl-peptidase-4 and dromedary camel-dipeptidyl-peptidase-4 as the receptors for cell entry. Flow cytometry, co-immunoprecipitation and surface plasmon resonance assays show that Tylonycteris-bat-CoV-HKU4-receptor-binding-domain can bind human-dipeptidyl-peptidase-4, dromedary camel-dipeptidyl-peptidase-4, and Tylonycteris pachypus-dipeptidyl-peptidase-4. Tylonycteris-bat-CoV-HKU4 can infect human-dipeptidyl-peptidase-4-transgenic mice by intranasal inoculation with self-limiting disease. Positive virus and inflammatory changes were detected in lungs and brains of infected mice, associated with suppression of antiviral cytokines and activation of proinflammatory cytokines and chemokines. The results suggest that MERS-related bat coronaviruses may overcome species barrier by utilizing dipeptidyl-peptidase-4 and potentially emerge in humans by direct bat-to-human transmission. Several human coronaviruses (CoV) have been proposed to emerge from bats but evidence of direct bat-to-human transmission is slim. In this work, the authors isolate a MERS-related CoV strain directly from bats and show that it infects target cells in vitro and engineered mice through the human DDP4 receptor.
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Kangabam R, Sahoo S, Ghosh A, Roy R, Silla Y, Misra N, Suar M. Next-generation computational tools and resources for coronavirus research: From detection to vaccine discovery. Comput Biol Med 2021; 128:104158. [PMID: 33301953 PMCID: PMC7705366 DOI: 10.1016/j.compbiomed.2020.104158] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 12/14/2022]
Abstract
The COVID-19 pandemic has affected 215 countries and territories around the world with 60,187,347 coronavirus cases and 17,125,719 currently infected patients confirmed as of the November 25, 2020. Currently, many countries are working on developing new vaccines and therapeutic drugs for this novel virus strain, and a few of them are in different phases of clinical trials. The advancement in high-throughput sequence technologies, along with the application of bioinformatics, offers invaluable knowledge on genomic characterization and molecular pathogenesis of coronaviruses. Recent multi-disciplinary studies using bioinformatics methods like sequence-similarity, phylogenomic, and computational structural biology have provided an in-depth understanding of the molecular and biochemical basis of infection, atomic-level recognition of the viral-host receptor interaction, functional annotation of important viral proteins, and evolutionary divergence across different strains. Additionally, various modern immunoinformatic approaches are also being used to target the most promiscuous antigenic epitopes from the SARS-CoV-2 proteome for accelerating the vaccine development process. In this review, we summarize various important computational tools and databases available for systematic sequence-structural study on coronaviruses. The features of these public resources have been comprehensively discussed, which may help experimental biologists with predictive insights useful for ongoing research efforts to find therapeutics against the infectious COVID-19 disease.
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Affiliation(s)
- Rajiv Kangabam
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Susrita Sahoo
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Arpan Ghosh
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India; School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Riya Roy
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Yumnam Silla
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, 785006, India
| | - Namrata Misra
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India; School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Mrutyunjay Suar
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India; School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India.
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37
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Mulabbi EN, Tweyongyere R, Byarugaba DK. The history of the emergence and transmission of human coronaviruses. Onderstepoort J Vet Res 2020. [DOI: 10.4102/ojvr.v87i1.1872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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38
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Kuzmin K, Adeniyi AE, DaSouza AK, Lim D, Nguyen H, Molina NR, Xiong L, Weber IT, Harrison RW. Machine learning methods accurately predict host specificity of coronaviruses based on spike sequences alone. Biochem Biophys Res Commun 2020; 533:553-558. [PMID: 32981683 PMCID: PMC7500881 DOI: 10.1016/j.bbrc.2020.09.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/06/2020] [Indexed: 11/19/2022]
Abstract
Coronaviruses infect many animals, including humans, due to interspecies transmission. Three of the known human coronaviruses: MERS, SARS-CoV-1, and SARS-CoV-2, the pathogen for the COVID-19 pandemic, cause severe disease. Improved methods to predict host specificity of coronaviruses will be valuable for identifying and controlling future outbreaks. The coronavirus S protein plays a key role in host specificity by attaching the virus to receptors on the cell membrane. We analyzed 1238 spike sequences for their host specificity. Spike sequences readily segregate in t-SNE embeddings into clusters of similar hosts and/or virus species. Machine learning with SVM, Logistic Regression, Decision Tree, Random Forest gave high average accuracies, F1 scores, sensitivities and specificities of 0.95-0.99. Importantly, sites identified by Decision Tree correspond to protein regions with known biological importance. These results demonstrate that spike sequences alone can be used to predict host specificity.
