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Lin HF, Liu MQ, Jiang RD, Gong QC, Su J, Guo ZS, Chen Y, Jia JK, Dong TY, Zhu Y, Li A, Shen XR, Wang Y, Li B, Xie TT, Yang XL, Hu B, Shi ZL. Characterization of a mouse-adapted strain of bat severe acute respiratory syndrome-related coronavirus. J Virol 2023; 97:e0079023. [PMID: 37607058 PMCID: PMC10537601 DOI: 10.1128/jvi.00790-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 06/18/2023] [Indexed: 08/24/2023] Open
Abstract
Bats carry genetically diverse severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs). Some of them utilize human angiotensin-converting enzyme 2 (hACE2) as a receptor and cannot efficiently replicate in wild-type mice. Our previous study demonstrated that the bat SARSr-CoV rRsSHC014S induces respiratory infection and lung damage in hACE2 transgenic mice but not wild-type mice. In this study, we generated a mouse-adapted strain of rRsSHC014S, which we named SMA1901, by serial passaging of wild-type virus in BALB/c mice. SMA1901 showed increased infectivity in mouse lungs and induced interstitial lung pneumonia in both young and aged mice after intranasal inoculation. Genome sequencing revealed mutations in not only the spike protein but the whole genome, which may be responsible for the enhanced pathogenicity of SMA1901 in wild-type BALB/c mice. SMA1901 induced age-related mortality similar to that observed in SARS and COVID-19. Drug testing using antibodies and antiviral molecules indicated that this mouse-adapted virus strain can be used to test prophylactic and therapeutic drug candidates against SARSr-CoVs. IMPORTANCE The genetic diversity of SARSr-CoVs in wildlife and their potential risk of cross-species infection highlights the importance of developing a powerful animal model to evaluate the antibodies and antiviral drugs. We acquired the mouse-adapted strain of a bat-origin coronavirus named SMA1901 by natural serial passaging of rRsSHC014S in BALB/c mice. The SMA1901 infection caused interstitial pneumonia and inflammatory immune responses in both young and aged BALB/c mice after intranasal inoculation. Our model exhibited age-related mortality similar to SARS and COVID-19. Therefore, our model will be of high value for investigating the pathogenesis of bat SARSr-CoVs and could serve as a prospective test platform for prophylactic and therapeutic candidates.
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Affiliation(s)
- Hao-Feng Lin
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Qin Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ren-Di Jiang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Qian-Chun Gong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jia Su
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Shuo Guo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing-Kun Jia
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tian-Yi Dong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ang Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xu-Rui Shen
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
| | - Yi Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ting-Ting Xie
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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Starr TN, Zepeda SK, Walls AC, Greaney AJ, Alkhovsky S, Veesler D, Bloom JD. ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. Nature 2022; 603:913-918. [PMID: 35114688 PMCID: PMC8967715 DOI: 10.1038/s41586-022-04464-z] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 01/25/2022] [Indexed: 11/08/2022]
Abstract
Two different sarbecoviruses have caused major human outbreaks in the past two decades1,2. Both of these sarbecoviruses, SARS-CoV-1 and SARS-CoV-2, engage ACE2 through the spike receptor-binding domain2-6. However, binding to ACE2 orthologues of humans, bats and other species has been observed only sporadically among the broader diversity of bat sarbecoviruses7-11. Here we use high-throughput assays12 to trace the evolutionary history of ACE2 binding across a diverse range of sarbecoviruses and ACE2 orthologues. We find that ACE2 binding is an ancestral trait of sarbecovirus receptor-binding domains that has subsequently been lost in some clades. Furthermore, we reveal that bat sarbecoviruses from outside Asia can bind to ACE2. Moreover, ACE2 binding is highly evolvable-for many sarbecovirus receptor-binding domains, there are single amino-acid mutations that enable binding to new ACE2 orthologues. However, the effects of individual mutations can differ considerably between viruses, as shown by the N501Y mutation, which enhances the human ACE2-binding affinity of several SARS-CoV-2 variants of concern12 but substantially decreases it for SARS-CoV-1. Our results point to the deep ancestral origin and evolutionary plasticity of ACE2 binding, broadening the range of sarbecoviruses that should be considered to have spillover potential.
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Affiliation(s)
- Tyler N Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Allison J Greaney
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sergey Alkhovsky
- N.F. Gamleya National Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - David Veesler
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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3
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Alkhovsky S, Lenshin S, Romashin A, Vishnevskaya T, Vyshemirsky O, Bulycheva Y, Lvov D, Gitelman A. SARS-like Coronaviruses in Horseshoe Bats ( Rhinolophus spp.) in Russia, 2020. Viruses 2022; 14:v14010113. [PMID: 35062318 PMCID: PMC8779456 DOI: 10.3390/v14010113] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/24/2021] [Accepted: 01/06/2022] [Indexed: 02/05/2023] Open
Abstract
We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the greater (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern regions of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found evidence of recombination events in the evolutionary history of Khosta-1, which involved the acquisition of the structural proteins S, E, and M, as well as the nonstructural genes ORF3, ORF6, ORF7a, and ORF7b, from a virus that is related to the Kenyan isolate BtKY72. The examination of bats by RT-PCR revealed that 62.5% of the greater horseshoe bats in one of the caves were positive for Khosta-1 virus, while its overall prevalence was 14%. The prevalence of Khosta-2 was 1.75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region, and we provide new data on their genetic diversity.
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Affiliation(s)
- Sergey Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamleya National Center for Epidemiology and Microbiology of Ministry of Health of Russian Federation, 18 Gamaleya Street, 123098 Moscow, Russia; (T.V.); (Y.B.); (D.L.); (A.G.)
- Reference Center on Coronavirus Infection of N.F. Gamleya National Center for Epidemiology and Microbiology of Ministry of Health of Russian Federation, 18 Gamaleya Street, 123098 Moscow, Russia
- Correspondence:
| | - Sergey Lenshin
- Scientific Research Institute of Medical Primatology of Russian Academy of Science, 177 Mira Street, Veseoloe Village, 354376 Sochi, Russia; (S.L.); (O.V.)
| | - Alexey Romashin
- Federal State Budgetary Institution Sochi National Park of Ministry of Natural Resources and Environment of Russian Federation, 74 Kurortniy Avenue, 354002 Sochi, Russia;
| | - Tatyana Vishnevskaya
- D.I. Ivanovsky Institute of Virology of N.F. Gamleya National Center for Epidemiology and Microbiology of Ministry of Health of Russian Federation, 18 Gamaleya Street, 123098 Moscow, Russia; (T.V.); (Y.B.); (D.L.); (A.G.)
- Reference Center on Coronavirus Infection of N.F. Gamleya National Center for Epidemiology and Microbiology of Ministry of Health of Russian Federation, 18 Gamaleya Street, 123098 Moscow, Russia
| | - Oleg Vyshemirsky
- Scientific Research Institute of Medical Primatology of Russian Academy of Science, 177 Mira Street, Veseoloe Village, 354376 Sochi, Russia; (S.L.); (O.V.)
| | - Yulia Bulycheva
- D.I. Ivanovsky Institute of Virology of N.F. Gamleya National Center for Epidemiology and Microbiology of Ministry of Health of Russian Federation, 18 Gamaleya Street, 123098 Moscow, Russia; (T.V.); (Y.B.); (D.L.); (A.G.)
| | - Dmitry Lvov
- D.I. Ivanovsky Institute of Virology of N.F. Gamleya National Center for Epidemiology and Microbiology of Ministry of Health of Russian Federation, 18 Gamaleya Street, 123098 Moscow, Russia; (T.V.); (Y.B.); (D.L.); (A.G.)
| | - Asya Gitelman
- D.I. Ivanovsky Institute of Virology of N.F. Gamleya National Center for Epidemiology and Microbiology of Ministry of Health of Russian Federation, 18 Gamaleya Street, 123098 Moscow, Russia; (T.V.); (Y.B.); (D.L.); (A.G.)
