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Li W, Tahiri N. Host-Virus Cophylogenetic Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts. Viruses 2024; 16:1133. [PMID: 39066295 PMCID: PMC11281392 DOI: 10.3390/v16071133] [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: 06/04/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Bats, with their virus tolerance, social behaviors, and mobility, are reservoirs for emerging viruses, including coronaviruses (CoVs) known for genetic flexibility. Studying the cophylogenetic link between bats and CoVs provides vital insights into transmission dynamics and host adaptation. Prior research has yielded valuable insights into phenomena such as host switching, cospeciation, and other dynamics concerning the interaction between CoVs and bats. Nonetheless, a distinct gap exists in the current literature concerning a comparative cophylogenetic analysis focused on elucidating the contributions of sequence fragments to the co-evolution between hosts and viruses. In this study, we analyzed the cophylogenetic patterns of 69 host-virus connections. Among the 69 host-virus links examined, 47 showed significant cophylogeny based on ParaFit and PACo analyses, affirming strong associations. Focusing on two proteins, ORF1ab and spike, we conducted a comparative analysis of host and CoV phylogenies. For ORF1ab, the specific window ranged in multiple sequence alignment (positions 520-680, 770-870, 2930-3070, and 4910-5080) exhibited the lowest Robinson-Foulds (RF) distance (i.e., 84.62%), emphasizing its higher contribution in the cophylogenetic association. Similarly, within the spike region, distinct window ranges (positions 0-140, 60-180, 100-410, 360-550, and 630-730) displayed the lowest RF distance at 88.46%. Our analysis identified six recombination regions within ORF1ab (positions 360-1390, 550-1610, 680-1680, 700-1710, 2060-3090, and 2130-3250), and four within the spike protein (positions 10-510, 50-560, 170-710, and 230-730). The convergence of minimal RF distance regions with combination regions robustly affirms the pivotal role of recombination in viral adaptation to host selection pressures. Furthermore, horizontal gene transfer reveals prominent instances of partial gene transfer events, occurring not only among variants within the same host species but also crossing host species boundaries. This suggests a more intricate pattern of genetic exchange. By employing a multifaceted approach, our comprehensive strategy offers a nuanced understanding of the intricate interactions that govern the co-evolutionary dynamics between bat hosts and CoVs. This deeper insight enhances our comprehension of viral evolution and adaptation mechanisms, shedding light on the broader dynamics that propel viral diversity.
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Affiliation(s)
| | - Nadia Tahiri
- Department of Computer Science, University of Sherbrooke, 2500 Bd University, Sherbrooke, QC J1K 2R1, Canada;
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2
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Dunowska M, More GD, Biggs PJ, Cave NJ. Genomic analysis of canine pneumoviruses and canine respiratory coronavirus from New Zealand. N Z Vet J 2024; 72:191-200. [PMID: 38650102 DOI: 10.1080/00480169.2024.2339845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
AIMS To isolate canine respiratory coronavirus (CRCoV) and canine pneumovirus (CnPnV) in cell culture and to compare partial genomic sequences of CRCoV and CnPnV from New Zealand with those from other countries. METHODS Oropharyngeal swab samples from dogs affected by canine infectious respiratory disease syndrome that were positive for CnPnV (n = 15) or CRCoV (n = 1) by virus-specific reverse transcriptase quantitative PCR (RT-qPCR) in a previous study comprised the starting material. Virus isolation was performed in HRT-18 cells for CRCoV and RAW 264.7 and Vero cells for CnPnV. The entire sequence of CnPnV G protein (1,266 nucleotides) and most (8,063/9,707 nucleotides) of the 3' region of CRCoV that codes for 10 structural and accessory proteins were amplified and sequenced. The sequences were analysed and compared with other sequences available in GenBank using standard molecular tools including phylogenetic analysis. RESULTS Virus isolation was unsuccessful for both CRCoV and CnPnV. Pneumovirus G protein was amplified from 3/15 (20%) samples that were positive for CnPnV RNA by RT-qPCR. Two of these (NZ-048 and NZ-049) were 100% identical to each other, and 90.9% identical to the third one (NZ-007). Based on phylogenetic analysis of the G protein gene, CnPnV NZ-048 and NZ-049 clustered with sequences from the USA, Thailand and Italy in group A, and CnPnV NZ-007 clustered with sequences from the USA in group B. The characteristics of the predicted genes (length, position) and their putative protein products (size, predicted structure, presence of N- and O-glycosylation sites) of the New Zealand CRCoV sequence were consistent with those reported previously, except for the region located between open reading frame (ORF)3 (coding for S protein) and ORF6 (coding for E protein). The New Zealand virus was predicted to encode 5.9 kDa, 27 kDa and 12.7 kDa proteins, which differed from the putative coding capacity of this region reported for CRCoV from other countries. CONCLUSIONS This report represents the first characterisation of partial genomic sequences of CRCoV and CnPnV from New Zealand. Our results suggest that the population of CnPnV circulating in New Zealand is not homogeneous, and that the viruses from two clades described overseas are also present here. Limited conclusions can be made based on only one CRCoV sequence, but the putative differences in the coding capacity of New Zealand CRCoV support the previously reported variability of this region. The reasons for such variability and its biological implications need to be further elucidated.
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Affiliation(s)
- M Dunowska
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - G D More
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - P J Biggs
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - N J Cave
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
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3
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Zhang M, Qian B, Veit M. Engineering and characterizing porcine reproductive and respiratory syndrome virus with separated and tagged genes encoding the minor glycoproteins. Vet Microbiol 2024; 294:110125. [PMID: 38795404 DOI: 10.1016/j.vetmic.2024.110125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/13/2024] [Accepted: 05/18/2024] [Indexed: 05/27/2024]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major pathogen affecting pigs and belongs to the enveloped plus-stranded RNA virus family Arteriviridae. A unique feature of Arteriviruses is that the genes encoding the structural proteins overlap at their 3` and 5` ends. This impedes mutagenesis opportunities and precludes the binding of short peptides for antibody detection, as this would alter the amino acids encoded by the overlapping gene. In this study, we aimed to generate infectious PRRSV variants with separated genes encoding the minor glycoproteins Gp2, Gp3, and Gp4, accompanied by appended tags for detection. All recombinant genomes facilitate the release of infectious virus particles into the supernatant of transfected 293 T cells, as evidenced by immunofluorescence of infected MARC-145 cells using anti-nucleocapsid antibodies. Furthermore, expression of Gp2-Myc and Gp3-HA was confirmed through immunofluorescence and western blot analysis with tag-specific antibodies. However, after two passages of Gp2-Myc and Gp3-HA viruses, the appended tags were completely removed as indicated by sequencing the viral genome. Recombinant viruses with separated Gp2 and Gp3 genes remained stable for at least nine passages, while those with Gp3 and Gp4 genes separated reverted to wild type after only four passages. Notably, this virus exhibited significantly reduced titers in growth assays. Furthermore, we introduced a tag to the C-terminus of Gp4. The Gp4-HA virus was consistently stable for at least 10 passages, and the HA-tag was detectable by western blotting and immunofluorescence.
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Affiliation(s)
- Minze Zhang
- Free University Berlin, Faculty of Veterinary Medicine, Institute of Virology, Robert von Ostertagstr 7, Berlin 14163, Germany
| | - Bang Qian
- Free University Berlin, Faculty of Veterinary Medicine, Institute of Virology, Robert von Ostertagstr 7, Berlin 14163, Germany
| | - Michael Veit
- Free University Berlin, Faculty of Veterinary Medicine, Institute of Virology, Robert von Ostertagstr 7, Berlin 14163, Germany.
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4
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Ujike M, Suzuki T. Progress of research on coronaviruses and toroviruses in large domestic animals using reverse genetics systems. Vet J 2024; 305:106122. [PMID: 38641200 DOI: 10.1016/j.tvjl.2024.106122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/24/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
The generation of genetically engineered recombinant viruses from modified DNA/RNA is commonly referred to as reverse genetics, which allows the introduction of desired mutations into the viral genome. Reverse genetics systems (RGSs) are powerful tools for studying fundamental viral processes, mechanisms of infection, pathogenesis and vaccine development. However, establishing RGS for coronaviruses (CoVs) and toroviruses (ToVs), which have the largest genomes among vertebrate RNA viruses, is laborious and hampered by technical constraints. Hence, little research has focused on animal CoVs and ToVs using RGSs, especially in large domestic animals such as pigs and cattle. In the last decade, however, studies of porcine CoVs and bovine ToVs using RGSs have been reported. In addition, the coronavirus disease-2019 pandemic has prompted the development of new and simple CoV RGSs, which will accelerate RGS-based research on animal CoVs and ToVs. In this review, we summarise the general characteristics of CoVs and ToVs, the RGSs available for CoVs and ToVs and the progress made in the last decade in RGS-based research on porcine CoVs and bovine ToVs.
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Affiliation(s)
- Makoto Ujike
- Laboratory of Veterinary Infectious Diseases, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan; Research Center for Animal Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan.
| | - Tohru Suzuki
- Division of Zoonosis Research, Sapporo Research Station, National Institute of Animal Health, NARO, Sapporo, Hokkaido 062-0045, Japan
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Liao Y, Wang H, Liao H, Sun Y, Tan L, Song C, Qiu X, Ding C. Classification, replication, and transcription of Nidovirales. Front Microbiol 2024; 14:1291761. [PMID: 38328580 PMCID: PMC10847374 DOI: 10.3389/fmicb.2023.1291761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry,as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.
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Affiliation(s)
- Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huiyu Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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Lin CH, Hsieh FC, Wang M, Hsu C, Hsu HW, Yang CC, Yang CY, Wu HY. Identification of subgenomic mRNAs derived from the coronavirus 1a/1b protein gene: Implications for coronavirus transcription. Virology 2024; 589:109920. [PMID: 37952466 DOI: 10.1016/j.virol.2023.109920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023]
Abstract
Synthesis of coronavirus subgenomic mRNA (sgmRNA) is guided by the transcription regulatory sequence (TRS). sgmRNA derived from the body TRS (TRS-B) located at the 1a/1b protein gene is designated 1ab/sgmRNA. In the current study, we comprehensively identified the 1ab/sgmRNAs synthesized from TRS-Bs located at the 1a/1b protein genes of different coronavirus genera both in vitro and in vivo by RT‒PCR and sequencing. The results suggested that the degree of sequence homology between the leader TRS (TRS-L) and TRS-B may not be a decisive factor for 1ab/sgmRNA synthesis. This observation led us to revisit the coronavirus transcription mechanism and to propose that the disassociation of coronavirus polymerase from the viral genome may be a prerequisite for sgmRNA synthesis. Once the polymerase can disassociate at TRS-B, the sequence homology between TRS-L and TRS-B is important for sgmRNA synthesis. The study therefore extends our understanding of transcription mechanisms.
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Affiliation(s)
- Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Feng-Cheng Hsieh
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Meilin Wang
- Department of Microbiology and Immunology, School of Medicine, Chung-Shan Medical University and Clinical Laboratory, Chung-Shan Medical University Hospital, Taichung, 40201, Taiwan
| | - Chieh Hsu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hsuan-Wei Hsu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Chun-Chun Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Cheng-Yao Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan.
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan.
