1
|
Wang X, Chen Y, Qi C, Li F, Zhang Y, Zhou J, Wu H, Zhang T, Qi A, Ouyang H, Xie Z, Pang D. Mechanism, structural and functional insights into nidovirus-induced double-membrane vesicles. Front Immunol 2024; 15:1340332. [PMID: 38919631 PMCID: PMC11196420 DOI: 10.3389/fimmu.2024.1340332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/22/2024] [Indexed: 06/27/2024] Open
Abstract
During infection, positive-stranded RNA causes a rearrangement of the host cell membrane, resulting in specialized membrane structure formation aiding viral genome replication. Double-membrane vesicles (DMVs), typical structures produced by virus-induced membrane rearrangements, are platforms for viral replication. Nidoviruses, one of the most complex positive-strand RNA viruses, have the ability to infect not only mammals and a few birds but also invertebrates. Nidoviruses possess a distinctive replication mechanism, wherein their nonstructural proteins (nsps) play a crucial role in DMV biogenesis. With the participation of host factors related to autophagy and lipid synthesis pathways, several viral nsps hijack the membrane rearrangement process of host endoplasmic reticulum (ER), Golgi apparatus, and other organelles to induce DMV formation. An understanding of the mechanisms of DMV formation and its structure and function in the infectious cycle of nidovirus may be essential for the development of new and effective antiviral strategies in the future.
Collapse
Affiliation(s)
- Xi Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Yiwu Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Chunyun Qi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Feng Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Yuanzhu Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Jian Zhou
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Heyong Wu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Tianyi Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Aosi Qi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Hongsheng Ouyang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
- Chongqing Research Institute, Jilin University, Chongqing, China
- Center for Animal Science and Technology Research, Chongqing Jitang Biotechnology Research Institute Co., Ltd, Chongqing, China
| | - Zicong Xie
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
- Chongqing Research Institute, Jilin University, Chongqing, China
| | - Daxin Pang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun, Jilin, China
- Chongqing Research Institute, Jilin University, Chongqing, China
- Center for Animal Science and Technology Research, Chongqing Jitang Biotechnology Research Institute Co., Ltd, Chongqing, China
| |
Collapse
|
2
|
Guo H, Ha S, Botten JW, Xu K, Zhang N, An Z, Strohl WR, Shiver JW, Fu TM. SARS-CoV-2 Omicron: Viral Evolution, Immune Evasion, and Alternative Durable Therapeutic Strategies. Viruses 2024; 16:697. [PMID: 38793580 PMCID: PMC11125895 DOI: 10.3390/v16050697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Since the SARS-CoV-2 Omicron virus has gained dominance worldwide, its continual evolution with unpredictable mutations and patterns has revoked all authorized immunotherapeutics. Rapid viral evolution has also necessitated several rounds of vaccine updates in order to provide adequate immune protection. It remains imperative to understand how Omicron evolves into different subvariants and causes immune escape as this could help reevaluate the current intervention strategies mostly implemented in the clinics as emergency measures to counter the pandemic and, importantly, develop new solutions. Here, we provide a review focusing on the major events of Omicron viral evolution, including the features of spike mutation that lead to immune evasion against monoclonal antibody (mAb) therapy and vaccination, and suggest alternative durable options such as the ACE2-based experimental therapies superior to mAbs to address this unprecedented evolution of Omicron virus. In addition, this type of unique ACE2-based virus-trapping molecules can counter all zoonotic SARS coronaviruses, either from unknown animal hosts or from established wild-life reservoirs of SARS-CoV-2, and even seasonal alpha coronavirus NL63 that depends on human ACE2 for infection.
Collapse
Affiliation(s)
- Hailong Guo
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Sha Ha
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Jason W. Botten
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Kai Xu
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | | | | | | |
Collapse
|
3
|
Zhu R, Cao R, Wang L, Gong Y, Cheng Q, Long H, Xia D, Song Q, Xia Z, Liu M, Du H, Song J, Han J, Gao C. Seasonal human coronavirus NL63 epidemics in children in Guilin, China, reveal the emergence of a new subgenotype of HCoV-NL63. Front Cell Infect Microbiol 2024; 14:1378804. [PMID: 38736749 PMCID: PMC11082418 DOI: 10.3389/fcimb.2024.1378804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/11/2024] [Indexed: 05/14/2024] Open
Abstract
Introduction Seasonal human coronavirus NL63 (HCoV-NL63) is a frequently encountered virus linked to mild upper respiratory infections. However, its potential to cause more severe or widespread disease remains an area of concern. This study aimed to investigate a rare localized epidemic of HCoV-NL63-induced respiratory infections among pediatric patients in Guilin, China, and to understand the viral subtype distribution and genetic characteristics. Methods In this study, 83 pediatric patients hospitalized with acute respiratory infections and positive for HCoV-NL63 were enrolled. Molecular analysis was conducted to identify the viral subgenotypes and to assess genetic variations in the receptor-binding domain of the spiking protein. Results Among the 83 HCoV-NL63-positive children, three subgenotypes were identified: C4, C3, and B. Notably, 21 cases exhibited a previously unreported subtype, C4. Analysis of the C4 subtype revealed a unique amino acid mutation (I507L) in the receptor-binding domain of the spiking protein, which was also observed in the previously reported C3 genotype. This mutation may suggest potential increases in viral transmissibility and pathogenicity. Discussion The findings of this study highlight the rapid mutation dynamics of HCoV-NL63 and its potential for increased virulence and epidemic transmission. The presence of a unique mutation in the C4 subtype, shared with the C3 genotype, raises concerns about the virus's evolving nature and its potential public health implications. This research contributes valuable insights into the understanding of HCoV-NL63's epidemiology and pathogenesis, which is crucial for effective disease prevention and control strategies. Future studies are needed to further investigate the biological significance of the observed mutation and its potential impact on the virus's transmissibility and pathogenicity.
