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Hussein HAM, Thabet AA, Wardany AA, El-Adly AM, Ali M, Hassan MEA, Abdeldayem MAB, Mohamed ARMA, Sobhy A, El-Mokhtar MA, Afifi MM, Fathy SM, Sultan S. SARS-CoV-2 outbreak: role of viral proteins and genomic diversity in virus infection and COVID-19 progression. Virol J 2024; 21:75. [PMID: 38539202 PMCID: PMC10967059 DOI: 10.1186/s12985-024-02342-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 03/12/2024] [Indexed: 05/15/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is the cause of coronavirus disease 2019 (COVID-19); a severe respiratory distress that has emerged from the city of Wuhan, Hubei province, China during December 2019. COVID-19 is currently the major global health problem and the disease has now spread to most countries in the world. COVID-19 has profoundly impacted human health and activities worldwide. Genetic mutation is one of the essential characteristics of viruses. They do so to adapt to their host or to move to another one. Viral genetic mutations have a high potentiality to impact human health as these mutations grant viruses unique unpredicted characteristics. The difficulty in predicting viral genetic mutations is a significant obstacle in the field. Evidence indicates that SARS-CoV-2 has a variety of genetic mutations and genomic diversity with obvious clinical consequences and implications. In this review, we comprehensively summarized and discussed the currently available knowledge regarding SARS-CoV-2 outbreaks with a fundamental focus on the role of the viral proteins and their mutations in viral infection and COVID-19 progression. We also summarized the clinical implications of SARS-CoV-2 variants and how they affect the disease severity and hinder vaccine development. Finally, we provided a massive phylogenetic analysis of the spike gene of 214 SARS-CoV-2 isolates from different geographical regions all over the world and their associated clinical implications.
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Affiliation(s)
- Hosni A M Hussein
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt.
| | - Ali A Thabet
- Department of Zoology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed A Wardany
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed M El-Adly
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed Ali
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed E A Hassan
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A B Abdeldayem
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | | | - Ali Sobhy
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A El-Mokhtar
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos Campus, Lebanon
| | - Magdy M Afifi
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - Samah M Fathy
- Department of Zoology, Faculty of Science, Fayoum University, Fayoum, Egypt.
| | - Serageldeen Sultan
- Department of Microbiology, Virology Division, Faculty of Veterinary medicine, South Valley University, 83523, Qena, Egypt.
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2
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Wang HC, Wang YC, Wu CJ. Phylogenetic characteristics of Non-SARS human coronavirus in southern Taiwan, 2012-2013. Biomed J 2023; 46:100555. [PMID: 35964939 PMCID: PMC9367205 DOI: 10.1016/j.bj.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: 05/16/2022] [Revised: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 11/11/2022] Open
Abstract
This study characterizes the phylogenetic relatedness of non-SARS human coronaviruses (HCoVs) in southern Taiwan by sequencing the nucleocapsid (N), spike (S), and RNA-dependent RNA polymerase (RdRp) genes directly from ten HCoV PCR-positive respiratory samples collected during 2012-2013. In the N, S1, and RdRp phylogeny, HCoV-OC43 in one and three samples was clustered with genotypes F and G, respectively, and HCoV-OC43 in sample YC101/TWN/2013 represented a recombination event between genotypes F and G. Amino acid substitutions in the S1 protein of HCoV-OC43 were also identified. In the N phylogeny, HCoV-HKU1 in one and two samples clustered with genotypes A and B, respectively, and HCoV-229E in two samples was clustered with genogroup 6. The genotypes and genogroup detected here were in line with the prevalent phylogenetic lineages reported outside of Taiwan during the contemporary period. In summary, three species of non-SARS HCoVs with different genotypes cocirculated in the community, with genetic evolution observed in HCoV-OC43.
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Affiliation(s)
- Hsuan-Chen Wang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
| | - Yu-Chun Wang
- Center for Genomic Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chi-Jung Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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3
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Kadja T, Sun Y, Chodavarapu VP. Low-Cost, Real-Time Polymerase Chain Reaction System with Integrated RNA Extraction. SENSORS (BASEL, SWITZERLAND) 2023; 23:4604. [PMID: 37430517 DOI: 10.3390/s23104604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/01/2023] [Accepted: 05/06/2023] [Indexed: 07/12/2023]
Abstract
Rapid, easy-to-use, and low-cost systems for biological sample testing are important for point-of-care diagnostics and various other health applications. The recent pandemic of Coronavirus Disease 2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed an urgent need to rapidly and accurately identify the genetic material of SARS-CoV-2, an enveloped ribonucleic acid (RNA) virus, in upper respiratory specimens from people. In general, sensitive testing methods require genetic material extraction from the specimen. Unfortunately, current commercially available extraction kits are expensive and involve time-consuming and laborious extraction procedures. To overcome the difficulties associated with common extraction methods, we propose a simple enzymatic assay for the nucleic acid extraction step using heat mediation to improve the polymerase chain reaction (PCR) reaction sensitivity. Our protocol was tested on Human Coronavirus 229E (HCoV-229E) as an example, which comes from the large coronaviridae family of viruses that affect birds, amphibians, and mammals, of which SARS-CoV-2 is a member. The proposed assay was performed using a low-cost, custom-made, real-time PCR system that incorporates thermal cycling and fluorescence detection. It had fully customizable reaction settings to allow versatile biological sample testing for various applications, including point-of-care medical diagnosis, food and water quality testing, and emergency health situations. Our results show that heat-mediated RNA extraction is a viable extraction method when compared to commercial extraction kits. Further, our study showed that extraction has a direct impact on purified laboratory samples of HCoV-229E, but no direct impact on infected human cells. This is clinically relevant, as it allows us to circumvent the extraction step on clinical samples when using PCR.
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Affiliation(s)
- Tchamie Kadja
- Department of Electrical and Computer Engineering, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Yvonne Sun
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Vamsy P Chodavarapu
- Department of Electrical and Computer Engineering, University of Dayton, 300 College Park, Dayton, OH 45469, USA
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4
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Becerra-Artiles A, Nanaware PP, Muneeruddin K, Weaver GC, Shaffer SA, Calvo-Calle JM, Stern LJ. Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.01.518643. [PMID: 36482973 PMCID: PMC9727760 DOI: 10.1101/2022.12.01.518643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Seasonal "common-cold" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but identification and characterization of the T cell response to seasonal human coronaviruses remain largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal human coronavirus OC43. We identified MHC-I and MHC-II bound peptides derived from the viral spike, nucleocapsid, hemagglutinin-esterase, 3C-like proteinase, and envelope proteins. Only three MHC-I bound OC43-derived peptides were observed, possibly due to the potent MHC-I downregulation induced by OC43 infection. By contrast, 80 MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. These peptides elicited low-abundance recall T cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T cell lines. Among the validated epitopes, S 903-917 presented by DPA1*01:03/DPB1*04:01 and S 1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. N 54-68 and HE 128-142 presented by DRB1*15:01 and HE 259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow T cell cross-reactivity after infection or vaccination and could aid in the selection of epitopes for inclusion in pan-coronavirus vaccines. Author Summary There is much current interest in cellular immune responses to seasonal common-cold coronaviruses because of their possible role in mediating protection against SARS-CoV-2 infection or pathology. However, identification of relevant T cell epitopes and systematic studies of the T cell responses responding to these viruses are scarce. We conducted a study to identify naturally processed and presented MHC-I and MHC-II epitopes from human cells infected with the seasonal coronavirus HCoV-OC43, and to characterize the T cell responses associated with these epitopes. We found epitopes specific to the seasonal coronaviruses, as well as epitopes cross-reactive between HCoV-OC43 and SARS-CoV-2. These epitopes should be useful in following immune responses to seasonal coronaviruses and identifying their roles in COVID-19 vaccination, infection, and pathogenesis.
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Affiliation(s)
- Aniuska Becerra-Artiles
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Padma P. Nanaware
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Khaja Muneeruddin
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury MA
| | - Grant C. Weaver
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Scott A. Shaffer
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury MA
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - J. Mauricio Calvo-Calle
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Lawrence J. Stern
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA 01655, USA
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Identification of a novel neutralizing epitope on the N-terminal domain of the HCoV-229E spike protein. J Virol 2021; 96:e0195521. [PMID: 34908442 DOI: 10.1128/jvi.01955-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The receptor binding domain (RBD) of the coronavirus spike protein (S) has been verified to be the main target for potent neutralizing antibodies (nAbs) in most coronaviruses, and the N-terminal domain (NTD) of some betacoronaviruses has also been indicated to induce nAbs. For alphacoronavirus HCoV-229E, its RBD has been shown to have neutralizing epitopes, and these epitopes could change over time. However, whether neutralizing epitopes exist on the NTD and whether these epitopes change like those of the RBD are still unknown. Here, we verified that neutralizing epitopes exist on the NTD of HCoV-229E. Furthermore, we characterized an NTD targeting nAb 5H10, which could neutralize both pseudotyped and authentic HCoV-229E VR740 in vitro. Epitope mapping indicated that 5H10 targeted motif E1 (147-167 aa) and identified F159 as critical for 5H10 binding. More importantly, our results revealed that motif E1 was highly conserved among clinical isolates except for F159. Further data proved that mutations at position 159 gradually appeared over time and could completely abolish the neutralizing ability of 5H10, supporting the notion that position 159 may be under selective pressure during the human epidemic. In addition, we also found that contemporary clinical serum has a stronger binding capacity for the NTD of contemporary strains than historic strains, proving that the epitope on the NTD could change over time. In summary, these findings define a novel neutralizing epitope on the NTD of HCoV-229E S and provide a theoretical basis for the design of vaccines against HCoV-229E or related coronaviruses. Importance Characterization of the neutralizing epitope of the spike (S) protein, the major invasion protein of coronaviruses, can help us better understand the evolutionary characteristics of these viruses and promote vaccine development. To date, the neutralizing epitope distribution of alphacoronaviruses is not well known. Here, we identified a neutralizing antibody that targeted the N-terminal domain (NTD) of the alphacoronavirus HCoV-229E S protein. Epitope mapping revealed a novel epitope that was not previously discovered in HCoV-229E. Further studies identified an important residue, F159. Mutations that gradually appeared over time at this site abolished the neutralizing ability of 5H10, indicating that selective pressure occurred at this position in the spread of HCoV-229E. Furthermore, we found that the epitopes within the NTD also changed over time. Taken together, our findings defined a novel neutralizing epitope and highlighted the role of the NTD in the future prevention and control of HCoV-229E or related coronaviruses.
