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Yousefi M, Lee WS, Chan WOY, He W, Mah MG, Yong CL, Deerain JM, Wang L, Arcinas C, Yan B, Tan D, Sia WR, Gamage AM, Yang J, Hsu ACY, Li S, Linster M, Yang X, Ghosh S, Anderson DE, Smith GJD, Tan CW, Wang LF, Ooi YS. Betacoronaviruses SARS-CoV-2 and HCoV-OC43 infections in IGROV-1 cell line require aryl hydrocarbon receptor. Emerg Microbes Infect 2023; 12:2256416. [PMID: 37672505 PMCID: PMC10512916 DOI: 10.1080/22221751.2023.2256416] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/01/2023] [Indexed: 09/08/2023]
Abstract
The emergence of novel betacoronaviruses has posed significant financial and human health burdens, necessitating the development of appropriate tools to combat future outbreaks. In this study, we have characterized a human cell line, IGROV-1, as a robust tool to detect, propagate, and titrate betacoronaviruses SARS-CoV-2 and HCoV-OC43. IGROV-1 cells can be used for serological assays, antiviral drug testing, and isolating SARS-CoV-2 variants from patient samples. Using time-course transcriptomics, we confirmed that IGROV-1 cells exhibit a robust innate immune response upon SARS-CoV-2 infection, recapitulating the response previously observed in primary human nasal epithelial cells. We performed genome-wide CRISPR knockout genetic screens in IGROV-1 cells and identified Aryl hydrocarbon receptor (AHR) as a critical host dependency factor for both SARS-CoV-2 and HCoV-OC43. Using DiMNF, a small molecule inhibitor of AHR, we observed that the drug selectively inhibits HCoV-OC43 infection but not SARS-CoV-2. Transcriptomic analysis in primary normal human bronchial epithelial cells revealed that DiMNF blocks HCoV-OC43 infection via basal activation of innate immune responses. Our findings highlight the potential of IGROV-1 cells as a valuable diagnostic and research tool to combat betacoronavirus diseases.
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Affiliation(s)
- Meisam Yousefi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Wai Suet Lee
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Wharton O. Y. Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Wei He
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Marcus G. Mah
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Cythia Lingli Yong
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Joshua M. Deerain
- Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Lijin Wang
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Camille Arcinas
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Biaoguo Yan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Dewei Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Wan Rong Sia
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Akshamal M. Gamage
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Jinxuan Yang
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People’s Republic of China
| | - Alan Chen-Yu Hsu
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, Australia
- College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, Australia
| | - Shang Li
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Martin Linster
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Xinglou Yang
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People’s Republic of China
| | - Sujoy Ghosh
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Danielle E. Anderson
- Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Gavin J. D. Smith
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Chee Wah Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- Infectious Diseases Translation Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lin-Fa Wang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Yaw Shin Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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2
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Tan CW, Lim CK, Prestedge J, Batty M, Mah YY, O'Han M, Wang LF, Kilby D, Anderson DE. Use of a point-of-care test to rapidly assess levels of SARS-CoV-2 nasal neutralising antibodies in vaccines and breakthrough infected individuals. Sci Rep 2023; 13:20263. [PMID: 37985674 PMCID: PMC10662396 DOI: 10.1038/s41598-023-47613-8] [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: 09/25/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023] Open
Abstract
Despite SARS-CoV-2 vaccines eliciting systemic neutralising antibodies (nAbs), breakthrough infections still regularly occur. Infection helps to generate mucosal immunity, possibly reducing disease transmission. Monitoring mucosal nAbs is predominantly restricted to lab-based assays, which have limited application to the public. In this multi-site study, we used lateral-flow surrogate neutralisation tests to measure mucosal and systemic nAbs in vaccinated and breakthrough infected individuals in Australia and Singapore. Using three lateral flow assays to detect SARS-CoV-2 nAbs, we demonstrated that nasal mucosal nAbs were present in 71.4 (95% CI 56.3-82.9%) to 85.7% (95% CI 71.8-93.7%) of individuals with breakthrough infection (positivity rate was dependent upon the type of test), whereas only 20.7 (95% CI 17.1-49.4%) to 34.5% (95% CI 19.8-52.7%) of vaccinated individuals without breakthrough infection had detectible nasal mucosal nAbs. Of the individuals with breakthrough infection, collective mucosal anti-S antibody detection in confirmatory assays was 92.9% (95% CI 80.3-98.2%) of samples, while 72.4% (95% CI 54.1-85.5%) of the vaccinated individuals who had not experienced a breakthrough infection were positive to anti-S antibody. All breakthrough infected individuals produced systemic anti-N antibodies; however, these antibodies were not detected in the nasal cavity. Mucosal immunity is likely to play a role in limiting the transmission of SARS-CoV-2 and lateral flow neutralisation tests provide a rapid readout of mucosal nAbs at the point-of-care.
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Affiliation(s)
- Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117547, Singapore
| | - Chuan Kok Lim
- Victorian Infectious Diseases Reference Laboratory, Melbourne Health, The Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Australia
- Department of Infectious Diseases, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, 3000, Australia
| | - Jacqueline Prestedge
- Victorian Infectious Diseases Reference Laboratory, Melbourne Health, The Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Australia
- Department of Infectious Diseases, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, 3000, Australia
| | - Mitchell Batty
- Victorian Infectious Diseases Reference Laboratory, Melbourne Health, The Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Australia
- Department of Infectious Diseases, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, 3000, Australia
| | - Yun Yan Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Michelle O'Han
- Impact Biotech Healthcare, Level 30 Australia Square, 264 George St, Sydney, NSW, 2000, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Dean Kilby
- Impact Biotech Healthcare, Level 30 Australia Square, 264 George St, Sydney, NSW, 2000, Australia
| | - Danielle E Anderson
- Victorian Infectious Diseases Reference Laboratory, Melbourne Health, The Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Australia.
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, 3000, Australia.
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3
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Saron WAA, Shanmugam K, Tung CC, Patmanathan RK, Rathore APS, Anderson DE, St John AL. Exacerbated Zika virus-induced neuropathology and microcephaly in fetuses of dengue-immune nonhuman primates. Sci Transl Med 2023; 15:eadd2420. [PMID: 37878671 DOI: 10.1126/scitranslmed.add2420] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/04/2023] [Indexed: 10/27/2023]
Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus that can vertically transmit from mother to fetus, potentially causing congenital defects, including microcephaly. It is not fully understood why some fetuses experience severe complications after in utero exposure to ZIKV, whereas others do not. Given the antigenic similarity between ZIKV and the closely related virus dengue (DENV) and the potential of DENV-specific antibodies to enhance ZIKV disease severity in mice, we questioned whether maternal DENV immunity could influence fetal outcomes in a nonhuman primate model of ZIKV vertical transmission. We found significantly increased severity of congenital Zika syndrome (CZS) in fetuses of DENV-immune cynomolgus macaques infected with ZIKV in early pregnancy compared with naïve controls, which occurred despite no effect on maternal ZIKV infection or antibody responses. Ultrasound measurements of head circumference and biparietal diameter measurements taken sequentially throughout pregnancy demonstrated CZS in fetuses of DENV-immune pregnant macaques. Furthermore, severe CZS enhanced by DENV immunity was typified by reduced cortical thickness and increased frequency of neuronal death, hemorrhaging, cellular infiltrations, calcifications, and lissencephaly in fetal brains. This study shows that maternal immunity to DENV can worsen ZIKV neurological outcomes in fetal primates, and it provides an animal model of vertical transmission closely approximating human developmental timelines that could be used to investigate severe ZIKV disease outcomes and interventions in fetuses.
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Affiliation(s)
- Wilfried A A Saron
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Keerthana Shanmugam
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Chi-Ching Tung
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | | | - Abhay P S Rathore
- Department of Pathology, Duke University Medical Center, Durham, NC 27705, USA
| | - Danielle E Anderson
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
- Victorian Infectious Diseases Reference Laboratory, Melbourne, Victoria 3000, Australia
| | - Ashley L St John
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
- Department of Pathology, Duke University Medical Center, Durham, NC 27705, USA
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
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4
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Tan JY, Anderson DE, Rathore AP, O’Neill A, Mantri CK, Saron WA, Lee CQ, Cui CW, Kang AE, Foo R, Kalimuddin S, Low JG, Ho L, Tambyah P, Burke TW, Woods CW, Chan KR, Karhausen J, St. John AL. Mast cell activation in lungs during SARS-CoV-2 infection associated with lung pathology and severe COVID-19. J Clin Invest 2023; 133:e149834. [PMID: 37561585 PMCID: PMC10541193 DOI: 10.1172/jci149834] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 03/23/2021] [Accepted: 08/08/2023] [Indexed: 08/12/2023] Open
Abstract
Lung inflammation is a hallmark of Coronavirus disease 2019 (COVID-19) in patients who are severely ill, and the pathophysiology of disease is thought to be immune mediated. Mast cells (MCs) are polyfunctional immune cells present in the airways, where they respond to certain viruses and allergens and often promote inflammation. We observed widespread degranulation of MCs during acute and unresolved airway inflammation in SARS-CoV-2-infected mice and nonhuman primates. Using a mouse model of MC deficiency, MC-dependent interstitial pneumonitis, hemorrhaging, and edema in the lung were observed during SARS-CoV-2 infection. In humans, transcriptional changes in patients requiring oxygen supplementation also implicated cells with a MC phenotype in severe disease. MC activation in humans was confirmed through detection of MC-specific proteases, including chymase, the levels of which were significantly correlated with disease severity and with biomarkers of vascular dysregulation. These results support the involvement of MCs in lung tissue damage during SARS-CoV-2 infection in animal models and the association of MC activation with severe COVID-19 in humans, suggesting potential strategies for intervention.
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Affiliation(s)
- Janessa Y.J. Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Danielle E. Anderson
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, Melbourne, Victoria, Australia
| | - Abhay P.S. Rathore
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - Aled O’Neill
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | | | | | - Cheryl Q.E. Lee
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore
| | - Chu Wern Cui
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore
| | - Adrian E.Z. Kang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Randy Foo
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Shirin Kalimuddin
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Jenny G. Low
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Lena Ho
- Duke-NUS Medical School, Program in Cardiovascular and Metabolic Disorders, Singapore
| | - Paul Tambyah
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Infectious Disease, University Medicine Cluster, National University Hospital, Singapore
| | - Thomas W. Burke
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Christopher W. Woods
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, North Carolina, USA
- Division of Infectious Diseases, Duke University Medical Center, Durham VA Medical Center, Durham, North Carolina, USA
| | - Kuan Rong Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jörn Karhausen
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Ashley L. St. John
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Microbiology and Immunology, National University of Singapore, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
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5
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Yong KSM, Anderson DE, Zheng AKE, Liu M, Tan SY, Tan WWS, Chen Q, Wang LF. Comparison of infection and human immune responses of two SARS-CoV-2 strains in a humanized hACE2 NIKO mouse model. Sci Rep 2023; 13:12484. [PMID: 37528224 PMCID: PMC10394059 DOI: 10.1038/s41598-023-39628-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/27/2023] [Indexed: 08/03/2023] Open
Abstract
The COVID-19 pandemic has sickened millions, cost lives and has devastated the global economy. Various animal models for experimental infection with SARS-CoV-2 have played a key role in many aspects of COVID-19 research. Here, we describe a humanized hACE2 (adenovirus expressing hACE2) NOD-SCID IL2Rγ-/- (NIKO) mouse model and compare infection with ancestral and mutant (SARS-CoV-2-∆382) strains of SARS-CoV-2. Immune cell infiltration, inflammation, lung damage and pro-inflammatory cytokines and chemokines was observed in humanized hACE2 NIKO mice. Humanized hACE2 NIKO mice infected with the ancestral and mutant SARS-CoV-2 strain had lung inflammation and production of pro-inflammatory cytokines and chemokines. This model can aid in examining the pathological basis of SARS-CoV-2 infection in a human immune environment and evaluation of therapeutic interventions.
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Affiliation(s)
- Kylie Su Mei Yong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Adrian Kang Eng Zheng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Min Liu
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Sue Yee Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Wilson Wei Sheng Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Qingfeng Chen
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
- Singhealth Duke-NUS Global Health Institute, Singapore, Singapore.
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6
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Wang Y, Xu Y, Tan CW, Qiao L, Chia WN, Zhang H, Huang Q, Deng Z, Wang Z, Wang X, Shen X, Liu C, Pei R, Liu Y, Xue S, Kong D, Anderson DE, Cai F, Zhou P, Wang LF, Ye H. Author Correction: Engineering antiviral immune-like systems for autonomous virus detection and inhibition in mice. Nat Commun 2023; 14:3969. [PMID: 37407578 DOI: 10.1038/s41467-023-39774-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Affiliation(s)
- Yidan Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
- Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing, 401120, China
| | - Ying Xu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Longliang Qiao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Hongyi Zhang
- Department of Breast Surgery, Yangpu Hospital, School of Medicine, Tongji University, 450 Tengyue Road, Shanghai, 200090, China
| | - Qin Huang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Zhenqiang Deng
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Ziwei Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Xi Wang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xurui Shen
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Canyu Liu
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
| | - Rongjuan Pei
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
| | - Yuanxiao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Shuai Xue
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058, Basel, Switzerland
| | - Deqiang Kong
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Fengfeng Cai
- Department of Breast Surgery, Yangpu Hospital, School of Medicine, Tongji University, 450 Tengyue Road, Shanghai, 200090, China
| | - Peng Zhou
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
- SingHealth Duke-NUS Global Health Institute, Singapore, Singapore.
| | - Haifeng Ye
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China.
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7
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Vesikari T, Langley JM, Spaans JN, Petrov I, Popovic V, Yassin-Rajkumar B, Anderson DE, Diaz-Mitoma F. The persistence of seroprotective levels of antibodies after vaccination with PreHevbrio, a 3-antigen hepatitis B vaccine. Vaccine 2023:S0264-410X(23)00528-5. [PMID: 37179167 DOI: 10.1016/j.vaccine.2023.05.010] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/11/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023]
Abstract
Prevention of hepatitis B virus (HBV) infection by vaccination can potentially eliminate HBV-related diseases. PreHevbrio™/PreHevbri® is a 3-antigen (S, preS1, preS2) HBV vaccine (3A-HBV) recently licensed for adults in the US, EU and Canada. This study evaluated antibody persistence in a subset of fully vaccinated and seroprotected (anti-HBs ≥ 10 mIU/mL) Finnish participants from the phase 3 trial (PROTECT) of 3A-HBV versus single-antigen HBV vaccine (1A-HBV). 465/528 eligible subjects were enrolled (3A-HBV: 244; 1A-HBV: 221). Baseline characteristics were balanced. After 2.5 years, more 3A-HBV subjects remained seroprotected (88.1 % [95 %CI: 84.1,92.2]) versus 1A-HBV (72.4 % [95 %CI: 66.6,78.3)], p < 0.0001) and had higher mean anti-HBs [1382.9 mIU/mL (95 %CI: 1013.8,1751.9) versus 252.6 mIU/mL (95 %CI: 127.5,377.6), p < 0.0001]. In multiple variable logistic regression analysis including age, vaccine, initial vaccine response, sex and BMI, only higher post dose 3 (Day 196) antibody titers significantly reduced the odds of losing seroprotection.