Collapse
Affiliation(s)
- Renhe Zhu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Rundong Cao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lulu Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yue Gong
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qian Cheng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hu Long
- Epidemic Prevention and Control Department, Guilin Center for Disease Control and Prevention, Guilin, China
| | - Dong Xia
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qinqin Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhiqiang Xia
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mi Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - HaiJun Du
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Juan Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Han
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chen Gao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| |
Collapse
|
4
|
Zhang M, Leong MW, Mitch WA, Blish CA, Boehm A. Persistence and free chlorine disinfection of human coronaviruses and their surrogates in water. Appl Environ Microbiol 2024; 90:e0005524. [PMID: 38511945 PMCID: PMC11022552 DOI: 10.1128/aem.00055-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The coronavirus disease 2019 pandemic illustrates the importance of understanding the behavior and control of human pathogenic viruses in the environment. Exposure via water (drinking, bathing, and recreation) is a known route of transmission of viruses to humans, but the literature is relatively void of studies on the persistence of many viruses, especially coronaviruses, in water and their susceptibility to chlorine disinfection. To fill that knowledge gap, we evaluated the persistence and free chlorine disinfection of human coronavirus OC43 (HCoV-OC43) and its surrogates, murine hepatitis virus (MHV) and porcine transmissible gastroenteritis virus (TGEV), in drinking water and laboratory buffer using cell culture methods. The decay rate constants of human coronavirus and its surrogates in water varied, depending on virus and water matrix. In drinking water without disinfectant addition, MHV showed the largest decay rate constant (estimate ± standard error, 2.25 ± 0.09 day-1) followed by HCoV-OC43 (0.99 ± 0.12 day-1) and TGEV (0.65 ± 0.06 day-1), while in phosphate buffer without disinfectant addition, HCoV-OC43 (0.51 ± 0.10 day-1) had a larger decay rate constant than MHV (0.28 ± 0.03 day-1) and TGEV (0.24 ± 0.02 day-1). Upon free chlorine disinfection, the inactivation rates of coronaviruses were independent of free chlorine concentration and were not affected by water matrix, though they still varied between viruses. TGEV showed the highest susceptibility to free chlorine disinfection with the inactivation rate constant of 113.50 ± 7.50 mg-1 min-1 L, followed by MHV (81.33 ± 4.90 mg-1 min-1 L) and HCoV-OC43 (59.42 ± 4.41 mg-1 min-1 L). IMPORTANCE This study addresses an important knowledge gap on enveloped virus persistence and disinfection in water. Results have immediate practical applications for shaping evidence-based water policies, particularly in the development of disinfection strategies for pathogenic virus control.
Collapse
Affiliation(s)
- Mengyang Zhang
- Department of Civil and Environmental Engineering, School of Engineering and Doerr School of Sustainability, Stanford University, Stanford, California, USA
| | - Michelle Wei Leong
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - William A. Mitch
- Department of Civil and Environmental Engineering, School of Engineering and Doerr School of Sustainability, Stanford University, Stanford, California, USA
| | - Catherine A. Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Alexandria Boehm
- Department of Civil and Environmental Engineering, School of Engineering and Doerr School of Sustainability, Stanford University, Stanford, California, USA
| |
Collapse
|
5
|
Guo H, Cho B, Hinton PR, He S, Yu Y, Ramesh AK, Sivaccumar JP, Ku Z, Campo K, Holland S, Sachdeva S, Mensch C, Dawod M, Whitaker A, Eisenhauer P, Falcone A, Honce R, Botten JW, Carroll SF, Keyt BA, Womack AW, Strohl WR, Xu K, Zhang N, An Z, Ha S, Shiver JW, Fu TM. An ACE2 decamer viral trap as a durable intervention solution for current and future SARS-CoV. Emerg Microbes Infect 2023; 12:2275598. [PMID: 38078382 PMCID: PMC10768737 DOI: 10.1080/22221751.2023.2275598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/19/2023] [Indexed: 12/18/2023]
Abstract
The capacity of SARS-CoV-2 to evolve poses challenges to conventional prevention and treatment options such as vaccination and monoclonal antibodies, as they rely on viral receptor binding domain (RBD) sequences from previous strains. Additionally, animal CoVs, especially those of the SARS family, are now appreciated as a constant pandemic threat. We present here a new antiviral approach featuring inhalation delivery of a recombinant viral trap composed of ten copies of angiotensin-converting enzyme 2 (ACE2) fused to the IgM Fc. This ACE2 decamer viral trap is designed to inhibit SARS-CoV-2 entry function, regardless of viral RBD sequence variations as shown by its high neutralization potency against all known SARS-CoV-2 variants, including Omicron BQ.1, BQ.1.1, XBB.1 and XBB.1.5. In addition, it demonstrates potency against SARS-CoV-1, human NL63, as well as bat and pangolin CoVs. The multivalent trap is effective in both prophylactic and therapeutic settings since a single intranasal dosing confers protection in human ACE2 transgenic mice against viral challenges. Lastly, this molecule is stable at ambient temperature for more than twelve weeks and can sustain physical stress from aerosolization. These results demonstrate the potential of a decameric ACE2 viral trap as an inhalation solution for ACE2-dependent coronaviruses of current and future pandemic concerns.
