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Lam TTY, Hon CC, Tang JW. Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections. Crit Rev Clin Lab Sci 2010; 47:5-49. [PMID: 20367503 DOI: 10.3109/10408361003633318] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Since DNA sequencing techniques first became available almost 30 years ago, the amount of nucleic acid sequence data has increased enormously. Phylogenetics, which is widely applied to compare and analyze such data, is particularly useful for the analysis of genes from rapidly evolving viruses. It has been used extensively to describe the molecular epidemiology and transmission of the human immunodeficiency virus (HIV), the origins and subsequent evolution of the severe acute respiratory syndrome (SARS)-associated coronavirus (SCoV), and, more recently, the evolving epidemiology of avian influenza as well as seasonal and pandemic human influenza viruses. Recent advances in phylogenetic methods can infer more in-depth information about the patterns of virus emergence, adding to the conventional approaches in viral epidemiology. Examples of this information include estimations (with confidence limits) of the actual time of the origin of a new viral strain or its emergence in a new species, viral recombination and reassortment events, the rate of population size change in a viral epidemic, and how the virus spreads and evolves within a specific population and geographical region. Such sequence-derived information obtained from the phylogenetic tree can assist in the design and implementation of public health and therapeutic interventions. However, application of many of these advanced phylogenetic methods are currently limited to specialized phylogeneticists and statisticians, mainly because of their mathematical basis and their dependence on the use of a large number of computer programs. This review attempts to bridge this gap by presenting conceptual, technical, and practical aspects of applying phylogenetic methods in studies of influenza, HIV, and SCoV. It aims to provide, with minimal mathematics and statistics, a practical overview of how phylogenetic methods can be incorporated into virological studies by clinical and laboratory specialists.
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Affiliation(s)
- Tommy Tsan-Yuk Lam
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, China
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Molecular and Biochemical Characterization of the SARS-CoV Accessory Proteins ORF8a, ORF8b and ORF8ab. MOLECULAR BIOLOGY OF THE SARS-CORONAVIRUS 2010. [PMCID: PMC7176222 DOI: 10.1007/978-3-642-03683-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
A novel coronavirus was identified as the aetiological agent for the global outbreak of severe acute respiratory syndrome (SARS) at the beginning of the twenty-first century. The SARS coronavirus genome encodes for proteins that are common to all members of the coronavirus, i.e. replicase polyproteins (pp1a and pp1b) and structural proteins (spike, membrane, nucleocapsid and envelope), as well as eight accessory proteins. The accessory proteins have been designated as open reading frames (ORF) 3a, 3b, 6, 7a, 7b, 8a, 8b and 9b, and they do not show significant homology to viral proteins of other known coronaviruses. Epidemiological studies have revealed that the part of the viral genome that encodes for ORF8a and ORF8b showed major variations and the animal isolates contain an additional 29-nucleotide sequence which is absent in most of the human isolates. As a result, ORF8a and ORF8b in the human isolates become one ORF, termed ORF8ab. In this chapter, we will discuss the genetic variation in the ORF8 region, expression of ORF8a, ORF8b and ORF8ab during infection, cellular localization and posttranslational modification of ORF8a, ORF8b and ORF8ab, participation of ORF8a, ORF8b and ORF8ab in viral–viral interactions, their effects on other viral proteins and impact on viral replication and/or pathogenesis.
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Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission. J Virol 2009; 84:3134-46. [PMID: 19906932 DOI: 10.1128/jvi.01394-09] [Citation(s) in RCA: 473] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Over the past 30 years, several cross-species transmission events, as well as changes in virus tropism, have mediated significant animal and human diseases. Most notable is severe acute respiratory syndrome (SARS), a lower respiratory tract disease of humans that was first reported in late 2002 in Guangdong Province, China. The disease, which quickly spread worldwide over a period of 4 months spanning late 2002 and early 2003, infected over 8,000 individuals and killed nearly 800 before it was successfully contained by aggressive public health intervention strategies. A coronavirus (SARS-CoV) was identified as the etiological agent of SARS, and initial assessments determined that the virus crossed to human hosts from zoonotic reservoirs, including bats, Himalayan palm civets (Paguma larvata), and raccoon dogs (Nyctereutes procyonoides), sold in exotic animal markets in Guangdong Province. In this review, we discuss the molecular mechanisms that govern coronavirus cross-species transmission both in vitro and in vivo, using the emergence of SARS-CoV as a model. We pay particular attention to how changes in the Spike attachment protein, both within and outside of the receptor binding domain, mediate the emergence of coronaviruses in new host populations.
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Yip CW, Hon CC, Shi M, Lam TTY, Chow KYC, Zeng F, Leung FCC. Phylogenetic perspectives on the epidemiology and origins of SARS and SARS-like coronaviruses. INFECTION GENETICS AND EVOLUTION 2009; 9:1185-96. [PMID: 19800030 PMCID: PMC7106296 DOI: 10.1016/j.meegid.2009.09.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2009] [Revised: 08/09/2009] [Accepted: 09/24/2009] [Indexed: 11/24/2022]
Abstract
Severe Acute Respiratory Syndrome (SARS) is a respiratory disease caused by a zoonotic coronavirus (CoV) named SARS-CoV (SCoV), which rapidly swept the globe after its emergence in rural China during late 2002. The origins of SCoV have been mysterious and controversial, until the recent discovery of SARS-like CoV (SLCoV) in bats and the proposal of bats as the natural reservior of the Coronaviridae family. In this article, we focused on discussing how phylogenetics contributed to our understanding towards the emergence and transmission of SCoV. We first reviewed the epidemiology of SCoV from a phylogenetic perspective and discussed the controversies over its phylogenetic origins. Then, we summarized the phylogenetic findings in relation to its zoonotic origins and the proposed inter-species viral transmission events. Finally, we also discussed how the discoveries of SCoV and SLCoV expanded our knowledge on the evolution of the Coronaviridae family as well as its implications on the possible future re-emergence of SCoV.
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Affiliation(s)
- Chi Wai Yip
- The School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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Du L, He Y, Zhou Y, Liu S, Zheng BJ, Jiang S. The spike protein of SARS-CoV--a target for vaccine and therapeutic development. Nat Rev Microbiol 2009; 7:226-36. [PMID: 19198616 PMCID: PMC2750777 DOI: 10.1038/nrmicro2090] [Citation(s) in RCA: 1150] [Impact Index Per Article: 76.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This Review provides an overview on the spike (S) protein of severe acute respiratory syndrome-coronavirus (SARS-CoV) as a target for the development of vaccines and therapeutics for the prevention and treatment of SARS. SARS is a newly emerging infectious disease, caused by SARS-CoV, a novel coronavirus that caused a global outbreak of SARS. SARS-CoV S protein mediates binding of the virus with its receptor angiotensin-converting enzyme 2 and promotes the fusion between the viral and host cell membranes and virus entry into the host cell. SARS-CoV S protein induces humoral and cellular immune responses against SARS-CoV. SARS S protein is the target of new SARS vaccines. These vaccines are based on SARS-CoV full-length S protein and its receptor-binding domain, including DNA-, viral vector- and subunit-based vaccines Peptides, antibodies, organic compounds and short interfering RNAs are additional anti-SARS-CoV therapeutics that target the S protein. The work on SARS-CoV S protein-based vaccines and drugs will be useful as a model for the development of prophylactic strategies and therapies against other viruses with class I fusion proteins that can cause emerging infectious diseases.
The outbreaks of severe acute respiratory syndrome (SARS) between 2002 and 2004 killed hundreds of people. Vaccines against the SARS coronavirus (SARS-CoV) could protect the population during future outbreaks. In this Review, Shibo Jiang and colleagues describe such vaccines, as well as other therapeutics, based on the SARS-CoV spike protein. Severe acute respiratory syndrome (SARS) is a newly emerging infectious disease caused by a novel coronavirus, SARS-coronavirus (SARS-CoV). The SARS-CoV spike (S) protein is composed of two subunits; the S1 subunit contains a receptor-binding domain that engages with the host cell receptor angiotensin-converting enzyme 2 and the S2 subunit mediates fusion between the viral and host cell membranes. The S protein plays key parts in the induction of neutralizing-antibody and T-cell responses, as well as protective immunity, during infection with SARS-CoV. In this Review, we highlight recent advances in the development of vaccines and therapeutics based on the S protein.
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Affiliation(s)
- Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, 310 East 67th Street, New York, NY 10065, USA
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Yang J, James E, Roti M, Huston L, Gebe JA, Kwok WW. Searching immunodominant epitopes prior to epidemic: HLA class II-restricted SARS-CoV spike protein epitopes in unexposed individuals. Int Immunol 2008; 21:63-71. [PMID: 19050106 PMCID: PMC2638843 DOI: 10.1093/intimm/dxn124] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Identification of dominant T cell epitopes within newly emerging and re-emerging infectious organisms is valuable in understanding pathogenic immune responses and potential vaccine designs. However, difficulties in obtaining samples from patients or convalescent subjects have hampered research in this direction. We demonstrated a strategy, tetramer-guided epitope mapping, that specific CD4+ T cell epitopes can be identified by using PBMC from subjects that have not been exposed to the infectious organism. Sixteen HLA-DR0401- and 14 HLA-DR0701-restricted epitopes within spike protein of severe acute respiratory syndrome-coronavirus (SARS-CoV) were identified. Among these, spike protein residues 159-171, 166-178, 449-461 and 1083-1097 were identified to contain naturally processed immunodominant epitopes based on strong in vitro T cell responses of PBMC (as assayed by tetramer staining) to intact spike protein stimulation. These immunodominant epitopes were confirmed in vivo in HLA-DR0401 transgenic mice by immunizing with spike protein. Furthermore, the epitope-specific T cells from naive donors secreted IFN-gamma and IL-13 upon re-stimulation with corresponding tetramers. Our study demonstrates a strategy to determine potential immunodominant epitopes for emerging infectious pathogens prior to their epidemic circulation.