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Sarker MT, Hasan AQF, Rafi MO, Hossain MJ, El-Mageed HRA, Elsapagh RM, Capasso R, Emran TB. A Comprehensive Overview of the Newly Emerged COVID-19 Pandemic: Features, Origin, Genomics, Epidemiology, Treatment, and Prevention. BIOLOGICS 2021; 1:357-383. [DOI: 10.3390/biologics1030021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The coronavirus disease 2019 (COVID-19), a life-threatening pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has resulted in massive destruction and is still continuously adding to its death toll. The advent of this global outbreak has not yet been confirmed; however, investigation for suitable prophylaxis against this lethal virus is being carried out by experts all around the globe. The SARS-CoV-2 belongs to the Coronaviridae superfamily, like the other previously occurring human coronavirus variants. To better understand a new virus variant, such as the SARS-CoV-2 delta variant, it is vital to investigate previous virus strains, including their genomic composition and functionality. Our study aimed at addressing the basic overview of the virus’ profile that may provide the scientific community with evidence-based insights into COVID-19. Therefore, this study accomplished a comprehensive literature review that includes the virus’ origin, classification, structure, life cycle, genome, mutation, epidemiology, and subsequent essential factors associated with host–virus interaction. Moreover, we summarized the considerable diagnostic measures, treatment options, including multiple therapeutic approaches, and prevention, as well as future directions that may reduce the impact and misery caused by this devastating pandemic. The observations and data provided here have been screened and accumulated through extensive literature study, hence this study will help the scientific community properly understand this new virus and provide further leads for therapeutic interventions.
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7
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Singh J, Pandit P, McArthur AG, Banerjee A, Mossman K. Evolutionary trajectory of SARS-CoV-2 and emerging variants. Virol J 2021; 18:166. [PMID: 34389034 PMCID: PMC8361246 DOI: 10.1186/s12985-021-01633-w] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.
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Affiliation(s)
- Jalen Singh
- School of Interdisciplinary Science, McMaster University, Hamilton, ON, Canada
| | - Pranav Pandit
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
| | - Karen Mossman
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.
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8
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Antigenic sites in SARS-CoV-2 spike RBD show molecular similarity with pathogenic antigenic determinants and harbors peptides for vaccine development. Immunobiology 2021; 226:152091. [PMID: 34303920 PMCID: PMC8297981 DOI: 10.1016/j.imbio.2021.152091] [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: 06/13/2020] [Revised: 03/13/2021] [Accepted: 03/30/2021] [Indexed: 01/22/2023]
Abstract
The spike protein of coronavirus is key target for drug development and other pharmacological interventions. In current study, we performed an integrative approach to predict antigenic sites in SARS-CoV-2 spike receptor binding domain and found nine potential antigenic sites. The predicted antigenic sites were then assessed for possible molecular similarity with other known antigens in different organisms. Out of nine sites, seven sites showed molecular similarity with 54 antigenic determinants found in twelve pathogenic bacterial species (Mycobacterium tuberculosis, Mycobacterium leprae, Bacillus anthracis, Borrelia burgdorferi, Clostridium perfringens, Clostridium tetani, Helicobacter Pylori, Listeria monocytogenes, Staphylococcus aureus, Streptococcus pyogenes, Vibrio cholera and Yersinia pestis), two malarial parasites (Plasmodium falciparum and Plasmodium knowlesi) and influenza virus A. Most of the bacterial antigens that displayed molecular similarity with antigenic sites in SARS-CoV-2 RBD (receptor binding domain) were toxins and virulent factors. Antigens from Mycobacterium that showed similarity were mainly involved in modulating host cell immune response and ensuring persistence and survival of pathogen in host cells. Presence of a large number of antigenic determinants, similar to those in highly pathogenic microorganisms, not merely accounts for complex etiology of the disease but also provides an explanation for observed pathophysiological complications, such as deregulated immune response, unleashed or dysregulated cytokine secretion (cytokine storm), multiple organ failure etc., that are more evident in aged and immune-compromised patients. Over-representation of antigenic determinants from Plasmodium and Mycobacterium in all antigenic sites suggests that anti-malarial and anti-TB drugs can prove to be clinical beneficial for COVID-19 treatment. Besides this, anti-leprosy, anti-lyme, anti-plague, anti-anthrax drugs/vaccine etc. are also expected to be beneficial in COVID-19 treatment. Moreover, individuals previously immunized/vaccinated or had previous history of malaria, tuberculosis or other disease caused by fifteen microorganisms are expected to display a considerable degree of resistance against SARS-CoV-2 infection. Out of the seven antigenic sites predicted in SARS-CoV-2, a part of two antigenic sites were also predicted as potent T-cell epitopes (KVGGNYNYL444-452 and SVLYNSASF366-374) against MHC class I and three (KRISNCVADYSVLYN356-370, DLCFTNVYADSFVI389-402, and YRVVVLSFELLHA508-520) against MHC class II. All epitopes possessed significantly lower predicted IC50 value which is a prerequisite for a preferred vaccine candidate for COVID-19.
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9
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Richards KA, Glover M, Crawford JC, Thomas PG, White C, Sant AJ. Circulating CD4 T Cells Elicited by Endemic Coronaviruses Display Vast Disparities in Abundance and Functional Potential Linked to Antigen Specificity and Age. J Infect Dis 2021; 223:1555-1563. [PMID: 33556959 PMCID: PMC7928818 DOI: 10.1093/infdis/jiab076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/03/2021] [Indexed: 01/12/2023] Open
Abstract
Repeated infections with endemic human coronaviruses (hCoV) are thought to reflect lack of long-lasting protective immunity. We evaluated circulating human CD4 T cells collected prior to 2020 for reactivity towards hCoV spike proteins, probing for the ability to produce interferon-γ, interleukin-2, or granzyme B. We found robust reactivity to spike-derived epitopes, comparable to influenza, but highly variable abundance and functional potential across subjects, depending on age and viral antigen specificity. To explore potential of these memory cells to be recruited in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, we examined the subjects for cross-reactive recognition of epitopes from SARS-CoV-2 nucleocapsid, membrane/envelope, and spike. Functional potential of these cross-reactive CD4 T cells was highly variable; nucleocapsid-specific CD4 T cells but not spike-reactive cells showed exceptionally high levels of granzyme production upon stimulation. These results are considered in light of recruitment of hCoV-reactive cells into responses to SARS-CoV infections or vaccinations.
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Affiliation(s)
- Katherine A Richards
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Maryah Glover
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Jeremy C Crawford
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Chantelle White
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Andrea J Sant
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
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10
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Zhang BZ, Wang X, Yuan S, Li W, Dou Y, Poon VKM, Chan CCS, Cai JP, Chik KK, Tang K, Chan CCY, Hu YF, Hu JC, Badea SR, Gong HR, Lin X, Chu H, Li X, To KKW, Liu L, Chen Z, Hung IFN, Yuen KY, Chan JFW, Huang JD. A novel linker-immunodominant site (LIS) vaccine targeting the SARS-CoV-2 spike protein protects against severe COVID-19 in Syrian hamsters. Emerg Microbes Infect 2021; 10:874-884. [PMID: 33890550 PMCID: PMC8118541 DOI: 10.1080/22221751.2021.1921621] [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] [Indexed: 12/18/2022]
Abstract
The Coronavirus Disease 2019 (COVID-19) pandemic is unlikely to abate until sufficient herd immunity is built up by either natural infection or vaccination. We previously identified ten linear immunodominant sites on the SARS-CoV-2 spike protein of which four are located within the RBD. Therefore, we designed two linkerimmunodominant site (LIS) vaccine candidates which are composed of four immunodominant sites within the RBD (RBD-ID) or all the 10 immunodominant sites within the whole spike (S-ID). They were administered by subcutaneous injection and were tested for immunogenicity and in vivo protective efficacy in a hamster model for COVID-19. We showed that the S-ID vaccine induced significantly better neutralizing antibody response than RBD-ID and alum control. As expected, hamsters vaccinated by S-ID had significantly less body weight loss, lung viral load, and histopathological changes of pneumonia. The S-ID has the potential to be an effective vaccine for protection against COVID-19.