Collapse
Affiliation(s)
| | | | | | - Sijia He
- IGM Biosciences, Mountain View, CA, USA
| | | | - Ashwin Kumar Ramesh
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jwala Priyadarsini Sivaccumar
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | | | | | | | | | - Annalis Whitaker
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT, USA
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Philip Eisenhauer
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Allison Falcone
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Rebekah Honce
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
| | - Jason W. Botten
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont, Burlington, VT, USA
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | | | | | | | | | - Kai Xu
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sha Ha
- IGM Biosciences, Mountain View, CA, USA
| | | | | |
Collapse
|
6
|
Watanabe N, Hirose R, Yamauchi K, Miyazaki H, Bandou R, Yoshida T, Doi T, Inoue K, Dohi O, Yoshida N, Uchiyama K, Ishikawa T, Takagi T, Konishi H, Ikegaya H, Nakaya T, Itoh Y. Evaluation of Environmental Stability and Disinfectant Effectiveness for Human Coronavirus OC43 on Human Skin Surface. Microbiol Spectr 2023; 11:e0238122. [PMID: 36840603 PMCID: PMC10100891 DOI: 10.1128/spectrum.02381-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/04/2023] [Indexed: 02/24/2023] Open
Abstract
The environmental stability of human coronavirus OC43 (HCoV-OC43) on the surface of human skin and the effectiveness of disinfectant against HCoV-OC43, which are important to prevent contact transmission, have not been clarified in previous studies. Using previously generated models, we evaluated HCoV-OC43 stability and disinfection effectiveness. Then we compared the results with those for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The median survival time of HCoV-OC43 on the surface of human skin was 24.6 h (95% confidence interval, 19.7 to 29.6 h), which was higher than that of SARS-CoV-2 (10.8 h). Although the in vitro disinfectant effectiveness evaluation showed that HCoV-OC43 has a higher ethanol resistance than SARS-CoV-2, HCoV-OC43 on the skin surface was completely inactivated by a minimum of 50% ethanol within 5 s (the log reduction values were >4.0). Moreover, 1.0% chlorhexidine gluconate and 0.2% benzalkonium chloride showed relatively high disinfectant effectiveness, and the log reduction values when these disinfectants were applied for 15 s were >3.0. HCoV-OC43 is highly stable on the skin surface, which may increase the risk of contact transmission. Although HCoV-OC43 has relatively high ethanol resistance, appropriate hand hygiene practices with current alcohol-based disinfectants sufficiently reduce the risk of contact transmission. IMPORTANCE This study revealed the environmental stability of HCoV-OC43 and disinfectant effectiveness against HCoV-OC43, which had not been demonstrated in previous studies. HCoV-OC43 is highly stable on the surface of human skin, with a survival time of approximately 25 h. High stability of HCoV-OC43 may increase the risk of contact transmission. Furthermore, the in vitro disinfectant effectiveness evaluation showed that HCoV-OC43, which is classified as an envelope virus, has a relatively high ethanol resistance. This finding suggests that disinfectant effectiveness may vary greatly depending on the virus and that each virus targeted for infection control should be evaluated individually. HCoV-OC43 on the skin surface was rapidly inactivated by 50% ethanol, which suggests that appropriate hand hygiene practices with current alcohol-based disinfectants can sufficiently reduce the risk of HCoV-OC43 contact transmission.
Collapse
Affiliation(s)
- Naoto Watanabe
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryohei Hirose
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Katsuma Yamauchi
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hajime Miyazaki
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Risa Bandou
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Forensics Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takuma Yoshida
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Toshifumi Doi
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ken Inoue
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Osamu Dohi
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naohisa Yoshida
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazuhiko Uchiyama
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takeshi Ishikawa
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomohisa Takagi
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hideyuki Konishi
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroshi Ikegaya
- Department of Forensics Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshito Itoh
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| |
Collapse
|
7
|
Zhang Z, Liu W, Zhang S, Wei P, Zhang L, Chen D, Qiu S, Li X, Zhao J, Shi Y, Zhou R, Wang Y, Zhao J. Two novel human coronavirus OC43 genotypes circulating in hospitalized children with pneumonia in China. Emerg Microbes Infect 2021; 11:168-171. [PMID: 34907853 PMCID: PMC8741245 DOI: 10.1080/22221751.2021.2019560] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
HCoV-OC43 is one of the mildly pathogenic coronaviruses with high infection rates in common population. Here, 43 HCoV-OC43 related cases with pneumonia were reported, corresponding genomes of HCoV-OC43 were obtained. Phylogenetic analyses based on complete genome, orf1ab and spike genes revealed that two novel genotypes of HCoV-OC43 have emerged in China. Obvious recombinant events also can be detected in the analysis of the evolutionary dynamics of novel HCoV-OC43 genotypes. Estimated divergence time analysis indicated that the two novel genotypes had apparently independent evolutionary routes. Efforts should be conducted for further investigation of genomic diversity and evolution analysis of mildly pathogenic coronaviruses.
