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Zheng X, Zhao K, Xue B, Deng Y, Xu X, Yan W, Rong C, Leung K, Wu JT, Leung GM, Peiris M, Poon LLM, Zhang T. Tracking diarrhea viruses and mpox virus using the wastewater surveillance network in Hong Kong. Water Res 2024; 255:121513. [PMID: 38555782 DOI: 10.1016/j.watres.2024.121513] [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] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 03/14/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
The wastewater surveillance network successfully established for COVID-19 showed great potential to monitor other infectious viruses, such as norovirus, rotavirus and mpox virus. In this study, we established and validated detection methods for these viruses in wastewater. We developed a supernatant-based method to detect RNA viruses from wastewater samples and applied it to the monthly diarrhea viruses (norovirus genogroup I & II, and rotavirus) surveillance in wastewater treatment plants (WWTPs) at a city-wide level for 16 months. Significant correlations were observed between the diarrhea viruses concentrations in wastewater and detection rates in faecal specimens by clinical surveillance. The highest norovirus concentration in wastewater was obtained in winter, consistent with the seasonal pattern of norovirus outbreak in Hong Kong. Additionally, we established a pellet-based method to monitor DNA viruses in wastewater and detected weak signals for mpox virus in wastewater from a WWTP serving approximately 16,700 people, when the first mpox patient in Hong Kong was admitted to the hospital within the catchment area. Genomic sequencing provided confirmatory evidence for the validity of the results. Our findings emphasized the efficacy of the wastewater surveillance network in WWTPs as a cost-effective tool to track the transmission trend of diarrhea viruses and to provide sensitive detection of novel emerging viruses such as mpox virus in low-prevalence areas. The developed methods and surveillance results provide confidence for establishing robust wastewater surveillance programs to control infectious diseases in the post-pandemic era.
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Affiliation(s)
- Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Keyue Zhao
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Bingjie Xue
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Weifu Yan
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chao Rong
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China; Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong, China; The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China; Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong, China; The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China; Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong, China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong, China; Centre For Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong, China; Centre For Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China; School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China; Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, Hong Kong, China.
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Jia JZ, Cohen CA, Gu H, McLean MR, Varadarajan R, Bhandari N, Peiris M, Leung GM, Poon LLM, Tsang T, Chung AW, Cowling BJ, Leung NHL, Valkenburg SA. Influenza antibody breadth and effector functions are immune correlates from acquisition of pandemic infection of children. Nat Commun 2024; 15:3210. [PMID: 38615070 PMCID: PMC11016072 DOI: 10.1038/s41467-024-47590-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 04/04/2024] [Indexed: 04/15/2024] Open
Abstract
Cross-reactive antibodies with Fc receptor (FcR) effector functions may mitigate pandemic virus impact in the absence of neutralizing antibodies. In this exploratory study, we use serum from a randomized placebo-controlled trial of seasonal trivalent influenza vaccination in children (NCT00792051) conducted at the onset of the 2009 H1N1 pandemic (pH1N1) and monitored for infection. We found that seasonal vaccination increases pH1N1 specific antibodies and FcR effector functions. Furthermore, prospective baseline antibody profiles after seasonal vaccination, prior to pH1N1 infection, show that unvaccinated uninfected children have elevated ADCC effector function, FcγR3a and FcγR2a binding antibodies to multiple pH1N1 proteins, past seasonal and avian (H5, H7 and H9) strains. Whereas, children that became pH1N1 infected after seasonal vaccination have antibodies focussed to seasonal strains without FcR functions, and greater aggregated HA-specific profiles for IgM and IgG3. Modeling to predict infection susceptibility, ranked baseline hemagglutination antibody inhibition as the highest contributor to lack of pH1N1 infection, in combination with features that include pH1-IgG1, H1-stem responses and FcR binding to seasonal vaccine and pH1 proteins. Thus, seasonal vaccination can have benefits against pandemic influenza viruses, and some children already have broadly reactive antibodies with Fc potential without vaccination and may be considered 'elite influenza controllers'.
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Affiliation(s)
- Janice Z Jia
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Carolyn A Cohen
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Haogao Gu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Milla R McLean
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | | | - Nisha Bhandari
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Malik Peiris
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
- Centre for Immunology and Infection (C2i), Hong Kong Science and Technology Park, Hong Kong, SAR, China
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, Hong Kong, SAR, China
| | - Leo L M Poon
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
- Centre for Immunology and Infection (C2i), Hong Kong Science and Technology Park, Hong Kong, SAR, China
| | - Tim Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Amy W Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Nancy H L Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.
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3
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Zumla A, Peiris M, Memish ZA, Perlman S. Anticipating a MERS-like coronavirus as a potential pandemic threat. Lancet 2024:S0140-6736(24)00641-X. [PMID: 38604210 DOI: 10.1016/s0140-6736(24)00641-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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024]
Affiliation(s)
- Alimuddin Zumla
- Department of Infection, Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, London, UK; NIHR Biomedical Research Centre, University College London Hospitals, London, UK
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong Special Administrative Region, China
| | - Ziad A Memish
- Research and Innovation Center, King Saud Medical City, Ministry of Health and College of Medicine, Al Faisal University, Riyadh, Saudi Arabia; Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA; Division of Infectious Diseases, Kyung Hee University, Seoul, South Korea
| | - Stanley Perlman
- Department of Microbiology and Immunology and Department of Pediatrics, University of Iowa, Iowa City, IA 52246, USA.
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Rosa Duque JS, Cheng SMS, Cohen CA, Leung D, Wang X, Mu X, Chung Y, Lau TM, Wang M, Zhang W, Zhang Y, Wong HHW, Tsang LCH, Chaothai S, Kwan TC, Li JKC, Chan KCK, Luk LLH, Ho JCH, Li WY, Lee AMT, Lam JHY, Chan SM, Wong WHS, Tam IYS, Mori M, Valkenburg SA, Peiris M, Tu W, Lau YL. Superior antibody and membrane protein-specific T-cell responses to CoronaVac by intradermal versus intramuscular routes in adolescents. World J Pediatr 2024; 20:353-370. [PMID: 38085470 PMCID: PMC11052846 DOI: 10.1007/s12519-023-00764-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/18/2023] [Indexed: 04/29/2024]
Abstract
BACKGROUND Optimising the immunogenicity of COVID-19 vaccines to improve their protection against disease is necessary. Fractional dosing by intradermal (ID) administration has been shown to be equally immunogenic as intramuscular (IM) administration for several vaccines, but the immunogenicity of ID inactivated whole severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the full dose is unknown. This study (NCT04800133) investigated the superiority of antibody and T-cell responses of full-dose CoronaVac by ID over IM administration in adolescents. METHODS Participants aged 11-17 years received two doses of IM or ID vaccine, followed by the 3rd dose 13-42 days later. Humoral and cellular immunogenicity outcomes were measured post-dose 2 (IM-CC versus ID-CC) and post-dose 3 (IM-CCC versus ID-CCC). Doses 2 and 3 were administered to 173 and 104 adolescents, respectively. RESULTS Spike protein (S) immunoglobulin G (IgG), S-receptor-binding domain (RBD) IgG, S IgG Fcγ receptor IIIa (FcγRIIIa)-binding, SNM [sum of individual (S), nucleocapsid protein (N), and membrane protein (M) peptide pool]-specific interleukin-2 (IL-2)+CD4+, SNM-specific IL-2+CD8+, S-specific IL-2+CD8+, N-specific IL-2+CD4+, N-specific IL-2+CD8+ and M-specific IL-2+CD4+ responses fulfilled the superior and non-inferior criteria for ID-CC compared to IM-CC, whereas IgG avidity was inferior. For ID-CCC, S-RBD IgG, surrogate virus neutralisation test, 90% plaque reduction neutralisation titre (PRNT90), PRNT50, S IgG avidity, S IgG FcγRIIIa-binding, M-specific IL-2+CD4+, interferon-γ+CD8+ and IL-2+CD8+ responses were superior and non-inferior to IM-CCC. The estimated vaccine efficacies were 49%, 52%, 66% and 79% for IM-CC, ID-CC, IM-CCC and ID-CCC, respectively. The ID groups reported more local, mild adverse reactions. CONCLUSION This is the first study to demonstrate superior antibody and M-specific T-cell responses by ID inactivated SARS-CoV-2 vaccination and serves as the basis for future research to improve the immunogenicity of inactivated vaccines.
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Affiliation(s)
- Jaime S Rosa Duque
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Samuel M S Cheng
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Carolyn A Cohen
- School of Public Health, The University of Hong Kong, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Daniel Leung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Xiwei Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Xiaofeng Mu
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuet Chung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Tsun Ming Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Manni Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Wenyue Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yanmei Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Howard H W Wong
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Leo C H Tsang
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Sara Chaothai
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Tsz Chun Kwan
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - John K C Li
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Karl C K Chan
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Leo L H Luk
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Jenson C H Ho
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Wing Yan Li
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Amos M T Lee
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jennifer H Y Lam
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Sau Man Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Wilfred H S Wong
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Issan Y S Tam
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Masashi Mori
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
| | - Sophie A Valkenburg
- School of Public Health, The University of Hong Kong, Hong Kong, China.
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China.
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection, and Immunity, University of Melbourne, Melbourne, VIC, Australia.
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong, China.
- Center for Immunology and Infection C2i, Hong Kong, China.
| | - Wenwei Tu
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China.
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China.
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5
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Cheng SMS, Mok CKP, Li JKC, Chan KKP, Luk KS, Lee BHW, Gu H, Chan KCK, Tsang LCH, Yiu KYS, Ling KKC, Tang YS, Luk LLH, Yu JKM, Pekosz A, Webby RJ, Cowling BJ, Hui DSC, Peiris M. Cross-neutralizing antibody against emerging Omicron subvariants of SARS-CoV-2 in infection-naïve individuals with homologous BNT162b2 or BNT162b2(WT + BA.4/5) bivalent booster vaccination. Virol J 2024; 21:70. [PMID: 38515117 PMCID: PMC10956325 DOI: 10.1186/s12985-024-02335-9] [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: 02/14/2024] [Accepted: 03/02/2024] [Indexed: 03/23/2024] Open
Abstract
Since the emergence of SARS-CoV-2, different variants and subvariants successively emerged to dominate global virus circulation as a result of immune evasion, replication fitness or both. COVID-19 vaccines continue to be updated in response to the emergence of antigenically divergent viruses, the first being the bivalent RNA vaccines that encodes for both the Wuhan-like and Omicron BA.5 subvariant spike proteins. Repeated infections and vaccine breakthrough infections have led to complex immune landscapes in populations making it increasingly difficult to assess the intrinsic neutralizing antibody responses elicited by the vaccines. Hong Kong's intensive COVID-19 containment policy through 2020-2021 permitted us to identify sera from a small number of infection-naïve individuals who received 3 doses of the RNA BNT162b2 vaccine encoding the Wuhan-like spike (WT) and were boosted with a fourth dose of the WT vaccine or the bivalent WT and BA.4/5 spike (WT + BA.4/5). While neutralizing antibody to wild-type virus was comparable in both vaccine groups, BNT162b2 (WT + BA.4/BA.5) bivalent vaccine elicited significantly higher plaque neutralizing antibodies to Omicron subvariants BA.5, XBB.1.5, XBB.1.16, XBB.1.9.1, XBB.2.3.2, EG.5.1, HK.3, BA.2.86 and JN.1, compared to BNT162b2 monovalent vaccine. The single amino acid substitution that differentiates the spike of JN.1 from BA.2.86 resulted in a profound antigenic change.
