1
|
Akaishi T, Fujiwara K, Ishii T. Genetic Recombination Sites Away from the Insertion/Deletion Hotspots in SARS-Related Coronaviruses. TOHOKU J EXP MED 2023; 259:17-26. [PMID: 36351613 DOI: 10.1620/tjem.2022.j093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Affiliation(s)
| | - Kei Fujiwara
- Department of Gastroenterology and Metabolism, Nagoya City University
| | - Tadashi Ishii
- Department of Education and Support for Regional Medicine, Tohoku University
| |
Collapse
|
2
|
Akaishi T, Fujiwara K, Ishii T. Insertion/deletion hotspots in the Nsp2, Nsp3, S1, and ORF8 genes of SARS-related coronaviruses. BMC Ecol Evol 2022; 22:123. [PMID: 36307763 PMCID: PMC9616624 DOI: 10.1186/s12862-022-02078-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/11/2022] [Indexed: 11/20/2022] Open
Abstract
The genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains many insertions/deletions (indels) from the genomes of other SARS-related coronaviruses. Some of the identified indels have recently reported to involve relatively long segments of 10-300 consecutive bases and with diverse RNA sequences around gaps between virus species, both of which are different characteristics from the classical shorter in-frame indels. These non-classical complex indels have been identified in non-structural protein 3 (Nsp3), the S1 domain of the spike (S), and open reading frame 8 (ORF8). To determine whether the occurrence of these non-classical indels in specific genomic regions is ubiquitous among broad species of SARS-related coronaviruses in different animal hosts, the present study compared SARS-related coronaviruses from humans (SARS-CoV and SARS-CoV-2), bats (RaTG13 and Rc-o319), and pangolins (GX-P4L), by performing multiple sequence alignment. As a result, indel hotspots with diverse RNA sequences of different lengths between the viruses were confirmed in the Nsp2 gene (approximately 2500-2600 base positions in the overall 29,900 bases), Nsp3 gene (approximately 3000-3300 and 3800-3900 base positions), N-terminal domain of the spike protein (21,500-22,500 base positions), and ORF8 gene (27,800-28,200 base positions). Abnormally high rate of point mutations and complex indels in these regions suggest that the occurrence of mutations in these hotspots may be selectively neutral or even benefit the survival of the viruses. The presence of such indel hotspots has not been reported in different human SARS-CoV-2 strains in the last 2 years, suggesting a lower rate of indels in human SARS-CoV-2. Future studies to elucidate the mechanisms enabling the frequent development of long and complex indels in specific genomic regions of SARS-related coronaviruses would offer deeper insights into the process of viral evolution.
Collapse
Affiliation(s)
- Tetsuya Akaishi
- grid.69566.3a0000 0001 2248 6943Department of Education and Support for Regional Medicine, Tohoku University, Seiryo-machi 1-1, Aoba-ku, 980-8574 Sendai, Miyagi Japan ,grid.69566.3a0000 0001 2248 6943COVID-19 Testing Center, Tohoku University, Sendai, Japan
| | - Kei Fujiwara
- grid.260433.00000 0001 0728 1069Department of Gastroenterology and Metabolism, Nagoya City University, Nagoya, Japan
| | - Tadashi Ishii
- grid.69566.3a0000 0001 2248 6943Department of Education and Support for Regional Medicine, Tohoku University, Seiryo-machi 1-1, Aoba-ku, 980-8574 Sendai, Miyagi Japan ,grid.69566.3a0000 0001 2248 6943COVID-19 Testing Center, Tohoku University, Sendai, Japan
| |
Collapse
|
3
|
Sequence Exchange Involving Dozens of Consecutive Bases with External Origin in SARS-Related Coronaviruses. J Virol 2022; 96:e0100222. [PMID: 35856673 PMCID: PMC9364795 DOI: 10.1128/jvi.01002-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
|
4
|
Insertion-and-Deletion Mutations between the Genomes of SARS-CoV, SARS-CoV-2, and Bat Coronavirus RaTG13. Microbiol Spectr 2022; 10:e0071622. [PMID: 35658573 PMCID: PMC9241832 DOI: 10.1128/spectrum.00716-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The evolutional process of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) development remains inconclusive. This study compared the genome sequences of severe acute respiratory syndrome coronavirus (SARS-CoV), bat coronavirus RaTG13, and SARS-CoV-2. In total, the genomes of SARS-CoV-2 and RaTG13 were 77.9% and 77.7% identical to the genome of SARS-CoV, respectively. A total of 3.6% (1,068 bases) of the SARS-CoV-2 genome was derived from insertion and/or deletion (indel) mutations, and 18.6% (5,548 bases) was from point mutations from the genome of SARS-CoV. At least 35 indel sites were confirmed in the genome of SARS-CoV-2, in which 17 were with ≥10 consecutive bases long. Ten of these relatively long indels were located in the spike (S) gene, five in nonstructural protein 3 (Nsp3) gene of open reading frame (ORF) 1a, and one in ORF8 and noncoding region. Seventeen (48.6%) of the 35 indels were based on insertion-and-deletion mutations with exchanged gene sequences of 7–325 consecutive bases. Almost the complete ORF8 gene was replaced by a single 325 consecutive base-long indel. The distribution of these indels was roughly in accordance with the distribution of the rate of point mutation rate around the indels. The genome sequence of SARS-CoV-2 was 96.0% identical to that of RaTG13. There was no long insertion-and-deletion mutation between the genomes of RaTG13 and SARS-CoV-2. The findings of the uneven distribution of multiple indels and the presence of multiple long insertion-and-deletion mutations with exchanged consecutive base sequences in the viral genome may provide insights into SARS-CoV-2 development. IMPORTANCE The developmental mechanism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains inconclusive. This study compared the base sequence one-by-one between severe acute respiratory syndrome coronavirus (SARS-CoV) or bat coronavirus RaTG13 and SARS-CoV-2. The genomes of SARS-CoV-2 and RaTG13 were 77.9% and 77.7% identical to the genome of SARS-CoV, respectively. Seventeen of the 35 sites with insertion and/or deletion mutations between SARS-CoV-2 and SARS-CoV were based on insertion-and-deletion mutations with the replacement of 7–325 consecutive bases. Most of these long insertion-and-deletion sites were concentrated in the nonstructural protein 3 (Nsp3) gene of open reading frame (ORF) 1a, S1 domain of the spike protein, and ORF8 genes. Such long insertion-and-deletion mutations were not observed between the genomes of RaTG13 and SARS-CoV-2. The presence of multiple long insertion-and-deletion mutations in the genome of SARS-CoV-2 and their uneven distributions may provide further insights into the development of the virus.
Collapse
|
5
|
Corpuz MVA, Buonerba A, Vigliotta G, Zarra T, Ballesteros F, Campiglia P, Belgiorno V, Korshin G, Naddeo V. Viruses in wastewater: occurrence, abundance and detection methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:140910. [PMID: 32758747 PMCID: PMC7368910 DOI: 10.1016/j.scitotenv.2020.140910] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 04/14/2023]
Abstract
This paper presents an updated and comprehensive review on the different methods used for detection and quantification of viruses in wastewater treatment systems. The analysis of viability of viruses in wastewater and sludge is another thrust of this review. Recent studies have mostly focused on determining the abundance and diversity of viruses in wastewater influents, in samples from primary, secondary, and tertiary treatment stages, and in final effluents. A few studies have also examined the occurrence and diversity of viruses in raw and digested sludge samples. Recent efforts to improve efficiency of virus detection and quantification methods in the complex wastewater and sludge matrices are highlighted in this review. A summary and a detailed comparison of the pre-treatment methods that have been utilized for wastewater and sludge samples are also presented. The role of metagenomics or sequencing analysis in monitoring wastewater systems to predict disease outbreaks, to conduct public health surveillance, to assess the efficiency of existing treatment systems in virus removal, and to re-evaluate current regulations regarding pathogenic viruses in wastewater is discussed in this paper. Challenges and future perspectives in the detection of viruses, including emerging and newly emerged viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in wastewater systems are discussed in this review.
Collapse
Affiliation(s)
- Mary Vermi Aizza Corpuz
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines.
| | - Antonio Buonerba
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Giovanni Vigliotta
- Laboratory of Microbiology, University of Salerno, 84084 Fisciano, Italy.
| | - Tiziano Zarra
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Florencio Ballesteros
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines; Department of Chemical Engineering, College of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines.