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7
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Lin CH, Chen B, Chao DY, Hsieh FC, Lai CC, Wang WC, Kuo CY, Yang CC, Hsu HW, Tam HMH, Wu HY. Biological characterization of coronavirus noncanonical transcripts in vitro and in vivo. Virol J 2023; 20:232. [PMID: 37828527 PMCID: PMC10571414 DOI: 10.1186/s12985-023-02201-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND In addition to the well-known coronavirus genomes and subgenomic mRNAs, the existence of other coronavirus RNA species, which are collectively referred to as noncanonical transcripts, has been suggested; however, their biological characteristics have not yet been experimentally validated in vitro and in vivo. METHODS To comprehensively determine the amounts, species and structures of noncanonical transcripts for bovine coronavirus in HRT-18 cells and mouse hepatitis virus A59, a mouse coronavirus, in mouse L cells and mice, nanopore direct RNA sequencing was employed. To experimentally validate the synthesis of noncanonical transcripts under regular infection, Northern blotting was performed. Both Northern blotting and nanopore direct RNA sequencing were also applied to examine the reproducibility of noncanonical transcripts. In addition, Northern blotting was also employed to determine the regulatory features of noncanonical transcripts under different infection conditions, including different cells, multiplicities of infection (MOIs) and coronavirus strains. RESULTS In the current study, we (i) experimentally determined that coronavirus noncanonical transcripts were abundantly synthesized, (ii) classified the noncanonical transcripts into seven populations based on their structures and potential synthesis mechanisms, (iii) showed that the species and amounts of the noncanonical transcripts were reproducible during regular infection but regulated in altered infection environments, (iv) revealed that coronaviruses may employ various mechanisms to synthesize noncanonical transcripts, and (v) found that the biological characteristics of coronavirus noncanonical transcripts were similar between in vitro and in vivo conditions. CONCLUSIONS The biological characteristics of noncanonical coronavirus transcripts were experimentally validated for the first time. The identified features of noncanonical transcripts in terms of abundance, reproducibility and variety extend the current model for coronavirus gene expression. The capability of coronaviruses to regulate the species and amounts of noncanonical transcripts may contribute to the pathogenesis of coronaviruses during infection, posing potential challenges in disease control. Thus, the biology of noncanonical transcripts both in vitro and in vivo revealed here can provide a database for biological research, contributing to the development of antiviral strategies.
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Affiliation(s)
- Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - BoJia Chen
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, 40227, Taiwan
| | - Day-Yu Chao
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, 40227, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Feng-Cheng Hsieh
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, College of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Wei-Chen Wang
- Institute of Molecular Biology, College of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Cheng-Yu Kuo
- Institute of Molecular Biology, College of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Chun-Chun Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hsuan-Wei Hsu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hon-Man-Herman Tam
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan.
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Wang C, Chen Y, Hu S, Liu X. Insights into the function of ESCRT and its role in enveloped virus infection. Front Microbiol 2023; 14:1261651. [PMID: 37869652 PMCID: PMC10587442 DOI: 10.3389/fmicb.2023.1261651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/20/2023] [Indexed: 10/24/2023] Open
Abstract
The endosomal sorting complex required for transport (ESCRT) is an essential molecular machinery in eukaryotic cells that facilitates the invagination of endosomal membranes, leading to the formation of multivesicular bodies (MVBs). It participates in various cellular processes, including lipid bilayer remodeling, cytoplasmic separation, autophagy, membrane fission and re-modeling, plasma membrane repair, as well as the invasion, budding, and release of certain enveloped viruses. The ESCRT complex consists of five complexes, ESCRT-0 to ESCRT-III and VPS4, along with several accessory proteins. ESCRT-0 to ESCRT-II form soluble complexes that shuttle between the cytoplasm and membranes, mainly responsible for recruiting and transporting membrane proteins and viral particles, as well as recruiting ESCRT-III for membrane neck scission. ESCRT-III, a soluble monomer, directly participates in vesicle scission and release, while VPS4 hydrolyzes ATP to provide energy for ESCRT-III complex disassembly, enabling recycling. Studies have confirmed the hijacking of ESCRT complexes by enveloped viruses to facilitate their entry, replication, and budding. Recent research has focused on the interaction between various components of the ESCRT complex and different viruses. In this review, we discuss how different viruses hijack specific ESCRT regulatory proteins to impact the viral life cycle, aiming to explore commonalities in the interaction between viruses and the ESCRT system.
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Affiliation(s)
- Chunxuan Wang
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yu Chen
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Shunlin Hu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
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Yuan X, Zhang X, Wang H, Mao X, Sun Y, Tan L, Song C, Qiu X, Ding C, Liao Y. The Ubiquitin-Proteasome System Facilitates Membrane Fusion and Uncoating during Coronavirus Entry. Viruses 2023; 15:2001. [PMID: 37896778 PMCID: PMC10610886 DOI: 10.3390/v15102001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/08/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Although the involvement of the ubiquitin-proteasome system (UPS) in several coronavirus-productive infections has been reported, whether the UPS is required for infectious bronchitis virus (IBV) and porcine epidemic diarrhea virus (PEDV) infections is unclear. In this study, the role of UPS in the IBV and PEDV life cycles was investigated. When the UPS was suppressed by pharmacological inhibition at the early infection stage, IBV and PEDV infectivity were severely impaired. Further study showed that inhibition of UPS did not change the internalization of virus particles; however, by using R18 and DiOC-labeled virus particles, we found that inhibition of UPS prevented the IBV and PEDV membrane fusion with late endosomes or lysosomes. In addition, proteasome inhibitors blocked the degradation of the incoming viral protein N, suggesting the uncoating process and genomic RNA release were suppressed. Subsequently, the initial translation of genomic RNA was blocked. Thus, UPS may target the virus-cellular membrane fusion to facilitate the release of incoming viruses from late endosomes or lysosomes, subsequently blocking the following virus uncoating, initial translation, and replication events. Similar to the observation of proteasome inhibitors, ubiquitin-activating enzyme E1 inhibitor PYR-41 also impaired the entry of IBV, enhanced the accumulation of ubiquitinated proteins, and depleted mono-ubiquitin. In all, this study reveals an important role of UPS in coronavirus entry by preventing membrane fusion and identifies UPS as a potential target for developing antiviral therapies for coronavirus.
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Affiliation(s)
- Xiao Yuan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (X.Y.); (X.Z.); (H.W.); (X.M.); (Y.S.); (L.T.); (C.S.); (X.Q.); (C.D.)
| | - Xiaoman Zhang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (X.Y.); (X.Z.); (H.W.); (X.M.); (Y.S.); (L.T.); (C.S.); (X.Q.); (C.D.)
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (X.Y.); (X.Z.); (H.W.); (X.M.); (Y.S.); (L.T.); (C.S.); (X.Q.); (C.D.)
| | - Xiang Mao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (X.Y.); (X.Z.); (H.W.); (X.M.); (Y.S.); (L.T.); (C.S.); (X.Q.); (C.D.)
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (X.Y.); (X.Z.); (H.W.); (X.M.); (Y.S.); (L.T.); (C.S.); (X.Q.); (C.D.)
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (X.Y.); (X.Z.); (H.W.); (X.M.); (Y.S.); (L.T.); (C.S.); (X.Q.); (C.D.)
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (X.Y.); (X.Z.); (H.W.); (X.M.); (Y.S.); (L.T.); (C.S.); (X.Q.); (C.D.)
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (X.Y.); (X.Z.); (H.W.); (X.M.); (Y.S.); (L.T.); (C.S.); (X.Q.); (C.D.)
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (X.Y.); (X.Z.); (H.W.); (X.M.); (Y.S.); (L.T.); (C.S.); (X.Q.); (C.D.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (X.Y.); (X.Z.); (H.W.); (X.M.); (Y.S.); (L.T.); (C.S.); (X.Q.); (C.D.)
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10
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Scutari R, Renica S, Cento V, Nava A, Sammartino JC, Ferrari A, Pani A, Merli M, Fanti D, Vismara C, Scaglione F, Puoti M, Bandera A, Gori A, Piralla A, Baldanti F, Perno CF, Alteri C. Quantitative SARS-CoV-2 subgenomic RNA as a surrogate marker for viral infectivity: Comparison between culture isolation and direct sgRNA quantification. PLoS One 2023; 18:e0291120. [PMID: 37656746 PMCID: PMC10473502 DOI: 10.1371/journal.pone.0291120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 08/22/2023] [Indexed: 09/03/2023] Open
Abstract
Detection of subgenomic (sg) SARS-CoV-2 RNAs are frequently used as a correlate of viral infectiousness, but few data about correlation between sg load and viable virus are available. Here, we defined concordance between culture isolation and E and N sgRNA quantification by ddPCR assays in 51 nasopharyngeal swabs collected from SARS-CoV-2 positive hospitalized patients. Among the 51 samples, 14 were SARS-CoV-2 culture-positive and 37 were negative. According to culture results, the sensitivity and specificity of E and N sgRNA assays were 100% and 100%, and 84% and 86%, respectively. ROC analysis showed that the best E and N cut-offs to predict positive culture isolation were 32 and 161 copies/mL respectively, with an AUC (95% CI) of 0.96 (0.91-1.00) and 0.96 (0.92-1.00), and a diagnostic accuracy of 88% and 92%, respectively. Even if no significant correlations were observed between sgRNA amount and clinical presentation, a higher number of moderate/severe cases and lower number of days from symptoms onset characterized patients with sgRNA equal to or higher than sgRNA cut-offs. Overall, this study suggests that SARS-CoV-2 sgRNA quantification could be helpful to estimate the replicative activity of SARS-CoV-2 and can represent a valid surrogate marker to efficiently recognize patients with active infection. The inclusion of this assay in available SARS-CoV-2 diagnostics procedure might help in optimizing fragile patients monitoring and management.
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Affiliation(s)
- Rossana Scutari
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
- Multimodal Research Area, Bambino Gesù Children Hospital IRCCS, Rome, Italy
| | - Silvia Renica
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Valeria Cento
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IRCSS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Alice Nava
- Chemical-Clinical and Microbiological Analysis, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | - Alessandro Ferrari
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Arianna Pani
- Chemical-Clinical and Microbiological Analysis, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Marco Merli
- Infectious Diseases Unit, Azienda Socio-Sanitaria Territoriale (ASST) Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Diana Fanti
- Chemical-Clinical and Microbiological Analysis, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Chiara Vismara
- Chemical-Clinical and Microbiological Analysis, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Francesco Scaglione
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
- Chemical-Clinical and Microbiological Analysis, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Massimo Puoti
- Infectious Diseases Unit, Azienda Socio-Sanitaria Territoriale (ASST) Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Alessandra Bandera
- Infectious Diseases Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | | | - Claudia Alteri
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
- Multimodal Research Area, Bambino Gesù Children Hospital IRCCS, Rome, Italy
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11
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Flies AS, Flies EJ, Fountain-Jones NM, Musgrove RE, Hamede RK, Philips A, Perrott MRF, Dunowska M. Wildlife nidoviruses: biology, epidemiology, and disease associations of selected nidoviruses of mammals and reptiles. mBio 2023; 14:e0071523. [PMID: 37439571 PMCID: PMC10470586 DOI: 10.1128/mbio.00715-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023] Open
Abstract
Wildlife is the source of many emerging infectious diseases. Several viruses from the order Nidovirales have recently emerged in wildlife, sometimes with severe consequences for endangered species. The order Nidovirales is currently classified into eight suborders, three of which contain viruses of vertebrates. Vertebrate coronaviruses (suborder Cornidovirineae) have been extensively studied, yet the other major suborders have received less attention. The aim of this minireview was to summarize the key findings from the published literature on nidoviruses of vertebrate wildlife from two suborders: Arnidovirineae and Tornidovirineae. These viruses were identified either during investigations of disease outbreaks or through molecular surveys of wildlife viromes, and include pathogens of reptiles and mammals. The available data on key biological features, disease associations, and pathology are presented, in addition to data on the frequency of infections among various host populations, and putative routes of transmission. While nidoviruses discussed here appear to have a restricted in vivo host range, little is known about their natural life cycle. Observational field-based studies outside of the mortality events are needed to facilitate an understanding of the virus-host-environment interactions that lead to the outbreaks. Laboratory-based studies are needed to understand the pathogenesis of diseases caused by novel nidoviruses and their evolutionary histories. Barriers preventing research progress include limited funding and the unavailability of virus- and host-specific reagents. To reduce mortalities in wildlife and further population declines, proactive development of expertise, technologies, and networks should be developed. These steps would enable effective management of future outbreaks and support wildlife conservation.