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Affiliation(s)
- Junbao Yang
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
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Sui J, Aird DR, Tamin A, Murakami A, Yan M, Yammanuru A, Jing H, Kan B, Liu X, Zhu Q, Yuan QA, Adams GP, Bellini WJ, Xu J, Anderson LJ, Marasco WA. Broadening of neutralization activity to directly block a dominant antibody-driven SARS-coronavirus evolution pathway. PLoS Pathog 2008; 4:e1000197. [PMID: 18989460 PMCID: PMC2572002 DOI: 10.1371/journal.ppat.1000197] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 10/09/2008] [Indexed: 01/01/2023] Open
Abstract
Phylogenetic analyses have provided strong evidence that amino acid changes in spike (S) protein of animal and human SARS coronaviruses (SARS-CoVs) during and between two zoonotic transfers (2002/03 and 2003/04) are the result of positive selection. While several studies support that some amino acid changes between animal and human viruses are the result of inter-species adaptation, the role of neutralizing antibodies (nAbs) in driving SARS-CoV evolution, particularly during intra-species transmission, is unknown. A detailed examination of SARS-CoV infected animal and human convalescent sera could provide evidence of nAb pressure which, if found, may lead to strategies to effectively block virus evolution pathways by broadening the activity of nAbs. Here we show, by focusing on a dominant neutralization epitope, that contemporaneous- and cross-strain nAb responses against SARS-CoV spike protein exist during natural infection. In vitro immune pressure on this epitope using 2002/03 strain-specific nAb 80R recapitulated a dominant escape mutation that was present in all 2003/04 animal and human viruses. Strategies to block this nAb escape/naturally occurring evolution pathway by generating broad nAbs (BnAbs) with activity against 80R escape mutants and both 2002/03 and 2003/04 strains were explored. Structure-based amino acid changes in an activation-induced cytidine deaminase (AID) “hot spot” in a light chain CDR (complementarity determining region) alone, introduced through shuffling of naturally occurring non-immune human VL chain repertoire or by targeted mutagenesis, were successful in generating these BnAbs. These results demonstrate that nAb-mediated immune pressure is likely a driving force for positive selection during intra-species transmission of SARS-CoV. Somatic hypermutation (SHM) of a single VL CDR can markedly broaden the activity of a strain-specific nAb. The strategies investigated in this study, in particular the use of structural information in combination of chain-shuffling as well as hot-spot CDR mutagenesis, can be exploited to broaden neutralization activity, to improve anti-viral nAb therapies, and directly manipulate virus evolution. The SARS-CoV caused a worldwide epidemic of SARS in 2002/03 and was responsible for this zoonotic infectious disease. The role of neutralizing antibody (nAb) mediated immune pressure in the evolution of SARS-CoV during the 2002/03 outbreak and a second 2003/04 zoonotic transmission is unknown. Here we demonstrate nAb responses elicited during natural infection clearly have strain-specific components which could have been the driving force for virus evolution in spike protein during intra-species transmission. In vitro immune pressure using 2002/03 strain-specific nAb 80R recapitulate a dominant escape mutation that was present in all 2003/04 animal and human viruses. We investigated how to generate a single broad nAb (BnAb) with activity against various natural viral variants of the 2002/03 and 2003/04 outbreaks as well as nAb escape mutants. Remarkably, amino acid changes in an activation-induced cytidine deaminase (AID) “hot spot” of somatic hypermutation and localized to a single VL CDR were successful in generating BnAbs. These results provide an effective strategy for generating BnAbs that should be generally useful for improving immune based anti-viral therapies as well as providing a foundation to directly manipulate virus evolution by blocking escape pathways.
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Affiliation(s)
- Jianhua Sui
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute; Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (JS); (WAM)
| | - Daniel R. Aird
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute; Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Azaibi Tamin
- National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Akikazu Murakami
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute; Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Meiying Yan
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Anuradha Yammanuru
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute; Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Huaiqi Jing
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Xin Liu
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute; Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Quan Zhu
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute; Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Qing-an Yuan
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Gregory P. Adams
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - William J. Bellini
- National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Larry J. Anderson
- National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Wayne A. Marasco
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute; Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (JS); (WAM)
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Kammila S, Das D, Bhatnagar PK, Sunwoo HH, Zayas-Zamora G, King M, Suresh MR. A rapid point of care immunoswab assay for SARS-CoV detection. J Virol Methods 2008; 152:77-84. [PMID: 18620761 PMCID: PMC2678951 DOI: 10.1016/j.jviromet.2008.05.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 04/18/2008] [Accepted: 05/08/2008] [Indexed: 01/09/2023]
Abstract
The emergence of severe acute respiratory syndrome (SARS) resulted in several outbreaks worldwide. Early tests for diagnosis were not always conclusive in identifying a SARS suspected patient. Nucleocapsid protein (NP) is the most predominant virus derived structural protein which is shed in high amounts in serum and nasopharyngeal aspirate during the first week of infection. As part of such efforts, a simple, easy to use immunoswab method was developed by generating a panel of monoclonal antibodies (MAbs), Bispecific MAbs and chicken polyclonal IgY antibody against the SARS-CoV nucleocapsid protein (NP). Employing the MAb-based immunoswab, an NP concentration of 200 pg/mL in saline and pig nasopharyngeal aspirate, and 500 pg/mL in rabbit serum were detected. BsMAb-based immunoswabs detected an NP concentration of 20 pg/mL in saline, 500 pg/mL in rabbit serum and 20-200 pg/mL in pig nasopharyngeal aspirate. Polyclonal IgY-based immunoswabs detected an NP concentration of 10 pg/mL in pig nasopharyngeal aspirate providing the most sensitive SARS point of care assay. Results show that the robust immunoswab method of detecting SARS-CoV NP antigen can be developed into an easy and effective way of identifying SARS suspected individuals during a future SARS epidemic, thereby reducing and containing the transmission. The key feature of this simple immunoswab diagnostic assay is its ability to detect the presence of the SARS-CoV antigen within 45-60 min with the availability of the body fluid samples.
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Affiliation(s)
- Sriram Kammila
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, 11304-89 Avenue, Edmonton, Alberta, Canada T6G 2N8
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Structural analysis of major species barriers between humans and palm civets for severe acute respiratory syndrome coronavirus infections. J Virol 2008; 82:6984-91. [PMID: 18448527 DOI: 10.1128/jvi.00442-08] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
It is believed that a novel coronavirus, severe acute respiratory syndrome coronavirus (SARS-CoV), was passed from palm civets to humans and caused the epidemic of SARS in 2002 to 2003. The major species barriers between humans and civets for SARS-CoV infections are the specific interactions between a defined receptor-binding domain (RBD) on a viral spike protein and its host receptor, angiotensin-converting enzyme 2 (ACE2). In this study a chimeric ACE2 bearing the critical N-terminal helix from civet and the remaining peptidase domain from human was constructed, and it was shown that this construct has the same receptor activity as civet ACE2. In addition, crystal structures of the chimeric ACE2 complexed with RBDs from various human and civet SARS-CoV strains were determined. These structures, combined with a previously determined structure of human ACE2 complexed with the RBD from a human SARS-CoV strain, have revealed a structural basis for understanding the major species barriers between humans and civets for SARS-CoV infections. They show that the major species barriers are determined by interactions between four ACE2 residues (residues 31, 35, 38, and 353) and two RBD residues (residues 479 and 487), that early civet SARS-CoV isolates were prevented from infecting human cells due to imbalanced salt bridges at the hydrophobic virus/receptor interface, and that SARS-CoV has evolved to gain sustained infectivity for human cells by eliminating unfavorable free charges at the interface through stepwise mutations at positions 479 and 487. These results enhance our understanding of host adaptations and cross-species infections of SARS-CoV and other emerging animal viruses.
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Is the anti-psychotic, 10-(3-(dimethylamino)propyl)phenothiazine (promazine), a potential drug with which to treat SARS infections? Lack of efficacy of promazine on SARS-CoV replication in a mouse model. Antiviral Res 2008; 79:105-13. [PMID: 18423639 PMCID: PMC2582943 DOI: 10.1016/j.antiviral.2007.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 08/03/2007] [Accepted: 12/13/2007] [Indexed: 01/20/2023]
Abstract
Phenothiazine and derivatives were tested for inhibition of SARS-CoV replication. Phenothiazine slightly inhibited SARS-CoV replication in a neutral red (NR) uptake assay. Adding a propylamino group to give promazine reduced virus yields (VYR assay) with an EC90 = 8.3 ± 2.8 μM, but without selectivity. Various substitutions in the basic phenothiazine structure did not promote efficacy. Phenazine ethosulfate was the most potent compound by VYR assay (EC90 = 6.1 ± 4.3 μM). All compounds were toxic (IC50 = 6.6–74.5 μM) except for phenoxathiin (IC50 = 858 ± 208 μM) and 10-(alpha-diethylamino-propionyl) phenothiazine·HCl (IC50 = 195 ± 71.2 μM). Consequently, none were selective inhibitors of SARS-CoV replication (SI values <1–3.3 μM). These data portended the poor efficacy of promazine in a SARS-CoV mouse lung replication model. Intraperitoneal treatment with promazine using a prophylactic (−4 h)/therapeutic regimen of 1, 10, or 50 mg/(kg day) did not reduce virus lung titers at day 3, yet prolonged virus replication to 14 days. Similar therapeutic promazine doses were not efficacious. Thus, promazine did not affect SARS-CoV replication in vitro or in vivo, nor were any other phenothiazines efficacious in reducing virus replication. Therefore, treating SARS infections with compounds like promazine is not warranted.
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Poutanen SM. Human Coronaviruses. PRINCIPLES AND PRACTICE OF PEDIATRIC INFECTIOUS DISEASE 2008. [PMCID: PMC7310927 DOI: 10.1016/b978-0-7020-3468-8.50228-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ruan L, Zeng G. SARS Epidemic: SARS Outbreaks in Inner-land of China. EMERGING INFECTIONS IN ASIA 2008. [PMCID: PMC7122843 DOI: 10.1007/978-0-387-75722-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Severe Acute Respiratory Syndrome (SARS), also known in China as Infectious Atypical Pneumonia (IAP), is the 21st century’s first infectious disease to severely threaten the public health of the human population (WHO, 2003a). A respiratory transmitted disease caused by a virus, SARS is highly infectious and is rapidly transmitted, inflicting severe complications and a high case fatality rate. The first round of the SARS pandemic led to global panic and billions of dollars economic losses, for due to lack of effective SARS drugs, governments throughout the world had to take rigid steps toward prevention and treatment of the disease. The SARS epidemic began with the first reported case in Guangzhou, China (Wang et al., 2004), on 16 November 2002. Eight months later, the disease had spread to 26 countries in Asia, America, and Europe, resulting in a reported 8,096 cases and 774 deaths (WHO, 2004). In this global epidemic, China, with 7,429 cases and 685 deaths, accounted for 91.8% of the world’s reported cases and 88.5% of the deaths (5,327 SARS cases and 349 deaths were reported in 24 provinces in the inner-land of China – mostly in Beijing and Guangzhou, which, with a combined 4,033 cases, accounted for 75.7% of the total number in the inner-land of China; Hong Kong had 1,755 cases, 299 deaths; Taiwan: 346 cases, 37 deaths; Macao: 1 case, 0 deaths) (He et al., 2003; Peng et al., 2003; Yang et al., 2003; Leadership Group of SARS Prevention and Control in Beijing, 2003; Chinese Center for Disease Control and Prevention, 2003).