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Affiliation(s)
- Samuel M S Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Chris K P Mok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- SH Ho Research Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - John K C Li
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ken K P Chan
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kristine S Luk
- Princess Margaret Hospital, Hospital Authority, Hong Kong SAR, China
| | - Ben H W Lee
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Karl C K Chan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Leo C H Tsang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Karen Y S Yiu
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ken K C Ling
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yun Sang Tang
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Leo L H Luk
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jennifer K M Yu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Richard J Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benjamin J Cowling
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - David S C Hui
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- SH Ho Research Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China.
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Murphy C, Kwan MYW, Chan ELY, Wong JSC, Sullivan SG, Peiris M, Cowling BJ, Lee SL. Influenza vaccine effectiveness against hospitalizations associated with influenza A(H3N2) in Hong Kong children aged 9 months to 17 years, June-November 2023. Vaccine 2024; 42:1878-1882. [PMID: 38395722 PMCID: PMC10947845 DOI: 10.1016/j.vaccine.2024.02.056] [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: 12/05/2023] [Revised: 02/05/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
A test negative study was carried out from 13 June through to 15 November 2023 enrolling 3183 children hospitalized with acute respiratory illness in Hong Kong. Influenza A and B viruses were detected in 528 (16.6%) children, among which 419 (79.4%) were influenza A(H3N2). The overall vaccine effectiveness against hospitalization associated with any influenza virus infection was estimated as 22.4% (95% CI: -11.7%, 46.1%), and against influenza A(H3N2) specifically was 14.3% (95% CI: -29.2%, 43.2%). Despite the moderate to low VE estimated here, which could be a result of waning immunity and antigenic drift, influenza vaccination remains an important approach to reduce the impact of influenza in children.
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Affiliation(s)
- Caitriona Murphy
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Mike Y W Kwan
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Eunice L Y Chan
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Joshua S C Wong
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, and Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Department of Epidemiology, University of California, Los Angeles, California
| | - Malik Peiris
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Centre for Immunology & Infection, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China.
| | - So-Lun Lee
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region
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7
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Cheng SMS, Lau JJ, Tsang LCH, Leung K, Lee CK, Hachim A, Kavian N, Chaothai S, Wong RWK, Yu JKM, Chai ZYH, Mori M, Wu C, Yiu K, Hui DSC, Amarasinghe GK, Poon LLM, Wu JT, Valkenburg SA, Peiris M. Serological assays for differentiating natural COVID-19 infection from vaccine induced immunity. J Clin Virol 2024; 170:105621. [PMID: 38056114 DOI: 10.1016/j.jcv.2023.105621] [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] [Received: 09/06/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Natural SARS-CoV-2 infection may elicit antibodies to a range of viral proteins including non-structural protein ORF8. RNA, adenovirus vectored and sub-unit vaccines expressing SARS-CoV-2 spike would be only expected to elicit S-antibodies and antibodies to distinct domains of nucleocapsid (N) protein may reliably differentiate infection from vaccine-elicited antibody. However, inactivated whole virus vaccines may potentially elicit antibody to wider range of viral proteins, including N protein. We hypothesized that antibody to ORF8 protein will discriminate natural infection from vaccination irrespective of vaccine type. METHODS We optimized and validated the anti-ORF8 and anti-N C-terminal domain (NCTD) ELISA assays using sera from pre-pandemic, RT-PCR confirmed natural infection sera and BNT162b2 (BNT) or CoronaVac vaccinees. We then applied these optimized assays to a cohort of blood donor sera collected in April-July 2022 with known vaccination and self-reported infection status. RESULTS We optimized cut-off values for the anti-ORF8 and anti-N-CTD IgG ELISA assays using receiver-operating-characteristic (ROC) curves. The sensitivity of the anti-ORF8 and anti-N-CTD ELISA for detecting past infection was 83.2% and 99.3%, respectively. Specificity of anti-ORF8 ELISA was 96.8 % vs. the pre-pandemic cohort or 93% considering the pre-pandemic and vaccine cohorts together. The anti-N-CTD ELISA specificity of 98.9% in the pre-pandemic cohort, 93% in BNT vaccinated and only 4 % in CoronaVac vaccinated cohorts. Anti-N-CTD antibody was longer-lived than anti-ORF8 antibody after natural infection. CONCLUSIONS Anti-N-CTD antibody assays provide good discrimination between natural infection and vaccination in BNT162b2 vaccinated individuals. Anti-ORF8 antibody can help discriminate infection from vaccination in either type of vaccine and help estimate infection attack rates (IAR) in communities.
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Affiliation(s)
- Samuel M S Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jonathan J Lau
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Leo C H Tsang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kathy Leung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Cheuk Kwong Lee
- Hong Kong Red Cross Blood Transfusion Service, Hospital Authority, Hong Kong SAR, China
| | - Asmaa Hachim
- HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Niloufar Kavian
- HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, & Assistance Publique-Hôpitaux de Paris, Hôpital Universitaire Paris Centre, Centre Hospitalier Universitaire Cochin, Service d'Immunologie Biologique, Paris, France
| | - Sara Chaothai
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ricky W K Wong
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jennifer K M Yu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Zacary Y H Chai
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Masashi Mori
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
| | - Chao Wu
- Shenzhen Bay Laboratory, Guangdong, China
| | - Karen Yiu
- Department of Medicine and Therapeutics and SH Ho Research Center for Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong SAR, China
| | - David S C Hui
- Department of Medicine and Therapeutics and SH Ho Research Center for Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine at St. Louis, St. Louis, Missouri, United States
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Joseph T Wu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Centre for Immunology and Infection(C2i), Hong Kong Science Park, Hong Kong SAR, China.
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8
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Wang Y, Zhang Z, Yang M, Xiong X, Yan Q, Cao L, Wei P, Zhang Y, Zhang L, Lv K, Chen J, Liu X, Zhao X, Xiao J, Zhang S, Zhu A, Gan M, Zhang J, Cai R, Zhuo J, Zhang Y, Rao H, Qu B, Zhang Y, Chen L, Dai J, Cheng L, Hu Q, Chen Y, Lv H, So RTY, Peiris M, Zhao J, Liu X, Mok CKP, Wang X, Zhao J. Identification of a broad sarbecovirus neutralizing antibody targeting a conserved epitope on the receptor-binding domain. Cell Rep 2024; 43:113653. [PMID: 38175758 DOI: 10.1016/j.celrep.2023.113653] [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] [Received: 06/24/2023] [Revised: 11/11/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024] Open
Abstract
Omicron, as the emerging variant with enhanced vaccine tolerance, has sharply disrupted most therapeutic antibodies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the subgenus Sarbecovirus, members of which share high sequence similarity. Herein, we report one sarbecovirus antibody, 5817, which has broad-spectrum neutralization capacity against SARS-CoV-2 variants of concern (VOCs) and SARS-CoV, as well as related bat and pangolin viruses. 5817 can hardly compete with six classes of receptor-binding-domain-targeted antibodies grouped by structural classifications. No obvious impairment in the potency is detected against SARS-CoV-2 Omicron and subvariants. The cryoelectron microscopy (cryo-EM) structure of neutralizing antibody 5817 in complex with Omicron spike reveals a highly conserved epitope, only existing at the receptor-binding domain (RBD) open state. Prophylactic and therapeutic administration of 5817 potently protects mice from SARS-CoV-2 Beta, Delta, Omicron, and SARS-CoV infection. This study reveals a highly conserved cryptic epitope targeted by a broad sarbecovirus neutralizing antibody, which would be beneficial to meet the potential threat of pre-emergent SARS-CoV-2 VOCs.
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Affiliation(s)
- Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China; Clinical Laboratory Medicine Department, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Minnan Yang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xinyi Xiong
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qihong Yan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lei Cao
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Peilan Wei
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Guangzhou National Laboratory, Bio-Island, Guangzhou, China
| | - Yuting Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lu Zhang
- Health and Quarantine Laboratory, Guangzhou Customs District Technology Centre, Guangzhou, China
| | - Kexin Lv
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Jiantao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xuesong Liu
- Department of Critical Care Medicine, State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaochu Zhao
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Juxue Xiao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shengnan Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Mian Gan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jingjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ruoxi Cai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jianfen Zhuo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Haiyue Rao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Bin Qu
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yuanyuan Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lei Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jun Dai
- Health and Quarantine Laboratory, Guangzhou Customs District Technology Centre, Guangzhou, China
| | - Linling Cheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qingtao Hu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yaoqing Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ray T Y So
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Guangzhou National Laboratory, Bio-Island, Guangzhou, China
| | - Xiaoqing Liu
- Department of Critical Care Medicine, State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Chris Ka Pun Mok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; S.H. Ho Research Centre for Infectious Diseases, Chinese University of Hong Kong, Hong Kong, China.
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Guangzhou National Laboratory, Bio-Island, Guangzhou, China; Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
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9
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Lau JJ, Cheng SMS, Leung K, Lee CK, Hachim A, Tsang LCH, Yam KWH, Chaothai S, Kwan KKH, Chai ZYH, Lo THK, Mori M, Wu C, Valkenburg SA, Amarasinghe GK, Lau EHY, Hui DSC, Leung GM, Peiris M, Wu JT. Author Correction: Real-world COVID-19 vaccine effectiveness against the Omicron BA.2 variant in a SARS-CoV-2 infection-naive population. Nat Med 2024; 30:305. [PMID: 37875568 PMCID: PMC10803247 DOI: 10.1038/s41591-023-02648-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Affiliation(s)
- Jonathan J Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Samuel M S Cheng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Cheuk Kwong Lee
- Hong Kong Red Cross Blood Transfusion Service, Hong Kong SAR, People's Republic of China
| | - Asmaa Hachim
- HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Leo C H Tsang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kenny W H Yam
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sara Chaothai
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kelvin K H Kwan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Zacary Y H Chai
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tiffany H K Lo
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Masashi Mori
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
| | - Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine at St. Louis, St. Louis, MO, USA
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine at St. Louis, St. Louis, MO, USA
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - David S C Hui
- Department of Medicine and Therapeutics and Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection, Hong Kong SAR, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China.
