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O’Dowd K, Isham IM, Vatandour S, Boulianne M, Dozois CM, Gagnon CA, Barjesteh N, Abdul-Careem MF. Host Immune Response Modulation in Avian Coronavirus Infection: Tracheal Transcriptome Profiling In Vitro and In Vivo. Viruses 2024; 16:605. [PMID: 38675946 PMCID: PMC11053446 DOI: 10.3390/v16040605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Infectious bronchitis virus (IBV) is a highly contagious Gammacoronavirus causing moderate to severe respiratory infection in chickens. Understanding the initial antiviral response in the respiratory mucosa is crucial for controlling viral spread. We aimed to characterize the impact of IBV Delmarva (DMV)/1639 and IBV Massachusetts (Mass) 41 at the primary site of infection, namely, in chicken tracheal epithelial cells (cTECs) in vitro and the trachea in vivo. We hypothesized that some elements of the induced antiviral responses are distinct in both infection models. We inoculated cTECs and infected young specific pathogen-free (SPF) chickens with IBV DMV/1639 or IBV Mass41, along with mock-inoculated controls, and studied the transcriptome using RNA-sequencing (RNA-seq) at 3 and 18 h post-infection (hpi) for cTECs and at 4 and 11 days post-infection (dpi) in the trachea. We showed that IBV DMV/1639 and IBV Mass41 replicate in cTECs in vitro and the trachea in vivo, inducing host mRNA expression profiles that are strain- and time-dependent. We demonstrated the different gene expression patterns between in vitro and in vivo tracheal IBV infection. Ultimately, characterizing host-pathogen interactions with various IBV strains reveals potential mechanisms for inducing and modulating the immune response during IBV infection in the chicken trachea.
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Affiliation(s)
- Kelsey O’Dowd
- Health Research Innovation Centre, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (K.O.); (I.M.I.)
| | - Ishara M. Isham
- Health Research Innovation Centre, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (K.O.); (I.M.I.)
| | - Safieh Vatandour
- Department of Animal and Poultry Science, Islamic Azad University, Qaemshahr Branch, Qaem Shahr 4765161964, Iran;
| | - Martine Boulianne
- Swine and Poultry Infectious Diseases Research Centre–Fonds de Recherche du Québec (CRIPA-FRQ), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (M.B.); (C.M.D.); (C.A.G.); (N.B.)
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Charles M. Dozois
- Swine and Poultry Infectious Diseases Research Centre–Fonds de Recherche du Québec (CRIPA-FRQ), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (M.B.); (C.M.D.); (C.A.G.); (N.B.)
- Institut National de Recherche Scientifique-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
| | - Carl A. Gagnon
- Swine and Poultry Infectious Diseases Research Centre–Fonds de Recherche du Québec (CRIPA-FRQ), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (M.B.); (C.M.D.); (C.A.G.); (N.B.)
- Molecular Diagnostic and Virology Laboratories, Centre de Diagnostic Vétérinaire de l’Université de Montréal (CDVUM), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Neda Barjesteh
- Swine and Poultry Infectious Diseases Research Centre–Fonds de Recherche du Québec (CRIPA-FRQ), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (M.B.); (C.M.D.); (C.A.G.); (N.B.)
| | - Mohamed Faizal Abdul-Careem
- Health Research Innovation Centre, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (K.O.); (I.M.I.)
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Wang Y, Zheng S, Zeng W, Yin J, Li Y, Ren Y, Mo X, Shi C, Bergmann SM, Wang Q. Comparative transcriptional analysis between virulent isolate HN1307 and avirulent isolate GD1108 of grass carp reovirus genotype II. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104893. [PMID: 37451563 DOI: 10.1016/j.dci.2023.104893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
As a widespread epidemic virus, genotype II of the grass carp reovirus poses a significant threat to the grass carp farming industry in China. Different genotype II isolates cause different degrees of virulence, although the underlying pathogenic mechanisms remain largely unknown. In this work, infections of grass carp with the virulent isolate grass carp reovirus (GCRV)-HN1307 and the avirulent isolate GCRV-GD1108 were performed to reveal a possible mutual transcriptional discrepancy. More differentially expressed genes (DEGs) were identified in the HN1307-infected group, which defined a grossly similar gene ontology (GO) pattern and different pathway landscape as the GD1108-infected group. Gene set enrichment analysis revealed that pathways related to innate immunity and metabolism were reciprocally activated and suppressed, respectively, following infection withHN1307, compared with GD1108. The trend analysis further indicated that immune-related pathways were involved in one of the four statistically significant profiles. Network analysis of transcription factor-gene interactions and protein-protein interactions on the immune-related profile suggested that among the core transcriptional factors (TFs) (UBTF, HCFC1, MAZ, MAX, and NRF1) and the hub proteins (Tlr3, Tlr7, Tlr9, Irf3, and Irf7), the latter were highly enriched in the toll-like receptor signaling pathway. Real-time quantitative PCR performed on the selected mRNAs validated the relative expression. This work will provide insights into the distinct transcriptional signatures from avirulent and virulent isolates of GCRV, which may contribute to the development of products for prevention.