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Severe acute respiratory syndrome (SARS) vaccines. Vaccines (Basel) 2008. [PMCID: PMC7315341 DOI: 10.1016/b978-1-4160-3611-1.50060-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Investigation of Animal Reservoir(s) of SARS-CoV. EMERGING INFECTIONS IN ASIA 2008. [PMCID: PMC7121429 DOI: 10.1007/978-0-387-75722-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Severe acute respiratory syndrome (SARS) is a novel infectious disease in the new millennium. It has been ascertained that a new coronavirus, SARS-CoV, is the etiological agent of SARS. While the extraordinarily rapid isolation and full genome sequencing of SARS-CoV constituted a remarkable scientific achievement, identification of the actual animal reservoir(s) of SARS-CoV is more difficult. Initial evidences indicated that the masked palm civet (Paguma larvata) was the primary suspect of the animal origin of SARS (Guan et al., 2003; Song et al., 2005). Recent studies suggested that horseshoe bat is one of the real reservoirs (Lau et al., 2005; Li et al., 2005) and masked palm civet may have only served as an intermediate amplification host for SARS-CoV and fulfilled efficient interspecies transmission (Lau et al., 2005). This chapter will summarize the studies on the animal reservoir(s) of SARS-CoV.
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Yu M, Stevens V, Berry JD, Crameri G, McEachern J, Tu C, Shi Z, Liang G, Weingartl H, Cardosa J, Eaton BT, Wang LF. Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species. J Immunol Methods 2007; 331:1-12. [PMID: 18191140 PMCID: PMC7094251 DOI: 10.1016/j.jim.2007.11.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 11/03/2007] [Accepted: 11/14/2007] [Indexed: 02/08/2023]
Abstract
Knowledge of immunodominant regions in major viral antigens is important for rational design of effective vaccines and diagnostic tests. Although there have been many reports of such work done for SARS–CoV, these were mainly focused on the immune responses of humans and mice. In this study, we aim to search for and compare immunodominant regions of the spike (S) and nucleocapsid (N) proteins which are recognized by sera from different animal species, including mouse, rat, rabbit, civet, pig and horse. Twelve overlapping recombinant protein fragments were produced in Escherichia coli, six each for the S and N proteins, which covered the entire coding region of the two proteins. Using a membrane-strip based Western blot approach, the reactivity of each antigen fragment against a panel of animal sera was determined. Immunodominant regions containing linear epitopes, which reacted with sera from all the species tested, were identified for both proteins. The S3 fragment (aa 402–622) and the N4 fragment (aa 220–336) were the most immunodominant among the six S and N fragments, respectively. Antibodies raised against the S3 fragment were able to block the binding of a panel of S-specific monoclonal antibodies (mAb) to SARS–CoV in ELISA, further demonstrating the immunodominance of this region. Based on these findings, one-step competition ELISAs were established which were able to detect SARS–CoV antibodies from human and at least seven different animal species. Considering that a large number of animal species are known to be susceptible to SARS–CoV, these assays will be a useful tool to trace the origin and transmission of SARS–CoV and to minimise the risk of animal-to-human transmission.
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Affiliation(s)
- Meng Yu
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria, Australia
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Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Clin Microbiol Rev 2007; 20:660-94. [PMID: 17934078 DOI: 10.1128/cmr.00023-07] [Citation(s) in RCA: 657] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Before the emergence of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) in 2003, only 12 other animal or human coronaviruses were known. The discovery of this virus was soon followed by the discovery of the civet and bat SARS-CoV and the human coronaviruses NL63 and HKU1. Surveillance of coronaviruses in many animal species has increased the number on the list of coronaviruses to at least 36. The explosive nature of the first SARS epidemic, the high mortality, its transient reemergence a year later, and economic disruptions led to a rush on research of the epidemiological, clinical, pathological, immunological, virological, and other basic scientific aspects of the virus and the disease. This research resulted in over 4,000 publications, only some of the most representative works of which could be reviewed in this article. The marked increase in the understanding of the virus and the disease within such a short time has allowed the development of diagnostic tests, animal models, antivirals, vaccines, and epidemiological and infection control measures, which could prove to be useful in randomized control trials if SARS should return. The findings that horseshoe bats are the natural reservoir for SARS-CoV-like virus and that civets are the amplification host highlight the importance of wildlife and biosecurity in farms and wet markets, which can serve as the source and amplification centers for emerging infections.
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68
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Zhu Z, Chakraborti S, He Y, Roberts A, Sheahan T, Xiao X, Hensley LE, Prabakaran P, Rockx B, Sidorov IA, Corti D, Vogel L, Feng Y, Kim JO, Wang LF, Baric R, Lanzavecchia A, Curtis KM, Nabel GJ, Subbarao K, Jiang S, Dimitrov DS. Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies. Proc Natl Acad Sci U S A 2007; 104:12123-8. [PMID: 17620608 PMCID: PMC1924550 DOI: 10.1073/pnas.0701000104] [Citation(s) in RCA: 240] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) caused a worldwide epidemic in late 2002/early 2003 and a second outbreak in the winter of 2003/2004 by an independent animal-to-human transmission. The GD03 strain, which was isolated from an index patient of the second outbreak, was reported to resist neutralization by the human monoclonal antibodies (hmAbs) 80R and S3.1, which can potently neutralize isolates from the first outbreak. Here we report that two hmAbs, m396 and S230.15, potently neutralized GD03 and representative isolates from the first SARS outbreak (Urbani, Tor2) and from palm civets (SZ3, SZ16). These antibodies also protected mice challenged with the Urbani or recombinant viruses bearing the GD03 and SZ16 spike (S) glycoproteins. Both antibodies competed with the SARS-CoV receptor, ACE2, for binding to the receptor-binding domain (RBD), suggesting a mechanism of neutralization that involves interference with the SARS-CoV-ACE2 interaction. Two putative hot-spot residues in the RBD (Ile-489 and Tyr-491) were identified within the SARS-CoV spike that likely contribute to most of the m396-binding energy. Residues Ile-489 and Tyr-491 are highly conserved within the SARS-CoV spike, indicating a possible mechanism of the m396 cross-reactivity. Sequence analysis and mutagenesis data show that m396 might neutralize all zoonotic and epidemic SARS-CoV isolates with known sequences, except strains derived from bats. These antibodies exhibit cross-reactivity against isolates from the two SARS outbreaks and palm civets and could have potential applications for diagnosis, prophylaxis, and treatment of SARS-CoV infections.
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Affiliation(s)
- Zhongyu Zhu
- *Protein Interactions Group, Center for Cancer Research Nanobiology Program, and
- Basic Research Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702
| | - Samitabh Chakraborti
- Basic Research Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702
| | - Yuxian He
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10021
| | | | - Tim Sheahan
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599
| | - Xiaodong Xiao
- *Protein Interactions Group, Center for Cancer Research Nanobiology Program, and
| | - Lisa E. Hensley
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702
| | - Ponraj Prabakaran
- *Protein Interactions Group, Center for Cancer Research Nanobiology Program, and
| | - Barry Rockx
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599
| | - Igor A. Sidorov
- *Protein Interactions Group, Center for Cancer Research Nanobiology Program, and
| | - Davide Corti
- **Institute for Research in Biomedicine, Via Vela 6, CH 6500 Belllinzona, Switzerland; and
| | | | - Yang Feng
- *Protein Interactions Group, Center for Cancer Research Nanobiology Program, and
| | - Jae-Ouk Kim
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Lin-Fa Wang
- CSIRO Livestock Industries, Australian Animal Health Laboratory and Australian Biosecurity Cooperative Research Center for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599
| | - Antonio Lanzavecchia
- **Institute for Research in Biomedicine, Via Vela 6, CH 6500 Belllinzona, Switzerland; and
| | - Kristopher M. Curtis
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702
| | - Gary J. Nabel
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | | | - Shibo Jiang
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10021
| | - Dimiter S. Dimitrov
- *Protein Interactions Group, Center for Cancer Research Nanobiology Program, and
- To whom correspondence should be addressed at:
Protein Interactions, Center for Cancer Research Nanobiology Program, National Cancer Institute, National Institutes of Health, P.O. Box B, Building 469, Room 150B, Frederick, MD 21702-1201. E-mail:
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69
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Hamming I, Cooper ME, Haagmans BL, Hooper NM, Korstanje R, Osterhaus ADME, Timens W, Turner AJ, Navis G, van Goor H. The emerging role of ACE2 in physiology and disease. J Pathol 2007; 212:1-11. [PMID: 17464936 PMCID: PMC7167724 DOI: 10.1002/path.2162] [Citation(s) in RCA: 324] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The renin–angiotensin–aldosterone system (RAAS) is a key regulator of systemic blood pressure and renal function and a key player in renal and cardiovascular disease. However, its (patho)physiological roles and its architecture are more complex than initially anticipated. Novel RAAS components that may add to our understanding have been discovered in recent years. In particular, the human homologue of ACE (ACE2) has added a higher level of complexity to the RAAS. In a short period of time, ACE2 has been cloned, purified, knocked‐out, knocked‐in; inhibitors have been developed; its 3D structure determined; and new functions have been identified. ACE2 is now implicated in cardiovascular and renal (patho)physiology, diabetes, pregnancy, lung disease and, remarkably, ACE2 serves as a receptor for SARS and NL63 coronaviruses. This review covers available information on the genetic, structural and functional properties of ACE2. Its role in a variety of (patho)physiological conditions and therapeutic options of modulation are discussed. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- I Hamming
- Department of Pathology and Laboratory Medicine, University Medical Center Groningen and University of Groningen, The Netherlands.
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70
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Abstract
TOC Summary: The discovery of SARS-like coronaviruses in horseshoe bats highlights the possibility of future outbreaks caused by different coronaviruses of bat origin. Bats have been identified as a natural reservoir for an increasing number of emerging zoonotic viruses, including henipaviruses and variants of rabies viruses. Recently, we and another group independently identified several horseshoe bat species (genus Rhinolophus) as the reservoir host for a large number of viruses that have a close genetic relationship with the coronavirus associated with severe acute respiratory syndrome (SARS). Our current research focused on the identification of the reservoir species for the progenitor virus of the SARS coronaviruses responsible for outbreaks during 2002–2003 and 2003–2004. In addition to SARS-like coronaviruses, many other novel bat coronaviruses, which belong to groups 1 and 2 of the 3 existing coronavirus groups, have been detected by PCR. The discovery of bat SARS-like coronaviruses and the great genetic diversity of coronaviruses in bats have shed new light on the origin and transmission of SARS coronaviruses.