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy.
| | - Vincenzo Belgiorno
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Gregory Korshin
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA 98105-2700, United States.
| | - Vincenzo Naddeo
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| |
Collapse
|
6
|
SARS-CoV-2 and Three Related Coronaviruses Utilize Multiple ACE2 Orthologs and Are Potently Blocked by an Improved ACE2-Ig. J Virol 2020; 94:JVI.01283-20. [PMID: 32847856 PMCID: PMC7592233 DOI: 10.1128/jvi.01283-20] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of the currently uncontrolled coronavirus disease 2019 (COVID-19) pandemic. It is important to study the host range of SARS-CoV-2, because some domestic species might harbor the virus and transmit it back to humans. In addition, insight into the ability of SARS-CoV-2 and SARS-like viruses to utilize animal orthologs of the SARS-CoV-2 receptor ACE2 might provide structural insight into improving ACE2-based viral entry inhibitors. In this study, we found that ACE2 orthologs of a wide range of domestic and wild animals can support cell entry of SARS-CoV-2 and three related coronaviruses, providing insights into identifying animal hosts of these viruses. We also developed recombinant ACE2-Ig proteins that are able to potently block these viral infections, providing a promising approach to developing antiviral proteins broadly effective against these distinct coronaviruses. The ongoing coronavirus disease 2019 (COVID-19) pandemic has caused >20 million infections and >750,000 deaths. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, has been found closely related to the bat coronavirus strain RaTG13 (Bat-CoV RaTG13) and a recently identified pangolin coronavirus (Pangolin-CoV-2020). Here, we first investigated the ability of SARS-CoV-2 and three related coronaviruses to utilize animal orthologs of angiotensin-converting enzyme 2 (ACE2) for cell entry. We found that ACE2 orthologs of a wide range of domestic and wild mammals, including camels, cattle, horses, goats, sheep, cats, rabbits, and pangolins, were able to support cell entry of SARS-CoV-2, suggesting that these species might be able to harbor and spread this virus. In addition, the pangolin and bat coronaviruses, Pangolin-CoV-2020 and Bat-CoV RaTG13, were also found able to utilize human ACE2 and a number of animal-ACE2 orthologs for cell entry, indicating risks of spillover of these viruses into humans in the future. We then developed potently anticoronavirus ACE2-Ig proteins that are broadly effective against the four distinct coronaviruses. In particular, through truncating ACE2 at its residue 740 but not 615, introducing a D30E mutation, and adopting an antibody-like tetrameric-ACE2 configuration, we generated an ACE2-Ig variant that neutralizes SARS-CoV-2 at picomolar range. These data demonstrate that the improved ACE2-Ig variants developed in this study could potentially be developed to protect from SARS-CoV-2 and some other SARS-like viruses that might spillover into humans in the future. IMPORTANCE The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of the currently uncontrolled coronavirus disease 2019 (COVID-19) pandemic. It is important to study the host range of SARS-CoV-2, because some domestic species might harbor the virus and transmit it back to humans. In addition, insight into the ability of SARS-CoV-2 and SARS-like viruses to utilize animal orthologs of the SARS-CoV-2 receptor ACE2 might provide structural insight into improving ACE2-based viral entry inhibitors. In this study, we found that ACE2 orthologs of a wide range of domestic and wild animals can support cell entry of SARS-CoV-2 and three related coronaviruses, providing insights into identifying animal hosts of these viruses. We also developed recombinant ACE2-Ig proteins that are able to potently block these viral infections, providing a promising approach to developing antiviral proteins broadly effective against these distinct coronaviruses.
Collapse
|
7
|
Lam SD, Bordin N, Waman VP, Scholes HM, Ashford P, Sen N, van Dorp L, Rauer C, Dawson NL, Pang CSM, Abbasian M, Sillitoe I, Edwards SJL, Fraternali F, Lees JG, Santini JM, Orengo CA. SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals. Sci Rep 2020; 10:16471. [PMID: 33020502 PMCID: PMC7536205 DOI: 10.1038/s41598-020-71936-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/17/2020] [Indexed: 01/04/2023] Open
Abstract
SARS-CoV-2 has a zoonotic origin and was transmitted to humans via an undetermined intermediate host, leading to infections in humans and other mammals. To enter host cells, the viral spike protein (S-protein) binds to its receptor, ACE2, and is then processed by TMPRSS2. Whilst receptor binding contributes to the viral host range, S-protein:ACE2 complexes from other animals have not been investigated widely. To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We also analysed structural interactions to better understand the key residues contributing to affinity. We predict that mutations are more detrimental in ACE2 than TMPRSS2. Finally, we demonstrate phylogenetically that human SARS-CoV-2 strains have been isolated in animals. Our results suggest that SARS-CoV-2 can infect a broad range of mammals, but few fish, birds or reptiles. Susceptible animals could serve as reservoirs of the virus, necessitating careful ongoing animal management and surveillance.
Collapse
Affiliation(s)
- S D Lam
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - N Bordin
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - V P Waman
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - H M Scholes
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - P Ashford
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - N Sen
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
- Indian Institute of Science Education and Research, Pune, 411008, India
| | - L van Dorp
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - C Rauer
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - N L Dawson
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - C S M Pang
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - M Abbasian
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - I Sillitoe
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - S J L Edwards
- Department of Science and Technology Studies, University College London, London, WC1E 6BT, UK
| | - F Fraternali
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, New Hunt's House, King's College London, London, SE1 1UL, UK
| | - J G Lees
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 OBP, UK
| | - J M Santini
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - C A Orengo
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
| |
Collapse
|
8
|
Shirani K, Sheikhbahaei E, Torkpour Z, Ghadiri Nejad M, Kamyab Moghadas B, Ghasemi M, Akbari Aghdam H, Ehsani A, Saber-Samandari S, Khandan A. A Narrative Review of COVID-19: The New Pandemic Disease. IRANIAN JOURNAL OF MEDICAL SCIENCES 2020; 45:233-249. [PMID: 32801413 PMCID: PMC7395956 DOI: 10.30476/ijms.2020.85869.1549] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/06/2020] [Accepted: 05/18/2020] [Indexed: 01/21/2023]
Abstract
Nearly every 100 years, humans collectively face a pandemic crisis. After the Spanish flu, now the world is in the grip of coronavirus disease 2019 (COVID-19). First detected in 2019 in the Chinese city of Wuhan, COVID-19 causes severe acute respiratory distress syndrome. Despite the initial evidence indicating a zoonotic origin, the contagion is now known to primarily spread from person to person through respiratory droplets. The precautionary measures recommended by the scientific community to halt the fast transmission of the disease failed to prevent this contagious disease from becoming a pandemic for a whole host of reasons. After an incubation period of about two days to two weeks, a spectrum of clinical manifestations can be seen in individuals afflicted by COVID-19: from an asymptomatic condition that can spread the virus in the environment, to a mild/moderate disease with cold/flu-like symptoms, to deteriorated conditions that need hospitalization and intensive care unit management, and then a fatal respiratory distress syndrome that becomes refractory to oxygenation. Several diagnostic modalities have been advocated and evaluated; however, in some cases, diagnosis is made on the clinical picture in order not to lose time. A consensus on what constitutes special treatment for COVID-19 has yet to emerge. Alongside conservative and supportive care, some potential drugs have been recommended and a considerable number of investigations are ongoing in this regard.
Collapse
Affiliation(s)
- Kiana Shirani
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Erfan Sheikhbahaei
- Student Research Committee, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zahra Torkpour
- Student Research Committee, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mazyar Ghadiri Nejad
- Industrial Engineering Department, Girne American University, Kyrenia, TRNC, Turkey
| | | | - Matina Ghasemi
- Faculty of Business and Economics, Business Department, Girne American University, Kyrenia, TRNC, Turkey
| | - Hossein Akbari Aghdam
- Department of Orthopedic Surgery, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Athena Ehsani
- Department of Biomedical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Amirsalar Khandan
- Department of Electrical Engineering, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
- 0Technology Incubator Center, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
| |
Collapse
|
9
|
Affiliation(s)
- David S Hui
- Department of Medicine and Therapeutics, and Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China.
| |
Collapse
|
10
|
Darai G, Handermann M, Sonntag HG, Zöller L. Neue Infektionserreger mit pandemischem Potential: Ursache – Verbreitung – Management. LEXIKON DER INFEKTIONSKRANKHEITEN DES MENSCHEN 2012. [PMCID: PMC7123822 DOI: 10.1007/978-3-642-17158-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Die im vergangenen Jahrhundert errungenen Erfolge bei der Reduzierung der Mortalität durch Infektionskrankheiten können nicht verdecken, dass beständig neue Infektionskrankheiten mit weltweiter Verbreitung auftreten. Diese gehen entweder auf „neue“ Erreger zurück („emerging diseases“), oder sind durch bekannte Erreger bedingt, die neue Verbreitungsgebiete erobert haben. Bei der Expansion der endemischen Zirkulation von Infektionserregern spielen anthropogene Faktoren eine entscheidende Rolle, und eine große Zahl völlig unterschiedlicher Erreger kommt für solche Geschehen in Betracht (Kaufmann 2010).
Collapse
Affiliation(s)
| | - Michaela Handermann
- Sektion Nephrologie, Medizinische Universitätsklinik, Im Neuenheimer Feld 162, 69120 Heidelberg
| | - Hans-Günther Sonntag
- Institut für Hygiene und Medizinische Mikrobiologie, Universität Heidelberg, Im Neuenheimer Feld 346, 69120 Heidelberg
| | - Lothar Zöller
- Institut für Mikrobiologie der Bundeswehr, Neuherbergstraße 11, 80937 München
| |
Collapse
|
11
|
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.