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Affiliation(s)
- Yingying Wang
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fishery Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Shucheng Zheng
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fishery Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Weiwei Zeng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China.
| | - Jiyuan Yin
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fishery Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Yingying Li
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fishery Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Yan Ren
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fishery Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Xubing Mo
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fishery Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Cunbin Shi
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fishery Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Sven M Bergmann
- Institute of Infectology, Friedrich-Loffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany.
| | - Qing Wang
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fishery Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
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3
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Lafon-Hughes L. Towards Understanding Long COVID: SARS-CoV-2 Strikes the Host Cell Nucleus. Pathogens 2023; 12:806. [PMID: 37375496 DOI: 10.3390/pathogens12060806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Despite what its name suggests, the effects of the COVID-19 pandemic causative agent "Severe Acute Respiratory Syndrome Coronavirus-2" (SARS-CoV-2) were not always confined, neither temporarily (being long-term rather than acute, referred to as Long COVID) nor spatially (affecting several body systems). Moreover, the in-depth study of this ss(+) RNA virus is defying the established scheme according to which it just had a lytic cycle taking place confined to cell membranes and the cytoplasm, leaving the nucleus basically "untouched". Cumulative evidence shows that SARS-CoV-2 components disturb the transport of certain proteins through the nuclear pores. Some SARS-CoV-2 structural proteins such as Spike (S) and Nucleocapsid (N), most non-structural proteins (remarkably, Nsp1 and Nsp3), as well as some accessory proteins (ORF3d, ORF6, ORF9a) can reach the nucleoplasm either due to their nuclear localization signals (NLS) or taking a shuttle with other proteins. A percentage of SARS-CoV-2 RNA can also reach the nucleoplasm. Remarkably, controversy has recently been raised by proving that-at least under certain conditions-, SARS-CoV-2 sequences can be retrotranscribed and inserted as DNA in the host genome, giving rise to chimeric genes. In turn, the expression of viral-host chimeric proteins could potentially create neo-antigens, activate autoimmunity and promote a chronic pro-inflammatory state.
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Affiliation(s)
- Laura Lafon-Hughes
- Departamento de Genética, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo 11600, Uruguay
- Grupo de Biofisicoquímica, Departamento de Ciencias Biológicas, Centro Universitario Regional Litoral Norte, Universidad de la República (CENUR-UdelaR), Salto 50000, Uruguay
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Allan MF, Brivanlou A, Rouskin S. RNA levers and switches controlling viral gene expression. Trends Biochem Sci 2023; 48:391-406. [PMID: 36710231 DOI: 10.1016/j.tibs.2022.12.002] [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: 09/12/2022] [Revised: 11/27/2022] [Accepted: 12/15/2022] [Indexed: 01/29/2023]
Abstract
RNA viruses are diverse and abundant pathogens that are responsible for numerous human diseases. RNA viruses possess relatively compact genomes and have therefore evolved multiple mechanisms to maximize their coding capacities, often by encoding overlapping reading frames. These reading frames are then decoded by mechanisms such as alternative splicing and ribosomal frameshifting to produce multiple distinct proteins. These solutions are enabled by the ability of the RNA genome to fold into 3D structures that can mimic cellular RNAs, hijack host proteins, and expose or occlude regulatory protein-binding motifs to ultimately control key process in the viral life cycle. We highlight recent findings focusing on less conventional mechanisms of gene expression and new discoveries on the role of RNA structures.
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Affiliation(s)
- Matthew F Allan
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amir Brivanlou
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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5
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Keep S, Dowgier G, Lulla V, Britton P, Oade M, Freimanis G, Tennakoon C, Jonassen CM, Tengs T, Bickerton E. Deletion of the s2m RNA Structure in the Avian Coronavirus Infectious Bronchitis Virus and Human Astrovirus Results in Sequence Insertions. J Virol 2023; 97:e0003823. [PMID: 36779761 PMCID: PMC10062133 DOI: 10.1128/jvi.00038-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/25/2023] [Indexed: 02/14/2023] Open
Abstract
Coronaviruses infect a wide variety of host species, resulting in a range of diseases in both humans and animals. The coronavirus genome consists of a large positive-sense single-stranded molecule of RNA containing many RNA structures. One structure, denoted s2m and consisting of 41 nucleotides, is located within the 3' untranslated region (3' UTR) and is shared between some coronavirus species, including infectious bronchitis virus (IBV), severe acute respiratory syndrome coronavirus (SARS-CoV), and SARS-CoV-2, as well as other pathogens, including human astrovirus. Using a reverse genetic system to generate recombinant viruses, we investigated the requirement of the s2m structure in the replication of IBV, a globally distributed economically important Gammacoronavirus that infects poultry causing respiratory disease. Deletion of three nucleotides predicted to destabilize the canonical structure of the s2m or the deletion of the nucleotides corresponding to s2m impacted viral replication in vitro. In vitro passaging of the recombinant IBV with the s2m sequence deleted resulted in a 36-nucleotide insertion in place of the deletion, which was identified to be composed of a duplication of flanking sequences. A similar result was observed following serial passage of human astrovirus with a deleted s2m sequence. RNA modeling indicated that deletion of the nucleotides corresponding to the s2m impacted other RNA structures present in the IBV 3' UTR. Our results indicated for both IBV and human astrovirus a preference for nucleotide occupation in the genome location corresponding to the s2m, which is independent of the specific s2m sequence. IMPORTANCE Coronaviruses infect many species, including humans and animals, with substantial effects on livestock, particularly with respect to poultry. The coronavirus RNA genome consists of structural elements involved in viral replication whose roles are poorly understood. We investigated the requirement of the RNA structural element s2m in the replication of the Gammacoronavirus infectious bronchitis virus, an economically important viral pathogen of poultry. Using reverse genetics to generate recombinant IBVs with either a disrupted or deleted s2m, we showed that the s2m is not required for viral replication in cell culture; however, replication is decreased in tracheal tissue, suggesting a role for the s2m in the natural host. Passaging of these viruses as well as human astrovirus lacking the s2m sequence demonstrated a preference for nucleotide occupation, independent of the s2m sequence. RNA modeling suggested deletion of the s2m may negatively impact other essential RNA structures.