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Affiliation(s)
- Lin-Fa Wang
- Australian Animal Health Laboratory, Geelong, Victoria, Australia.
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71
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Shi Z, Hu Z. A review of studies on animal reservoirs of the SARS coronavirus. Virus Res 2007; 133:74-87. [PMID: 17451830 PMCID: PMC7114516 DOI: 10.1016/j.virusres.2007.03.012] [Citation(s) in RCA: 207] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 03/04/2007] [Accepted: 03/15/2007] [Indexed: 12/02/2022]
Abstract
In this review, we summarize the researches on animal reservoirs of the SARS coronavirus (SARS-CoV). Masked palm civets were suspected as the origin of the SARS outbreak in 2003 and was confirmed as the direct origin of SARS cases with mild symptom in 2004. Sequence analysis of the SARS-CoV-like virus in masked palm civets indicated that they were highly homologous to human SARS-CoV with nt identity over 99.6%, indicating the virus has not been circulating in the population of masked palm civets for a very long time. Alignment of 10 complete viral genome sequences from masked palm civets with those of human SARS-CoVs revealed 26 conserved single-nucleotide variations (SNVs) in the viruses from masked palm civets. These conserved SNVs were gradually lost from the genomes of viruses isolated from the early phase to late phase human patients of the 2003 SARS epidemic. In 2005, horseshoe bats were identified as the natural reservoir of a group of coronaviruses that are distantly related to SARS-CoV. The genome sequences of bat SARS-like coronavirus had about 88–92% nt identity with that of the SARS-CoV. The prevalence of antibodies and viral RNA in different bat species and the characteristics of the bat SARS-like coronavirus were elucidated. Apart from masked palm civets and bats, 29 other animal species had been tested for the SARS-CoV, and the results are summarized in this paper.
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Affiliation(s)
- Zhengli Shi
- State Key Laboratory of Virology and Joint-Lab of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
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72
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A retrospective serological study of severe acute respiratory syndrome cases in Guangdong province, China. Chin Med J (Engl) 2007. [DOI: 10.1097/00029330-200704020-00020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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73
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Burrer R, Neuman BW, Ting JPC, Stein DA, Moulton HM, Iversen PL, Kuhn P, Buchmeier MJ. Antiviral effects of antisense morpholino oligomers in murine coronavirus infection models. J Virol 2007; 81:5637-48. [PMID: 17344287 PMCID: PMC1900280 DOI: 10.1128/jvi.02360-06] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The recent emergence of novel pathogenic human and animal coronaviruses has highlighted the need for antiviral therapies that are effective against a spectrum of these viruses. We have used several strains of murine hepatitis virus (MHV) in cell culture and in vivo in mouse models to investigate the antiviral characteristics of peptide-conjugated antisense phosphorodiamidate morpholino oligomers (P-PMOs). Ten P-PMOs directed against various target sites in the viral genome were tested in cell culture, and one of these (5TERM), which was complementary to the 5' terminus of the genomic RNA, was effective against six strains of MHV. Further studies were carried out with various arginine-rich peptides conjugated to the 5TERM PMO sequence in order to evaluate efficacy and toxicity and thereby select candidates for in vivo testing. In uninfected mice, prolonged P-PMO treatment did not result in weight loss or detectable histopathologic changes. 5TERM P-PMO treatment reduced viral titers in target organs and protected mice against virus-induced tissue damage. Prophylactic 5TERM P-PMO treatment decreased the amount of weight loss associated with infection under most experimental conditions. Treatment also prolonged survival in two lethal challenge models. In some cases of high-dose viral inoculation followed by delayed treatment, 5TERM P-PMO treatment was not protective and increased morbidity in the treated group, suggesting that P-PMO may cause toxic effects in diseased mice that were not apparent in the uninfected animals. However, the strong antiviral effect observed suggests that with further development, P-PMO may provide an effective therapeutic approach against a broad range of coronavirus infections.
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Affiliation(s)
- Renaud Burrer
- The Scripps Research Institute, Department of Molecular and Integrative Neurosciences, Mail Drop SP30-2020, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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74
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Abstract
Emerging viral infections are becoming a serious problem in Europe in the recent years. This is particularly true for severe acute respiratory syndrome (SARS), West Nile virus (WNV) disease, Toscana virus (TOSV) disease, and potentially for avian influenza virus (H5N1). In contrast, emergence or re-emergence of severe viral infections, including tick borne encephalitis virus, and viral haemorrhagic fever caused by Hantavirus and dengue virus have been frequently reported in several European countries. Laboratory diagnosis of these viral infections based on viral isolation or detection by immune electron microscopy, immunoassay and polymerase chain reaction (PCR) has dramatically improved in the recent years, and SARS represents a good example of a diagnostic approach to emerging viral infections. Finally, old and new promising agents are in the pipeline of pharmaceutical companies to treat emerging viral infections. However only prevention based on large epidemiological studies, and research and development of new vaccines may be able to control and eventually eradicate these deadly viral infections.
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Affiliation(s)
- Agostino Pugliese
- Department of Medical and Surgical Sciences, Section of Clinical Microbiology of Turin University, Amedeo di Savoia Hospital, Turin, Italy.
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75
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Zhang Y, Zheng N, Nan P, Cao Y, Hasegawa M, Zhong Y. Computational simulation of interactions between SARS coronavirus spike mutants and host species-specific receptors. Comput Biol Chem 2007; 31:134-7. [PMID: 17368104 PMCID: PMC7106403 DOI: 10.1016/j.compbiolchem.2007.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2006] [Accepted: 02/13/2007] [Indexed: 02/02/2023]
Abstract
As a critical adaptive mechanism, amino acid replacements on the severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein could alter the receptor-binding specificity of this envelope glycoprotein and in turn lead to the emergence or reemergence of this viral zoonosis. Based on the X-ray structures of SARS-CoV spike receptor-binding domain (RBD) in complex with its functional receptor (angiotensin-converting enzyme 2, ACE2), we perform computational simulations of interactions between three representative RBD mutants and four host species-specific receptors. The comparisons between computational predictions and experimental evidences validate our structural bioinformatics approaches. And the predictions further indicate that some viral prototypes might utilize the rat ACE2 while rats might serve as a vector or reservoir of SARS-CoV.
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Affiliation(s)
- Yuan Zhang
- School of Life Sciences, Fudan University, Shanghai 200433, China.
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76
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Haynes LM, Miao C, Harcourt JL, Montgomery JM, Le MQ, Dryga SA, Kamrud KI, Rivers B, Babcock GJ, Oliver JB, Comer JA, Reynolds M, Uyeki TM, Bausch D, Ksiazek T, Thomas W, Alterson H, Smith J, Ambrosino DM, Anderson LJ. Recombinant protein-based assays for detection of antibodies to severe acute respiratory syndrome coronavirus spike and nucleocapsid proteins. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2007; 14:331-3. [PMID: 17229882 PMCID: PMC1828864 DOI: 10.1128/cvi.00351-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Recombinant severe acute respiratory syndrome (SARS) nucleocapsid and spike protein-based immunoglobulin G immunoassays were developed and evaluated. Our assays demonstrated high sensitivity and specificity to the SARS coronavirus in sera collected from patients as late as 2 years postonset of symptoms. These assays will be useful not only for routine SARS coronavirus diagnostics but also for epidemiological and antibody kinetic studies.
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Affiliation(s)
- Lia M Haynes
- National Centers for Immunization and Respiratory Diseases, Division of Viral Diseases, Respiratory and Gastroenteritis Viruses Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-18, Atlanta, GA 30333.
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77
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Kuhn JH, Li W, Radoshitzky SR, Choe H, Farzan M. Severe Acute Respiratory Syndrome Coronavirus Entry as a Target of Antiviral Therapies. Antivir Ther 2007. [DOI: 10.1177/135965350701200s05.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The identification in 2003 of a coronavirus as the aetiological agent of severe acute respiratory syndrome (SARS) intensified efforts to understand the biology of corona-viruses in general and SARS coronavirus (SARS-CoV) in particular. Rapid progress was made in describing the SARS-CoV genome, evolution and lifecycle. Identification of angiotensin-converting enzyme 2 (ACE2) as an obligate cellular receptor for SARS-CoV contributed to understanding of the SARS-CoV entry process, and helped to characterize two targets of antiviral therapeutics: the SARS-CoV spike protein and ACE2. Here we describe the role of these proteins in SARS-CoV replication and potential therapeutic strategies aimed at preventing entry of SARS-CoV into target cells.
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Affiliation(s)
- Jens H Kuhn
- Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, MA, USA
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Wenhui Li
- Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, MA, USA
| | - Sheli R Radoshitzky
- Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, MA, USA
| | - Hyeryun Choe
- Department of Pediatrics, Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Farzan
- Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, MA, USA
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78
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Abstract
Severe acute respiratory syndrome (SARS) is caused by a coronavirus (CoV), SARSCoV. SARS-CoV belongs to the family Coronaviridae, which are enveloped RNA viruses in the order Nidovirales. Global research efforts are continuing to increase the understanding of the virus, the pathogenesis of the disease it causes (SARS), and the “heterogeneity of individual infectiousness” as well as shedding light on how to prepare for other emerging viral diseases. Promising drugs and vaccines have been identified. The milestones achieved have resulted from a truly international effort. Molecular studies dissected the adaptation of this virus as it jumped from an intermediary animal, the civet, to humans, thus providing valuable insights into processes of molecular emergence.