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Affiliation(s)
- T Vesikari
- Nordic Research Network Oy, Tampere, Finland
| | - J M Langley
- Canadian Center for Vaccinology (Dalhousie University, IWK and Nova Scotia Health), Canada
| | - J N Spaans
- VBI Vaccines Inc, Cambridge, MA, United States
| | - I Petrov
- VBI Vaccines Inc, Cambridge, MA, United States
| | - V Popovic
- VBI Vaccines Inc, Cambridge, MA, United States
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8
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Speck P, Mackenzie J, Bull RA, Slobedman B, Drummer H, Fraser J, Herrero L, Helbig K, Londrigan S, Moseley G, Prow N, Hansman G, Edwards R, Ahlenstiel C, Abendroth A, Tscharke D, Hobson-Peters J, Kriiger-Loterio R, Parry R, Marsh G, Harding E, Jacques DA, Gartner MJ, Lee WS, McAuley J, Vaz P, Sainsbury F, Tate MD, Sinclair J, Imrie A, Rawlinson S, Harman A, Carr JM, Monson EA, Hibma M, Mahony TJ, Tu T, Center RJ, Shrestha LB, Hall R, Warner M, Ward V, Anderson DE, Eyre NS, Netzler NE, Peel AJ, Revill P, Beard M, Legione AR, Spencer AJ, Idris A, Forwood J, Sarker S, Purcell DFJ, Bartlett N, Deerain JM, Brew BJ, Asgari S, Farrell H, Khromykh A, Enosi Tuipulotu D, Anderson D, Mese S, Tayyar Y, Edenborough K, Uddin JM, Hussain A, Daymond CJI, Agius J, Johnson KN, Shirmast P, Abedinzadeshahri M, MacDiarmid R, Ashley CL, Laws J, Furfaro LL, Burton TD, Johnson SMR, Telikani Z, Petrone M, Roby JA, Samer C, Suhrbier A, Van Der Kamp A, Cunningham A, Donato C, Mahar J, Black WD, Vasudevan S, Lenchine R, Spann K, Rawle DJ, Rudd P, Neil J, Kingston R, Newsome TP, Kim KW, Mak J, Lowry K, Bryant N, Meers J, Roberts JA, McMillan N, Labzin LI, Slonchak A, Hugo LE, Henzeler B, Newton ND, David CT, Reading PC, Esneau C, Briody T, Nasr N, McNeale D, McSharry B, Fakhri O, Horsburgh BA, Logan G, Howley P, Young P. Statement in Support of: "Virology under the Microscope-a Call for Rational Discourse". mBio 2023:e0081523. [PMID: 37097032 DOI: 10.1128/mbio.00815-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Affiliation(s)
- Peter Speck
- Flinders University, Bedford Park, South Australia
| | - Jason Mackenzie
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Rowena A Bull
- Kirby Institute, University of New South Wales, Sydney, Australia
| | | | | | | | - Lara Herrero
- Griffith University, Southport, Queensland, Australia
| | - Karla Helbig
- La Trobe University, Melbourne, Victoria, Australia
| | - Sarah Londrigan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | - Natalie Prow
- Hull York Medical School, University of York, York, United Kingdom
| | - Grant Hansman
- Griffith University, Southport, Queensland, Australia
| | | | | | | | - David Tscharke
- Australian National University, Canberra, Australian Capital Territory, Australia
| | | | | | - Rhys Parry
- University of Queensland, St. Lucia, Queensland, Australia
| | - Glenn Marsh
- Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia
| | - Emma Harding
- University of New South Wales, Sydney, New South Wales, Australia
| | - David A Jacques
- University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew J Gartner
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Wen Shi Lee
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Julie McAuley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Paola Vaz
- University of Melbourne, Melbourne, Victoria, Australia
| | | | - Michelle D Tate
- Monash University, Melbourne, Victoria, Australia
- Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Jane Sinclair
- University of Queensland, St. Lucia, Queensland, Australia
| | - Allison Imrie
- University of Western Australia, Perth, Western Australia, Australia
| | | | - Andrew Harman
- The University of Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | | | | | | | | | - Thomas Tu
- The University of Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | | | | | - Robyn Hall
- Ausvet Pty Ltd., Canberra, Australian Capital Territory, Australia
- Commonwealth Scientific and Industrial Research Organisation, Black Mountain, Australian Capital Territory, Australia
| | - Morgyn Warner
- University of Adelaide, Adelaide, South Australia, Australia
- SA Pathology, Adelaide, South Australia, Australia
| | | | - Danielle E Anderson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | - Natalie E Netzler
- University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre of Research Excellence, Auckland, New Zealand
| | | | - Peter Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michael Beard
- University of Adelaide, Adelaide, South Australia, Australia
| | | | | | - Adi Idris
- Griffith University, Southport, Queensland, Australia
- Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jade Forwood
- Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Subir Sarker
- La Trobe University, Melbourne, Victoria, Australia
| | - Damian F J Purcell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Nathan Bartlett
- The University of Newcastle, Newcastle, New South Wales, Australia
| | - Joshua M Deerain
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Bruce J Brew
- University of New South Wales, Sydney, New South Wales, Australia
- University of Notre Dame, Sydney, New South Wales, Australia
- St. Vincent's Hospital, Sydney, New South Wales, Australia
| | - Sassan Asgari
- University of Queensland, St. Lucia, Queensland, Australia
| | - Helen Farrell
- University of Queensland, St. Lucia, Queensland, Australia
| | | | | | | | - Sevim Mese
- University of Queensland, St. Lucia, Queensland, Australia
- Istanbul University, Istanbul, Turkey
| | - Yaman Tayyar
- Griffith University, Southport, Queensland, Australia
- Prorenata Biotech, Moledinar, Queensland, Australia
| | | | | | - Abrar Hussain
- Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Connor J I Daymond
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | | | | | - Robin MacDiarmid
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | | | - Jay Laws
- La Trobe University, Melbourne, Victoria, Australia
| | - Lucy L Furfaro
- University of Western Australia, Perth, Western Australia, Australia
| | | | | | | | - Mary Petrone
- The University of Sydney, New South Wales, Australia
| | - Justin A Roby
- Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Carolyn Samer
- The University of Sydney, New South Wales, Australia
| | - Andreas Suhrbier
- University of Queensland, St. Lucia, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | | | - Anthony Cunningham
- The University of Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Celeste Donato
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Jackie Mahar
- The University of Sydney, New South Wales, Australia
| | - Wesley D Black
- Biotopia Environmental Assessment Pty Ltd., Melbourne, Victoria, Australia
| | | | | | - Kirsten Spann
- Queensland University of Technology, Brisbane, Queensland, Australia
| | - Daniel J Rawle
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Penny Rudd
- Griffith University, Southport, Queensland, Australia
| | - Jessica Neil
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | - Ki Wook Kim
- University of New South Wales, Sydney, New South Wales, Australia
| | - Johnson Mak
- Griffith University, Southport, Queensland, Australia
| | - Kym Lowry
- University of Queensland, St. Lucia, Queensland, Australia
| | - Nathan Bryant
- The University of Newcastle, Newcastle, New South Wales, Australia
| | - Joanne Meers
- University of Queensland, St. Lucia, Queensland, Australia
| | - Jason A Roberts
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | | | | | - Leon E Hugo
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | | | | | | | - Patrick C Reading
- University of Melbourne, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, Australia
| | - Camille Esneau
- The University of Newcastle, Newcastle, New South Wales, Australia
| | - Tatiana Briody
- University of Queensland, St. Lucia, Queensland, Australia
| | - Najla Nasr
- The University of Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | | | - Brian McSharry
- Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Omid Fakhri
- Commonwealth Scientific and Industrial Research Organisation, Black Mountain, Australian Capital Territory, Australia
| | | | - Grant Logan
- Children's Medical Research Institute, Westmead, NSW, Australia
| | - Paul Howley
- Vaxmed Pty Ltd., Berwick, Victoria, Australia
| | - Paul Young
- University of Queensland, St. Lucia, Queensland, Australia
| |
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9
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Speck P, Mackenzie J, Bull RA, Slobedman B, Drummer H, Fraser J, Herrero L, Helbig K, Londrigan S, Moseley G, Prow N, Hansman G, Edwards R, Ahlenstiel C, Abendroth A, Tscharke D, Hobson-Peters J, Kriiger-Loterio R, Parry R, Marsh G, Harding E, Jacques DA, Gartner MJ, Lee WS, McAuley J, Vaz P, Sainsbury F, Tate MD, Sinclair J, Imrie A, Rawlinson S, Harman A, Carr JM, Monson EA, Hibma M, Mahony TJ, Tu T, Center RJ, Shrestha LB, Hall R, Warner M, Ward V, Anderson DE, Eyre NS, Netzler NE, Peel AJ, Revill P, Beard M, Legione AR, Spencer AJ, Idris A, Forwood J, Sarker S, Purcell DFJ, Bartlett N, Deerain JM, Brew BJ, Asgari S, Farrell H, Khromykh A, Enosi Tuipulotu D, Anderson D, Mese S, Tayyar Y, Edenborough K, Uddin JM, Hussain A, Daymond CJI, Agius J, Johnson KN, Shirmast P, Abedinzadeshahri M, MacDiarmid R, Ashley CL, Laws J, Furfaro LL, Burton TD, Johnson SMR, Telikani Z, Petrone M, Roby JA, Samer C, Suhrbier A, Van Der Kamp A, Cunningham A, Donato C, Mahar J, Black WD, Vasudevan S, Lenchine R, Spann K, Rawle DJ, Rudd P, Neil J, Kingston R, Newsome TP, Kim KW, Mak J, Lowry K, Bryant N, Meers J, Roberts JA, McMillan N, Labzin LI, Slonchak A, Hugo LE, Henzeler B, Newton ND, David CT, Reading PC, Esneau C, Briody T, Nasr N, McNeale D, McSharry B, Fakhri O, Horsburgh BA, Logan G, Howley P, Young P. Statement in Support of: "Virology under the Microscope-a Call for Rational Discourse". mSphere 2023:e0016523. [PMID: 37097028 DOI: 10.1128/msphere.00165-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Affiliation(s)
- Peter Speck
- Flinders University, Bedford Park, South Australia
| | - Jason Mackenzie
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Rowena A Bull
- Kirby Institute, University of New South Wales, Sydney, Australia
| | | | | | | | - Lara Herrero
- Griffith University, Southport, Queensland, Australia
| | - Karla Helbig
- La Trobe University, Melbourne, Victoria, Australia
| | - Sarah Londrigan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | - Natalie Prow
- Hull York Medical School, University of York, York, United Kingdom
| | - Grant Hansman
- Griffith University, Southport, Queensland, Australia
| | | | | | | | - David Tscharke
- Australian National University, Canberra, Australian Capital Territory, Australia
| | | | | | - Rhys Parry
- University of Queensland, St. Lucia, Queensland, Australia
| | - Glenn Marsh
- Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia
| | - Emma Harding
- University of New South Wales, Sydney, New South Wales, Australia
| | - David A Jacques
- University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew J Gartner
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Wen Shi Lee
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Julie McAuley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Paola Vaz
- University of Melbourne, Melbourne, Victoria, Australia
| | | | - Michelle D Tate
- Monash University, Melbourne, Victoria, Australia
- Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Jane Sinclair
- University of Queensland, St. Lucia, Queensland, Australia
| | - Allison Imrie
- University of Western Australia, Perth, Western Australia, Australia
| | | | - Andrew Harman
- The University of Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | | | | | | | | | - Thomas Tu
- The University of Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | | | | | - Robyn Hall
- Ausvet Pty Ltd., Canberra, Australian Capital Territory, Australia
- Commonwealth Scientific and Industrial Research Organisation, Black Mountain, Australian Capital Territory, Australia
| | - Morgyn Warner
- University of Adelaide, Adelaide, South Australia, Australia
- SA Pathology, Adelaide, South Australia, Australia
| | | | - Danielle E Anderson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | - Natalie E Netzler
- University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre of Research Excellence, Auckland, New Zealand
| | | | - Peter Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michael Beard
- University of Adelaide, Adelaide, South Australia, Australia
| | | | | | - Adi Idris
- Griffith University, Southport, Queensland, Australia
- Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jade Forwood
- Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Subir Sarker
- La Trobe University, Melbourne, Victoria, Australia
| | - Damian F J Purcell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Nathan Bartlett
- The University of Newcastle, Newcastle, New South Wales, Australia
| | - Joshua M Deerain
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Bruce J Brew
- University of New South Wales, Sydney, New South Wales, Australia
- University of Notre Dame, Sydney, New South Wales, Australia
- St. Vincent's Hospital, Sydney, New South Wales, Australia
| | - Sassan Asgari
- University of Queensland, St. Lucia, Queensland, Australia
| | - Helen Farrell
- University of Queensland, St. Lucia, Queensland, Australia
| | | | | | | | - Sevim Mese
- University of Queensland, St. Lucia, Queensland, Australia
- Istanbul University, Istanbul, Turkey
| | - Yaman Tayyar
- Griffith University, Southport, Queensland, Australia
- Prorenata Biotech, Moledinar, Queensland, Australia
| | | | | | - Abrar Hussain
- Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Connor J I Daymond
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | | | | | - Robin MacDiarmid
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | | | - Jay Laws
- La Trobe University, Melbourne, Victoria, Australia
| | - Lucy L Furfaro
- University of Western Australia, Perth, Western Australia, Australia
| | | | | | | | - Mary Petrone
- The University of Sydney, New South Wales, Australia
| | - Justin A Roby
- Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Carolyn Samer
- The University of Sydney, New South Wales, Australia
| | - Andreas Suhrbier
- University of Queensland, St. Lucia, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | | | - Anthony Cunningham
- The University of Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Celeste Donato
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Jackie Mahar
- The University of Sydney, New South Wales, Australia
| | - Wesley D Black
- Biotopia Environmental Assessment Pty Ltd., Melbourne, Victoria, Australia
| | | | | | - Kirsten Spann
- Queensland University of Technology, Brisbane, Queensland, Australia
| | - Daniel J Rawle
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Penny Rudd
- Griffith University, Southport, Queensland, Australia
| | - Jessica Neil
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | - Ki Wook Kim
- University of New South Wales, Sydney, New South Wales, Australia
| | - Johnson Mak
- Griffith University, Southport, Queensland, Australia
| | - Kym Lowry
- University of Queensland, St. Lucia, Queensland, Australia
| | - Nathan Bryant
- The University of Newcastle, Newcastle, New South Wales, Australia
| | - Joanne Meers
- University of Queensland, St. Lucia, Queensland, Australia
| | - Jason A Roberts
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | | | | | - Leon E Hugo
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | | | | | | | - Patrick C Reading
- University of Melbourne, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, Australia
| | - Camille Esneau
- The University of Newcastle, Newcastle, New South Wales, Australia
| | - Tatiana Briody
- University of Queensland, St. Lucia, Queensland, Australia
| | - Najla Nasr
- The University of Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | | | - Brian McSharry
- Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Omid Fakhri
- Commonwealth Scientific and Industrial Research Organisation, Black Mountain, Australian Capital Territory, Australia
| | | | - Grant Logan
- Children's Medical Research Institute, Westmead, NSW, Australia
| | - Paul Howley
- Vaxmed Pty Ltd., Berwick, Victoria, Australia
| | - Paul Young
- University of Queensland, St. Lucia, Queensland, Australia
| |
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10
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Speck P, Mackenzie J, Bull RA, Slobedman B, Drummer H, Fraser J, Herrero L, Helbig K, Londrigan S, Moseley G, Prow N, Hansman G, Edwards R, Ahlenstiel C, Abendroth A, Tscharke D, Hobson-Peters J, Kriiger-Loterio R, Parry R, Marsh G, Harding E, Jacques DA, Gartner MJ, Lee WS, McAuley J, Vaz P, Sainsbury F, Tate MD, Sinclair J, Imrie A, Rawlinson S, Harman A, Carr JM, Monson EA, Hibma M, Mahony TJ, Tu T, Center RJ, Shrestha LB, Hall R, Warner M, Ward V, Anderson DE, Eyre NS, Netzler NE, Peel AJ, Revill P, Beard M, Legione AR, Spencer AJ, Idris A, Forwood J, Sarker S, Purcell DFJ, Bartlett N, Deerain JM, Brew BJ, Asgari S, Farrell H, Khromykh A, Enosi Tuipulotu D, Anderson D, Mese S, Tayyar Y, Edenborough K, Uddin JM, Hussain A, Daymond CJI, Agius J, Johnson KN, Shirmast P, Abedinzadeshahri M, MacDiarmid R, Ashley CL, Laws J, Furfaro LL, Burton TD, Johnson SMR, Telikani Z, Petrone M, Roby JA, Samer C, Suhrbier A, Van Der Kamp A, Cunningham A, Donato C, Mahar J, Black WD, Vasudevan S, Lenchine R, Spann K, Rawle DJ, Rudd P, Neil J, Kingston R, Newsome TP, Kim KW, Mak J, Lowry K, Bryant N, Meers J, Roberts JA, McMillan N, Labzin LI, Slonchak A, Hugo LE, Henzeler B, Newton ND, David CT, Reading PC, Esneau C, Briody T, Nasr N, McNeale D, McSharry B, Fakhri O, Horsburgh BA, Logan G, Howley P, Young P. Statement in Support of: "Virology under the Microscope-a Call for Rational Discourse". J Virol 2023; 97:e0045123. [PMID: 37097023 DOI: 10.1128/jvi.00451-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Affiliation(s)
- Peter Speck
- Flinders University, Bedford Park, South Australia
| | - Jason Mackenzie
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Rowena A Bull
- Kirby Institute, University of New South Wales, Sydney, Australia
| | | | | | | | - Lara Herrero
- Griffith University, Southport, Queensland, Australia
| | - Karla Helbig
- La Trobe University, Melbourne, Victoria, Australia
| | - Sarah Londrigan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | - Natalie Prow
- Hull York Medical School, University of York, York, United Kingdom
| | - Grant Hansman
- Griffith University, Southport, Queensland, Australia
| | | | | | | | - David Tscharke
- Australian National University, Canberra, Australian Capital Territory, Australia
| | | | | | - Rhys Parry
- University of Queensland, St. Lucia, Queensland, Australia
| | - Glenn Marsh
- Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia
| | - Emma Harding
- University of New South Wales, Sydney, New South Wales, Australia
| | - David A Jacques
- University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew J Gartner
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Wen Shi Lee
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Julie McAuley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Paola Vaz
- University of Melbourne, Melbourne, Victoria, Australia
| | | | - Michelle D Tate
- Monash University, Melbourne, Victoria, Australia
- Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Jane Sinclair
- University of Queensland, St. Lucia, Queensland, Australia
| | - Allison Imrie
- University of Western Australia, Perth, Western Australia, Australia
| | | | - Andrew Harman
- The University of Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | | | | | | | | | - Thomas Tu
- The University of Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | | | | | - Robyn Hall