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Affiliation(s)
- Kiril Kuzmin
- Department of Computer Science, Georgia State University, 1 Park Place, Atlanta, GA, 30303, USA.
| | | | - Arthur Kevin DaSouza
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA, 30303, USA
| | - Deuk Lim
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA, 30303, USA
| | - Huyen Nguyen
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA, 30303, USA
| | - Nuria Ramirez Molina
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA, 30303, USA
| | - Lanqiao Xiong
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA, 30303, USA
| | - Irene T Weber
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA, 30303, USA
| | - Robert W Harrison
- Department of Computer Science, Georgia State University, 1 Park Place, Atlanta, GA, 30303, USA; Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA, 30303, USA.
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Zhu W, Yang J, Lu S, Lan R, Jin D, Luo XL, Pu J, Wu S, Xu J. Beta- and Novel Delta-Coronaviruses Are Identified from Wild Animals in the Qinghai-Tibetan Plateau, China. Virol Sin 2020; 36:402-411. [PMID: 33259031 PMCID: PMC7706178 DOI: 10.1007/s12250-020-00325-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/27/2020] [Indexed: 12/02/2022] Open
Abstract
Outbreaks of severe virus infections with the potential to cause global pandemics are increasingly concerning. One type of those commonly emerging and re-emerging pathogens are coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2). Wild animals are hosts of different coronaviruses with the potential risk of cross-species transmission. However, little is known about the reservoir and host of coronaviruses in wild animals in Qinghai Province, where has the greatest biodiversity among the world’s high-altitude regions. Here, from the next-generation sequencing data, we obtained a known beta-coronavirus (beta-CoV) genome and a novel delta-coronavirus (delta-CoV) genome from faecal samples of 29 marmots, 50 rats and 25 birds in Yushu Tibetan Autonomous Prefecture, Qinghai Province, China in July 2019. According to the phylogenetic analysis, the beta-CoV shared high nucleotide identity with Coronavirus HKU24. Although the novel delta-CoV (MtCoV) was closely related to Sparrow deltacoronavirus ISU42824, the protein spike of the novel delta-CoV showed highest amino acid identity to Sparrow coronavirus HKU17 (73.1%). Interestingly, our results identified a novel host (Montifringilla taczanowskii) for the novel delta-CoV and the potential cross-species transmission. The most recent common ancestor (tMRCA) of MtCoVs along with other closest members of the species of Coronavirus HKU15 was estimated to be 289 years ago. Thus, this study increases our understanding of the genetic diversity of beta-CoVs and delta-CoVs, and also provides a new perspective of the coronavirus hosts.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xue-Lian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, 815000, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China. .,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China. .,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China. .,Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, China.
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40
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Lam SD, Bordin N, Waman VP, Scholes HM, Ashford P, Sen N, van Dorp L, Rauer C, Dawson NL, Pang CSM, Abbasian M, Sillitoe I, Edwards SJL, Fraternali F, Lees JG, Santini JM, Orengo CA. SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals. Sci Rep 2020; 10:16471. [PMID: 33020502 PMCID: PMC7536205 DOI: 10.1038/s41598-020-71936-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/17/2020] [Indexed: 01/04/2023] Open
Abstract
SARS-CoV-2 has a zoonotic origin and was transmitted to humans via an undetermined intermediate host, leading to infections in humans and other mammals. To enter host cells, the viral spike protein (S-protein) binds to its receptor, ACE2, and is then processed by TMPRSS2. Whilst receptor binding contributes to the viral host range, S-protein:ACE2 complexes from other animals have not been investigated widely. To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We also analysed structural interactions to better understand the key residues contributing to affinity. We predict that mutations are more detrimental in ACE2 than TMPRSS2. Finally, we demonstrate phylogenetically that human SARS-CoV-2 strains have been isolated in animals. Our results suggest that SARS-CoV-2 can infect a broad range of mammals, but few fish, birds or reptiles. Susceptible animals could serve as reservoirs of the virus, necessitating careful ongoing animal management and surveillance.