- Reference Center on Coronavirus Infection of N.F. Gamleya National Center for Epidemiology and Microbiology of Ministry of Health of Russian Federation, 18 Gamaleya Street, 123098 Moscow, Russia
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Guo H, Hu B, Si HR, Zhu Y, Zhang W, Li B, Li A, Geng R, Lin HF, Yang XL, Zhou P, Shi ZL. Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor. Emerg Microbes Infect 2021; 10:1507-1514. [PMID: 34263709 PMCID: PMC8344244 DOI: 10.1080/22221751.2021.1956373] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022]
Abstract
Severe respiratory disease coronavirus-2 (SARS-CoV-2) has been the most devastating disease COVID-19 in the century. One of the unsolved scientific questions of SARS-CoV-2 is the animal origin of this virus. Bats and pangolins are recognized as the most probable reservoir hosts that harbour highly similar SARS-CoV-2 related viruses (SARSr-CoV-2). This study identified a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015. Although RaTG15 and the related viruses share 97.2% amino acid sequence identities with SARS-CoV-2 in the conserved ORF1b region, it only shows less than 77.6% nucleotide identity to all known SARSr-CoVs at the genome level, thus forming a distinct lineage in the Sarbecovirus phylogenetic tree. We found that the RaTG15 receptor-binding domain (RBD) can bind to ACE2 from Rhinolophus affinis, Malayan pangolin, and use it as an entry receptor, except for ACE2 from humans. However, it contains a short deletion and has different key residues responsible for ACE2 binding. In addition, we showed that none of the known viruses in bat SARSr-CoV-2 lineage discovered uses human ACE2 as efficiently as the pangolin-derived SARSr-CoV-2 or some viruses in the SARSr-CoV-1 lineage. Therefore, further systematic and longitudinal studies in bats are needed to prevent future spillover events caused by SARSr-CoVs or to understand the origin of SARS-CoV-2 better.
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Affiliation(s)
- Hua Guo
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
| | - Hao-Rui Si
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
| | - Wei Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
| | - Ang Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Rong Geng
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Hao-Feng Lin
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
| | - Peng Zhou
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
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5
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Pollett S, Conte MA, Sanborn M, Jarman RG, Lidl GM, Modjarrad K, Maljkovic Berry I. A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic. Sci Rep 2021; 11:17365. [PMID: 34462471 PMCID: PMC8405798 DOI: 10.1038/s41598-021-96626-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/09/2021] [Indexed: 11/11/2022] Open
Abstract
The SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in the non-ORF1 region of the genome containing structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.
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Affiliation(s)
- Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Matthew A Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mark Sanborn
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Grace M Lidl
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
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Santacroce L, Charitos IA, Carretta DM, De Nitto E, Lovero R. The human coronaviruses (HCoVs) and the molecular mechanisms of SARS-CoV-2 infection. J Mol Med (Berl) 2021; 99:93-106. [PMID: 33269412 PMCID: PMC7710368 DOI: 10.1007/s00109-020-02012-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/31/2020] [Accepted: 11/18/2020] [Indexed: 12/13/2022]
Abstract
In humans, coronaviruses can cause infections of the respiratory system, with damage of varying severity depending on the virus examined: ranging from mild-to-moderate upper respiratory tract diseases, such as the common cold, pneumonia, severe acute respiratory syndrome, kidney failure, and even death. Human coronaviruses known to date, common throughout the world, are seven. The most common-and least harmful-ones were discovered in the 1960s and cause a common cold. Others, more dangerous, identified in the early 2000s and cause more severe respiratory tract infections. Among these the SARS-CoV, isolated in 2003 and responsible for the severe acute respiratory syndrome (the so-called SARS), which appeared in China in November 2002, the coronavirus 2012 (2012-nCoV) cause of the Middle Eastern respiratory syndrome (MERS) from coronavirus, which exploded in June 2012 in Saudi Arabia, and actually SARS-CoV-2. On December 31, 2019, a new coronavirus strain was reported in Wuhan, China, identified as a new coronavirus beta strain ß-CoV from group 2B, with a genetic similarity of approximately 70% to SARS-CoV, the virus responsible of SARS. In the first half of February, the International Committee on Taxonomy of Viruses (ICTV), in charge of the designation and naming of the viruses (i.e., species, genus, family, etc.), thus definitively named the new coronavirus as SARS-CoV-2. This article highlights the main knowledge we have about the biomolecular and pathophysiologic mechanisms of SARS-CoV-2.
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Affiliation(s)
- Luigi Santacroce
- Department of Interdisciplinary Medicine, Microbiology and Virology Laboratory, University Hospital of Bari, Università degli Studi di Bari, p.zza G. Cesare, 11, 70124, Bari, Italy.
| | - Ioannis A Charitos
- Department of Emergency and Urgency, National Poisoning Centre, Riuniti University Hospital of Foggia, viale Pinto, 1, Foggia, 71122, Italy
| | - Domenico M Carretta
- Syncope Unit at Cardio-Thoracic Department, Policlinico Consorziale, U.O.S. Coronary Unit and Electrophysiology/Pacing Unit, p.zza G. Cesare 11, Bari, 70124, Italy
| | - Emanuele De Nitto
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, Section of Biochemistry, University of Bari "Aldo Moro", p.zza G. Cesare, 11, 70124, Bari, Italy
| | - Roberto Lovero
- Clinical Pathology Unit, AOU Policlinico Consorziale di Bari - Ospedale Giovanni XXIII, p.zza G. Cesare 11, 70124, Bari, Italy
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Kirtipal N, Bharadwaj S, Kang SG. From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses. Infect Genet Evol 2020; 85:104502. [PMID: 32798769 PMCID: PMC7425554 DOI: 10.1016/j.meegid.2020.104502] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/10/2020] [Indexed: 01/08/2023]
Abstract
Human Coronaviruses (HCoV), periodically emerging across the world, are potential threat to humans such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) - diseases termed as COVID-19. Current SARS-CoV-2 outbreak have fueled ongoing efforts to exploit various viral target proteins for therapy, but strategies aimed at blocking the viral proteins as in drug and vaccine development have largely failed. In fact, evidence has now shown that coronaviruses undergoes rapid recombination to generate new strains of altered virulence; additionally, escaped the host antiviral defense system and target humoral immune system which further results in severe deterioration of the body such as by cytokine storm. This demands the understanding of phenotypic and genotypic classification, and pathogenesis of SARS-CoV-2 for the production of potential therapy. In lack of clear clinical evidences for the pathogenesis of COVID-19, comparative analysis of previous pandemic HCoVs associated immunological responses can provide insights into COVID-19 pathogenesis. In this review, we summarize the possible origin and transmission mode of CoVs and the current understanding on the viral genome integrity of known pandemic virus against SARS-CoV-2. We also consider the host immune response and viral evasion based on available clinical evidences which would be helpful to remodel COVID-19 pathogenesis; and hence, development of therapeutics against broad spectrum of coronaviruses.
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Affiliation(s)
- Nikhil Kirtipal
- Department of Science, Modern Institute of Technology, Dhalwala, Rishikesh, Uttarakhand, India
| | - Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
| | - Sang Gu Kang
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
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Paul T, Vainio S, Roning J. Clustering and classification of virus sequence through music communication protocol and wavelet transform. Genomics 2020; 113:778-784. [PMID: 33069829 PMCID: PMC7561519 DOI: 10.1016/j.ygeno.2020.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/13/2020] [Indexed: 01/19/2023]
Abstract
The coronavirus pandemic became a major risk in global public health. The outbreak is caused by SARS-CoV-2, a member of the coronavirus family. Though the images of the virus are familiar to us, in the present study, an attempt is made to hear the coronavirus by translating its protein spike into audio sequences. The musical features such as pitch, timbre, volume and duration are mapped based on the coronavirus protein sequence. Three different viruses Influenza, Ebola and Coronavirus were studied and compared through their auditory virus sequences by implementing Haar wavelet transform. The sonification of the coronavirus benefits in understanding the protein structures by enhancing the hidden features. Further, it makes a clear difference in the representation of coronavirus compared with other viruses, which will help in various research works related to virus sequence. This evolves as a simplified and novel way of representing the conventional computational methods.
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Affiliation(s)
- Tirthankar Paul
- InfoTech Oulu, Biomimetics and Intelligent Systems Group (BISG), Faculty of Information Technology and Electrical Engineering, University of Oulu, Oulu, Finland.
| | - Seppo Vainio
- InfoTech Oulu, Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, Laboratory of Development Biology, University of Oulu, Oulu, Finland.
| | - Juha Roning
- InfoTech Oulu, Biomimetics and Intelligent Systems Group (BISG), Faculty of Information Technology and Electrical Engineering, University of Oulu, Oulu, Finland.