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Affiliation(s)
- Bao-Zhong Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Xiaolei Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Wenjun Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Ying Dou
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Vincent Kwok-Man Poon
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Chris Chung-Sing Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Jian-Piao Cai
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Kenn KaHeng Chik
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Kaiming Tang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Chris Chun-Yiu Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Ye-Fan Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Jing-Chu Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Smaranda Ruxandra Badea
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Hua-Rui Gong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Xuansheng Lin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Xuechen Li
- Department of Chemistry, Faculty of Science, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Li Liu
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China.,AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, People's Republic of China
| | - Zhiwei Chen
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China.,AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, People's Republic of China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Kwok Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
| | - Jian-Dong Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, People's Republic of China
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11
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El-Sayed A, Kamel M. Coronaviruses in humans and animals: the role of bats in viral evolution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:19589-19600. [PMID: 33655480 PMCID: PMC7924989 DOI: 10.1007/s11356-021-12553-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/14/2021] [Indexed: 04/15/2023]
Abstract
Bats act as a natural reservoir for many viruses, including coronaviruses, and have played a crucial epidemiological role in the emergence of many viral diseases. Coronaviruses have been known for 60 years. They are usually responsible for the induction of mild respiratory signs in humans. However, since 2002, the bat-borne virus started to induce fatal epidemics according to WHO reports. In this year, the first serious human coronavirus epidemic (severe acute respiratory syndrome; SARS) occurred (China, 8098 cases, 774 deaths [9.5% of the cases] in 17 countries). The case fatality was higher in elderly patients above 60 years and reached 50% of the cases. SARS epidemic was followed 10 years later by the emergence of the middle east respiratory syndrome (MERS) in Saudi Arabia (in 2012, 2260 cases, 803 deaths [35.5% of the cases] in 27 countries). Finally, in December 2019, a new epidemic in Wuhan, China, (corona virus disease 2019, COVID-19) emerged and could spread to 217 countries infecting more than 86,255,226 cases and killing 1,863,973 people by the end of 2020. There are many reasons why bats are ideal reservoir hosts for viral diseases such as the tolerance of their immune system to the invading viruses for several months. They can actively shed the viruses, although they develop no clinical signs (will be discussed in details later in the review). Bats were directly or indirectly involved in the three previous coronavirus epidemics. The indirect transmission takes place via intermediate hosts including civet cats for SARS and dromedary camels in the case of MERS. Although bats are believed to be the source of COVID-19 pandemic, direct pieces of evidence are still lacking. Therefore, coronaviruses' role in epidemics induction and the epidemiological role of bats are discussed. The current work also presents different evidence (phylogenetic data, animal experiments, bats artificial infection studies, and computerized models of SARS-CoV2 evolution) that underline the involvement of bats in the epidemiology of the pandemic.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Medicine and Infectious Diseases, Cairo University, Giza, 12211, Egypt
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Medicine and Infectious Diseases, Cairo University, Giza, 12211, Egypt.
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12
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Eguia RT, Crawford KHD, Stevens-Ayers T, Kelnhofer-Millevolte L, Greninger AL, Englund JA, Boeckh MJ, Bloom JD. A human coronavirus evolves antigenically to escape antibody immunity. PLoS Pathog 2021; 17:e1009453. [PMID: 33831132 PMCID: PMC8031418 DOI: 10.1371/journal.ppat.1009453] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
There is intense interest in antibody immunity to coronaviruses. However, it is unknown if coronaviruses evolve to escape such immunity, and if so, how rapidly. Here we address this question by characterizing the historical evolution of human coronavirus 229E. We identify human sera from the 1980s and 1990s that have neutralizing titers against contemporaneous 229E that are comparable to the anti-SARS-CoV-2 titers induced by SARS-CoV-2 infection or vaccination. We test these sera against 229E strains isolated after sera collection, and find that neutralizing titers are lower against these "future" viruses. In some cases, sera that neutralize contemporaneous 229E viral strains with titers >1:100 do not detectably neutralize strains isolated 8-17 years later. The decreased neutralization of "future" viruses is due to antigenic evolution of the viral spike, especially in the receptor-binding domain. If these results extrapolate to other coronaviruses, then it may be advisable to periodically update SARS-CoV-2 vaccines.
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Affiliation(s)
- Rachel T. Eguia
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Katharine H. D. Crawford
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
| | - Terry Stevens-Ayers
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | | | - Alexander L. Greninger
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Janet A. Englund
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Michael J. Boeckh
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jesse D. Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
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13
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Lee CY, Amrun SN, Chee RS, Goh YS, Mak T, Octavia S, Yeo NK, Chang ZW, Tay MZ, Torres‐Ruesta A, Carissimo G, Poh CM, Fong S, Bei W, Lee S, Young BE, Tan S, Leo Y, Lye DC, Lin RTP, Maurer‐Stroh S, Lee B, Wang C, Renia L, Ng LFP. Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Clin Transl Immunology 2021; 10:e1241. [PMID: 33628442 PMCID: PMC7899292 DOI: 10.1002/cti2.1241] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVES The emergence of a SARS-CoV-2 variant with a point mutation in the spike (S) protein, D614G, has taken precedence over the original Wuhan isolate by May 2020. With an increased infection and transmission rate, it is imperative to determine whether antibodies induced against the D614 isolate may cross-neutralise against the G614 variant. METHODS Antibody profiling against the SARS-CoV-2 S protein of the D614 variant by flow cytometry and assessment of neutralising antibody titres using pseudotyped lentiviruses expressing the SARS-CoV-2 S protein of either the D614 or G614 variant tagged with a luciferase reporter were performed on plasma samples from COVID-19 patients with known D614G status (n = 44 infected with D614, n = 6 infected with G614, n = 7 containing all other clades: O, S, L, V, G, GH or GR). RESULTS Profiling of the anti-SARS-CoV-2 humoral immunity reveals similar neutralisation profiles against both S protein variants, albeit waning neutralising antibody capacity at the later phase of infection. Of clinical importance, patients infected with either the D614 or G614 clade elicited a similar degree of neutralisation against both pseudoviruses, suggesting that the D614G mutation does not impact the neutralisation capacity of the elicited antibodies. CONCLUSIONS Cross-reactivity occurs at the functional level of the humoral response on both the S protein variants, which suggests that existing serological assays will be able to detect both D614 and G614 clades of SARS-CoV-2. More importantly, there should be negligible impact towards the efficacy of antibody-based therapies and vaccines that are currently being developed.
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Affiliation(s)
- Cheryl Yi‐Pin Lee
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Siti Naqiah Amrun
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Rhonda Sin‐Ling Chee
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Yun Shan Goh
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Tze‐Minn Mak
- National Centre for Infectious DiseasesSingapore
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
| | - Sophie Octavia
- National Centre for Infectious DiseasesSingapore
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
| | - Nicholas Kim‐Wah Yeo
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Zi Wei Chang
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Matthew Zirui Tay
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Anthony Torres‐Ruesta
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Guillaume Carissimo
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Chek Meng Poh
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Siew‐Wai Fong
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Wang Bei
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Sandy Lee
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Barnaby Edward Young
- National Centre for Infectious DiseasesSingapore
- Department of Infectious DiseasesTan Tock Seng HospitalSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore
| | - Seow‐Yen Tan
- Department of Infectious DiseasesChangi General HospitalSingapore
| | - Yee‐Sin Leo
- National Centre for Infectious DiseasesSingapore
- Department of Infectious DiseasesTan Tock Seng HospitalSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore
- Yong Loo Lin School of MedicineNational University of Singapore and National University Health SystemSingapore
| | - David C Lye
- National Centre for Infectious DiseasesSingapore
- Department of Infectious DiseasesTan Tock Seng HospitalSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore
- Yong Loo Lin School of MedicineNational University of Singapore and National University Health SystemSingapore
| | - Raymond TP Lin
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
- Department of Microbiology and ImmunologyYong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Sebastien Maurer‐Stroh
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- National Centre for Infectious DiseasesSingapore
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
- Department of Biological SciencesNational University of SingaporeSingapore
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR)Singapore
| | - Bernett Lee
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Cheng‐I Wang
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Laurent Renia
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Lisa FP Ng
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingapore
- National Institute of Health ResearchHealth Protection Research Unit in Emerging and Zoonotic InfectionsUniversity of LiverpoolLiverpoolUK
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolLiverpoolUK
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14
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Ng KT, Mohd-Ismail NK, Tan YJ. Spike S2 Subunit: The Dark Horse in the Race for Prophylactic and Therapeutic Interventions against SARS-CoV-2. Vaccines (Basel) 2021; 9:178. [PMID: 33672450 PMCID: PMC7923282 DOI: 10.3390/vaccines9020178] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 11/16/2022] Open
Abstract
In the midst of the unceasing COVID-19 pandemic, the identification of immunogenic epitopes in the SARS-CoV-2 spike (S) glycoprotein plays a vital role in the advancement and development of intervention strategies. S is expressed on the exterior of the SARS-CoV-2 virion and contains two subunits, namely the N-terminal S1 and C-terminal S2. It is the key element for mediating viral entry as well as a crucial antigenic determinant capable of stimulating protective immune response through elicitation of anti-SARS-CoV-2 antibodies and activation of CD4+ and CD8+ cells in COVID-19 patients. Given that S2 is highly conserved in comparison to the S1, here, we provide a review of the latest findings on the SARS-CoV-2 S2 subunit and further discuss its potential as an attractive and promising target for the development of prophylactic vaccines and therapeutic agents against COVID-19.
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Affiliation(s)
- Kim Tien Ng
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; (K.T.N.); (N.K.M.-I.)
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Nur Khairiah Mohd-Ismail
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; (K.T.N.); (N.K.M.-I.)
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Yee-Joo Tan
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; (K.T.N.); (N.K.M.-I.)
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore 138673, Singapore
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15
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Molecular Evolution of Human Coronavirus 229E in Hong Kong and a Fatal COVID-19 Case Involving Coinfection with a Novel Human Coronavirus 229E Genogroup. mSphere 2021; 6:6/1/e00819-20. [PMID: 33568452 PMCID: PMC8544887 DOI: 10.1128/msphere.00819-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Compared to other human coronaviruses, the genetic diversity and evolution of human coronavirus 229E (HCoV-229E) are relatively understudied. We report a fatal case of COVID-19 pneumonia coinfected with HCoV-229E in Hong Kong. Genome sequencing of SARS-CoV-2 and HCoV-229E from a nasopharyngeal sample of the patient showed that the SARS-CoV-2 strain HK13 was most closely related to SARS-CoV-2 type strain Wuhan-Hu-1 (99.99% nucleotide identity), compatible with his recent history of travel to Wuhan. The HCoV-229E strain HK20-42 was most closely related to HCoV-229E strain SC0865 from the United States (99.86% nucleotide identity). To investigate if it may represent a newly emerged HCoV-229E genotype in Hong Kong, we retrieved 41 archived respiratory samples that tested positive for HCoV-229E from 2004 to 2019. Pneumonia and exacerbations of chronic airway diseases were common among infected patients. Complete RdRp, S, and N gene sequencing of the 41 HCoV-229E strains revealed that our contemporary HCoV-229E strains have undergone significant genetic drift with clustering of strains in chronological order. Two novel genogroups were identified, in addition to previously described genogroups 1 to 4, with recent circulating strains including strain HK20-42 belonging to novel genogroup 6. Positive selection was detected in the spike protein and receptor-binding domain, which may be important for viral evolution at the receptor-binding interphase. Molecular dating analysis showed that HCoV-229E shared the most recent common ancestor with bat and camel/alpaca 229E-related viruses at ∼1884, while camel/alpaca viruses had a relatively recent common ancestor at ∼1999. Further studies are required to ascertain the evolutionary origin and path of HCoV-229E.IMPORTANCE Since its first appearance in the 1960s, the genetic diversity and evolution of human coronavirus 229E (HCoV-229E) have been relatively understudied. In this study, we report a fatal case of COVID-19 coinfected with HCoV-229E in Hong Kong. Genome sequencing revealed that our SARS-CoV-2 strain is highly identical to the SARS-CoV-2 strain from Wuhan, compatible with the patient's recent travel history, whereas our HCoV-229E strain in this study is highly identical to a recent strain in the United States. We also retrieved 41 archived HCoV-229E strains from 2004 to 2019 in Hong Kong for sequence analysis. Pneumonia and exacerbations of chronic airway diseases were common diagnoses among the 41 patients. The results showed that HCoV-229E was evolving in chronological order. Two novel genogroups were identified in addition to the four preexisting HCoV-229E genogroups, with recent circulating strains belonging to novel genogroup 6. Molecular clock analysis dated bat-to-human and bat-to-camelid transmission to as early as 1884.