Collapse
Affiliation(s)
- Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Shengnan Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Peilan Wei
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Lu Zhang
- Guangzhou Customs District Technology Centre, Guangzhou, People's Republic of China
| | - Dehui Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Shuyan Qiu
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Xiaobo Li
- Guangzhou Customs District Technology Centre, Guangzhou, People's Republic of China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Yongxia Shi
- Guangzhou Customs District Technology Centre, Guangzhou, People's Republic of China
| | - Rong Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China.,Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China.,Guangzhou Laboratory, Bio-island, Guangzhou, Guangdong, People's Republic of China
| |
Collapse
|
8
|
Islam A, Ferdous J, Islam S, Sayeed MA, Dutta Choudhury S, Saha O, Hassan MM, Shirin T. Evolutionary Dynamics and Epidemiology of Endemic and Emerging Coronaviruses in Humans, Domestic Animals, and Wildlife. Viruses 2021; 13:1908. [PMID: 34696338 PMCID: PMC8537103 DOI: 10.3390/v13101908] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 12/21/2022] Open
Abstract
Diverse coronavirus (CoV) strains can infect both humans and animals and produce various diseases. CoVs have caused three epidemics and pandemics in the last two decades, and caused a severe impact on public health and the global economy. Therefore, it is of utmost importance to understand the emergence and evolution of endemic and emerging CoV diversity in humans and animals. For diverse bird species, the Infectious Bronchitis Virus is a significant one, whereas feline enteric and canine coronavirus, recombined to produce feline infectious peritonitis virus, infects wild cats. Bovine and canine CoVs have ancestral relationships, while porcine CoVs, especially SADS-CoV, can cross species barriers. Bats are considered as the natural host of diverse strains of alpha and beta coronaviruses. Though MERS-CoV is significant for both camels and humans, humans are nonetheless affected more severely. MERS-CoV cases have been reported mainly in the Arabic peninsula since 2012. To date, seven CoV strains have infected humans, all descended from animals. The severe acute respiratory syndrome coronaviruses (SARS-CoV and SARS-CoV-2) are presumed to be originated in Rhinolopoid bats that severely infect humans with spillover to multiple domestic and wild animals. Emerging alpha and delta variants of SARS-CoV-2 were detected in pets and wild animals. Still, the intermediate hosts and all susceptible animal species remain unknown. SARS-CoV-2 might not be the last CoV to cross the species barrier. Hence, we recommend developing a universal CoV vaccine for humans so that any future outbreak can be prevented effectively. Furthermore, a One Health approach coronavirus surveillance should be implemented at human-animal interfaces to detect novel coronaviruses before emerging to humans and to prevent future epidemics and pandemics.
Collapse
Affiliation(s)
- Ariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, VIC 3216, Australia
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Jinnat Ferdous
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia
| | - Shariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Md. Abu Sayeed
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Shusmita Dutta Choudhury
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh;
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh;
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| |
Collapse
|
9
|
Park DE, Higdon MM, Prosperi C, Baggett HC, Brooks WA, Feikin DR, Hammitt LL, Howie SRC, Kotloff KL, Levine OS, Madhi SA, Murdoch DR, O’Brien KL, Scott JAG, Thea DM, Antonio M, Awori JO, Baillie VL, Bunthi C, Kwenda G, Mackenzie GA, Moore DP, Morpeth SC, Mwananyanda L, Paveenkittiporn W, Ziaur Rahman M, Rahman M, Rhodes J, Sow SO, Tapia MD, Deloria Knoll M. Upper Respiratory Tract Co-detection of Human Endemic Coronaviruses and High-density Pneumococcus Associated With Increased Severity Among HIV-Uninfected Children Under 5 Years Old in the PERCH Study. Pediatr Infect Dis J 2021; 40:503-512. [PMID: 33883479 PMCID: PMC8104011 DOI: 10.1097/inf.0000000000003139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Severity of viral respiratory illnesses can be increased with bacterial coinfection and can vary by sex, but influence of coinfection and sex on human endemic coronavirus (CoV) species, which generally cause mild to moderate respiratory illness, is unknown. We evaluated CoV and pneumococcal co-detection by sex in childhood pneumonia. METHODS In the 2011-2014 Pneumonia Etiology Research for Child Health study, nasopharyngeal and oropharyngeal (NP/OP) swabs and other samples were collected from 3981 children <5 years hospitalized with severe or very severe pneumonia in 7 countries. Severity by NP/OP detection status of CoV (NL63, 229E, OC43 or HKU1) and high-density (≥6.9 log10 copies/mL) pneumococcus (HDSpn) by real-time polymerase chain reaction was assessed by sex using logistic regression adjusted for age and site. RESULTS There were 43 (1.1%) CoV+/HDSpn+, 247 CoV+/HDSpn-, 449 CoV-/HDSpn+ and 3149 CoV-/HDSpn- cases with no significant difference in co-detection frequency by sex (range 51.2%-64.0% male, P = 0.06). More CoV+/HDSpn+ pneumonia was very severe compared with other groups for both males (13/22, 59.1% versus range 29.1%-34.7%, P = 0.04) and females (10/21, 47.6% versus 32.5%-43.5%, P = 0.009), but only male CoV+/HDSpn+ required supplemental oxygen more frequently (45.0% versus 20.6%-28.6%, P < 0.001) and had higher mortality (35.0% versus 5.3%-7.1%, P = 0.004) than other groups. For females with CoV+/HDSpn+, supplemental oxygen was 25.0% versus 24.8%-33.3% (P = 0.58) and mortality was 10.0% versus 9.2%-12.9% (P = 0.69). CONCLUSIONS Co-detection of endemic CoV and HDSpn was rare in children hospitalized with pneumonia, but associated with higher severity and mortality in males. Findings may warrant investigation of differences in severity by sex with co-detection of HDSpn and SARS-CoV-2.