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Lokman SM, Rasheduzzaman M, Salauddin A, Barua R, Tanzina AY, Rumi MH, Hossain MI, Siddiki AMAMZ, Mannan A, Hasan MM. Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach. Infect Genet Evol 2020; 84:104389. [PMID: 32502733 PMCID: PMC7266584 DOI: 10.1016/j.meegid.2020.104389] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/12/2020] [Accepted: 05/31/2020] [Indexed: 12/14/2022]
Abstract
The newly identified SARS-CoV-2 has now been reported from around 185 countries with more than a million confirmed human cases including more than 120,000 deaths. The genomes of SARS-COV-2 strains isolated from different parts of the world are now available and the unique features of constituent genes and proteins need to be explored to understand the biology of the virus. Spike glycoprotein is one of the major targets to be explored because of its role during the entry of coronaviruses into host cells. We analyzed 320 whole-genome sequences and 320 spike protein sequences of SARS-CoV-2 using multiple sequence alignment. In this study, 483 unique variations have been identified among the genomes of SARS-CoV-2 including 25 nonsynonymous mutations and one deletion in the spike (S) protein. Among the 26 variations detected in S, 12 variations were located at the N-terminal domain (NTD) and 6 variations at the receptor-binding domain (RBD) which might alter the interaction of S protein with the host receptor angiotensin-converting enzyme 2 (ACE2). Besides, 22 amino acid insertions were identified in the spike protein of SARS-CoV-2 in comparison with that of SARS-CoV. Phylogenetic analyses of spike protein revealed that Bat coronavirus have a close evolutionary relationship with circulating SARS-CoV-2. The genetic variation analysis data presented in this study can help a better understanding of SARS-CoV-2 pathogenesis. Based on results reported herein, potential inhibitors against S protein can be designed by considering these variations and their impact on protein structure.
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Affiliation(s)
- Syed Mohammad Lokman
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Md Rasheduzzaman
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Asma Salauddin
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Rocktim Barua
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Afsana Yeasmin Tanzina
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Meheadi Hasan Rumi
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - Md Imran Hossain
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh
| | - A M A M Zonaed Siddiki
- Department of Pathology and Parasitology, Chittagong Veterinary and Animal Sciences University, Chattogram 4202, Bangladesh
| | - Adnan Mannan
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh.
| | - Md Mahbub Hasan
- Department of Genetic Engineering & Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh; Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
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10
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Uddin MB, Hasan M, Harun-Al-Rashid A, Ahsan MI, Imran MAS, Ahmed SSU. Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective. Infect Genet Evol 2020; 84:104440. [PMID: 32622082 PMCID: PMC7327474 DOI: 10.1016/j.meegid.2020.104440] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 12/22/2022]
Abstract
SARS-CoV-2, a new coronavirus strain responsible for COVID-19, has emerged in Wuhan City, China, and continuing its global pandemic nature. The availability of the complete gene sequences of the virus helps to know about the origin and molecular characteristics of this virus. In the present study, we performed bioinformatic analysis of the available gene sequence data of SARS-CoV-2 for the understanding of evolution and molecular characteristics and immunogenic resemblance of the circulating viruses. Phylogenetic analysis was performed for four types of representative viral proteins (spike, membrane, envelope and nucleoprotein) of SARS-CoV-2, HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1, MERS-CoV, HKU4, HKU5 and BufCoV-HKU26. The findings demonstrated that SARS-CoV-2 exhibited convergent evolutionary relation with previously reported SARS-CoV. It was also depicted that SARS-CoV-2 proteins were highly similar and identical to SARS-CoV proteins, though proteins from other coronaviruses showed a lower level of resemblance. The cross-checked conservancy analysis of SARS-CoV-2 antigenic epitopes showed significant conservancy with antigenic epitopes derived from SARS-CoV. Descriptive epidemiological analysis on several epidemiological indices was performed on available epidemiological outbreak information from several open databases on COVID-19 (SARS-CoV-2). Satellite-derived imaging data have been employed to understand the role of temperature in the environmental persistence of the virus. Findings of the descriptive analysis were used to describe the global impact of newly emerged SARS-CoV-2, and the risk of an epidemic in Bangladesh.
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MESH Headings
- Alphacoronavirus/classification
- Alphacoronavirus/genetics
- Alphacoronavirus/metabolism
- Amino Acid Sequence
- Animals
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/metabolism
- Bangladesh/epidemiology
- Base Sequence
- Betacoronavirus/classification
- Betacoronavirus/genetics
- Betacoronavirus/metabolism
- Binding Sites
- COVID-19
- Chiroptera/virology
- Computational Biology
- Coronavirus 229E, Human/classification
- Coronavirus 229E, Human/genetics
- Coronavirus 229E, Human/metabolism
- Coronavirus Infections/epidemiology
- Coronavirus Infections/virology
- Coronavirus NL63, Human/classification
- Coronavirus NL63, Human/genetics
- Coronavirus NL63, Human/metabolism
- Coronavirus OC43, Human/classification
- Coronavirus OC43, Human/genetics
- Coronavirus OC43, Human/metabolism
- Genome, Viral
- Humans
- Middle East Respiratory Syndrome Coronavirus/classification
- Middle East Respiratory Syndrome Coronavirus/genetics
- Middle East Respiratory Syndrome Coronavirus/metabolism
- Models, Molecular
- Mutation
- Nucleoproteins/chemistry
- Nucleoproteins/genetics
- Nucleoproteins/metabolism
- Pandemics
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/virology
- Protein Binding
- Protein Interaction Domains and Motifs
- Severe acute respiratory syndrome-related coronavirus/classification
- Severe acute respiratory syndrome-related coronavirus/genetics
- Severe acute respiratory syndrome-related coronavirus/metabolism
- SARS-CoV-2
- Sequence Alignment
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Viral Envelope Proteins/chemistry
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/metabolism
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Affiliation(s)
- Md Bashir Uddin
- Department of Medicine, Sylhet Agricultural University, Sylhet-3100, Bangladesh.
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Ahmed Harun-Al-Rashid
- Department of Aquatic Resource Management, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Md Irtija Ahsan
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Md Abdus Shukur Imran
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Syed Sayeem Uddin Ahmed
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet-3100, Bangladesh.
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11
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Abstract
A severe upper respiratory tract syndrome caused by the new coronavirus has now spread to the entire world as a highly contagious pandemic. The large scale explosion of the disease is conventionally traced back to January of this year in the Chinese province of Hubei, the wet markets of the principal city of Wuhan being assumed to have been the specific causative locus of the sudden explosion of the infection. A number of findings that are now coming to light show that this interpretation of the origin and history of the pandemic is overly simplified. A number of variants of the coronavirus would in principle have had the ability to initiate the pandemic well before January of this year. However, even if the COVID-19 had become, so to say, ready, conditions in the local environment would have had to prevail to induce the loss of the biodiversity's "dilution effect" that kept the virus under control, favoring its spillover from its bat reservoir to the human target. In the absence of these appropriate conditions only abortive attempts to initiate the pandemic could possibly occur: a number of them did indeed occur in China, and probably elsewhere as well. These conditions were unfortunately present at the wet marked in Wuhan at the end of last year.
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Affiliation(s)
- Sara Platto
- China Biodiversity Conservation and Green Development Foundation, Beijing, China.
- Department of Biotechnology, College of Life Sciences, Jianghan University, Wuhan, China.
| | - Tongtong Xue
- Department of Biotechnology, College of Life Sciences, Jianghan University, Wuhan, China
| | - Ernesto Carafoli
- Venetian Institute of molecular Medicine, University of Padova, Padova, Italy
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12
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Tan HW, Xu Y, Lau ATY. Angiotensin-converting enzyme 2: The old door for new severe acute respiratory syndrome coronavirus 2 infection. Rev Med Virol 2020; 30:e2122. [PMID: 32602627 PMCID: PMC7361198 DOI: 10.1002/rmv.2122] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 02/05/2023]
Abstract
Coronavirus (CoV) disease 2019 (COVID-19) is an ongoing pandemic caused by severe acute respiratory syndrome CoV 2 (SARS-CoV-2). The highly contagious SARS-CoV-2 belongs to the genus Betacoronavirus, and it is phylogenetically closely related to SARS-CoV, a human CoV that caused an outbreak back in 2002 to 2003. Both SARS-CoV-2 and SARS-CoV enter human cells via the interactions between viral crown-like spike protein and human angiotensin-converting enzyme 2 (ACE2) receptor. Here, we aim to review the involvement of ACE2 in human CoV infections by discussing the roles of ACE2 in CoV evolution, cross-species transmissibility, and COVID-19 susceptibility. We also provide our perspectives on COVID-19 treatment and prevention.