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Affiliation(s)
- Tommy R Tong
- Department of Pathology, Princess Margaret Hospital, Laichikok, Kowloon, Hong Kong, China
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79
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Du L, Zhao G, He Y, Guo Y, Zheng BJ, Jiang S, Zhou Y. Receptor-binding domain of SARS-CoV spike protein induces long-term protective immunity in an animal model. Vaccine 2006; 25:2832-8. [PMID: 17092615 PMCID: PMC7115660 DOI: 10.1016/j.vaccine.2006.10.031] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2006] [Revised: 09/10/2006] [Accepted: 10/17/2006] [Indexed: 12/16/2022]
Abstract
Development of effective vaccines against severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) is still a priority in prevention of re-emergence of SARS. Our previous studies have shown that the receptor-binding domain (RBD) of SARS-CoV spike (S) protein elicits highly potent neutralizing antibody responses in the immunized animals. But it is unknown whether RBD can also induce protective immunity in an animal model, a key aspect for vaccine development. In this study, BALB/c mice were vaccinated intramuscularly (i.m.) with 10 μg of RBD-Fc (RBD fused with human IgG1 Fc) and boosted twice at 3-week intervals and one more time at 12th month. Humoral immune responses of vaccinated mice were investigated for up to 12 months at a 1-month interval and the neutralizing titers of produced antibodies were reported at months 0, 3, 6 and 12 post-vaccination. Mice were challenged with the homologous strain of SARS-CoV 5 days after the last boost, and sacrificed 5 days after the challenge. Mouse lung tissues were collected for detection of viral load, virus replication and histopathological effects. Our results showed that RBD-Fc vaccination induced high titer of S-specific antibodies with long-term and potent SARS-CoV neutralizing activity. Four of five vaccinated mice were protected from subsequent SARS-CoV challenge because no significant virus replication, and no obvious histopathological changes were found in the lung tissues of the vaccinated mice challenged with SARS-CoV. Only one vaccinated mouse had mild alveolar damage in the lung tissues. In contrast, high copies of SARS-CoV RNA and virus replication were detected, and pathological changes were observed in the lung tissues of the control mice. In conclusion, our findings suggest that RBD, which can induce protective antibodies to SARS-CoV, may be further developed as a safe and effective SARS subunit vaccine.
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Affiliation(s)
- Lanying Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
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80
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He Y, Li J, Heck S, Lustigman S, Jiang S. Antigenic and immunogenic characterization of recombinant baculovirus-expressed severe acute respiratory syndrome coronavirus spike protein: implication for vaccine design. J Virol 2006; 80:5757-67. [PMID: 16731915 PMCID: PMC1472569 DOI: 10.1128/jvi.00083-06] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The spike (S) glycoprotein of severe acute respiratory syndrome coronavirus (SARS-CoV) mediates the receptor interaction and immune recognition and is considered a major target for vaccine design. However, its antigenic and immunogenic properties remain to be elucidated. In this study, we immunized mice with full-length S protein (FL-S) or its extracellular domain (EC-S) expressed by recombinant baculoviruses in insect cells. We found that the immunized mice developed high titers of anti-S antibodies with potent neutralizing activities against SARS pseudoviruses constructed with the S proteins of Tor2, GD03T13, and SZ3, the representative strains of 2002 to 2003 and 2003 to 2004 human SARS-CoV and palm civet SARS-CoV, respectively. These data suggest that the recombinant baculovirus-expressed S protein vaccines possess excellent immunogenicity, thereby inducing highly potent neutralizing responses against human and animal SARS-CoV variants. The antigenic structure of the S protein was characterized by a panel of 38 monoclonal antibodies (MAbs) isolated from the immunized mice. The epitopes of most anti-S MAbs (32 of 38) were localized within the S1 domain, and those of the remaining 6 MAbs were mapped to the S2 domain. Among the anti-S1 MAbs, 17 MAbs targeted the N-terminal region (amino acids [aa] 12 to 327), 9 MAbs recognized the receptor-binding domain (RBD; aa 318 to 510), and 6 MAbs reacted with the C-terminal region of S1 domain that contains the major immunodominant site (aa 528 to 635). Strikingly, all of the RBD-specific MAbs had potent neutralizing activity, 6 of which efficiently blocked the receptor binding, confirming that the RBD contains the main neutralizing epitopes and that blockage of the receptor association is the major mechanism of SARS-CoV neutralization. Five MAbs specific for the S1 N-terminal region exhibited moderate neutralizing activity, but none of the MAbs reacting with the S2 domain and the major immunodominant site in S1 showed neutralizing activity. All of the neutralizing MAbs recognize conformational epitopes. These data provide important information for understanding the antigenicity and immunogenicity of S protein and for designing SARS vaccines. This panel of anti-S MAbs can be used as tools for studying the structure and function of the SARS-CoV S protein.
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Affiliation(s)
- Yuxian He
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10021, USA.
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81
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Keng CT, Choi YW, Welkers MRA, Chan DZL, Shen S, Gee Lim S, Hong W, Tan YJ. The human severe acute respiratory syndrome coronavirus (SARS-CoV) 8b protein is distinct from its counterpart in animal SARS-CoV and down-regulates the expression of the envelope protein in infected cells. Virology 2006; 354:132-42. [PMID: 16876844 PMCID: PMC7111915 DOI: 10.1016/j.virol.2006.06.026] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 06/15/2006] [Accepted: 06/17/2006] [Indexed: 12/14/2022]
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV), isolated from humans infected during the peak of epidemic, encodes two accessory proteins termed as 8a and 8b. Interestingly, the SARS-CoV isolated from animals contains an extra 29-nucleotide in this region such that these proteins are fused to become a single protein, 8ab. Here, we compared the cellular properties of the 8a, 8b and 8ab proteins by examining their cellular localizations and their abilities to interact with other SARS-CoV proteins. These results may suggest that the conformations of 8a and 8b are different from 8ab although nearly all the amino acids in 8a and 8b are found in 8ab. In addition, the expression of the structural protein, envelope (E), was down-regulated by 8b but not 8a or 8ab. Consequently, E was not detectable in SARS-CoV-infected cells that were expressing high levels of 8b. These findings suggest that 8b may modulate viral replication and/or pathogenesis.
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Affiliation(s)
- Choong-Tat Keng
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore, 138673
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82
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ter Meulen J, van den Brink EN, Poon LLM, Marissen WE, Leung CSW, Cox F, Cheung CY, Bakker AQ, Bogaards JA, van Deventer E, Preiser W, Doerr HW, Chow VT, de Kruif J, Peiris JSM, Goudsmit J. Human monoclonal antibody combination against SARS coronavirus: synergy and coverage of escape mutants. PLoS Med 2006; 3:e237. [PMID: 16796401 PMCID: PMC1483912 DOI: 10.1371/journal.pmed.0030237] [Citation(s) in RCA: 493] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Accepted: 04/03/2006] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Experimental animal data show that protection against severe acute respiratory syndrome coronavirus (SARS-CoV) infection with human monoclonal antibodies (mAbs) is feasible. For an effective immune prophylaxis in humans, broad coverage of different strains of SARS-CoV and control of potential neutralization escape variants will be required. Combinations of virus-neutralizing, noncompeting mAbs may have these properties. METHODS AND FINDINGS Human mAb CR3014 has been shown to completely prevent lung pathology and abolish pharyngeal shedding of SARS-CoV in infected ferrets. We generated in vitro SARS-CoV variants escaping neutralization by CR3014, which all had a single P462L mutation in the glycoprotein spike (S) of the escape virus. In vitro experiments confirmed that binding of CR3014 to a recombinant S fragment (amino acid residues 318-510) harboring this mutation was abolished. We therefore screened an antibody-phage library derived from blood of a convalescent SARS patient for antibodies complementary to CR3014. A novel mAb, CR3022, was identified that neutralized CR3014 escape viruses, did not compete with CR3014 for binding to recombinant S1 fragments, and bound to S1 fragments derived from the civet cat SARS-CoV-like strain SZ3. No escape variants could be generated with CR3022. The mixture of both mAbs showed neutralization of SARS-CoV in a synergistic fashion by recognizing different epitopes on the receptor-binding domain. Dose reduction indices of 4.5 and 20.5 were observed for CR3014 and CR3022, respectively, at 100% neutralization. Because enhancement of SARS-CoV infection by subneutralizing antibody concentrations is of concern, we show here that anti-SARS-CoV antibodies do not convert the abortive infection of primary human macrophages by SARS-CoV into a productive one. CONCLUSIONS The combination of two noncompeting human mAbs CR3014 and CR3022 potentially controls immune escape and extends the breadth of protection. At the same time, synergy between CR3014 and CR3022 may allow for a lower total antibody dose to be administered for passive immune prophylaxis of SARS-CoV infection.
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MESH Headings
- Amino Acid Substitution
- Animals
- Antibodies, Monoclonal/administration & dosage
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antibody Affinity
- Antibody Specificity
- Antigen-Antibody Reactions
- Antigenic Variation
- Antigens, Viral/immunology
- Base Sequence
- Binding Sites
- Cells, Cultured/virology
- Chlorocebus aethiops
- Disease Outbreaks
- Dose-Response Relationship, Immunologic
- Drug Synergism
- Epitopes/immunology
- Humans
- Immune Sera
- Immunization, Passive
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Heavy Chains/immunology
- Immunoglobulin Light Chains/genetics
- Immunoglobulin Light Chains/immunology
- Immunoglobulin Variable Region/chemistry
- Immunoglobulin Variable Region/immunology
- Macrophages/virology
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/immunology
- Membrane Glycoproteins/physiology
- Molecular Sequence Data
- Mutation, Missense
- Nandiniidae/virology
- Neutralization Tests
- Point Mutation
- Protein Structure, Tertiary
- Recombinant Fusion Proteins/immunology
- Severe acute respiratory syndrome-related coronavirus/genetics
- Severe acute respiratory syndrome-related coronavirus/immunology
- Severe Acute Respiratory Syndrome/drug therapy
- Severe Acute Respiratory Syndrome/epidemiology
- Severe Acute Respiratory Syndrome/prevention & control
- Severe Acute Respiratory Syndrome/therapy
- Severe Acute Respiratory Syndrome/virology
- Spike Glycoprotein, Coronavirus
- Surface Plasmon Resonance
- Vero Cells
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/immunology
- Viral Envelope Proteins/physiology
- Virus Replication
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83
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Muller MP, Richardson SE, McGeer A, Dresser L, Raboud J, Mazzulli T, Loeb M, Louie M. Early diagnosis of SARS: lessons from the Toronto SARS outbreak. Eur J Clin Microbiol Infect Dis 2006; 25:230-7. [PMID: 16586072 PMCID: PMC7087683 DOI: 10.1007/s10096-006-0127-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The clinical presentation of SARS is nonspecific and diagnostic tests do not provide accurate results early in the disease course. Initial diagnosis remains reliant on clinical assessment. To identify features of the clinical assessment that are useful in SARS diagnosis, the exposure status and the prevalence and timing of symptoms, signs, laboratory and radiographic findings were determined for all adult patients admitted with suspected SARS during the Toronto SARS outbreak. Findings were compared between patients with laboratory-confirmed SARS and those in whom SARS was excluded by laboratory or public health investigation. Of 364 cases, 273 (75%) had confirmed SARS, 30 (8%) were excluded, and 61 (17%) remained indeterminate. Among confirmed cases, exposure occurred in the healthcare environment (80%) or in the households of affected patients (17%); community or travel-related cases were rare (<3%). Fever occurred in 97% of patients by the time of admission. Respiratory findings including cough, dyspnea and pulmonary infiltrates evolved later and were present in only 59, 37 and 68% of patients, respectively, at admission. Direct exposure, fever on the first day of illness, and elevated temperature, pulmonary infiltrates, lymphopenia and thrombocytopenia at admission were associated with confirmed cases. Rhinorrhea, sore throat, and an elevated neutrophil count at admission were associated with excluded cases. In the absence of fever or significant exposure, SARS is unlikely. Other clinical, laboratory and radiographic findings further raise or lower the likelihood of SARS and provide a rational basis for estimating the likelihood of SARS and directing initial management.