- Ausvet Pty Ltd., Canberra, Australian Capital Territory, Australia
- Commonwealth Scientific and Industrial Research Organisation, Black Mountain, Australian Capital Territory, Australia
| | - Morgyn Warner
- University of Adelaide, Adelaide, South Australia, Australia
- SA Pathology, Adelaide, South Australia, Australia
| | | | - Danielle E Anderson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | - Natalie E Netzler
- University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre of Research Excellence, Auckland, New Zealand
| | | | - Peter Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michael Beard
- University of Adelaide, Adelaide, South Australia, Australia
| | | | | | - Adi Idris
- Griffith University, Southport, Queensland, Australia
- Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jade Forwood
- Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Subir Sarker
- La Trobe University, Melbourne, Victoria, Australia
| | - Damian F J Purcell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Nathan Bartlett
- The University of Newcastle, Newcastle, New South Wales, Australia
| | - Joshua M Deerain
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Bruce J Brew
- University of New South Wales, Sydney, New South Wales, Australia
- University of Notre Dame, Sydney, New South Wales, Australia
- St. Vincent's Hospital, Sydney, New South Wales, Australia
| | - Sassan Asgari
- University of Queensland, St. Lucia, Queensland, Australia
| | - Helen Farrell
- University of Queensland, St. Lucia, Queensland, Australia
| | | | | | | | - Sevim Mese
- University of Queensland, St. Lucia, Queensland, Australia
- Istanbul University, Istanbul, Turkey
| | - Yaman Tayyar
- Griffith University, Southport, Queensland, Australia
- Prorenata Biotech, Moledinar, Queensland, Australia
| | | | | | - Abrar Hussain
- Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Connor J I Daymond
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | | | | | - Robin MacDiarmid
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | | | - Jay Laws
- La Trobe University, Melbourne, Victoria, Australia
| | - Lucy L Furfaro
- University of Western Australia, Perth, Western Australia, Australia
| | | | | | | | - Mary Petrone
- The University of Sydney, New South Wales, Australia
| | - Justin A Roby
- Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Carolyn Samer
- The University of Sydney, New South Wales, Australia
| | - Andreas Suhrbier
- University of Queensland, St. Lucia, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | | | - Anthony Cunningham
- The University of Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Celeste Donato
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Jackie Mahar
- The University of Sydney, New South Wales, Australia
| | - Wesley D Black
- Biotopia Environmental Assessment Pty Ltd., Melbourne, Victoria, Australia
| | | | | | - Kirsten Spann
- Queensland University of Technology, Brisbane, Queensland, Australia
| | - Daniel J Rawle
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Penny Rudd
- Griffith University, Southport, Queensland, Australia
| | - Jessica Neil
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | - Ki Wook Kim
- University of New South Wales, Sydney, New South Wales, Australia
| | - Johnson Mak
- Griffith University, Southport, Queensland, Australia
| | - Kym Lowry
- University of Queensland, St. Lucia, Queensland, Australia
| | - Nathan Bryant
- The University of Newcastle, Newcastle, New South Wales, Australia
| | - Joanne Meers
- University of Queensland, St. Lucia, Queensland, Australia
| | - Jason A Roberts
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | | | | | - Leon E Hugo
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | | | | | | | - Patrick C Reading
- University of Melbourne, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, Australia
| | - Camille Esneau
- The University of Newcastle, Newcastle, New South Wales, Australia
| | - Tatiana Briody
- University of Queensland, St. Lucia, Queensland, Australia
| | - Najla Nasr
- The University of Sydney, New South Wales, Australia
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | | | - Brian McSharry
- Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Omid Fakhri
- Commonwealth Scientific and Industrial Research Organisation, Black Mountain, Australian Capital Territory, Australia
| | | | - Grant Logan
- Children's Medical Research Institute, Westmead, NSW, Australia
| | - Paul Howley
- Vaxmed Pty Ltd., Berwick, Victoria, Australia
| | - Paul Young
- University of Queensland, St. Lucia, Queensland, Australia
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11
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Montgomerie I, Bird TW, Palmer OR, Mason NC, Pankhurst TE, Lawley B, Hernández LC, Harfoot R, Authier-Hall A, Anderson DE, Hilligan KL, Buick KH, Mbenza NM, Mittelstädt G, Maxwell S, Sinha S, Kuang J, Subbarao K, Parker EJ, Sher A, Hermans IF, Ussher JE, Quiñones-Mateu ME, Comoletti D, Connor LM. Incorporation of SARS-CoV-2 spike NTD to RBD protein vaccine improves immunity against viral variants. iScience 2023; 26:106256. [PMID: 36845030 PMCID: PMC9940465 DOI: 10.1016/j.isci.2023.106256] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/10/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Emerging SARS-CoV-2 variants pose a threat to human health worldwide. SARS-CoV-2 receptor binding domain (RBD)-based vaccines are suitable candidates for booster vaccines, eliciting a focused antibody response enriched for virus neutralizing activity. Although RBD proteins are manufactured easily, and have excellent stability and safety properties, they are poorly immunogenic compared to the full-length spike protein. We have overcome this limitation by engineering a subunit vaccine composed of an RBD tandem dimer fused to the N-terminal domain (NTD) of the spike protein. We found that inclusion of the NTD (1) improved the magnitude and breadth of the T cell and anti-RBD response, and (2) enhanced T follicular helper cell and memory B cell generation, antibody potency, and cross-reactive neutralization activity against multiple SARS-CoV-2 variants, including B.1.1.529 (Omicron BA.1). In summary, our uniquely engineered RBD-NTD-subunit protein vaccine provides a promising booster vaccination strategy capable of protecting against known SARS-CoV-2 variants of concern.
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Affiliation(s)
- Isabelle Montgomerie
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Thomas W Bird
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Olga R Palmer
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | | | | | - Blair Lawley
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Leonor C Hernández
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Rhodri Harfoot
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Danielle E Anderson
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kerry L Hilligan
- Malaghan Institute of Medical Research, Wellington, New Zealand
- Laboratory of Parasitic Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kaitlin H Buick
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Naasson M Mbenza
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Gerd Mittelstädt
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Samara Maxwell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Shubhra Sinha
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Joanna Kuang
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Kanta Subbarao
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, VIC, Australia
| | - Emily J Parker
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Alan Sher
- Laboratory of Parasitic Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ian F Hermans
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - James E Ussher
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Miguel E Quiñones-Mateu
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Webster Centre for Infectious Diseases, University of Otago, Dunedin, New Zealand
| | - Davide Comoletti
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Lisa M Connor
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Malaghan Institute of Medical Research, Wellington, New Zealand
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12
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Paskey AC, Lim XF, Ng JHJ, Rice GK, Chia WN, Philipson CW, Foo R, Cer RZ, Long KA, Lueder MR, Glang L, Frey KG, Hamilton T, Mendenhall IH, Smith GJ, Anderson DE, Wang LF, Bishop-Lilly KA. Genomic Characterization of a Relative of Mumps Virus in Lesser Dawn Bats of Southeast Asia. Viruses 2023; 15:v15030659. [PMID: 36992368 PMCID: PMC10053730 DOI: 10.3390/v15030659] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
The importance of genomic surveillance on emerging diseases continues to be highlighted with the ongoing SARS-CoV-2 pandemic. Here, we present an analysis of a new bat-borne mumps virus (MuV) in a captive colony of lesser dawn bats (Eonycteris spelaea). This report describes an investigation of MuV-specific data originally collected as part of a longitudinal virome study of apparently healthy, captive lesser dawn bats in Southeast Asia (BioProject ID PRJNA561193) which was the first report of a MuV-like virus, named dawn bat paramyxovirus (DbPV), in bats outside of Africa. More in-depth analysis of these original RNA sequences in the current report reveals that the new DbPV genome shares only 86% amino acid identity with the RNA-dependent RNA polymerase of its closest relative, the African bat-borne mumps virus (AbMuV). While there is no obvious immediate cause for concern, it is important to continue investigating and monitoring bat-borne MuVs to determine the risk of human infection.
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Affiliation(s)
- Adrian C. Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Xiao Fang Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Justin H. J. Ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Gregory K. Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Casandra W. Philipson
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Randy Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | - Kyle A. Long
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Matthew R. Lueder
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Lindsay Glang
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Kenneth G. Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Gavin J. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Danielle E. Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Correspondence:
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13
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Wang LF, Mani S, Tan CW, Anderson DE. Assays for Detecting Henipavirus Antibodies. Methods Mol Biol 2023; 2682:245-258. [PMID: 37610587 DOI: 10.1007/978-1-0716-3283-3_18] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
While molecular detection has increasingly become the detection method of choice for infectious diseases, antibody detection remains an important approach for diagnosis and surveillance. For henipaviruses, antibody detection methods such as ELISA and Western blot played a key role in the initial discovery of bats as the natural reservoir host. Here, we will describe three additional antibody detection methods (LIPS, Luminex, and pseudovirus systems), which can be used in most BSL2 laboratories without the need for live virus and a high containment BSL4 facility.
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Affiliation(s)
- Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| | - Shailendra Mani
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- NCR Biotech Science Cluster, Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity , Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
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14
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Gamage AM, Chan WOY, Zhu F, Lim YT, Long S, Ahn M, Tan CW, Hiang Foo RJ, Sia WR, Lim XF, He H, Zhai W, Anderson DE, Sobota RM, Dutertre CA, Wang LF. Single-cell transcriptome analysis of the in vivo response to viral infection in the cave nectar bat Eonycteris spelaea. Immunity 2022; 55:2187-2205.e5. [PMID: 36351376 DOI: 10.1016/j.immuni.2022.10.008] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 07/19/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022]
Abstract
Bats are reservoir hosts of many zoonotic viruses with pandemic potential. We utilized single-cell transcriptome sequencing (scRNA-seq) to analyze the immune response in bat lungs upon in vivo infection with a double-stranded RNA virus, Pteropine orthoreovirus PRV3M. Bat neutrophils were distinguished by high basal IDO1 expression. NK cells and T cells were the most abundant immune cells in lung tissue. Three distinct CD8+ effector T cell populations could be delineated by differential expression of KLRB1, GFRA2, and DPP4. Select NK and T clusters increased expression of genes involved in T cell activation and effector function early after viral infection. Alveolar macrophages and classical monocytes drove antiviral interferon signaling. Infection expanded a CSF1R+ population expressing collagen-like genes, which became the predominant myeloid cell type post-infection. This work uncovers features relevant to viral disease tolerance in bats, lays a foundation for future experimental work, and serves as a resource for comparative immunology studies.
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Affiliation(s)
- Akshamal M Gamage
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Wharton O Y Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Yan Ting Lim
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Sandy Long
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Matae Ahn
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Randy Jee Hiang Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Wan Rong Sia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Xiao Fang Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Haopeng He
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, P.R. China; Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, 138672, Singapore, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore; Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Victoria, Australia
| | - Radoslaw Mikolaj Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Charles-Antoine Dutertre
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Gustave Roussy Cancer Campus, Villejuif, France
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore; Singhealth Duke-NUS Global Health Institute, Singapore, Singapore.
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15
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Zhang XA, Li H, Jiang FC, Zhu F, Zhang YF, Chen JJ, Tan CW, Anderson DE, Fan H, Dong LY, Li C, Zhang PH, Li Y, Ding H, Fang LQ, Wang LF, Liu W. A Zoonotic Henipavirus in Febrile Patients in China. N Engl J Med 2022; 387:470-472. [PMID: 35921459 DOI: 10.1056/nejmc2202705] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xiao-Ai Zhang
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hao Li
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fa-Chun Jiang
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China
| | - Feng Zhu
- Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Yun-Fa Zhang
- State Key Laboratory of Pathogens and Biosecurity, Beijing, China
| | - Jin-Jin Chen
- State Key Laboratory of Pathogens and Biosecurity, Beijing, China
| | - Chee-Wah Tan
- Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Danielle E Anderson
- Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Hang Fan
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Li-Yan Dong
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China
| | - Chang Li
- Changchun Institute of Veterinary Medicine, Changchun, China
| | - Pan-He Zhang
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yue Li
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Heng Ding
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Li-Qun Fang
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin-Fa Wang
- Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Wei Liu
- Beijing Institute of Microbiology and Epidemiology, Beijing, China
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16
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Miller MB, Ooi EE, Rhoads DD, Kulldorff M, Anderson DE, Lee H, Gupta S, Mel K. As Omicron Takes Hold and Other New Variants Arise, COVID-19 Testing Remains the Universally Agreed Tool to Effect Transition From Pandemic to Endemic State. Front Public Health 2022; 10:883066. [PMID: 35602143 PMCID: PMC9121917 DOI: 10.3389/fpubh.2022.883066] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
The COVID-19 pandemic has caused more than 448 million cases and 6 million deaths worldwide to date. Omicron is now the dominant SARS-CoV-2 variant, making up more than 90% of cases in countries reporting sequencing data. As the pandemic continues into its third year, continued testing is a strategic and necessary tool for transitioning to an endemic state of COVID-19. Here, we address three critical topics pertaining to the transition from pandemic to endemic: defining the endemic state for COVID-19, highlighting the role of SARS-CoV-2 testing as endemicity is approached, and recommending parameters for SARS-CoV-2 testing once endemicity is reached. We argue for an approach that capitalizes on the current public health momentum to increase capacity for PCR-based testing and whole genome sequencing to monitor emerging infectious diseases. Strategic development and utilization of testing, including viral panels in addition to vaccination, can keep SARS-CoV-2 in a manageable endemic state and build a framework of preparedness for the next pandemic.
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Affiliation(s)
- Melissa B Miller
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.,Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Daniel D Rhoads
- Department of Pathology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States.,Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, United States
| | - Martin Kulldorff
- Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Danielle E Anderson
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Hyukmin Lee
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Krajden Mel
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
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17
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Zhu F, Duong V, Lim XF, Hul V, Chawla T, Keatts L, Goldstein T, Hassanin A, Tu VT, Buchy P, Sessions OM, Wang LF, Dussart P, Anderson DE. Presence of Recombinant Bat Coronavirus GCCDC1 in Cambodian Bats. Viruses 2022; 14:v14020176. [PMID: 35215769 PMCID: PMC8877364 DOI: 10.3390/v14020176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/31/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 12/04/2022] Open
Abstract
Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extreme example is the insertion of the P10 gene from reoviruses in the bat CoV GCCDC1, first discovered in Rousettus leschenaultii bats in China. Here, we report the detection of GCCDC1 in four different bat species (Eonycteris spelaea, Cynopterus sphinx, Rhinolophus shameli and Rousettus sp.) in Cambodia. This finding demonstrates a much broader geographic and bat species range for this virus and indicates common cross-species transmission. Interestingly, one of the bat samples showed a co-infection with an Alpha CoV most closely related to RsYN14, a virus recently discovered in the same genus (Rhinolophus) of bat in Yunnan, China, 2020. Taken together, our latest findings highlight the need to conduct active surveillance in bats to assess the risk of emerging CoVs, especially in Southeast Asia.