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16
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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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17
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Abstract
Community protective immunity can affect RNA virus evolution by selecting for new antigenic variants on the scale of years, exemplified by the need of annual evaluation of influenza vaccines. The extent to which this process termed antigenic drift affects coronaviruses remains unknown. Alike the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), seasonal human coronaviruses (HCoV) likely emerged from animal reservoirs as new human pathogens in the past. We therefore analyzed the long-term evolutionary dynamics of the ubiquitous HCoV-229E and HCoV-OC43 in comparison with human influenza A virus (IAV) subtype H3N2. We focus on viral glycoprotein genes that mediate viral entry into cells and are major targets of host neutralizing antibody responses. Maximum likelihood and Bayesian phylogenies of publicly available gene datasets representing about three decades of HCoV and IAV evolution showed that all viruses had similar ladder-like tree shapes compatible with antigenic drift, supported by different tree shape statistics. Evolutionary rates inferred in a Bayesian framework were 6.5 × 10-4 (95% highest posterior density (HPD), 5.4-7.5 × 10-4) substitutions per site per year (s/s/y) for HCoV-229E spike (S) genes and 5.7 × 10-4 (95% HPD, 5-6.5 × 10-4) s/s/y for HCoV-OC43 S genes, which were about fourfold lower than the 2.5 × 10-3 (95% HPD, 2.3-2.7 × 10-3) s/s/y rate for IAV hemagglutinin (HA) genes. Coronavirus S genes accumulated about threefold less (P < 0.001) non-synonymous mutations (dN) over time than IAV HA genes. In both IAV and HCoV, the average rate of dN within the receptor binding domains (RBD) was about fivefold higher (P < 0.0001) than in other glycoprotein gene regions. Similarly, most sites showing evidence for positive selection occurred within the RBD (HCoV-229E, 6/14 sites, P < 0.05; HCoV-OC43, 23/38 sites, P < 0.01; IAV, 13/15 sites, P = 0.08). In sum, the evolutionary dynamics of HCoV and IAV showed several similarities, yet amino acid changes potentially representing antigenic drift occurred on a lower scale in endemic HCoV compared to IAV. It seems likely that pandemic SARS-CoV-2 evolution will bear similarities with IAV evolution including accumulation of adaptive changes in the RBD, requiring vaccines to be updated regularly, whereas higher SARS-CoV-2 evolutionary stability resembling endemic HCoV can be expected in the post-pandemic stage.
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Affiliation(s)
- Wendy K Jo
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Christian Drosten
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), associated partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Felix Drexler
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), associated partner Charité-Universitätsmedizin Berlin, Berlin, Germany
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18
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Amitai A. Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.10.20.347641. [PMID: 33106808 PMCID: PMC7587782 DOI: 10.1101/2020.10.20.347641] [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: 10/27/2022]
Abstract
The evolution of circulating viruses is shaped by their need to evade antibody response, which mainly targets the glycoprotein (spike). However, not all antigenic sites are targeted equally by antibodies, leading to complex immunodominance patterns. We used 3D computational models to estimate antibody pressure on the seasonal influenza H1N1 and SARS spikes. Analyzing publically available sequences, we show that antibody pressure, through the geometrical organization of spikes on the viral surface, shaped their mutability. Studying the mutability patterns of SARS-CoV-2 and the 2009 H1N1 pandemic spikes, we find that they are not predominantly shaped by antibody pressure. However, for SARS-CoV-2, we find that over time, it acquired mutations at antibody-accessible positions, which could indicate possible escape as define by our model. We offer a geometry-based approach to predict and rank the probability of surface resides of SARS-CoV-2 spike to acquire antibody escaping mutations.
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Affiliation(s)
- Assaf Amitai
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
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19
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Abstract
Animal and human endemic coronaviruses have been known for decades, as has their capacity to re-infect. In the COVID-19 pandemic, it is key to reveal the factors that influence reinfection susceptibility. In this commentary, I provide a view on endemic animal and human coronaviruses and the correlates of protection to reinfection.
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20
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Sofi MS, Hamid A, Bhat SU. SARS-CoV-2: A critical review of its history, pathogenesis, transmission, diagnosis and treatment. BIOSAFETY AND HEALTH 2020; 2:217-225. [PMID: 33196035 PMCID: PMC7648888 DOI: 10.1016/j.bsheal.2020.11.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 01/08/2023] Open
Abstract
The outbreak of the deadly virus (novel coronavirus or Severe Acute Respiratory Syndrome Coronavirus-2) that emerged in December 2019, remained a controversial subject of intense speculations regarding its origin, became a worldwide health problem resulting in serious coronavirus disease 2019 (acronym COVID-19). The concern regarding this new viral strain "Severe Acute Respiratory Syndrome Coronavirus-2" (acronym SARS-CoV-2) and diseases it causes (COVID-19) is well deserved at all levels. The incidence of COVID-19 infection and infectious patients are increasing at a high rate. Coronaviruses (CoVs), enclosed positive-sense RNA viruses, are distinguished by club-like spikes extending from their surface, an exceptionally large genome of RNA, and a special mechanism for replication. Coronaviruses are associated with a broad variety of human and other animal diseases spanning from enteritis in cattle and pigs and upper chicken respiratory disease to extremely lethal human respiratory infections. With World Health Organization (WHO) declaring COVID-19 as pandemic, we deemed it necessary to provide a detailed review of coronaviruses discussing their history, current situation, coronavirus classification, pathogenesis, structure, mode of action, diagnosis and treatment, the effect of environmental factors, risk reduction and guidelines to understand the virus and develop ways to control it.
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Affiliation(s)
| | | | - Sami Ullah Bhat
- Corresponding author: Department of Environmental Science, School of Earth and Environmental Science, University of Kashmir, 190006, India
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21
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Edridge AWD, Kaczorowska J, Hoste ACR, Bakker M, Klein M, Loens K, Jebbink MF, Matser A, Kinsella CM, Rueda P, Ieven M, Goossens H, Prins M, Sastre P, Deijs M, van der Hoek L. Seasonal coronavirus protective immunity is short-lasting. Nat Med 2020. [PMID: 32929268 DOI: 10.1101/2020.05.11.20086439] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A key unsolved question in the current coronavirus disease 2019 (COVID-19) pandemic is the duration of acquired immunity. Insights from infections with the four seasonal human coronaviruses might reveal common characteristics applicable to all human coronaviruses. We monitored healthy individuals for more than 35 years and determined that reinfection with the same seasonal coronavirus occurred frequently at 12 months after infection.
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Affiliation(s)
- Arthur W D Edridge
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Joanna Kaczorowska
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Michelle Klein
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Katherine Loens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
- Department of Microbiology, University Hospital Antwerp, Edegem, Belgium
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Amy Matser
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
| | - Cormac M Kinsella
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Paloma Rueda
- INGENASA, Inmunología y Genética Aplicada S. A., Madrid, Spain
| | - Margareta Ieven
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
| | - Herman Goossens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Wilrijk, Belgium
- Department of Microbiology, University Hospital Antwerp, Edegem, Belgium
| | - Maria Prins
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Department of Infectious Diseases, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Patricia Sastre
- INGENASA, Inmunología y Genética Aplicada S. A., Madrid, Spain
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
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22
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Flanagan KL, Best E, Crawford NW, Giles M, Koirala A, Macartney K, Russell F, Teh BW, Wen SCH. Progress and Pitfalls in the Quest for Effective SARS-CoV-2 (COVID-19) Vaccines. Front Immunol 2020; 11:579250. [PMID: 33123165 PMCID: PMC7566192 DOI: 10.3389/fimmu.2020.579250] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/31/2020] [Indexed: 12/15/2022] Open
Abstract
There are currently around 200 SARS-CoV-2 candidate vaccines in preclinical and clinical trials throughout the world. The various candidates employ a range of vaccine strategies including some novel approaches. Currently, the goal is to prove that they are safe and immunogenic in humans (phase 1/2 studies) with several now advancing into phase 2 and 3 trials to demonstrate efficacy and gather comprehensive data on safety. It is highly likely that many vaccines will be shown to stimulate antibody and T cell responses in healthy individuals and have an acceptable safety profile, but the key will be to confirm that they protect against COVID-19. There is much hope that SARS-CoV-2 vaccines will be rolled out to the entire world to contain the pandemic and avert its most damaging impacts. However, in all likelihood this will initially require a targeted approach toward key vulnerable groups. Collaborative efforts are underway to ensure manufacturing can occur at the unprecedented scale and speed required to immunize billions of people. Ensuring deployment also occurs equitably across the globe will be critical. Careful evaluation and ongoing surveillance for safety will be required to address theoretical concerns regarding immune enhancement seen in previous contexts. Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. We provide details of some of the frontrunner vaccines and discuss potential issues including adverse effects, scale-up and delivery.