Collapse
Affiliation(s)
- Daniel E. Park
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, District of Columbia
| | - Melissa M. Higdon
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Christine Prosperi
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Henry C. Baggett
- Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - W. Abdullah Brooks
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh
| | - Daniel R. Feikin
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Laura L. Hammitt
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Steve R. C. Howie
- Medical Research Council Unit, Basse, The Gambia
- Department of Paediatrics, University of Auckland, New Zealand
| | - Karen L. Kotloff
- Department of Pediatrics and Department of Medicine, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Orin S. Levine
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shabir A. Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - David R. Murdoch
- Department of Pathology and Biomedical Sciences, University of Otago
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Katherine L. O’Brien
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - J. Anthony G. Scott
- KEMRI Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Donald M. Thea
- Department of Global Health and Development, Boston University School of Public Health, Boston, Massachusetts
| | - Martin Antonio
- Medical Research Council Unit, Basse, The Gambia
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Juliet O. Awori
- KEMRI Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
| | - Vicky L. Baillie
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
| | - Charatdao Bunthi
- Division of Global Health Protection, Thailand Ministry of Public Health–US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Geoffrey Kwenda
- Right to Care-Zambia
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Grant A. Mackenzie
- Medical Research Council Unit, Basse, The Gambia
- Murdoch Children’s Research Institute, Melbourne, Australia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Paediatrics, University of Melbourne, Australia
| | - David P. Moore
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit
- Department of Paediatrics & Child Health, Chris Hani Baragwanath Academic Hospital and University of the Witwatersrand, South Africa
| | - Susan C. Morpeth
- KEMRI Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Microbiology Laboratory, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - Lawrence Mwananyanda
- Department of Global Health and Development, Boston University School of Public Health, Boston, Massachusetts
- EQUIP-Zambia, Lusaka, Zambia
| | | | - Mohammed Ziaur Rahman
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh
| | - Mustafizur Rahman
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh
| | - Julia Rhodes
- Division of Global Health Protection, Thailand Ministry of Public Health–US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Samba O. Sow
- Centre pour le Développement des Vaccins (CVD-Mali), Bamako, Mali
| | - Milagritos D. Tapia
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Maria Deloria Knoll
- From the Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| |
Collapse
|
10
|
Nicol MP, MacGinty R, Workman L, Stadler JAM, Myer L, Allen V, Ah Tow Edries L, Zar HJ. A Longitudinal Study of the Epidemiology of Seasonal Coronaviruses in an African Birth Cohort. J Pediatric Infect Dis Soc 2021; 10:607-614. [PMID: 33528016 PMCID: PMC7928775 DOI: 10.1093/jpids/piaa168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/17/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Since non-epidemic, seasonal human coronaviruses (sHCoV) commonly infect children, an improved understanding of the epidemiology of these infections may offer insights into the context of severe acute respiratory syndrome (SARS)-CoV-2. We investigated the epidemiology of sHCoV infection during the first year of life, including risk factors and association with lower respiratory tract infection (LRTI). METHODS We conducted a nested case-control study of infants enrolled in a birth cohort near Cape Town, South Africa, from 2012 to 2015. LRTI surveillance was implemented, and nasopharyngeal swabs were collected fortnightly over infancy. Quantitative PCR detected respiratory pathogens, including coronaviruses-229E, -NL63, -OC43, and -HKU1. Swabs were tested from infants at the time of LRTI and from the 90 days prior as well as from age-matched control infants from the cohort over the equivalent period. RESULTS In total, 885 infants were included, among whom 464 LRTI events occurred. Of the 4751 samples tested for sHCoV, 9% tested positive, with HCoV-NL63 the most common. Seasonal HCoV detection was associated with LRTI; this association was strongest for coronavirus-OC43, which was also found in all sHCoV-associated hospitalizations. Birth in winter was associated with sHCoV-LRTI, but there were no clear seasonal differences in detection. Co-detection of Streptococcus pneumoniae was weakly associated with sHCoV-LRTI (odds ratio: 1.8; 95% confidence interval: 0.9-3.6); detection of other respiratory viruses or bacteria was not associated with sHCoV status. CONCLUSIONS Seasonal HCoV infections were common and associated with LRTI, particularly sHCoV-OC43, which is most closely related to the SARS group of coronaviruses. Interactions of coronaviruses with bacteria in the pathogenesis of LRTI require further study.