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Affiliation(s)
- Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
| | - Xiao Fang Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Vibol Hul
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
- Unité des Virus Émergents, (UVÉ: Aix-Marseille Univ-IRD 190-INSERM 1207), 13005 Marseille, France
| | - Tanu Chawla
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Lucy Keatts
- Wildlife Conservation Society, Health Program, Bronx, NY 10460, USA;
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité, Sorbonne Université, MNHN, CNRS, EPHE, UA, 75005 Paris, France;
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, No. 18, Hoang Quoc Viet Road, Cau Giay District, Hanoi 10072, Vietnam;
| | - Philippe Buchy
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
| | - October M. Sessions
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
- Correspondence: (L.-F.W.); (P.D.); (D.E.A.)
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
- Correspondence: (L.-F.W.); (P.D.); (D.E.A.)
| | - Danielle E. Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
- Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, University of Melbourne, Melbourne 3000, Australia
- Correspondence: (L.-F.W.); (P.D.); (D.E.A.)
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18
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Monaco DR, Kottapalli SV, Breitwieser FP, Anderson DE, Wijaya L, Tan K, Chia WN, Kammers K, Caturegli P, Waugh K, Roederer M, Petri M, Goldman DW, Rewers M, Wang LF, Larman HB. Deconvoluting virome-wide antibody epitope reactivity profiles. EBioMedicine 2022; 75:103747. [PMID: 34922324 PMCID: PMC8688874 DOI: 10.1016/j.ebiom.2021.103747] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 06/10/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Comprehensive characterization of exposures and immune responses to viral infections is critical to a basic understanding of human health and disease. We previously developed the VirScan system, a programmable phage-display technology for profiling antibody binding to a library of peptides designed to span the human virome. Previous VirScan analytical approaches did not carefully account for antibody cross-reactivity among sequences shared by related viruses or for the disproportionate representation of individual viruses in the library. METHODS Here we present the AntiViral Antibody Response Deconvolution Algorithm (AVARDA), a multi-module software package for analyzing VirScan datasets. AVARDA provides a probabilistic assessment of infection with species-level resolution by considering sequence alignment of all library peptides to each other and to all human viruses. We employed AVARDA to analyze VirScan data from a cohort of encephalitis patients with either known viral infections or undiagnosed etiologies. We further assessed AVARDA's utility in associating viral infection with type 1 diabetes and lupus. FINDINGS By comparing acute and convalescent sera, AVARDA successfully confirmed or detected encephalitis-associated responses to human herpesviruses 1, 3, 4, 5, and 6, improving the rate of diagnosing viral encephalitis in this cohort by 44%. AVARDA analyses of VirScan data from the type 1 diabetes and lupus cohorts implicated enterovirus and herpesvirus infections, respectively. INTERPRETATION AVARDA, in combination with VirScan and other pan-pathogen serological techniques, is likely to find broad utility in the epidemiology and diagnosis of infectious diseases. FUNDING This work was made possible by support from the National Institutes of Health (NIH), the US Army Research Office, the Singapore Infectious Diseases Initiative (SIDI), the Singapore Ministry of Health's National Medical Research Council (NMRC) and the Singapore National Research Foundation (NRF).
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Affiliation(s)
- Daniel R Monaco
- Department of Pathology, Division of Immunology, Institute of Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sanjay V Kottapalli
- Department of Pathology, Division of Immunology, Institute of Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Florian P Breitwieser
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Limin Wijaya
- Department of Infectious Diseases, Singapore General Hospital, 20 College Road, 169856, Singapore
| | - Kevin Tan
- National Neuroscience Institute, 11 Jalan Tan Tock Seng, 308433, Singapore
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Kai Kammers
- Department of Oncology, Division of Biostatistics and Bioinformatics, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patrizio Caturegli
- Department of Pathology, Division of Immunology, Institute of Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kathleen Waugh
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michelle Petri
- Department of Medicine, Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel W Goldman
- Department of Medicine, Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - H Benjamin Larman
- Department of Pathology, Division of Immunology, Institute of Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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19
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Lam JH, Khan AK, Cornell TA, Chia TW, Dress RJ, Yeow WWW, Mohd-Ismail NK, Venkataraman S, Ng KT, Tan YJ, Anderson DE, Ginhoux F, Nallani M. Polymersomes as Stable Nanocarriers for a Highly Immunogenic and Durable SARS-CoV-2 Spike Protein Subunit Vaccine. ACS Nano 2021; 15:15754-15770. [PMID: 34618423 PMCID: PMC8525042 DOI: 10.1021/acsnano.1c01243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/30/2021] [Indexed: 05/05/2023]
Abstract
Multiple successful vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently needed to address the ongoing coronavirus disease 2019 (Covid-19) pandemic. In the present work, we describe a subunit vaccine based on the SARS-CoV-2 spike protein coadministered with CpG adjuvant. To enhance the immunogenicity of our formulation, both antigen and adjuvant were encapsulated with our proprietary artificial cell membrane (ACM) polymersome technology. Structurally, ACM polymersomes are self-assembling nanoscale vesicles made up of an amphiphilic block copolymer comprising poly(butadiene)-b-poly(ethylene glycol) and a cationic lipid, 1,2-dioleoyl-3-trimethylammonium-propane. Functionally, ACM polymersomes serve as delivery vehicles that are efficiently taken up by dendritic cells (DC1 and DC2), which are key initiators of the adaptive immune response. Two doses of our formulation elicit robust neutralizing antibody titers in C57BL/6 mice that persist at least 40 days. Furthermore, we confirm the presence of functional memory CD4+ and CD8+ T cells that produce T helper type 1 cytokines. This study is an important step toward the development of an efficacious vaccine in humans.
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Affiliation(s)
| | - Amit K. Khan
- ACM
Biolabs Pte Ltd, Singapore 638075, Singapore
| | | | | | - Regine J. Dress
- Singapore Immunology
Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | | | - Nur Khairiah Mohd-Ismail
- Infectious
Diseases Translational Research Program, Department of Microbiology
and Immunology, Yong Loo Lin School of Medicine, National University
Health System, National University of Singapore, Singapore 117545, Singapore
| | | | - Kim Tien Ng
- Infectious
Diseases Translational Research Program, Department of Microbiology
and Immunology, Yong Loo Lin School of Medicine, National University
Health System, National University of Singapore, Singapore 117545, Singapore
| | - Yee-Joo Tan
- Infectious
Diseases Translational Research Program, Department of Microbiology
and Immunology, Yong Loo Lin School of Medicine, National University
Health System, National University of Singapore, Singapore 117545, Singapore
- Institute
of Molecular and Cell Biology, Agency for Science, Technology
and Research, Singapore 138673, Singapore
| | - Danielle E. Anderson
- Program
in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore 169857, Singapore
| | - Florent Ginhoux
- Singapore Immunology
Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
- SingHealth
Translational Immunology and Inflammation Centre, Singapore 169856, Singapore
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20
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Wang J, Anderson DE, Halpin K, Hong X, Chen H, Walker S, Valdeter S, van der Heide B, Neave MJ, Bingham J, O'Brien D, Eagles D, Wang LF, Williams DT. A new Hendra virus genotype found in Australian flying foxes. Virol J 2021; 18:197. [PMID: 34641882 PMCID: PMC8510678 DOI: 10.1186/s12985-021-01652-7] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hendra virus (HeV) has caused lethal disease outbreaks in humans and horses in Australia. Flying foxes are the wildlife reservoir from which the virus was first isolated in 1996. Following a heat stress mortality event in Australian flying foxes in 2013, a novel HeV variant was discovered. This study describes the subsequent surveillance of Australian flying foxes for this novel virus over a nine year period using qRT-PCR testing of tissues from flying foxes submitted primarily for Australian bat lyssavirus diagnosis. Genome sequencing and characterisation of the novel HeV variant was also undertaken. METHODS Spleen and kidney samples harvested from flying fox carcasses were initially screened with two real-time qRT-PCR assays specific for the prototype HeV. Two additional qRT-PCR assays were developed specific for the HeV variant first detected in samples from a flying fox in 2013. Next-generation sequencing and virus isolation was attempted from selected samples to further characterise the new virus. RESULTS Since 2013, 98 flying foxes were tested and 11 were positive for the new HeV variant. No samples were positive for the original HeV. Ten of the positive samples were from grey-headed flying foxes (GHFF, Pteropus poliocephalus), however this species was over-represented in the opportunistic sampling (83% of bats tested were GHFF). The positive GHFF samples were collected from Victoria and South Australia and one positive Little red flying fox (LRFF, Pteropus scapulatus) was collected from Western Australia. Immunohistochemistry confirmed the presence of henipavirus antigen, associated with an inflammatory lesion in cardiac blood vessels of one GHFF. Positive samples were sequenced and the complete genome was obtained from three samples. When compared to published HeV genomes, there was 84% sequence identity at the nucleotide level. Based on phylogenetic analyses, the newly detected HeV belongs to the HeV species but occupies a distinct lineage. We have therefore designated this virus HeV genotype 2 (HeV-g2). Attempts to isolate virus from PCR positive samples have not been successful. CONCLUSIONS A novel HeV genotype (HeV-g2) has been identified in two flying fox species submitted from three states in Australia, indicating that the level of genetic diversity for HeV is broader than first recognised. Given its high genetic relatedness to HeV, HeV-g2 is a zoonotic pathogen.
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Affiliation(s)
- Jianning Wang
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Australia.
| | - Danielle E Anderson
- Programme in Emerging, Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Kim Halpin
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Australia
| | - Xiao Hong
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Australia
| | - Honglei Chen
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Australia
| | - Som Walker
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Australia
| | - Stacey Valdeter
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Australia
| | - Brenda van der Heide
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Australia
| | - Matthew J Neave
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Australia
| | - John Bingham
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Australia
| | - Dwane O'Brien
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Australia
| | - Debbie Eagles
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Australia
| | - Lin-Fa Wang
- Programme in Emerging, Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore, Singapore
| | - David T Williams
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Australia
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21
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Wittwer K, Anderson DE, Pfeffermann K, Cox RM, Wolf JD, Santibanez S, Mankertz A, Plesker R, Sticher ZM, Kolkykhalov AA, Natchus MG, Pfaller CK, Plemper RK, von Messling V. Small-molecule polymerase inhibitor protects non-human primates from measles and reduces shedding. Nat Commun 2021; 12:5233. [PMID: 34475387 PMCID: PMC8413292 DOI: 10.1038/s41467-021-25497-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 08/12/2021] [Indexed: 01/26/2023] Open
Abstract
Measles virus (MeV) is a highly contagious pathogen that enters the human host via the respiratory route. Besides acute pathologies including fever, cough and the characteristic measles rash, the infection of lymphocytes leads to substantial immunosuppression that can exacerbate the outcome of infections with additional pathogens. Despite the availability of effective vaccine prophylaxis, measles outbreaks continue to occur worldwide. We demonstrate that prophylactic and post-exposure therapeutic treatment with an orally bioavailable small-molecule polymerase inhibitor, ERDRP-0519, prevents measles disease in squirrel monkeys (Saimiri sciureus). Treatment initiation at the onset of clinical signs reduced virus shedding, which may support outbreak control. Results show that this clinical candidate has the potential to alleviate clinical measles and augment measles virus eradication. Measles virus is highly contagious and outbreaks occur worldwide. Here the authors show that the orally bioavailable small-molecule polymerase inhibitor ERDRP-0519 prevents measles disease in squirrel monkeys and reduces virus shedding.
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Affiliation(s)
- Kevin Wittwer
- Veterinary Medicine Division, Paul-Ehrlich-Institute, Langen, Germany
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | | | - Robert M Cox
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Josef D Wolf
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sabine Santibanez
- WHO European Regional Reference Laboratory for Measles and Rubella, Robert Koch-Institute, Berlin, Germany
| | - Annette Mankertz
- WHO European Regional Reference Laboratory for Measles and Rubella, Robert Koch-Institute, Berlin, Germany
| | - Roland Plesker
- Veterinary Medicine Division, Paul-Ehrlich-Institute, Langen, Germany
| | - Zachary M Sticher
- Emory Institute for Drug Development, Emory University, Atlanta, GA, USA
| | | | - Michael G Natchus
- Emory Institute for Drug Development, Emory University, Atlanta, GA, USA
| | | | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
| | - Veronika von Messling
- Veterinary Medicine Division, Paul-Ehrlich-Institute, Langen, Germany.,Life Sciences Unit, Federal Ministry of Education and Research, Berlin, Germany
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22
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de Alwis R, Zellweger RM, Chua E, Wang LF, Chawla T, Sessions OM, Marlier D, Connolly JE, von Messling V, Anderson DE. Systemic inflammation, innate immunity and pathogenesis after Zika virus infection in cynomolgus macaques are modulated by strain-specificity within the Asian lineage. Emerg Microbes Infect 2021; 10:1457-1470. [PMID: 34120576 PMCID: PMC8300938 DOI: 10.1080/22221751.2021.1943536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Zika virus (ZIKV) is an emerging arbovirus with recent global expansion. Historically, ZIKV infections with Asian lineages have been associated with mild disease such as rash and fever. However, recent Asian sub-lineages have caused outbreaks in the South Pacific and Latin America with increased prevalence of neurological disorders in infants and adults. Asian sub-lineage differences may partially explain the range of disease severity observed. However, the effect of Asian sub-lineage differences on pathogenesis remains poorly characterized. Current study conducts a head-to-head comparison of three Asian sub-lineages that are representative of the circulating ancestral mild Asian strain (ZIKV-SG), the 2007 epidemic French Polynesian strain (ZIKV-FP), and the 2013 epidemic Brazil strain (ZIKV-Brazil) in adult Cynomolgus macaques. Animals infected intervenously or subcutaneously with either of the three clinical isolates showed sub-lineage-specific differences in viral pathogenesis, early innate immune responses and systemic inflammation. Despite the lack of neurological symptoms in infected animals, the epidemiologically neurotropic ZIKV sub-lineages (ZIKV-Brazil and/or ZIKV-FP) were associated with more sustained viral replication, higher systemic inflammation (i.e. higher levels of TNFα, MCP-1, IL15 and G-CSF) and greater percentage of CD14+ monocytes and dendritic cells in blood. Multidimensional analysis showed clustering of ZIKV-SG away from ZIKV-Brazil and ZIKV-FP, further confirming sub-lineage differences in the measured parameters. These findings highlight greater systemic inflammation and monocyte recruitment as possible risk factors of adult ZIKV disease observed during the 2007 FP and 2013 Brazil epidemics. Future studies should explore the use of anti-inflammatory therapeutics as early treatment to prevent ZIKV-associated disease in adults.
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Affiliation(s)
- Ruklanthi de Alwis
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,Viral Research and Experimental Medicine Centre, SingHealth-Duke NUS, Singapore
| | | | - Edmond Chua
- Institute of Molecular and Cell Biology, A*STAR, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Tanu Chawla
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - October M Sessions
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,Department of Pharmacy, National University of Singapore, Singapore
| | - Damien Marlier
- Institute of Molecular and Cell Biology, A*STAR, Singapore
| | - John E Connolly
- Institute of Molecular and Cell Biology, A*STAR, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Institute of Biomedical Studies, Baylor University, Waco, TX, USA
| | - Veronika von Messling
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,Veterinary Medicine Division, Paul-Ehrlich-Institute, Langen, Germany
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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23
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Tan J, Anderson DE, Rathore APS, O'Neill A, Mantri CK, Saron WAA, Lee C, Cui CW, Kang AEZ, Foo R, Kalimuddin S, Low JG, Ho L, Tambyah P, Burke TW, Woods CW, Chan KR, Karhausen J, John ALS. Signatures of mast cell activation are associated with severe COVID-19. medRxiv 2021. [PMID: 34100020 DOI: 10.1101/2021.05.31.21255594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Lung inflammation is a hallmark of Coronavirus disease 2019 (COVID-19) in severely ill patients and the pathophysiology of disease is thought to be immune-mediated. Mast cells (MCs) are polyfunctional immune cells present in the airways, where they respond to certain viruses and allergens, often promoting inflammation. We observed widespread degranulation of MCs during acute and unresolved airway inflammation in SARS-CoV-2-infected mice and non-human primates. In humans, transcriptional changes in patients requiring oxygen supplementation also implicated cells with a MC phenotype. MC activation in humans was confirmed, through detection of the MC-specific protease, chymase, levels of which were significantly correlated with disease severity. These results support the association of MC activation with severe COVID-19, suggesting potential strategies for intervention.