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Affiliation(s)
- M P Muller
- Department of Microbiology, Mount Sinai Hospital, 600 University Avenue, M5G 1X5 Toronto, Canada.
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84
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He Y, Li J, Li W, Lustigman S, Farzan M, Jiang S. Cross-neutralization of human and palm civet severe acute respiratory syndrome coronaviruses by antibodies targeting the receptor-binding domain of spike protein. THE JOURNAL OF IMMUNOLOGY 2006; 176:6085-92. [PMID: 16670317 DOI: 10.4049/jimmunol.176.10.6085] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The spike (S) protein of severe acute respiratory syndrome coronavirus (SARS-CoV) is considered as a protective Ag for vaccine design. We previously demonstrated that the receptor-binding domain (RBD) of S protein contains multiple conformational epitopes (Conf I-VI) that confer the major target of neutralizing Abs. Here we show that the recombinant RBDs derived from the S protein sequences of Tor2, GD03, and SZ3, the representative strains of human 2002-2003 and 2003-2004 SARS-CoV and palm civet SARS-CoV, respectively, induce in the immunized mice and rabbits high titers of cross-neutralizing Abs against pseudoviruses expressing S proteins of Tor2, GD03, and SZ3. We also demonstrate that the Tor2-RBD induced-Conf I-VI mAbs can potently neutralize both human SARS-CoV strains, Tor2 and GD03. However, only the Conf IV-VI, but not Conf I-III mAbs, neutralize civet SARS-CoV strain SZ3. All these mAbs reacted significantly with each of the three RBD variants (Tor2-RBD, GD03-RBD, and SZ3-RBD) that differ at several amino acids. Regardless, the Conf I-IV and VI epitopes were completely disrupted by single-point mutation of the conserved residues in the RBD (e.g., D429A, R441A, or D454A) and the Conf III epitope was significantly affected by E452A or D463A substitution. Interestingly, the Conf V epitope, which may overlap the receptor-binding motif and induce most potent neutralizing Abs, was conserved in these mutants. These data suggest that the major neutralizing epitopes of SARS-CoV have been apparently maintained during cross-species transmission, and that RBD-based vaccines may induce broad protection against both human and animal SARS-CoV variants.
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Affiliation(s)
- Yuxian He
- Lindsley F. Kimball Research Institute, New York Blood Center, 310 East 67th Street, New York, NY 10021, USA.
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85
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Zhu QY, Qin ED, Wang W, Yu J, Liu BH, Hu Y, Hu JF, Cao WC. Fatal infection with influenza A (H5N1) virus in China. N Engl J Med 2006; 354:2731-2. [PMID: 16790715 DOI: 10.1056/nejmc066058] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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86
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Tan YJ, Lim SG, Hong W. Understanding the accessory viral proteins unique to the severe acute respiratory syndrome (SARS) coronavirus. Antiviral Res 2006; 72:78-88. [PMID: 16820226 PMCID: PMC7114237 DOI: 10.1016/j.antiviral.2006.05.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Revised: 04/29/2006] [Accepted: 05/15/2006] [Indexed: 12/14/2022]
Abstract
A novel coronavirus, termed the severe acute respiratory syndrome coronavirus (SARS-CoV), infected humans in Guangdong, China, in November 2002 and the subsequent efficient human-to-human transmissions of this virus caused profound disturbances in over 30 countries worldwide in 2003. Eventually, this epidemic was controlled by isolation and there has been no human infection reported since January 2004. However, research on different aspects of the SARS-CoV is not waning, as it is not known if this virus will re-emerge, especially since its origins and potential reservoir(s) are unresolved. The SARS-CoV genome is nearly 30 kb in length and contains 14 potential open reading frames (ORFs). Some of these ORFs encode for genes that are homologous to proteins found in all known coronaviruses, namely the replicase genes (ORFs 1a and 1b) and the four structural proteins: nucleocapsid, spike, membrane and envelope, and these proteins are expected to be essential for the replication of the virus. The remaining eight ORFs encodes for accessory proteins, varying in length from 39 to 274 amino acids, which are unique to SARS-CoV. This review will summarize the expeditious research on these accessory viral proteins in three major areas: (i) the detection of antibodies against accessory proteins in the serum of infected patients, (ii) the expression, processing and cellular localization of the accessory proteins, and (iii) the effects of the accessory proteins on cellular functions. These in-depth molecular and biochemical characterizations of the SARS-CoV accessory proteins, which have no homologues in other coronaviruses, may offer clues as to why the SARS-CoV causes such a severe and rapid attack in humans, while other coronaviruses that infect humans seem to be more forgiving.
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Affiliation(s)
- Yee-Joo Tan
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.
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87
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Li W, Wong SK, Li F, Kuhn JH, Huang IC, Choe H, Farzan M. Animal origins of the severe acute respiratory syndrome coronavirus: insight from ACE2-S-protein interactions. J Virol 2006; 80:4211-9. [PMID: 16611880 PMCID: PMC1472041 DOI: 10.1128/jvi.80.9.4211-4219.2006] [Citation(s) in RCA: 210] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Wenhui Li
- Department of Microbiology and Molecular Genetics, Harvard Medical School and New England Primate Research Center, Southborough, Massachusetts, USA.
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88
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Che XY, Di B, Zhao GP, Wang YD, Qiu LW, Hao W, Wang M, Qin PZ, Liu YF, Chan KH, Cheng VCC, Yuen KY. A patient with asymptomatic severe acute respiratory syndrome (SARS) and antigenemia from the 2003-2004 community outbreak of SARS in Guangzhou, China. Clin Infect Dis 2006; 43:e1-5. [PMID: 16758408 PMCID: PMC7108013 DOI: 10.1086/504943] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Accepted: 03/18/2006] [Indexed: 01/08/2023] Open
Abstract
An asymptomatic case of severe acute respiratory syndrome (SARS) occurred early in 2004, during a community outbreak of SARS in Guangzhou, China. This was the first time that a case of asymptomatic SARS was noted in an individual with antigenemia and seroconversion. The asymptomatic case patient and the second index case patient with SARS in the 2003-2004 outbreak both worked in the same restaurant, where they served palm civets, which were found to carry SARS-associated coronaviruses. Epidemiological information and laboratory findings suggested that the findings for the patient with asymptomatic infection, together with the findings from previously reported serological analyses of handlers of wild animals and the 4 index case patients from the 2004 community outbreak, reflected a likely intermediate phase of animal-to-human transmission of infection, rather than a case of human-to-human transmission. This intermediate phase may be a critical stage for virus evolution and disease prevention.
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Affiliation(s)
- Xiao-yan Che
- Center of Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou
- Reprints or correspondence: Dr. Xiao-yan Che, Center of Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, People's Republic of China ()
| | - Biao Di
- Center for Disease Control and Prevention of Guangzhou, Guangzhou
| | - Guo-ping Zhao
- Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai
- Dr. Guo-ping Zhao, Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, People's Republic of China ()
| | - Ya-di Wang
- Center of Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou
| | - Li-wen Qiu
- Center of Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou
| | - Wei Hao
- Center of Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou
| | - Ming Wang
- Center for Disease Control and Prevention of Guangzhou, Guangzhou
| | - Peng-zhe Qin
- Center for Disease Control and Prevention of Guangzhou, Guangzhou
| | - Yu-fei Liu
- Center for Disease Control and Prevention of Guangzhou, Guangzhou
| | - Kwok-hong Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Vincent C. C. Cheng
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Kwok-yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
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89
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Lim W, Ng KC, Tsang DNC. Laboratory Containment of SARS Virus. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2006. [DOI: 10.47102/annals-acadmedsg.v35n5p354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Following the severe acute respiratory syndrome (SARS) outbreak in 2003, a large number of clinical and environmental samples containing/potentially containing SARS coronavirus (SARS-CoV) as well as SARS-CoV stocks were retained in clinical and research laboratories. The importance of laboratory biosafety was demonstrated by the occurrence of laboratory incidents in Singapore, Taiwan and Beijing. It is imperative that safe practice and techniques, safety equipment and appropriate facility design should be in place to reduce or eliminate exposure of laboratory workers, other persons and the outside environment to SARS-CoV containing materials. Discussion on laboratory containment of SARS-CoV was initiated in Hong Kong in August 2003. It was agreed that an inventory of all specimens with the potential presence of SARS-CoV collected for any diagnostic or research purposes from November 2002 to July 2003 should be established in each laboratory. They should be stored in a secure place at the appropriate biosafety level with access control. Un-needed samples collected during the period should be destroyed. These laboratories should be audited to ensure inventories are updated. The audit should include safety and security measures to detect irregularities. Any laboratory accidents involving materials suspected of containing SARS-CoV should be reported to the authorities and all personnel exposed closely followed medically. A contingency plan should be in place in the laboratory and a drill conducted regularly to test its efficacy. By January 2004, all clinical laboratories performing SARS-CoV testing in Hong Kong set up inventories to document location and types of SARS-CoV containing materials retained in their laboratory. Audits of these laboratories in 2004 showed that laboratory safety and containment requirements as recommended were generally met.
Key words: Contingency plan, Laboratory safety, Virus inventory, Virus survival
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Affiliation(s)
- Wilina Lim
- Centre for Health Protection, Department of Health, Hong Kong
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90
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Pien BC, Saah JR, Miller SE, Woods CW. Use of sentinel laboratories by clinicians to evaluate potential bioterrorism and emerging infections. Clin Infect Dis 2006; 42:1311-24. [PMID: 16586392 PMCID: PMC7107841 DOI: 10.1086/503260] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Accepted: 01/11/2006] [Indexed: 11/13/2022] Open
Abstract
With the persistent threat of emerging infectious diseases and bioterrorism, it has become increasingly important that clinicians be able to identify the diseases that might signal the occurrence of these unusual events. Essential to a thoughtful diagnostic approach is understanding when to initiate a public health investigation and how to appropriately use commonly performed microbiology procedures in the sentinel laboratory to evaluate potential pathogens. Although diagnostic test development is evolving rapidly, recognizing many of these pathogens continues to challenge the capabilities of most sentinel laboratories. Therefore, effective, ongoing communication and education among clinicians, infection control personnel, sentinel laboratorians, public health authorities, and Laboratory Response Network reference laboratorians is the key to preparedness.