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Affiliation(s)
- Sarah Keep
- The Pirbright Institute, Woking, United Kingdom
| | | | - Valeria Lulla
- Department of Pathology, University of Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom
| | | | - Michael Oade
- Department of Pathology, University of Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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Yuan LX, Yang B, Fung TS, Chen RA, Liu DX. Transcriptomic analysis reveals crucial regulatory roles of immediate-early response genes and related signaling pathways in coronavirus infectious bronchitis virus infection. Virology 2022; 575:1-9. [PMID: 35987078 PMCID: PMC9375846 DOI: 10.1016/j.virol.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022]
Abstract
Coronavirus infection of cells differentially regulates the expression of host genes and their related pathways. In this study, we present the transcriptomic profile of cells infected with gammacoronavirus infectious bronchitis virus (IBV). In IBV-infected human non-small cell lung carcinoma cells (H1299 cells), a total of 1162 differentially expressed genes (DEGs), including 984 upregulated and 178 downregulated genes, was identified. These DEGs were mainly enriched in MAPK and Wnt signaling pathways, and 5 out of the 10 top upregulated genes in all transcripts were immediate-early response genes (IEGs). In addition, the induction of 11 transcripts was validated in IBV-infected H1299 and Vero cells by RT-qPCR. The accuracy, reliability and genericity of the transcriptomic data were demonstrated by functional characterization of these IEGs in cells infected with different coronaviruses in our previous publications. This study provides a reliable transcriptomic profile of host genes and pathways regulated by coronavirus infection.
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Affiliation(s)
- Li Xia Yuan
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China; Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, 526000, Guangdong, China
| | - Bei Yang
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - To Sing Fung
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Rui Ai Chen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, 526000, Guangdong, China
| | - Ding Xiang Liu
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China; Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, 526000, Guangdong, China.
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7
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The Translational Landscape of SARS-CoV-2-infected Cells Reveals Suppression of Innate Immune Genes. mBio 2022; 13:e0081522. [PMID: 35604092 PMCID: PMC9239271 DOI: 10.1128/mbio.00815-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes a number of strategies to modulate viral and host mRNA translation. Here, we used ribosome profiling in SARS-CoV-2-infected model cell lines and primary airway cells grown at an air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We found that SARS-CoV-2 mRNAs dominate the cellular mRNA pool but are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy despite notable accumulation of ribosomes within the slippery sequence on the frameshifting element. In a highly permissive cell line model, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokine, cytokine, and interferon-stimulated genes, many of these mRNAs were not translated efficiently. The impact of SARS-CoV-2 on host mRNA translation was more subtle in primary cells, with marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data reveal the key role of mRNA translation in SARS-CoV-2 replication and highlight unique mechanisms for therapeutic development.
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Eriani G, Martin F. Viral and cellular translation during SARS‐CoV‐2 infection. FEBS Open Bio 2022; 12:1584-1601. [PMID: 35429230 PMCID: PMC9110871 DOI: 10.1002/2211-5463.13413] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/30/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
SARS‐CoV‐2 is a betacoronavirus that emerged in China in December 2019 and which is the causative agent of the Covid‐19 pandemic. This enveloped virus contains a large positive‐sense single‐stranded RNA genome. In this review, we summarize the current knowledge on the molecular mechanisms for the translation of both viral transcripts and cellular messenger RNAs. Non‐structural proteins are encoded by the genomic RNA and are produced in the early steps of infection. In contrast, the structural proteins are produced from subgenomic RNAs that are translated in the late phase of the infectious program. Non‐structural protein 1 (NSP1) is a key molecule that regulates both viral and cellular translation. In addition, NSP1 interferes with multiple steps of the interferon I pathway and thereby blocks host antiviral responses. Therefore, NSP1 is a drug target of choice for the development of antiviral therapies.
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Affiliation(s)
- Gilbert Eriani
- Université de Strasbourg Institut de Biologie Moléculaire et Cellulaire Architecture et Réactivité de l’ARN CNRS UPR9002 2, allée Konrad Roentgen F‐67084 Strasbourg France
| | - Franck Martin
- Université de Strasbourg Institut de Biologie Moléculaire et Cellulaire Architecture et Réactivité de l’ARN CNRS UPR9002 2, allée Konrad Roentgen F‐67084 Strasbourg France
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9
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Identification of Amino Acids within Nonstructural Proteins 10 and 14 of the Avian Coronavirus Infectious Bronchitis Virus That Result in Attenuation In Vivo and In Ovo. J Virol 2022; 96:e0205921. [PMID: 35044208 PMCID: PMC8941869 DOI: 10.1128/jvi.02059-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gammacoronavirus infectious bronchitis virus (IBV) is a highly contagious global pathogen prevalent in all types of poultry flocks. IBV is responsible for economic losses and welfare issues in domestic poultry, resulting in a significant risk to food security. IBV vaccines are currently generated by serial passage of virulent IBV field isolates through embryonated hens' eggs. The different patterns of genomic variation accumulated during this process means that the exact mechanism of attenuation is unknown and presents a risk of reversion to virulence. Additionally, the passaging process adapts the virus to replicate in chicken embryos, increasing embryo lethality. Vaccines produced in this manner are therefore unsuitable for in ovo application. We have developed a reverse genetics system, based on the pathogenic IBV strain M41, to identify genes which can be targeted for rational attenuation. During the development of this reverse genetics system, we identified four amino acids, located in nonstructural proteins (nsps) 10, 14, 15, and 16, which resulted in attenuation both in vivo and in ovo. Further investigation highlighted a role of amino acid changes, Pro85Leu in nsp 10 and Val393Leu in nsp 14, in the attenuated in vivo phenotype observed. This study provides evidence that mutations in nsps offer a promising mechanism for the development of rationally attenuated live vaccines against IBV, which have the potential for in ovo application. IMPORTANCE The Gammacoronavirus infectious bronchitis virus (IBV) is the etiological agent of infectious bronchitis, an acute, highly contagious, economically important disease of poultry. Vaccination is achieved using a mixture of live attenuated vaccines for young chicks and inactivated vaccines as boosters for laying hens. Live attenuated vaccines are generated through serial passage in embryonated hens' eggs, an empirical process which achieves attenuation but retains immunogenicity. However, these vaccines have a risk of reversion to virulence, and they are lethal to the embryo. In this study, we identified amino acids in the replicase gene which attenuated IBV strain M41, both in vivo and in ovo. Stability assays indicate that the attenuating amino acids are stable and unlikely to revert. The data in this study provide evidence that specific modifications in the replicase gene offer a promising direction for IBV live attenuated vaccine development, with the potential for in ovo application.