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Affiliation(s)
- Katie L. Flanagan
- Department of Infectious Diseases, Launceston General Hospital, Launceston, TAS, Australia
- Faculty of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS, Australia
- School of Health and Biomedical Science, Royal Melbourne Institute of Technology (RMIT) University, Melbourne, VIC, Australia
- Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia
| | - Emma Best
- Department of Paediatric Infectious Diseases, Starship Children's Hospital, Auckland, New Zealand
- Department of Paediatrics: Child and Youth Health, University of Auckland, Auckland, New Zealand
| | - Nigel W. Crawford
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital Immunisation Service, Melbourne, VIC, Australia
| | - Michelle Giles
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, VIC, Australia
- Infectious Diseases Unit, Alfred Health, Melbourne, VIC, Australia
| | - Archana Koirala
- Department of Child and Adolescent Health, University of Sydney, Sydney, NSW, Australia
- National Centre for Immunisation Research & Surveillance (NCIRS), Sydney, NSW, Australia
- Department of Infectious Diseases, Nepean Hospital, Sydney, NSW, Australia
| | - Kristine Macartney
- Department of Child and Adolescent Health, University of Sydney, Sydney, NSW, Australia
- National Centre for Immunisation Research & Surveillance (NCIRS), Sydney, NSW, Australia
| | - Fiona Russell
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital Immunisation Service, Melbourne, VIC, Australia
| | - Benjamin W. Teh
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Sophie CH Wen
- Infection Management Prevention Services, Queensland Children's Hospital, South Brisbane, QLD, Australia
- University of Queensland Centre for Clinical Research (UQCCR), University of Queensland, Brisbane, QLD, Australia
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23
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Ling J, Hickman RA, Li J, Lu X, Lindahl JF, Lundkvist Å, Järhult JD. Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. Viruses 2020; 12:E1026. [PMID: 32937868 PMCID: PMC7551444 DOI: 10.3390/v12091026] [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: 08/26/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND During the COVID-19 pandemic, the virus evolved, and we therefore aimed to provide an insight into which genetic variants were enriched, and how they spread in Sweden. METHODS We analyzed 348 Swedish SARS-CoV-2 sequences freely available from GISAID obtained from 7 February 2020 until 14 May 2020. RESULTS We identified 14 variant sites ≥5% frequency in the population. Among those sites, the D936Y substitution in the viral Spike protein was under positive selection. The variant sites can distinguish 11 mutational profiles in Sweden. Nine of the profiles appeared in Stockholm in March 2020. Mutational profiles 3 (B.1.1) and 6 (B.1), which contain the D936Y mutation, became the predominant profiles over time, spreading from Stockholm to other Swedish regions during April and the beginning of May. Furthermore, Bayesian phylogenetic analysis indicated that SARS-CoV-2 could have emerged in Sweden on 27 December 2019, and community transmission started on February 1st with an evolutionary rate of 1.5425 × 10-3 substitutions per year. CONCLUSIONS Our study provides novel knowledge on the spatio-temporal dynamics of Swedish SARS-CoV-2 variants during the early pandemic. Characterization of these viral variants can provide precious insights on viral pathogenesis and can be valuable for diagnostic and drug development approaches.
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Affiliation(s)
- Jiaxin Ling
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
| | - Rachel A. Hickman
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
| | - Jinlin Li
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Xi Lu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
| | - Johanna F. Lindahl
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
- International Livestock Research Institute, Nairobi 00100, Kenya
- Swedish University of Agricultural Research, SE-750 07 Uppsala, Sweden
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
| | - Josef D. Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, SE-751 23 Uppsala, Sweden;
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24
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Wang Y, Grunewald M, Perlman S. Coronaviruses: An Updated Overview of Their Replication and Pathogenesis. Methods Mol Biol 2020; 2203:1-29. [PMID: 32833200 DOI: 10.1007/978-1-0716-0900-2_1] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. CoVs cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs, and upper respiratory tract and kidney disease in chickens to lethal human respiratory infections. Most recently, the novel coronavirus, SARS-CoV-2, which was first identified in Wuhan, China in December 2019, is the cause of a catastrophic pandemic, COVID-19, with more than 8 million infections diagnosed worldwide by mid-June 2020. Here we provide a brief introduction to CoVs discussing their replication, pathogenicity, and current prevention and treatment strategies. We will also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV), which are relevant for understanding COVID-19.
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Affiliation(s)
- Yuhang Wang
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Matthew Grunewald
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA.
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25
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Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020; 182:812-827.e19. [PMID: 32697968 PMCID: PMC7332439 DOI: 10.1016/j.cell.2020.06.043] [Citation(s) in RCA: 2795] [Impact Index Per Article: 698.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/10/2020] [Accepted: 06/26/2020] [Indexed: 02/08/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
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26
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Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020. [PMID: 32697968 DOI: 10.1016/j.cell.2020.06.043%0asummary] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
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27
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Lundstrom K. Coronavirus Pandemic-Therapy and Vaccines. Biomedicines 2020; 8:E109. [PMID: 32375268 PMCID: PMC7277397 DOI: 10.3390/biomedicines8050109] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/13/2022] Open
Abstract
The current coronavirus COVID-19 pandemic, which originated in Wuhan, China, has raised significant social, psychological and economic concerns in addition to direct medical issues. The rapid spread of severe acute respiratory syndrome-coronavirus (SARS-CoV)-2 to almost every country on the globe and the failure to contain the infections have contributed to fear and panic worldwide. The lack of available and efficient antiviral drugs or vaccines has further worsened the situation. For these reasons, it cannot be overstated that an accelerated effort for the development of novel drugs and vaccines is needed. In this context, novel approaches in both gene therapy and vaccine development are essential. Previous experience from SARS- and MERS-coronavirus vaccine and drug development projects have targeted glycoprotein epitopes, monoclonal antibodies, angiotensin receptor blockers and gene silencing technologies, which may be useful for COVID-19 too. Moreover, existing antivirals used for other types of viral infections have been considered as urgent action is necessary. This review aims at providing a background of coronavirus genetics and biology, examples of therapeutic and vaccine strategies taken and potential innovative novel approaches in progress.
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28
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Islam MT, Sarkar C, El-Kersh DM, Jamaddar S, Uddin SJ, Shilpi JA, Mubarak MS. Natural products and their derivatives against coronavirus: A review of the non-clinical and pre-clinical data. Phytother Res 2020; 34:2471-2492. [PMID: 32248575 DOI: 10.1002/ptr.6700] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/19/2020] [Accepted: 03/28/2020] [Indexed: 01/08/2023]
Abstract
Several corona viral infections have created serious threats in the last couple of decades claiming the death of thousands of human beings. Recently, corona viral epidemic raised the issue of developing effective antiviral agents at the earliest to prevent further losses. Natural products have always played a crucial role in drug development process against various diseases, which resulted in screening of such agents to combat emergent mutants of corona virus. This review focuses on those natural compounds that showed promising results against corona viruses. Although inhibition of viral replication is often considered as a general mechanism for antiviral activity of most of the natural products, studies have shown that some natural products can interact with key viral proteins that are associated with virulence. In this context, some of the natural products have antiviral activity in the nanomolar concentration (e.g., lycorine, homoharringtonine, silvestrol, ouabain, tylophorine, and 7-methoxycryptopleurine) and could be leads for further drug development on their own or as a template for drug design. In addition, a good number of natural products with anti-corona virus activity are the major constituents of some common dietary supplements, which can be exploited to improve the immunity of the general population in certain epidemics.
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Affiliation(s)
- Muhammad T Islam
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam.,Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Chandan Sarkar
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Bangladesh, Gopalganj, Bangladesh
| | - Dina M El-Kersh
- Pharmacognosy Department, Faculty of Pharmacy, The British University in Egypt (BUE), El Sherouk, Cairo Governorate, Egypt
| | - Sarmin Jamaddar
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Bangladesh, Gopalganj, Bangladesh
| | - Shaikh J Uddin
- Pharmacy Discipline, Khulna University, Khulna, Bangladesh
| | - Jamil A Shilpi
- Pharmacy Discipline, Khulna University, Khulna, Bangladesh
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29
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Wong AHM, Tomlinson ACA, Zhou D, Satkunarajah M, Chen K, Sharon C, Desforges M, Talbot PJ, Rini JM. Receptor-binding loops in alphacoronavirus adaptation and evolution. Nat Commun 2017; 8:1735. [PMID: 29170370 PMCID: PMC5701055 DOI: 10.1038/s41467-017-01706-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/06/2017] [Indexed: 02/08/2023] Open
Abstract
RNA viruses are characterized by a high mutation rate, a buffer against environmental change. Nevertheless, the means by which random mutation improves viral fitness is not well characterized. Here we report the X-ray crystal structure of the receptor-binding domain (RBD) of the human coronavirus, HCoV-229E, in complex with the ectodomain of its receptor, aminopeptidase N (APN). Three extended loops are solely responsible for receptor binding and the evolution of HCoV-229E and its close relatives is accompanied by changing loop–receptor interactions. Phylogenetic analysis shows that the natural HCoV-229E receptor-binding loop variation observed defines six RBD classes whose viruses have successively replaced each other in the human population over the past 50 years. These RBD classes differ in their affinity for APN and their ability to bind an HCoV-229E neutralizing antibody. Together, our results provide a model for alphacoronavirus adaptation and evolution based on the use of extended loops for receptor binding. Coronaviruses have a relatively high mutation rate, potentially allowing fast adaptation to changing pressures. Here, Wong et al. provide the structure of the receptor-binding domain (RBD) of the human coronavirus HCoV-229E and its receptor and analyze the evolution of the RBD over the past 50 years.
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Affiliation(s)
- Alan H M Wong
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Aidan C A Tomlinson
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Dongxia Zhou
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Malathy Satkunarajah
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Kevin Chen
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Chetna Sharon
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Marc Desforges
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, 531 Boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Pierre J Talbot
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, 531 Boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - James M Rini
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8. .,Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8.