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, China.
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10
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Daulagala P, Cheng SM, Chin A, Luk LL, Leung K, Wu JT, Poon LL, Peiris M, Yen HL. Avian Influenza A(H5N1) Neuraminidase Inhibition Antibodies in Healthy Adults after Exposure to Influenza A(H1N1)pdm09. Emerg Infect Dis 2024; 30:168-171. [PMID: 38147510 PMCID: PMC10756388 DOI: 10.3201/eid3001.230756] [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: 12/28/2023] Open
Abstract
We detected high titers of cross-reactive neuraminidase inhibition antibodies to influenza A(H5N1) virus clade 2.3.4.4b in 96.8% (61/63) of serum samples from healthy adults in Hong Kong in 2020. In contrast, antibodies at low titers were detected in 42% (21/50) of serum samples collected in 2009. Influenza A(H1N1)pdm09 and A(H5N1) titers were correlated.
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Affiliation(s)
- Pavithra Daulagala
- School of Public Health, The University of Hong Kong, Hong Kong, China (P. Daulagala, S.M.S. Cheng, A. Chin, L.H.L. Luk, K. Leung, J.T. Wu, L.L.M. Poon, M. Peiris, H.L. Yen)
- The University of Hong Kong–Shenzhen Hospital, Shenzhen, China (K. Leung)
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong (L.L.M. Poon, M. Peiris)
| | - Samuel M.S. Cheng
- School of Public Health, The University of Hong Kong, Hong Kong, China (P. Daulagala, S.M.S. Cheng, A. Chin, L.H.L. Luk, K. Leung, J.T. Wu, L.L.M. Poon, M. Peiris, H.L. Yen)
- The University of Hong Kong–Shenzhen Hospital, Shenzhen, China (K. Leung)
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong (L.L.M. Poon, M. Peiris)
| | - Alex Chin
- School of Public Health, The University of Hong Kong, Hong Kong, China (P. Daulagala, S.M.S. Cheng, A. Chin, L.H.L. Luk, K. Leung, J.T. Wu, L.L.M. Poon, M. Peiris, H.L. Yen)
- The University of Hong Kong–Shenzhen Hospital, Shenzhen, China (K. Leung)
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong (L.L.M. Poon, M. Peiris)
| | - Leo L.H. Luk
- School of Public Health, The University of Hong Kong, Hong Kong, China (P. Daulagala, S.M.S. Cheng, A. Chin, L.H.L. Luk, K. Leung, J.T. Wu, L.L.M. Poon, M. Peiris, H.L. Yen)
- The University of Hong Kong–Shenzhen Hospital, Shenzhen, China (K. Leung)
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong (L.L.M. Poon, M. Peiris)
| | - Kathy Leung
- School of Public Health, The University of Hong Kong, Hong Kong, China (P. Daulagala, S.M.S. Cheng, A. Chin, L.H.L. Luk, K. Leung, J.T. Wu, L.L.M. Poon, M. Peiris, H.L. Yen)
- The University of Hong Kong–Shenzhen Hospital, Shenzhen, China (K. Leung)
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong (L.L.M. Poon, M. Peiris)
| | - Joseph T. Wu
- School of Public Health, The University of Hong Kong, Hong Kong, China (P. Daulagala, S.M.S. Cheng, A. Chin, L.H.L. Luk, K. Leung, J.T. Wu, L.L.M. Poon, M. Peiris, H.L. Yen)
- The University of Hong Kong–Shenzhen Hospital, Shenzhen, China (K. Leung)
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong (L.L.M. Poon, M. Peiris)
| | - Leo L.M. Poon
- School of Public Health, The University of Hong Kong, Hong Kong, China (P. Daulagala, S.M.S. Cheng, A. Chin, L.H.L. Luk, K. Leung, J.T. Wu, L.L.M. Poon, M. Peiris, H.L. Yen)
- The University of Hong Kong–Shenzhen Hospital, Shenzhen, China (K. Leung)
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong (L.L.M. Poon, M. Peiris)
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11
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So RTY, Chu DKW, Hui KPY, Mok CKP, Shum MHH, Sanyal S, Nicholls JM, Ho JCW, Cheung MC, Ng KC, Yeung HW, Chan MCW, Poon LLM, Zhao J, Lam TTY, Peiris M. Amino acid substitution L232F in non-structural protein 6 identified as a possible human-adaptive mutation in clade B MERS coronaviruses. J Virol 2023; 97:e0136923. [PMID: 38038429 PMCID: PMC10734512 DOI: 10.1128/jvi.01369-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE Viral host adaptation plays an important role in inter-species transmission of coronaviruses and influenza viruses. Multiple human-adaptive mutations have been identified in influenza viruses but not so far in MERS-CoV that circulates widely in dromedary camels in the Arabian Peninsula leading to zoonotic transmission. Here, we analyzed clade B MERS-CoV sequences and identified an amino acid substitution L232F in nsp6 that repeatedly occurs in human MERS-CoV. Using a loss-of-function reverse genetics approach, we found the nsp6 L232F conferred increased viral replication competence in vitro, in cultures of the upper human respiratory tract ex vivo, and in lungs of mice infected in vivo. Our results showed that nsp6 L232F may be an adaptive mutation associated with zoonotic transmission of MERS-CoV. This study highlighted the capacity of MERS-CoV to adapt to transmission to humans and also the need for continued surveillance of MERS-CoV in camels.
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Affiliation(s)
- Ray T. Y. So
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Daniel K. W. Chu
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- UK Health Security Agency, London, United Kingdom
| | - Kenrie P. Y. Hui
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Chris K. P. Mok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, People's Republic of China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Marcus H. H. Shum
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - John M. Nicholls
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - John C. W. Ho
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Man-chun Cheung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Ka-chun Ng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Hin-Wo Yeung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Michael C. W. Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Leo L. M. Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Tommy T. Y. Lam
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
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12
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Wong CKH, Lau JJ, Au ICH, Lau KTK, Hung IFN, Peiris M, Leung GM, Wu JT. Optimal timing of nirmatrelvir/ritonavir treatment after COVID-19 symptom onset or diagnosis: target trial emulation. Nat Commun 2023; 14:8377. [PMID: 38104114 PMCID: PMC10725470 DOI: 10.1038/s41467-023-43706-0] [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: 04/16/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023] Open
Abstract
Reports of symptomatic rebound and/or test re-positivity among COVID-19 patients following the standard five-day treatment course of nirmatrelvir/ritonavir have sparked debates regarding optimal treatment timing and dosage. It is unclear whether initiating nirmatrelvir/ritonavir immediately after symptom onset would improve clinical outcomes and/or lead to post-treatment viral burden rebound due to inadequate viral clearance during treatment. Here we show that, by emulating a randomized target trial using real-world electronic medical record data from all 87,070 adult users of nirmatrelvir/ritonavir in Hong Kong between 16th March 2022 and 15th January 2023, early initiation of nirmatrelvir/ritonavir treatment (0 to 1 days after symptom onset or diagnosis) significantly reduced the incidence of 28-day all-cause mortality and hospitalization compared to delayed initiation (2 or more days) (absolute risk reduction [ARR]: 1.50% (95% confidence interval 1.17-1.80%); relative risk [RR]: 0.77 (0.73, 0.82)), but may be associated with a significant elevated risk of viral burden rebound (ARR: -1.08% (-1.55%, -0.46%)), although the latter estimates were associated with high uncertainty due to limited sample sizes. As such, patients should continue to initiate nirmatrelvir/ritonavir early after symptom onset or diagnosis to better protect against the more serious outcomes of hospitalization and mortality.
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Affiliation(s)
- Carlos K H Wong
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Family Medicine and Primary Care, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Vaccine Confidence Project, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Jonathan J Lau
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ivan C H Au
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kristy T K Lau
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ivan F N Hung
- Infectious Diseases Division, Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection, Hong Kong SAR, China
| | - Gabriel M Leung
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Joseph T Wu
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China.
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
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13
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Zhou Z, Ali A, Walelign E, Demissie GF, El Masry I, Abayneh T, Getachew B, Krishnan P, Ng DY, Gardner E, Makonnen Y, Miguel E, Chevalier V, Chu DK, So RTY, Von Dobschuetz S, Mamo G, Poon LLM, Peiris M. Genetic diversity and molecular epidemiology of Middle East Respiratory Syndrome Coronavirus in dromedaries in Ethiopia, 2017-2020. Emerg Microbes Infect 2023; 12:e2164218. [PMID: 36620913 PMCID: PMC9888459 DOI: 10.1080/22221751.2022.2164218] [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] [Indexed: 01/10/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary camels and causes zoonotic infection and disease in humans. Although over 80% of the global population of infected dromedary camels are found in Africa, zoonotic disease had only been reported in the Arabia Peninsula and travel-associated disease has been reported elsewhere. In this study, genetic diversity and molecular epidemiology of MERS-CoV in dromedary camels in Ethiopia were investigated during 2017-2020. Of 1766 nasal swab samples collected, 61 (3.5%) were detected positive for MERS-CoV RNA. Of 484 turbinate swab samples collected, 10 (2.1%) were detected positive for MERS-CoV RNA. Twenty-five whole genome sequences were obtained from these MERS-CoV positive samples. Phylogenetically, these Ethiopian camel-originated MERS-CoV belonged to clade C2, clustering with other East African camel strains. Virus sequences from camel herds clustered geographically while in an abattoir, two distinct phylogenetic clusters of MERS-CoVs were observed in two sequential sampling collections, which indicates the greater genetic diversity of MERS-CoV in abattoirs. In contrast to clade A and B viruses from the Arabian Peninsula, clade C camel-originated MERS-CoV from Ethiopia had various nucleotide insertions and deletions in non-structural gene nsp3, accessory genes ORF3 and ORF5 and structural gene N. This study demonstrates the genetic instability of MERS-CoV in dromedaries in East Africa, which indicates that the virus is still actively adapting to its camel host. The impact of the observed nucleotide insertions and deletions on virus evolution, viral fitness, and zoonotic potential deserves further study.