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Affiliation(s)
- S D Lam
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - N Bordin
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - V P Waman
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - H M Scholes
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - P Ashford
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - N Sen
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
- Indian Institute of Science Education and Research, Pune, 411008, India
| | - L van Dorp
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - C Rauer
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - N L Dawson
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - C S M Pang
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - M Abbasian
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - I Sillitoe
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - S J L Edwards
- Department of Science and Technology Studies, University College London, London, WC1E 6BT, UK
| | - F Fraternali
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, New Hunt's House, King's College London, London, SE1 1UL, UK
| | - J G Lees
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 OBP, UK
| | - J M Santini
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - C A Orengo
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
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41
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Witkowska D. Mass Spectrometry and Structural Biology Techniques in the Studies on the Coronavirus-Receptor Interaction. Molecules 2020; 25:E4133. [PMID: 32927621 PMCID: PMC7571139 DOI: 10.3390/molecules25184133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/01/2020] [Accepted: 09/09/2020] [Indexed: 12/15/2022] Open
Abstract
Mass spectrometry and some other biophysical methods, have made substantial contributions to the studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human proteins interactions. The most interesting feature of SARS-CoV-2 seems to be the structure of its spike (S) protein and its interaction with the human cell receptor. Mass spectrometry of spike S protein revealed how the glycoforms are distributed across the S protein surface. X-ray crystallography and cryo-electron microscopy made huge impact on the studies on the S protein and ACE2 receptor protein interaction, by elucidating the three-dimensional structures of these proteins and their conformational changes. The findings of the most recent studies in the scope of SARS-CoV-2-Human protein-protein interactions are described here.
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MESH Headings
- Amino Acid Sequence
- Angiotensin-Converting Enzyme 2
- Betacoronavirus/chemistry
- Betacoronavirus/pathogenicity
- Binding Sites
- COVID-19
- Coronavirus Infections/epidemiology
- Coronavirus Infections/virology
- Gene Expression
- Host-Pathogen Interactions
- Humans
- Models, Molecular
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/genetics
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/virology
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Severe acute respiratory syndrome-related coronavirus/chemistry
- Severe acute respiratory syndrome-related coronavirus/pathogenicity
- SARS-CoV-2
- Sequence Alignment
- Severe Acute Respiratory Syndrome/epidemiology
- Severe Acute Respiratory Syndrome/virology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Danuta Witkowska
- Institute of Health Sciences, Opole University, Katowicka 68, 45-060 Opole, Poland
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42
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Domańska-Blicharz K, Woźniakowski G, Konopka B, Niemczuk K, Welz M, Rola J, Socha W, Orłowska A, Antas M, Śmietanka K, Cuvelier-Mizak B. Animal Coronaviruses in the Light of COVID-19. J Vet Res 2020; 64:333-345. [PMID: 32984621 PMCID: PMC7497757 DOI: 10.2478/jvetres-2020-0050] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022] Open
Abstract
Coronaviruses are extremely susceptible to genetic changes due to the characteristic features of the genome structure, life cycle and environmental pressure. Their remarkable variability means that they can infect many different species of animals and cause different disease symptoms. Moreover, in some situations, coronaviruses might be transmitted across species. Although they are commonly found in farm, companion and wild animals, causing clinical and sometimes serious signs resulting in significant economic losses, not all of them have been classified by the World Organization for Animal Health (OIE) as hazardous and included on the list of notifiable diseases. Currently, only three diseases caused by coronaviruses are on the OIE list of notifiable terrestrial and aquatic animal diseases. However, none of these three entails any administrative measures. The emergence of the SARS-CoV-2 infections that have caused the COVID-19 pandemic in humans has proved that the occurrence and variability of coronaviruses is highly underestimated in the animal reservoir and reminded us of the critical importance of the One Health approach. Therefore, domestic and wild animals should be intensively monitored, both to broaden our knowledge of the viruses circulating among them and to understand the mechanisms of the emergence of viruses of relevance to animal and human health.