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10
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Cook GM, Brown K, Shang P, Li Y, Soday L, Dinan AM, Tumescheit C, Mockett APA, Fang Y, Firth AE, Brierley I. Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression. eLife 2022; 11:e75668. [PMID: 35226596 PMCID: PMC9000960 DOI: 10.7554/elife.75668] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/26/2022] [Indexed: 11/13/2022] Open
Abstract
The arterivirus porcine reproductive and respiratory syndrome virus (PRRSV) causes significant economic losses to the swine industry worldwide. Here we apply ribosome profiling (RiboSeq) and parallel RNA sequencing (RNASeq) to characterise the transcriptome and translatome of both species of PRRSV and to analyse the host response to infection. We calculated programmed ribosomal frameshift (PRF) efficiency at both sites on the viral genome. This revealed the nsp2 PRF site as the second known example where temporally regulated frameshifting occurs, with increasing -2 PRF efficiency likely facilitated by accumulation of the PRF-stimulatory viral protein, nsp1β. Surprisingly, we find that PRF efficiency at the canonical ORF1ab frameshift site also increases over time, in contradiction of the common assumption that RNA structure-directed frameshift sites operate at a fixed efficiency. This has potential implications for the numerous other viruses with canonical PRF sites. Furthermore, we discovered several highly translated additional viral ORFs, the translation of which may be facilitated by multiple novel viral transcripts. For example, we found a highly expressed 125-codon ORF overlapping nsp12, which is likely translated from novel subgenomic RNA transcripts that overlap the 3' end of ORF1b. Similar transcripts were discovered for both PRRSV-1 and PRRSV-2, suggesting a potential conserved mechanism for temporally regulating expression of the 3'-proximal region of ORF1b. We also identified a highly translated, short upstream ORF in the 5' UTR, the presence of which is highly conserved amongst PRRSV-2 isolates. These findings reveal hidden complexity in the gene expression programmes of these important nidoviruses.
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Affiliation(s)
- Georgia M Cook
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Katherine Brown
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Pengcheng Shang
- Department of Diagnostic Medicine and Pathobiology, Kansas State UniversityManhattanUnited States
| | - Yanhua Li
- Department of Diagnostic Medicine and Pathobiology, Kansas State UniversityManhattanUnited States
| | - Lior Soday
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Adam M Dinan
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | | | | | - Ying Fang
- Department of Diagnostic Medicine and Pathobiology, Kansas State UniversityManhattanUnited States
| | - Andrew E Firth
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Ian Brierley
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
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11
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Hill CH, Cook GM, Napthine S, Kibe A, Brown K, Caliskan N, Firth AE, Graham SC, Brierley I. Investigating molecular mechanisms of 2A-stimulated ribosomal pausing and frameshifting in Theilovirus. Nucleic Acids Res 2021; 49:11938-11958. [PMID: 34751406 PMCID: PMC8599813 DOI: 10.1093/nar/gkab969] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 12/02/2022] Open
Abstract
The 2A protein of Theiler's murine encephalomyelitis virus (TMEV) acts as a switch to stimulate programmed -1 ribosomal frameshifting (PRF) during infection. Here, we present the X-ray crystal structure of TMEV 2A and define how it recognises the stimulatory RNA element. We demonstrate a critical role for bases upstream of the originally predicted stem-loop, providing evidence for a pseudoknot-like conformation and suggesting that the recognition of this pseudoknot by beta-shell proteins is a conserved feature in cardioviruses. Through examination of PRF in TMEV-infected cells by ribosome profiling, we identify a series of ribosomal pauses around the site of PRF induced by the 2A-pseudoknot complex. Careful normalisation of ribosomal profiling data with a 2A knockout virus facilitated the identification, through disome analysis, of ribosome stacking at the TMEV frameshifting signal. These experiments provide unparalleled detail of the molecular mechanisms underpinning Theilovirus protein-stimulated frameshifting.
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Affiliation(s)
- Chris H Hill
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Georgia M Cook
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Sawsan Napthine
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Anuja Kibe
- Helmholtz Institute for RNA-based Infection Research (HIRI), Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
| | - Katherine Brown
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
- Medical Faculty, Julius-Maximilians University Würzburg, 97074 Würzburg, Germany
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Stephen C Graham
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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12
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Puray-Chavez M, Lee N, Tenneti K, Wang Y, Vuong HR, Liu Y, Horani A, Huang T, Gunsten SP, Case JB, Yang W, Diamond MS, Brody SL, Dougherty J, Kutluay SB. The translational landscape of SARS-CoV-2 and infected cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.11.03.367516. [PMID: 33173862 PMCID: PMC7654850 DOI: 10.1101/2020.11.03.367516] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SARS-CoV-2 utilizes a number of strategies to modulate viral and host mRNA translation. Here, we used ribosome profiling in SARS-CoV-2 infected model cell lines and primary airway cells grown at the air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We find that SARS-CoV-2 mRNAs dominate the cellular mRNA pool but are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy in comparison to HIV-1, suggesting utilization of distinct structural elements. In the highly permissive cell models, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokines, cytokines and interferon stimulated genes, many of these mRNAs were not translated efficiently. Impact of SARS-CoV-2 on host mRNA translation was more subtle in primary cells, with marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data reveal the key role of mRNA translation in SARS-CoV-2 replication and highlight unique mechanisms for therapeutic development.