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Affiliation(s)
- Ziqi Zhou
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Abraham Ali
- Bacterial, Parasitic and Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia,Department of Veterinary Microbiology, Immunology and Public Health, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
| | - Elias Walelign
- Food and Agriculture Organization, Emergency Centre for Transboundary Animal Diseases, Addis Ababa, Ethiopia
| | - Getnet F. Demissie
- College of Veterinary Medicine, Department of Veterinary Epidemiology, Microbiology and Public Health, Haramaya University, Haramaya, Ethiopia
| | - Ihab El Masry
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | | | | | - Pavithra Krishnan
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Daisy Y.M. Ng
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Emma Gardner
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Yilma Makonnen
- Food and Agriculture Organization, Subregional Office for Eastern Africa, Addis Ababa, Ethiopia
| | - Eve Miguel
- Animal, Santé, Territoires, Risques et Ecosystèmes, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut National de la Recherche Agronomique, Université de Montpellier, Montpellier, France,Maladies Infectieuses et Vecteurs: Ecologie Genetique, Evolution et Controle, L’Institut de Recherche pour le Developpment, CNRS, Montpellier, France
| | - Véronique Chevalier
- International Center of Research in Agriculture for Development (CIRAD), UMR ASTRE, Montpellier, France,CIRAD, UMR ASTRE, Antananarivo, Madagascar,Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Daniel K. Chu
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China,UK Health Security Agency, London, UK
| | - Ray T. Y. So
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | | | - Gezahegne Mamo
- Department of Veterinary Microbiology, Immunology and Public Health, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
| | - Leo L. M. Poon
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China, Malik Peiris
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14
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El Masry I, Al Makhladi S, Al Abdwany M, Al Subhi A, Eltahir H, Cheng S, Peiris M, Gardner E, Von Dobschuetz S, Soumare B, Dhingra M, Sumption K, Tibbo M. Serological evidence of SARS-CoV-2 infection in dromedary camels and domestic bovids in Oman. Emerg Microbes Infect 2023; 12:2220577. [PMID: 37306181 DOI: 10.1080/22221751.2023.2220577] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
SARS-CoV-2 has demonstrated the ability to infect a wide range of animal species. Here, we investigated SARS-CoV-2 infection in livestock species in Oman and provided serological evidence of SARS-CoV-2 infection in cattle, sheep, goats, and dromedary camel using the surrogate virus neutralization and plaque reduction neutralization tests. To better understand the extent of SARS-CoV-2 infection in animals and associated risks, "One Health" epidemiological investigations targeting animals exposed to COVID-19 human cases should be implemented with integrated data analysis of the epidemiologically linked human and animal cases.
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Affiliation(s)
- Ihab El Masry
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Salim Al Makhladi
- Animal Health Research Center, Ministry of Agriculture, Fisheries and Water Resources, Muscat, Oman
| | - Mohsin Al Abdwany
- Animal Health Research Center, Ministry of Agriculture, Fisheries and Water Resources, Muscat, Oman
| | - Afrah Al Subhi
- Animal Health Research Center, Ministry of Agriculture, Fisheries and Water Resources, Muscat, Oman
| | - Hatim Eltahir
- Animal Health Research Center, Ministry of Agriculture, Fisheries and Water Resources, Muscat, Oman
| | - Samuel Cheng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Emma Gardner
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | | | - Baba Soumare
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Madhur Dhingra
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Keith Sumption
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Markos Tibbo
- Food and Agriculture Organization of the United Nations, Subregional Office for the Gulf Cooperation Council States and Yemen, Abu Dhabi, UAE
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15
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Cowling BJ, Kwan MYW, Murphy C, Chan ELY, Wong JSC, Sullivan SG, Peiris M, Lee SL. Influenza Vaccine Effectiveness Against Influenza-Associated Hospitalization in Hong Kong Children Aged 9 Months to 17 Years, March-June 2023. J Pediatric Infect Dis Soc 2023; 12:586-589. [PMID: 37818976 PMCID: PMC10687596 DOI: 10.1093/jpids/piad083] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/09/2023] [Indexed: 10/13/2023]
Abstract
In March-June 2023, we conducted a test-negative study in 1671 children who were hospitalized with acute respiratory illness in Hong Kong. Two hundred and eighty-six children (17.2%) were tested positive for influenza virus including 188 with A(H1N1). We estimated influenza vaccine effectiveness against influenza-associated hospitalization as 69.6% (95% confidence interval: 49.3%, 81.7%).
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Affiliation(s)
- Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Mike Y W Kwan
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Caitriona Murphy
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eunice L Y Chan
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Joshua S C Wong
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, and Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Epidemiology, University of California, Los Angeles, California, USA
| | - Malik Peiris
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - So-Lun Lee
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China
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16
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Zhong S, Ng TWY, Skowronski DM, Iuliano AD, Leung NHL, Perera RAPM, Ho F, Fang VJ, Tam YH, Ip DKM, Havers FG, Fry AM, Aziz-Baumgartner E, Barr IG, Peiris M, Thompson MG, Cowling BJ. Standard-dose versus MF59-adjuvanted, high-dose or recombinant-hemagglutinin influenza vaccine immunogenicity in older adults: comparison of A(H3N2) antibody response by prior season's vaccine status. J Infect Dis 2023:jiad497. [PMID: 37950884 DOI: 10.1093/infdis/jiad497] [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: 07/01/2023] [Revised: 10/19/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023] Open
Abstract
BACKGROUND Annual influenza vaccination is recommended for older adults but repeated vaccination with standard-dose influenza vaccine has been linked to reduced immunogenicity and effectiveness, especially against A(H3N2) viruses. METHODS Community-dwelling Hong Kong adults aged 65-82 years were randomly allocated to receive 2017/18 standard-dose quadrivalent, MF59-adjuvanted trivalent, high-dose trivalent, and recombinant-HA quadrivalent vaccination. Antibody response to unchanged A(H3N2) vaccine antigen was compared among participants with and without self-reported prior year (2016/17) standard-dose vaccination. RESULTS Mean fold rise (MFR) in antibody titers from Day 0 to Day 30 by hemagglutination inhibition and virus microneutralization assays were lower among 2017/18 standard-dose and enhanced vaccine recipients with (range, 1.7-3.0) vs. without (range, 4.3-14.3) prior 2016/17 vaccination. MFR was significantly reduced by about one half to four fifths for previously vaccinated recipients of standard-dose and all three enhanced vaccines (β range, 0.21-0.48). Among prior-year vaccinated older adults, enhanced vaccines induced higher 1.43 to 2.39-fold geometric mean titers and 1.28 to 1.74-fold MFR vs. standard-dose vaccine by microneutralization assay. CONCLUSIONS In the context of unchanged A(H3N2) vaccine strain, prior-year vaccination was associated with reduced antibody response among both standard-dose and enhanced influenza vaccine recipients. Enhanced vaccines improved antibody response among older adults with prior-year standard-dose vaccination.
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Affiliation(s)
- Shuyi Zhong
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Tiffany W Y Ng
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Danuta M Skowronski
- British Columbia Centre for Disease Control, Vancouver, Canada
- University of British Columbia, Vancouver, Canada
| | - A Danielle Iuliano
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nancy H L Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Ranawaka A P M Perera
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Faith Ho
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Vicky J Fang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yat Hung Tam
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Dennis K M Ip
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Fiona G Havers
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Alicia M Fry
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Ian G Barr
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - Malik Peiris
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre of Immunology and Infection, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Mark G Thompson
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
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17
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Leung D, Chan EYH, Mu X, Rosa Duque JS, Cheng SM, Ho FTW, Tong PC, Lai WM, Lee MH, Chim S, Tam IY, Tsang LC, Kwan KK, Chung Y, Wong HH, Lee AM, Li WY, Sze ST, Lam JH, Lee DH, Chan SM, Tu W, Peiris M, Ma ALT, Lau YL. Humoral and Cellular Immunogenicity of 3 Doses of BNT162b2 in Children With Kidney Diseases. Kidney Int Rep 2023; 8:2356-2367. [PMID: 38025215 PMCID: PMC10658278 DOI: 10.1016/j.ekir.2023.08.014] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Patients with severe kidney diseases are at risk of complications from COVID-19; however, little is known about the effectiveness of COVID-19 vaccines in children and adolescents with kidney diseases. Methods We investigated the immunogenicity and safety of an accelerated 3-dose primary series of COVID-19 vaccination among 59 pediatric patients with chronic kidney disease (CKD) (mean age 12.9 years; 30 male) with or without immunosuppression, dialysis, or kidney transplant. Dosage was 0.1 ml BNT162b2 to those aged 5 to 11 years, and 0.3 ml BNT162b2 to those aged 11 to 18 years. Results Three doses of either vaccine type elicited significant antibody responses that included spike receptor-binding domain (S-RBD) IgG (90.5%-93.8% seropositive) and surrogate virus neutralization (geometric mean sVNT% level, 78.6%-79.3%). There were notable T cell responses. Weaker neutralization responses were observed among those on immunosuppression, especially those receiving higher number of immunosuppressants or on mycophenolate mofetil. Neutralization was reduced against Omicron BA.1 compared to wild type (WT, i.e., ancestral) (post-dose 3 sVNT% level; 82.7% vs. 27.4%; P < 0.0001). However, the T cell response against Omicron BA.1 was preserved, which likely confers protection against severe COVID-19. Infected patients exhibited hybrid immunity after vaccination, as evidenced by the higher Omicron BA.1 neutralization response among these infected patients who received 2 doses compared with those who were uninfected. Generally mild or moderate adverse reactions following vaccines were reported. Conclusion An accelerated 3-dose primary series with BNT162b2 is immunogenic and safe in young children and adolescents with kidney diseases.