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24
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Tan CW, Yang X, Anderson DE, Wang LF. Bat virome research: the past, the present and the future. Curr Opin Virol 2021; 49:68-80. [PMID: 34052731 DOI: 10.1016/j.coviro.2021.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023]
Abstract
Bats have been increasingly recognised as an exceptional reservoir for emerging zoonotic viruses for the past few decades. Recent studies indicate that the unique bat immune system may be partially responsible for their ability to co-exist with viruses with minimal or no clinical diseases. In this review, we discuss the history and importance of bat virome studies and contrast the vast difference between such studies before and after the introduction of next generation sequencing (NGS) in this area of research. We also discuss the role of discovery serology and high-throughput single cell RNA-seq in future bat virome research.
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Affiliation(s)
- Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Xinglou Yang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; SingHealth Duke-NUS Global Health Institute, 169857, Singapore.
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25
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Yeo JG, Leong JY, Tay SH, Nadua KD, Anderson DE, Lim AJM, Ng XW, Poh SL, Guo D, Yaung KN, Kumar P, Wasser M, Hazirah SN, Sutamam N, Chua CJH, Qui M, Foo R, Gamage AM, Yeo KT, Ramakrishna L, Arkachaisri T, Young BE, Lye DC, Wang LF, Chong CY, Tan NWH, Li J, Kam KQ, Ginhoux F, Thoon KC, Chan JKY, Yung CF, Albani S. A Virus-Specific Immune Rheostat in the Immunome of Patients Recovering From Mild COVID-19. Front Immunol 2021; 12:674279. [PMID: 34113347 PMCID: PMC8185226 DOI: 10.3389/fimmu.2021.674279] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/05/2021] [Indexed: 01/10/2023] Open
Abstract
An accurate depiction of the convalescent COVID-19 immunome will help delineate the immunological milieu crucial for disease resolution and protection. Using mass cytometry, we characterized the immune architecture in patients recovering from mild COVID-19. We identified a virus-specific immune rheostat composed of an effector T (Teff) cell recall response that is balanced by the enrichment of a highly specialized regulatory T (Treg) cell subset. Both components were reactive against a peptide pool covering the receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein. We also observed expansion of IFNγ+ memory CD4+ T cells and virus-specific follicular helper T (TFH) cells. Overall, these findings pinpoint critical immune effector and regulatory mechanisms essential for a potent, yet harmless resolution of COVID-19 infection.
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Affiliation(s)
- Joo Guan Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.,Rheumatology and Immunology Service, Department of Pediatric Subspecialities, KK Women's and Children's Hospital, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Jing Yao Leong
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Shi Huan Tay
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Karen Donceras Nadua
- Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore.,Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | | | - Amanda Jin Mei Lim
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Xiang Wen Ng
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Su Li Poh
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Dianyan Guo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Katherine Nay Yaung
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Pavanish Kumar
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Martin Wasser
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Sharifah Nur Hazirah
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Nursyuhadah Sutamam
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Camillus Jian Hui Chua
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Martin Qui
- Duke-NUS Medical School, Singapore, Singapore
| | - Randy Foo
- Duke-NUS Medical School, Singapore, Singapore
| | | | - Kee Thai Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore.,Department of Neonatology, KK Women's and Children's Hospital, Singapore, Singapore
| | - Lakshmi Ramakrishna
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Thaschawee Arkachaisri
- Rheumatology and Immunology Service, Department of Pediatric Subspecialities, KK Women's and Children's Hospital, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Barnaby E Young
- Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore.,National Centre for Infectious Diseases, Singapore, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - David Chien Lye
- Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore.,National Centre for Infectious Diseases, Singapore, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore.,Lee Kong Chian School of Medicine, Singapore, Singapore
| | - Lin-Fa Wang
- Duke-NUS Medical School, Singapore, Singapore
| | - Chia Yin Chong
- Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore.,Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,Lee Kong Chian School of Medicine, Singapore, Singapore
| | - Natalie Woon Hui Tan
- Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore.,Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,Lee Kong Chian School of Medicine, Singapore, Singapore
| | - Jiahui Li
- Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore.,Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Kai-Qian Kam
- Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore.,Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Florent Ginhoux
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore.,Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Koh Cheng Thoon
- Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore.,Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,Lee Kong Chian School of Medicine, Singapore, Singapore
| | - Jerry Kok Yen Chan
- Duke-NUS Medical School, Singapore, Singapore.,Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Chee Fu Yung
- Duke-NUS Medical School, Singapore, Singapore.,Infectious Disease Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,Lee Kong Chian School of Medicine, Singapore, Singapore
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.,Rheumatology and Immunology Service, Department of Pediatric Subspecialities, KK Women's and Children's Hospital, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
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26
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Young BE, Wei WE, Fong SW, Mak TM, Anderson DE, Chan YH, Pung R, Heng CS, Ang LW, Zheng AKE, Lee B, Kalimuddin S, Pada S, Tambyah PA, Parthasarathy P, Tan SY, Sun L, Smith GJ, Lin RTP, Leo YS, Renia L, Wang LF, Ng LF, Maurer-Stroh S, Lye DC, Lee VJ. Association of SARS-CoV-2 clades with clinical, inflammatory and virologic outcomes: An observational study. EBioMedicine 2021; 66:103319. [PMID: 33840632 PMCID: PMC8027908 DOI: 10.1016/j.ebiom.2021.103319] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 11/30/2020] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Host determinants of severe coronavirus disease 2019 include advanced age, comorbidities and male sex. Virologic factors may also be important in determining clinical outcome and transmission rates, but limited patient-level data is available. METHODS We conducted an observational cohort study at seven public hospitals in Singapore. Clinical and laboratory data were collected and compared between individuals infected with different SARS-CoV-2 clades. Firth's logistic regression was used to examine the association between SARS-CoV-2 clade and development of hypoxia, and quasi-Poisson regression to compare transmission rates. Plasma samples were tested for immune mediator levels and the kinetics of viral replication in cell culture were compared. FINDINGS 319 patients with PCR-confirmed SARS-CoV-2 infection had clinical and virologic data available for analysis. 29 (9%) were infected with clade S, 90 (28%) with clade L/V, 96 (30%) with clade G (containing D614G variant), and 104 (33%) with other clades 'O' were assigned to lineage B.6. After adjusting for age and other covariates, infections with clade S (adjusted odds ratio (aOR) 0·030 (95% confidence intervals (CI): 0·0002-0·29)) or clade O (B·6) (aOR 0·26 (95% CI 0·064-0·93)) were associated with lower odds of developing hypoxia requiring supplemental oxygen compared with clade L/V. Patients infected with clade L/V had more pronounced systemic inflammation with higher concentrations of pro-inflammatory cytokines, chemokines and growth factors. No significant difference in the severity of clade G infections was observed (aOR 0·95 (95% CI: 0·35-2·52). Though viral loads were significantly higher, there was no evidence of increased transmissibility of clade G, and replicative fitness in cell culture was similar for all clades. INTERPRETATION Infection with clades L/V was associated with increased severity and more systemic release of pro-inflammatory cytokines. Infection with clade G was not associated with changes in severity, and despite higher viral loads there was no evidence of increased transmissibility.
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Affiliation(s)
- Barnaby E Young
- National Centre for Infectious Diseases, Singapore; Deaprtment of Infectious Diseases, Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Wycliffe E Wei
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore; Singapore Ministry of Health, Singapore
| | - Siew-Wai Fong
- A*STAR ID Labs, Agency for Science, Technology and Research (A*STAR), Singapore; Singapore Immunology Network, A*STAR, Singapore; Department of Biological Science, National University of Singapore, Singapore
| | - Tze-Minn Mak
- National Centre for Infectious Diseases, Singapore
| | | | - Yi-Hao Chan
- Singapore Immunology Network, A*STAR, Singapore; Singapore Immunology Network, A*STAR, Singapore
| | - Rachael Pung
- Singapore Ministry of Health, Singapore; London School of Hygiene and Tropical Medicine, London, UK
| | | | - Li Wei Ang
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore
| | | | - Bernett Lee
- Singapore Immunology Network, A*STAR, Singapore
| | - Shirin Kalimuddin
- Duke NUS Medical School, Singapore; Singapore General Hospital of Singapore, Singapore
| | | | - Paul A Tambyah
- National University Health System, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | | | | | | | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore; Deaprtment of Infectious Diseases, Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Laurent Renia
- Singapore Immunology Network, A*STAR, Singapore; Singapore Immunology Network, A*STAR, Singapore
| | | | - Lisa Fp Ng
- Singapore Immunology Network, A*STAR, Singapore; Singapore Immunology Network, A*STAR, Singapore
| | | | - David Chien Lye
- National Centre for Infectious Diseases, Singapore; Deaprtment of Infectious Diseases, Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vernon J Lee
- Singapore Ministry of Health, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
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27
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Affiliation(s)
- Linfa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
| | - Matae Ahn
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
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28
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Mai HK, Trieu NB, Long TH, Thanh HT, Luong ND, Huy LX, Nguyet LA, Man DNH, Anderson DE, Thanh TT, Chau NVV, Thwaites G, Wang LF, Van Tan L, Hung DT. Long-Term Humoral Immune Response in Persons with Asymptomatic or Mild SARS-CoV-2 Infection, Vietnam. Emerg Infect Dis 2021; 27:663-666. [PMID: 33496647 PMCID: PMC7853537 DOI: 10.3201/eid2702.204226] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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] [Indexed: 01/09/2023] Open
Abstract
Antibody response against nucleocapsid and spike proteins of SARS-CoV-2 in 11 persons with mild or asymptomatic infection rapidly increased after infection. At weeks 18–30 after diagnosis, all remained seropositive but spike protein–targeting antibody titers declined. These data may be useful for vaccine development.
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29
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Johannesdottir F, Allaire B, Kopperdahl DL, Keaveny TM, Sigurdsson S, Bredella MA, Anderson DE, Samelson EJ, Kiel DP, Gudnason VG, Bouxsein ML. Bone density and strength from thoracic and lumbar CT scans both predict incident vertebral fractures independently of fracture location. Osteoporos Int 2021; 32:261-269. [PMID: 32748310 PMCID: PMC8265597 DOI: 10.1007/s00198-020-05528-4] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/30/2020] [Indexed: 01/01/2023]
Abstract
UNLABELLED In a population-based study, we found that computed tomography (CT)-based bone density and strength measures from the thoracic spine predicted new vertebral fracture as well as measures from the lumbar spine, suggesting that CT scans at either the thorax or abdominal regions are useful to assess vertebral fracture risk. INTRODUCTION Prior studies have shown that computed tomography (CT)-based lumbar bone density and strength measurements predict incident vertebral fracture. This study investigated whether CT-based bone density and strength measurements from the thoracic spine predict incident vertebral fracture and compared the performance of thoracic and lumbar bone measurements to predict incident vertebral fracture. METHODS This case-control study of community-based men and women (age 74.6 ± 6.6) included 135 cases with incident vertebral fracture at any level and 266 age- and sex-matched controls. We used baseline CT scans to measure integral and trabecular volumetric bone mineral density (vBMD) and vertebral strength (via finite element analysis, FEA) at the T8 and L2 levels. Association between these measurements and vertebral fracture was determined by using conditional logistic regression. Sensitivity and specificity for predicting incident vertebral fracture were determined for lumbar spine and thoracic bone measurements. RESULTS Bone measurements from T8 and L2 predicted incident vertebral fracture equally well, regardless of fracture location. Specifically, for predicting vertebral fracture at any level, the odds ratio (per 1-SD decrease) for the vBMD and strength measurements at L2 and T8 ranged from 2.0 to 2.7 (p < 0.0001) and 1.8 to 2.8 (p < 0.0001), respectively. Results were similar when predicting fracture only in the thoracic versus the thoracolumbar spine. Lumbar and thoracic spine bone measurements had similar sensitivity and specificity for predicting incident vertebral fracture. CONCLUSION These findings indicated that like those from the lumbar spine, CT-based bone density and strength measurements from the thoracic spine may be useful for identifying individuals at high risk for vertebral fracture.
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Affiliation(s)
- F Johannesdottir
- Center for Advanced Orthopaedic Studies, Beth Israel Deaconess Medical Center, RN115, 330 Brookline Avenue, Boston, MA, 02215, USA.
- Harvard Medical School, Boston, MA, USA.
| | - B Allaire
- Center for Advanced Orthopaedic Studies, Beth Israel Deaconess Medical Center, RN115, 330 Brookline Avenue, Boston, MA, 02215, USA
| | | | - T M Keaveny
- Department of Mechanical Engineering, University of California, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | | | - M A Bredella
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - D E Anderson
- Center for Advanced Orthopaedic Studies, Beth Israel Deaconess Medical Center, RN115, 330 Brookline Avenue, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, USA
| | - E J Samelson
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
| | - D P Kiel
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
| | - V G Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - M L Bouxsein
- Center for Advanced Orthopaedic Studies, Beth Israel Deaconess Medical Center, RN115, 330 Brookline Avenue, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, USA
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30
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Mattar CN, Kalimuddin S, Sadarangani SP, Tagore S, Thain S, Thoon KC, Hong EY, Kanneganti A, Ku CW, Chan GM, Lee KZ, Yap JJ, Tan SS, Yan B, Young BE, Lye DC, Anderson DE, Yang L, Su LL, Somani J, Tan LK, Choolani MA, Chan JK. Pregnancy Outcomes in COVID-19: A Prospective Cohort Study in Singapore. Ann Acad Med Singap 2021. [PMID: 33381779 DOI: 10.47102/annals-acadmedsg.2020437] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION Pregnant women are reported to be at increased risk of severe coronavirus disease 2019 (COVID-19) due to underlying immunosuppression during pregnancy. However, the clinical course of COVID-19 in pregnancy and risk of vertical and horizontal transmission remain relatively unknown. We aim to describe and evaluate outcomes in pregnant women with COVID-19 in Singapore. METHODS Prospective observational study of 16 pregnant patients admitted for COVID-19 to 4 tertiary hospitals in Singapore. Outcomes included severe disease, pregnancy loss, and vertical and horizontal transmission. RESULTS Of the 16 patients, 37.5%, 43.8% and 18.7% were infected in the first, second and third trimesters, respectively. Two gravidas aged ≥35 years (12.5%) developed severe pneumonia; one patient (body mass index 32.9kg/m2) required transfer to intensive care. The median duration of acute infection was 19 days; one patient remained reverse transcription polymerase chain reaction (RT-PCR) positive >11 weeks from diagnosis. There were no maternal mortalities. Five pregnancies produced term live-births while 2 spontaneous miscarriages occurred at 11 and 23 weeks. RT-PCR of breast milk and maternal and neonatal samples taken at birth were negative; placenta and cord histology showed non-specific inflammation; and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific immunoglobulins were elevated in paired maternal and umbilical cord blood (n=5). CONCLUSION The majority of COVID-19 infected pregnant women had mild disease and only 2 women with risk factors (obesity, older age) had severe infection; this represents a slightly higher incidence than observed in age-matched non-pregnant women. Among the women who delivered, there was no definitive evidence of mother-to-child transmission via breast milk or placenta.
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Affiliation(s)
- Citra Nz Mattar
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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31
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Irving AT, Ahn M, Goh G, Anderson DE, Wang LF. Lessons from the host defences of bats, a unique viral reservoir. Nature 2021; 589:363-370. [PMID: 33473223 DOI: 10.1038/s41586-020-03128-0] [Citation(s) in RCA: 170] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/03/2020] [Indexed: 01/30/2023]
Abstract
There have been several major outbreaks of emerging viral diseases, including Hendra, Nipah, Marburg and Ebola virus diseases, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS)-as well as the current pandemic of coronavirus disease 2019 (COVID-19). Notably, all of these outbreaks have been linked to suspected zoonotic transmission of bat-borne viruses. Bats-the only flying mammal-display several additional features that are unique among mammals, such as a long lifespan relative to body size, a low rate of tumorigenesis and an exceptional ability to host viruses without presenting clinical disease. Here we discuss the mechanisms that underpin the host defence system and immune tolerance of bats, and their ramifications for human health and disease. Recent studies suggest that 64 million years of adaptive evolution have shaped the host defence system of bats to balance defence and tolerance, which has resulted in a unique ability to act as an ideal reservoir host for viruses. Lessons from the effective host defence of bats would help us to better understand viral evolution and to better predict, prevent and control future viral spillovers. Studying the mechanisms of immune tolerance in bats could lead to new approaches to improving human health. We strongly believe that it is time to focus on bats in research for the benefit of both bats and humankind.