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Affiliation(s)
- Andrew S. Flies
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Emily J. Flies
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- Healthy Landscapes Research Group, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Ruth E. Musgrove
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo K. Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Annie Philips
- Natural Resources and Environment Tasmania, Hobart, Tasmania, Australia
| | | | - Magdalena Dunowska
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
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12
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François S, Nazki S, Vickers SH, Fournié G, Perrins CM, Broadbent AJ, Pybus OG, Hill SC. Genetic diversity, recombination and cross-species transmission of a waterbird gammacoronavirus in the wild. J Gen Virol 2023; 104. [PMID: 37589541 DOI: 10.1099/jgv.0.001883] [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] [Indexed: 08/18/2023] Open
Abstract
Viruses emerging from wildlife can cause outbreaks in humans and domesticated animals. Predicting the emergence of future pathogens and mitigating their impacts requires an understanding of what shapes virus diversity and dynamics in wildlife reservoirs. In order to better understand coronavirus ecology in wild species, we sampled birds within a coastal freshwater lagoon habitat across 5 years, focussing on a large population of mute swans (Cygnus olor) and the diverse species that they interact with. We discovered and characterised the full genome of a divergent gammacoronavirus belonging to the Goose coronavirus CB17 species. We investigated the genetic diversity and dynamics of this gammacoronavirus using untargeted metagenomic sequencing of 223 faecal samples from swans of known age and sex, and RT-PCR screening of 1632 additional bird samples. The virus circulated persistently within the bird community; virus prevalence in mute swans exhibited seasonal variations, but did not change with swan age-class or epidemiological year. One whole genome was fully characterised, and revealed that the virus originated from a recombination event involving an undescribed gammacoronavirus species. Multiple lineages of this gammacoronavirus co-circulated within our study population. Viruses from this species have recently been detected in aquatic birds from both the Anatidae and Rallidae families, implying that host species habitat sharing may be important in shaping virus host range. As the host range of the Goose coronavirus CB17 species is not limited to geese, we propose that this species name should be updated to 'Waterbird gammacoronavirus 1'. Non-invasive sampling of bird coronaviruses may provide a tractable model system for understanding the evolutionary and cross-species dynamics of coronaviruses.
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Affiliation(s)
- Sarah François
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
| | - Salik Nazki
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
| | - Stephen H Vickers
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Guillaume Fournié
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Gènes-Champanelle, France
| | | | - Andrew J Broadbent
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD20742, USA
| | - Oliver G Pybus
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Sarah C Hill
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
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13
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Fritch EJ, Sanders W, Sims AC, Herring LE, Barker NK, Schepmoes AA, Weitz KK, Texier JR, Dittmer DP, Graves LM, Smith RD, Waters KM, Moorman NJ, Baric RS, Graham RL. Metatranscriptomics analysis reveals a novel transcriptional and translational landscape during Middle East respiratory syndrome coronavirus infection. iScience 2023; 26:106780. [PMID: 37193127 PMCID: PMC10152751 DOI: 10.1016/j.isci.2023.106780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/31/2023] [Accepted: 04/25/2023] [Indexed: 05/18/2023] Open
Abstract
Among all RNA viruses, coronavirus RNA transcription is the most complex and involves a process termed "discontinuous transcription" that results in the production of a set of 3'-nested, co-terminal genomic and subgenomic RNAs during infection. While the expression of the classic canonical set of subgenomic RNAs depends on the recognition of a 6- to 7-nt transcription regulatory core sequence (TRS), here, we use deep sequence and metagenomics analysis strategies and show that the coronavirus transcriptome is even more vast and more complex than previously appreciated and involves the production of leader-containing transcripts that have canonical and noncanonical leader-body junctions. Moreover, by ribosome protection and proteomics analyses, we show that both positive- and negative-sense transcripts are translationally active. The data support the hypothesis that the coronavirus proteome is much vaster than previously noted in the literature.
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Affiliation(s)
- Ethan J. Fritch
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wes Sanders
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Amy C. Sims
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura E. Herring
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Michael Hooker Proteomics Core Facility, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie K. Barker
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Michael Hooker Proteomics Core Facility, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Athena A. Schepmoes
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99394, USA
| | - Karl K. Weitz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99394, USA
| | - Jordan R. Texier
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dirk P. Dittmer
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lee M. Graves
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Michael Hooker Proteomics Core Facility, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Richard D. Smith
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99394, USA
| | - Katrina M. Waters
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99394, USA
| | - Nathaniel J. Moorman
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ralph S. Baric
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rachel L. Graham
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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14
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Mah MG, Linster M, Low DHW, Zhuang Y, Jayakumar J, Samsudin F, Wong FY, Bond PJ, Mendenhall IH, Su YCF, Smith GJD. Spike-Independent Infection of Human Coronavirus 229E in Bat Cells. Microbiol Spectr 2023; 11:e0348322. [PMID: 37199653 PMCID: PMC10269751 DOI: 10.1128/spectrum.03483-22] [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: 09/06/2022] [Accepted: 04/17/2023] [Indexed: 05/19/2023] Open
Abstract
Bats are the reservoir for numerous human pathogens, including coronaviruses. Despite many coronaviruses having descended from bat ancestors, little is known about virus-host interactions and broader evolutionary history involving bats. Studies have largely focused on the zoonotic potential of coronaviruses with few infection experiments conducted in bat cells. To determine genetic changes derived from replication in bat cells and possibly identify potential novel evolutionary pathways for zoonotic virus emergence, we serially passaged six human 229E isolates in a newly established Rhinolophus lepidus (horseshoe bat) kidney cell line. Here, we observed extensive deletions within the spike and open reading frame 4 (ORF4) genes of five 229E viruses after passaging in bat cells. As a result, spike protein expression and infectivity of human cells was lost in 5 of 6 viruses, but the capability to infect bat cells was maintained. Only viruses that expressed the spike protein could be neutralized by 229E spike-specific antibodies in human cells, whereas there was no neutralizing effect on viruses that did not express the spike protein inoculated on bat cells. However, one isolate acquired an early stop codon, abrogating spike expression but maintaining infection in bat cells. After passaging this isolate in human cells, spike expression was restored due to acquisition of nucleotide insertions among virus subpopulations. Spike-independent infection of human coronavirus 229E may provide an alternative mechanism for viral maintenance in bats that does not rely on the compatibility of viral surface proteins and known cellular entry receptors. IMPORTANCE Many viruses, including coronaviruses, originated from bats. Yet, we know little about how these viruses switch between hosts and enter human populations. Coronaviruses have succeeded in establishing in humans at least five times, including endemic coronaviruses and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In an approach to identify requirements for host switches, we established a bat cell line and adapted human coronavirus 229E viruses by serial passage. The resulting viruses lost their spike protein but maintained the ability to infect bat cells, but not human cells. Maintenance of 229E viruses in bat cells appears to be independent of a canonical spike receptor match, which in turn might facilitate cross-species transmission in bats.
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Affiliation(s)
- Marcus G. Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Martin Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Dolyce H. W. Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yan Zhuang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jayanthi Jayakumar
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Firdaus Samsudin
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore
| | - Foong Ying Wong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Gavin J. D. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
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15
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Gul I, Hassan A, Haq E, Ahmad SM, Shah RA, Ganai NA, Chikan NA, Abdul-Careem MF, Shabir N. An Investigation of the Antiviral Potential of Phytocompounds against Avian Infectious Bronchitis Virus through Template-Based Molecular Docking and Molecular Dynamics Simulation Analysis. Viruses 2023; 15:v15040847. [PMID: 37112828 PMCID: PMC10144825 DOI: 10.3390/v15040847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Vaccination is widely used to control Infectious Bronchitis in poultry; however, the limited cross-protection and safety issues associated with these vaccines can lead to vaccination failures. Keeping these limitations in mind, the current study explored the antiviral potential of phytocompounds against the Infectious Bronchitis virus using in silico approaches. A total of 1300 phytocompounds derived from fourteen botanicals were screened for their potential ability to inhibit the main protease, papain-like protease or RNA-dependent RNA–polymerase of the virus. The study identified Methyl Rosmarinate, Cianidanol, Royleanone, and 6,7-Dehydroroyleanone as dual-target inhibitors against any two of the key proteins. At the same time, 7-alpha-Acetoxyroyleanone from Rosmarinus officinalis was found to be a multi-target protein inhibitor against all three proteins. The potential multi-target inhibitor was subjected to molecular dynamics simulations to assess the stability of the protein–ligand complexes along with the corresponding reference ligands. The findings specified stable interactions of 7-alpha-Acetoxyroyleanone with the protein targets. The results based on the in silico study indicate that the phytocompounds can potentially inhibit the essential proteins of the Infectious Bronchitis virus; however, in vitro and in vivo studies are required for validation. Nevertheless, this study is a significant step in exploring the use of botanicals in feed to control Infectious Bronchitis infections in poultry.
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Affiliation(s)
- Irfan Gul
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
- Department of Biotechnology, University of Kashmir, Srinagar 190006, India
| | - Amreena Hassan
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
- Department of Biotechnology, University of Kashmir, Srinagar 190006, India
| | - Ehtishamul Haq
- Department of Biotechnology, University of Kashmir, Srinagar 190006, India
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
| | - Riaz Ahmad Shah
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
| | - Nazir Ahmad Ganai
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
| | - Naveed Anjum Chikan
- Division of Computational Biology, Daskdan Innovations, Pvt. Ltd., Kashmir 190006, India
| | - Mohamed Faizal Abdul-Careem
- Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
- Correspondence: (M.F.A.-C.); (N.S.)
| | - Nadeem Shabir
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
- Correspondence: (M.F.A.-C.); (N.S.)
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16
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Dunowska M. Cross-species transmission of coronaviruses with a focus on severe acute respiratory syndrome coronavirus 2 infection in animals: a review for the veterinary practitioner. N Z Vet J 2023:1-13. [PMID: 36927253 DOI: 10.1080/00480169.2023.2191349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
AbstractIn 2019 a novel coronavirus termed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged from an unidentified source and spread rapidly among humans worldwide. While many human infections are mild, some result in severe clinical disease that in a small proportion of infected people is fatal. The pandemic spread of SARS-CoV-2 has been facilitated by efficient human-to-human transmission of the virus, with no data to indicate that animals contributed to this global health crisis. However, a range of domesticated and wild animals are also susceptible to SARS-CoV-2 infection under both experimental and natural conditions. Humans are presumed to be the source of most animal infections thus far, although natural transmission between mink and between free-ranging deer has occurred, and occasional natural transmission between cats cannot be fully excluded. Considering the ongoing circulation of the virus among people, together with its capacity to evolve through mutation and recombination, the risk of the emergence of animal-adapted variants is not negligible. If such variants remain infectious to humans, this could lead to the establishment of an animal reservoir for the virus, which would complicate control efforts. As such, minimising human-to-animal transmission of SARS-CoV-2 should be considered as part of infection control efforts. The aim of this review is to summarise what is currently known about the species specificity of animal coronaviruses, with an emphasis on SARS-CoV-2, in the broader context of factors that facilitate cross-species transmission of viruses.
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Affiliation(s)
- M Dunowska
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
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17
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Sattar S, Kabat J, Jerome K, Feldmann F, Bailey K, Mehedi M. Nuclear translocation of spike mRNA and protein is a novel feature of SARS-CoV-2. Front Microbiol 2023; 14:1073789. [PMID: 36778849 PMCID: PMC9909199 DOI: 10.3389/fmicb.2023.1073789] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/12/2023] [Indexed: 01/27/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes severe pathophysiology in vulnerable older populations and appears to be highly pathogenic and more transmissible than other coronaviruses. The spike (S) protein appears to be a major pathogenic factor that contributes to the unique pathogenesis of SARS-CoV-2. Although the S protein is a surface transmembrane type 1 glycoprotein, it has been predicted to be translocated into the nucleus due to the novel nuclear localization signal (NLS) "PRRARSV," which is absent from the S protein of other coronaviruses. Indeed, S proteins translocate into the nucleus in SARS-CoV-2-infected cells. S mRNAs also translocate into the nucleus. S mRNA colocalizes with S protein, aiding the nuclear translocation of S mRNA. While nuclear translocation of nucleoprotein (N) has been shown in many coronaviruses, the nuclear translocation of both S mRNA and S protein reveals a novel feature of SARS-CoV-2.