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Affiliation(s)
- Daniel Leung
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Eugene Yu-hin Chan
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, China
| | - Xiaofeng Mu
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jaime S. Rosa Duque
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Samuel M.S. Cheng
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Fanny Tsz-wai Ho
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, China
| | - Pak-chiu Tong
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, China
| | - Wai-ming Lai
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, China
| | - Matthew H.L. Lee
- Department of Pediatrics and Adolescent Medicine, Queen Mary Hospital, Hong Kong, China
| | - Stella Chim
- Department of Pediatrics and Adolescent Medicine, Queen Mary Hospital, Hong Kong, China
| | - Issan Y.S. Tam
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Leo C.H. Tsang
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Kelvin K.H. Kwan
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Yuet Chung
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Howard H.W. Wong
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Amos M.T. Lee
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Wing Yan Li
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Summer T.K. Sze
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jennifer H.Y. Lam
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Derek H.L. Lee
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Sau Man Chan
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Wenwei Tu
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection C2i, Hong Kong, China
| | - Alison Lap-tak Ma
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, China
| | - Yu Lung Lau
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
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18
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Zheng X, Zhao K, Xu X, Deng Y, Leung K, Wu JT, Leung GM, Peiris M, Poon LLM, Zhang T. Development and application of influenza virus wastewater surveillance in Hong Kong. Water Research 2023; 245:120594. [PMID: 37741039 DOI: 10.1016/j.watres.2023.120594] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/25/2023]
Abstract
Wastewater surveillance is considered as a powerful tool in providing cost-effective, population-wide and near real-time surveillance results for controlling infectious diseases (i.e., SARS-CoV-2, influenza virus), complementary to clinical surveillance. To facilitate the utility of this emerging tool, we developed two preanalytical protocols (supernatant-based and pellet-based) for influenza A/B virus (IAV/IBV) wastewater surveillance and applied them to the established wastewater surveillance network for large-scale longitudinal monitoring in Hong Kong. We tested 724 wastewater samples from 24 stationary sites for weekly surveillance for 8 months and 458 wastewater samples from 11 wastewater treatment plants (WWTPs) for more frequent (three times per week) city-wide surveillance for 4 months when influenza season commenced. We found the city-wide IAV virus concentration in wastewater were associated with the detection rate and influenza-like illness plus rates (ILI+) of clinical respiratory specimens and increased significantly after the cancelling of mask mandate that was in place for COVID-19. IBV was at low detection rates and low virus concentration levels, consistent with the low detection rates observed by clinical surveillance. In addition, we conducted virus subtype identification in selected wastewater samples, and observed the H1pdm was the major circulation subtype. Moreover, the obtained virus signals were confirmed by Sanger sequencing of PCR products, suggesting the feasibility and applicability of established methods for rapid detection of influenza virus types and subtypes in wastewater surveillance. This study demonstrates the applicability of IAV/IBV wastewater surveillance to current wastewater infrastructures and it could be used as a rapid and cost-effective surveillance strategy to track virus transmission patterns in the community for timely public health actions in the future.
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Affiliation(s)
- Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Keyue Zhao
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China; Laboratory of Data Discovery for Health Limited (D(2)4H), Hong Kong Science Park, Hong Kong SAR, China; The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China; Laboratory of Data Discovery for Health Limited (D(2)4H), Hong Kong Science Park, Hong Kong SAR, China; The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China; Laboratory of Data Discovery for Health Limited (D(2)4H), Hong Kong Science Park, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China; School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China; Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau SAR, China.
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19
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Zhao S, Lok KYW, Sin ZY, Peng Y, Fan HSL, Nagesh N, Choi MSL, Kwok JYY, Choi EPH, Zhang X, Wai HKF, Tsang LCH, Cheng SSM, Wong MKL, Zhu J, Mok CKP, Ng SC, Chan FKL, Peiris M, Poon LLM, Tun HM. COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition. NPJ Vaccines 2023; 8:151. [PMID: 37798293 PMCID: PMC10556030 DOI: 10.1038/s41541-023-00745-4] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023] Open
Abstract
Newborns can acquire immunological protection to SARS-CoV-2 through vaccine-conferred antibodies in human breast milk. However, there are some concerns around lactating mothers with regards to potential short- and long-term adverse events and vaccine-induced changes to their breast milk microbiome composition, which helps shape the early-life microbiome. Thus, we sought to explore if SARS-CoV-2 mRNA vaccine could change breast milk microbiota and how the changes impact the levels of antibodies in breast milk. We recruited 49 lactating mothers from Hong Kong who received two doses of BNT162b2 vaccine between June 2021 and August 2021. Breast milk samples were self-collected by participants pre-vaccination, one week post-first dose, one week post-second dose, and one month post-second dose. The levels of SARS-CoV-2 spike-specific IgA and IgG in breast milk peaked at one week post-second dose. Subsequently, the levels of both antibodies rapidly waned in breast milk, with IgA levels returning to baseline levels one month post-second dose. The richness and composition of human breast milk microbiota changed dynamically throughout the vaccination regimen, but the abundances of beneficial microbes such as Bifidobacterium species did not significantly change after vaccination. Additionally, we found that baseline breast milk bacterial composition can predict spike-specific IgA levels at one week post-second dose (Area Under Curve: 0.72, 95% confidence interval: 0.58-0.85). Taken together, our results identified specific breast milk microbiota markers associated with high levels of IgA in the breast milk following BNT162b2 vaccine. Furthermore, in lactating mothers, BNT162b2 vaccines did not significantly reduce probiotic species in breast milk.
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Affiliation(s)
- Shilin Zhao
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Kris Y W Lok
- School of Nursing, The University of Hong Kong, Hong Kong, China.
| | - Zhen Y Sin
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ye Peng
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Heidi S L Fan
- School of Nursing, The University of Hong Kong, Hong Kong, China
| | - Nitya Nagesh
- School of Nursing, The University of Hong Kong, Hong Kong, China
| | - Martha S L Choi
- School of Nursing, The University of Hong Kong, Hong Kong, China
| | - Jojo Y Y Kwok
- School of Nursing, The University of Hong Kong, Hong Kong, China
| | - Edmond P H Choi
- School of Nursing, The University of Hong Kong, Hong Kong, China
| | - Xi Zhang
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hogan Kok-Fung Wai
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Leo C H Tsang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Samuel S M Cheng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | | | - Jie Zhu
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Chris K P Mok
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Francis K L Chan
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hein M Tun
- Microbiota I-Center (MagIC), Hong Kong SAR, China.
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
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20
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Chan EYH, Leung D, Cheng SM, Rosa Duque JS, Mu X, Ho FTW, Tong PC, Lai WM, Lee MH, Chim S, Tam IY, Tsang LC, Kwan KK, Chung Y, Wong HH, Lee AM, Li WY, Sze ST, Lam JH, Lee DH, Chan SM, Tu W, Peiris M, Ma ALT, Lau YL. Humoral and Cellular Immunogenicity and Safety of 3-Dose Inactivated COVID-19 Vaccine in Young Children Less Than 5 Years With Kidney Diseases. Kidney Int Rep 2023; 8:2177-2179. [PMID: 37850008 PMCID: PMC10577489 DOI: 10.1016/j.ekir.2023.08.012] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/17/2023] [Accepted: 08/14/2023] [Indexed: 10/19/2023] Open
Affiliation(s)
- Eugene Yu-Hin Chan
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Kowloon City, Hong Kong, China
| | - Daniel Leung
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Samuel M.S. Cheng
- School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Jaime S. Rosa Duque
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Xiaofeng Mu
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Fanny Tsz-Wai Ho
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Kowloon City, Hong Kong, China
| | - Pak-Chiu Tong
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Kowloon City, Hong Kong, China
| | - Wai-Ming Lai
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Kowloon City, Hong Kong, China
| | - Matthew H.L. Lee
- Department of Pediatrics and Adolescent Medicine, Queen Mary Hospital, Pok Fu Lam, Hong Kong, China
| | - Stella Chim
- Department of Pediatrics and Adolescent Medicine, Queen Mary Hospital, Pok Fu Lam, Hong Kong, China
| | - Issan Y.S. Tam
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Leo C.H. Tsang
- School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Kelvin K.H. Kwan
- School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Yuet Chung
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Howard H.W. Wong
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Amos M.T. Lee
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Wing Yan Li
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Summer T.K. Sze
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Jennifer H.Y. Lam
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Derek H.L. Lee
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Sau Man Chan
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Wenwei Tu
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
- Centre for Immunology and Infection C2i, Shatin, Hong Kong, China
| | - Alison Lap-Tak Ma
- Pediatric Nephrology Centre, Department of Pediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Kowloon City, Hong Kong, China
| | - Yu Lung Lau
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
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21
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Xu X, Deng Y, Ding J, Zheng X, Wang C, Wang D, Liu L, Gu H, Peiris M, Poon LLM, Zhang T. Wastewater genomic sequencing for SARS-CoV-2 variants surveillance in wastewater-based epidemiology applications. Water Res 2023; 244:120444. [PMID: 37579567 DOI: 10.1016/j.watres.2023.120444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/16/2023]
Abstract
Wastewater-based epidemiology (WBE) has been widely used as a complementary approach to SARS-CoV-2 clinical surveillance. Wastewater genomic sequencing could provide valuable information on the genomic diversity of SARS-CoV-2 in the surveyed population. However, reliable detection and quantification of variants or mutations remain challenging. In this study, we used mock wastewater samples created by spiking SARS-CoV-2 variant standard RNA into wastewater RNA to evaluate the impacts of sequencing throughput on various aspects such as genome coverage, mutation detection, and SARS-CoV-2 variant deconvolution. We found that wastewater datasets with sequencing throughput greater than 0.5 Gb yielded reliable results in genomic analysis. In addition, using in silico mock datasets, we evaluated the performance of the adopted pipeline for variant deconvolution. By sequencing 86 wastewater samples covering more than 6 million people over 7 months, we presented two use cases of wastewater genomic sequencing for surveying COVID-19 in Hong Kong in WBE applications, including the replacement of Delta variants by Omicron variants, and the prevalence and development trends of three Omicron sublineages. Importantly, the wastewater genomic sequencing data were able to reveal the variant trends 16 days before the clinical data did. By investigating mutations of the spike (S) gene of the SARS-CoV-2 virus, we also showed the potential of wastewater genomic sequencing in identifying novel mutations and unique alleles. Overall, our study demonstrated the crucial role of wastewater genomic surveillance in providing valuable insights into the emergence and monitoring of new SARS-CoV-2 variants and laid a solid foundation for the development of genomic analysis methodologies for WBE of other novel emerging viruses in the future.