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Affiliation(s)
- Heng Wee Tan
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and GeneticsShantou University Medical CollegeShantouGuangdongPeople's Republic of China
| | - Yan‐Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and GeneticsShantou University Medical CollegeShantouGuangdongPeople's Republic of China
| | - Andy T. Y. Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and GeneticsShantou University Medical CollegeShantouGuangdongPeople's Republic of China
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13
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Gautam A, Kaphle K, Shrestha B, Phuyal S. Susceptibility to SARS, MERS, and COVID-19 from animal health perspective. Open Vet J 2020; 10:164-177. [PMID: 32821661 PMCID: PMC7419072 DOI: 10.4314/ovj.v10i2.6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/01/2020] [Indexed: 12/11/2022] Open
Abstract
Viruses are having great time as they seem to have bogged humans down. Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and novel coronavirus (COVID-19) are the three major coronaviruses of present-day global human and animal health concern. COVID-19 caused by SARS-CoV-2 is identified as the newest disease, presumably of bat origin. Different theories on the evolution of viruses are in circulation, yet there is no denying the fact that the animal source is the skeleton. The whole world is witnessing the terror of the COVID-19 pandemic that is following the same path of SARS and MERS, and seems to be more severe. In addition to humans, several species of animals are reported to have been infected with these life-threatening viruses. The possible routes of transmission and their zoonotic potentialities are the subjects of intense research. This review article aims to overview the link of all these three deadly coronaviruses among animals along with their phylogenic evolution and cross-species transmission. This is essential since animals as pets or food are said to pose some risk, and their better understanding is a must in order to prepare a possible plan for future havoc in both human and animal health. Although COVID-19 is causing a human health hazard globally, its reporting in animals are limited compared to SARS and MERS. Non-human primates and carnivores are most susceptible to SARS-coronavirus and SARS-CoV-2, respectively, whereas the dromedary camel is susceptible to MERS-coronavirus. Phylogenetically, the trio viruses are reported to have originated from bats and have special capacity to undergo mutation and genomic recombination in order to infect humans through its reservoir or replication host. However, it is difficult to analyze how the genomic pattern of coronaviruses occurs. Thus, increased possibility of new virus-variants infecting humans and animals in the upcoming days seems to be the biggest challenge for the future of the world. One health approach is portrayed as our best way ahead, and understanding the animal dimension will go a long way in formulating such preparedness plans.
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Affiliation(s)
- Aasish Gautam
- Institute of Agriculture and Animal Science, Tribhuvan University, Rupandehi, Nepal
| | - Krishna Kaphle
- Veterinary Teaching Hospital, Institute of Agriculture and Animal Science, Tribhuvan University, Rupandehi, Nepal
| | - Birendra Shrestha
- Institute of Agriculture and Animal Science, Tribhuvan University, Rupandehi, Nepal
| | - Samiksha Phuyal
- Institute of Agriculture and Animal Science, Tribhuvan University, Rupandehi, Nepal
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14
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Yang Y, Xiao Z, Ye K, He X, Sun B, Qin Z, Yu J, Yao J, Wu Q, Bao Z, Zhao W. SARS-CoV-2: characteristics and current advances in research. Virol J 2020; 17:117. [PMID: 32727485 PMCID: PMC7387805 DOI: 10.1186/s12985-020-01369-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection has spread rapidly across the world and become an international public health emergency. Both SARS-CoV-2 and SARS-CoV belong to subfamily Coronavirinae in the family Coronaviridae of the order Nidovirales and they are classified as the SARS-like species while belong to different cluster. Besides, viral structure, epidemiology characteristics and pathological characteristics are also different. We present a comprehensive survey of the latest coronavirus-SARS-CoV-2-from investigating its origin and evolution alongside SARS-CoV. Meanwhile, pathogenesis, cardiovascular disease in COVID-19 patients, myocardial injury and venous thromboembolism induced by SARS-CoV-2 as well as the treatment methods are summarized in this review.
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Affiliation(s)
- Yicheng Yang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Zhiqiang Xiao
- Department of clinical medicine, Zhengzhou university, 100 Science Avenue, Zhengzhou, 450001, China
| | - Kaiyan Ye
- Second Clinical Medical College, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoen He
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Bo Sun
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Zhiran Qin
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jianghai Yu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jinxiu Yao
- Yang Jiang Hospital, Yangjiang, 510515, Guangdong Province, China
| | - Qinghua Wu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Zhang Bao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
| | - Wei Zhao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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15
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Matyášek R, Kovařík A. Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts. Genes (Basel) 2020; 11:E761. [PMID: 32646049 PMCID: PMC7397057 DOI: 10.3390/genes11070761] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 12/17/2022] Open
Abstract
The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated from Rhinolophus affinis (a horseshoe bat). We also evaluated the CpG dinucleotide contents in SARS-CoV-2 and other human and animal coronavirus genomes. Out of 1136 single nucleotide variations (~4% divergence) between human SARS-CoV-2 and bat RaTG13, 682 (60%) can be attributed to C>U and U>C substitutions, far exceeding other types of substitutions. An accumulation of C>U mutations was also observed in SARS-CoV2 variants that arose within the human population. Globally, the C>U substitutions increased the frequency of codons for hydrophobic amino acids in SARS-CoV-2 peptides, while U>C substitutions decreased it. In contrast to most other coronaviruses, both SARS-CoV-2 and RaTG13 exhibited CpG depletion in their genomes. The data suggest that C-to-U conversion mediated by C deamination played a significant role in the evolution of the SARS-CoV-2 coronavirus. We hypothesize that the high frequency C>U transitions reflect virus adaptation processes in their hosts, and that SARS-CoV-2 could have been evolving for a relatively long period in humans following the transfer from animals before spreading worldwide.
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Affiliation(s)
| | - Aleš Kovařík
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic;
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16
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Gorbalenya AE, Krupovic M, Mushegian A, Kropinski AM, Siddell SG, Varsani A, Adams MJ, Davison AJ, Dutilh BE, Harrach B, Harrison RL, Junglen S, King AMQ, Knowles NJ, Lefkowitz EJ, Nibert ML, Rubino L, Sabanadzovic S, Sanfaçon H, Simmonds P, Walker PJ, Zerbini FM, Kuhn JH. The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks. Nat Microbiol 2020; 5:668-674. [PMID: 32341570 PMCID: PMC7186216 DOI: 10.1038/s41564-020-0709-x] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/11/2020] [Indexed: 01/17/2023]
Abstract
Virus taxonomy emerged as a discipline in the middle of the twentieth century. Traditionally, classification by virus taxonomists has been focussed on the grouping of relatively closely related viruses. However, during the past few years, the International Committee on Taxonomy of Viruses (ICTV) has recognized that the taxonomy it develops can be usefully extended to include the basal evolutionary relationships among distantly related viruses. Consequently, the ICTV has changed its Code to allow a 15-rank classification hierarchy that closely aligns with the Linnaean taxonomic system and may accommodate the entire spectrum of genetic divergence in the virosphere. The current taxonomies of three human pathogens, Ebola virus, severe acute respiratory syndrome coronavirus and herpes simplex virus 1 are used to illustrate the impact of the expanded rank structure. This new rank hierarchy of virus taxonomy will stimulate further research on virus origins and evolution, and vice versa, and could promote crosstalk with the taxonomies of cellular organisms.
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17
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Gorbalenya AE, Baker SC, Baric RS, de Groot RJ, Drosten C, Gulyaeva AA, Haagmans BL, Lauber C, Leontovich AM, Neuman BW, Penzar D, Perlman S, Poon LLM, Samborskiy DV, Sidorov IA, Sola I, Ziebuhr J. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 2020; 5:536-544. [PMID: 32123347 PMCID: PMC7095448 DOI: 10.1038/s41564-020-0695-z] [Citation(s) in RCA: 4330] [Impact Index Per Article: 1082.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 02/19/2020] [Indexed: 02/06/2023]
Abstract
The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.
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18
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Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 2020; 5:536-44. [PMID: 32123347 DOI: 10.1038/s41564-020-0695-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.
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19
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Gorbalenya AE, Baker SC, Baric RS, de Groot RJ, Drosten C, Gulyaeva AA, Haagmans BL, Lauber C, Leontovich AM, Neuman BW, Penzar D, Perlman S, Poon LL, Samborskiy D, Sidorov IA, Sola I, Ziebuhr J. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 2020; 5:536-544. [PMID: 32123347 DOI: 10.1101/2020.02.07.937862] [Citation(s) in RCA: 392] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 02/19/2020] [Indexed: 05/21/2023]
Abstract
The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.
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20
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Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 2020; 5:536-44. [PMID: 32123347 DOI: 10.1038/s41564-020-0695-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.
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21
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Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 2020. [PMID: 32015507 DOI: 10.1038/s415+86-020-2012-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats1-4. Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans5-7. Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor-angiotensin converting enzyme II (ACE2)-as SARS-CoV.