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Affiliation(s)
- Maritza Puray-Chavez
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Nakyung Lee
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Kasyap Tenneti
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yiqing Wang
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Hung R Vuong
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Amjad Horani
- Department of Pediatrics, Allergy, Immunology and Pulmonary Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Tao Huang
- Department of Medicine, Pulmonary and Critical Care Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Sean P Gunsten
- Department of Medicine, Pulmonary and Critical Care Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - James B Case
- Department of Medicine, Infectious Disease Division, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Wei Yang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Medicine, Infectious Disease Division, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Steven L Brody
- Department of Medicine, Pulmonary and Critical Care Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Joseph Dougherty
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Sebla B Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
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13
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A high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome. Nat Commun 2021; 12:5120. [PMID: 34433827 PMCID: PMC8387416 DOI: 10.1038/s41467-021-25361-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 08/02/2021] [Indexed: 12/15/2022] Open
Abstract
COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which infected >200 million people resulting in >4 million deaths. However, temporal landscape of the SARS-CoV-2 translatome and its impact on the human genome remain unexplored. Here, we report a high-resolution atlas of the translatome and transcriptome of SARS-CoV-2 for various time points after infecting human cells. Intriguingly, substantial amount of SARS-CoV-2 translation initiates at a novel translation initiation site (TIS) located in the leader sequence, termed TIS-L. Since TIS-L is included in all the genomic and subgenomic RNAs, the SARS-CoV-2 translatome may be regulated by a sophisticated interplay between TIS-L and downstream TISs. TIS-L functions as a strong translation enhancer for ORF S, and as translation suppressors for most of the other ORFs. Our global temporal atlas provides compelling insight into unique regulation of the SARS-CoV-2 translatome and helps comprehensively evaluate its impact on the human genome. Here, Kim et al. apply various sequencing techniques (RPF-seq, QTI-seq, mRNA-seq, sRNA-seq) to unravel the high-resolution, longitudinal translatome and transcriptome of SARS-CoV-2. They identify a translation initiation site in the leader sequence of all genomic and subgenomic RNAs and show its relevance for the SARS-CoV-2 translatome.
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14
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Atkins JF, O’Connor KM, Bhatt PR, Loughran G. From Recoding to Peptides for MHC Class I Immune Display: Enriching Viral Expression, Virus Vulnerability and Virus Evasion. Viruses 2021; 13:1251. [PMID: 34199077 PMCID: PMC8310308 DOI: 10.3390/v13071251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/11/2021] [Accepted: 06/19/2021] [Indexed: 01/02/2023] Open
Abstract
Many viruses, especially RNA viruses, utilize programmed ribosomal frameshifting and/or stop codon readthrough in their expression, and in the decoding of a few a UGA is dynamically redefined to specify selenocysteine. This recoding can effectively increase viral coding capacity and generate a set ratio of products with the same N-terminal domain(s) but different C-terminal domains. Recoding can also be regulatory or generate a product with the non-universal 21st directly encoded amino acid. Selection for translation speed in the expression of many viruses at the expense of fidelity creates host immune defensive opportunities. In contrast to host opportunism, certain viruses, including some persistent viruses, utilize recoding or adventitious frameshifting as part of their strategy to evade an immune response or specific drugs. Several instances of recoding in small intensively studied viruses escaped detection for many years and their identification resolved dilemmas. The fundamental importance of ribosome ratcheting is consistent with the initial strong view of invariant triplet decoding which however did not foresee the possibility of transitory anticodon:codon dissociation. Deep level dynamics and structural understanding of recoding is underway, and a high level structure relevant to the frameshifting required for expression of the SARS CoV-2 genome has just been determined.
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Affiliation(s)
- John F. Atkins
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
| | - Kate M. O’Connor
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
| | - Pramod R. Bhatt
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Gary Loughran
- Schools of Biochemistry and Microbiology, University College Cork, T12 XF62 Cork, Ireland; (K.M.O.); (P.R.B.); (G.L.)
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15
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Transcriptome analysis of primary chicken cells infected with infectious bronchitis virus strain K047-12 isolated in Korea. Arch Virol 2021; 166:2291-2298. [PMID: 34089367 PMCID: PMC8178662 DOI: 10.1007/s00705-021-05124-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/15/2021] [Indexed: 01/21/2023]
Abstract
Infectious bronchitis virus (IBV), an avian coronavirus, is highly contagious. Chickens with IBV infection develop acute pathogenesis in multiple organs, including the respiratory and urogenital tracts. Frequent recombination in the spike (S) glycoprotein gene has made vaccine strategies ineffective. To understand IBV pathogenesis, we analyzed the genetic distance between Korean IBV isolates and other coronaviruses, including SARS-CoV-2. To obtain comprehensive information about early immune responses such as innate cytokine production and associated immune regulation during IBV infection, we infected primary chicken embryonic kidney cells and performed transcriptome analysis. We observed that the functional pathways of innate immunity are regulated and confirmed expression of genes that coordinate early immune responses. Understanding the immune profile of the host cell may assist in vaccine development.
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16
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Franzo G, Tucciarone CM, Legnardi M, Cecchinato M. Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues. BMC Genomics 2021; 22:244. [PMID: 33827429 PMCID: PMC8025453 DOI: 10.1186/s12864-021-07559-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/26/2021] [Indexed: 11/10/2022] Open
Abstract
Background Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues. Results The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle. Conclusions The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07559-5.