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Affiliation(s)
- Xiaoqing Xu
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yu Deng
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jiahui Ding
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiawan Zheng
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Chunxiao Wang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Dou Wang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Lei Liu
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Haogao Gu
- Li Ka Shing Faculty of Medicine, School of Public Health, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Malik Peiris
- Li Ka Shing Faculty of Medicine, School of Public Health, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Leo L M Poon
- Li Ka Shing Faculty of Medicine, School of Public Health, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Tong Zhang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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22
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Aquino Y, Bisiaux A, Li Z, O'Neill M, Mendoza-Revilla J, Merkling SH, Kerner G, Hasan M, Libri V, Bondet V, Smith N, de Cevins C, Ménager M, Luca F, Pique-Regi R, Barba-Spaeth G, Pietropaoli S, Schwartz O, Leroux-Roels G, Lee CK, Leung K, Wu JT, Peiris M, Bruzzone R, Abel L, Casanova JL, Valkenburg SA, Duffy D, Patin E, Rotival M, Quintana-Murci L. Dissecting human population variation in single-cell responses to SARS-CoV-2. Nature 2023; 621:120-128. [PMID: 37558883 PMCID: PMC10482701 DOI: 10.1038/s41586-023-06422-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 11/10/2022] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Humans display substantial interindividual clinical variability after SARS-CoV-2 infection1-3, the genetic and immunological basis of which has begun to be deciphered4. However, the extent and drivers of population differences in immune responses to SARS-CoV-2 remain unclear. Here we report single-cell RNA-sequencing data for peripheral blood mononuclear cells-from 222 healthy donors of diverse ancestries-that were stimulated with SARS-CoV-2 or influenza A virus. We show that SARS-CoV-2 induces weaker, but more heterogeneous, interferon-stimulated gene activity compared with influenza A virus, and a unique pro-inflammatory signature in myeloid cells. Transcriptional responses to viruses display marked population differences, primarily driven by changes in cell abundance including increased lymphoid differentiation associated with latent cytomegalovirus infection. Expression quantitative trait loci and mediation analyses reveal a broad effect of cell composition on population disparities in immune responses, with genetic variants exerting a strong effect on specific loci. Furthermore, we show that natural selection has increased population differences in immune responses, particularly for variants associated with SARS-CoV-2 response in East Asians, and document the cellular and molecular mechanisms by which Neanderthal introgression has altered immune functions, such as the response of myeloid cells to viruses. Finally, colocalization and transcriptome-wide association analyses reveal an overlap between the genetic basis of immune responses to SARS-CoV-2 and COVID-19 severity, providing insights into the factors contributing to current disparities in COVID-19 risk.
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Affiliation(s)
- Yann Aquino
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Aurélie Bisiaux
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Zhi Li
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Mary O'Neill
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Javier Mendoza-Revilla
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Sarah Hélène Merkling
- Insect-Virus Interactions Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Gaspard Kerner
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Milena Hasan
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
| | - Valentina Libri
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
| | - Vincent Bondet
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Nikaïa Smith
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Camille de Cevins
- Université Paris Cité, Imagine Institute, Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Atip-Avenir Team, INSERM UMR1163, Paris, France
| | - Mickaël Ménager
- Université Paris Cité, Imagine Institute, Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Atip-Avenir Team, INSERM UMR1163, Paris, France
- Labtech Single-Cell@Imagine, Imagine Institute, INSERM UMR1163, Paris, France
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Giovanna Barba-Spaeth
- Structural Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Stefano Pietropaoli
- Structural Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | | | - Cheuk-Kwong Lee
- Hong Kong Red Cross Blood Transfusion Service, Hospital Authority, Hong Kong SAR, China
| | - Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Malik Peiris
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Roberto Bruzzone
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Université Paris Cité, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Université Paris Cité, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Maxime Rotival
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France.
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France.
- Chair Human Genomics and Evolution, Collège de France, Paris, France.
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23
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Abstract
No abstract available
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Affiliation(s)
- Malik Peiris
- School of Public Health, The University of Hong Kong. Hong Kong Special Administrative Region, China
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24
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Hui KPY, Chin AWH, Ehret J, Ng KC, Peiris M, Poon LLM, Wong KHM, Chan MCW, Hosegood I, Nicholls JM. Stability of SARS-CoV-2 on Commercial Aircraft Interior Surfaces with Implications for Effective Control Measures. Int J Environ Res Public Health 2023; 20:6598. [PMID: 37623181 PMCID: PMC10454724 DOI: 10.3390/ijerph20166598] [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] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/02/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND The COVID-19 pandemic from 2019 to 2022 devastated many aspects of life and the economy, with the commercial aviation industry being no exception. One of the major concerns during the pandemic was the degree to which the internal aircraft environment contributed to virus transmission between humans and, in particular, the stability of SARS-CoV-2 on contact surfaces in the aircraft cabin interior. METHOD In this study, the stability of various major strains of SARS-CoV-2 on interior aircraft surfaces was evaluated using the TCID50 assessment. RESULTS In contrast to terrestrial materials, SARS-CoV-2 was naturally less stable on common contact points in the aircraft interior, and, over a 4 h time period, there was a 90% reduction in culturable virus. Antiviral and surface coatings were extremely effective at mitigating the persistence of the virus on surfaces; however, their benefit was diminished by regular cleaning and were ineffective after 56 days of regular use and cleaning. Finally, successive strains of SARS-CoV-2 have not evolved to be more resilient to survival on aircraft surfaces. CONCLUSIONS We conclude that the mitigation strategies for SARS-CoV-2 on interior aircraft surfaces are more than sufficient, and epidemiological evidence over the past three years has not found that surface spread is a major route of transmission.
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Affiliation(s)
- Kenrie P. Y. Hui
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China; (K.P.Y.H.)
- Centre for Immunology & Infection, Hong Kong Science Park HKG, Hong Kong SAR, China
| | - Alex W. H. Chin
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China; (K.P.Y.H.)
- Centre for Immunology & Infection, Hong Kong Science Park HKG, Hong Kong SAR, China
| | - John Ehret
- Qantas Airways Ltd., Qantas 10 Bourke Rd Mascot, Sydney, NSW 2020, Australia
| | - Ka-Chun Ng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China; (K.P.Y.H.)
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China; (K.P.Y.H.)
- Centre for Immunology & Infection, Hong Kong Science Park HKG, Hong Kong SAR, China
| | - Leo L. M. Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China; (K.P.Y.H.)
- Centre for Immunology & Infection, Hong Kong Science Park HKG, Hong Kong SAR, China
| | - Karen H. M. Wong
- Electron Microscopy Unit, Queen Mary Hospital, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China
| | - Michael C. W. Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China; (K.P.Y.H.)
- Centre for Immunology & Infection, Hong Kong Science Park HKG, Hong Kong SAR, China
| | - Ian Hosegood
- Qantas Airways Ltd., Qantas 10 Bourke Rd Mascot, Sydney, NSW 2020, Australia
| | - John M. Nicholls
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam HKG, Hong Kong SAR, China
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25
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Chia WN, Tan CW, Tan AWK, Young B, Starr TN, Lopez E, Fibriansah G, Barr J, Cheng S, Yeoh AYY, Yap WC, Lim BL, Ng TS, Sia WR, Zhu F, Chen S, Zhang J, Kwek MSS, Greaney AJ, Chen M, Au GG, Paradkar PN, Peiris M, Chung AW, Bloom JD, Lye D, Lok S, Wang LF. Potent pan huACE2-dependent sarbecovirus neutralizing monoclonal antibodies isolated from a BNT162b2-vaccinated SARS survivor. Sci Adv 2023; 9:eade3470. [PMID: 37494438 PMCID: PMC10371021 DOI: 10.1126/sciadv.ade3470] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern such as Omicron hampered efforts in controlling the ongoing coronavirus disease 2019 pandemic due to their ability to escape neutralizing antibodies induced by vaccination or prior infection, highlighting the need to develop broad-spectrum vaccines and therapeutics. Most human monoclonal antibodies (mAbs) reported to date have not demonstrated true pan-sarbecovirus neutralizing breadth especially against animal sarbecoviruses. Here, we report the isolation and characterization of highly potent mAbs targeting the receptor binding domain (RBD) of huACE2-dependent sarbecovirus from a SARS-CoV survivor vaccinated with BNT162b2. Among the six mAbs identified, one (E7) showed better huACE2-dependent sarbecovirus neutralizing potency and breadth than any other mAbs reported to date. Mutagenesis and cryo-electron microscopy studies indicate that these mAbs have a unique RBD contact footprint and that E7 binds to a quaternary structure-dependent epitope.
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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
| | - Aaron Wai Kit Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Barnaby Young
- National Center of Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Ester Lopez
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Guntur Fibriansah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Jennifer Barr
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Samuel Cheng
- School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Aileen Ying-Yan Yeoh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Wee Chee Yap
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Beng Lee Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Thiam-Seng Ng
- 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
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Shiwei Chen
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Jinyan Zhang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Madeline Sheng Si Kwek
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA, USA
| | - Mark Chen
- National Center of Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Gough G. Au
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Prasad N. Paradkar
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong, China
- Centre for Immunology & Infection, New Territories, Hong Kong, China
- HKU-Pasteur Research Pole, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Amy W. Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA, USA
| | - David Lye
- National Center of 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
| | - Sheemei Lok
- 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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Cheung J, Bui AN, Younas S, Edwards KM, Nguyen HQ, Pham NT, Bui VN, Peiris M, Dhanasekaran V. Long-Term Epidemiology and Evolution of Swine Influenza Viruses, Vietnam. Emerg Infect Dis 2023; 29:1397-1406. [PMID: 37347532 PMCID: PMC10310380 DOI: 10.3201/eid2907.230165] [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] [Indexed: 06/23/2023] Open
Abstract
Influenza A viruses are a One Health threat because they can spill over between host populations, including among humans, swine, and birds. Surveillance of swine influenza virus in Hanoi, Vietnam, during 2013-2019 revealed gene pool enrichment from imported swine from Asia and North America and showed long-term maintenance, persistence, and reassortment of virus lineages. Genome sequencing showed continuous enrichment of H1 and H3 diversity through repeat introduction of human virus variants and swine influenza viruses endemic in other countries. In particular, the North American H1-δ1a strain, which has a triple-reassortant backbone that potentially results in increased human adaptation, emerged as a virus that could pose a zoonotic threat. Co-circulation of H1-δ1a viruses with other swine influenza virus genotypes raises concerns for both human and animal health.