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Complete Genome Sequence of Human Coronavirus Strain 229E Isolated from Plasma Collected from a Haitian Child in 2016. GENOME ANNOUNCEMENTS 2017; 5:5/47/e01313-17. [PMID: 29167251 PMCID: PMC5701476 DOI: 10.1128/genomea.01313-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Human coronavirus strain 229E (HCoV-229E) and human alphaherpesvirus 1 were isolated from the plasma of a Haitian child in 2016 with suspected arbovirus diseases. To our knowledge, this is the first description of HCoV-229E in human plasma, which is the focus of this article.
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Clinical Isolates of Human Coronavirus 229E Bypass the Endosome for Cell Entry. J Virol 2016; 91:JVI.01387-16. [PMID: 27733646 DOI: 10.1128/jvi.01387-16] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/04/2016] [Indexed: 11/20/2022] Open
Abstract
Human coronavirus 229E (HCoV-229E), a causative agent of the common cold, enters host cells via two distinct pathways: one is mediated by cell surface proteases, particularly transmembrane protease serine 2 (TMPRSS2), and the other by endosomal cathepsin L. Thus, specific inhibitors of these proteases block virus infection. However, it is unclear which of these pathways is actually utilized by HCoV-229E in the human respiratory tract. Here, we examined the mechanism of cell entry used by a pseudotyped virus bearing the HCoV-229E spike (S) protein in the presence or absence of protease inhibitors. We found that, compared with a laboratory strain isolated in 1966 and passaged for a half century, clinical isolates of HCoV-229E were less likely to utilize cathepsin L; rather, they showed a preference for TMPRSS2. Two amino acid substitutions (R642M and N714K) in the S protein of HCoV-229E clinical isolates altered their sensitivity to a cathepsin L inhibitor, suggesting that these amino acids were responsible for cathepsin L use. After 20 passages in HeLa cells, the ability of the isolate to use cathepsin increased so that it was equal to that of the laboratory strain; this increase was caused by an amino acid substitution (I577S) in the S protein. The passaged virus showed a reduced ability to replicate in differentiated airway epithelial cells cultured at an air-liquid interface. These results suggest that the endosomal pathway is disadvantageous for HCoV-229E infection of human airway epithelial cells; therefore, clinical isolates are less able to use cathepsin. IMPORTANCE Many enveloped viruses enter cells through endocytosis. Viral spike proteins drive the fusion of viral and endosomal membranes to facilitate insertion of the viral genome into the cytoplasm. Human coronavirus 229E (HCoV-229E) utilizes endosomal cathepsin L to activate the spike protein after receptor binding. Here, we found that clinical isolates of HCoV-229E preferentially utilize the cell surface protease TMPRSS2 rather than endosomal cathepsin L. The endosome is a main site of Toll-like receptor recognition, which then triggers an innate immune response; therefore, HCoV-229E presumably evolved to bypass the endosome by entering the cell via TMPRSS2. Thus, the virus uses a simple mechanism to evade the host innate immune system. Therefore, therapeutic agents for coronavirus-mediated diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), should target cell surface TMPRSS2 rather than endosomal cathepsin.
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Abstract
The four human coronaviruses (HCoVs) are globally endemic respiratory pathogens. The Middle East respiratory syndrome (MERS) coronavirus (CoV) is an emerging CoV with a known zoonotic source in dromedary camels. Little is known about the origins of endemic HCoVs. Studying these viruses' evolutionary history could provide important insight into CoV emergence. In tests of MERS-CoV-infected dromedaries, we found viruses related to an HCoV, known as HCoV-229E, in 5.6% of 1,033 animals. Human- and dromedary-derived viruses are each monophyletic, suggesting ecological isolation. One gene of dromedary viruses exists in two versions in camels, full length and deleted, whereas only the deleted version exists in humans. The deletion increased in size over a succession starting from camelid viruses via old human viruses to contemporary human viruses. Live isolates of dromedary 229E viruses were obtained and studied to assess human infection risks. The viruses used the human entry receptor aminopeptidase N and replicated in human hepatoma cells, suggesting a principal ability to cause human infections. However, inefficient replication in several mucosa-derived cell lines and airway epithelial cultures suggested lack of adaptation to the human host. Dromedary viruses were as sensitive to the human type I interferon response as HCoV-229E. Antibodies in human sera neutralized dromedary-derived viruses, suggesting population immunity against dromedary viruses. Although no current epidemic risk seems to emanate from these viruses, evolutionary inference suggests that the endemic human virus HCoV-229E may constitute a descendant of camelid-associated viruses. HCoV-229E evolution provides a scenario for MERS-CoV emergence.
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Al-Khannaq MN, Ng KT, Oong XY, Pang YK, Takebe Y, Chook JB, Hanafi NS, Kamarulzaman A, Tee KK. Diversity and Evolutionary Histories of Human Coronaviruses NL63 and 229E Associated with Acute Upper Respiratory Tract Symptoms in Kuala Lumpur, Malaysia. Am J Trop Med Hyg 2016; 94:1058-64. [PMID: 26928836 DOI: 10.4269/ajtmh.15-0810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/13/2016] [Indexed: 01/06/2023] Open
Abstract
The human alphacoronaviruses HCoV-NL63 and HCoV-229E are commonly associated with upper respiratory tract infections (URTI). Information on their molecular epidemiology and evolutionary dynamics in the tropical region of southeast Asia however is limited. Here, we analyzed the phylogenetic, temporal distribution, population history, and clinical manifestations among patients infected with HCoV-NL63 and HCoV-229E. Nasopharyngeal swabs were collected from 2,060 consenting adults presented with acute URTI symptoms in Kuala Lumpur, Malaysia, between 2012 and 2013. The presence of HCoV-NL63 and HCoV-229E was detected using multiplex polymerase chain reaction (PCR). The spike glycoprotein, nucleocapsid, and 1a genes were sequenced for phylogenetic reconstruction and Bayesian coalescent inference. A total of 68/2,060 (3.3%) subjects were positive for human alphacoronavirus; HCoV-NL63 and HCoV-229E were detected in 45 (2.2%) and 23 (1.1%) patients, respectively. A peak in the number of HCoV-NL63 infections was recorded between June and October 2012. Phylogenetic inference revealed that 62.8% of HCoV-NL63 infections belonged to genotype B, 37.2% was genotype C, while all HCoV-229E sequences were clustered within group 4. Molecular dating analysis indicated that the origin of HCoV-NL63 was dated to 1921, before it diverged into genotype A (1975), genotype B (1996), and genotype C (2003). The root of the HCoV-229E tree was dated to 1955, before it diverged into groups 1-4 between the 1970s and 1990s. The study described the seasonality, molecular diversity, and evolutionary dynamics of human alphacoronavirus infections in a tropical region.
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Affiliation(s)
- Maryam Nabiel Al-Khannaq
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan; School of Medicine, Yokohama City University, Kanagawa, Japan; Department of Health Sciences, Faculty of Health and Life Sciences, Management and Science University, Selangor, Malaysia; Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kim Tien Ng
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan; School of Medicine, Yokohama City University, Kanagawa, Japan; Department of Health Sciences, Faculty of Health and Life Sciences, Management and Science University, Selangor, Malaysia; Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Xiang Yong Oong
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan; School of Medicine, Yokohama City University, Kanagawa, Japan; Department of Health Sciences, Faculty of Health and Life Sciences, Management and Science University, Selangor, Malaysia; Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan; School of Medicine, Yokohama City University, Kanagawa, Japan; Department of Health Sciences, Faculty of Health and Life Sciences, Management and Science University, Selangor, Malaysia; Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yutaka Takebe
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan; School of Medicine, Yokohama City University, Kanagawa, Japan; Department of Health Sciences, Faculty of Health and Life Sciences, Management and Science University, Selangor, Malaysia; Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jack Bee Chook
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan; School of Medicine, Yokohama City University, Kanagawa, Japan; Department of Health Sciences, Faculty of Health and Life Sciences, Management and Science University, Selangor, Malaysia; Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Nik Sherina Hanafi
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan; School of Medicine, Yokohama City University, Kanagawa, Japan; Department of Health Sciences, Faculty of Health and Life Sciences, Management and Science University, Selangor, Malaysia; Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Adeeba Kamarulzaman
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan; School of Medicine, Yokohama City University, Kanagawa, Japan; Department of Health Sciences, Faculty of Health and Life Sciences, Management and Science University, Selangor, Malaysia; Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Keng Tee
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan; School of Medicine, Yokohama City University, Kanagawa, Japan; Department of Health Sciences, Faculty of Health and Life Sciences, Management and Science University, Selangor, Malaysia; Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia; Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Matoba Y, Aoki Y, Tanaka S, Yahagi K, Itagaki T, Matsuzaki Y, Mizuta K. Picornavirus-like cytopathic effects on RD-18S cell lines were induced by human coronavirus 229E not picornaviruses. Jpn J Infect Dis 2016; 68:78-9. [PMID: 25702793 DOI: 10.7883/yoken.jjid.2014.487] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Yohei Matoba
- Department of Microbiology, Yamagata Prefectural Institute of Public Health
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Evidence for an Ancestral Association of Human Coronavirus 229E with Bats. J Virol 2015; 89:11858-70. [PMID: 26378164 DOI: 10.1128/jvi.01755-15] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/07/2015] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED We previously showed that close relatives of human coronavirus 229E (HCoV-229E) exist in African bats. The small sample and limited genomic characterizations have prevented further analyses so far. Here, we tested 2,087 fecal specimens from 11 bat species sampled in Ghana for HCoV-229E-related viruses by reverse transcription-PCR (RT-PCR). Only hipposiderid bats tested positive. To compare the genetic diversity of bat viruses and HCoV-229E, we tested historical isolates and diagnostic specimens sampled globally over 10 years. Bat viruses were 5- and 6-fold more diversified than HCoV-229E in the RNA-dependent RNA polymerase (RdRp) and spike genes. In phylogenetic analyses, HCoV-229E strains were monophyletic and not intermixed with animal viruses. Bat viruses formed three large clades in close and more distant sister relationships. A recently described 229E-related alpaca virus occupied an intermediate phylogenetic position between bat and human viruses. According to taxonomic criteria, human, alpaca, and bat viruses form a single CoV species showing evidence for multiple recombination events. HCoV-229E and the alpaca virus showed a major deletion in the spike S1 region compared to all bat viruses. Analyses of four full genomes from 229E-related bat CoVs revealed an eighth open reading frame (ORF8) located at the genomic 3' end. ORF8 also existed in the 229E-related alpaca virus. Reanalysis of HCoV-229E sequences showed a conserved transcription regulatory sequence preceding remnants of this ORF, suggesting its loss after acquisition of a 229E-related CoV by humans. These data suggested an evolutionary origin of 229E-related CoVs in hipposiderid bats, hypothetically with camelids as intermediate hosts preceding the establishment of HCoV-229E. IMPORTANCE The ancestral origins of major human coronaviruses (HCoVs) likely involve bat hosts. Here, we provide conclusive genetic evidence for an evolutionary origin of the common cold virus HCoV-229E in hipposiderid bats by analyzing a large sample of African bats and characterizing several bat viruses on a full-genome level. Our evolutionary analyses show that animal and human viruses are genetically closely related, can exchange genetic material, and form a single viral species. We show that the putative host switches leading to the formation of HCoV-229E were accompanied by major genomic changes, including deletions in the viral spike glycoprotein gene and loss of an open reading frame. We reanalyze a previously described genetically related alpaca virus and discuss the role of camelids as potential intermediate hosts between bat and human viruses. The evolutionary history of HCoV-229E likely shares important characteristics with that of the recently emerged highly pathogenic Middle East respiratory syndrome (MERS) coronavirus.