Collapse
Affiliation(s)
- Tommy Tsan-Yuk Lam
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | | | | |
Collapse
|
12
|
Ma Y, Feng Y, Liu D, Gao GF. Avian influenza virus, Streptococcus suis serotype 2, severe acute respiratory syndrome-coronavirus and beyond: molecular epidemiology, ecology and the situation in China. Philos Trans R Soc Lond B Biol Sci 2009; 364:2725-37. [PMID: 19687041 PMCID: PMC2865088 DOI: 10.1098/rstb.2009.0093] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The outbreak and spread of severe acute respiratory syndrome-associated coronavirus and the subsequent identification of its animal origin study have heightened the world's awareness of animal-borne or zoonotic pathogens. In addition to SARS, the highly pathogenic avian influenza virus (AIV), H5N1, and the lower pathogenicity H9N2 AIV have expanded their host ranges to infect human beings and other mammalian species as well as birds. Even the ‘well-known’ reservoir animals for influenza virus, migratory birds, became victims of the highly pathogenic H5N1 virus. Not only the viruses, but bacteria can also expand their host range: a new disease, streptococcal toxic shock syndrome, caused by human Streptococcus suis serotype 2 infection, has been observed in China with 52 human fatalities in two separate outbreaks (1998 and 2005, respectively). Additionally, enterohaemorrhagic Escherichia coli O157:H7 infection has increased worldwide with severe disease. Several outbreaks and sporadic isolations of this pathogen in China have made it an important target for disease control. A new highly pathogenic variant of porcine reproductive and respiratory syndrome virus (PRRSV) has been isolated in both China and Vietnam recently; although PRRSV is not a zoonotic human pathogen, its severe outbreaks have implications for food safety. All of these pathogens occur in Southeast Asia, including China, with severe consequences; therefore, we discuss the issues in this article by addressing the situation of the zoonotic threat in China.
Collapse
Affiliation(s)
- Ying Ma
- CAS Key Laboratory of Pathogenic Microbiology and Immunology (CASPMI), Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, The People's Republic of China
| | | | | | | |
Collapse
|
13
|
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.
Collapse
Affiliation(s)
- Chi Wai Yip
- The School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | | | | | | | | | | | | |
Collapse
|
14
|
Abstract
In this work, severe acute respiratory syndrome associated coronavirus (SARS-CoV) genome BJ202 (AY864806) was completely sequenced. The genome was directly accessed from the stool sample of a patient in Beijing. Comparative genomics methods were used to analyze the sequence variations of 116 SARS-CoV genomes (including BJ202) available in the NCBI Gen-Bank. With the genome sequence of GZ02 as the reference, there were 41 polymorphic sites identified in BJ202 and a total of 278 polymorphic sites present in at least two of the 116 genomes. The distribution of the polymorphic sites was biased over the whole genome. Nearly half of the variations (50.4%, 140/278) clustered in the one third of the whole genome at the 3′ end (19.0 kb-29.7 kb). Regions encoding Orf10–11, Orf3/4, E, M and S protein had the highest mutation rates. A total of 15 PCR products (about 6.0 kb of the genome) including 11 fragments containing 12 known polymorphic sites and 4 fragments without identified polymorphic sites were cloned and sequenced. Results showed that 3 unique polymorphic sites of BJ202 (positions 13 804, 15 031 and 20 792) along with 3 other polymorphic sites (26 428, 26 477 and 27 243) all contained 2 kinds of nucleotides. It is interesting to find that position 18379 which has not been identified to be polymorphic in any of the other 115 published SARS-CoV genomes is actually a polymorphic site. The nucleotide composition of this site is A (8) to G (6). Among 116 SARS-CoV genomes, 18 types of deletions and 2 insertions were identified. Most of them were related to a 300 bp region (27 700–28 000) which encodes parts of the putative ORF9 and ORF10–11. A phylogenetic tree illustrating the divergence of whole BJ202 genome from 115 other completely sequenced SARS-CoVs was also constructed. BJ202 was phylogeneticly closer to BJ01 and LLJ-2004.
Collapse
Affiliation(s)
- Lei Shang
- James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
| | | | | | | | | | | | | |
Collapse
|
15
|
Chu LHM, Chan SH, Tsai SN, Wang Y, Cheng CHK, Wong KB, Waye MMY, Ngai SM. Fusion core structure of the severe acute respiratory syndrome coronavirus (SARS-CoV): in search of potent SARS-CoV entry inhibitors. J Cell Biochem 2008; 104:2335-47. [PMID: 18442051 PMCID: PMC7166385 DOI: 10.1002/jcb.21790] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Severe acute respiratory coronavirus (SARS‐CoV) spike (S) glycoprotein fusion core consists of a six‐helix bundle with the three C‐terminal heptad repeat (HR2) helices packed against a central coiled‐coil of the other three N‐terminal heptad repeat (HR1) helices. Each of the three peripheral HR2 helices shows prominent contacts with the hydrophobic surface of the central HR1 coiled‐coil. The concerted protein–protein interactions among the HR helices are responsible for the fusion event that leads to the release of the SARS‐CoV nucleocapsid into the target host‐cell. In this investigation, we applied recombinant protein and synthetic peptide‐based biophysical assays to characterize the biological activities of the HR helices. In a parallel experiment, we employed a HIV‐luc/SARS pseudotyped virus entry inhibition assay to screen for potent inhibitory activities on HR peptides derived from the SARS‐CoV S protein HR regions and a series of other small‐molecule drugs. Three HR peptides and five small‐molecule drugs were identified as potential inhibitors. ADS‐J1, which has been used to interfere with the fusogenesis of HIV‐1 onto CD4+ cells, demonstrated the highest HIV‐luc/SARS pseudotyped virus‐entry inhibition activity among the other small‐molecule drugs. Molecular modeling analysis suggested that ADS‐J1 may bind to the deep pocket of the hydrophobic groove on the surface of the central coiled‐coil of SARS‐CoV S HR protein and prevent the entrance of the SARS‐CoV into the host cells. J. Cell. Biochem. 104: 2335–2347, 2008. © 2008 Wiley‐Liss, Inc.
Collapse
Affiliation(s)
- Ling-Hon Matthew Chu
- Molecular Biotechnology Program, The Chinese University of Hong Kong, Hong Kong, China
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Lu Y, Essex M, Roberts B. The 2003 SARS Outbreaks in Taiwan. EMERGING INFECTIONS IN ASIA 2008. [PMCID: PMC7120672 DOI: 10.1007/978-0-387-75722-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Severe acute respiratory syndrome (SARS) is caused by SARS-associated coronaviruses (SARS-CoVs) (Drosten et al., 2003; Fouchier et al., 2003; Peiris et al., 2003b; Ksiazek et al., 2003). The first known outbreak of SARS occurred in China’s Guangdong province in November, 2002 (Chinese SARS Molecular Epidemiology Consortium, 2004). By August 7 of the following year, SARS had spread to more than 30 countries, affecting 8,096 people and resulting in 774 deaths worldwide (World Health Organization, 2004). In 2003, Taiwan experienced a series of SARS outbreaks and the Municipal Hoping Hospital (referred to hereafter as HP) in Taipei City suffered the first and the most serious outbreak of SARS-CoV nosocomial infections: 137 probable cases and 26 deaths (Division of Surveillance and Investigation, Center for Disease Control, Taiwan, 2003; Lan et al., 2005b). According to the Center for Disease Control (CDC) in Taiwan, 364 of the 664 probable Taiwanese SARS cases reported to the World Health Organization were confirmed by reverse transcriptase-polymerase chain reaction (RT-PCR) and/or neutralizing antibody tests (Center for Disease Control, 2003a). In this chapter, we will discuss the molecular and clinical epidemiology of SARS infection in Taiwan during 2003.
Collapse
Affiliation(s)
- Yichen Lu
- Harvard School of Public Health, 02115 Boston, MA USA
| | - M. Essex
- Harvard School of Public Health, 02115 Boston, MA USA
| | | |
Collapse
|
17
|
Cheung YK, Cheng SCS, Sin FWY, Chan KT, Xie Y. Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope. Vaccine 2007; 25:6070-7. [PMID: 17629360 PMCID: PMC7115375 DOI: 10.1016/j.vaccine.2007.05.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Revised: 05/03/2007] [Accepted: 05/12/2007] [Indexed: 12/23/2022]
Abstract
The severe acute respiratory syndrome coronavirus nucleocapsid protein (SARS-CoV N) is one of the major targets for SARS vaccine due to its high potency in triggering immune responses. In this study, we have identified a novel HLA-A*0201 restricted epitope, N220 (LALLLLDRL), of the SARS-CoV N-protein through bioinformatics analysis. The N-protein peptide N220 shows a high binding affinity towards human MHC class I in T2-cells, and is capable of activating cytotoxic T-cells in human peripheral blood mononuclear cells (PBMCs). The application of using the N220 peptide sequence with a single-chain-trimer (SCT) approach to produce a potential DNA vaccine candidate was investigated in HLA-A2.1K(b) transgenic mice. Cytotoxicity assay clearly showed that the T-cells obtained from the vaccinated animals were able to kill the N-protein expressing cells with a cytotoxicity level of 86% in an effector cells/target cells ratio of 81:1 one week after the last vaccination, which is significantly higher than other N-protein peptides previously described. The novel immunogenic N-protein peptide revealed in the present study provides valuable information for therapeutic SARS vaccine design.