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Affiliation(s)
- Sarah Sattar
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
| | - Juraj Kabat
- Biological Imaging Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kailey Jerome
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
| | - Friederike Feldmann
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Kristina Bailey
- Department of Internal Medicine, Pulmonary, Critical Care, and Sleep and Allergy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Masfique Mehedi
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
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18
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Lamkiewicz K, Esquivel Gomez LR, Kühnert D, Marz M. Genome Structure, Life Cycle, and Taxonomy of Coronaviruses and the Evolution of SARS-CoV-2. Curr Top Microbiol Immunol 2023; 439:305-339. [PMID: 36592250 DOI: 10.1007/978-3-031-15640-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Coronaviruses have a broad host range and exhibit high zoonotic potential. In this chapter, we describe their genomic organization in terms of encoded proteins and provide an introduction to the peculiar discontinuous transcription mechanism. Further, we present evolutionary conserved genomic RNA secondary structure features, which are involved in the complex replication mechanism. With a focus on computational methods, we review the emergence of SARS-CoV-2 starting with the 2019 strains. In that context, we also discuss the debated hypothesis of whether SARS-CoV-2 was created in a laboratory. We focus on the molecular evolution and the epidemiological dynamics of this recently emerged pathogen and we explain how variants of concern are detected and characterised. COVID-19, the disease caused by SARS-CoV-2, can spread through different transmission routes and also depends on a number of risk factors. We describe how current computational models of viral epidemiology, or more specifically, phylodynamics, have facilitated and will continue to enable a better understanding of the epidemic dynamics of SARS-CoV-2.
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Affiliation(s)
- Kevin Lamkiewicz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743, Jena, Germany
- European Virus Bioinformatics Center, Leutragraben 1, 07743, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103, Leipzig, Germany
| | - Luis Roger Esquivel Gomez
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745, Jena, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745, Jena, Germany
- European Virus Bioinformatics Center, Leutragraben 1, 07743, Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743, Jena, Germany.
- European Virus Bioinformatics Center, Leutragraben 1, 07743, Jena, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103, Leipzig, Germany.
- FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745, Jena, Germany.
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19
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Shannon A, Sama B, Gauffre P, Guez T, Debart F, Vasseur JJ, Decroly E, Canard B, Ferron F. A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome. Nucleic Acids Res 2022; 50:11186-11198. [PMID: 36265859 DOI: 10.1093/nar/gkac876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 09/29/2022] [Indexed: 11/12/2022] Open
Abstract
The order Nidovirales is a diverse group of (+)RNA viruses, with a common genome organization and conserved set of replicative and editing enzymes. In particular, RNA methyltransferases play a central role in mRNA stability and immune escape. However, their presence and distribution in different Nidovirales families is not homogeneous. In Coronaviridae, the best characterized family, two distinct methytransferases perform methylation of the N7-guanine and 2'-OH of the RNA-cap to generate a cap-1 structure (m7GpppNm). The genes of both of these enzymes are located in the ORF1b genomic region. While 2'-O-MTases can be identified for most other families based on conservation of both sequence motifs and genetic loci, identification of the N7-guanine methyltransferase has proved more challenging. Recently, we identified a putative N7-MTase domain in the ORF1a region (N7-MT-1a) of certain members of the large genome Tobaniviridae family. Here, we demonstrate that this domain indeed harbors N7-specific methyltransferase activity. We present its structure as the first N7-specific Rossmann-fold (RF) MTase identified for (+)RNA viruses, making it remarkably different from that of the known Coronaviridae ORF1b N7-MTase gene. We discuss the evolutionary implications of such an appearance in this unexpected location in the genome, which introduces a split-off in the classification of Tobaniviridae.
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Affiliation(s)
- Ashleigh Shannon
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Bhawna Sama
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Pierre Gauffre
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Théo Guez
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Françoise Debart
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | | | - Etienne Decroly
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Bruno Canard
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - François Ferron
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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20
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Sattar S, Kabat J, Jerome K, Feldmann F, Bailey K, Mehedi M. Nuclear translocation of spike mRNA and protein is a novel pathogenic feature of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.27.509633. [PMID: 36203551 PMCID: PMC9536038 DOI: 10.1101/2022.09.27.509633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes severe pathophysiology in vulnerable older populations and appears to be highly pathogenic and more transmissible than SARS-CoV or MERS-CoV [1, 2]. The spike (S) protein appears to be a major pathogenic factor that contributes to the unique pathogenesis of SARS-CoV-2. Although the S protein is a surface transmembrane type 1 glycoprotein, it has been predicted to be translocated into the nucleus due to the novel nuclear localization signal (NLS) "PRRARSV", which is absent from the S protein of other coronaviruses. Indeed, S proteins translocate into the nucleus in SARS-CoV-2-infected cells. To our surprise, S mRNAs also translocate into the nucleus. S mRNA colocalizes with S protein, aiding the nuclear translocation of S mRNA. While nuclear translocation of nucleoprotein (N) has been shown in many coronaviruses, the nuclear translocation of both S mRNA and S protein reveals a novel pathogenic feature of SARS-CoV-2. Author summary One of the novel sequence insertions resides at the S1/S2 boundary of Spike (S) protein and constitutes a functional nuclear localization signal (NLS) motif "PRRARSV", which may supersede the importance of previously proposed polybasic furin cleavage site "RRAR". Indeed, S protein's NLS-driven nuclear translocation and its possible role in S mRNA's nuclear translocation reveal a novel pathogenic feature of SARS-CoV-2.
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Affiliation(s)
- Sarah Sattar
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, USA
| | - Juraj Kabat
- Biological Imaging Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kailey Jerome
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, USA
| | - Friederike Feldmann
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kristina Bailey
- Department of Internal Medicine, Pulmonary, Critical Care, and Sleep and Allergy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Masfique Mehedi
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND, USA
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21
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Deming ME, Dong TQ, Agrawal V, Mills MG, Huang MLW, Greninger AL, Jerome KR, Wener MH, Paasche-Orlow MK, Kissinger P, Luk A, Hoffman RM, Stewart J, Kottkamp AC, Bershteyn A, Chu HY, Stankiewicz Karita HC, Johnston CM, Wald A, Barnabas R, Brown ER, Neuzil KM. Detection and Kinetics of Subgenomic Severe Acute Respiratory Syndrome Coronavirus 2 RNA Viral Load in Longitudinal Diagnostic RNA-Positive Samples. J Infect Dis 2022; 226:788-796. [PMID: 35150571 PMCID: PMC8903395 DOI: 10.1093/infdis/jiac048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/09/2022] [Indexed: 11/14/2022] Open
Abstract
While detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by diagnostic reverse-transcription polymerase chain reaction (RT-PCR) is highly sensitive for viral RNA, the nucleic acid amplification of subgenomic RNAs (sgRNAs) that are the product of viral replication may more accurately identify replication. We characterized the diagnostic RNA and sgRNA detection by RT-PCR from nasal swab samples collected daily by participants in postexposure prophylaxis or treatment studies for SARS-CoV-2. Among 1932 RT-PCR-positive swab samples with sgRNA tests, 40% (767) had detectable sgRNA. Above a diagnostic RNA viral load (VL) threshold of 5.1 log10 copies/mL, 96% of samples had detectable sgRNA with VLs that followed a linear trend. The trajectories of diagnostic RNA and sgRNA VLs differed, with 80% peaking on the same day but duration of sgRNA detection being shorter (8 vs 14 days). With a large sample of daily swab samples we provide comparative sgRNA kinetics and a diagnostic RNA threshold that correlates with replicating virus independent of symptoms or duration of illness.
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Affiliation(s)
- Meagan E Deming
- The Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Tracy Q Dong
- Vaccine and Infectious Disease Division, Fred Hutchinson, Cancer Research Center, Seattle, Washington, USA
| | - Vaidehi Agrawal
- The Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Margaret G Mills
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Meei Li W Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson, Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson, Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Mark H Wener
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Michael K Paasche-Orlow
- Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Patricia Kissinger
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine
| | - Alfred Luk
- Section of Infectious Diseases, John W. Deming, Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Risa M Hoffman
- Division of Infectious Diseases, David Geffen School of Medicine at the University of California, Los Angeles, California, USA
| | - Jenell Stewart
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Division of Infectious Diseases & Immunology, Department of Medicine, New York University Grossman, School of Medicine, New York, New York, USA
| | - Angelica C Kottkamp
- Department of Population Health; New York University, Grossman School of Medicine, New York, New York, USA
| | - Anna Bershteyn
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Helen Y Chu
- Division of Infectious Diseases & Immunology, Department of Medicine, New York University Grossman, School of Medicine, New York, New York, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Christine M Johnston
- Vaccine and Infectious Disease Division, Fred Hutchinson, Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Division of Infectious Diseases & Immunology, Department of Medicine, New York University Grossman, School of Medicine, New York, New York, USA
| | - Anna Wald
- Vaccine and Infectious Disease Division, Fred Hutchinson, Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Division of Infectious Diseases & Immunology, Department of Medicine, New York University Grossman, School of Medicine, New York, New York, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Ruanne Barnabas
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Division of Infectious Diseases & Immunology, Department of Medicine, New York University Grossman, School of Medicine, New York, New York, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Elizabeth R Brown
- Vaccine and Infectious Disease Division, Fred Hutchinson, Cancer Research Center, Seattle, Washington, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Kathleen M Neuzil
- The Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
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22
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Otieno JR, Cherry JL, Spiro DJ, Nelson MI, Trovão NS. Origins and Evolution of Seasonal Human Coronaviruses. Viruses 2022; 14:1551. [PMID: 35891531 PMCID: PMC9320361 DOI: 10.3390/v14071551] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Four seasonal human coronaviruses (sHCoVs) are endemic globally (229E, NL63, OC43, and HKU1), accounting for 5-30% of human respiratory infections. However, the epidemiology and evolution of these CoVs remain understudied due to their association with mild symptomatology. Using a multigene and complete genome analysis approach, we find the evolutionary histories of sHCoVs to be highly complex, owing to frequent recombination of CoVs including within and between sHCoVs, and uncertain, due to the under sampling of non-human viruses. The recombination rate was highest for 229E and OC43 whereas substitutions per recombination event were highest in NL63 and HKU1. Depending on the gene studied, OC43 may have ungulate, canine, or rabbit CoV ancestors. 229E may have origins in a bat, camel, or an unsampled intermediate host. HKU1 had the earliest common ancestor (1809-1899) but fell into two distinct clades (genotypes A and B), possibly representing two independent transmission events from murine-origin CoVs that appear to be a single introduction due to large gaps in the sampling of CoVs in animals. In fact, genotype B was genetically more diverse than all the other sHCoVs. Finally, we found shared amino acid substitutions in multiple proteins along the non-human to sHCoV host-jump branches. The complex evolution of CoVs and their frequent host switches could benefit from continued surveillance of CoVs across non-human hosts.
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Affiliation(s)
- James R. Otieno
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Joshua L. Cherry
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - David J. Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
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23
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Alamri MA, Mirza MU, Adeel MM, Ashfaq UA, Tahir ul Qamar M, Shahid F, Ahmad S, Alatawi EA, Albalawi GM, Allemailem KS, Almatroudi A. Structural Elucidation of Rift Valley Fever Virus L Protein towards the Discovery of Its Potential Inhibitors. Pharmaceuticals (Basel) 2022; 15:659. [PMID: 35745579 PMCID: PMC9228520 DOI: 10.3390/ph15060659] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 12/17/2022] Open
Abstract
Rift valley fever virus (RVFV) is the causative agent of a viral zoonosis that causes a significant clinical burden in domestic and wild ruminants. Major outbreaks of the virus occur in livestock, and contaminated animal products or arthropod vectors can transmit the virus to humans. The viral RNA-dependent RNA polymerase (RdRp; L protein) of the RVFV is responsible for viral replication and is thus an appealing drug target because no effective and specific vaccine against this virus is available. The current study reported the structural elucidation of the RVFV-L protein by in-depth homology modeling since no crystal structure is available yet. The inhibitory binding modes of known potent L protein inhibitors were analyzed. Based on the results, further molecular docking-based virtual screening of Selleckchem Nucleoside Analogue Library (156 compounds) was performed to find potential new inhibitors against the RVFV L protein. ADME (Absorption, Distribution, Metabolism, and Excretion) and toxicity analysis of these compounds was also performed. Besides, the binding mechanism and stability of identified compounds were confirmed by a 50 ns molecular dynamic (MD) simulation followed by MM/PBSA binding free energy calculations. Homology modeling determined a stable multi-domain structure of L protein. An analysis of known L protein inhibitors, including Monensin, Mycophenolic acid, and Ribavirin, provide insights into the binding mechanism and reveals key residues of the L protein binding pocket. The screening results revealed that the top three compounds, A-317491, Khasianine, and VER155008, exhibited a high affinity at the L protein binding pocket. ADME analysis revealed good pharmacodynamics and pharmacokinetic profiles of these compounds. Furthermore, MD simulation and binding free energy analysis endorsed the binding stability of potential compounds with L protein. In a nutshell, the present study determined potential compounds that may aid in the rational design of novel inhibitors of the RVFV L protein as anti-RVFV drugs.