Collapse
Affiliation(s)
- Mark P Nicol
- Division of Infection and Immunity, School of Biomedical Sciences, Faculty of Health Sciences, University of Western Australia, Perth, Australia
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Rae MacGinty
- Department of Paediatrics and Child Health and SA-MRC Unit on Child & Adolescent Health, Red Cross War Memorial Children’s Hospital and University of Cape Town, Cape Town, South Africa
| | - Lesley Workman
- Department of Paediatrics and Child Health and SA-MRC Unit on Child & Adolescent Health, Red Cross War Memorial Children’s Hospital and University of Cape Town, Cape Town, South Africa
| | - Jacob A M Stadler
- Department of Paediatrics and Child Health and SA-MRC Unit on Child & Adolescent Health, Red Cross War Memorial Children’s Hospital and University of Cape Town, Cape Town, South Africa
| | - Landon Myer
- Division of Epidemiology and Biostatistics, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Veronica Allen
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Lemese Ah Tow Edries
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health and SA-MRC Unit on Child & Adolescent Health, Red Cross War Memorial Children’s Hospital and University of Cape Town, Cape Town, South Africa
| |
Collapse
|
11
|
Wang X, Xia S, Zhu Y, Lu L, Jiang S. Pan-coronavirus fusion inhibitors as the hope for today and tomorrow. Protein Cell 2021; 12:84-88. [PMID: 33420956 PMCID: PMC7796682 DOI: 10.1007/s13238-020-00806-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Affiliation(s)
- Xinling Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yun Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
12
|
Uhteg K, Carroll KC, Mostafa HH. Coronavirus Detection in the Clinical Microbiology Laboratory: Are We Ready for Identifying and Diagnosing a Novel Virus? Clin Lab Med 2020; 40:459-472. [PMID: 33121615 PMCID: PMC7414311 DOI: 10.1016/j.cll.2020.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Endemic species of coronavirus (HCoV-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1) are frequent causes of upper respiratory tract infections. Three highly pathogenic coronaviruses have been associated with outbreaks and epidemics and have challenged clinical microbiology laboratories to quickly develop assays for diagnosis. Their initial characterization was achieved by molecular methods. With the great advance in metagenomic whole-genome sequencing directly from clinical specimens, diagnosis of novel coronaviruses could be quickly implemented into the workflow of managing cases of pneumonia of unknown cause, which will markedly affect the time of the initial characterization and accelerate the initiation of outbreak control measures.
Collapse
|
13
|
Ezzikouri S, Nourlil J, Benjelloun S, Kohara M, Tsukiyama-Kohara K. Coronavirus disease 2019-Historical context, virology, pathogenesis, immunotherapy, and vaccine development. Hum Vaccin Immunother 2020; 16:2992-3000. [PMID: 32755425 PMCID: PMC8641599 DOI: 10.1080/21645515.2020.1787068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/20/2020] [Accepted: 06/09/2020] [Indexed: 01/08/2023] Open
Abstract
The current Coronavirus Disease 2019 (COVID-19) pandemic is causing great alarm around the world. The pathogen for COVID-19 - severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) - is the seventh known coronavirus to cause pneumonia in humans. While much remains unknown about SARS-CoV-2, physicians and researchers have begun to publish relevant findings, and much evidence is available on coronaviruses previously circulating in human and animal populations. In this review, we situate COVID-19 in its context as a transboundary viral disease, and provide a comprehensive discussion focused on the discovery, spread, virology, pathogenesis, and clinical features of this disease, its causative coronaviral pathogen, and approaches to combating the disease through immunotherapies and other treatments and vaccine development. An epidemiological survey revealed a potentially large number of asymptomatic SARS-CoV-2 carriers within the population, which may hamper efforts against COVID-19. Finally, we emphasize that vaccines against SARS-CoV-2, which may be developed by 2021, will be essential for prevention of COVID-19.
Collapse
Affiliation(s)
- Sayeh Ezzikouri
- Virology Unit¸ Viral Hepatitis Laboratory, Institut Pasteur Du Maroc, Casablanca, Morocco
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Jalal Nourlil
- Medical Virology and BSL3 Laboratory, Institut Pasteur Du Maroc, Casablanca, Morocco
| | - Soumaya Benjelloun
- Virology Unit¸ Viral Hepatitis Laboratory, Institut Pasteur Du Maroc, Casablanca, Morocco
| | - Michinori Kohara
- Department of Microbiology and Cell Biology, The Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| |
Collapse
|
14
|
Stein RA, Young LM. From ACE2 to COVID-19: A multiorgan endothelial disease. Int J Infect Dis 2020; 100:425-430. [PMID: 32896660 PMCID: PMC7832810 DOI: 10.1016/j.ijid.2020.08.083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Affiliation(s)
- Richard A Stein
- NYU Tandon School of Engineering, Department of Chemical and Biomolecular Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA; LaGuardia Community College, Department of Natural Sciences, City University of New York, New York, NY 11101, USA.
| | - Lauren M Young
- University of Chicago, Department of Internal Medicine, 5841 S Maryland Ave, Chicago, IL 60637, USA.
| |
Collapse
|
15
|
A 14-year Prospective Study of Human Coronavirus Infections in Hospitalized Children: Comparison With Other Respiratory Viruses. Pediatr Infect Dis J 2020; 39:653-657. [PMID: 32453196 DOI: 10.1097/inf.0000000000002760] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Human coronaviruses (HCoVs) have been recognized as causative agents of respiratory tract infections.Our aim was to describe HCoV infections in hospitalized children in a prospective surveillance study for 14 years and compare them with other respiratory viruses. METHODS As a part of an ongoing prospective study to identify the etiology of viral respiratory infections in Spain, we performed the analysis of HCoV infections in children hospitalized in a secondary hospital in Madrid, between October 2005 and June 2018. Clinical data of HCoV patients were compared with those infected by rhinovirus, respiratory syncytial virus and influenza. RESULTS The study population consisted of 5131 hospitalizations for respiratory causes in children. A total of 3901 cases (75.9%) had a positive viral identification and 205 cases (4.1%) were positive for HCoV. Only 41 cases (20%) of HCoV infection were detected as single infections. Episodes of recurrent wheezing were the most common diagnosis, and 112 children (54%) had hypoxia. Clinical data in HCoV cases were similar to those associated with rhinovirus; however, patients with HCoV were younger. Other viruses were associated with hypoxia more frequently than cases with HCoV; high fever was more common in influenza infections and bronchiolitis in respiratory syncytial virus group. Although a slight peak of circulation appears mostly in winter, HCoV has been detected throughout the year as well. CONCLUSIONS HCoV infections represent a small fraction of respiratory infections that require hospitalization in children and their characteristics do not differ greatly from other respiratory viral infections.