Collapse
Affiliation(s)
| | | | | | | | - Yong Xie
- Department of Biology, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| |
Collapse
|
18
|
Feng Y, Gao GF. Towards our understanding of SARS-CoV, an emerging and devastating but quickly conquered virus. Comp Immunol Microbiol Infect Dis 2007; 30:309-27. [PMID: 17640731 PMCID: PMC7112560 DOI: 10.1016/j.cimid.2007.05.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Accepted: 05/16/2007] [Indexed: 12/30/2022]
Abstract
Severe acute respiratory syndrome (SARS) is a newly emerging infectious disease caused by a novel coronavirus (SARS-CoV), which has overwhelmed more than 30 countries claiming nearly 8400 cases with over 800 fatalities. Thanks to the unprecedented international collaboration, the whole-genomes of SARS-CoVs were successfully deciphered shortly after the identification of the causative pathogen for outbreak of SARS in southern China, in 2003. Hitherto, the SARS-CoV, as a viral paradigm of emerging infectious entities, has been extensively studied that has ranged from epidemiology, molecular virology/immunology to structural genomics. Also, several lines of breakthroughs have been record-brokenly obtained, that included the finding of ACE2, a functional receptor for the SARS-CoV, solution of the 3CL(pro) structure, a first crystal structure of SARS-related macromolecules, revealing of bats as natural reservoirs for SARS-like viruses and the possible involvement of civet cats in the SARS emergence. This review intends to outline the major progress in the journey of SARS-related exploration, by emphasizing those inaugurated studies with milestone-like significance contributed by Chinese research groups.
Collapse
Affiliation(s)
- Youjun Feng
- Center for Molecular Virology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
- Graduate University, Chinese Academy of Sciences, Beijing 100049, China
| | - George F. Gao
- Center for Molecular Virology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
- Corresponding author. Tel.: +86 10 64807688; fax: +86 10 64807365.
| |
Collapse
|
19
|
Chim SSC, Chiu RWK, Lo YMD. Genomic sequencing of the severe acute respiratory syndrome-coronavirus. Methods Mol Biol 2006; 336:177-94. [PMID: 16916263 PMCID: PMC7121524 DOI: 10.1385/1-59745-074-x:177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
The polymerase chain reaction (PCR), which can exponentially replicate a target DNA sequence, has formed the basis for the sensitive and direct examination of clinical samples for evidence of infection. During the epidemic of severe acute respiratory syndrome (SARS) in 2003, PCR not only offered a rapid way to diagnose SARS-coronavirus (SARS-CoV) infection, but also made the molecular analysis of its genomic sequence possible. Sequence variations were observed in the SAR-CoV obtained from different patients in this epidemic. These unique viral genetic signatures can be applied as a powerful molecular tool in tracing the route of transmission and in studying the genome evolution of SARS-CoV. To extract this wealth of information from the limited primary clinical specimens of SARS patients, we were presented with the challenge of efficiently amplifying fragments of the SARS-CoV genome for analysis. In this chapter, we will discuss how we managed to accomplish this task with our optimized protocols on reverse-transcription, nested PCR amplification, and DNA cycle sequencing. We will also discuss the sequence variations that typified some strains of SARS-CoV in the different phases during this epidemic. PCR amplification of the viral sequence and genomic sequencing of these critical sequence variations of re-emerging SARS-CoV strains would give us quick insights into the virus.
Collapse
Affiliation(s)
- Stephen S C Chim
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR
| | | | | |
Collapse
|
20
|
Brierley I, Dos Ramos FJ. Programmed ribosomal frameshifting in HIV-1 and the SARS-CoV. Virus Res 2005; 119:29-42. [PMID: 16310880 PMCID: PMC7114087 DOI: 10.1016/j.virusres.2005.10.008] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Revised: 07/31/2005] [Accepted: 10/19/2005] [Indexed: 01/11/2023]
Abstract
Ribosomal frameshifting is a mechanism of gene expression used by several RNA viruses to express replicase enzymes. This article focuses on frameshifting in two human pathogens, the retrovirus human immunodeficiency virus type 1 (HIV-1) and the coronavirus responsible for severe acute respiratory syndrome (SARS). The nature of the frameshift signals of HIV-1 and the SARS–CoV will be described and the impact of this knowledge on models of frameshifting will be considered. The role of frameshifting in the replication cycle of the two pathogens and potential antiviral therapies targeting frameshifting will also be discussed.
Collapse
Affiliation(s)
- Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
| | | |
Collapse
|
21
|
Geng H, Liu YM, Chan WS, Lo AWI, Au DMY, Waye MMY, Ho YY. The putative protein 6 of the severe acute respiratory syndrome-associated coronavirus: expression and functional characterization. FEBS Lett 2005; 579:6763-8. [PMID: 16310783 PMCID: PMC7094358 DOI: 10.1016/j.febslet.2005.11.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 10/07/2005] [Accepted: 11/03/2005] [Indexed: 01/30/2023]
Abstract
The SARS‐CoV open reading frame 6 (ORF6) is transcribed into mRNA6 and encodes a putative 7.5 kDa accessory protein, SARS 6, with unknown function. In this study, we have confirmed the SARS 6 protein expression in lung and intestine tissues of the SARS patients and in SARS‐CoV infected Vero E6 cells by immunohistochemistry. Further studies by immunoblot and confocal microscopy analyses revealed the expression and the endoplasmic reticulum (ER) localization of the recombinant SARS 6 protein in mammalian cells. Expression of SARS 6 protein in mammalian cells elicits biological activity of stimulating cellular DNA synthesis.
Collapse
Affiliation(s)
- Hua Geng
- Department of Biochemistry, MMW509C, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Yuet-Man Liu
- Department of Biochemistry, MMW509C, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Wai-Sing Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong SAR, China
| | - Anthony Wing-Ip Lo
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong SAR, China
| | | | - Mary Miu-Yee Waye
- Department of Biochemistry, MMW509C, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
- Croucher Laboratory for Human Genomics, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Yuan-Yuan Ho
- Department of Biochemistry, MMW509C, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| |
Collapse
|
22
|
Wang ZG, Zheng ZH, Shang L, Li LJ, Cong LM, Feng MG, Luo Y, Cheng SY, Zhang YJ, Ru MG, Wang ZX, Bao QY. Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV. FEBS Lett 2005; 579:4928-36. [PMID: 16112670 PMCID: PMC7118731 DOI: 10.1016/j.febslet.2005.07.075] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Accepted: 07/15/2005] [Indexed: 01/19/2023]
Abstract
In this study, we have identified 876 polymorphism sites in 145 complete or partial genomes of SARS-CoV available in the NCBI GenBank. One hundred and seventy-four of these sites existed in two or more SARS-CoV genome sequences. According to the sequence polymorphism, all SARS-CoVs can be divided into three groups: (I) group 1, animal-origin viruses (such as SARS-CoV SZ1, SZ3, SZ13 and SZ16); (II) group 2, all viruses with clinical origin during first epidemic; and (III) group 3, SARS-CoV GD03T0013. According to 10 special loci, group 2 again can be divided into genotypes C and T, which can be further divided into sub-genotypes C1-C4 and T1-T4. Positive Darwinian selections were identified between any pair of these three groups. Genotype C gives neutral selection. Genotype T, however, shows negative selection. By comparing the death rates of SARS patients in the different regions, it was found that the death rate caused by the viruses of the genotype C was lower than that of the genotype T. SARS-CoVs might originate from an unknown ancestor.
Collapse
Affiliation(s)
- Zhi-Gang Wang
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Zhi-Hua Zheng
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Lei Shang
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China
| | - Lan-Juan Li
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Li-Ming Cong
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Ming-Guang Feng
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China
| | - Yun Luo
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Su-Yun Cheng
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Yan-Jun Zhang
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Miao-Gui Ru
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Zan-Xin Wang
- Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China
| | - Qi-Yu Bao
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China
- Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, China
| |
Collapse
|
23
|
Vabret A, Mourez T, Dina J, van der Hoek L, Gouarin S, Petitjean J, Brouard J, Freymuth F. Human coronavirus NL63, France. Emerg Infect Dis 2005; 11:1225-9. [PMID: 16102311 PMCID: PMC3320486 DOI: 10.3201/eid1108.050110] [Citation(s) in RCA: 191] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Coronavirus NL63 was found in hospitalized children with upper and lower respiratory infections. The human coronavirus NL63 (HCoV-NL63) was first identified in the Netherlands, and its circulation in France has not been investigated. We studied HCoV-NL63 infection in hospitalized children diagnosed with respiratory tract infections. From November 2002 to April 2003, we evaluated 300 respiratory specimens for HCoV-NL63. Of the 300 samples, 28 (9.3%) were positive for HCoV-NL63. The highest prevalence was found in February (18%). The main symptoms were fever (61%), rhinitis (39%), bronchiolitis (39%), digestive problems (33%), otitis (28%), pharyngitis (22%), and conjunctivitis (17%). A fragment of the spike protein gene was sequenced to determine the variety of circulating HCoV-NL63. Phylogenetic analysis indicated that strains with different genetic markers cocirculate in France.