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Affiliation(s)
| | - Grzegorz Woźniakowski
- Department of Swine Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
| | | | - Krzysztof Niemczuk
- Director General, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Mirosław Welz
- General Veterinary Inspectorate, 00-930Warsaw, Poland
| | - Jerzy Rola
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Wojciech Socha
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Anna Orłowska
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Marta Antas
- Department of Swine Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Krzysztof Śmietanka
- Department of Poultry Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Beata Cuvelier-Mizak
- Department of Veterinary Pharmacy, National Veterinary Research Institute, 24-100Puławy, Poland
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43
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MALIK YASHPALSINGH, SIRCAR SHUBHANKAR, BHAT SUDIPTA, R VINODHKUMARO, TIWARI RUCHI, SAH RANJIT, RABAAN ALIA, RODRIGUEZ-MORALES ALFONSOJ, DHAMA KULDEEP. Emerging Coronavirus Disease (COVID-19), a pandemic public health emergency with animal linkages: Current status update. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2020. [DOI: 10.56093/ijans.v90i3.102316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
After the appearance of first cases of ‘pneumonia of unknown origin’ in the Wuhan city, China, during late 2019, the disease progressed fast. Its cause was identified as a novel coronavirus, named provisionally 2019-nCoV. Subsequently, an official name was given as SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) by the International Committee on Taxonomy of Viruses (ICTV) study group. The World Health Organization (WHO) named the Coronavirus disease-2019 as COVID-19. The epidemics of COVID-2019 have been recorded over 113 countries/territories/areas apart from China and filched more than 4,292 humans, affecting severely around 1,18,326 cases in a short span. The status of COVID-2019 emergency revised by the WHO within 42 days from Public Health International Emergency (January 30, 2020) to a pandemic (March 11, 2020). Nonetheless, the case fatality rate (CFR) of the current epidemic is on the rise (between 2–4%), relatively is lower than the previous SARS-CoV (2002/2003) and MERS-CoV (2012) outbreaks. Even though investigations are on its way, the researchers across the globe have assumptions of animal-origin of current SARS-CoV-2. A recent case report provides evidence of mild COVID-2019 infection in a pet dog that acquired COVID-2019 infection from his owner in Hong Kong. The news on travellers associated spread across the globe have also put many countries on alert with the cancellation of tourist visa to all affected countries and postponement of events where international visits were required. A few diagnostic approaches, including quantitative and differential real-time polymerase chain reaction assays, have been recommended for the screening of the individuals at risk. In the absence of any selective vaccine against SARS-CoV-2, re-purposed drugs are advocated in many studies. This article discourse the current worldwide situation of COVID-2019 with information on virus, epidemiology, host, the role of animals, effective diagnosis, therapeutics, preventive and control approaches making people aware on the disease outcomes.
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44
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Nasir A, Shaukat K, Hameed IA, Luo S, Alam TM, Iqbal F. A Bibliometric Analysis of Corona Pandemic in Social Sciences: A Review of Influential Aspects and Conceptual Structure. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2020; 8:133377-133402. [PMID: 34812340 PMCID: PMC8545329 DOI: 10.1109/access.2020.3008733] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 07/06/2020] [Indexed: 05/07/2023]
Abstract
Corona pandemic has affected the whole world, and it is a highly researched area in biological sciences. As the current pandemic has affected countries socially and economically, the purpose of this bibliometric analysis is to provide a holistic review of the corona pandemic in the field of social sciences. This study aims to highlight significant, influential aspects, research streams, and themes. We have reviewed 395 journal articles related to coronavirus in the field of social sciences from 2003 to 2020. We have deployed 'biblioshiny' a web-interface of the 'bibliometrix 3.0' package of R-studio to conduct bibliometric analysis and visualization. In the field of social sciences, we have reported influential aspects of coronavirus literature. We have found that the 'Morbidity and Mortality Weekly Report' is the top journal. The core article of coronavirus literature is 'Guidelines for preventing health-care-associated pneumonia'. The most commonly used word, in titles, abstracts, author's keywords, and keywords plus, is 'SARS'. Top affiliation is 'The University of Hong Kong'. Hong Kong is a leading country based on citations, and the USA is on top based on total publications. We have used a conceptual framework to identify potential research streams and themes in coronavirus literature. Four research streams are found by deploying a co-occurrence network. These research streams are 'Social and economic effects of epidemic disease', 'Infectious disease calamities and control', 'Outbreak of COVID 19,' and 'Infectious diseases and the role of international organizations'. Finally, a thematic map is used to provide a holistic understanding by dividing significant themes into basic or transversal, emerging or declining, motor, highly developed, but isolated themes. These themes and subthemes have proposed future directions and critical areas of research.