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Affiliation(s)
- Mubarak A. Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 16273, Saudi Arabia;
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada;
| | - Muhammad Muzammal Adeel
- 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China;
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (U.A.A.); (F.S.)
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (U.A.A.); (F.S.)
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (U.A.A.); (F.S.)
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan;
| | - Eid A. Alatawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia;
| | - Ghadah M. Albalawi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (G.M.A.); (A.A.)
- Department of Laboratory and Blood Bank, King Fahd Specialist Hospital, Tabuk 47717, Saudi Arabia
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (G.M.A.); (A.A.)
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (G.M.A.); (A.A.)
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24
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Grellet E, L'Hôte I, Goulet A, Imbert I. Replication of the coronavirus genome: A paradox among positive-strand RNA viruses. J Biol Chem 2022; 298:101923. [PMID: 35413290 PMCID: PMC8994683 DOI: 10.1016/j.jbc.2022.101923] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 01/18/2023] Open
Abstract
Coronavirus (CoV) genomes consist of positive-sense single-stranded RNA and are among the largest viral RNAs known to date (∼30 kb). As a result, CoVs deploy sophisticated mechanisms to replicate these extraordinarily large genomes as well as to transcribe subgenomic messenger RNAs. Since 2003, with the emergence of three highly pathogenic CoVs (SARS-CoV, MERS-CoV, and SARS-CoV-2), significant progress has been made in the molecular characterization of the viral proteins and key mechanisms involved in CoV RNA genome replication. For example, to allow for the maintenance and integrity of their large RNA genomes, CoVs have acquired RNA proofreading 3'-5' exoribonuclease activity (in nonstructural protein nsp14). In order to replicate the large genome, the viral-RNA-dependent RNA polymerase (RdRp; in nsp12) is supplemented by a processivity factor (made of the viral complex nsp7/nsp8), making it the fastest known RdRp. Lastly, a viral structural protein, the nucleocapsid (N) protein, which is primarily involved in genome encapsidation, is required for efficient viral replication and transcription. Therefore, CoVs are a paradox among positive-strand RNA viruses in the sense that they use both a processivity factor and have proofreading activity reminiscent of DNA organisms in addition to structural proteins that mediate efficient RNA synthesis, commonly used by negative-strand RNA viruses. In this review, we present a historical perspective of these unsuspected discoveries and detail the current knowledge on the core replicative machinery deployed by CoVs.
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Affiliation(s)
- Emeline Grellet
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France
| | - India L'Hôte
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France
| | - Adeline Goulet
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France
| | - Isabelle Imbert
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France.
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25
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Ugolini C, Mulroney L, Leger A, Castelli M, Criscuolo E, Williamson MK, Davidson AD, Almuqrin A, Giambruno R, Jain M, Frigè G, Olsen H, Tzertzinis G, Schildkraut I, Wulf MG, Corrêa IR, Ettwiller L, Clementi N, Clementi M, Mancini N, Birney E, Akeson M, Nicassio F, Matthews D, Leonardi T. Nanopore ReCappable sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs. Nucleic Acids Res 2022; 50:3475-3489. [PMID: 35244721 PMCID: PMC8989550 DOI: 10.1093/nar/gkac144] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/05/2022] [Accepted: 02/16/2022] [Indexed: 01/09/2023] Open
Abstract
The SARS-CoV-2 virus has a complex transcriptome characterised by multiple, nested subgenomic RNAsused to express structural and accessory proteins. Long-read sequencing technologies such as nanopore direct RNA sequencing can recover full-length transcripts, greatly simplifying the assembly of structurally complex RNAs. However, these techniques do not detect the 5' cap, thus preventing reliable identification and quantification of full-length, coding transcript models. Here we used Nanopore ReCappable Sequencing (NRCeq), a new technique that can identify capped full-length RNAs, to assemble a complete annotation of SARS-CoV-2 sgRNAs and annotate the location of capping sites across the viral genome. We obtained robust estimates of sgRNA expression across cell lines and viral isolates and identified novel canonical and non-canonical sgRNAs, including one that uses a previously un-annotated leader-to-body junction site. The data generated in this work constitute a useful resource for the scientific community and provide important insights into the mechanisms that regulate the transcription of SARS-CoV-2 sgRNAs.
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Affiliation(s)
- Camilla Ugolini
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Logan Mulroney
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
- Biomolecular Engineering Department, UC Santa Cruz, CA 95064, USA
| | - Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Matteo Castelli
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
| | - Elena Criscuolo
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
| | - Maia Kavanagh Williamson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Abdulaziz Almuqrin
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
- Department of Clinical Laboratory Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Roberto Giambruno
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Miten Jain
- Biomolecular Engineering Department, UC Santa Cruz, CA 95064, USA
| | - Gianmaria Frigè
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139 Milano, Italy
| | - Hugh Olsen
- Biomolecular Engineering Department, UC Santa Cruz, CA 95064, USA
| | | | | | | | | | | | - Nicola Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute; via Olgettina 60, 20132 Milan, Italy
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute; via Olgettina 60, 20132 Milan, Italy
| | - Nicasio Mancini
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University; via Olgettina 58, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute; via Olgettina 60, 20132 Milan, Italy
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Mark Akeson
- Biomolecular Engineering Department, UC Santa Cruz, CA 95064, USA
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - David A Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol BS8 1TD, UK
| | - Tommaso Leonardi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
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26
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Di Gioacchino A, Legendre R, Rahou Y, Najburg V, Charneau P, Greenbaum BD, Tangy F, van der Werf S, Cocco S, Komarova AV. sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs. RNA (NEW YORK, N.Y.) 2022; 28:277-289. [PMID: 34937774 PMCID: PMC8848934 DOI: 10.1261/rna.078969.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study the growing number of next-generation sequencing (NGS) data of SARS-CoV-2. We introduced sgDI-tector to identify and quantify sgRNA in SARS-CoV-2 NGS data. sgDI-tector allowed detection of sgRNA without initial knowledge of the transcription-regulatory sequences. We produced NGS data and successfully detected the nested set of sgRNAs with the ranking M > ORF3a > N>ORF6 > ORF7a > ORF8 > S > E>ORF7b. We also compared the level of sgRNA production with other types of viral RNA products such as defective interfering viral genomes.
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Affiliation(s)
- Andrea Di Gioacchino
- Sorbonne Université, Université de Paris, Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, 75005, Paris, France
| | - Rachel Legendre
- Institut Pasteur, Université de Paris, Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, 75015, Paris, France
| | - Yannis Rahou
- Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France
| | - Valérie Najburg
- Institut Pasteur, Université de Paris, Laboratory of Innovative Vaccines, 75015, Paris, France
| | - Pierre Charneau
- Institut Pasteur, Pasteur-TheraVectys joined unit, 75015, Paris, France
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York 10065, USA
- Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York 10065, USA
| | - Frédéric Tangy
- Institut Pasteur, Université de Paris, Laboratory of Innovative Vaccines, 75015, Paris, France
| | - Sylvie van der Werf
- Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France
| | - Simona Cocco
- Sorbonne Université, Université de Paris, Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, 75005, Paris, France
| | - Anastassia V Komarova
- Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France
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Tumor Susceptibility Gene 101 (TSG101) Contributes to Virion Formation of Porcine Reproductive and Respiratory Syndrome Virus via Interaction with the Nucleocapsid (N) Protein along with the Early Secretory Pathway. J Virol 2022; 96:e0000522. [PMID: 35080428 PMCID: PMC8941886 DOI: 10.1128/jvi.00005-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) has caused huge economic losses to global swine industry. As an intracellular obligate pathogen, PRRSV exploits host cellular machinery to establish infection. The endocytic sorting complex required for transport (ESCRT) system has been shown to participate in different life cycle stages of multiple viruses. In the current study, a systematic small interference RNA (siRNA) screening assay identified that certain ESCRT components contributed to PRRSV infection. Among them, tumor susceptibility gene 101 (TSG101) was demonstrated to be important for PRRSV infection by knockdown and overexpression assays. TSG101 was further revealed to be involved in virion formation rather than viral attachment, internalization, RNA replication and nucleocapsid (N) protein translation within the first round of PRRSV life cycle. In detail, TSG101 was determined to specially interact with PRRSV N protein and take effect on its subcellular localization along with the early secretory pathway. Taken together, these results provide evidence that TSG101 is a pro-viral cellular factor for PRRSV assembly, which will be a promising target to interfere with the viral infection. IMPORTANCE PRRSV infection results in a serious swine disease affecting pig farming in the world. However, efficient prevention and control of PRRSV is hindered by its complicated infection process. Up to now, our understanding of PRRSV assembly during infection is especially limited. Here, we identified that TSG101, an ESCRT-I subunit, facilitated virion formation of PRRSV via interaction with the viral N protein along with the early secretory pathway. Our work actually expands the knowledge of PRRSV infection and provides a novel therapeutic target for prevention and control of the virus.
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Malone B, Urakova N, Snijder EJ, Campbell EA. Structures and functions of coronavirus replication-transcription complexes and their relevance for SARS-CoV-2 drug design. Nat Rev Mol Cell Biol 2022; 23:21-39. [PMID: 34824452 PMCID: PMC8613731 DOI: 10.1038/s41580-021-00432-z] [Citation(s) in RCA: 197] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2021] [Indexed: 02/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed millions of people and continues to cause massive global upheaval. Coronaviruses are positive-strand RNA viruses with an unusually large genome of ~30 kb. They express an RNA-dependent RNA polymerase and a cohort of other replication enzymes and supporting factors to transcribe and replicate their genomes. The proteins performing these essential processes are prime antiviral drug targets, but drug discovery is hindered by our incomplete understanding of coronavirus RNA synthesis and processing. In infected cells, the RNA-dependent RNA polymerase must coordinate with other viral and host factors to produce both viral mRNAs and new genomes. Recent research aiming to decipher and contextualize the structures, functions and interplay of the subunits of the SARS-CoV-2 replication and transcription complex proteins has burgeoned. In this Review, we discuss recent advancements in our understanding of the molecular basis and complexity of the coronavirus RNA-synthesizing machinery. Specifically, we outline the mechanisms and regulation of RNA translation, replication and transcription. We also discuss the composition of the replication and transcription complexes and their suitability as targets for antiviral therapy.
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Affiliation(s)
- Brandon Malone
- grid.134907.80000 0001 2166 1519Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY USA
| | - Nadya Urakova
- grid.10419.3d0000000089452978Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Eric J. Snijder
- grid.10419.3d0000000089452978Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Elizabeth A. Campbell
- grid.134907.80000 0001 2166 1519Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY USA
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29
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WGS- versus ORF5-Based Typing of PRRSV: A Belgian Case Study. Viruses 2021; 13:v13122419. [PMID: 34960688 PMCID: PMC8707199 DOI: 10.3390/v13122419] [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: 10/15/2021] [Revised: 11/17/2021] [Accepted: 11/24/2021] [Indexed: 12/18/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of one of the most widespread and economically devastating diseases in the swine industry. Typing circulating PRRSV strains by means of sequencing is crucial for developing adequate control strategies. Most genetic studies only target the highly variable open reading frame (ORF) 5, for which an extensive database is available. In this study, we performed whole-genome sequencing (WGS) on a collection of 124 PRRSV-1 positive serum samples that were collected over a 5-year period (2015–2019) in Belgium. Our results show that (nearly) complete PRRSV genomes can be obtained directly from serum samples with a high success rate. Analysis of the coding regions confirmed the exceptionally high genetic diversity, even among Belgian PRRSV-1 strains. To gain more insight into the added value of WGS, we performed phylogenetic cluster analyses on separate ORF datasets as well as on a single, concatenated dataset (CDS) containing all ORFs. A comparison between the CDS and ORF clustering schemes revealed numerous discrepancies. To explain these differences, we performed a large-scale recombination analysis, which allowed us to identify a large number of potential recombination events that were scattered across the genome. As PRRSV does not contain typical recombination hot-spots, typing PRRSV strains based on a single ORF is not recommended. Although the typing accuracy can be improved by including multiple regions, our results show that the full genetic diversity among PRRSV strains can only be captured by analysing (nearly) complete genomes. Finally, we also identified several vaccine-derived recombinant strains, which once more raises the question of the safety of these vaccines.