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Affiliation(s)
- Peng Zhou
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | | | - Ben Hu
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Lei Zhang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Wei Zhang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Hao-Rui Si
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | | | | | - Jing Chen
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun Luo
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hua Guo
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ren-Di Jiang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Qin Liu
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Chen
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xu-Rui Shen
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xi Wang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Shuang Zheng
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kai Zhao
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Quan-Jiao Chen
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Fei Deng
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Lin-Lin Liu
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Bing Yan
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Fa-Xian Zhan
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Yan-Yi Wang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Geng-Fu Xiao
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
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22
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Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 2020; 579:270-273. [PMID: 32015507 PMCID: PMC7095418 DOI: 10.1038/s41586-020-2012-7] [Citation(s) in RCA: 13197] [Impact Index Per Article: 3299.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 01/29/2020] [Indexed: 12/15/2022]
Abstract
Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats1-4. Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans5-7. Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor-angiotensin converting enzyme II (ACE2)-as SARS-CoV.
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Affiliation(s)
- Peng Zhou
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | | | - Ben Hu
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Lei Zhang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Wei Zhang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Hao-Rui Si
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | | | | | - Jing Chen
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun Luo
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hua Guo
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ren-Di Jiang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Qin Liu
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Chen
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xu-Rui Shen
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xi Wang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Shuang Zheng
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kai Zhao
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Quan-Jiao Chen
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Fei Deng
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Lin-Lin Liu
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Bing Yan
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Fa-Xian Zhan
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Yan-Yi Wang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Geng-Fu Xiao
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
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23
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Chuck CP, Ke ZH, Chen C, Wan DCC, Chow HF, Wong KB. Profiling of substrate-specificity and rational design of broad-spectrum peptidomimetic inhibitors for main proteases of coronaviruses. Hong Kong Med J 2014; 20 Suppl 4:22-25. [PMID: 25224114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Affiliation(s)
- C P Chuck
- School of Life Sciences, The Chinese University of Hong Kong
| | - Z H Ke
- Department of Chemistry, The Chinese University of Hong Kong
| | - C Chen
- Department of Chemistry, The Chinese University of Hong Kong
| | - D C C Wan
- School of Biomedical Sciences, The Chinese University of Hong Kong
| | - H F Chow
- Department of Chemistry, The Chinese University of Hong Kong
| | - K B Wong
- School of Life Sciences, The Chinese University of Hong Kong
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24
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Xu D, Sun H, Su H, Zhang L, Zhang J, Wang B, Xu R. SARS coronavirus without reservoir originated from an unnatural evolution, experienced the reverse evolution, and finally disappeared in the world. Chin Med J (Engl) 2014; 127:2537-2542. [PMID: 24985597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Affiliation(s)
- Dezhong Xu
- Department of Epidemiology, Fourth Military Medical University, Xi'an, Shaanxi 710032, China; Clinical Epidemiological Unit, Fourth Military Medical University, China Clinical Epidemiological Network, International Clinical Epidemiological Network, Xi'an, Shaanxi 710032, China.
| | - Huimin Sun
- Department of Epidemiology, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Haixia Su
- Department of Epidemiology, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Lei Zhang
- Department of Epidemiology, Fourth Military Medical University, Xi'an, Shaanxi 710032, China; Clinical Epidemiological Unit, Fourth Military Medical University, China Clinical Epidemiological Network, International Clinical Epidemiological Network, Xi'an, Shaanxi 710032, China
| | - Jingxia Zhang
- Department of Epidemiology, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Bo Wang
- Department of Epidemiology, Fourth Military Medical University, Xi'an, Shaanxi 710032, China; Clinical Epidemiological Unit, Fourth Military Medical University, China Clinical Epidemiological Network, International Clinical Epidemiological Network, Xi'an, Shaanxi 710032, China
| | - Rui Xu
- Department of Epidemiology, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
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25
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Affiliation(s)
- Guangwen Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Di Liu
- Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
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26
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Gouilh MA, Puechmaille SJ, Gonzalez JP, Teeling E, Kittayapong P, Manuguerra JC. SARS-Coronavirus ancestor's foot-prints in South-East Asian bat colonies and the refuge theory. Infect Genet Evol 2011; 11:1690-702. [PMID: 21763784 PMCID: PMC7106191 DOI: 10.1016/j.meegid.2011.06.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 06/29/2011] [Accepted: 06/30/2011] [Indexed: 12/20/2022]
Abstract
One of the great challenges in the ecology of infectious diseases is to understand what drives the emergence of new pathogens including the relationship between viruses and their hosts. In the case of the emergence of SevereAcute Respiratory Syndrome Coronavirus (SARS-CoV), several studies have shown coronavirus diversity in bats as well as the existence of SARS-CoV infection in apparently healthy bats, suggesting that bats may be a crucial host in the genesis of this disease. To elucidate the biogeographic origin of SARS-CoV and investigate the role that bats played in its emergence, we amplified coronavirus sequences from bat species captured throughout Thailand and assessed the phylogenetic relationships to each other and to other published coronavirus sequences. To this end, RdRp sequence of Coronavirinae was targeted by RT-PCR in non-invasive samples from bats collected in Thailand. Two new coronaviruses were detected in two bat species: one Betacoronavirus in Hipposideros larvatus and one Alphacoronavirus in Hipposiderosarmiger. Interestingly, these viruses from South-East Asia are related to those previously detected in Africa (Betacoronavirus-b) or in Europe (Alphacoronavirus & Betacoronavirus-b). These findings illuminate the origin and the evolutionary history of the SARS-CoV group found in bats by pushing forward the hypothesis of a Betacoronavirus spill-over from Hipposideridae to Rhinolophidae and then from Rhinolophidae to civets and Human. All reported Betacoronaviruses-b (SARS-CoV group) of Hipposideridae and Rhinolophidae respectively cluster in two groups despite their broad geographic distribution and the sympatry of their hosts, which is in favor of an ancient and genetically independent evolution of Betacoronavirus-b clusters in these families. Moreover, despite its probable pathogenicity, we found that a Betacoronavirus-b can persistently infect a medium-sized hipposiderid bat colony. These findings illustrate the importance of the host phylogeny and the host/pathogen ecological interactions in the description and the understanding of pathogen emergence. The host's phylogeny, biogeography and behaviour, combined with already described roles of pathogen plasticity and anthropic changes are likely to be co-factors of disease emergence. Elucidating the common ancestor of Hipposideridae and Rhinolophidae is key to understanding the evolutionary history of actual betacoronaviruses and therefore to get an insight of the deep origin of SARS-CoV.
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Affiliation(s)
- Meriadeg Ar Gouilh
- Institut Pasteur, CIBU, Department Infection and Epidemiology, 75724 Paris, France
- Center of Excellence for Vectors and Vector-Borne Diseases, Mahidol University at Salaya, Nakhon Pathom, Thailand
| | | | | | - Emma Teeling
- School of Biological and Environmental Sciences, University College Dublin, Dublin, Ireland
| | - Pattamaporn Kittayapong
- Center of Excellence for Vectors and Vector-Borne Diseases, Mahidol University at Salaya, Nakhon Pathom, Thailand
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27
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Affiliation(s)
- David S C Hui
- Division of Respiratory Medicine, Stanley Ho Center for Emerging Infectious Diseases, Prince of Wales Hospital, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.
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Chen SC, Olsthoorn RCL. Group-specific structural features of the 5'-proximal sequences of coronavirus genomic RNAs. Virology 2010; 401:29-41. [PMID: 20202661 PMCID: PMC7111916 DOI: 10.1016/j.virol.2010.02.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 01/06/2010] [Accepted: 02/05/2010] [Indexed: 01/24/2023]
Abstract
Global predictions of the secondary structure of coronavirus (CoV) 5′ untranslated regions and adjacent coding sequences revealed the presence of conserved structural elements. Stem loops (SL) 1, 2, 4, and 5 were predicted in all CoVs, while the core leader transcription-regulating sequence (L-TRS) forms SL3 in only some CoVs. SL5 in group I and II CoVs, with the exception of group IIa CoVs, is characterized by the presence of a large sequence insertion capable of forming hairpins with the conserved 5′-UUYCGU-3′ loop sequence. Structure probing confirmed the existence of these hairpins in the group I Human coronavirus-229E and the group II Severe acute respiratory syndrome coronavirus (SARS-CoV). In general, the pattern of the 5′ cis-acting elements is highly related to the lineage of CoVs, including features of the conserved hairpins in SL5. The function of these conserved hairpins as a putative packaging signal is discussed.