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Affiliation(s)
- Brian C. Pien
- Division of Infectious Diseases and Clinical Microbiology Laboratory, Duke University Medical Center, Durham
| | - J. Royden Saah
- Bioterrorism and Emerging Pathogens Unit, North Carolina State Laboratory of Public Health, Raleigh, North Carolina
| | - Sara E. Miller
- Departments of Pathology, Duke University Medical Center, Durham
- Molecular Genetics and Microbiology, Duke University Medical Center, Duke University Medical Center, Durham
| | - Christopher W. Woods
- Departments of Medicine, Duke University Medical Center, Durham
- Pathology, Durham Veterans Administration Medical Center, Duke University Medical Center, Durham
- Reprints or correspondence: Dr. Christopher W. Woods, Chief, Infectious Diseases, Section 113, Durham VA Medical Center, Durham, NC 27705 ()
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91
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Zhou Z, Post P, Chubet R, Holtz K, McPherson C, Petric M, Cox M. A recombinant baculovirus-expressed S glycoprotein vaccine elicits high titers of SARS-associated coronavirus (SARS-CoV) neutralizing antibodies in mice. Vaccine 2006; 24:3624-31. [PMID: 16497416 PMCID: PMC7115485 DOI: 10.1016/j.vaccine.2006.01.059] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Revised: 01/17/2006] [Accepted: 01/24/2006] [Indexed: 12/28/2022]
Abstract
A recombinant SARS-CoV spike (S) glycoprotein vaccine produced in insect cells in a pre-clinical development stage is described. A truncated version of S glycoprotein, containing only the ecto-domain, as well as a His-tagged full-length version were cloned and expressed in a serum-free insect cell line, ExpresSF+. The proteins, purified to apparent homogeneity by liquid column chromatography, were formulated without adjuvant at 3, 9, 27, and 50 microg per dose in phosphate saline and used to immunize mice. Both antigens in each formulation elicited a strong immune response after two or three vaccinations with the antigen. Neutralizing antibody titers correlated closely with standard ELISA reactivity against the S glycoprotein. The truncated S protein was also formulated with an adjuvant, aluminum hydroxide, at 1 microg per dose (+/-adjuvant), and 5 microg per dose (+/-adjuvant). Significantly enhanced immune responses, manifested by higher titers of serum ELISA and viral neutralizing antibodies, were achieved in adjuvanted groups with fewer doses and lower concentration of S glycoprotein. These findings indicate that the ecto-domain of SARS-CoV S glycoprotein vaccine, with or without adjuvant, is immunogenic and induces high titers of virus neutralizing antibodies to levels similar to those achieved with the full S glycoprotein vaccine.
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Affiliation(s)
- Zhimin Zhou
- Protein Sciences Corporation, 1000 Research Parkway, Meriden, CT 06540, USA.
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92
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Kong WP, Xu L, Stadler K, Ulmer JB, Abrignani S, Rappuoli R, Nabel GJ. Modulation of the immune response to the severe acute respiratory syndrome spike glycoprotein by gene-based and inactivated virus immunization. J Virol 2006; 79:13915-23. [PMID: 16254327 PMCID: PMC1280202 DOI: 10.1128/jvi.79.22.13915-13923.2005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although the initial isolates of the severe acute respiratory syndrome (SARS) coronavirus (CoV) are sensitive to neutralization by antibodies through their spike (S) glycoprotein, variants of S have since been identified that are resistant to such inhibition. Optimal vaccine strategies would therefore make use of additional determinants of immune recognition, either through cellular or expanded, cross-reactive humoral immunity. Here, the cellular and humoral immune responses elicited by different combinations of gene-based and inactivated viral particles with various adjuvants have been assessed. The T-cell response was altered by different prime-boost immunizations, with the optimal CD8 immunity induced by DNA priming and replication-defective adenoviral vector boosting. The humoral immune response was enhanced most effectively through the use of inactivated virus with adjuvants, either MF59 or alum, and was associated with stimulation of the CD4 but not the CD8 response. The use of inactivated SARS virus with MF59 enhanced the CD4 and antibody response even after gene-based vaccination. Because both cellular and humoral immune responses are generated by gene-based vaccination and inactivated viral boosting, this strategy may prove useful in the generation of SARS-CoV vaccines.
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Affiliation(s)
- Wing-pui Kong
- Vaccine Research Center, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bldg. 40, Room 4502, MSC-3005, 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
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93
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Perlman S, Holmes KV. Insights from the association of SARS-CoV S-protein with its receptor, ACE2. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2006; 581:209-18. [PMID: 17037532 PMCID: PMC7123956 DOI: 10.1007/978-0-387-33012-9_36] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Stanley Perlman
- Department of Pediatrics, University of Iowa, 52242 Iowa City, IA USA
| | - Kathryn V. Holmes
- Department of Microbiology, University of Colorado Health Sciences Center at Fitzsimons, 80045-8333 Aurora, CO USA
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94
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Kan B, Wang M, Jing H, Xu H, Jiang X, Yan M, Liang W, Zheng H, Wan K, Liu Q, Cui B, Xu Y, Zhang E, Wang H, Ye J, Li G, Li M, Cui Z, Qi X, Chen K, Du L, Gao K, Zhao YT, Zou XZ, Feng YJ, Gao YF, Hai R, Yu D, Guan Y, Xu J. Molecular evolution analysis and geographic investigation of severe acute respiratory syndrome coronavirus-like virus in palm civets at an animal market and on farms. J Virol 2005; 79:11892-900. [PMID: 16140765 PMCID: PMC1212604 DOI: 10.1128/jvi.79.18.11892-11900.2005] [Citation(s) in RCA: 252] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Massive numbers of palm civets were culled to remove sources for the reemergence of severe acute respiratory syndrome (SARS) in Guangdong Province, China, in January 2004, following SARS coronavirus detection in market animals. The virus was identified in all 91 palm civets and 15 raccoon dogs of animal market origin sampled prior to culling, but not in 1,107 palm civets later sampled at 25 farms, spread over 12 provinces, which were claimed to be the source of traded animals. Twenty-seven novel signature variation residues (SNVs) were identified on the spike gene and were analyzed for their phylogenetic relationships, based on 17 sequences obtained from animals in our study and from other published studies. Analysis indicated that the virus in palm civets at the live-animal market had evolved to infect humans. The evolutionary starting point was a prototype group consisting of three viral sequences of animal origin. Initially, seven SNV sites caused six amino acid changes, at positions 147, 228, 240, 479, 821, and 1080 of the spike protein, to generate low-pathogenicity viruses. One of these was linked to the first SARS patient in the 2003-2004 period. A further 14 SNVs caused 11 amino acid residue changes, at positions 360, 462, 472, 480, 487, 609, 613, 665, 743, 765, and 1163. The resulting high-pathogenicity groups were responsible for infections during the so-called early-phase epidemic of 2003. Finally, the remaining six SNVs caused four amino acid changes, at positions 227, 244, 344, and 778, which resulted in the group of viruses responsible for the global epidemic.
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Affiliation(s)
- Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control (China CDC), Chinese Center for Disease Control and Prevention, P.O. Box 5, Changping, Beijing 102206, People's Republic of China
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95
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Tripp RA, Haynes LM, Moore D, Anderson B, Tamin A, Harcourt BH, Jones LP, Yilla M, Babcock GJ, Greenough T, Ambrosino DM, Alvarez R, Callaway J, Cavitt S, Kamrud K, Alterson H, Smith J, Harcourt JL, Miao C, Razdan R, Comer JA, Rollin PE, Ksiazek TG, Sanchez A, Rota PA, Bellini WJ, Anderson LJ. Monoclonal antibodies to SARS-associated coronavirus (SARS-CoV): identification of neutralizing and antibodies reactive to S, N, M and E viral proteins. J Virol Methods 2005; 128:21-8. [PMID: 15885812 PMCID: PMC7112802 DOI: 10.1016/j.jviromet.2005.03.021] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Revised: 03/23/2005] [Accepted: 03/23/2005] [Indexed: 11/26/2022]
Abstract
Monoclonal antibodies (Mabs) against the Urbani strain of the SARS-associated coronavirus (SARS-CoV) were developed and characterized for reactivity to SARS-CoV and SARS-CoV S, N, M, and E proteins using enzyme-linked immunoabsorbent (ELISA), radioimmunoprecipitation, immunofluorescence, Western Blot and microneutralization assays. Twenty-six mAbs were reactive to SARS-CoV by ELISA, and nine were chosen for detailed characterization. Five mAbs reacted against the S protein, two against the M protein, and one each against the N and E proteins. Two of five S protein mAbs neutralized SARS-CoV infection of Vero E6 cells and reacted to an epitope within amino acids 490–510 in the S protein. While two of the three non-neutralizing antibodies recognized at second epitope within amino acids 270–350. The mAbs characterized should prove useful for developing SARS-CoV diagnostic assays and for studying the biology of infection and pathogenesis of disease.