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A Novel Potentially Recombinant Rodent Coronavirus with a Polybasic Cleavage Site in the Spike Protein. J Virol 2021; 95:e0117321. [PMID: 34431700 PMCID: PMC8549509 DOI: 10.1128/jvi.01173-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reignited global interest in animal coronaviruses and their potential for human transmission. While bats are thought to be the wildlife reservoir of SARS-CoV and SARS-CoV-2, the widespread human coronavirus OC43 is thought to have originated in rodents. Here, we sampled 297 rodents and shrews, representing eight species, from three municipalities of southern China. We report coronavirus prevalences of 23.3% and 0.7% in Guangzhou and Guilin, respectively, with samples from urban areas having significantly higher coronavirus prevalences than those from rural areas. We obtained three coronavirus genome sequences from Rattus norvegicus, including a Betacoronavirus (rat coronavirus [RCoV] GCCDC3), an Alphacoronavirus (RCoV-GCCDC5), and a novel Betacoronavirus (RCoV-GCCDC4). Recombination analysis suggests that there was a potential recombination event involving RCoV-GCCDC4, murine hepatitis virus (MHV), and Longquan Rl rat coronavirus (LRLV). Furthermore, we uncovered a polybasic cleavage site, RARR, in the spike (S) protein of RCoV-GCCDC4, which is dominant in RCoV. These findings provide further information on the potential for interspecies transmission of coronaviruses and demonstrate the value of a One Health approach to virus discovery. IMPORTANCE Surveillance of viruses among rodents in rural and urban areas of South China identified three rodent coronaviruses, RCoV-GCCDC3, RCoV-GCCDC4, and RCoV-GCCDC5, one of which was identified as a novel potentially recombinant coronavirus with a polybasic cleavage site in the spike (S) protein. Through reverse transcription-PCR (RT-PCR) screening of coronaviruses, we found that coronavirus prevalence in urban areas is much higher than that in rural areas. Subsequently, we obtained three coronavirus genome sequences by deep sequencing. After different method-based analyses, we found that RCoV-GCCDC4 was a novel potentially recombinant coronavirus with a polybasic cleavage site in the S protein, dominant in RCoV. This newly identified coronavirus RCoV-GCCDC4 with its potentially recombinant genome and polybasic cleavage site provides a new insight into the evolution of coronaviruses. Furthermore, our results provide further information on the potential for interspecies transmission of coronaviruses and demonstrate the necessity of a One Health approach for zoonotic disease surveillance.
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31
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Parrish K, Kirkland PD, Skerratt LF, Ariel E. Nidoviruses in Reptiles: A Review. Front Vet Sci 2021; 8:733404. [PMID: 34621811 PMCID: PMC8490724 DOI: 10.3389/fvets.2021.733404] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/19/2021] [Indexed: 12/17/2022] Open
Abstract
Since their discovery in 2014, reptile nidoviruses (also known as serpentoviruses) have emerged as significant pathogens worldwide. They are known for causing severe and often fatal respiratory disease in various captive snake species, especially pythons. Related viruses have been detected in other reptiles with and without respiratory disease, including captive and wild populations of lizards, and wild populations of freshwater turtles. There are many opportunities to better understand the viral diversity, species susceptibility, and clinical presentation in different species in this relatively new field of research. In captive snake collections, reptile nidoviruses can spread quickly and be associated with high morbidity and mortality, yet the potential disease risk to wild reptile populations remains largely unknown, despite reptile species declining on a global scale. Experimental studies or investigations of disease outbreaks in wild reptile populations are scarce, leaving the available literature limited mostly to exploring findings of naturally infected animals in captivity. Further studies into the pathogenesis of different reptile nidoviruses in a variety of reptile species is required to explore the complexity of disease and routes of transmission. This review focuses on the biology of these viruses, hosts and geographic distribution, clinical signs and pathology, laboratory diagnosis and management of reptile nidovirus infections to better understand nidovirus infections in reptiles.
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Affiliation(s)
- Kate Parrish
- Virology Laboratory, Elizabeth Macarthur Agricultural Institute, New South Wales (NSW) Department of Primary Industries, Menangle, NSW, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Peter D Kirkland
- Virology Laboratory, Elizabeth Macarthur Agricultural Institute, New South Wales (NSW) Department of Primary Industries, Menangle, NSW, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Lee F Skerratt
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, VIC, Australia
| | - Ellen Ariel
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
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32
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Bioinformatics Analysis Identifies a Small ORF in the Genome of Fish Nidoviruses of Genus Oncotshavirus Predicted to Encode a Novel Integral Protein. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12040055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Genome sequence analysis of Atlantic salmon bafinivirus (ASBV) revealed a small open reading frame (ORF) predicted to encode a Type I membrane protein with an N-terminal cleaved signal sequence (110 aa), likely an envelope (E) protein. Bioinformatic analyses showed that the predicted protein is strikingly similar to the coronavirus E protein in structure. This is the first report to identify a putative E protein ORF in the genome of members of the Oncotshavirus genus (subfamily Piscavirinae, family Tobaniviridae, order Nidovirales) and, if expressed would be the third family (after Coronaviridae and Arteriviridae) within the order to have the E protein as a major structural protein.
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33
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Long S. SARS-CoV-2 Subgenomic RNAs: Characterization, Utility, and Perspectives. Viruses 2021; 13:1923. [PMID: 34696353 PMCID: PMC8539008 DOI: 10.3390/v13101923] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/12/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2, the etiologic agent at the root of the ongoing COVID-19 pandemic, harbors a large RNA genome from which a tiered ensemble of subgenomic RNAs (sgRNAs) is generated. Comprehensive definition and investigation of these RNA products are important for understanding SARS-CoV-2 pathogenesis. This review summarizes the recent progress on SARS-CoV-2 sgRNA identification, characterization, and application as a viral replication marker. The significance of these findings and potential future research areas of interest are discussed.
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Affiliation(s)
- Samuel Long
- Independent Researcher, Clarksburg, MD 20871, USA
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34
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Telwatte S, Kumar N, Vallejo-Gracia A, Kumar GR, Lu CM, Ott M, Wong JK, Yukl SA. Novel RT-ddPCR assays for simultaneous quantification of multiple noncoding and coding regions of SARS-CoV-2 RNA. J Virol Methods 2021; 292:114115. [PMID: 33667568 PMCID: PMC7923865 DOI: 10.1016/j.jviromet.2021.114115] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/02/2021] [Accepted: 02/25/2021] [Indexed: 12/19/2022]
Abstract
A hallmark of coronavirus transcription is the generation of negative-sense RNA intermediates that serve as the templates for the synthesis of positive-sense genomic RNA (gRNA) and an array of subgenomic mRNAs (sgRNAs) encompassing sequences arising from discontinuous transcription. Existing PCR-based diagnostic assays for SAR-CoV-2 are qualitative or semi-quantitative and do not provide the resolution needed to assess the complex transcription dynamics of SARS-CoV-2 over the course of infection. We developed and validated a novel panel of sensitive, quantitative RT-ddPCR assays designed to target regions spanning the genome of SARS-CoV-2. Our assays target untranslated regions (5', 3') as well as different coding regions, including non-structural genes that are only found in full length (genomic) RNA and structural genes that are found in genomic as well as different subgenomic RNAs. Application of these assays to clinically relevant samples will enhance our understanding of SARS-CoV-2 gene expression and may also inform the development of improved diagnostic tools and therapeutics.
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Affiliation(s)
- Sushama Telwatte
- Department of Medicine, University of California, San Francisco, CA, USA; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Nitasha Kumar
- Department of Medicine, University of California, San Francisco, CA, USA; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, USA
| | | | - G Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Chuanyi M Lu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA; Department of Laboratory Medicine, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Melanie Ott
- Department of Medicine, University of California, San Francisco, CA, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Joseph K Wong
- Department of Medicine, University of California, San Francisco, CA, USA; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Steven A Yukl
- Department of Medicine, University of California, San Francisco, CA, USA; Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, USA.
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35
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Yan S, Wu G. Potential 3-chymotrypsin-like cysteine protease cleavage sites in the coronavirus polyproteins pp1a and pp1ab and their possible relevance to COVID-19 vaccine and drug development. FASEB J 2021; 35:e21573. [PMID: 33913206 PMCID: PMC8206714 DOI: 10.1096/fj.202100280rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/04/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023]
Abstract
Coronavirus (CoV) 3-chymotrypsin (C)-like cysteine protease (3CLpro ) is a target for anti-CoV drug development and drug repurposing because along with papain-like protease, it cleaves CoV-encoded polyproteins (pp1a and pp1ab) into nonstructural proteins (nsps) for viral replication. However, the cleavage sites of 3CLpro and their relevant nsps remain unclear, which is the subject of this perspective. Here, we address the subject from three standpoints. First, we explore the inconsistency in the cleavage sites and relevant nsps across CoVs, and investigate the function of nsp11. Second, we consider the nsp16 mRNA overlapping of the spike protein mRNA, and analyze the effect of this overlapping on mRNA vaccines. Finally, we study nsp12, whose existence depends on ribosomal frameshifting, and investigate whether 3CLpro requires a large number of inhibitors to achieve full inhibition. This perspective helps us to clarify viral replication and is useful for developing anti-CoV drugs with 3CLpro as a target in the current coronavirus disease 2019 (COVID-19) pandemic.
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Affiliation(s)
- Shaomin Yan
- National Engineering Research Center for Non‐Food Biorefinery, State Key Laboratory of Non‐Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Guangxi Key Laboratory of BiorefineryGuangxi Academy of SciencesNanningChina
| | - Guang Wu
- National Engineering Research Center for Non‐Food Biorefinery, State Key Laboratory of Non‐Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Guangxi Key Laboratory of BiorefineryGuangxi Academy of SciencesNanningChina
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36
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Zhang L, Zhang L, Pan Y, Gao J, Xu Y, Li X, Tian Z, Chen H, Wang Y. Downregulation of miR-218 by porcine reproductive and respiratory syndrome virus facilitates viral replication via inhibition of type I interferon responses. J Biol Chem 2021; 296:100683. [PMID: 33887325 PMCID: PMC8131720 DOI: 10.1016/j.jbc.2021.100683] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 04/14/2021] [Accepted: 04/18/2021] [Indexed: 12/15/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a devastating pathogen in the swine industry worldwide. miRNAs are reported to be involved in virus-host interaction. Here, we used high-throughput sequencing and miRNA inhibitors to screen possible miRNAs that can inhibit PRRSV infection on its target cell, porcine alveolar macrophages. We observed that miR-218 was downregulated upon virus infection, and knockdown of miR-218 significantly enhanced PRRSV replication. Overexpression of miR-218 resulted in a decrease in PRRSV replication, and this overexpression did not alter viral genomic RNA levels, but rather increased antiviral interferon signaling. Further analysis revealed that miR-218 regulated PRRSV replication by directly targeting porcine suppressor of cytokine signaling 3 (SOCS3), a JAK2 kinase inhibitor. Knockdown of the endogenous SOCS3 expression led to augmentation of type I interferon genes and resulted in decreased PRRSV replication, and vice versa. During PRRSV infection in vivo and in vitro, cellular miR-218 expression was downregulated and SOCS3 expression was upregulated, further supporting the inverse correlation between miR-218 and SOCS3 expression. The data on SOCS3 depletion in combination with miR-218 inhibition suggested that the antiviral activity of miR-218 required the SOCS3-mediated signaling pathway. Similarly, miR-218 negatively regulated PRRSV replication in Marc-145 cells, as well as the replication of porcine epidemic diarrhea virus and transmissible gastroenteritis virus in Vero and ST cells respectively. Taken together, these results demonstrate that PRRSV-induced miR-218 downregulation serves to inhibit the type I interferon response and may provide a novel therapeutic target for treatment of PRRSV and other viral infections.