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Genetic drift of human coronavirus OC43 spike gene during adaptive evolution. Sci Rep 2015; 5:11451. [PMID: 26099036 PMCID: PMC4476415 DOI: 10.1038/srep11451] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/26/2015] [Indexed: 11/08/2022] Open
Abstract
Coronaviruses (CoVs) continuously threaten human health. However, to date, the evolutionary mechanisms that govern CoV strain persistence in human populations have not been fully understood. In this study, we characterized the evolution of the major antigen-spike (S) gene in the most prevalent human coronavirus (HCoV) OC43 using phylogenetic and phylodynamic analysis. Among the five known HCoV-OC43 genotypes (A to E), higher substitution rates and dN/dS values as well as more positive selection sites were detected in the S gene of genotype D, corresponding to the most dominant HCoV epidemic in recent years. Further analysis showed that the majority of substitutions were located in the S1 subunit. Among them, seven positive selection sites were chronologically traced in the temporal evolution routes of genotype D, and six were located around the critical sugar binding region in the N-terminal domain (NTD) of S protein, an important sugar binding domain of CoV. These findings suggest that the genetic drift of the S gene may play an important role in genotype persistence in human populations, providing insights into the mechanisms of HCoV-OC43 adaptive evolution.
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Fehr AR, Perlman S. Coronaviruses: an overview of their replication and pathogenesis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2015. [PMID: 25720466 DOI: 10.1007/978‐1‐4939‐2438‐7_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. Coronaviruses cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs and upper respiratory disease in chickens to potentially lethal human respiratory infections. Here we provide a brief introduction to coronaviruses discussing their replication and pathogenicity, and current prevention and treatment strategies. We also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the recently identified Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV).
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Affiliation(s)
- Anthony R Fehr
- Department of Microbiology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
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38
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Abstract
Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. Coronaviruses cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs and upper respiratory disease in chickens to potentially lethal human respiratory infections. Here we provide a brief introduction to coronaviruses discussing their replication and pathogenicity, and current prevention and treatment strategies. We also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the recently identified Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV).
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Affiliation(s)
- Helena Jane Maier
- grid.63622.330000000403887540The Pirbright Institute, Compton, United Kingdom
| | - Erica Bickerton
- grid.63622.330000000403887540The Pirbright Institute, Compton, United Kingdom
| | - Paul Britton
- grid.63622.330000000403887540The Pirbright Institute, Compton, United Kingdom
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Shirato K, Imada Y, Kawase M, Nakagaki K, Matsuyama S, Taguchi F. Possible involvement of infection with human coronavirus 229E, but not NL63, in Kawasaki disease. J Med Virol 2014; 86:2146-53. [PMID: 24760654 PMCID: PMC7166330 DOI: 10.1002/jmv.23950] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2014] [Indexed: 11/08/2022]
Abstract
Although human coronavirus (HCoV)‐NL63 was once considered a possible causative agent of Kawasaki disease based on RT‐PCR analyses, subsequent studies could not confirm the result. In this study, this possibility was explored using serological tests. To evaluate the role of HCoV infection in patients with Kawasaki disease, immunofluorescence assays and virus neutralizing tests were performed. Paired serum samples were obtained from patients with Kawasaki disease who had not been treated with γ‐globulin. HCoV‐NL63 and two antigenically different isolates of HCoV‐229E (ATCC‐VR740 and a new isolate, Sendai‐H) were examined as controls. Immunofluorescence assays detected no difference in HCoV‐NL63 antibody positivity between the patients with Kawasaki disease and controls, whereas the rate of HCoV‐229E antibody positivity was higher in the patients with Kawasaki disease than that in controls. The neutralizing tests revealed no difference in seropositivity between the acute and recovery phases of patients with Kawasaki disease for the two HCoV‐229Es. However, the Kawasaki disease specimens obtained from patients in recovery phase displayed significantly higher positivity for Sendai‐H, but not for ATCC‐VR740, as compared to the controls. The serological test supported no involvement of HCoV‐NL63 but suggested the possible involvement of HCoV‐229E in the development of Kawasaki disease. J. Med. Virol. 86:2146–2153, 2014. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Kazuya Shirato
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Japan
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Crossley BM, Mock RE, Callison SA, Hietala SK. Identification and characterization of a novel alpaca respiratory coronavirus most closely related to the human coronavirus 229E. Viruses 2012; 4:3689-700. [PMID: 23235471 PMCID: PMC3528286 DOI: 10.3390/v4123689] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 11/13/2012] [Accepted: 11/23/2012] [Indexed: 12/27/2022] Open
Abstract
In 2007, a novel coronavirus associated with an acute respiratory disease in alpacas (Alpaca Coronavirus, ACoV) was isolated. Full-length genomic sequencing of the ACoV demonstrated the genome to be consistent with other Alphacoronaviruses. A putative additional open-reading frame was identified between the nucleocapsid gene and 3'UTR. The ACoV was genetically most similar to the common human coronavirus (HCoV) 229E with 92.2% nucleotide identity over the entire genome. A comparison of spike gene sequences from ACoV and from HCoV-229E isolates recovered over a span of five decades showed the ACoV to be most similar to viruses isolated in the 1960's to early 1980's. The true origin of the ACoV is unknown, however a common ancestor between the ACoV and HCoV-229E appears to have existed prior to the 1960's, suggesting virus transmission, either as a zoonosis or anthroponosis, has occurred between alpacas and humans.
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Affiliation(s)
- Beate M. Crossley
- California Animal Health and Food Safety Laboratory System, University of California-Davis, Davis, West Health Sciences Drive, CA 95616, USA; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: Tel.: +1-530-752-5662; Fax: +1-530-752-6253
| | - Richard E. Mock
- North Carolina Veterinary Diagnostic Laboratory System, Raleigh, NC 27699, USA; E-Mail:
| | | | - Sharon K. Hietala
- California Animal Health and Food Safety Laboratory System, University of California-Davis, Davis, West Health Sciences Drive, CA 95616, USA; E-Mail:
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The first complete genome sequences of clinical isolates of human coronavirus 229E. Virus Genes 2012; 45:433-9. [PMID: 22926811 PMCID: PMC7088690 DOI: 10.1007/s11262-012-0807-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 08/10/2012] [Indexed: 12/20/2022]
Abstract
Human coronavirus 229E has been identified in the mid-1960s, yet still only one full-genome sequence is available. This full-length sequence has been determined from the cDNA-clone Inf-1 that is based on the lab-adapted strain VR-740. Lab-adaptation might have resulted in genomic changes, due to insufficient pressure to maintain gene integrity of non-essential genes. We present here the first full-length genome sequence of two clinical isolates. Each encoded gene was compared to Inf-1. In general, little sequence changes were noted, most could be attributed to genetic drift, since the clinical isolates originate from 2009 to 2010 and VR740 from 1962. Hot spots of substitutions were situated in the S1 region of the Spike, the nucleocapsid gene, and the non-structural protein 3 gene, whereas several deletions were detected in the 3′UTR. Most notable was the difference in genome organization: instead of an ORF4A and ORF4B, an intact ORF4 was present in clinical isolates.
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Shirato K, Kawase M, Watanabe O, Hirokawa C, Matsuyama S, Nishimura H, Taguchi F. Differences in neutralizing antigenicity between laboratory and clinical isolates of HCoV-229E isolated in Japan in 2004-2008 depend on the S1 region sequence of the spike protein. J Gen Virol 2012; 93:1908-1917. [PMID: 22673931 DOI: 10.1099/vir.0.043117-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Human coronavirus (HCoV) is a causative agent of the common cold. Although HCoV is highly prevalent in the world, studies of the genomic and antigenic details of circulating HCoV strains have been limited. In this study, we compared four Japanese isolates with the standard HCoV-229E strain obtained from ATCC (ATCC-VR740) by focusing on the spike (S) protein, a major determinant of neutralizing antigen and pathogenicity. The isolates were found to have nucleotide deletions and a number of sequence differences in the S1 region of the S protein. We compared two of the Japanese isolates with the ATCC-VR740 strain by using virus-neutralizing assays consisting of infectious HCoV-229E particles and vesicular stomatitis virus (VSV)-pseudotyped virus carrying the HCoV-229E S protein. The two clinical isolates (Sendai-H/1121/04 and Niigata/01/08) did not react with antiserum to the ATCC-VR740 strain via the neutralizing test. We then constructed a pseudotype VSV-harboured chimeric S protein with the ATCC S1 and Sendai S2 regions or that with Sendai S1 and ATCC S2 regions and compared them by a neutralization test. The results revealed that the difference in the neutralizing antigenicity depends on the S1 region. This different antigenic phenotype was also confirmed by a neutralizing test with clinically isolated human sera. These results suggest that the HCoV-229E viruses prevalent in Japan are quite different from the laboratory strain ATCC-VR740 in terms of the S sequence and neutralization antigenicity, which is attributed to the difference in the S1 region.