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Affiliation(s)
- Giovanni Franzo
- Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy.
| | - Claudia Maria Tucciarone
- Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy
| | - Matteo Legnardi
- Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy
| | - Mattia Cecchinato
- Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy
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17
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Zhao MM, Yang WL, Yang FY, Zhang L, Huang WJ, Hou W, Fan CF, Jin RH, Feng YM, Wang YC, Yang JK. Cathepsin L plays a key role in SARS-CoV-2 infection in humans and humanized mice and is a promising target for new drug development. Signal Transduct Target Ther 2021; 6:134. [PMID: 33774649 PMCID: PMC7997800 DOI: 10.1038/s41392-021-00558-8] [Citation(s) in RCA: 276] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/02/2021] [Accepted: 02/20/2021] [Indexed: 02/06/2023] Open
Abstract
To discover new drugs to combat COVID-19, an understanding of the molecular basis of SARS-CoV-2 infection is urgently needed. Here, for the first time, we report the crucial role of cathepsin L (CTSL) in patients with COVID-19. The circulating level of CTSL was elevated after SARS-CoV-2 infection and was positively correlated with disease course and severity. Correspondingly, SARS-CoV-2 pseudovirus infection increased CTSL expression in human cells in vitro and human ACE2 transgenic mice in vivo, while CTSL overexpression, in turn, enhanced pseudovirus infection in human cells. CTSL functionally cleaved the SARS-CoV-2 spike protein and enhanced virus entry, as evidenced by CTSL overexpression and knockdown in vitro and application of CTSL inhibitor drugs in vivo. Furthermore, amantadine, a licensed anti-influenza drug, significantly inhibited CTSL activity after SARS-CoV-2 pseudovirus infection and prevented infection both in vitro and in vivo. Therefore, CTSL is a promising target for new anti-COVID-19 drug development.
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Affiliation(s)
- Miao-Miao Zhao
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wei-Li Yang
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Fang-Yuan Yang
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Li Zhang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Wei-Jin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Wei Hou
- Department of Science and Technology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Chang-Fa Fan
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control, Beijing, China
| | - Rong-Hua Jin
- Department of Science and Technology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Ying-Mei Feng
- Department of Science and Technology, Beijing Youan Hospital, Capital Medical University, Beijing, China.
| | - You-Chun Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China.
| | - Jin-Kui Yang
- Department of Endocrinology, Beijing Tongren Hospital, Capital Medical University, Beijing, China.
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18
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Al-Qaaneh AM, Alshammari T, Aldahhan R, Aldossary H, Alkhalifah ZA, Borgio JF. Genome composition and genetic characterization of SARS-CoV-2. Saudi J Biol Sci 2021; 28:1978-1989. [PMID: 33519278 PMCID: PMC7834485 DOI: 10.1016/j.sjbs.2020.12.053] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is a type of Betacoronaviruses responsible for COVID-19 pandemic disease, with more than 1.745 million fatalities globally as of December-2020. Genetically, it is considered the second largest genome of all RNA viruses with a 5' cap and 3' poly-A tail. Phylogenetic analyses of coronaviruses reveal that SARS-CoV-2 is genetically closely related to the Bat-SARS Like-Corona virus (Bat-SL-Cov) with 96% whole-genome identity. SARS-CoV-2 genome consists of 15 ORFs coded into 29 proteins. At the 5' terminal of the genome, we have ORF1ab and ORF1a, which encode the 1ab and 1a polypeptides that are proteolytically cleaved into 16 different nonstructural proteins (NSPs). The 3' terminal of the genome represents four structural (spike, envelope, matrix, and nucleocapsid) and nine accessory (3a, 3b, 6, 7a, 7b, 8b, 9a, 9b, and orf10) proteins. As the number of COVID-19 patients increases dramatically worldwide, there is an urgent need to find a quick and sensitive diagnostic tool for controlling the outbreak of SARS-CoV-2 in the community. Today, molecular testing methods utilizing viral genetic material (e.g., PCR) represent the crucial diagnostic tool for the SARS-CoV-2 virus despite its low sensitivity in the early stage of viral infection. This review summarizes the genome composition and genetic characterization of the SARS-CoV-2.
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Affiliation(s)
- Ayman M. Al-Qaaneh
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
- Drug Information Center, Pharmacy Services Department, Johns Hopkins Aramco Healthcare (JHAH), Dhahran 31311, Saudi Arabia
| | - Thamer Alshammari
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Razan Aldahhan
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Hanan Aldossary
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
- Department of Epidemic Diseases Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Zahra Abduljaleel Alkhalifah
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
- Department of Epidemic Diseases Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
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19
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Keep S, Oade MS, Lidzbarski-Silvestre F, Bentley K, Stevenson-Leggett P, Freimanis GL, Tennakoon C, Sanderson N, Hammond JA, Jones RC, Britton P, Bickerton E. Multiple novel non-canonically transcribed sub-genomic mRNAs produced by avian coronavirus infectious bronchitis virus. J Gen Virol 2020; 101:1103-1118. [PMID: 32720890 PMCID: PMC7660457 DOI: 10.1099/jgv.0.001474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/01/2020] [Indexed: 12/15/2022] Open
Abstract
Coronavirus sub-genomic mRNA (sgmRNA) synthesis occurs via a process of discontinuous transcription involving complementary transcription regulatory sequences (TRSs), one (TRS-L) encompassing the leader sequence of the 5' untranslated region (UTR), and the other upstream of each structural and accessory gene (TRS-B). Several coronaviruses have an ORF located between the N gene and the 3'-UTR, an area previously thought to be non-coding in the Gammacoronavirus infectious bronchitis virus (IBV) due to a lack of a canonical TRS-B. Here, we identify a non-canonical TRS-B allowing for a novel sgmRNA relating to this ORF to be produced in several strains of IBV: Beaudette, CR88, H120, D1466, Italy-02 and QX. Interestingly, the potential protein produced by this ORF is prematurely truncated in the Beaudette strain. A single nucleotide deletion was made in the Beaudette strain allowing for the generation of a recombinant IBV (rIBV) that had the potential to express a full-length protein. Assessment of this rIBV in vitro demonstrated that restoration of the full-length potential protein had no effect on viral replication. Further assessment of the Beaudette-derived RNA identified a second non-canonically transcribed sgmRNA located within gene 2. Deep sequencing analysis of allantoic fluid from Beaudette-infected embryonated eggs confirmed the presence of both the newly identified non-canonically transcribed sgmRNAs and highlighted the potential for further yet unidentified sgmRNAs. This HiSeq data, alongside the confirmation of non-canonically transcribed sgmRNAs, indicates the potential of the coronavirus genome to encode a larger repertoire of genes than has currently been identified.