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Affiliation(s)
- Lin Zhang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lu Zhang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yu Pan
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Junxin Gao
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yunfei Xu
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xi Li
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhijun Tian
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yue Wang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
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37
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Ullah A, Ullah K. Inhibition of SARS-CoV-2 3CL M pro by Natural and Synthetic Inhibitors: Potential Implication for Vaccine Production Against COVID-19. Front Mol Biosci 2021; 8:640819. [PMID: 33912587 PMCID: PMC8072276 DOI: 10.3389/fmolb.2021.640819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/10/2021] [Indexed: 12/24/2022] Open
Abstract
COVID-19 has created a pandemic situation all over the world. It has spread in nearly every continent. Researchers all over the world are trying to produce an effective vaccine against this virus, however; no specific treatment for COVID-19 has been discovered -so far. The current work describes the inhibition study of the SARS-CoV-2 main proteinase or 3CL Mpro by natural and synthetic inhibitors, which include 2S albumin and flocculating protein from Moringa oleifera (M. oleifera) and Suramin. Molecular Docking study was carried out using the programs like AutoDock 4.0, HADDOCK2.4, patchdock, pardock, and firedock. The global binding energy of Suramin, 2S albumin, and flocculating proteins were −41.96, −9.12, and −14.78 kJ/mol, respectively. The docking analysis indicates that all three inhibitors bind at the junction of domains II and III. The catalytic function of 3CL Mpro is dependent on its dimeric form, and the flexibility of domain III is considered important for this dimerization. Our study showed that all three inhibitors reduce this flexibility and restrict their motion. The decrease in flexibility of domain III was further confirmed by analysis coming from Molecular dynamic simulation. The analysis results indicate that the temperature B-factor of the enzyme decreases tremendously when the inhibitors bind to it. This study will further explore the possibility of producing an effective treatment against COVID-19.
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Affiliation(s)
- Anwar Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Kifayat Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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38
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Ujike M, Taguchi F. Recent Progress in Torovirus Molecular Biology. Viruses 2021; 13:435. [PMID: 33800523 PMCID: PMC7998386 DOI: 10.3390/v13030435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 11/16/2022] Open
Abstract
Torovirus (ToV) has recently been classified into the new family Tobaniviridae, although it belonged to the Coronavirus (CoV) family historically. ToVs are associated with enteric diseases in animals and humans. In contrast to CoVs, which are recognised as pathogens of veterinary and medical importance, little attention has been paid to ToVs because their infections are usually asymptomatic or not severe; for a long time, only one equine ToV could be propagated in cultured cells. However, bovine ToVs, which predominantly cause diarrhoea in calves, have been detected worldwide, leading to economic losses. Porcine ToVs have also spread globally; although they have not caused serious economic losses, coinfections with other pathogens can exacerbate their symptoms. In addition, frequent inter- or intra-recombination among ToVs can increase pathogenesis or unpredicted host adaptation. These findings have highlighted the importance of ToVs as pathogens and the need for basic ToV research. Here, we review recent progress in the study of ToV molecular biology including reverse genetics, focusing on the similarities and differences between ToVs and CoVs.
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Affiliation(s)
- Makoto Ujike
- Laboratory of Veterinary Infectious Diseases, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan;
- Research Center for Animal Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan
| | - Fumihiro Taguchi
- Laboratory of Veterinary Infectious Diseases, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan;
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Mirzaei A, Moghim S. SARS-CoV-2, SARS and MERS: Three formidable
coronaviruses which have originated from bats. POSTEP HIG MED DOSW 2021. [DOI: 10.5604/01.3001.0014.7476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The recent continuously emerging rampancy of novel coronavirus (SARS-CoV-2) that started in
Wuhan in late December 2019 has become an international public health emergency and is still
spreading rapidly in the world. Up to October 11, 2020, 37.109.6851 confirmed cases of COVID-19
have been announced with 2.8 percent death, which means 1.070.355 confirmed death cases.
At the moment, a specific vaccine or drug for the new coronavirus is not available; thus, the
development of a drug with far-reaching HCoV inhibitory activity is an urgent medical need.
It is, however, vital to first comprehend the nature of this family and other coronaviruses that
have caused the outbreak. Here, we relate the epidemiological and virological characteristics
of the COVID-19, SARS, and MERS rampancy.
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Affiliation(s)
- Arezoo Mirzaei
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Sharareh Moghim
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Science, Isfahan, Iran
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40
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Zhu Z, Liu G, Meng K, Yang L, Liu D, Meng G. Rapid Spread of Mutant Alleles in Worldwide SARS-CoV-2 Strains Revealed by Genome-Wide Single Nucleotide Polymorphism and Variation Analysis. Genome Biol Evol 2021; 13:evab015. [PMID: 33512495 PMCID: PMC7883668 DOI: 10.1093/gbe/evab015] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2021] [Indexed: 12/13/2022] Open
Abstract
The novel coronavirus (SARS-CoV-2) has become a pandemic and is threatening human health globally. Here, we report nine newly evolved SARS-CoV-2 single nucleotide polymorphism (SNP) alleles those underwent a rapid increase (seven cases) or decrease (two cases) in their frequency for 30-80% in the initial four months, which are further confirmed by intrahost single nucleotide variation analysis using raw sequence data including 8,217 samples. The nine SNPs are mostly (8/9) located in the coding region and are mainly (6/9) nonsynonymous substitutions. The nine SNPs show a complete linkage in SNP pairs and belong to three different linkage groups, named LG_1 to LG_3. Analyses in population genetics show signatures of adaptive selection toward the mutants in LG_1, but no signal of selection for LG_2. Population genetic analysis results on LG_3 show geological differentiation. Analyses on geographic COVID-19 cases and published clinical data provide evidence that the mutants in LG_1 and LG_3 benefit virus replication and those in LG_1 have a positive correlation with the disease severity in COVID-19-infected patients. The mutants in LG_2 show a bias toward mildness of the disease based on available public clinical data. Our findings may be instructive for epidemiological surveys and disease control of COVID-19 in the future.
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Affiliation(s)
- Zhenglin Zhu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Gexin Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Kaiwen Meng
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Liuqing Yang
- Chongqing Occupational Disease Prevention Hospital, Chongqing, China
| | - Di Liu
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for 25 Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Geng Meng
- College of Veterinary Medicine, China Agricultural University, Beijing, China
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41
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Rosenke K, Leventhal S, Moulton HM, Hatlevig S, Hawman D, Feldmann H, Stein DA. Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino oligomers. J Antimicrob Chemother 2021; 76:413-417. [PMID: 33164048 PMCID: PMC7717290 DOI: 10.1093/jac/dkaa460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/02/2020] [Indexed: 02/07/2023] Open
Abstract
Background As the causative agent of COVID-19, SARS-CoV-2 is a pathogen of immense importance to global public health. Development of innovative direct-acting antiviral agents is sorely needed to address this virus. Peptide-conjugated morpholino oligomers (PPMO) are antisense compounds composed of a phosphorodiamidate morpholino oligomer covalently conjugated to a cell-penetrating peptide. PPMO require no delivery assistance to enter cells and are able to reduce expression of targeted RNA through sequence-specific steric blocking. Methods Five PPMO designed against sequences of genomic RNA in the SARS-CoV-2 5′-untranslated region and a negative control PPMO of random sequence were synthesized. Each PPMO was evaluated for its effect on the viability of uninfected cells and its inhibitory effect on the replication of SARS-CoV-2 in Vero-E6 cell cultures. Cell viability was evaluated with an ATP-based method using a 48 h PPMO treatment time. Viral growth was measured with quantitative RT–PCR and TCID50 infectivity assays from experiments where cells received a 5 h PPMO treatment time. Results PPMO designed to base-pair with sequence in the 5′ terminal region or the leader transcription regulatory sequence region of SARS-CoV-2 genomic RNA were highly efficacious, reducing viral titres by up to 4–6 log10 in cell cultures at 48–72 h post-infection, in a non-toxic and dose-responsive manner. Conclusions The data indicate that PPMO have the ability to potently and specifically suppress SARS-CoV-2 growth and are promising candidates for further preclinical development.
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Affiliation(s)
- Kyle Rosenke
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Shanna Leventhal
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Hong M Moulton
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Susan Hatlevig
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - David Hawman
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - David A Stein
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
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42
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Kistler KE, Bedford T. Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e. eLife 2021; 10:64509. [PMID: 33463525 PMCID: PMC7861616 DOI: 10.7554/elife.64509] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/12/2020] [Indexed: 11/13/2022] Open
Abstract
Seasonal coronaviruses (OC43, 229E, NL63, and HKU1) are endemic to the human population, regularly infecting and reinfecting humans while typically causing asymptomatic to mild respiratory infections. It is not known to what extent reinfection by these viruses is due to waning immune memory or antigenic drift of the viruses. Here we address the influence of antigenic drift on immune evasion of seasonal coronaviruses. We provide evidence that at least two of these viruses, OC43 and 229E, are undergoing adaptive evolution in regions of the viral spike protein that are exposed to human humoral immunity. This suggests that reinfection may be due, in part, to positively selected genetic changes in these viruses that enable them to escape recognition by the immune system. It is possible that, as with seasonal influenza, these adaptive changes in antigenic regions of the virus would necessitate continual reformulation of a vaccine made against them.
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Affiliation(s)
- Kathryn E Kistler
- Molecular and Cellular Biology Program, University of Washington, Seattle, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Trevor Bedford
- Molecular and Cellular Biology Program, University of Washington, Seattle, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
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43
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Telwatte S, Kumar N, Vallejo-Gracia A, Kumar GR, Lu CM, Ott M, Wong JK, Yukl SA. Novel RT-ddPCR Assays for determining the transcriptional profile of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.12.425991. [PMID: 33469579 PMCID: PMC7814816 DOI: 10.1101/2021.01.12.425991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The exact mechanism of coronavirus replication and transcription is not fully understood; however, a hallmark of coronavirus transcription is the generation of negative-sense RNA intermediates that serve as the templates for the synthesis of positive-sense genomic RNA (gRNA) and an array of subgenomic mRNAs (sgRNAs) encompassing sequences arising from discontinuous transcription. Existing PCR-based diagnostic assays for SAR-CoV-2 are qualitative or semi-quantitative and do not provide the resolution needed to assess the complex transcription dynamics of SARS-CoV-2 over the course of infection. We developed and validated a novel panel of specially designed SARS-CoV-2 ddPCR-based assays to map the viral transcription profile. Application of these assays to clinically relevant samples will enhance our understanding of SARS-CoV-2 replication and transcription and may also inform the development of improved diagnostic tools and therapeutics.
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Affiliation(s)
- Sushama Telwatte
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Nitasha Kumar
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
| | | | - G. Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Chuanyi M. Lu
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Melanie Ott
- Department of Medicine, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Joseph K. Wong
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Steven A. Yukl
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
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44
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Yang M, He S, Chen X, Huang Z, Zhou Z, Zhou Z, Chen Q, Chen S, Kang S. Structural Insight Into the SARS-CoV-2 Nucleocapsid Protein C-Terminal Domain Reveals a Novel Recognition Mechanism for Viral Transcriptional Regulatory Sequences. Front Chem 2021; 8:624765. [PMID: 33511102 PMCID: PMC7835709 DOI: 10.3389/fchem.2020.624765] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/08/2020] [Indexed: 11/22/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has caused massive disruptions to society and the economy, and the transcriptional regulatory mechanisms behind the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are poorly understood. Herein, we determined the crystal structure of the SARS-CoV-2 nucleocapsid protein C-terminal domain (CTD) at a resolution of 2.0 Å, and demonstrated that the CTD has a comparable distinct electrostatic potential surface to equivalent domains of other reported CoVs, suggesting that the CTD has novel roles in viral RNA binding and transcriptional regulation. Further in vitro biochemical assays demonstrated that the viral genomic intergenic transcriptional regulatory sequences (TRSs) interact with the SARS-CoV-2 nucleocapsid protein CTD with a flanking region. The unpaired adeno dinucleotide in the TRS stem-loop structure is a major determining factor for their interactions. Taken together, these results suggested that the nucleocapsid protein CTD is responsible for the discontinuous viral transcription mechanism by recognizing the different patterns of viral TRS during transcription.