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Affiliation(s)
- Aaron T Irving
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore. .,Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China. .,Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Matae Ahn
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Geraldine Goh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore. .,SingHealth Duke-NUS Global Health Institute, Singapore, Singapore.
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32
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Gamage AM, Tan KS, Chan WOY, Liu J, Tan CW, Ong YK, Thong M, Andiappan AK, Anderson DE, Wang DY, Wang LF. Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles. PLoS Pathog 2020; 16:e1009130. [PMID: 33284849 PMCID: PMC7746279 DOI: 10.1371/journal.ppat.1009130] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/17/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023] Open
Abstract
The novel coronavirus SARS-CoV-2 is the causative agent of Coronavirus Disease 2019 (COVID-19), a global healthcare and economic catastrophe. Understanding of the host immune response to SARS-CoV-2 is still in its infancy. A 382-nt deletion strain lacking ORF8 (Δ382 herein) was isolated in Singapore in March 2020. Infection with Δ382 was associated with less severe disease in patients, compared to infection with wild-type SARS-CoV-2. Here, we established Nasal Epithelial cells (NECs) differentiated from healthy nasal-tissue derived stem cells as a suitable model for the ex-vivo study of SARS-CoV-2 mediated pathogenesis. Infection of NECs with either SARS-CoV-2 or Δ382 resulted in virus particles released exclusively from the apical side, with similar replication kinetics. Screening of a panel of 49 cytokines for basolateral secretion from infected NECs identified CXCL10 as the only cytokine significantly induced upon infection, at comparable levels in both wild-type and Δ382 infected cells. Transcriptome analysis revealed the temporal up-regulation of distinct gene subsets during infection, with anti-viral signaling pathways only detected at late time-points (72 hours post-infection, hpi). This immune response to SARS-CoV-2 was significantly attenuated when compared to infection with an influenza strain, H3N2, which elicited an inflammatory response within 8 hpi, and a greater magnitude of anti-viral gene up-regulation at late time-points. Remarkably, Δ382 induced a host transcriptional response nearly identical to that of wild-type SARS-CoV-2 at every post-infection time-point examined. In accordance with previous results, Δ382 infected cells showed an absence of transcripts mapping to ORF8, and conserved expression of other SARS-CoV-2 genes. Our findings shed light on the airway epithelial response to SARS-CoV-2 infection, and demonstrate a non-essential role for ORF8 in modulating host gene expression and cytokine production from infected cells.
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Affiliation(s)
- Akshamal M. Gamage
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Kai Sen Tan
- Department of Otolaryngology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Wharton O. Y. Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jing Liu
- Department of Otolaryngology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yew Kwang Ong
- Department of Otolaryngology, Head & Neck Surgery, National University Health System, National University Hospital, Singapore
| | - Mark Thong
- Department of Otolaryngology, Head & Neck Surgery, National University Health System, National University Hospital, Singapore
| | | | | | - De Yun Wang
- Department of Otolaryngology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Singhealth Duke-NUS Global Health Institute, Singapore
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33
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Lim LW, Tan GS, Yong V, Anderson DE, Lye DC, Young B, Agrawal R. Acute Onset of Bilateral Follicular Conjunctivitis in two Patients with Confirmed SARS-CoV-2 Infections. Ocul Immunol Inflamm 2020; 28:1280-1284. [PMID: 33021847 DOI: 10.1080/09273948.2020.1821901] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
PURPOSE To report bilateral follicular conjunctivitis in two confirmed Coronavirus (COVID-19) patients with the presence of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) in conjunctival swab specimens. PARTICIPANTS AND METHODS Two unrelated patients with confirmed SARS-CoV-2 infection and bilateral acute conjunctivitis were examined. Conjunctival swabs were assessed for the presence of SARS-CoV-2 by quantitative real-time polymerase chain reaction (RT-PCR) and viral culture. RESULTS Both patients developed eye redness 3 days after the onset of COVID-19 symptoms. Slit lamp examination showed bilateral acute follicular conjunctivitis, which was resolved within 6 days. RT-PCR demonstrated the presence of viral RNA in conjunctival specimens from both eyes, which was unrelated to viral RNA from throat swabs. CONCLUSION SARS-CoV-2 may cause ocular manifestations such as viral conjunctivitis. Conjunctival sampling may be useful for infected patients with conjunctivitis and fever. Precautionary measures are recommended when examining infected patients throughout the clinical course of the infection.
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Affiliation(s)
- Louis W Lim
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital , Singapore, Singapore.,Tan Tock Seng Hospital , Singapore
| | - Glorijoy S Tan
- Tan Tock Seng Hospital , Singapore.,National Centre for Infectious Diseases , Singapore, Singapore
| | - Vernon Yong
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital , Singapore, Singapore.,Tan Tock Seng Hospital , Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School , Singapore, Singapore
| | - David C Lye
- National Centre for Infectious Diseases , Singapore, Singapore.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School , Singapore, Singapore.,Lee Kong Chian School of Medicine , Singapore, Singapore.,Yong Loo Lin School of Medicine , Singapore, Singapore
| | - Barnaby Young
- Tan Tock Seng Hospital , Singapore.,National Centre for Infectious Diseases , Singapore, Singapore.,Lee Kong Chian School of Medicine , Singapore, Singapore
| | - Rupesh Agrawal
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital , Singapore, Singapore.,Tan Tock Seng Hospital , Singapore.,National Centre for Infectious Diseases , Singapore, Singapore.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School , Singapore, Singapore.,Lee Kong Chian School of Medicine , Singapore, Singapore.,Yong Loo Lin School of Medicine , Singapore, Singapore.,Moorfields Eye Hospital, NHS Foundation Trust , London, UK
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Anderson DE, Sivalingam V, Kang AEZ, Ananthanarayanan A, Arumugam H, Jenkins TM, Hadjiat Y, Eggers M. Povidone-Iodine Demonstrates Rapid In Vitro Virucidal Activity Against SARS-CoV-2, The Virus Causing COVID-19 Disease. Infect Dis Ther 2020; 9:669-675. [PMID: 32643111 PMCID: PMC7341475 DOI: 10.1007/s40121-020-00316-3] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Indexed: 01/13/2023] Open
Abstract
INTRODUCTION As of 22 June 2020, Severe Acute Respiratory Syndrome (SARS)-coronavirus (CoV)-2 has infected more than 8.95 million people worldwide, causing > 468,000 deaths. The virus is transmitted through respiratory droplets and physical contact from contaminated surfaces to the mucosa. Hand hygiene and oral decontamination among other measures are key to preventing the spread of the virus. We report the in vitro virucidal activity of topical and oral povidone-iodine (PVP-I) products against SARS-CoV-2. METHODS Suspension assays were used to assess the virucidal activity of PVP-I against SARS-CoV-2. Products were tested at a contact time of 30 s for virucidal activity. Viral titres were calculated using the Spearman-Kärber method and reported as median tissue culture infectious dose (TCID50)/mL. RESULTS All four products [antiseptic solution (PVP-I 10%), skin cleanser (PVP-I 7.5%), gargle and mouth wash (PVP-I 1%) and throat spray (PVP-I 0.45%)] achieved ≥ 99.99% virucidal activity against SARS-CoV-2, corresponding to ≥ 4 log10 reduction of virus titre, within 30 s of contact. CONCLUSION This study provides evidence of rapid and effective virucidal activity of PVP-I against SARS-CoV-2. PVP-I-based products are widely available for medical and personal use for hand hygiene and oral decontamination, and could be readily integrated into coronavirus disease, COVID-19, infection control measures in hospital and community settings.
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Affiliation(s)
- Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| | - Velraj Sivalingam
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Adrian Eng Zheng Kang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | | | - Harsha Arumugam
- Mundipharma Singapore Holding Pte. Limited, Singapore, Singapore
| | | | - Yacine Hadjiat
- Mundipharma Singapore Holding Pte. Limited, Singapore, Singapore
| | - Maren Eggers
- Labor Prof. Dr. G. Enders MVZ GbR, Stuttgart, Germany.
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35
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Young BE, Fong SW, Chan YH, Mak TM, Ang LW, Anderson DE, Lee CYP, Amrun SN, Lee B, Goh YS, Su YCF, Wei WE, Kalimuddin S, Chai LYA, Pada S, Tan SY, Sun L, Parthasarathy P, Chen YYC, Barkham T, Lin RTP, Maurer-Stroh S, Leo YS, Wang LF, Renia L, Lee VJ, Smith GJD, Lye DC, Ng LFP. Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study. Lancet 2020; 396:603-611. [PMID: 32822564 PMCID: PMC7434477 DOI: 10.1016/s0140-6736(20)31757-8] [Citation(s) in RCA: 308] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with a 382-nucleotide deletion (∆382) in the open reading frame 8 (ORF8) region of the genome have been detected in Singapore and other countries. We investigated the effect of this deletion on the clinical features of infection. METHODS We retrospectively identified patients who had been screened for the ∆382 variant and recruited to the PROTECT study-a prospective observational cohort study conducted at seven public hospitals in Singapore. We collected clinical, laboratory, and radiological data from patients' electronic medical records and serial blood and respiratory samples taken during hospitalisation and after discharge. Individuals infected with the ∆382 variant were compared with those infected with wild-type SARS-CoV-2. Exact logistic regression was used to examine the association between the infection groups and the development of hypoxia requiring supplemental oxygen (an indicator of severe COVID-19, the primary endpoint). Follow-up for the study's primary endpoint is completed. FINDINGS Between Jan 22 and March 21, 2020, 278 patients with PCR-confirmed SARS-CoV-2 infection were screened for the ∆382 deletion and 131 were enrolled onto the study, of whom 92 (70%) were infected with the wild-type virus, ten (8%) had a mix of wild-type and ∆382-variant viruses, and 29 (22%) had only the ∆382 variant. Development of hypoxia requiring supplemental oxygen was less frequent in the ∆382 variant group (0 [0%] of 29 patients) than in the wild-type only group (26 [28%] of 92; absolute difference 28% [95% CI 14-28]). After adjusting for age and presence of comorbidities, infection with the ∆382 variant only was associated with lower odds of developing hypoxia requiring supplemental oxygen (adjusted odds ratio 0·07 [95% CI 0·00-0·48]) compared with infection with wild-type virus only. INTERPRETATION The ∆382 variant of SARS-CoV-2 seems to be associated with a milder infection. The observed clinical effects of deletions in ORF8 could have implications for the development of treatments and vaccines. FUNDING National Medical Research Council Singapore.
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Affiliation(s)
- Barnaby E Young
- National Centre for Infectious Diseases, Singapore; Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Siew-Wai Fong
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore; Department of Biological Sciences, National University of Singapore, Singapore
| | - Yi-Hao Chan
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore
| | | | - Li Wei Ang
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore
| | | | - Cheryl Yi-Pin Lee
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore
| | - Siti Naqiah Amrun
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore
| | - Yun Shan Goh
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore
| | - Yvonne C F Su
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Wycliffe E Wei
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore
| | - Shirin Kalimuddin
- Duke-NUS Medical School, National University of Singapore, Singapore; Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Louis Yi Ann Chai
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Medicine, National University Health System, Singapore
| | - Surinder Pada
- Department of Medicine, Infectious Diseases Service, Ng Teng Fong General Hospital, Singapore
| | - Seow Yen Tan
- Department of Infectious Diseases, Changi General Hospital, Singapore
| | | | | | | | - Timothy Barkham
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Sebastian Maurer-Stroh
- National Centre for Infectious Diseases, Singapore; Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore; Department of Biological Sciences, National University of Singapore, Singapore; Global Initiative on Sharing All Influenza Data, Munich, Germany
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore; Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Lin-Fa Wang
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Laurent Renia
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore
| | - Vernon J Lee
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Ministry of Health, Singapore
| | - Gavin J D Smith
- Duke-NUS Medical School, National University of Singapore, Singapore.
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore; Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lisa F P Ng
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore.
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36
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Young BE, Ong SWX, Ng LFP, Anderson DE, Chia WN, Chia PY, Ang LW, Mak TM, Kalimuddin S, Chai LYA, Pada S, Tan SY, Sun L, Parthasarathy P, Fong SW, Chan YH, Tan CW, Lee B, Rötzschke O, Ding Y, Tambyah P, Low JGH, Cui L, Barkham T, Lin RTP, Leo YS, Renia L, Wang LF, Lye DC. Viral dynamics and immune correlates of COVID-19 disease severity. Clin Infect Dis 2020; 73:e2932-e2942. [PMID: 32856707 PMCID: PMC7499509 DOI: 10.1093/cid/ciaa1280] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/26/2020] [Indexed: 12/13/2022] Open
Abstract
Background Key knowledge gaps remain in the understanding of viral dynamics and immune response of SARS-CoV-2 infection. Methods We evaluated these characteristics and established their association with clinical severity in a prospective observational cohort study of 100 patients with PCR-confirmed SARS-CoV-2 infection (mean age 46 years, 56% male, 38% with comorbidities). Respiratory samples (n=74) were collected for viral culture, serum samples for measurement of IgM/IgG levels (n=30), and plasma samples for levels of inflammatory cytokines and chemokines (n=81). Disease severity was correlated with results from viral culture, serologic testing, and immune markers. Results 57 (57%) patients developed viral pneumonia, of whom 20 (20%) required supplemental oxygen including 12 (12%) invasive mechanical ventilation. Viral culture from respiratory samples was positive for 19 of 74 patients (26%). No virus was isolated when the PCR cycle threshold (Ct) value was >30 or >14 days after symptom onset. Seroconversion occurred at a median of 12.5 days (IQR 9-18) for IgM and 15.0 days (IQR 12-20) for IgG; 54/62 patients (87.1%) sampled at day 14 or later seroconverted. Severe infections were associated with earlier seroconversion and higher peak IgM and IgG levels. Levels of IP-10, HGF, IL-6, MCP-1, MIP-1α, IL-12p70, IL-18, VEGF-A, PDGF-BB and IL-1RA significantly correlated with disease severity. Conclusion We found virus viability was associated with lower PCR Ct value in early illness. A stronger antibody response was associated with disease severity. The overactive proinflammatory immune signatures offers targets for host-directed immunotherapy which should be evaluated in randomised controlled trials.