Collapse
|
16
|
Recommendations on the clinical management of the COVID-19 infection by the «new coronavirus» SARS-CoV2. Spanish Paediatric Association working group. An Pediatr (Barc) 2020; 92:241.e1-241.e11. [PMID: 32341943 PMCID: PMC7182532 DOI: 10.1016/j.anpede.2020.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/11/2022] Open
Abstract
On 31 December 2019, the Wuhan Municipal Committee of Health and Healthcare (Hubei Province, China) reported that there were 27 cases of pneumonia of unknown origin with symptoms starting on the 8 December. There were 7 serious cases with common exposure in market with shellfish, fish, and live animals, in the city of Wuhan. On 7 January 2020, the Chinese authorities identified that the agent causing the outbreak was a new type of virus of the Coronaviridae family, temporarily called «new coronavirus», 2019-nCoV. On January 30th, 2020, the World Health Organisation (WHO) declared the outbreak an International Emergency. On 11 February 2020 the WHO assigned it the name of SARS-CoV2 and COVID-19 (SARS-CoV2 and COVID-19). The Ministry of Health summoned the Specialties Societies to prepare a clinical protocol for the management of COVID-19. The Spanish Paediatric Association appointed a Working Group of the Societies of Paediatric Infectious Diseases and Paediatric Intensive Care to prepare the present recommendations with the evidence available at the time of preparing them.
Collapse
|
17
|
Calvo C, García López-Hortelano M, de Carlos Vicente JC, Vázquez Martínez JL. [Recommendations on the clinical management of the COVID-19 infection by the «new coronavirus» SARS-CoV2. Spanish Paediatric Association working group]. An Pediatr (Barc) 2020. [PMID: 32173188 DOI: 10.1016/j.anpedi.2020.02.001"] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022] Open
Abstract
On 31 December 2019, the Wuhan Municipal Committee of Health and Healthcare (Hubei Province, China) reported that there were 27 cases of pneumonia of unknown origin with symptoms starting on the 8 December. There were 7 serious cases with common exposure in market with shellfish, fish, and live animals, in the city of Wuhan. On 7 January 2020, the Chinese authorities identified that the agent causing the outbreak was a new type of virus of the Coronaviridae family, temporarily called «new coronavirus», 2019-nCoV. On January 30th, 2020, the World Health Organisation (WHO) declared the outbreak an International Emergency. On 11 February 2020 the WHO assigned it the name of SARS-CoV2 and COVID-19 (SARS-CoV2 and COVID-19). The Ministry of Health summoned the Specialties Societies to prepare a clinical protocol for the management of COVID-19. The Spanish Paediatric Association appointed a Working Group of the Societies of Paediatric Infectious Diseases and Paediatric Intensive Care to prepare the present recommendations with the evidence available at the time of preparing them.
Collapse
Affiliation(s)
- Cristina Calvo
- Sociedad Española de Infectología Pediátrica (SEIP); Servicio de Pediatría, Enfermedades Infecciosas y Tropicales, Hospital Universitario La Paz, Madrid, España.
| | - Milagros García López-Hortelano
- Sociedad Española de Infectología Pediátrica (SEIP); Servicio de Pediatría, Enfermedades Infecciosas y Tropicales, Hospital Universitario La Paz, Madrid, España; Unidad de Aislamiento de Alto Nivel (UAAN), Hospital La Paz-Carlos III, Madrid, España
| | - Juan Carlos de Carlos Vicente
- Sociedad Española de Cuidados Intensivos Pediátricos (SECIP); Unidad de Cuidados Intensivos Pediátricos, Hospital Son Espases, Palma de Mallorca, España
| | - Jose Luis Vázquez Martínez
- Sociedad Española de Cuidados Intensivos Pediátricos (SECIP); Unidad de Cuidados Intensivos Pediátricos, Hospital Ramón y Cajal, Madrid, España
| | | | | |
Collapse
|
18
|
[Recommendations on the clinical management of the COVID-19 infection by the «new coronavirus» SARS-CoV2. Spanish Paediatric Association working group]. An Pediatr (Barc) 2020; 92:241.e1-241.e11. [PMID: 32173188 PMCID: PMC7118614 DOI: 10.1016/j.anpedi.2020.02.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/22/2022] Open
Abstract
On 31 December 2019, the Wuhan Municipal Committee of Health and Healthcare (Hubei Province, China) reported that there were 27 cases of pneumonia of unknown origin with symptoms starting on the 8 December. There were 7 serious cases with common exposure in market with shellfish, fish, and live animals, in the city of Wuhan. On 7 January 2020, the Chinese authorities identified that the agent causing the outbreak was a new type of virus of the Coronaviridae family, temporarily called «new coronavirus», 2019-nCoV. On January 30th, 2020, the World Health Organisation (WHO) declared the outbreak an International Emergency. On 11 February 2020 the WHO assigned it the name of SARS-CoV2 and COVID-19 (SARS-CoV2 and COVID-19). The Ministry of Health summoned the Specialties Societies to prepare a clinical protocol for the management of COVID-19. The Spanish Paediatric Association appointed a Working Group of the Societies of Paediatric Infectious Diseases and Paediatric Intensive Care to prepare the present recommendations with the evidence available at the time of preparing them.