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Affiliation(s)
- Mei Yang
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.,Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Suhua He
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Xiaoxue Chen
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Zhaoxia Huang
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Ziliang Zhou
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Zhechong Zhou
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Qiuyue Chen
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Shoudeng Chen
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.,Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Sisi Kang
- Guangdong Provincial Key Laboratory of Biomedical Imaging, Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.,Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
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45
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da Silva PG, Mesquita JR, de São José Nascimento M, Ferreira VAM. Viral, host and environmental factors that favor anthropozoonotic spillover of coronaviruses: An opinionated review, focusing on SARS-CoV, MERS-CoV and SARS-CoV-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:141483. [PMID: 32829257 PMCID: PMC7405882 DOI: 10.1016/j.scitotenv.2020.141483] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 05/21/2023]
Abstract
Environmental factors play a key role in the zoonotic transmission of emerging pathogenic viruses as mankind is constantly disturbing wildlife's ecosystems usually by cutting down forests to build human settlements or by catching wild animals for food, which deprives the viruses of their natural hosts and gives them opportunity to infect humans. In December 2019, a new coronavirus emerged from bats and was named SARS-CoV-2 by the International Committee for Taxonomy of Viruses, and the disease it causes named COVID-19 by the World Health Organization. Disease outbreaks such as SARS in 2002-2003, MERS in 2012 and the current COVID-19 pandemic are the result of higher mutation rates of coronaviruses and their unique capacity for genetic recombination, resulting in adaptations that make them more suitable to cross the species barriers and infect other species. This ability for host switching and interspecies infection is often attributed to the great diversity of these viruses, which is a result of viral and host factors such as the low fidelity of their RNA-dependent RNA polymerase, the high frequency of their homologous RNA recombination, and the adaptation of the S protein to bind host receptors like the angiotensin converting enzyme 2 (ACE2) in the case of SARS-CoV and SARS-CoV-2, and dipeptidyl peptidase 4 (DDP4) in MERS-CoV. This review presents an overview of the zoonotic transmission of SARS, MERS and COVID-19, focusing on the viral, host and environmental factors that favor the spillover of these viruses into humans, as well as the biological and ecological factors that make bats the perfect animal reservoir of infection for these viruses.
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Affiliation(s)
| | - João Rodrigo Mesquita
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal; Epidemiology Research Unit (EPIUnit), Institute of Public Health, University of Porto, Porto, Portugal
| | - Maria de São José Nascimento
- Epidemiology Research Unit (EPIUnit), Institute of Public Health, University of Porto, Porto, Portugal; Faculty of Pharmacy, University of Porto (FFUP), Porto, Portugal
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46
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The zoonotic potential of bat-borne coronaviruses. Emerg Top Life Sci 2020; 4:353-369. [PMID: 33258903 DOI: 10.1042/etls20200097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023]
Abstract
Seven zoonoses - human infections of animal origin - have emerged from the Coronaviridae family in the past century, including three viruses responsible for significant human mortality (SARS-CoV, MERS-CoV, and SARS-CoV-2) in the past twenty years alone. These three viruses, in addition to two older CoV zoonoses (HCoV-229E and HCoV-NL63) are believed to be originally derived from wild bat reservoir species. We review the molecular biology of the bat-derived Alpha- and Betacoronavirus genera, highlighting features that contribute to their potential for cross-species emergence, including the use of well-conserved mammalian host cell machinery for cell entry and a unique capacity for adaptation to novel host environments after host switching. The adaptive capacity of coronaviruses largely results from their large genomes, which reduce the risk of deleterious mutational errors and facilitate range-expanding recombination events by offering heightened redundancy in essential genetic material. Large CoV genomes are made possible by the unique proofreading capacity encoded for their RNA-dependent polymerase. We find that bat-borne SARS-related coronaviruses in the subgenus Sarbecovirus, the source clade for SARS-CoV and SARS-CoV-2, present a particularly poignant pandemic threat, due to the extraordinary viral genetic diversity represented among several sympatric species of their horseshoe bat hosts. To date, Sarbecovirus surveillance has been almost entirely restricted to China. More vigorous field research efforts tracking the circulation of Sarbecoviruses specifically and Betacoronaviruses more generally is needed across a broader global range if we are to avoid future repeats of the COVID-19 pandemic.
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47
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Abozeid HH, Naguib MM. Infectious Bronchitis Virus in Egypt: Genetic Diversity and Vaccination Strategies. Vet Sci 2020; 7:vetsci7040204. [PMID: 33348570 PMCID: PMC7766096 DOI: 10.3390/vetsci7040204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
Infectious bronchitis virus (IBV) is a highly evolving avian pathogen that has increasingly imposed a negative impact on poultry industry worldwide. In the last 20 years, IBV has been continuously circulating among chicken flocks in Egypt causing huge economic losses to poultry production. Multiple IBV genotypes, namely, GI-1, GI-13, GI-16, and GI-23 have been reported in Egypt possessing different genetic and pathogenic features. Different vaccine programs are being used to control the spread of the disease in Egypt. However, the virus continues to spread and evolve where multiple IBV variants and several recombination evidence have been described. In this review, we highlight the current knowledge concerning IBV circulation, genesis, and vaccination strategies in Egypt. In addition, we analyze representative Egyptian IBV strains from an evolutionary perspective based on available data of their S1 gene. We also provide insight into the importance of surveillance programs and share our perspectives for better control of IBV circulating in Egypt.
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Affiliation(s)
- Hassanein H. Abozeid
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt;
| | - Mahmoud M. Naguib
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 21 Uppsala, Sweden
- Correspondence:
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48
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Chakraborty J, Banerjee I, Vaishya R, Ghosh S. Bioengineered in Vitro Tissue Models to Study SARS-CoV-2 Pathogenesis and Therapeutic Validation. ACS Biomater Sci Eng 2020; 6:6540-6555. [PMID: 33320635 PMCID: PMC7688047 DOI: 10.1021/acsbiomaterials.0c01226] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/04/2020] [Indexed: 02/07/2023]
Abstract
Given the various viral outbreaks in the 21st century, specifically the present pandemic situation arising from SARS-CoV-2 or the coronavirus, of unknown magnitude, there is an unmet clinical need to develop effective therapeutic and diagnostic strategies to combat this infectious disease worldwide. To develop precise anticoronavirus drugs and prophylactics, tissue engineering and biomaterial research strategies can serve as a suitable alternative to the conventional treatment options. Therefore, in this Review, we have highlighted various tissue engineering-based diagnostic systems for SARS-CoV-2 and suggested how these strategies involving organ-on-a-chip, organoids, 3D bioprinting, and advanced bioreactor models can be employed to develop in vitro human tissue models, for more efficient diagnosis, drug/vaccine development, and focusing on the need for patient-specific therapy. We believe that combining the basics of virology with tissue engineering techniques can help the researchers to understand the molecular mechanism underlying viral infection, which is critical for effective drug design. In addition, it can also serve to be a suitable platform for drug testing and delivery of small molecules that can lead to therapeutic tools in this dreaded pandemic situation. Additionally, we have also discussed the essential biomaterial properties which polarize the immune system, including dendritic cells and macrophages, toward their inflammatory phenotype, which can thus serve as a reference for exhibiting the role of biomaterial in influencing the adaptive immune response involving B and T lymphocytes to foster a regenerative tissue microenvironment. The situation arising from SARS-CoV-2 poses a challenge to scientists from almost all disciplines, and we feel that tissue engineers can thus provide new translational opportunities in this dreadful pandemic situation.
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Affiliation(s)
- Juhi Chakraborty
- Department of Textile and Fibre Engineering,
Indian Institute of Technology Delhi, New Delhi-110016,
India
| | - Indranil Banerjee
- Department of Biological Sciences, Indian
Institute of Science Education and Research, Mohali (IISER Mohali), Sector
81, S.A.S. Nagar, Mohali-140306, Punjab, India
| | - Raju Vaishya
- Indraprastha Apollo Hospitals
Delhi, Delhi Mathura Road, Sarita Vihar, New Delhi,
India
| | - Sourabh Ghosh
- Department of Textile and Fibre Engineering,
Indian Institute of Technology Delhi, New Delhi-110016,
India
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49
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Krishnamoorthy S, Swain B, Verma RS, Gunthe SS. SARS-CoV, MERS-CoV, and 2019-nCoV viruses: an overview of origin, evolution, and genetic variations. Virusdisease 2020; 31:411-423. [PMID: 33102628 PMCID: PMC7567416 DOI: 10.1007/s13337-020-00632-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
Coronaviruses are single stranded RNA viruses usually present in bats (reservoir hosts), and are generally lethal, highly transmissible, and pathogenic viruses causing sever morbidity and mortality rates in human. Several animals including civets, camels, etc. have been identified as intermediate hosts enabling effective recombination of these viruses to emerge as new virulent and pathogenic strains. Among the seven known human coronaviruses SARS-CoV, MERS-CoV, and SARS-CoV-2 (2019-nCoV) have evolved as severe pathogenic forms infecting the human respiratory tract. About 8096 cases and 774 deaths were reported worldwide with the SARS-CoV infection during year 2002; 2229 cases and 791 deaths were reported for the MERS-CoV that emerged during 2012. Recently ~ 33,849,737 cases and 1,012,742 deaths (data as on 30 Sep 2020) were reported from the recent evolver SARS-CoV-2 infection. Studies on epidemiology and pathogenicity have shown that the viral spread was potentially caused by the contact route especially through the droplets, aerosols, and contaminated fomites. Genomic studies have confirmed the role of the viral spike protein in virulence and pathogenicity. They target the respiratory tract of the human causing severe progressive pneumonia affecting other organs like central nervous system in case of SARS-CoV, severe renal failure in MERS-CoV, and multi-organ failure in SARS-CoV-2. Herein, with respect to current awareness and role of coronaviruses in global public health, we review the various factors involving the origin, evolution, and transmission including the genetic variations observed, epidemiology, and pathogenicity of the three potential coronaviruses variants SARS-CoV, MERS-CoV, and 2019-nCoV.
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Affiliation(s)
- Sarayu Krishnamoorthy
- EWRE Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, 600 036 India
| | - Basudev Swain
- EWRE Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, 600 036 India
| | - R. S. Verma
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600 036 India
| | - Sachin S. Gunthe
- EWRE Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, 600 036 India
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50
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Banerjee A, Doxey AC, Tremblay BJM, Mansfield MJ, Subudhi S, Hirota JA, Miller MS, McArthur AG, Mubareka S, Mossman K. Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus. J Gen Virol 2020; 101:1251-1260. [PMID: 32902372 PMCID: PMC7819352 DOI: 10.1099/jgv.0.001491] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/12/2020] [Indexed: 01/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently emerged to cause widespread infections in humans. SARS-CoV-2 infections have been reported in the Kingdom of Saudi Arabia, where Middle East respiratory syndrome coronavirus (MERS-CoV) causes seasonal outbreaks with a case fatality rate of ~37 %. Here we show that there exists a theoretical possibility of future recombination events between SARS-CoV-2 and MERS-CoV RNA. Through computational analyses, we have identified homologous genomic regions within the ORF1ab and S genes that could facilitate recombination, and have analysed co-expression patterns of the cellular receptors for SARS-CoV-2 and MERS-CoV, ACE2 and DPP4, respectively, to identify human anatomical sites that could facilitate co-infection. Furthermore, we have investigated the likely susceptibility of various animal species to MERS-CoV and SARS-CoV-2 infection by comparing known virus spike protein-receptor interacting residues. In conclusion, we suggest that a recombination between SARS-CoV-2 and MERS-CoV RNA is possible and urge public health laboratories in high-risk areas to develop diagnostic capability for the detection of recombined coronaviruses in patient samples.
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Affiliation(s)
- Arinjay Banerjee
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Andrew C. Doxey
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
- Division of Respirology, Department of Medicine, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | | | - Michael J. Mansfield
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Sonu Subudhi
- Gastrointestinal Unit and Liver Center, Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA 02114, USA
| | - Jeremy A. Hirota
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Division of Respirology, Department of Medicine, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Matthew S. Miller
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Andrew G. McArthur
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Samira Mubareka
- Sunnybrook Health Sciences Centre, Toronto, Ontario, M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Karen Mossman
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
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