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Affiliation(s)
- Ralph A. Tripp
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
| | - Lia M. Haynes
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
- Corresponding author. Tel.: +1 404 639 4004; fax: +1 404 639 1307.
| | - Deborah Moore
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
| | - Barbara Anderson
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
| | - Azaibi Tamin
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
| | - Brian H. Harcourt
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
| | - Les P. Jones
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
| | - Mamadi Yilla
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
| | - Gregory J. Babcock
- Massachusetts Biologic Laboratories, University of Massachusetts Medical School, Jamaica Plain, MA 02130, USA
| | - Thomas Greenough
- Massachusetts Biologic Laboratories, University of Massachusetts Medical School, Jamaica Plain, MA 02130, USA
| | - Donna M. Ambrosino
- Massachusetts Biologic Laboratories, University of Massachusetts Medical School, Jamaica Plain, MA 02130, USA
| | - Rene Alvarez
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
| | | | | | - Kurt Kamrud
- AlphaVax Inc., Research Triangle Park, NC 27709, USA
| | | | | | - Jennifer L. Harcourt
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
| | - Congrong Miao
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
| | - Raj Razdan
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
| | - James A. Comer
- National Center for Infectious Diseases, Division of Viral and Rickettsial Diseases, Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Pierre E. Rollin
- National Center for Infectious Diseases, Division of Viral and Rickettsial Diseases, Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Thomas G. Ksiazek
- National Center for Infectious Diseases, Division of Viral and Rickettsial Diseases, Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Anthony Sanchez
- National Center for Infectious Diseases, Division of Viral and Rickettsial Diseases, Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Paul A. Rota
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
| | - William J. Bellini
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
| | - Larry J. Anderson
- National Centers for Infectious Diseases, Division of Viral and Rickettsial Diseases, Respiratory and Enteric Virus Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Mailstop G-09, Atlanta, GA 30333, USA
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96
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Abstract
Severe acute respiratory syndrome (SARS) is an emerging infectious disease caused by a new coronavirus (SARS-CoV). Recent studies suggest that SARS-CoV is zoonotic and may have a broad host range besides humans. Although the global outbreak of SARS has been contained, there are serious concerns over its re-emergence and bioterrorism potential. As a part of preparedness, development of a safe and effective vaccine is one of the highest priorities in fighting SARS. A number of candidate vaccines, using a variety of approaches, are under development. The first vaccine tested in clinical trial is made from the inactivated form of SARS-CoV. Several live attenuated, genetically engineered or vector vaccines encoding the SARS-CoV spike (S) protein have been in pre-clinical studies. These vaccine candidates are effective in terms of eliciting protective immunity in the vaccinated animals. However, caution should be taken with the safety of whole virus or full-length S protein-based immunogens in humans because they may induce harmful immune or inflammatory responses. We propose to use the receptor-binding domain (RBD) of SARS-CoV S protein (residues 318--510) for developing a safe and effective subunit SARS vaccine, as it is not only a functional domain that mediates virus-receptor binding but also a major neutralization determinant of SARSCoV. It has been demonstrated that the RBD of SARS-CoV S protein contains multiple conformational epitopes capable of inducing highly potent neutralizing antibody responses and protective immunity.
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Affiliation(s)
- Yuxian He
- Viral Immunology Laboratory, Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York 10021, USA
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97
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Li YH, Li J, Liu XE, Wang L, Li T, Zhou YH, Zhuang H. Detection of the nucleocapsid protein of severe acute respiratory syndrome coronavirus in serum: comparison with results of other viral markers. J Virol Methods 2005; 130:45-50. [PMID: 16024098 PMCID: PMC7112769 DOI: 10.1016/j.jviromet.2005.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Revised: 05/26/2005] [Accepted: 06/09/2005] [Indexed: 12/02/2022]
Abstract
A capture enzyme-enhanced chemiluminescence immunoassay (ECLIA) based on three specific monoclonal antibodies to detect the nucleocapsid (N) protein of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in the serial serum samples from SARS patients was developed. The anti-SARS-CoV IgG and the viral RNA were also detected in the sera by ELISA and RT-PCR, respectively. During the first 10 days after onset, anti-SARS-CoV IgG, SARS-CoV RNA and the N protein were detected in 21.4, 42.9, and 90% of the patients’ sera, respectively. The detection rate of the N protein during days 11–15 of the disease was still significantly higher than those of anti-SARS-CoV IgG and SARS-CoV RNA. The data demonstrated that detection of the N protein with the capture ECLIA appears to be more useful than detection of other viral makers for rapid diagnosis of SARS in patients.
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Affiliation(s)
| | | | | | | | | | | | - Hui Zhuang
- Corresponding author. Tel.: +86 10 8280 2221; fax: +86 10 8280 1617.
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98
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Di B, Hao W, Gao Y, Wang M, Wang YD, Qiu LW, Wen K, Zhou DH, Wu XW, Lu EJ, Liao ZY, Mei YB, Zheng BJ, Che XY. Monoclonal antibody-based antigen capture enzyme-linked immunosorbent assay reveals high sensitivity of the nucleocapsid protein in acute-phase sera of severe acute respiratory syndrome patients. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 2005; 12:135-40. [PMID: 15642998 PMCID: PMC540218 DOI: 10.1128/cdli.12.1.135-140.2005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Accurate and timely diagnosis of severe acute respiratory syndrome coronavirus (SARS-CoV) infection is a critical step in preventing another global outbreak. In this study, 829 serum specimens were collected from 643 patients initially reported to be infected with SARS-CoV. The sera were tested for the N protein of SARS-CoV by using an antigen capture enzyme-linked immunosorbent assay (ELISA) based on monoclonal antibodies against the N protein of SARS-CoV and compared to 197 control serum samples from healthy donors and non-SARS febrile patients. The results of the N protein detection analysis were directly related to the serological analysis data. From 27 SARS patients who tested positive with the neutralization test, 100% of the 24 sera collected from 1 to 10 days after the onset of symptoms were positive for the N protein. N protein was not detected beyond day 11 in this group. The positive rates of N protein for sera collected at 1 to 5, 6 to 10, 11 to 15, and 16 to 20 days after the onset of symptoms for 414 samples from 298 serologically confirmed patients were 92.9, 69.8, 36.4, and 21.1%, respectively. For 294 sera from 248 serological test-negative patients, the rates were 25.6, 16.7, 9.3, and 0%, respectively. The N protein was not detected in 66 patients with cases of what was initially suspected to be SARS but serologically proven to be negative for SARS and in 197 serum samples from healthy donors and non-SARS febrile patients. The specificity of the assay was 100%. Furthermore, of 16 sera collected from four patients during the SARS recurrence in Guangzhou, 5 sera collected from 7 to 9 days after the onset of symptoms were positive for the N protein. N protein detection exhibited a high positive rate, 96 to 100%, between day 3 and day 5 after the onset of symptoms for 27 neutralization test-positive SARS patients and 298 serologically confirmed patients. The N protein detection rate continually decreased beginning with day 10, and N protein was not detected beyond day 19 after the onset of symptoms. In conclusion, an antigen capture ELISA reveals a high N protein detection rate in acute-phase sera of patients with SARS, which makes it useful for early diagnosis of SARS.
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Affiliation(s)
- Biao Di
- Center for Disease Control and Prevention of Guangzhou, Guangzhou, People's Republic of China
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99
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Li W, Zhang C, Sui J, Kuhn JH, Moore MJ, Luo S, Wong SK, Huang IC, Xu K, Vasilieva N, Murakami A, He Y, Marasco WA, Guan Y, Choe H, Farzan M. Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2. EMBO J 2005; 24:1634-43. [PMID: 15791205 PMCID: PMC1142572 DOI: 10.1038/sj.emboj.7600640] [Citation(s) in RCA: 749] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2004] [Accepted: 03/04/2005] [Indexed: 12/05/2022] Open
Abstract
Human angiotensin-converting enzyme 2 (ACE2) is a functional receptor for SARS coronavirus (SARS-CoV). Here we identify the SARS-CoV spike (S)-protein-binding site on ACE2. We also compare S proteins of SARS-CoV isolated during the 2002-2003 SARS outbreak and during the much less severe 2003-2004 outbreak, and from palm civets, a possible source of SARS-CoV found in humans. All three S proteins bound to and utilized palm-civet ACE2 efficiently, but the latter two S proteins utilized human ACE2 markedly less efficiently than did the S protein obtained during the earlier human outbreak. The lower affinity of these S proteins could be complemented by altering specific residues within the S-protein-binding site of human ACE2 to those of civet ACE2, or by altering S-protein residues 479 and 487 to residues conserved during the 2002-2003 outbreak. Collectively, these data describe molecular interactions important to the adaptation of SARS-CoV to human cells, and provide insight into the severity of the 2002-2003 SARS epidemic.
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Affiliation(s)
- Wenhui Li
- Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, MA, USA
| | - Chengsheng Zhang
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong SAR, PRC
| | - Jianhua Sui
- Department of Medicine, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jens H Kuhn
- Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, MA, USA
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Michael J Moore
- Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, MA, USA
| | - Shiwen Luo
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong SAR, PRC
| | - Swee-Kee Wong
- Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, MA, USA
| | - I-Chueh Huang
- Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, MA, USA
| | - Keming Xu
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong SAR, PRC
| | - Natalya Vasilieva
- Department of Pediatrics, Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Akikazu Murakami
- Department of Medicine, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yaqing He
- Center for Disease Control and Prevention of Shenzhen, Shenzhen, Guangdong Province, PRC
| | - Wayne A Marasco
- Department of Medicine, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yi Guan
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong SAR, PRC
| | - Hyeryun Choe
- Department of Pediatrics, Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Farzan
- Department of Microbiology and Molecular Genetics, Harvard Medical School, New England Primate Research Center, Southborough, MA, USA
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100
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Song HD, Tu CC, Zhang GW, Wang SY, Zheng K, Lei LC, Chen QX, Gao YW, Zhou HQ, Xiang H, Zheng HJ, Chern SWW, Cheng F, Pan CM, Xuan H, Chen SJ, Luo HM, Zhou DH, Liu YF, He JF, Qin PZ, Li LH, Ren YQ, Liang WJ, Yu YD, Anderson L, Wang M, Xu RH, Wu XW, Zheng HY, Chen JD, Liang G, Gao Y, Liao M, Fang L, Jiang LY, Li H, Chen F, Di B, He LJ, Lin JY, Tong S, Kong X, Du L, Hao P, Tang H, Bernini A, Yu XJ, Spiga O, Guo ZM, Pan HY, He WZ, Manuguerra JC, Fontanet A, Danchin A, Niccolai N, Li YX, Wu CI, Zhao GP. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc Natl Acad Sci U S A 2005; 102:2430-5. [PMID: 15695582 PMCID: PMC548959 DOI: 10.1073/pnas.0409608102] [Citation(s) in RCA: 511] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genomic sequences of severe acute respiratory syndrome coronaviruses from human and palm civet of the 2003/2004 outbreak in the city of Guangzhou, China, were nearly identical. Phylogenetic analysis suggested an independent viral invasion from animal to human in this new episode. Combining all existing data but excluding singletons, we identified 202 single-nucleotide variations. Among them, 17 are polymorphic in palm civets only. The ratio of nonsynonymous/synonymous nucleotide substitution in palm civets collected 1 yr apart from different geographic locations is very high, suggesting a rapid evolving process of viral proteins in civet as well, much like their adaptation in the human host in the early 2002-2003 epidemic. Major genetic variations in some critical genes, particularly the Spike gene, seemed essential for the transition from animal-to-human transmission to human-to-human transmission, which eventually caused the first severe acute respiratory syndrome outbreak of 2002/2003.
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Affiliation(s)
- Huai-Dong Song
- State Key Laboratory for Medical Genomics/Pôle Sino-Français de Recherche en Sciences du Vivant et Génomique, Ruijin Hospital Affiliated to Shanghai Second Medical University, 197 Rui Jin Road II, Shanghai 200025, China
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