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Affiliation(s)
- Adeel Nasir
- Department of Management SciencesLahore College for Women UniversityLahore54000Pakistan
| | - Kamran Shaukat
- School of Electrical Engineering and ComputingThe University of NewcastleCallaghanNSW2308Australia
- Punjab University College of Information Technology, University of the PunjabLahore54590Pakistan
| | - Ibrahim A. Hameed
- Department of ICT and Natural SciencesNorwegian University of Science and Technology7491TrondheimNorway
| | - Suhuai Luo
- School of Electrical Engineering and ComputingThe University of NewcastleCallaghanNSW2308Australia
| | - Talha Mahboob Alam
- Department of Computer ScienceUniversity of Engineering and TechnologyLahore54890Pakistan
| | - Farhat Iqbal
- Punjab University College of Information Technology, University of the PunjabLahore54590Pakistan
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45
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On the Coronaviruses and Their Associations with the Aquatic Environment and Wastewater. WATER 2020. [DOI: 10.3390/w12061598] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The outbreak of Coronavirus Disease 2019 (COVID-19), a severe respiratory disease caused by betacoronavirus SARS-CoV-2, in 2019 that further developed into a pandemic has received an unprecedented response from the scientific community and sparked a general research interest into the biology and ecology of Coronaviridae, a family of positive-sense single-stranded RNA viruses. Aquatic environments, lakes, rivers and ponds, are important habitats for bats and birds, which are hosts for various coronavirus species and strains and which shed viral particles in their feces. It is therefore of high interest to fully explore the role that aquatic environments may play in coronavirus spread, including cross-species transmissions. Besides the respiratory tract, coronaviruses pathogenic to humans can also infect the digestive system and be subsequently defecated. Considering this, it is pivotal to understand whether wastewater can play a role in their dissemination, particularly in areas with poor sanitation. This review provides an overview of the taxonomy, molecular biology, natural reservoirs and pathogenicity of coronaviruses; outlines their potential to survive in aquatic environments and wastewater; and demonstrates their association with aquatic biota, mainly waterfowl. It also calls for further, interdisciplinary research in the field of aquatic virology to explore the potential hotspots of coronaviruses in the aquatic environment and the routes through which they may enter it.
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46
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Shchelkanov MY, Popova AY, Dedkov VG, Akimkin VG, Maleyev VV. History of investigation and current classification of coronaviruses ( Nidovirales: Coronaviridae). ACTA ACUST UNITED AC 2020. [DOI: 10.15789/2220-7619-hoi-1412] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- M. Yu. Shchelkanov
- International Scientific and Educational Center for Biological Security of Rospotrebnadzor; Federal Scientific Center of East Asia Terrestrial Biodiversity, Far Eastern Branch of RAS; Center of Hygiene and Epidemiology in the Primorsky Territory
| | - A. Yu. Popova
- Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor); Russian Medical Academy of Continuing Professional Education
| | | | - V. G. Akimkin
- Central Research Institute of Epidemiology and Microbiology of Rospotrebnadzor
| | - V. V. Maleyev
- Central Research Institute of Epidemiology and Microbiology of Rospotrebnadzor
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47
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Molecular Evolution and Structural Mapping of N-Terminal Domain in Spike Gene of Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Viruses 2020; 12:v12050502. [PMID: 32370153 PMCID: PMC7290774 DOI: 10.3390/v12050502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 01/10/2023] Open
Abstract
The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a lethal zoonotic pathogen circulating in the Arabian Peninsula since 2012. There is no vaccine for MERS and anti-viral treatment is generally not applicable. We investigated the evolution of the MERS-CoV spike gene sequences and changes in viral loads over time from patients in Saudi Arabia from 2105-2017. All the MERS-CoV strains belonged to lineage 5, and showed high sequence homology (99.9%) to 2017 strains. Recombination analysis showed a potential recombination event in study strains from patients in Saudi Arabia. The spike gene showed eight amino acid substitutions, especially between the A1 and B5 lineage, and contained positively selected codon 1020. We also determined that the viral loads were significantly (p < 0.001) higher in fatal cases, and virus shedding was prolonged in some fatal cases beyond 21 days. The viral concentration peaked during the first week of illness, and the lower respiratory specimens had higher levels of MERS-CoV RNA. The presence of the diversifying selection and the topologies with the structural mapping of residues under purifying selection suggested that codon 1020 might have a role in the evolution of spike gene during the divergence of different lineages. This study will im-prove our understanding of the evolution of MERS-CoV, and also highlights the need for enhanced surveillance in humans and dromedaries. The presence of amino acid changes at the N-terminal domain and structural mapping of residues under positive selection at heptad repeat 1 provides better insight into the adaptive evolution of the spike gene and might have a potential role in virus-host tropism and pathogenesis.