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Affiliation(s)
- Shih-Cheng Chen
- Leiden Institute of Chemistry, Department of Molecular Genetics, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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29
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Enjuanes L, Dediego ML, Alvarez E, Deming D, Sheahan T, Baric R. Vaccines to prevent severe acute respiratory syndrome coronavirus-induced disease. Virus Res 2008; 133:45-62. [PMID: 17416434 PMCID: PMC2633062 DOI: 10.1016/j.virusres.2007.01.021] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Accepted: 01/04/2007] [Indexed: 01/19/2023]
Abstract
An important effort has been performed after the emergence of severe acute respiratory syndrome (SARS) epidemic in 2003 to diagnose and prevent virus spreading. Several types of vaccines have been developed including inactivated viruses, subunit vaccines, virus-like particles (VLPs), DNA vaccines, heterologous expression systems, and vaccines derived from SARS-CoV genome by reverse genetics. This review describes several aspects essential to develop SARS-CoV vaccines, such as the correlates of protection, virus serotypes, vaccination side effects, and bio-safeguards that can be engineered into recombinant vaccine approaches based on the SARS-CoV genome. The production of effective and safe vaccines to prevent SARS has led to the development of promising vaccine candidates, in contrast to the design of vaccines for other coronaviruses, that in general has been less successful. After preclinical trials in animal models, efficacy and safety evaluation of the most promising vaccine candidates described has to be performed in humans.
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Affiliation(s)
- Luis Enjuanes
- Centro Nacional de Biotecnología (CNB), CSIC, Campus Universidad Autónoma, Cantoblanco, Darwin 3, 28049 Madrid, Spain.
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30
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Lam TTY, Hon CC, Lam PY, Yip CW, Zeng F, Leung FCC. Comments to the predecessor of human SARS coronavirus in 2003-2004 epidemic. Vet Microbiol 2007; 126:390-3. [PMID: 17884305 PMCID: PMC7117273 DOI: 10.1016/j.vetmic.2007.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Revised: 07/28/2007] [Accepted: 08/10/2007] [Indexed: 12/03/2022]
Affiliation(s)
| | | | | | | | | | - Frederick Chi-Ching Leung
- Corresponding author at: 5N-01, 5/F, North Wing, Kadoorie Biological Science Building, The University of Hong Kong, HKSAR, China. Tel.: +852 2299 0817; fax: +852 2857 4672.
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31
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Abstract
In this review, we summarize the researches on animal reservoirs of the SARS coronavirus (SARS-CoV). Masked palm civets were suspected as the origin of the SARS outbreak in 2003 and was confirmed as the direct origin of SARS cases with mild symptom in 2004. Sequence analysis of the SARS-CoV-like virus in masked palm civets indicated that they were highly homologous to human SARS-CoV with nt identity over 99.6%, indicating the virus has not been circulating in the population of masked palm civets for a very long time. Alignment of 10 complete viral genome sequences from masked palm civets with those of human SARS-CoVs revealed 26 conserved single-nucleotide variations (SNVs) in the viruses from masked palm civets. These conserved SNVs were gradually lost from the genomes of viruses isolated from the early phase to late phase human patients of the 2003 SARS epidemic. In 2005, horseshoe bats were identified as the natural reservoir of a group of coronaviruses that are distantly related to SARS-CoV. The genome sequences of bat SARS-like coronavirus had about 88–92% nt identity with that of the SARS-CoV. The prevalence of antibodies and viral RNA in different bat species and the characteristics of the bat SARS-like coronavirus were elucidated. Apart from masked palm civets and bats, 29 other animal species had been tested for the SARS-CoV, and the results are summarized in this paper.
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Affiliation(s)
- Zhengli Shi
- State Key Laboratory of Virology and Joint-Lab of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
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32
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Affiliation(s)
- Stephen J. Seligman
- Department of Microbiology and Immunology, New York Medical College, Valhalla
- Reprints or correspondence: Dr. Stephen J. Seligman, Dept. of Microbiology and Immunology, New York Medical College, Valhalla, NY 10595 ()
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33
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de Souza Luna LK, Heiser V, Regamey N, Panning M, Drexler JF, Mulangu S, Poon L, Baumgarte S, Haijema BJ, Kaiser L, Drosten C. Generic detection of coronaviruses and differentiation at the prototype strain level by reverse transcription-PCR and nonfluorescent low-density microarray. J Clin Microbiol 2007; 45:1049-52. [PMID: 17229859 PMCID: PMC1829107 DOI: 10.1128/jcm.02426-06] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A nonfluorescent low-cost, low-density oligonucleotide array was designed for detecting the whole coronavirus genus after reverse transcription (RT)-PCR. The limit of detection was 15.7 copies/reaction. The clinical detection limit in patients with severe acute respiratory syndrome was 100 copies/sample. In 39 children suffering from coronavirus 229E, NL63, OC43, or HKU1, the sensitivity was equal to that of individual real-time RT-PCRs.
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Affiliation(s)
- Luciano Kleber de Souza Luna
- Clinical Virology Section, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
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34
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Abstract
In February 2003, a severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in humans in Guangdong Province, China, and caused an epidemic that had severe impact on public health, travel, and economic trade. Coronaviruses are worldwide in distribution, highly infectious, and extremely difficult to control because they have extensive genetic diversity, a short generation time, and a high mutation rate. They can cause respiratory, enteric, and in some cases hepatic and neurological diseases in a wide variety of animals and humans. An enormous, previously unrecognized reservoir of coronaviruses exists among animals. Because coronaviruses have been shown, both experimentally and in nature, to undergo genetic mutations and recombination at a rate similar to that of influenza viruses, it is not surprising that zoonosis and host switching that leads to epidemic diseases have occurred among coronaviruses. Analysis of coronavirus genomic sequence data indicates that SARS-CoV emerged from an animal reservoir. Scientists examining coronavirus isolates from a variety of animals in and around Guangdong Province reported that SARS-CoV has similarities with many different coronaviruses including avian coronaviruses and SARS-CoV-like viruses from a variety of mammals found in live-animal markets. Although a SARS-like coronavirus isolated from a bat is thought to be the progenitor of SARS-CoV, a lack of genomic sequences for the animal coronaviruses has prevented elucidation of the true origin of SARS-CoV. Sequence analysis of SARS-CoV shows that the 5' polymerase gene has a mammalian ancestry; whereas the 3' end structural genes (excluding the spike glycoprotein) have an avian origin. Spike glycoprotein, the host cell attachment viral surface protein, was shown to be a mosaic of feline coronavirus and avian coronavirus sequences resulting from a recombination event. Based on phylogenetic analysis designed to elucidate evolutionary links among viruses, SARS-CoV is believed to have branched from the modern Group 2 coronaviruses, suggesting that it evolved relatively rapidly. This is significant because SARS-CoV is likely still circulating in an animal reservoir (or reservoirs) and has the potential to quickly emerge and cause a new epidemic.
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Affiliation(s)
- Mark W Jackwood
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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35
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Wang ZG, Xu SP, Zhang YJ, Bao QY. Genetic distance of SARS coronavirus from the recent natural case. Vet Microbiol 2006; 120:167-72. [PMID: 17141432 PMCID: PMC7117388 DOI: 10.1016/j.vetmic.2006.10.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Revised: 07/26/2006] [Accepted: 10/10/2006] [Indexed: 11/25/2022]
Abstract
Phylogenetic analysis of SARS coronavirus isolates based on the spike gene and protein sequence using Neighbor-Joining, maximum likelihood and Bayesian inference methods indicated that a recent human SARS-CoV isolate was closer to some human SARS-CoV isolates from earlier epidemic phase than to the SARS-CoV-like viruses isolated from wild animals during previous epidemic phase. A reasonable judgment based on phylogenetic relationship and sequence variations it is likely that the recent human SARS-CoV isolate is closer to an unknown SARS-CoV predecessor.
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Affiliation(s)
- Zhi-Gang Wang
- Zhejiang Provincial Center for Disease Prevention and Control, 17 Laozhedazhi Road, Hangzhou 310009, China.