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Affiliation(s)
- Sarah Keep
- The Pirbright Institute, Ash Road, Woking, GU24 0NF, UK
| | | | - Filip Lidzbarski-Silvestre
- The Pirbright Institute, Ash Road, Woking, GU24 0NF, UK
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Kirsten Bentley
- The Pirbright Institute, Ash Road, Woking, GU24 0NF, UK
- School of Biology, University of St Andrews, St Andrews, UK
| | | | | | | | - Nicholas Sanderson
- The Pirbright Institute, Ash Road, Woking, GU24 0NF, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Richard C. Jones
- School of Veterinary Science, University of Liverpool, Neston, UK
| | - Paul Britton
- The Pirbright Institute, Ash Road, Woking, GU24 0NF, UK
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20
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Khrustalev VV, Giri R, Khrustaleva TA, Kapuganti SK, Stojarov AN, Poboinev VV. Translation-Associated Mutational U-Pressure in the First ORF of SARS-CoV-2 and Other Coronaviruses. Front Microbiol 2020; 11:559165. [PMID: 33072018 PMCID: PMC7536284 DOI: 10.3389/fmicb.2020.559165] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Within 4 months of the ongoing COVID-19 pandemic caused by SARS-CoV-2, more than 250 nucleotide mutations have been detected in ORF1ab of the virus isolated from infected persons from different parts of the globe. These observations open up an obvious question about the rate and direction of mutational pressure for further vaccine and therapeutics designing. In this study, we did a comparative analysis of ORF1a and ORF1b by using the first isolate (Wuhan strain) as the parent sequence. We observed that most of the nucleotide mutations are C to U transitions. The rate of synonymous C to U transitions is significantly higher than the rate of non-synonymous ones, indicating negative selection on amino acid substitutions. Further, trends in nucleotide usage bias have been investigated in 49 coronaviruses species. A strong bias in nucleotide usage in fourfold degenerate sites toward uracil residues is seen in ORF1ab of all the studied coronaviruses: both in the ORF1a and in the ORF1b translated thanks to the programmed ribosomal frameshifting that has an efficiency of 14 – 45% in different species. A more substantial mutational U-pressure is observed in ORF1a than in ORF1b perhaps because ORF1a is translated more frequently than ORF1b. Mutational U-pressure is there even in ORFs that are not translated from genomic RNA plus strands, but the bias is weaker than in ORF1ab. Unlike other nucleotide mutations, mutational U-pressure caused by cytosine deamination, mostly occurring during the RNA plus strand replication and also translation, cannot be corrected by the proof-reading machinery of coronaviruses. The knowledge generated on the mutational U-pressure that becomes stronger during translation of viral RNA plus strands has implications for vaccine and nucleoside analog development for treating COVID-19 and other coronavirus infections.
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Affiliation(s)
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Tatyana Aleksandrovna Khrustaleva
- Biochemical Group of Multidisciplinary Diagnostic Laboratory, Institute of Physiology of the National Academy of Sciences of Belarus, Minsk, Belarus
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21
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Finkel Y, Mizrahi O, Nachshon A, Weingarten-Gabbay S, Morgenstern D, Yahalom-Ronen Y, Tamir H, Achdout H, Stein D, Israeli O, Beth-Din A, Melamed S, Weiss S, Israely T, Paran N, Schwartz M, Stern-Ginossar N. The coding capacity of SARS-CoV-2. Nature 2020; 589:125-130. [PMID: 32906143 DOI: 10.1038/s41586-020-2739-1] [Citation(s) in RCA: 352] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic1. To understand the pathogenicity and antigenic potential of SARS-CoV-2 and to develop therapeutic tools, it is essential to profile the full repertoire of its expressed proteins. The current map of SARS-CoV-2 coding capacity is based on computational predictions and relies on homology with other coronaviruses. As the protein complement varies among coronaviruses, especially in regard to the variety of accessory proteins, it is crucial to characterize the specific range of SARS-CoV-2 proteins in an unbiased and open-ended manner. Here, using a suite of ribosome-profiling techniques2-4, we present a high-resolution map of coding regions in the SARS-CoV-2 genome, which enables us to accurately quantify the expression of canonical viral open reading frames (ORFs) and to identify 23 unannotated viral ORFs. These ORFs include upstream ORFs that are likely to have a regulatory role, several in-frame internal ORFs within existing ORFs, resulting in N-terminally truncated products, as well as internal out-of-frame ORFs, which generate novel polypeptides. We further show that viral mRNAs are not translated more efficiently than host mRNAs; instead, virus translation dominates host translation because of the high levels of viral transcripts. Our work provides a resource that will form the basis of future functional studies.