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48
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Feasibility of Known RNA Polymerase Inhibitors as Anti-SARS-CoV-2 Drugs. Pathogens 2020; 9:pathogens9050320. [PMID: 32357471 PMCID: PMC7281371 DOI: 10.3390/pathogens9050320] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/22/2022] Open
Abstract
Coronaviruses (CoVs) are positive-stranded RNA viruses that infect humans and animals. Infection by CoVs such as HCoV-229E, -NL63, -OC43 and -HKU1 leads to the common cold, short lasting rhinitis, cough, sore throat and fever. However, CoVs such as Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and the newest SARS-CoV-2 (the causative agent of COVID-19) lead to severe and deadly diseases with mortality rates ranging between ~1 to 35% depending on factors such as age and pre-existing conditions. Despite continuous global health threats to humans, there are no approved vaccines or drugs targeting human CoVs, and the recent outbreak of COVID-19 emphasizes an urgent need for therapeutic interventions. Using computational and bioinformatics tools, here we present the feasibility of reported broad-spectrum RNA polymerase inhibitors as anti- SARS-CoV-2 drugs targeting its main RNA polymerase, suggesting that investigational and approved nucleoside RNA polymerase inhibitors have potential as anti-SARS-CoV-2 drugs. However, we note that it is also possible for SARS-CoV-2 to evolve and acquire drug resistance mutations against these nucleoside inhibitors.
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49
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Valencia DN. Brief Review on COVID-19: The 2020 Pandemic Caused by SARS-CoV-2. Cureus 2020; 12:e7386. [PMID: 32337113 PMCID: PMC7179986 DOI: 10.7759/cureus.7386] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 12/17/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the coronavirus disease of 2019 (COVID-19). First identified in Wuhan (Hubei, China) in December of 2019, it has since been declared a pandemic by the World Health Organization in March of 2020. In this study, we will provide a brief review of viral origin, identification, symptoms, transmission, diagnosis, and potential treatment strategies for the newly identified SARS-CoV-2 strain.
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50
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Yang YL, Meng F, Qin P, Herrler G, Huang YW, Tang YD. Trypsin promotes porcine deltacoronavirus mediating cell-to-cell fusion in a cell type-dependent manner. Emerg Microbes Infect 2020; 9:457-468. [PMID: 32090689 PMCID: PMC7054919 DOI: 10.1080/22221751.2020.1730245] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Porcine deltacoronavirus (PDCoV) is a newly emerging threat to the global porcine industry. PDCoV has been successfully isolated using various medium additives including trypsin, and although we know it is important for viral replication, the mechanism has not been fully elucidated. Here, we systematically investigated the role of trypsin in PDCoV replication including cell entry, cell-to-cell membrane fusion and virus release. Using pseudovirus entry assays, we demonstrated that PDCoV entry is not trypsin dependent. Furthermore, unlike porcine epidemic diarrhea virus (PEDV), in which trypsin is important for the release of virus from infected cells, PDCoV release was not affected by trypsin. We also demonstrated that trypsin promotes PDCoV replication by enhancing cell-to-cell membrane fusion. Most importantly, our study illustrates two distinct spreading patterns from infected cells to uninfected cells during PDCoV transmission, and the role of trypsin in PDCoV replication in cells with different virus spreading types. Overall, these results clarify that trypsin promotes PDCoV replication by mediating cell-to-cell fusion transmission but is not crucial for viral entry. This knowledge can potentially contribute to improvement of virus production efficiency in culture, not only for vaccine preparation but also to develop antiviral treatments.
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Affiliation(s)
- Yue-Lin Yang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Fandan Meng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Pan Qin
- Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Georg Herrler
- Institute for Virology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Yao-Wei Huang
- Institute of Preventive Veterinary Medicine and Key Laboratory of Animal Virology of Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
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