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Affiliation(s)
- Barnaby E Young
- National Centre for Infectious Diseases, Singapore.,Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Sean W X Ong
- National Centre for Infectious Diseases, Singapore.,Tan Tock Seng Hospital, Singapore
| | - Lisa F P Ng
- Infection Diseases Horizontal Technology Centre (ID HTC), Agency for Science, Technology and Research, Singapore.,Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | | | | | - Po Ying Chia
- National Centre for Infectious Diseases, Singapore.,Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Li Wei Ang
- National Centre for Infectious Diseases, Singapore
| | - Tze-Minn Mak
- National Centre for Infectious Diseases, Singapore
| | - Shirin Kalimuddin
- Duke-NUS Medical School, Singapore.,Singapore General Hospital, Singapore
| | - Louis Yi Ann Chai
- National University Health System, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | | | | | - Siew-Wai Fong
- Infection Diseases Horizontal Technology Centre (ID HTC), Agency for Science, Technology and Research, Singapore.,Singapore Immunology Network, Agency for Science, Technology and Research, Singapore.,Department of Biological Science, National University of Singapore, Singapore
| | - Yi-Hao Chan
- Infection Diseases Horizontal Technology Centre (ID HTC), Agency for Science, Technology and Research, Singapore.,Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Chee Wah Tan
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Olaf Rötzschke
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Ying Ding
- National Centre for Infectious Diseases, Singapore
| | - Paul Tambyah
- National University Health System, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jenny G H Low
- Duke-NUS Medical School, Singapore.,Singapore General Hospital, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore
| | - Timothy Barkham
- Tan Tock Seng Hospital, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore.,Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Laurent Renia
- Infection Diseases Horizontal Technology Centre (ID HTC), Agency for Science, Technology and Research, Singapore.,Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | | | - David Chien Lye
- National Centre for Infectious Diseases, Singapore.,Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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37
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Su YCF, Anderson DE, Young BE, Linster M, Zhu F, Jayakumar J, Zhuang Y, Kalimuddin S, Low JGH, Tan CW, Chia WN, Mak TM, Octavia S, Chavatte JM, Lee RTC, Pada S, Tan SY, Sun L, Yan GZ, Maurer-Stroh S, Mendenhall IH, Leo YS, Lye DC, Wang LF, Smith GJD. Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2. mBio 2020; 11:e01610-20. [PMID: 32694143 PMCID: PMC7374062 DOI: 10.1128/mbio.01610-20] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [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: 06/16/2020] [Accepted: 06/23/2020] [Indexed: 12/27/2022] Open
Abstract
To date, limited genetic changes in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome have been described. Here, we report a 382-nucleotide (nt) deletion in SARS-CoV-2 that truncates open reading frame 7b (ORF7b) and ORF8, removing the ORF8 transcription regulatory sequence (TRS) and eliminating ORF8 transcription. The earliest 382-nt deletion variant was detected in Singapore on 29 January 2020, with the deletion viruses circulating in the country and accounting for 23.6% (45/191) of SARS-CoV-2 samples screened in this study. SARS-CoV-2 with the same deletion has since been detected in Taiwan, and other ORF7b/8 deletions of various lengths, ranging from 62 nt to 345 nt, have been observed in other geographic locations, including Australia, Bangladesh, and Spain. Mutations or deletions in ORF8 of SARS-CoV have been associated with reduced replicative fitness and virus attenuation. In contrast, the SARS-CoV-2 382-nt deletion viruses showed significantly higher replicative fitness in vitro than the wild type, while no difference was observed in patient viral load, indicating that the deletion variant viruses retained their replicative fitness. A robust antibody response to ORF8 has been observed in SARS-CoV-2 infection, suggesting that the emergence of ORF8 deletions may be due to immune-driven selection and that further deletion variants may emerge during the sustained transmission of SARS-CoV-2 in humans.IMPORTANCE During the SARS epidemic in 2003/2004, a number of deletions were observed in ORF8 of SARS-CoV, and eventually deletion variants became predominant, leading to the hypothesis that ORF8 was an evolutionary hot spot for adaptation of SARS-CoV to humans. However, due to the successful control of the SARS epidemic, the importance of these deletions for the epidemiological fitness of SARS-CoV in humans could not be established. The emergence of multiple SARS-CoV-2 strains with ORF8 deletions, combined with evidence of a robust immune response to ORF8, suggests that the lack of ORF8 may assist with host immune evasion. In addition to providing a key insight into the evolutionary behavior of SARS-CoV-2 as the virus adapts to its new human hosts, the emergence of ORF8 deletion variants may also impact vaccination strategies.
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Affiliation(s)
- Yvonne C F Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Barnaby E Young
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
| | - Martin Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jayanthi Jayakumar
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yan Zhuang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Shirin Kalimuddin
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Singapore General Hospital, Singapore
| | - Jenny G H Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Singapore General Hospital, Singapore
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Tze Minn Mak
- National Centre for Infectious Diseases, Singapore
| | | | | | - Raphael T C Lee
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | | | | | | | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
- Duke Global Health Institute, Duke University, North Carolina, USA
| | - Gavin J D Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
- Duke Global Health Institute, Duke University, North Carolina, USA
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38
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Su YCF, Anderson DE, Young BE, Linster M, Zhu F, Jayakumar J, Zhuang Y, Kalimuddin S, Low JGH, Tan CW, Chia WN, Mak TM, Octavia S, Chavatte JM, Lee RTC, Pada S, Tan SY, Sun L, Yan GZ, Maurer-Stroh S, Mendenhall IH, Leo YS, Lye DC, Wang LF, Smith GJD. Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2. mBio 2020; 11:mBio.01610-20. [PMID: 32694143 DOI: 10.1101/2020.03.11.987222] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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] [Indexed: 05/22/2023] Open
Abstract
To date, limited genetic changes in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome have been described. Here, we report a 382-nucleotide (nt) deletion in SARS-CoV-2 that truncates open reading frame 7b (ORF7b) and ORF8, removing the ORF8 transcription regulatory sequence (TRS) and eliminating ORF8 transcription. The earliest 382-nt deletion variant was detected in Singapore on 29 January 2020, with the deletion viruses circulating in the country and accounting for 23.6% (45/191) of SARS-CoV-2 samples screened in this study. SARS-CoV-2 with the same deletion has since been detected in Taiwan, and other ORF7b/8 deletions of various lengths, ranging from 62 nt to 345 nt, have been observed in other geographic locations, including Australia, Bangladesh, and Spain. Mutations or deletions in ORF8 of SARS-CoV have been associated with reduced replicative fitness and virus attenuation. In contrast, the SARS-CoV-2 382-nt deletion viruses showed significantly higher replicative fitness in vitro than the wild type, while no difference was observed in patient viral load, indicating that the deletion variant viruses retained their replicative fitness. A robust antibody response to ORF8 has been observed in SARS-CoV-2 infection, suggesting that the emergence of ORF8 deletions may be due to immune-driven selection and that further deletion variants may emerge during the sustained transmission of SARS-CoV-2 in humans.IMPORTANCE During the SARS epidemic in 2003/2004, a number of deletions were observed in ORF8 of SARS-CoV, and eventually deletion variants became predominant, leading to the hypothesis that ORF8 was an evolutionary hot spot for adaptation of SARS-CoV to humans. However, due to the successful control of the SARS epidemic, the importance of these deletions for the epidemiological fitness of SARS-CoV in humans could not be established. The emergence of multiple SARS-CoV-2 strains with ORF8 deletions, combined with evidence of a robust immune response to ORF8, suggests that the lack of ORF8 may assist with host immune evasion. In addition to providing a key insight into the evolutionary behavior of SARS-CoV-2 as the virus adapts to its new human hosts, the emergence of ORF8 deletion variants may also impact vaccination strategies.
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Affiliation(s)
- Yvonne C F Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Barnaby E Young
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
| | - Martin Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jayanthi Jayakumar
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yan Zhuang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Shirin Kalimuddin
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Singapore General Hospital, Singapore
| | - Jenny G H Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Singapore General Hospital, Singapore
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Tze Minn Mak
- National Centre for Infectious Diseases, Singapore
| | | | | | - Raphael T C Lee
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | | | | | | | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
- Duke Global Health Institute, Duke University, North Carolina, USA
| | - Gavin J D Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
- Duke Global Health Institute, Duke University, North Carolina, USA
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39
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Chia WN, Tan CW, Foo R, Kang AEZ, Peng Y, Sivalingam V, Tiu C, Ong XM, Zhu F, Young BE, Chen MIC, Tan YJ, Lye DC, Anderson DE, Wang LF. Serological differentiation between COVID-19 and SARS infections. Emerg Microbes Infect 2020; 9:1497-1505. [PMID: 32529906 PMCID: PMC7473126 DOI: 10.1080/22221751.2020.1780951] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In response to the coronavirus disease 2019 (COVID-19) outbreak, caused by SARS-CoV-2, multiple diagnostic tests are required for acute disease diagnosis, contact tracing, monitoring asymptomatic infection rates and assessing herd immunity. While PCR remains the frontline test of choice in the acute diagnostic setting, serological tests are urgently needed. Unlike PCR tests which are highly specific, cross-reactivity is a major challenge for COVID-19 antibody tests considering there are six other coronaviruses known to infect humans. SARS-CoV is genetically related to SARS-CoV-2 sharing approximately 80% sequence identity and both belong to the species SARS related coronavirus in the genus Betacoronavirus of family Coronaviridae. We developed and compared the performance of four different serological tests to comprehensively assess the cross-reactivity between COVID-19 and SARS patient sera. There is significant cross-reactivity when N protein of either virus is used. The S1 or RBD regions from the spike (S) protein offers better specificity. Amongst the different platforms, capture ELISA performed best. We found that SARS survivors all have significant levels of antibodies remaining in their blood 17 years after infection. Anti-N antibodies waned more than anti-RBD antibodies, and the latter is known to play a more important role in providing protective immunity.
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Affiliation(s)
- Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Randy Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Adrian Eng Zheng Kang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Yilong Peng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Velraj Sivalingam
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Charles Tiu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Xin Mei Ong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Barnaby E Young
- National Centre for Infectious Diseases, Singapore, Singapore.,Tan Tock Seng Hospital, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Mark I-C Chen
- National Centre for Infectious Diseases, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yee-Joo Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore, Singapore.,Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - David C Lye
- National Centre for Infectious Diseases, Singapore, Singapore.,Tan Tock Seng Hospital, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
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40
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Seah IYJ, Anderson DE, Kang AEZ, Wang L, Rao P, Young BE, Lye DC, Agrawal R. Assessing Viral Shedding and Infectivity of Tears in Coronavirus Disease 2019 (COVID-19) Patients. Ophthalmology 2020; 127:977-979. [PMID: 32291098 PMCID: PMC7151491 DOI: 10.1016/j.ophtha.2020.03.026] [Citation(s) in RCA: 287] [Impact Index Per Article: 71.8] [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: 03/19/2020] [Revised: 03/21/2020] [Accepted: 03/21/2020] [Indexed: 01/08/2023] Open
Affiliation(s)
| | | | | | - Linfa Wang
- Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Pooja Rao
- Tan Tock Seng Hospital, Singapore, Republic of Singapore
| | - Barnaby Edward Young
- Tan Tock Seng Hospital, Singapore, Republic of Singapore; National Centre for Infectious Diseases, Singapore, Republic of Singapore; Lee Kong Chian School of Medicine, Singapore, Republic of Singapore
| | - David Chien Lye
- Tan Tock Seng Hospital, Singapore, Republic of Singapore; National Centre for Infectious Diseases, Singapore, Republic of Singapore; Lee Kong Chian School of Medicine, Singapore, Republic of Singapore; Yong Loo Lin School of Medicine, Singapore, Republic of Singapore
| | - Rupesh Agrawal
- Duke-NUS Medical School, Singapore, Republic of Singapore; Tan Tock Seng Hospital, Singapore, Republic of Singapore; Lee Kong Chian School of Medicine, Singapore, Republic of Singapore; Yong Loo Lin School of Medicine, Singapore, Republic of Singapore; Moorfields Eye Hospital, NHS Foundation Trust, London, United Kingdom.
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41
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Farrukee R, Tai CMK, Oh DY, Anderson DE, Gunalan V, Hibberd M, Lau GYF, Barr IG, von Messling V, Maurer-Stroh S, Hurt AC. Utilising animal models to evaluate oseltamivir efficacy against influenza A and B viruses with reduced in vitro susceptibility. PLoS Pathog 2020; 16:e1008592. [PMID: 32555740 PMCID: PMC7326275 DOI: 10.1371/journal.ppat.1008592] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/30/2020] [Accepted: 05/02/2020] [Indexed: 11/19/2022] Open
Abstract
The neuraminidase (NA) inhibitor (NAI) oseltamivir (OST) is the most widely used influenza antiviral drug. Several NA amino acid substitutions are reported to reduce viral susceptibility to OST in in vitro assays. However, whether there is a correlation between the level of reduction in susceptibility in vitro and the efficacy of OST against these viruses in vivo is not well understood. In this study, a ferret model was utilised to evaluate OST efficacy against circulating influenza A and B viruses with a range of in vitro generated 50% inhibitory concentrations (IC50) values for OST. OST efficacy against an A(H1N1)pdm09 and an A(H1N1)pdm09 virus with the H275Y substitution in neuraminidase was also tested in the macaque model. The results from this study showed that OST had a significant impact on virological parameters compared to placebo treatment of ferrets infected with wild-type influenza A viruses with normal IC50 values (~1 nM). However, this efficacy was lower against wild-type influenza B and other viruses with higher IC50 values. Differing pathogenicity of the viruses made evaluation of clinical parameters difficult, although some effect of OST in reducing clinical signs was observed with influenza A(H1N1) and A(H1N1)pdm09 (H275Y) viruses. Viral titres in macaques were too low to draw conclusive results. Analysis of the ferret data revealed a correlation between IC50 and OST efficacy in reducing viral shedding but highlighted that the current WHO guidelines/criteria for defining normal, reduced or highly reduced inhibition in influenza B viruses based on in vitro data are not well aligned with the low in vivo OST efficacy observed for both wild-type influenza B viruses and those with reduced OST susceptibility.
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Affiliation(s)
- Rubaiyea Farrukee
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Celeste Ming-Kay Tai
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ding Yuan Oh
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- School of Health and Life Sciences, Federation University, Churchill, Victoria, Australia
| | | | - Vithiagaran Gunalan
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Martin Hibberd
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Gary Yuk-Fai Lau
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Ian G. Barr
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- School of Health and Life Sciences, Federation University, Churchill, Victoria, Australia
| | - Veronika von Messling
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Veterinary Medicine Division, Paul-Ehrlich-Institute, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
- National Public Health Laboratories, National Centre for Infectious Diseases, Ministry of Health, Singapore
- Department of Biological Sciences, National University Singapore, Singapore
| | - Aeron C. Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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42
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Affiliation(s)
| | | | | | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Singapore; Yong Loo Lin School of Medicine, Singapore
| | - Rupesh Agrawal
- Duke-NUS Medical School, Singapore; Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Singapore; Yong Loo Lin School of Medicine, Singapore; Moorfields Eye Hospital, NHS Foundation Trust, London, UK.
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43
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Paskey AC, Ng JHJ, Rice GK, Chia WN, Philipson CW, Foo RJ, Cer RZ, Long KA, Lueder MR, Lim XF, Frey KG, Hamilton T, Anderson DE, Laing ED, Mendenhall IH, Smith GJ, Wang LF, Bishop-Lilly KA. Detection of Recombinant Rousettus Bat Coronavirus GCCDC1 in Lesser Dawn Bats ( Eonycteris spelaea) in Singapore. Viruses 2020; 12:E539. [PMID: 32422932 PMCID: PMC7291116 DOI: 10.3390/v12050539] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 03/22/2020] [Revised: 05/10/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023] Open
Abstract
Rousettus bat coronavirus GCCDC1 (RoBat-CoV GCCDC1) is a cross-family recombinant coronavirus that has previously only been reported in wild-caught bats in Yúnnan, China. We report the persistence of a related strain in a captive colony of lesser dawn bats captured in Singapore. Genomic evidence of the virus was detected using targeted enrichment sequencing, and further investigated using deeper, unbiased high throughput sequencing. RoBat-CoV GCCDC1 Singapore shared 96.52% similarity with RoBat-CoV GCCDC1 356 (NC_030886) at the nucleotide level, and had a high prevalence in the captive bat colony. It was detected at five out of six sampling time points across the course of 18 months. A partial segment 1 from an ancestral Pteropine orthoreovirus, p10, makes up the recombinant portion of the virus, which shares high similarity with previously reported RoBat-CoV GCCDC1 strains that were detected in Yúnnan, China. RoBat-CoV GCCDC1 is an intriguing, cross-family recombinant virus, with a geographical range that expands farther than was previously known. The discovery of RoBat-CoV GCCDC1 in Singapore indicates that this recombinant coronavirus exists in a broad geographical range, and can persist in bat colonies long-term.
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Affiliation(s)
- Adrian C. Paskey
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA; (A.C.P.); (E.D.L.)
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
- Leidos, Reston, VA 20190, USA
| | - Justin H. J. Ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Gregory K. Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
- Leidos, Reston, VA 20190, USA
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Casandra W. Philipson
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060 USA
| | - Randy J.H. Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
- Leidos, Reston, VA 20190, USA
| | - Kyle A. Long
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
- Leidos, Reston, VA 20190, USA
| | - Matthew R. Lueder
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
- Leidos, Reston, VA 20190, USA
| | - Xiao Fang Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Kenneth G. Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
| | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
| | - Danielle E. Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Eric D. Laing
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA; (A.C.P.); (E.D.L.)