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Affiliation(s)
- Yaara Finkel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Orel Mizrahi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shira Weingarten-Gabbay
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - David Morgenstern
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalised Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Hadas Tamir
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Hagit Achdout
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Dana Stein
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Sharon Melamed
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shay Weiss
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Michal Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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Keep S, Sives S, Stevenson-Leggett P, Britton P, Vervelde L, Bickerton E. Limited Cross-Protection against Infectious Bronchitis Provided by Recombinant Infectious Bronchitis Viruses Expressing Heterologous Spike Glycoproteins. Vaccines (Basel) 2020; 8:E330. [PMID: 32580371 PMCID: PMC7350270 DOI: 10.3390/vaccines8020330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 12/19/2022] Open
Abstract
Gammacoronavirus infectious bronchitis virus (IBV) causes an economically important respiratory disease of poultry. Protective immunity is associated with the major structural protein, spike (S) glycoprotein, which induces neutralising antibodies and defines the serotype. Cross-protective immunity between serotypes is limited and can be difficult to predict. In this study, the ability of two recombinant IBV vaccine candidates, BeauR-M41(S) and BeauR-4/91(S), to induce cross-protection against a third serotype, QX, was assessed. Both rIBVs are genetically based on the Beaudette genome with only the S gene derived from either M41 or 4/91, two unrelated serotypes. The use of these rIBVs allowed for the assessment of the potential of M41 and 4/91 S glycoproteins to induce cross-protective immunity against a heterologous QX challenge. The impact of the order of vaccination was also assessed. Homologous primary and secondary vaccination with BeauR-M41(S) or BeauR-4/91(S) resulted in a significant reduction of infectious QX load in the trachea at four days post-challenge, whereas heterologous primary and secondary vaccination with BeauR-M41(S) and BeauR-4/91(S) reduced viral RNA load in the conjunctiva-associated lymphoid tissue (CALT). Both homologous and heterologous vaccination regimes reduced clinical signs and birds recovered more rapidly as compared with an unvaccinated/challenge control group. Despite both rIBV BeauR-M41(S) and BeauR-4/91(S) displaying limited replication in vivo, serum titres in these vaccinated groups were higher as compared with the unvaccinated/challenge control group. This suggests that vaccination with rIBV primed the birds for a boosted humoral response to heterologous QX challenge. Collectively, vaccination with the rIBV elicited limited protection against challenge, with failure to protect against tracheal ciliostasis, clinical manifestations, and viral replication. The use of a less attenuated recombinant vector that replicates throughout the respiratory tract could be required to elicit a stronger and prolonged protective immune response.
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Affiliation(s)
- Sarah Keep
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (P.B.)
| | - Samantha Sives
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK; (S.S.); (L.V.)
| | | | - Paul Britton
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (P.B.)
| | - Lonneke Vervelde
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK; (S.S.); (L.V.)
| | - Erica Bickerton
- The Pirbright Institute, Pirbright, Surrey GU24 0NF, UK; (S.K.); (P.S.-L.); (P.B.)
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Comparative Analysis of Gene Expression in Virulent and Attenuated Strains of Infectious Bronchitis Virus at Subcodon Resolution. J Virol 2019; 93:JVI.00714-19. [PMID: 31243124 PMCID: PMC6714804 DOI: 10.1128/jvi.00714-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/17/2019] [Indexed: 12/27/2022] Open
Abstract
Like all coronaviruses, avian infectious bronchitis virus (IBV) possesses a long, single-stranded, positive-sense RNA genome (∼27 kb) and has a complex replication strategy that includes the production of a nested set of subgenomic mRNAs (sgmRNAs). Here, we used whole-transcriptome sequencing (RNASeq) and ribosome profiling (RiboSeq) to delineate gene expression in the IBV M41-CK and Beau-R strains at subcodon resolution. RNASeq facilitated a comparative analysis of viral RNA synthesis and revealed two novel transcription junction sites in the attenuated Beau-R strain, one of which would generate a sgmRNA encoding a ribosomally occupied open reading frame (dORF) located downstream of the nucleocapsid coding region. RiboSeq permitted quantification of the translational efficiency of virus gene expression and identified, for the first time, sites of ribosomal pausing on the genome. Quantification of reads flanking the programmed ribosomal frameshifting (PRF) signal at the genomic RNA ORF1a/ORF1b junction revealed that PRF in IBV is highly efficient (33 to 40%). Triplet phasing of RiboSeq data allowed precise determination of reading frames and revealed the translation of two ORFs (ORF4b and ORF4c on sgmRNA IR), which are widely conserved across IBV isolates. Analysis of differential gene expression in infected primary chick kidney cells indicated that the host cell response to IBV occurs primarily at the level of transcription, with global upregulation of immune-related mRNA transcripts following infection and comparatively modest changes in the translation efficiencies of host genes. Cellular genes and gene networks differentially expressed during virus infection were also identified, giving insights into the host cell response to IBV infection.IMPORTANCE IBV is a major avian pathogen and presents a substantial economic burden to the poultry industry. Improved vaccination strategies are urgently needed to curb the global spread of this virus, and the development of suitable vaccine candidates will be aided by an improved understanding of IBV molecular biology. Our high-resolution data have enabled a precise study of transcription and translation in cells infected with both pathogenic and attenuated forms of IBV and expand our understanding of gammacoronaviral gene expression. We demonstrate that gene expression shows considerable intraspecies variation, with single nucleotide polymorphisms being associated with altered production of sgmRNA transcripts, and our RiboSeq data sets enabled us to uncover novel ribosomally occupied ORFs in both strains. The numerous cellular genes and gene networks found to be differentially expressed during virus infection provide insights into the host cell response to IBV infection.
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