Collapse
|
24
|
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.
Collapse
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
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Zhu Y, Liu M, Zhao W, Zhang J, Zhang X, Wang K, Gu C, Wu K, Li Y, Zheng C, Xiao G, Yan H, Zhang J, Guo D, Tien P, Wu J. Isolation of virus from a SARS patient and genome-wide analysis of genetic mutations related to pathogenesis and epidemiology from 47 SARS-CoV isolates. Virus Genes 2005; 30:93-102. [PMID: 15744567 PMCID: PMC7089183 DOI: 10.1007/s11262-004-4586-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Accepted: 07/15/2004] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome (SARS) caused by SARS-associated coronavirus (SARS-CoV) is a fatal disease. Prevention of future outbreaks is essential and requires understanding pathogenesis and evolution of the virus. We have isolated a SARS-CoV in China and analyzed 47 SARS-CoV genomes with the aims to reveal the evolution trends of the virus and provide insights into understanding pathogenesis and SARS epidemic. Specimen from a SARS patient was inoculated into cell culture. The presence of SARS-CoV was determined by RT-PCR and confirmed by electron microscopy. Virus was isolated followed by the determination of its genome sequences, which were then analyzed by comparing with other 46 SARS-CoV genomes. Genetic mutations with potential implications to pathogenesis and the epidemic were characterized. This viral genome consists of 29,728 nucleotides with overall organization in agreement with that of published isolates. A total of 348 positions were mutated on 47 viral genomes. Among them 22 had mutations in more than three genomes. Hot spots of nucleotide variations and unique trends of mutations were identified on the viral genomes. Mutation rates were different from gene to gene and were correlated well with periodical or geographic characteristics of the epidemic.
Collapse
Affiliation(s)
- Ying Zhu
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Mo Liu
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Weiguang Zhao
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Jianlin Zhang
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Xue Zhang
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Ke Wang
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Chunfang Gu
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Kailang Wu
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Yan Li
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Congyi Zheng
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Gengfu Xiao
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Huimin Yan
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Jiamin Zhang
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Deyin Guo
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Po Tien
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Jianguo Wu
- Key Laboratory of Virology, Ministry of Education College of Life Sciences, Wuhan University, Wuhan, 430072 China
| |
Collapse
|
26
|
Chan HLY, Kwan ACP, To KF, Lai ST, Chan PKS, Leung WK, Lee N, Wu A, Sung JJY. Clinical significance of hepatic derangement in severe acute respiratory syndrome. World J Gastroenterol 2005; 11:2148-53. [PMID: 15810082 PMCID: PMC4305785 DOI: 10.3748/wjg.v11.i14.2148] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: Elevation of alanine aminotransferase (ALT) level is commonly seen among patients suffering from severe acute respiratory syndrome (SARS). We report the progression and clinical significance of liver derangement in a large cohort of SARS patient.
METHODS: Serial assay of serum ALT was followed in patients who fulfilled the WHO criteria of SARS. Those with elevated ALT were compared with those with normal liver functions for clinical outcome. Serology for hepatitis B virus (HBV) infection was checked. Adverse outcomes were defined as oxygen desaturation, need of intensive care unit (ICU) and mechanical ventilation and death.
RESULTS: Two hundred and ninety-four patients were included in this study. Seventy (24%) patients had elevated serum ALT on admission and 204 (69%) patients had elevated ALT during the subsequent course of illness. Using peak ALT > 5×ULN as a cut-off and after adjusting for potential confounding factors, the odds ratio of peak ALT > 5×ULN for oxygen desaturation was 3.24 (95%CI 1.23-8.59, P = 0.018), ICU care was 3.70 (95%CI 1.38-9.89, P = 0.009), mechanical ventilation was 6.64 (95%CI 2.22-19.81, P = 0.001) and death was 7.34 (95%CI 2.28-24.89, P = 0.001). Ninety-three percent of the survived patients had ALT levels normalized or were on the improving trend during follow-up. Chronic hepatitis B was not associated with worse clinical outcomes.
CONCLUSION: Reactive hepatitis is a common complication of SARS-coronavirus infection. Those patients with severe hepatitis had worse clinical outcome.
Collapse
Affiliation(s)
- Henry-Lik-Yuen Chan
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, China
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Chan KCA, Tang NLS, Hui DSC, Chung GTY, Wu AKL, Chim SSC, Chiu RWK, Lee N, Choi KW, Sung YM, Chan PKS, Tong YK, Lai ST, Yu WC, Tsang O, Lo YMD. Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study. BMC Infect Dis 2005; 5:26. [PMID: 15819995 PMCID: PMC1090578 DOI: 10.1186/1471-2334-5-26] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Accepted: 04/09/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It has been postulated that genetic predisposition may influence the susceptibility to SARS-coronavirus infection and disease outcomes. A recent study has suggested that the deletion allele (D allele) of the angiotensin converting enzyme (ACE) gene is associated with hypoxemia in SARS patients. Moreover, the ACE D allele has been shown to be more prevalent in patients suffering from adult respiratory distress syndrome (ARDS) in a previous study. Thus, we have investigated the association between ACE insertion/deletion (I/D) polymorphism and the progression to ARDS or requirement of intensive care in SARS patients. METHOD One hundred and forty genetically unrelated Chinese SARS patients and 326 healthy volunteers were recruited. The ACE I/D genotypes were determined by polymerase chain reaction and agarose gel electrophoresis. RESULTS There is no significant difference in the genotypic distributions and the allelic frequencies of the ACE I/D polymorphism between the SARS patients and the healthy control subjects. Moreover, there is also no evidence that ACE I/D polymorphism is associated with the progression to ARDS or the requirement of intensive care in the SARS patients. In multivariate logistic analysis, age is the only factor associated with the development of ARDS while age and male sex are independent factors associated with the requirement of intensive care. CONCLUSION The ACE I/D polymorphism is not directly related to increased susceptibility to SARS-coronavirus infection and is not associated with poor outcomes after SARS-coronavirus infection.
Collapse
Affiliation(s)
- KC Allen Chan
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Nelson LS Tang
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - David SC Hui
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Grace TY Chung
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Alan KL Wu
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Stephen SC Chim
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Rossa WK Chiu
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Nelson Lee
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - KW Choi
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - YM Sung
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - Paul KS Chan
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - YK Tong
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| | - ST Lai
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong
| | - WC Yu
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong
| | - Owen Tsang
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong
| | - YM Dennis Lo
- The Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong
| |
Collapse
|
28
|
Lan YC, Liu TT, Yang JY, Lee CM, Chen YJ, Chan YJ, Lu JJ, Liu HF, Hsiung CA, Ho MS, Hsiao KJ, Chen HY, Chen YMA. Molecular epidemiology of severe acute respiratory syndrome-associated coronavirus infections in Taiwan. J Infect Dis 2005; 191:1478-89. [PMID: 15809907 PMCID: PMC7199491 DOI: 10.1086/428591] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2004] [Accepted: 11/01/2004] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND In 2003, Taiwan experienced a series of outbreaks of severe acute respiratory syndrome (SARS) and 1 laboratory-contamination accident. Here we describe a new phylogenetic analytical method to study the sources and dissemination paths of SARS-associated coronavirus (SARS-CoV) infections in Taiwan. METHODS A phylogenetic analytical tool for combining nucleotide sequences from 6 variable regions of a SARS-CoV genome was developed by use of 20 published SARS-CoV sequences; and this method was validated by use of 80 published SARS-CoV sequences. Subsequently, this new tool was applied to provide a better understanding of the entire complement of Taiwanese SARS-CoV isolates, including 20 previously published and 19 identified in this study. The epidemiological data were integrated with the results from the phylogenetic tree and from the nucleotide-signature pattern. RESULTS The topologies of phylogenetic trees generated by the new and the conventional strategies were similar, with the former having better robustness than the latter, especially in comparison with the maximum-likelihood trees: the new strategy revealed that during 2003 there were 5 waves of epidemic SARS-CoV infection, which belonged to 3 phylogenetic clusters in Taiwan. CONCLUSIONS The new strategy is more efficient than its conventional counterparts. The outbreaks of SARS in Taiwan originated from multiple sources.