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36
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Tang JW, Cheung JLK, Chu IMT, Sung JJY, Peiris M, Chan PKS. The large 386-nt deletion in SARS-associated coronavirus: evidence for quasispecies? J Infect Dis 2006; 194:808-13. [PMID: 16941348 PMCID: PMC7109873 DOI: 10.1086/507044] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Accepted: 05/10/2006] [Indexed: 01/15/2023] Open
Abstract
The severe acute respiratory syndrome–associated coronavirus (SARS-CoV) is reported to have deletions of various sizes. Recently, the large 386-nucleotide deletion (L386del) comprising nucleotide positions 27719-28104 and spanning open reading frames 9–11 has been reported in the genomes of some human isolates from Hong Kong. In this study, archived specimens from 71 patients with SARS who were admitted to the New Territory East Cluster Hospitals in Hong Kong were analyzed to determine whether the L386del variant of SARS-CoV was present. There was no clear relationship between the presence of the L386del variant and SARS clinical severity as defined either by the need for intensive-care therapy and/or ventilation or by death. One patient had evidence of both the L386del variant and the wild-type variant in the same clinical specimen, supporting the idea that SARS-CoV exists as a quasispecies in some patients, although the clinical significance of these quasispecies remains unclear
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Affiliation(s)
| | | | | | - Joseph J. Y. Sung
- Medicine and Therapeutics, Centre for Emerging Infectious Diseases, and
- School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, and
| | - Malik Peiris
- Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Paul K. S. Chan
- Microbiology and
- School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, and
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37
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Sulaiman IM, Liu X, Frace M, Sulaiman N, Olsen-Rasmussen M, Neuhaus E, Rota PA, Wohlhueter RM. Evaluation of affymetrix severe acute respiratory syndrome resequencing GeneChips in characterization of the genomes of two strains of coronavirus infecting humans. Appl Environ Microbiol 2006; 72:207-11. [PMID: 16391044 PMCID: PMC1352236 DOI: 10.1128/aem.72.1.207-211.2006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome (SARS) was discovered during a recent global outbreak of atypical pneumonia. A number of immunologic and molecular studies of the clinical samples led to the conclusion that a novel coronavirus (SARS-CoV) was associated with the outbreak. Later, a SARS resequencing GeneChip was developed by Affymetrix to characterize the complete genome of SARS-CoV on a single GeneChip. The present study was carried out to evaluate the performance of SARS resequencing GeneChips. Two human SARS-CoV strains (CDC#200301157 and Urbani) were resequenced by the SARS GeneChips. Five overlapping PCR amplicons were generated for each strain and hybridized with these GeneChips. The successfully hybridized GeneChips generated nucleotide sequences of nearly complete genomes for the two SARS-CoV strains with an average call rate of 94.6%. Multiple alignments of nucleotide sequences obtained from SARS GeneChips and conventional sequencing revealed full concordance. Furthermore, the GeneChip-based analysis revealed no additional polymorphic sites. The results of this study suggest that GeneChip-based genome characterization is fast and reproducible. Thus, SARS resequencing GeneChips may be employed as an alternate tool to obtain genome sequences of SARS-CoV strains pathogenic for humans in order to further understand the transmission dynamics of these viruses.
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Affiliation(s)
- Irshad M Sulaiman
- Biotechnology Core Facility Branch, Scientific Resources Program, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Mailstop G-36, 1600 Clifton Road, Atlanta, GA 30333, USA.
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38
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Kim OJ, Lee DH, Lee CH. Close relationship between SARS-coronavirus and group 2 coronavirus. J Microbiol 2006; 44:83-91. [PMID: 16554722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The sudden appearance and potential lethality of severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) in humans has resulted in a focusing of new attention on the determination of both its origins and evolution. The relationship existing between SARS-CoV and other groups of coronaviruses was determined via analyses of phylogenetic trees and comparative genomic analyses of the coronavirus genes: polymerase (Orf1ab), spike (S), envelope (E), membrane (M) and nucleocapsid (N). Although the coronaviruses are traditionally classed into 3 groups, with SARS-CoV forming a 4th group, the phylogenetic position and origins of SARS-CoV remain a matter of some controversy. Thus, we conducted extensive phylogenetic analyses of the genes common to all coronavirus groups, using the Neighbor-joining, Maximum-likelihood, and Bayesian methods. Our data evidenced largely identical topology for all of the obtained phylogenetic trees, thus supporting the hypothesis that the relationship existing between SARS-CoV and group 2 coronavirus is a monophyletic one. Additional comparative genomic studies, including sequence similarity and protein secondary structure analyses, suggested that SARS-CoV may bear a closer relationship with group 2 than with the other coronavirus groups. Although our data strongly suggest that group 2 coronaviruses are most closely related with SARS-CoV, further and more detailed analyses may provide us with an increased amount of information regarding the origins and evolution of the coronaviruses, most notably SARS-CoV.
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Affiliation(s)
- Ok Ju Kim
- Division of Life Sciences and Research Institute for Biotechnology, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
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39
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Abstract
Measures of genetic distance based on alignment methods are confined to studying sequences that are conserved and identifiable in all organisms under study. A number of alignment-free techniques based on either statistical linguistics or information theory have been developed to overcome the limitations of alignment methods. We present a novel alignment-free approach to measuring the similarity among genetic sequences that incorporates elements from both word rank order-frequency statistics and information theory. We first validate this method on the human influenza A viral genomes as well as on the human mitochondrial DNA database. We then apply the method to study the origin of the SARS coronavirus. We find that the majority of the SARS genome is most closely related to group 1 coronaviruses, with smaller regions of matches to sequences from groups 2 and 3. The information based similarity index provides a new tool to measure the similarity between datasets based on their information content and may have a wide range of applications in the large-scale analysis of genomic databases.
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Affiliation(s)
- Albert C-C Yang
- Cardiovascular Division and Margret and H.A. Rey Institute for Nonlinear Dynamics in Medicine, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts 02215, USA
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40
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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41
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42
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Kan B, Wang M, Jing H, Xu H, Jiang X, Yan M, Liang W, Zheng H, Wan K, Liu Q, Cui B, Xu Y, Zhang E, Wang H, Ye J, Li G, Li M, Cui Z, Qi X, Chen K, Du L, Gao K, Zhao YT, Zou XZ, Feng YJ, Gao YF, Hai R, Yu D, Guan Y, Xu J. Molecular evolution analysis and geographic investigation of severe acute respiratory syndrome coronavirus-like virus in palm civets at an animal market and on farms. J Virol 2005; 79:11892-900. [PMID: 16140765 PMCID: PMC1212604 DOI: 10.1128/jvi.79.18.11892-11900.2005] [Citation(s) in RCA: 252] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Massive numbers of palm civets were culled to remove sources for the reemergence of severe acute respiratory syndrome (SARS) in Guangdong Province, China, in January 2004, following SARS coronavirus detection in market animals. The virus was identified in all 91 palm civets and 15 raccoon dogs of animal market origin sampled prior to culling, but not in 1,107 palm civets later sampled at 25 farms, spread over 12 provinces, which were claimed to be the source of traded animals. Twenty-seven novel signature variation residues (SNVs) were identified on the spike gene and were analyzed for their phylogenetic relationships, based on 17 sequences obtained from animals in our study and from other published studies. Analysis indicated that the virus in palm civets at the live-animal market had evolved to infect humans. The evolutionary starting point was a prototype group consisting of three viral sequences of animal origin. Initially, seven SNV sites caused six amino acid changes, at positions 147, 228, 240, 479, 821, and 1080 of the spike protein, to generate low-pathogenicity viruses. One of these was linked to the first SARS patient in the 2003-2004 period. A further 14 SNVs caused 11 amino acid residue changes, at positions 360, 462, 472, 480, 487, 609, 613, 665, 743, 765, and 1163. The resulting high-pathogenicity groups were responsible for infections during the so-called early-phase epidemic of 2003. Finally, the remaining six SNVs caused four amino acid changes, at positions 227, 244, 344, and 778, which resulted in the group of viruses responsible for the global epidemic.
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Affiliation(s)
- Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control (China CDC), Chinese Center for Disease Control and Prevention, P.O. Box 5, Changping, Beijing 102206, People's Republic of China
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43
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Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, Wang H, Crameri G, Hu Z, Zhang H, Zhang J, McEachern J, Field H, Daszak P, Eaton BT, Zhang S, Wang LF. Bats are natural reservoirs of SARS-like coronaviruses. Science 2005; 310:676-9. [PMID: 16195424 DOI: 10.1126/science.1118391] [Citation(s) in RCA: 1715] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Severe acute respiratory syndrome (SARS) emerged in 2002 to 2003 in southern China. The origin of its etiological agent, the SARS coronavirus (SARS-CoV), remains elusive. Here we report that species of bats are a natural host of coronaviruses closely related to those responsible for the SARS outbreak. These viruses, termed SARS-like coronaviruses (SL-CoVs), display greater genetic variation than SARS-CoV isolated from humans or from civets. The human and civet isolates of SARS-CoV nestle phylogenetically within the spectrum of SL-CoVs, indicating that the virus responsible for the SARS outbreak was a member of this coronavirus group.