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Affiliation(s)
- Jonathan Cheung
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
| | - Anh Ngoc Bui
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
| | - Sonia Younas
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
| | - Kimberly M. Edwards
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
| | - Huy Quang Nguyen
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
| | - Ngoc Thi Pham
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
| | - Vuong Nghia Bui
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
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27
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Ng WY, Thoe W, Yang R, Cheung WP, Chen CK, To KH, Pak KM, Leung HW, Lai WK, Wong TK, Lau TK, Au KW, Xu XQ, Zheng XW, Deng Y, Lau YK, To CK, Peiris M, Leung GM, Zhang T, Yang M, An W, Chen W, Wang C, Chui HK. The city-wide full-scale interactive application of sewage surveillance programme for assisting real-time COVID-19 pandemic control - A case study in Hong Kong. Sci Total Environ 2023; 875:162661. [PMID: 36898549 PMCID: PMC9991928 DOI: 10.1016/j.scitotenv.2023.162661] [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] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
The paper discusses the implementation of Hong Kong's tailor-made sewage surveillance programme led by the Government, which has demonstrated how an efficient and well-organized sewage surveillance system can complement conventional epidemiological surveillance to facilitate the planning of intervention strategies and actions for combating COVID-19 pandemic in real-time. This included the setting up of a comprehensive sewerage network-based SARS-CoV-2 virus surveillance programme with 154 stationary sites covering 6 million people (or 80 % of the total population), and employing an intensive monitoring programme to take samples from each stationary site every 2 days. From 1 January to 22 May 2022, the daily confirmed case count started with 17 cases per day on 1 January to a maximum of 76,991 cases on 3 March and dropped to 237 cases on 22 May. During this period, a total of 270 "Restriction-Testing Declaration" (RTD) operations at high-risk residential areas were conducted based on the sewage virus testing results, where over 26,500 confirmed cases were detected with a majority being asymptomatic. In addition, Compulsory Testing Notices (CTN) were issued to residents, and the distribution of Rapid Antigen Test kits was adopted as alternatives to RTD operations in areas of moderate risk. These measures formulated a tiered and cost-effective approach to combat the disease in the local setting. Some ongoing and future enhancement efforts to improve efficacy are discussed from the perspective of wastewater-based epidemiology. Forecast models on case counts based on sewage virus testing results were also developed with R2 of 0.9669-0.9775, which estimated that up to 22 May 2022, around 2,000,000 people (~67 % higher than the total number of 1,200,000 reported to the health authority, due to various constraints or limitations) had potentially contracted the disease, which is believed to be reflecting the real situation occurring in a highly urbanized metropolis like Hong Kong.
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Affiliation(s)
- Wai-Yin Ng
- Environmental Protection Department, Hong Kong SAR Government, China
| | - Wai Thoe
- Environmental Protection Department, Hong Kong SAR Government, China
| | - Rong Yang
- Environmental Protection Department, Hong Kong SAR Government, China
| | - Wai-Ping Cheung
- Environmental Protection Department, Hong Kong SAR Government, China
| | - Che-Kong Chen
- Environmental Protection Department, Hong Kong SAR Government, China
| | - King-Ho To
- Environmental Protection Department, Hong Kong SAR Government, China
| | - Kan-Ming Pak
- Drainage Service Department, Hong Kong SAR Government, China
| | - Hon-Wan Leung
- Drainage Service Department, Hong Kong SAR Government, China
| | - Wai-Kwan Lai
- Drainage Service Department, Hong Kong SAR Government, China
| | - Tsz-Kin Wong
- Drainage Service Department, Hong Kong SAR Government, China
| | - Tat-Kwong Lau
- Drainage Service Department, Hong Kong SAR Government, China
| | - Ka-Wing Au
- Centre for Health Protection, Department of Health, Hong Kong SAR Government, China
| | - Xiao-Qing Xu
- Department of Civil Engineering, The University of Hong Kong, China
| | - Xia-Wan Zheng
- Department of Civil Engineering, The University of Hong Kong, China
| | - Yu Deng
- Department of Civil Engineering, The University of Hong Kong, China
| | - Yan-Kin Lau
- CMA Industrial Development Foundation Limited, Hong Kong, China
| | - Chi-Kai To
- CMA Industrial Development Foundation Limited, Hong Kong, China
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, China
| | | | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, China
| | - Min Yang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wei An
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wenxiu Chen
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chen Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ho-Kwong Chui
- Environmental Protection Department, Hong Kong SAR Government, China; Hong Kong University of Science and Technology, China.
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28
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Yu MKL, Chan SHS, Cheng S, Leung D, Chan SM, Yan ASK, Wong WHS, Peiris M, Lau YL, Rosa Duque JS. Hesitancy, reactogenicity and immunogenicity of the mRNA and whole-virus inactivated Covid-19 vaccines in pediatric neuromuscular diseases. Hum Vaccin Immunother 2023:2206278. [PMID: 37157992 DOI: 10.1080/21645515.2023.2206278] [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] [Indexed: 05/10/2023] Open
Abstract
The mRNA-based BNT162b2 and inactivated whole-virus CoronaVac are two widely used COVID-19 vaccines that confer immune protection to healthy individuals. However, hesitancy toward COVID-19 vaccination appeared to be common for patients with neuromuscular diseases (NMDs) due to the paucity of data on the safety and efficacy in this high-risk patient population. Therefore, we examined the underlying factors associated with vaccine hesitancy across time for NMDs and assessed the reactogenicity and immunogenicity of these two vaccines. Patients aged 8-18 years with no cognitive delay were invited to complete surveys in January and April 2022. Patients aged 2-21 years were enrolled for COVID-19 vaccination between June 2021 and April 2022, and they recorded adverse reactions (ARs) for 7 days after vaccination. Peripheral blood was obtained before and within 49 days after vaccination to measure serological antibody responses compared to healthy children and adolescents. Forty-one patients completed vaccine hesitancy surveys for both timepoints, while 22 joined the reactogenicity and immunogenicity arm of the study. Two or more family members vaccinated against COVID-19 was positively associated with intention of vaccination (odds ratio 11.7, 95% CI 1.81-75.1, p = .010). Pain at the injection site, fatigue, and myalgia were the commonest ARs. Most ARs were mild (75.5%, n = 71/94). All 19 patients seroconverted against the wildtype SARS-CoV-2 after two doses of either vaccine, similar to 280 healthy counterparts. There was lower neutralization against the Omicron BA.1 variant. BNT162b2 and CoronaVac were safe and immunogenic for patients with NMDs, even in those on low-dose corticosteroids.
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Affiliation(s)
- Michael Kwan Leung Yu
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sophelia Hoi Shan Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Samuel Cheng
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Daniel Leung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sau Man Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Amy Suen Ka Yan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Wilfred Hing Sang Wong
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jaime S Rosa Duque
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
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29
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Xie R, Edwards KM, Adam DC, Leung KSM, Tsang TK, Gurung S, Xiong W, Wei X, Ng DYM, Liu GYZ, Krishnan P, Chang LDJ, Cheng SMS, Gu H, Siu GKH, Wu JT, Leung GM, Peiris M, Cowling BJ, Poon LLM, Dhanasekaran V. Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong. Nat Commun 2023; 14:2422. [PMID: 37105966 PMCID: PMC10134727 DOI: 10.1038/s41467-023-38201-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
Hong Kong experienced a surge of Omicron BA.2 infections in early 2022, resulting in one of the highest per-capita death rates of COVID-19. The outbreak occurred in a dense population with low immunity towards natural SARS-CoV-2 infection, high vaccine hesitancy in vulnerable populations, comprehensive disease surveillance and the capacity for stringent public health and social measures (PHSMs). By analyzing genome sequences and epidemiological data, we reconstructed the epidemic trajectory of BA.2 wave and found that the initial BA.2 community transmission emerged from cross-infection within hotel quarantine. The rapid implementation of PHSMs suppressed early epidemic growth but the effective reproduction number (Re) increased again during the Spring festival in early February and remained around 1 until early April. Independent estimates of point prevalence and incidence using phylodynamics also showed extensive superspreading at this time, which likely contributed to the rapid expansion of the epidemic. Discordant inferences based on genomic and epidemiological data underscore the need for research to improve near real-time epidemic growth estimates by combining multiple disparate data sources to better inform outbreak response policy.
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Affiliation(s)
- Ruopeng Xie
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kimberly M Edwards
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Dillon C Adam
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kathy S M Leung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tim K Tsang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shreya Gurung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Weijia Xiong
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaoman Wei
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Daisy Y M Ng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Gigi Y Z Liu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Pavithra Krishnan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lydia D J Chang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Samuel M S Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Gilman K H Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Joseph T Wu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, New Territories, Hong Kong SAR, China
| | - Gabriel M Leung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, New Territories, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, New Territories, Hong Kong SAR, China
| | - Benjamin J Cowling
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, New Territories, Hong Kong SAR, China
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, New Territories, Hong Kong SAR, China
| | - Vijaykrishna Dhanasekaran
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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30
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Hui KPY, Ho JCW, Ng KC, Cheng SMS, Sit KY, Au TWK, Poon LLM, Nicholls JM, Peiris M, Chan MCW. Replication of Novel Zoonotic-Like Influenza A(H3N8) Virus in Ex Vivo Human Bronchus and Lung. Emerg Infect Dis 2023; 29:1210-1214. [PMID: 37095078 DOI: 10.3201/eid2906.221680] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Human infection with avian influenza A(H3N8) virus is uncommon but can lead to acute respiratory distress syndrome. In explant cultures of the human bronchus and lung, novel H3N8 virus showed limited replication efficiency in bronchial and lung tissue but had a higher replication than avian H3N8 virus in lung tissue.