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Affiliation(s)
- Kazuya Shirato
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011 Japan
| | - Miyuki Kawase
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011 Japan
| | - Oshi Watanabe
- Virus Research Center, Sendai Medical Center, Sendai, Miyagi 983-8520, Japan
| | - Chika Hirokawa
- Virology Section, Niigata Prefectural Institute of Public Health and Environmental Sciences, Niigata 950-2144, Japan
| | - Shutoku Matsuyama
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011 Japan
| | - Hidekazu Nishimura
- Virus Research Center, Sendai Medical Center, Sendai, Miyagi 983-8520, Japan
| | - Fumihiro Taguchi
- Department of Veterinary Science, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan.,Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011 Japan
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Abstract
HCoV-NL63 and HCoV-229E are two of the four human coronaviruses that circulate worldwide. These two viruses are unique in their relationship towards each other. Phylogenetically, the viruses are more closely related to each other than to any other human coronavirus, yet they only share 65% sequence identity. Moreover, the viruses use different receptors to enter their target cell. HCoV-NL63 is associated with croup in children, whereas all signs suggest that the virus probably causes the common cold in healthy adults. HCoV-229E is a proven common cold virus in healthy adults, so it is probable that both viruses induce comparable symptoms in adults, even though their mode of infection differs. Here, we present an overview of the current knowledge on both human coronaviruses, focusing on similarities and differences.
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Affiliation(s)
- Ronald Dijkman
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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Voronin Y, Holte S, Overbaugh J, Emerman M. Genetic drift of HIV populations in culture. PLoS Genet 2009; 5:e1000431. [PMID: 19300501 PMCID: PMC2652835 DOI: 10.1371/journal.pgen.1000431] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 02/19/2009] [Indexed: 01/04/2023] Open
Abstract
Populations of Human Immunodeficiency Virus type 1 (HIV-1) undergo a surprisingly large amount of genetic drift in infected patients despite very large population sizes, which are predicted to be mostly deterministic. Several models have been proposed to explain this phenomenon, but all of them implicitly assume that the process of virus replication itself does not contribute to genetic drift. We developed an assay to measure the amount of genetic drift for HIV populations replicating in cell culture. The assay relies on creation of HIV populations of known size and measurements of variation in frequency of a neutral allele. Using this assay, we show that HIV undergoes approximately ten times more genetic drift than would be expected from its population size, which we defined as the number of infected cells in the culture. We showed that a large portion of the increase in genetic drift is due to non-synchronous infection of target cells. When infections are synchronized, genetic drift for the virus is only 3-fold higher than expected from its population size. Thus, the stochastic nature of biological processes involved in viral replication contributes to increased genetic drift in HIV populations. We propose that appreciation of these effects will allow better understanding of the evolutionary forces acting on HIV in infected patients. Genetic drift can be a strong evolutionary force, especially in small populations. Studies of HIV evolution within a single infected patient suggest that genetic drift plays an important role in the evolution of the virus, despite the large size of the viral population. The factors responsible for the high genetic drift are not known, but several models have been proposed to explain the phenomenon; all of them assume that the viral population is ideal. We measured the amount of genetic drift in HIV populations, replicating in the controlled environment of cell culture. We found that HIV populations exhibit approximately 10-fold more genetic drift than would be expected for an ideal population of similar size. Non-synchronous timing of infection is partially responsible for the increase, but other unidentified factors also contribute. While the increase in genetic drift observed for HIV in culture is not sufficient to explain the several orders of magnitude increase in intra-patient genetic drift, it provides strong experimental evidence for the intrinsic stochasticity of the HIV replication cycle. Understanding the sources of genetic drift is necessary to better understand the evolutionary forces that act upon HIV in vivo.
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Affiliation(s)
- Yegor Voronin
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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Pozo F, Casas I, Ruiz G, Falcón A, Pérez-Breña P. [Application of molecular methods in the diagnosis and epidemiological study of viral respiratory infections]. Enferm Infecc Microbiol Clin 2009; 26 Suppl 9:15-25. [PMID: 19195443 PMCID: PMC7130302 DOI: 10.1016/s0213-005x(08)76537-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hasta la fecha se han identificado más de 200 virus pertenecientes a 6 familias taxonómicas diferentes asociados con la infección del tracto respiratorio humano. La utilización generalizada de métodos moleculares en los laboratorios de microbiología clínica no sólo ha aportado grandes ventajas al diagnóstico de estas infecciones, sino también está permitiendo profundizar en el conocimiento de la enfermedad y el comportamiento epidemiológico de los virus causantes. Esta tecnología incrementa de manera notable el rendimiento de detección de virus en las muestras respiratorias, debido a su elevada sensibilidad en comparación con las técnicas clásicas y a la posibilidad de identificar virus no cultivables o de crecimiento fastidioso en las líneas celulares habituales, lo que permite realizar el diagnóstico etiológico con mayor rapidez. Sin embargo, también comporta algunos inconvenientes, como son detectar virus que se encuentran colonizando la mucosa respiratoria de personas asintomáticas, o en secreciones de pacientes que ya se han recuperado de una infección pasada, a consecuencia de excreción prolongada de éstos. La secuenciación de los productos obtenidos en la reacción de amplificación genómica permite caracterizar de forma adicional los virus detectados mediante su genotipado, realizar estudios de epidemiología molecular e identificar resistencias a determinados antivirales, por citar sólo algunos ejemplos.
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Affiliation(s)
- Francisco Pozo
- Laboratorio de Gripe y Virus Respiratorios, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, España.
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Abstract
In 2004, the novel respiratory human coronavirus NL63 (HCoV-NL63) was identified, and subsequent research revealed that the virus has spread worldwide. HCoV-229E is a close relative of HCoV-NL63, and infection with either virus can lead to the hospitalization of young children, immunocompromised persons, and the elderly. Children infected with HCoV-NL63 often develop croup, with obstruction of the airway. In this study we investigated at which age children are confronted for the first time with an HCoV-NL63 infection and, thus, at which age they seroconvert to HCoV-NL63 positivity. We designed a recombinant HCoV-229E and a recombinant HCoV-NL63 nucleocapsid protein enzyme-linked immunosorbent assay and performed a seroepidemiology survey on longitudinal and cross-sectional serum samples. The longitudinal serum samples were collected from 13 newborns, and data for those newborns were available from multiple time points spanning a period of at least 18 months. For the cross-sectional survey we tested serum samples of 139 children, including newborns to children 16 years of age. In examinations of the longitudinal serum samples we observed that all of the children had maternal anti-NL63 and anti-229E antibodies at birth that disappeared within 3 months. Seven of the 13 children became HCoV-NL63 seropositive during follow-up, whereas only 2 became HCoV-229E seropositive. The serology data of the cross-sectional serum samples revealed that 75% and 65% of the children in the age group 2.5 to 3.5 years were HCoV-NL63 and HCoV-229E seropositive, respectively. We conclude that on average, HCoV-NL63 and HCoV-229E seroconversion occurs before children reach the age of 3.5 years.
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Dijkman R, Jebbink MF, Wilbrink B, Pyrc K, Zaaijer HL, Minor PD, Franklin S, Berkhout B, Thiel V, van der Hoek L. Human coronavirus 229E encodes a single ORF4 protein between the spike and the envelope genes. Virol J 2006; 3:106. [PMID: 17194306 PMCID: PMC1774570 DOI: 10.1186/1743-422x-3-106] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Accepted: 12/28/2006] [Indexed: 11/12/2022] Open
Abstract
Background The genome of coronaviruses contains structural and non-structural genes, including several so-called accessory genes. All group 1b coronaviruses encode a single accessory protein between the spike and envelope genes, except for human coronavirus (HCoV) 229E. The prototype virus has a split gene, encoding the putative ORF4a and ORF4b proteins. To determine whether primary HCoV-229E isolates exhibit this unusual genome organization, we analyzed the ORF4a/b region of five current clinical isolates from The Netherlands and three early isolates collected at the Common Cold Unit (CCU) in Salisbury, UK. Results All Dutch isolates were identical in the ORF4a/b region at amino acid level. All CCU isolates are only 98% identical to the Dutch isolates at the nucleotide level, but more closely related to the prototype HCoV-229E (>98%). Remarkably, our analyses revealed that the laboratory adapted, prototype HCoV-229E has a 2-nucleotide deletion in the ORF4a/b region, whereas all clinical isolates carry a single ORF, 660 nt in size, encoding a single protein of 219 amino acids, which is a homologue of the ORF3 proteins encoded by HCoV-NL63 and PEDV. Conclusion Thus, the genome organization of the group 1b coronaviruses HCoV-NL63, PEDV and HCoV-229E is identical. It is possible that extensive culturing of the HCoV-229E laboratory strain resulted in truncation of ORF4. This may indicate that the protein is not essential in cell culture, but the highly conserved amino acid sequence of the ORF4 protein among clinical isolates suggests that the protein plays an important role in vivo.
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Affiliation(s)
- Ronald Dijkman
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Berry Wilbrink
- Laboratory for Infectious Diseases and Screening, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Krzysztof Pyrc
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Hans L Zaaijer
- Laboratory of Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Philip D Minor
- National Institute for Biological Standards and Controls (NIBSC), Hertfordshire, UK
| | - Sally Franklin
- National Institute for Biological Standards and Controls (NIBSC), Hertfordshire, UK
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Volker Thiel
- Kantonal Hospital St. Gallen, Research Department, St Gallen, Switzerland
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
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