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Affiliation(s)
- Wendong Li
- Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
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44
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Lau SKP, Woo PCY, Li KSM, Huang Y, Tsoi HW, Wong BHL, Wong SSY, Leung SY, Chan KH, Yuen KY. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci U S A 2005; 102:14040-5. [PMID: 16169905 PMCID: PMC1236580 DOI: 10.1073/pnas.0506735102] [Citation(s) in RCA: 1079] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Indexed: 11/18/2022] Open
Abstract
Although the finding of severe acute respiratory syndrome coronavirus (SARS-CoV) in caged palm civets from live animal markets in China has provided evidence for interspecies transmission in the genesis of the SARS epidemic, subsequent studies suggested that the civet may have served only as an amplification host for SARS-CoV. In a surveillance study for CoV in noncaged animals from the wild areas of the Hong Kong Special Administration Region, we identified a CoV closely related to SARS-CoV (bat-SARS-CoV) from 23 (39%) of 59 anal swabs of wild Chinese horseshoe bats (Rhinolophus sinicus) by using RT-PCR. Sequencing and analysis of three bat-SARS-CoV genomes from samples collected at different dates showed that bat-SARS-CoV is closely related to SARS-CoV from humans and civets. Phylogenetic analysis showed that bat-SARS-CoV formed a distinct cluster with SARS-CoV as group 2b CoV, distantly related to known group 2 CoV. Most differences between the bat-SARS-CoV and SARS-CoV genomes were observed in the spike genes, ORF 3 and ORF 8, which are the regions where most variations also were observed between human and civet SARS-CoV genomes. In addition, the presence of a 29-bp insertion in ORF 8 of bat-SARS-CoV genome, not in most human SARS-CoV genomes, suggests that it has a common ancestor with civet SARS-CoV. Antibody against recombinant bat-SARS-CoV nucleocapsid protein was detected in 84% of Chinese horseshoe bats by using an enzyme immunoassay. Neutralizing antibody to human SARS-CoV also was detected in bats with lower viral loads. Precautions should be exercised in the handling of these animals.
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Affiliation(s)
- Susanna K P Lau
- Department of Microbiology, Research Centre of Infection and Immunology, State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
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45
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Wang XW, Li JS, Guo TK, Zhen B, Kong QX, Yi B, Li Z, Song N, Jin M, Xiao WJ, Zhu XM, Gu CQ, Yin J, Wei W, Yao W, Liu C, Li JF, Ou GR, Wang MN, Fang TY, Wang GJ, Qiu YH, Wu HH, Chao FH, Li JW. Concentration and detection of SARS coronavirus in sewage from Xiao Tang Shan Hospital and the 309th Hospital. J Virol Methods 2005; 128:156-61. [PMID: 15964082 PMCID: PMC7112879 DOI: 10.1016/j.jviromet.2005.03.022] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 03/21/2005] [Accepted: 03/22/2005] [Indexed: 12/17/2022]
Abstract
The transmission of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is associated with close contact to SARS patients and droplet secretions of those patients. The finding of positive RT-PCR results from stools of SARS patients suggests that stools of SARS patients or sewage containing stools of patients could transmit SARS-CoV. We used a novel style of electropositive filter media particle to concentrate the SARS-CoV from the sewage of two hospitals receiving SARS patients in Beijing. We also used cell culture, RT-PCR and gene sequencing to detect and identify the viruses from sewage. No infectious SARS-CoV contamination was found in any of the samples collected, but the nucleic acid of SARS-CoV could be detected in the sewage from the two hospitals before disinfection. While the RNA was only detected in three samples from the 309th Hospital, the others were negative after disinfection. These findings provide strong evidence that SARS-CoV can be excreted through the stool/urine of patients into sewage system, thus making the sewage system a possible route of transmission.
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Affiliation(s)
- Xin-Wei Wang
- Tianjin Institute of Environment and Health, 1 Da Li Road, Tianjin 300050, PR China
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46
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Wu D, Tu C, Xin C, Xuan H, Meng Q, Liu Y, Yu Y, Guan Y, Jiang Y, Yin X, Crameri G, Wang M, Li C, Liu S, Liao M, Feng L, Xiang H, Sun J, Chen J, Sun Y, Gu S, Liu N, Fu D, Eaton BT, Wang LF, Kong X. Civets are equally susceptible to experimental infection by two different severe acute respiratory syndrome coronavirus isolates. J Virol 2005; 79:2620-5. [PMID: 15681462 PMCID: PMC546564 DOI: 10.1128/jvi.79.4.2620-2625.2005] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Severe acute respiratory syndrome (SARS) was caused by a novel virus now known as SARS coronavirus (SARS-CoV). The discovery of SARS-CoV-like viruses in masked palm civets (Paguma larvata) raises the possibility that civets play a role in SARS-CoV transmission. To test the susceptibility of civets to experimental infection by different SARS-CoV isolates, 10 civets were inoculated with two human isolates of SARS-CoV, BJ01 (with a 29-nucleotide deletion) and GZ01 (without the 29-nucleotide deletion). All inoculated animals displayed clinical symptoms, such as fever, lethargy, and loss of aggressiveness, and the infection was confirmed by virus isolation, detection of viral genomic RNA, and serum-neutralizing antibodies. Our data show that civets were equally susceptible to SARS-CoV isolates GZ01 and BJ01.
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Affiliation(s)
- Donglai Wu
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin 150001, China
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Lu SN, Jiang DDS, Liu JW, Lin MC, Chen CL, Su IJ, Chen SS. Outbreak of severe acute respiratory syndrome in southern Taiwan, 2003. Am J Trop Med Hyg 2005; 73:423-7. [PMID: 16103615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
This study describes the epidemiologic features of the severe acute respiratory syndrome (SARS) outbreak in southern Taiwan in 2003. According to the official files of reported cases of SARS from February 21 to June 19, 2003, there were 586 cases in southern Taiwan. Symptom onset occurred between February 21 and June 19 in reported cases, between March 13 and May 30 in probable cases, and between March 17 and May 23 in polymerase chain reaction (PCR)-positive probable cases. Dates of symptom onset were earliest for six imported cases, followed by 53 cases related to nosocomial infections and 51 cases without known sources of infection. The positive rates of the PCR for these three groups decreased from 50.0% to 28.3% to 3.9% , respectively (P < 0.001, by chi-square test for linear trend). Three other cases resulted from exposure to contaminated hospitals in northern Taiwan, one of which was the index case of the nosocomial infection. Imported cases following nosocomial infection were the major cause of SARS infections in southern Taiwan. Due to the low positive rate of the PCR for SARS coronavirus, and the low positive predictive value of reported cases, the factuality of cases with unknown sources of infection should be further verified.
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Affiliation(s)
- Sheng-Nan Lu
- Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
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48
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Oxford JS, Balasingam S, Chan C, Catchpole A, Lambkin R. New antiviral drugs, vaccines and classic public health interventions against SARS coronavirus. Antivir Chem Chemother 2005; 16:13-21. [PMID: 15739618 DOI: 10.1177/095632020501600102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Severe acute respiratory syndrome (SARS) is caused by one of two recently discovered coronaviruses. The virus is emergent from South East (SE) Asian mammals: either the civet cat, a related species or a rat species. The virus has a long incubation period and low reproduction number (R0 value) and hence the first outbreak in 2004 was controlled by hygiene and quarantine. However, the healthcare system was compromised and the economic cost was extremely high. Fortunately, the virus is easily cultivated in Vero E6 cells and therefore the search for new antivirals and vaccines was initiated within weeks of the discovery of the virus using classic techniques of cell culture and electron microscopy. Molecular diagnostics facilitated rapid and accurate diagnosis, a key factor in containing the outbreak. The broad-spectrum molecule ribavirin was used in SE Asia in infected patients alongside corticosteroids. In retrospect, many patients survived due to careful nursing. The only currently accepted intervention is interferon. Coronavirus replicon systems should facilitate rapid screening of new inhibitors and the complex mechanism of viral replication will ensure that drugs are developed against at least five molecular targets, in particular the viral protease.
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Affiliation(s)
- John S Oxford
- Retroscreen Virology Ltd, Centre for Infectious Diseases, Barts, UK.
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49
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Affiliation(s)
| | | | - Yu-kwan Tong
- The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | | | - Paul K.S. Chan
- The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Guo-ping Zhao
- The Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Y.M. Dennis Lo
- The Chinese University of Hong Kong, Shatin, Hong Kong SAR
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50
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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