Collapse
Affiliation(s)
- Yu-Ching Lan
- AIDS Prevention and Research Centre
- Institute of Public Health, and
- Reprints or correspondence: Prof. Yi-Ming A Chen, AIDS Prevention and Research Center, National Yang-Ming University, Li-Noun St., Section 2, Taipei, Taiwan 112 ()
| | - Tze-Tze Liu
- Genome Research Center, National Yang-Ming University, and
| | - Jyh-Yuan Yang
- Center for Disease Control, Department of Health, Executive Yuan, and
| | - Cheng-Ming Lee
- AIDS Prevention and Research Centre
- Institute of Public Health, and
| | - Yen-Ju Chen
- AIDS Prevention and Research Centre
- Institute of Public Health, and
| | - Yu-Jiun Chan
- AIDS Prevention and Research Centre
- Section of Virology, Department of Laboratory Medicine, Taipei Veterans General Hospital, and
| | - Jang-Jih Lu
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, and
| | - Hsin-Fu Liu
- Department of Medical Research, Taipei Mackay Memorial Hospital, and
| | | | - Mei-Shang Ho
- Institute of Biomedical Sciences, Academia Sinica, Taiwan, Republic of China
| | | | - Hour-Young Chen
- Center for Disease Control, Department of Health, Executive Yuan, and
| | | |
Collapse
|
29
|
Lan YC, Liu HF, Shih YP, Yang JY, Chen HY, Chen YMA. Phylogenetic analysis and sequence comparisons of structural and non-structural SARS coronavirus proteins in Taiwan. INFECTION GENETICS AND EVOLUTION 2004; 5:261-9. [PMID: 15737918 PMCID: PMC7106041 DOI: 10.1016/j.meegid.2004.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Accepted: 08/07/2004] [Indexed: 02/04/2023]
Abstract
Taiwan experienced a large number of severe acute respiratory syndrome (SARS) viral infections between March and July 2003; by September of that year, 346 SARS cases were confirmed by RT-PCR or serological tests. In order to better understand evolutionary relationships among SARS coronaviruses (SCoVs) from different international regions, we performed phylogenetic comparisons of full-length genomic and protein sequences from 45 human SCoVs (including 12 from Taiwan) and two civet SCoVs. All the Taiwanese SARS-CoV strains which associated with nosocomial infection formed a monophyletic clade within the late phase of the SARS epidemic. This Taiwanese clade could be further divided into two epidemic waves. Taiwan SCoVs in the first wave clustered with three isolates from the Amoy Gardens housing complex in Hong Kong indicating their possible origin. Of the 45 human SCoVs, one isolate from Guangdong province, China, exhibited an extra 29-nucleotide fragment between Orf 10 and Orf 11--similar to the civet SCoV genome. Nucleotide and protein sequence comparisons suggested that all SCoVs of late epidemic came from human-to-human transmission, while certain SCoVs of early epidemic might have originated in animals.
Collapse
Affiliation(s)
- Yu-Ching Lan
- AIDS Prevention and Research Center, Institute of Public Health, National Yang-Ming University, Taipei 112, Taiwan
| | - Hsin-Fu Liu
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yi-Ping Shih
- AIDS Prevention and Research Center, Institute of Public Health, National Yang-Ming University, Taipei 112, Taiwan
| | - Jyh-Yuan Yang
- Center for Disease Control, Department of Health, Executive Yuan, Taipei 100, Taiwan
| | - Hour-Young Chen
- Center for Disease Control, Department of Health, Executive Yuan, Taipei 100, Taiwan
| | - Yi-Ming Arthur Chen
- AIDS Prevention and Research Center, Institute of Public Health, National Yang-Ming University, Taipei 112, Taiwan
- Corresponding author. Tel.: +886 2 28267193; fax: +886 2 28270576.
| |
Collapse
|
30
|
Abstract
Severe acute respiratory syndrome (SARS) is a newly described respiratory infection with pandemic potential. The causative agent is a new strain of coronavirus most likely originating from wild animals. This disease first emerged in November 2002 in Guangdong Province, China. Early in the outbreak the infection had been transmitted primarily via household contacts and healthcare settings. In late February 2003 the infection was transmitted to Hong Kong when an infected doctor from the mainland visited there. During his stay in Hong Kong at least 17 guests and visitors were infected at the hotel at which he stayed. By modern day air travel, the infection was rapidly spread to other countries including Vietnam, Singapore and Canada by these infected guests. With the implementation of effective control strategies including early isolation of suspected cases, strict infection control measures in the hospital setting, meticulous contact tracing and quarantine, the outbreak was finally brought under control by July 2003. In addition, there were another two events of SARS in China between the end of December 2003 and January 2004 and from March to May 2004; both were readily controlled without significant patient spread.
Collapse
Affiliation(s)
- Nan-Shan Zhong
- Guangzhou Institute of Respiratory Diseases, Guangzhou, China
| | - Gary W.K. Wong
- Department of Paediatrics, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, New Territories, HKSAR, Hong Kong, China
- Correspondence to: G. W. K. Wong. Tel.: +852 2632 2981; Fax: +852 2636 0020.
| |
Collapse
|
31
|
Poon LLM, Guan Y, Nicholls JM, Yuen KY, Peiris JSM. The aetiology, origins, and diagnosis of severe acute respiratory syndrome. THE LANCET. INFECTIOUS DISEASES 2004; 4:663-71. [PMID: 15522678 PMCID: PMC7106534 DOI: 10.1016/s1473-3099(04)01172-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Severe acute respiratory syndrome (SARS) is a new infectious disease that first emerged in Guangdong province, China, in November, 2002. A novel coronavirus was later identified in patients with SARS. The detection of the virus in these patients, its absence in healthy controls or other patients with atypical pneumonia, and the reproduction of a similar disease in a relevant animal model fulfilled Koch's postulates for implicating this coronavirus as the causal agent of SARS. The full genome sequence was determined within weeks of the virus's identification. The rapid progress in the aetiology, the development of laboratory diagnostic tests, and the defining of routes of viral transmission were facilitated through a unique WHO-coordinated virtual network of laboratories, which shared information on a real-time basis through daily teleconferences. Subsequent studies have indicated that the SARS coronavirus is of animal origin, that its precursor is still present in animal populations within the region, and that live-animal markets in southern China may have provided the animal-human interphase that allowed this precursor virus to adapt to human-human transmission. These findings underscore the potential for the re-emergence of SARS and the need for laboratory tests for early diagnosis. However, the low viral load in the respiratory tract makes early diagnosis of SARS a diagnostic challenge, although improvements in the sensitivity of molecular diagnostic methods continue to be made.
Collapse
Affiliation(s)
- LLM Poon
- Department of Microbiology, University of Hong Kong, Hong Kong SAR, China
| | - Y Guan
- Department of Microbiology, University of Hong Kong, Hong Kong SAR, China
| | - JM Nicholls
- Department of Pathology, University of Hong Kong, Hong Kong SAR, China
| | - KY Yuen
- Department of Microbiology, University of Hong Kong, Hong Kong SAR, China
| | - JSM Peiris
- Department of Microbiology, University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
32
|
Chiu YC, Wu KL, Chou YP, Fong TV, Tsai TL, Kuo CM, Kuo CH, Chiu KW, Liu JW, Eng HL, Jawan B, Cheng YF, Chen CL. Diarrhea in medical care workers with severe acute respiratory syndrome. J Clin Gastroenterol 2004; 38:880-2. [PMID: 15492605 DOI: 10.1097/00004836-200411000-00009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND AND GOAL Several known coronavirus species cause a variety of diseases, including respiratory or enteric diseases. The purpose of this study was to investigate the interesting enteric symptoms of the medical care workers who were evidently infected with SARS by means of respiratory transmission. STUDY Between May 1 and June 16, 2003, we enrolled 16 medical care workers who fulfilled the definition of probable SARS. Samples used for the detection of coronavirus RNA by RT-PCR were collected from throat and rectal swabs during acute phase. Serum anti-SARS IgG was checked by enzyme-linked immunosorbent assays at the convalescent phase. RESULTS The incidence of watery diarrhea was 18.8% (3 of 16). The RT-PCR of coronavirus was positive in three (18.8%) of 16 throat swabs and in none (0%) of seven rectal swabs. Serum anti-coronavirus IgG was positive in 13 of the 15 patients (86.7%). The mortality rate was 6.25% (1 of 16). The diarrhea rate in our hospital was significantly lower in comparison with the 73% (55 of 75) of the Amoy Gardens outbreak in Hong Kong (P = 0.000073), and similar to the 19.6% (27 of 138) of the hospital-acquired outbreak in the Prince of Wales Hospital in Hong Kong (P = 0.798). In contrast to the high positive rate of feces RT-PCR (97%) in Amoy Gardens, our positive rate in rectal swab RT-PCT (0%) was significantly lower (P = 0.00000002). CONCLUSIONS Hospital-acquired SARS cases infected mainly by respiratory route less commonly presented with diarrhea. Lower intestinal viral load, when the virus spread by respiratory route, may be contributive to lower diarrhea rate and lower positive rate in rectal swab RT-PCR.