Collapse
|
19
|
Wang Y, Li X, Liu W, Gan M, Zhang L, Wang J, Zhang Z, Zhu A, Li F, Sun J, Zhang G, Zhuang Z, Luo J, Chen D, Qiu S, Zhang L, Xu D, Mok CKP, Zhang F, Zhao J, Zhou R, Zhao J. Discovery of a subgenotype of human coronavirus NL63 associated with severe lower respiratory tract infection in China, 2018. Emerg Microbes Infect 2020; 9:246-255. [PMID: 31996093 PMCID: PMC7034077 DOI: 10.1080/22221751.2020.1717999] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Human coronavirus NL63 (HCoV-NL63) is primarily associated with common cold in children, elderly and immunocompromised individuals. Outbreaks caused by HCoV-NL63 are rare. Here we report a cluster of HCoV-NL63 cases with severe lower respiratory tract infection that arose in Guangzhou, China, in 2018. Twenty-three hospitalized children were confirmed to be HCoV-NL63 positive, and most of whom were hospitalized with severe pneumonia or acute bronchitis. Whole genomes of HCoV-NL63 were obtained using next-generation sequencing. Phylogenetic and single amino acid polymorphism analyses showed that this outbreak was associated with two subgenotypes (C3 and B) of HCoV-NL63. Half of patients were identified to be related to a new subgenotype C3. One unique amino acid mutation at I507 L in spike protein receptor binding domain (RBD) was detected, which segregated this subgenotype C3 from other known subgenotypes. Pseudotyped virus bearing the I507 L mutation in RBD showed enhanced entry into host cells as compared to the prototype virus. This study proved that HCoV-NL63 was undergoing continuous mutation and has the potential to cause severe lower respiratory disease in humans.
Collapse
Affiliation(s)
- Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Xin Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Mian Gan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Lu Zhang
- Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jin Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Guoxian Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Zhen Zhuang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jiaying Luo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Dehui Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Shuyan Qiu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Li Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Duo Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Chris Ka Pun Mok
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China.,The HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Fuchun Zhang
- Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Rong Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China.,Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| |
Collapse
|
20
|
Abstract
The four endemic human coronaviruses HCoV-229E, -NL63, -OC43, and -HKU1 contribute a considerable share of upper and lower respiratory tract infections in adults and children. While their clinical representation resembles that of many other agents of the common cold, their evolutionary histories, and host associations could provide important insights into the natural history of past human pandemics. For two of these viruses, we have strong evidence suggesting an origin in major livestock species while primordial associations for all four viruses may have existed with bats and rodents. HCoV-NL63 and -229E may originate from bat reservoirs as assumed for many other coronaviruses, but HCoV-OC43 and -HKU1 seem more likely to have speciated from rodent-associated viruses. HCoV-OC43 is thought to have emerged from ancestors in domestic animals such as cattle or swine. The bovine coronavirus has been suggested to be a possible ancestor, from which HCoV-OC43 may have emerged in the context of a pandemic recorded historically at the end of the 19th century. New data suggest that HCoV-229E may actually be transferred from dromedary camels similar to Middle East respiratory syndrome (MERS) coronavirus. This scenario provides important ecological parallels to the present prepandemic pattern of host associations of the MERS coronavirus.
Collapse
Affiliation(s)
- Victor M Corman
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Berlin, Germany
| | - Doreen Muth
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Berlin, Germany
| | - Daniela Niemeyer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Christian Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Berlin, Germany.
| |
Collapse
|
21
|
Entry of Human Coronavirus NL63 into the Cell. J Virol 2018; 92:JVI.01933-17. [PMID: 29142129 DOI: 10.1128/jvi.01933-17] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 11/20/2022] Open
Abstract
The first steps of human coronavirus NL63 (HCoV-NL63) infection were previously described. The virus binds to target cells by use of heparan sulfate proteoglycans and interacts with the ACE2 protein. Subsequent events, including virus internalization and trafficking, remain to be elucidated. In this study, we mapped the process of HCoV-NL63 entry into the LLC-Mk2 cell line and ex vivo three-dimensional (3D) tracheobronchial tissue. Using a variety of techniques, we have shown that HCoV-NL63 virions require endocytosis for successful entry into the LLC-MK2 cells, and interaction between the virus and the ACE2 molecule triggers recruitment of clathrin. Subsequent vesicle scission by dynamin results in virus internalization, and the newly formed vesicle passes the actin cortex, which requires active cytoskeleton rearrangement. Finally, acidification of the endosomal microenvironment is required for successful fusion and release of the viral genome into the cytoplasm. For 3D tracheobronchial tissue cultures, we also observed that the virus enters the cell by clathrin-mediated endocytosis, but we obtained results suggesting that this pathway may be bypassed.IMPORTANCE Available data on coronavirus entry frequently originate from studies employing immortalized cell lines or undifferentiated cells. Here, using the most advanced 3D tissue culture system mimicking the epithelium of conductive airways, we systematically mapped HCoV-NL63 entry into susceptible cells. The data obtained allow for a better understanding of the infection process and may support development of novel treatment strategies.
Collapse
|