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Gavin J. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (J.H.J.N.); (W.N.C.); (R.J.H.F.); (X.F.L.); (D.E.A.); (I.H.M.); (G.J.S.); (L.-F.W.)
| | - Kimberly A. Bishop-Lilly
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA; (A.C.P.); (E.D.L.)
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center–Frederick, Fort Detrick, MD 21702 USA; (G.K.R.); (C.W.P.); (R.Z.C.); (K.A.L.); (M.R.L.); (K.G.F.); (T.H.)
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44
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Anderson DE, Tan CW, Chia WN, Young BE, Linster M, Low JH, Tan YJ, Chen MIC, Smith GJD, Leo YS, Lye DC, Wang LF. Lack of cross-neutralization by SARS patient sera towards SARS-CoV-2. Emerg Microbes Infect 2020; 9:900-902. [PMID: 32380903 PMCID: PMC7241448 DOI: 10.1080/22221751.2020.1761267] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Despite initial findings indicating that SARS-CoV and SARS-CoV-2 are genetically related belonging to the same virus species and that the two viruses used the same entry receptor, angiotensin-converting enzyme 2 (ACE2), our data demonstrated that there is no detectable cross-neutralization by SARS patient sera against SARS-CoV-2. We also found that there are significant levels of neutralizing antibodies in recovered SARS patients 9–17 years after initial infection. These findings will be of significant use in guiding the development of serologic tests, formulating convalescent plasma therapy strategies, and assessing the longevity of protective immunity for SARS-related coronaviruses in general as well as vaccine efficacy.
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Affiliation(s)
| | | | - Wan Ni Chia
- Duke-NUS Medical School, Singapore, Singapore
| | - Barnaby E Young
- National Center for Infectious Diseases, Singapore, Singapore
| | | | - JennyG H Low
- Singapore General Hospital, Singapore, Singapore
| | - Yee-Joo Tan
- National University of Singapore, Singapore, Singapore
| | - Mark I-C Chen
- National Center for Infectious Diseases, Singapore, Singapore
| | | | - Yee Sin Leo
- National Center for Infectious Diseases, Singapore, Singapore
| | - David C Lye
- National Center for Infectious Diseases, Singapore, Singapore
| | - Lin-Fa Wang
- Duke-NUS Medical School, Singapore, Singapore
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45
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Young BE, Ong SWX, Kalimuddin S, Low JG, Tan SY, Loh J, Ng OT, Marimuthu K, Ang LW, Mak TM, Lau SK, Anderson DE, Chan KS, Tan TY, Ng TY, Cui L, Said Z, Kurupatham L, Chen MIC, Chan M, Vasoo S, Wang LF, Tan BH, Lin RTP, Lee VJM, Leo YS, Lye DC. Epidemiologic Features and Clinical Course of Patients Infected With SARS-CoV-2 in Singapore. JAMA 2020; 323:1488-1494. [PMID: 32125362 PMCID: PMC7054855 DOI: 10.1001/jama.2020.3204] [Citation(s) in RCA: 1329] [Impact Index Per Article: 332.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China, in December 2019 and has spread globally with sustained human-to-human transmission outside China. OBJECTIVE To report the initial experience in Singapore with the epidemiologic investigation of this outbreak, clinical features, and management. DESIGN, SETTING, AND PARTICIPANTS Descriptive case series of the first 18 patients diagnosed with polymerase chain reaction (PCR)-confirmed SARS-CoV-2 infection at 4 hospitals in Singapore from January 23 to February 3, 2020; final follow-up date was February 25, 2020. EXPOSURES Confirmed SARS-CoV-2 infection. MAIN OUTCOMES AND MEASURES Clinical, laboratory, and radiologic data were collected, including PCR cycle threshold values from nasopharyngeal swabs and viral shedding in blood, urine, and stool. Clinical course was summarized, including requirement for supplemental oxygen and intensive care and use of empirical treatment with lopinavir-ritonavir. RESULTS Among the 18 hospitalized patients with PCR-confirmed SARS-CoV-2 infection (median age, 47 years; 9 [50%] women), clinical presentation was an upper respiratory tract infection in 12 (67%), and viral shedding from the nasopharynx was prolonged for 7 days or longer among 15 (83%). Six individuals (33%) required supplemental oxygen; of these, 2 required intensive care. There were no deaths. Virus was detectable in the stool (4/8 [50%]) and blood (1/12 [8%]) by PCR but not in urine. Five individuals requiring supplemental oxygen were treated with lopinavir-ritonavir. For 3 of the 5 patients, fever resolved and supplemental oxygen requirement was reduced within 3 days, whereas 2 deteriorated with progressive respiratory failure. Four of the 5 patients treated with lopinavir-ritonavir developed nausea, vomiting, and/or diarrhea, and 3 developed abnormal liver function test results. CONCLUSIONS AND RELEVANCE Among the first 18 patients diagnosed with SARS-CoV-2 infection in Singapore, clinical presentation was frequently a mild respiratory tract infection. Some patients required supplemental oxygen and had variable clinical outcomes following treatment with an antiretroviral agent.
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Affiliation(s)
- Barnaby Edward Young
- National Centre for Infectious Diseases,
Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine,
Singapore
| | - Sean Wei Xiang Ong
- National Centre for Infectious Diseases,
Singapore
- Tan Tock Seng Hospital, Singapore
| | - Shirin Kalimuddin
- Singapore General Hospital, Singapore
- Duke-NUS Medical School, Singapore
| | - Jenny G. Low
- Singapore General Hospital, Singapore
- Duke-NUS Medical School, Singapore
| | | | | | - Oon-Tek Ng
- National Centre for Infectious Diseases,
Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine,
Singapore
| | - Kalisvar Marimuthu
- National Centre for Infectious Diseases,
Singapore
- Tan Tock Seng Hospital, Singapore
- Yong Loo Lin School of Medicine, Singapore
| | - Li Wei Ang
- National Centre for Infectious Diseases,
Singapore
| | - Tze Minn Mak
- National Centre for Infectious Diseases,
Singapore
| | | | | | | | - Thean Yen Tan
- Duke-NUS Medical School, Singapore
- Changi General Hospital, Singapore
| | | | - Lin Cui
- National Centre for Infectious Diseases,
Singapore
| | | | | | - Mark I-Cheng Chen
- National Centre for Infectious Diseases,
Singapore
- Saw Swee Hock School of Public Health,
Singapore
| | - Monica Chan
- National Centre for Infectious Diseases,
Singapore
- Tan Tock Seng Hospital, Singapore
| | - Shawn Vasoo
- National Centre for Infectious Diseases,
Singapore
- Tan Tock Seng Hospital, Singapore
| | | | - Boon Huan Tan
- Lee Kong Chian School of Medicine,
Singapore
- DSO National Laboratories, Singapore
| | | | | | - Yee-Sin Leo
- National Centre for Infectious Diseases,
Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine,
Singapore
- Yong Loo Lin School of Medicine, Singapore
- Saw Swee Hock School of Public Health,
Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases,
Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine,
Singapore
- Yong Loo Lin School of Medicine, Singapore
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46
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Wang LF, Anderson DE, Mackenzie JS, Merson MH. From Hendra to Wuhan: what has been learned in responding to emerging zoonotic viruses. Lancet 2020; 395:e33-e34. [PMID: 32059799 PMCID: PMC7133556 DOI: 10.1016/s0140-6736(20)30350-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Lin-Fa Wang
- Programme in Emerging Infections Diseases, Duke-NUS Medical School, Singapore 169857; SingHealth Duke-NUS Global Health Institute, Singapore; Duke Global Health Institute, Duke University, Singapore.
| | - Danielle E Anderson
- Programme in Emerging Infections Diseases, Duke-NUS Medical School, Singapore 169857
| | | | - Michael H Merson
- SingHealth Duke-NUS Global Health Institute, Singapore; Duke Global Health Institute, Duke University, Singapore
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47
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Zhang W, Zheng XS, Agwanda B, Ommeh S, Zhao K, Lichoti J, Wang N, Chen J, Li B, Yang XL, Mani S, Ngeiywa KJ, Zhu Y, Hu B, Onyuok SO, Yan B, Anderson DE, Wang LF, Zhou P, Shi ZL. Serological evidence of MERS-CoV and HKU8-related CoV co-infection in Kenyan camels. Emerg Microbes Infect 2020; 8:1528-1534. [PMID: 31645223 PMCID: PMC6818114 DOI: 10.1080/22221751.2019.1679610] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Dromedary camels are important reservoir hosts of various coronaviruses, including Middle East respiratory syndrome coronavirus (MERS-CoV) that cause human infections. CoV genomes regularly undergo recombination during infection as observed in bat SARS-related CoVs. Here we report for the first time that only a small proportion of MERS-CoV receptor-binding domain positive (RBD) of spike protein positive camel sera in Kenya were also seropositive to MERS-CoV nucleocapsid (NP). In contrast, many of them contain antibodies against bat HKU8-related (HKU8r)-CoVs. Among 584 camel samples that were positive against MERS-CoV RBD, we found only 0.48 (8.22%) samples were also positive for NP. Furthermore, we found bat HKU8r-CoV NP antibody in 73 (12.5%) of the MERS-CoV RBD positive and NP negative samples, yet found only 3 (0.43%) of the HKU8r-CoV S1 antibody in the same samples. These findings may indicate co-infection with MERS-CoV and a HKU8r-CoV in camels. It may also raise the possibility of the circulation of a recombinant coronavirus virus with the spike of MERS-CoV and the NP of a HKU8r-CoV in Kenya. We failed to find molecular evidence of an HKU8r-CoV or a putative recombinant virus. Our findings should alert other investigators to look for molecular evidence of HKU8r-CoV or recombinants.
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Affiliation(s)
- Wei Zhang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Xiao-Shuang Zheng
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China.,University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya , Nairobi , Kenya
| | - Sheila Ommeh
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology , Nairobi , Kenya
| | - Kai Zhao
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China.,University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Jacqueline Lichoti
- Directorate of Veterinary Services, State Department of Livestock, Ministry of Agriculture , Livestock and Fisheries , Kenya
| | - Ning Wang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Jing Chen
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China.,University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Shailendra Mani
- Programme in Emerging Infectious Diseases Duke-NUS Medical School , Singapore , Singapore
| | - Kisa-Juma Ngeiywa
- Directorate of Veterinary Services, State Department of Livestock, Ministry of Agriculture , Livestock and Fisheries , Kenya.,Kenya Camel Association , Nairobi , Kenya
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Samson Omondi Onyuok
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Bing Yan
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases Duke-NUS Medical School , Singapore , Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases Duke-NUS Medical School , Singapore , Singapore
| | - Peng Zhou
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
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48
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Tan CW, Wittwer K, Lim XF, Uehara A, Mani S, Wang LF, Anderson DE. Serological evidence and experimental infection of cynomolgus macaques with pteropine orthoreovirus reveal monkeys as potential hosts for transmission to humans. Emerg Microbes Infect 2019; 8:787-795. [PMID: 31132935 PMCID: PMC6542153 DOI: 10.1080/22221751.2019.1621668] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Pteropine orthoreoviruses (PRV) are emerging bat-borne viruses with proven zoonotic transmission. We recently demonstrated human exposure to PRV in Singapore, which together with previous reports from Malaysia and Vietnam suggest that human infection of PRV may occur periodically in the region. This raises the question whether bats are the only sources of human infection. In this study, we screened 517 cynomolgus macaques caught in Singapore for evidence of exposure to PRV3M (also known as Melaka virus), which was first isolated from human patients in Melaka, Malaysia. We found that 67 serum samples were PRV3M positive by ELISA and 34 were also positive by virus neutralization assay. To investigate whether monkeys could act as hosts for PRV transmission, we experimentally infected cynomolgus macaques with PRV3M and housed these animals with uninfected monkeys. Although no clinical signs of infection were observed in infected animals, viral RNA was detected in nasal and rectal swabs and all infected macaques seroconverted. Additionally, one of the uninfected animals seroconverted, implying active shedding and transmission of PRV3M. We provide evidence that PRV exposure in the macaque population in Singapore occurs at a relatively high prevalence and this study suggests that cynomolgus macaques may be an intermediate or reservoir host for PRVs.
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Affiliation(s)
- Chee Wah Tan
- a Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore
| | - Kevin Wittwer
- a Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore.,b Veterinary Medicine Division , Paul-Ehrlich-Institute , Langen , Germany
| | - Xiao Fang Lim
- a Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore
| | - Anna Uehara
- a Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore
| | - Shailendra Mani
- a Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore
| | - Lin-Fa Wang
- a Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore
| | - Danielle E Anderson
- a Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore
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49
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Lim XF, Lee CB, Pascoe SM, How CB, Chan S, Tan JH, Yang X, Zhou P, Shi Z, Sessions OM, Wang LF, Ng LC, Anderson DE, Yap G. Detection and characterization of a novel bat-borne coronavirus in Singapore using multiple molecular approaches. J Gen Virol 2019; 100:1363-1374. [PMID: 31418677 PMCID: PMC7079695 DOI: 10.1099/jgv.0.001307] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bats are important reservoirs and vectors in the transmission of emerging infectious diseases. Many highly pathogenic viruses such as SARS-CoV and rabies-related lyssaviruses have crossed species barriers to infect humans and other animals. In this study we monitored the major roost sites of bats in Singapore, and performed surveillance for zoonotic pathogens in these bats. Screening of guano samples collected during the survey uncovered a bat coronavirus (Betacoronavirus) in Cynopterus brachyotis, commonly known as the lesser dog-faced fruit bat. Using a capture-enrichment sequencing platform, the full-length genome of the bat CoV was sequenced and found to be closely related to the bat coronavirus HKU9 species found in Leschenault’s rousette discovered in the Guangdong and Yunnan provinces.
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Affiliation(s)
- Xiao Fang Lim
- Environmental Health Institute, National Environment Agency, Singapore.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | | | | | - Choon Beng How
- Sungei Buloh Wetlands Reserve National Parks Board, Singapore
| | - Sharon Chan
- Sungei Buloh Wetlands Reserve National Parks Board, Singapore
| | - Jun Hao Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Xinglou Yang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Peng Zhou
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Zhengli Shi
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - October M Sessions
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,Department of Pharmacy, National University of Singapore, Singapore.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Grace Yap
- Environmental Health Institute, National Environment Agency, Singapore
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50
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Singanallur NB, Anderson DE, Sessions OM, Kamaraj US, Bowden TR, Horsington J, Cowled C, Wang LF, Vosloo W. Probe capture enrichment next-generation sequencing of complete foot-and-mouth disease virus genomes in clinical samples. J Virol Methods 2019; 272:113703. [PMID: 31336142 DOI: 10.1016/j.jviromet.2019.113703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/04/2019] [Accepted: 07/17/2019] [Indexed: 01/02/2023]
Abstract
Next-generation sequencing (NGS) techniques offer an unprecedented "step-change" increase in the quantity and quality of sequence data rapidly generated from a sample and can be applied to obtain ultra-deep coverage of viral genomes. This is not possible with the routinely used Sanger sequencing method that gives the consensus reads, or by cloning approaches. In this study, a targeted-enrichment methodology for the simultaneous acquisition of complete foot-and-mouth disease virus (FMDV) genomes directly from clinical samples is presented. Biotinylated oligonucleotide probes (120 nt) were used to capture and enrich viral RNA following library preparation. To create a virus capture panel targeting serotype O and A simultaneously, 18 baits targeting the highly conserved regions of the 8.3 kb FMDV genome were synthesised, with 14 common to both serotypes, 2 specific to serotype O and 2 specific to serotype A. These baits were used to capture and enrich FMDV RNA (as cDNA) from samples collected during one pathogenesis and two vaccine efficacy trials, where pigs were infected with serotype O or A viruses. After enrichment, FMDV-specific sequencing reads increased by almost 3000-fold. The sequence data were used in variant call analysis to identify single nucleotide polymorphisms (SNPs). This methodology was robust in its ability to capture diverse sequences, was shown to be highly sensitive, and can be easily scaled for large-scale epidemiological studies.
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Affiliation(s)
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - October M Sessions
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Department of Pharmacy, National University of Singapore, Singapore
| | - Uma S Kamaraj
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Timothy R Bowden
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Jacquelyn Horsington
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Christopher Cowled
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Wilna Vosloo
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
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