Collapse
Affiliation(s)
- Yi-Chun Chiu
- Division of Gastroenterology, Chang Gung University, Chang Gung Memorial Hospital, Kaohsiung Medical Center, Taiwan, Republic of China
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Hui DSC, Chan MCH, Wu AK, Ng PC. Severe acute respiratory syndrome (SARS): epidemiology and clinical features. Postgrad Med J 2004; 80:373-81. [PMID: 15254300 PMCID: PMC1743054 DOI: 10.1136/pgmj.2004.020263] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Severe acute respiratory syndrome (SARS) is a newly emerged infectious disease with a significant morbidity and mortality. The major clinical features include persistent fever, chills/rigor, myalgia, malaise, dry cough, headache, and dyspnoea. Older subjects may present without the typical febrile response. Common laboratory features include lymphopenia, thrombocytopenia, raised alanine transaminases, lactate dehydrogenase, and creatine kinase. The constellation of compatible clinical and laboratory findings, together with certain characteristic radiological features and lack of clinical response to broad spectrum antibiotics, should arouse suspicion of SARS. Measurement of serum RNA by real time reverse transcriptase-polymerase chain reaction technique has a detection rate of 75%-80% in the first week of the illness.
Collapse
Affiliation(s)
- D S C Hui
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong.
| | | | | | | |
Collapse
|
34
|
Lam CM, Wong SF, Leung TN, Chow KM, Yu WC, Wong TY, Lai ST, Ho LC. A case-controlled study comparing clinical course and outcomes of pregnant and non-pregnant women with severe acute respiratory syndrome. BJOG 2004; 111:771-4. [PMID: 15270922 PMCID: PMC7161819 DOI: 10.1111/j.1471-0528.2004.00199.x] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Objective To compare the clinical courses and outcomes of pregnant severe acute respiratory syndrome (SARS) patients and non‐pregnant SARS patients. Design A case–control study. Setting Tertiary Hospital for Infectious Disease. Sample Ten pregnant and 40 non‐pregnant female patients infected with SARS. Methods Clinical course and outcomes of pregnant SARS patients were compared with a group of non‐pregnant SARS patient. Cases and controls were matched with respect to sex, age, timing of contracting SARS, health care workers status and underlying illness. Main outcome measures The incidence of intensive care unit admission, intubation, medical complications and death rate. Results Pregnancy had no discernible impact on clinical symptoms and presentation delay. Four out of the 10 pregnant patients, nevertheless, required endotracheal intubation and six were admitted to the intensive care unit (ICU), as compared with 12.5% intubation rate (P= 0.065) and 17.5% ICU admission rate (P= 0.012) in the non‐pregnant group. More pregnant SARS patients developed renal failure (P= 0.006) and disseminated intravascular coagulopathy (P= 0.006), as compared with non‐pregnant SARS group. There were three deaths in the pregnant group, whereas there was no death in the non‐pregnant control group (P= 0.006). Conclusion Pregnant women with SARS experience a worse clinical course and poorer outcomes compared with non‐pregnant women.
Collapse
Affiliation(s)
- Chui Miu Lam
- Department of Obstetrics and Gynecology, Princess Margaret Hospital, Hong Kong, SAR, China
| | | | | | | | | | | | | | | |
Collapse
|
35
|
To KF, Lo AWI. Exploring the pathogenesis of severe acute respiratory syndrome (SARS): the tissue distribution of the coronavirus (SARS-CoV) and its putative receptor, angiotensin-converting enzyme 2 (ACE2). J Pathol 2004; 203:740-3. [PMID: 15221932 PMCID: PMC7167902 DOI: 10.1002/path.1597] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Severe acute respiratory syndrome (SARS) is an emerging infectious disease associated with a new coronavirus, SARS-CoV. Pulmonary involvement is the dominant clinical feature but extra-pulmonary manifestations are also common. Factors that account for the wide spectrum of organ system involvement and disease severity are poorly understood and the pathogenesis of SARS-CoV infection remains unclear. Angiotensin converting enzyme 2 (ACE2) has recently been identified as the functional cellular receptor for SARS-CoV. Studies of the tissue and cellular distribution of SARS-CoV, and ACE2 protein expression, reveal new insights into the pathogenesis of this deadly disease. ACE2 is expressed at high level in the primary target cells of SARS-CoV, namely pneumocytes and surface enterocytes of the small intestine. Despite the fact that SARS-CoV can infect the lung and intestine, the tissue responses in these two organs are different. All other tissues and cell types expressing ACE2 may be potential targets of SARS-CoV infection. Remarkably, endothelial cells, which express ACE2 to a high level, have not been shown to be infected by SARS-CoV. There is also evidence that cell types without detectable ACE2 expression may also be infected by the virus. Furthermore, studies in a new human cell culture model have indicated that the presence of ACE2 alone is not sufficient for maintaining viral infection. Therefore, other virus receptors or co-receptors may be required in different tissues. Moreover, the interaction between SARS-CoV and the immunological or lymphoid system remains to be defined. It is clear that we are only at the dawn of our understanding of the pathogenesis of SARS. As our knowledge of the pathogenic mechanisms improves, a more rational approach to therapeutic and vaccine development can be designed in order to combat this new and fatal human disease.
Collapse
Affiliation(s)
- K F To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | | |
Collapse
|
36
|
Tong S, Lingappa JR, Chen Q, Shu B, LaMonte AC, Cook BT, Birge C, Chern SWW, Liu X, Galloway R, Mai LQ, Ng WF, Yang JY, Butany J, Comer JA, Monroe SS, Beard SR, Ksiazek TG, Erdman D, Rota PA, Pallansch MA, Anderson LJ. Direct sequencing of SARS-coronavirus S and N genes from clinical specimens shows limited variation. J Infect Dis 2004; 190:1127-31. [PMID: 15319863 PMCID: PMC7199896 DOI: 10.1086/422849] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2004] [Accepted: 03/15/2004] [Indexed: 12/29/2022] Open
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) emerged, in November 2002, as a novel agent causing severe respiratory illness. To study sequence variation in the SARS-CoV genome, we determined the nucleic acid sequence of the S and N genes directly from clinical specimens from 10 patients--1 specimen with no matched SARS-CoV isolate, from 2 patients; multiple specimens from 3 patients; and matched clinical-specimen/cell-culture-isolate pairs from 6 patients. We identified 3 nucleotide substitutions that were most likely due to natural variation and 2 substitutions that arose after cell-culture passage of the virus. These data demonstrate the overall stability of the S and N genes of SARS-CoV over 3 months during which a minimum of 4 generations for transmission events occurred. These findings are a part of the expanding investigation of the evolution of how this virus adapts to a new host.
Collapse
Affiliation(s)
- Suxiang Tong
- National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS-G17, Atlanta, GA 30333, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Tang J, Chan R. Severe acute respiratory syndrome (SARS) in intensive care units (ICUs): limiting the risk to healthcare workers. CURRENT ANAESTHESIA AND CRITICAL CARE 2004; 15:143-155. [PMID: 32288321 PMCID: PMC7135788 DOI: 10.1016/j.cacc.2004.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The global epidemic of severe acute respiratory syndrome (SARS) during the first half of 2003 resulted in over 8000 cases with more than 800 deaths. Many of those who eventually died, did so in the critical (intensive) care units of various hospitals around the world, and many secondary cases of SARS arose in healthcare workers looking after such patients in these units. Research on SARS coronavirus (SARS CoV) demonstrated that this virus belongs to the same family of viruses, the Coronaviridae that causes the common cold, with some important differences. Properties of this virus have been discovered which can be used to develop important infection control policies within hospitals to limit the number of secondary cases. These properties include environmental survival, transmissibility, viral load in various organs and fluids and periods of symptomatic illness during which infectivity is greatest. Various barrier methods were used throughout the epidemic to protect healthcare workers from SARS, with varying degrees of success. Treatment of SARS patients has mainly involved steroid therapy, with or without ribavirin, but there is no consensus on the best treatment protocol, as yet. This review focuses on the implications of SARS for healthcare workers and patients on critical care units.
Collapse
Affiliation(s)
- J.W. Tang
- Royal Free and University College Medical Schools, Centre for Virology, Division of Infection and Immunity, Windeyer Building, 46 Cleveland Street, London W1T 4JF, UK
| | - R.C.W. Chan
- Department of Microbiology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administration Region (SAR), China
| |
Collapse
|
38
|
Abstract
PURPOSE OF REVIEW In November 2003, a new, life-threatening, respiratory illness named severe acute respiratory syndrome (SARS) arose from Guangdong Province in China. The illness spread across the globe, caused many major outbreaks, and had an overall mortality rate of 11%. The purpose of this review is primarily to review the clinical features, diagnosis, and management of SARS, but also to comment briefly on the epidemiology and pathogen. RECENT FINDINGS SARS is caused by a novel coronavirus that primarily affects the lower respiratory tract. It starts with an influenza-like illness characterized by nonspecific, systemic symptoms. This is followed by the rapid development of a non-specific bronchopneumonia associated with lower tract respiratory symptoms, or gastrointestinal symptoms. Most patients recover after a week or 2, but some go on to develop acute respiratory distress syndrome. There is no proven treatment, although cocktails of broad-spectrum antibiotics, antiviral, and immunomodulatory therapy have been tried. Secondary spread can be prevented and outbreaks brought under control provided that staff wear personal protective equipment and pay close attention to good personal hygiene, and patients are isolated. The most urgent needs at present are to develop a vaccine, to develop rapid, inexpensive, accurate diagnostic tests that can give results early in the illness and within a few hours of sampling. Other needs are to investigate which therapies have the lowest adverse event/efficacy ratios. SUMMARY Up-to-date knowledge of SARS should help in early detection, isolation of high-risk patients, to reduce mortality and morbidity, and to prevent a new global epidemic arising.
Collapse
Affiliation(s)
- Timothy H Rainer
- Accident and Emergency Medicine Academic Unit, The Chinese University of Hong Kong, Shatin, NT, Hong Kong.
| |
Collapse
|
39
|
Lai KN, Tsang KW, Seto WH, Ooi CGC. Clinical, Laboratory, and Radiologic Manifestation of SARS. Curr Infect Dis Rep 2004; 6:213-219. [PMID: 15142485 PMCID: PMC7088556 DOI: 10.1007/s11908-004-0011-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Severe acute respiratory syndrome (SARS) is a highly contagious and predominantly pneumonic illness caused by a novel coronavirus now commonly known as SARS-CoV. This article describes the key diagnostic clinical features, radiologic features, and investigation profiles of affected patients. We summarize our understanding from anecdotal experience and limited published data on the use of antiviral and corticosteroid therapy in the management of this highly contagious disease.
Collapse
Affiliation(s)
- Kar Neng Lai
- University Department of Medicine, The University of Hong Kong, Room 409, Professorial Block, Queen Mary Hospital, Pokfulam, Hong Kong.
| | | | | | | |
Collapse
|
40
|
Chim SS, Lo YD. Molecular epidemiology of the coronavirus associated with severe acute respiratory syndrome: a review of data from the Chinese University of Hong Kong. Clin Biochem Rev 2004; 25:143-147. [PMID: 18458710 PMCID: PMC1904414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The epidemic of the severe acute respiratory syndrome (SARS) has swept through the globe with more than 8000 reported probable cases. In Hong Kong, the hardest hit areas included our teaching hospital and the Amoy Gardens apartment complex. A novel coronavirus, SARS-coronavirus (SARS-CoV), with a single-stranded plus sense RNA genome, was promptly implicated as the causative agent and subsequently fulfilled Koch's postulates. To aid the understanding of SARS-CoV, groups of investigators rapidly sequenced viral isolates around the world. We were the third group in the world to release the complete SARS-CoV genome sequence (isolate CUHK-W1) on the world-wide web. With other isolates from patients of distinct epidemiological backgrounds, we additionally sequenced four complete (CUHK-Su10, CUHK-AG01, CUHK-AG02, CUHK-AG03) and two partial SARS-CoV genomes. The reviewed data obtained from representative patients from the hospital and community outbreaks has documented the evolution of the virus in this epidemic. Their sequence variations also revealed a remarkable epidemiological correlation. We demonstrate that sequence variations in the SARS-CoV genome can be applied as a powerful molecular tool in tracing the route of transmission, when used adjunctively with standard epidemiology.
Collapse
|
41
|
Abstract
Sixty-one SARS coronavirus genomic sequences derived from the early, middle, and late phases of the severe acute respiratory syndrome (SARS) epidemic were analyzed together with two viral sequences from palm civets. Genotypes characteristic of each phase were discovered, and the earliest genotypes were similar to the animal SARS-like coronaviruses. Major deletions were observed in the Orf8 region of the genome, both at the start and the end of the epidemic. The neutral mutation rate of the viral genome was constant but the amino acid substitution rate of the coding sequences slowed during the course of the epidemic. The spike protein showed the strongest initial responses to positive selection pressures, followed by subsequent purifying selection and eventual stabilization.
Collapse
|
42
|
Navas Elorza E. Síndrome respiratorio agudo grave. FMC : FORMACION MEDICA CONTINUADA EN ATENCION PRIMARIA 2004; 11:191-197. [PMID: 32288492 PMCID: PMC7144502 DOI: 10.1016/s1134-2072(04)75708-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
43
|
Jin W, Hu L, Du Z, Gao Q, Gao H, Ning Y, Feng J, Zhang J, Yin W, Li N. Genome sequence variation analysis of two SARS coronavirus isolates after passage in Vero cell culture. CHINESE SCIENCE BULLETIN-CHINESE 2004; 49:1824-1827. [PMID: 32214713 PMCID: PMC7089035 DOI: 10.1007/bf03183408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2004] [Accepted: 07/24/2004] [Indexed: 11/06/2022]
Abstract
SARS coronavirus is an RNA virus whose replication is error-prone, which provides possibility for escape of host defenses, and even leads to evolution of new viral strains during the passage or the transmission. Lots of variations have been detected among different SARS-CoV strains. And a study on these variations is helpful for development of efficient vaccine. Moreover, the test of nucleic acid characterization and genetic stability of SARS-CoV is important in the research of inactivated vaccine. The whole genome sequences of two SARS coronavirus strains after passage in Vero cell culture were determined and were compared with those of early passages, respectively. Results showed that both SARS coronavirus strains have high genetic stability, although nearly 10 generations were passed. Four nucleotide variations were observed between the second passage and the 11th passage of Sino1 strain for identification of SARS inactivated vaccine. Moreover, only one nucleotide was different between the third passage and the 10th passage of Sino3 strain for SARS inactivated vaccine. Therefore, this study suggested it was possible to develop inactivated vaccine against SARS-CoV in the future.
Collapse
Affiliation(s)
- Weiwu Jin
- State Key Laboratory for Agrobiotechnology, China Agricultural University, 100094 Beijing, China
| | - Liangxiang Hu
- Sino Biotech Co., Ltd., No. 39 Shangdi Xi Rd. Haidian District, 100085 Beijing, China
| | - Zhenglin Du
- State Key Laboratory for Agrobiotechnology, China Agricultural University, 100094 Beijing, China
| | - Qiang Gao
- Sino Biotech Co., Ltd., No. 39 Shangdi Xi Rd. Haidian District, 100085 Beijing, China
| | - Hong Gao
- Sino Biotech Co., Ltd., No. 39 Shangdi Xi Rd. Haidian District, 100085 Beijing, China
| | - Ye Ning
- Sino Biotech Co., Ltd., No. 39 Shangdi Xi Rd. Haidian District, 100085 Beijing, China
| | - Jidong Feng
- State Key Laboratory for Agrobiotechnology, China Agricultural University, 100094 Beijing, China
| | - Jiansan Zhang
- Sino Biotech Co., Ltd., No. 39 Shangdi Xi Rd. Haidian District, 100085 Beijing, China
| | - Weidong Yin
- Sino Biotech Co., Ltd., No. 39 Shangdi Xi Rd. Haidian District, 100085 Beijing, China
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, China Agricultural University, 100094 Beijing, China
| |
Collapse
|
44
|
Abstract
In this study, we analyzed the amino acid pairs affected by mutations in two spike proteins from human coronavirus strains 229E and OC43 by means of random analysis in order to gain some insight into the possible mutations in the spike protein from SARS-CoV. The results demonstrate that the randomly unpredictable amino acid pairs are more sensitive to the mutations. The larger is the difference between actual and predicted frequencies, the higher is the chance of mutation occurring. The effect induced by mutations is to reduce the difference between actual and predicted frequencies. The amino acid pairs whose actual frequencies are larger than their predicted frequencies are more likely to be targeted by mutations, whereas the amino acid pairs whose actual frequencies are smaller than their predicted frequencies are more likely to be formed after mutations. These findings are identical to our several recent studies, i.e. the mutations represent a process of degeneration inducing human diseases.
Collapse
Affiliation(s)
- Guang Wu
- DreamSciTech Consulting Co. Ltd., 301, Building 12, Nanyou A-zone, Jainnan Road, CN-518054, Shenzhen, PR China.
| | | |
Collapse
|
45
|
Chow KYC, Hon CC, Hui RKH, Wong RTY, Yip CW, Zeng F, Leung FCC. Molecular advances in severe acute respiratory syndrome-associated coronavirus (SARS-CoV). GENOMICS, PROTEOMICS & BIOINFORMATICS 2003; 1:247-62. [PMID: 15629054 PMCID: PMC5172416 DOI: 10.1016/s1672-0229(03)01031-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The sudden outbreak of severe acute respiratory syndrome (SARS) in 2002 prompted the establishment of a global scientific network subsuming most of the traditional rivalries in the competitive field of virology. Within months of the SARS outbreak, collaborative work revealed the identity of the disastrous pathogen as SARS-associated coronavirus (SARS-CoV). However, although the rapid identification of the agent represented an important breakthrough, our understanding of the deadly virus remains limited. Detailed biological knowledge is crucial for the development of effective countermeasures, diagnostic tests, vaccines and antiviral drugs against the SARS-CoV. This article reviews the present state of molecular knowledge about SARS-CoV, from the aspects of comparative genomics, molecular biology of viral genes, evolution, and epidemiology, and describes the diagnostic tests and the anti-viral drugs derived so far based on the available molecular information.
Collapse
|