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31
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Mok CKP, Chen C, Zhao S, Sun Y, Yiu K, Chan TO, Lai HL, Lai KC, Lau KM, Ling KC, Chan KKP, Ng SS, Ko FW, Peiris M, Hui DS. Omicron BA.1-specific T-cell responses in adults vaccinated with CoronaVac or BNT162b2 in Hong Kong: an observational cohort study. Lancet Microbe 2023:S2666-5247(23)00006-X. [PMID: 37086735 PMCID: PMC10115591 DOI: 10.1016/s2666-5247(23)00006-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/19/2022] [Accepted: 12/23/2022] [Indexed: 04/24/2023]
Abstract
BACKGROUND The primary aim of using vaccines in public health responses to SARS-CoV-2 variants of concern is to reduce incidence of severe disease, for which T-cell responses are essential. There is a paucity of data on vaccine-induced T-cell immunity to omicron (B.1.1.529). We aimed to compare SARS-CoV-2 omicron BA.1-specific T-cell responses in adults vaccinated with CoronaVac or BNT162b2. METHODS For this observational cohort, we recruited adults (aged ≥18 years) from three vaccination centres in Hong Kong. We included participants from four cohorts (cohort 1: participants who received two doses of either BNT162b2 or CoronaVac, cohort 2: participants who received two doses and a booster, cohort 3: participants who received two doses and a booster and had a breakthrough omicron infection, and cohort 4: participants who had a previous non-omicron infection and subsequently received one dose of vaccine). People with confirmed history of COVID-19 at recruitment were excluded from cohort 1 and cohort 2. We collected blood samples before vaccination (for cohort 1 and 2), 1-month following vaccination (for all cohorts), and during convalescence for cohort 3 and 4) and determined the proportion of IFNγ+CD4+ and IFNγ+CD8+ T cells in peripheral blood against SARS-CoV-2 using flow cytometry with peptide pools of SARS-CoV-2 wild type or omicron BA.1. The primary outcome was proportion of CD4+ and CD8+ T cells against SARS-CoV-2 1 month after exposure (ie, vaccination or breakthrough infection). FINDINGS Overall, between May 21, 2020, and Aug 31, 2021, we recruited 659 participants (231 [35%] men and 428 [65%] women). Of these participants, 428 were included in cohort 1 (214 [50%] received BNT162b2 and 214 [50%] received CoronaVac); 127 in cohort 2 (48 [38%] received all BNT162b2, 40 [31%] received all CoronaVac, and 39 [31%] received two CoronaVac and a booster with BNT162b2); 58 in cohort 3, and 46 in cohort 4 (16 [35%] received CoronaVac and 30 [65%] received BNT162b2). Vaccine-induced T-cell responses to the wild-type and omicron BA.1 variants were generally similar in adults receiving two doses of either CoronaVac (CD4+ cells p=0·33; CD8+ cells p=0·70) or BNT162b2 (CD4+ cells p=0·28; CD8+ cells p=1·0). Using a peptide pool of all structural proteins for stimulation, BNT162b2 induced a higher median frequency of omicron-specific CD4+ T cells in adults younger than 60 years (CD4+ cells 0·012% vs 0·010%, p=0·031; CD8+ cells 0·003% vs 0·000%, p=0·055) and omicron-specific CD8+ T cells in people aged 60 years or older (CD4+ cells 0·015% vs 0·006%, p=0·0070; CD8+ cells 0·007% vs 0·000%, p=0·035). A booster dose of either BNT162b2 or CoronaVac after two doses of CoronaVac boosted waning T-cell responses, but T-cell responses did not exceed those at 1 month after the second dose (CoronaVac CD4+ p=0·41, CD8+ p=0·79; BNT162b2 CD4+ p=0·70 CD8+ p=0·80). INTERPRETATION The evidence that mRNA and inactivated vaccines based on the ancestral SARS-CoV-2 virus elicited T-cell responses to SARS-CoV-2 omicron variants might explain the high observed vaccine effectiveness against severe COVID-19 shown by both types of vaccine, despite great differences in neutralising antibody responses. The use of either vaccine can be considered if the primary aim is to reduce severity and death caused by the new omicron subvariants; however, BNT162b2 is preferable for adults older than 60 years. FUNDING The Health and Medical Research Fund Commissioned Research on the Novel Coronavirus Disease and S H Ho Foundation.
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Affiliation(s)
- Chris Ka Pun Mok
- Jockey Club School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Chunke Chen
- Jockey Club School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Shilin Zhao
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yuanxin Sun
- Jockey Club School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Karen Yiu
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Tat-On Chan
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ho-Lun Lai
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kiu Cheung Lai
- Jockey Club School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ka Man Lau
- Jockey Club School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kwun Cheung Ling
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ken K P Chan
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Susanna S Ng
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Fanny W Ko
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China; School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China.
| | - David S Hui
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China.
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Daulagala P, Mann BR, Leung K, Lau EHY, Yung L, Lei R, Nizami SIN, Wu JT, Chiu SS, Daniels RS, Wu NC, Wentworth D, Peiris M, Yen HL. Imprinted Anti-Hemagglutinin and Anti-Neuraminidase Antibody Responses after Childhood Infections of A(H1N1) and A(H1N1)pdm09 Influenza Viruses. mBio 2023:e0008423. [PMID: 37070986 DOI: 10.1128/mbio.00084-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
Immune imprinting is a driver known to shape the anti-hemagglutinin (HA) antibody landscape of individuals born within the same birth cohort. With the HA and neuraminidase (NA) proteins evolving at different rates under immune selection pressures, anti-HA and anti-NA antibody responses since childhood influenza virus infections have not been evaluated in parallel at the individual level. This is partly due to the limited knowledge of changes in NA antigenicity, as seasonal influenza vaccines have focused on generating neutralizing anti-HA antibodies against HA antigenic variants. Here, we systematically characterized the NA antigenic variants of seasonal A(H1N1) viruses from 1977 to 1991 and completed the antigenic profile of N1 NAs from 1977 to 2015. We identified that NA proteins of A/USSR/90/77, A/Singapore/06/86, and A/Texas/36/91 were antigenically distinct and mapped N386K as a key determinant of the NA antigenic change from A/USSR/90/77 to A/Singapore/06/86. With comprehensive panels of HA and NA antigenic variants of A(H1N1) and A(H1N1)pdm09 viruses, we determined hemagglutinin inhibition (HI) and neuraminidase inhibition (NI) antibodies from 130 subjects born between 1950 and 2015. Age-dependent imprinting was observed for both anti-HA and anti-NA antibodies, with the peak HI and NI titers predominantly detected from subjects at 4 to 12 years old during the year of initial virus isolation, except the age-independent anti-HA antibody response against A(H1N1)pdm09 viruses. More participants possessed antibodies that reacted to multiple antigenically distinct NA proteins than those with antibodies that reacted to multiple antigenically distinct HA proteins. Our results support the need to include NA proteins in seasonal influenza vaccine preparations. IMPORTANCE Seasonal influenza vaccines have aimed to generate neutralizing anti-HA antibodies for protection since licensure. More recently, anti-NA antibodies have been established as an additional correlate of protection. While HA and NA antigenic changes occurred discordantly, the anti-HA and anti-NA antibody profiles have rarely been analyzed in parallel at the individual level, due to the limited knowledge on NA antigenic changes. By characterizing NA antigenic changes of A(H1N1) viruses, we determined the anti-HA and anti-NA antibody landscape against antigenically distinct A(H1N1) and A(H1N1)pdm09 viruses using sera of 130 subjects born between 1950 and 2015. We observed age-dependent imprinting of both anti-HA and anti-NA antibodies against strains circulated during the first decade of life. A total of 67.7% (88/130) and 90% (117/130) of participants developed cross-reactive antibodies to multiple HA and NA antigens at titers ≥1:40. With slower NA antigenic changes and cross-reactive anti-NA antibody responses, including NA protein in influenza vaccine preparation may enhance vaccine efficacy.
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Affiliation(s)
- Pavithra Daulagala
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Brian R Mann
- WHO Collaborating Center for Surveillance, Epidemiology and Control of Influenza, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kathy Leung
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
- University of Hong Kong, Shenzhen Hospital, Shenzhen, China
| | - Eric H Y Lau
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Louise Yung
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sarea I N Nizami
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Joseph T Wu
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Susan S Chiu
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital and Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Rodney S Daniels
- Francis Crick Institute, Crick Worldwide Influenza Centre, WHO Collaborating Centre for Reference and Research on Influenza, London, UK
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - David Wentworth
- WHO Collaborating Center for Surveillance, Epidemiology and Control of Influenza, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection (C2I), Hong Kong Science Park, Hong Kong SAR, China
| | - Hui-Ling Yen
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
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Chen R, Hui KPY, Liang Y, Ng KC, Nicholls JM, Ip MSM, Peiris M, Chan MCW, Mak JCW. SARS-CoV-2 infection aggravates cigarette smoke-exposed cell damage in primary human airway epithelia. Virol J 2023; 20:65. [PMID: 37041586 PMCID: PMC10089376 DOI: 10.1186/s12985-023-02008-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/08/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a worldwide pandemic with over 627 million cases and over 6.5 million deaths. It was reported that smoking-related chronic obstructive pulmonary disease (COPD) might be a crucial risk for COVID-19 patients to develop severe condition. As cigarette smoke (CS) is the major risk factor for COPD, we hypothesize that barrier dysfunction and an altered cytokine response in CS-exposed airway epithelial cells may contribute to increased SARS-CoV-2-induced immune response that may result in increased susceptibility to severe disease. The aim of this study was to evaluate the role of CS on SARS-CoV-2-induced immune and inflammatory responses, and epithelial barrier integrity leading to airway epithelial damage. METHODS Primary human airway epithelial cells were differentiated under air-liquid interface culture. Cells were then exposed to cigarette smoke medium (CSM) before infection with SARS-CoV-2 isolated from a local patient. The infection susceptibility, morphology, and the expression of genes related to host immune response, airway inflammation and damages were evaluated. RESULTS Cells pre-treated with CSM significantly caused higher replication of SARS-CoV-2 and more severe SARS-CoV-2-induced cellular morphological alteration. CSM exposure caused significant upregulation of long form angiotensin converting enzyme (ACE)2, a functional receptor for SARS-CoV-2 viral entry, transmembrane serine protease (TMPRSS)2 and TMPRSS4, which cleave the spike protein of SARS-CoV-2 to allow viral entry, leading to an aggravated immune response via inhibition of type I interferon pathway. In addition, CSM worsened SARS-CoV-2-induced airway epithelial cell damage, resulting in severe motile ciliary disorder, junctional disruption and mucus hypersecretion. CONCLUSION Smoking led to dysregulation of host immune response and cell damage as seen in SARS-CoV-2-infected primary human airway epithelia. These findings may contribute to increased disease susceptibility with severe condition and provide a better understanding of the pathogenesis of SARS-CoV-2 infection in smokers.
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Affiliation(s)
- Rui Chen
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Kenrie Pui-Yan Hui
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yingmin Liang
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ka-Chun Ng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - John Malcolm Nicholls
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mary Sau-Man Ip
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Malik Peiris
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Michael Chi-Wai Chan
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China.
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Judith Choi-Wo Mak
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Department of Pharmacology & Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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Gu H, Quadeer AA, Krishnan P, Ng DYM, Chang LDJ, Liu GYZ, Cheng SMS, Lam TTY, Peiris M, McKay MR, Poon LLM. Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals. Nat Commun 2023; 14:1793. [PMID: 37002233 PMCID: PMC10063955 DOI: 10.1038/s41467-023-37468-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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Viral and host factors can shape SARS-CoV-2 evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here, we analysed deep sequencing data from 2,820 SARS-CoV-2 respiratory samples with different viral lineages to describe the patterns of within-host diversity under different conditions, including vaccine-breakthrough infections. In unvaccinated individuals, variant of Concern (VOC) Alpha, Delta, and Omicron respiratory samples were found to have higher within-host diversity and were under neutral to purifying selection at the full genome level compared to non-VOC SARS-CoV-2. Breakthrough infections in 2-dose or 3-dose Comirnaty and CoronaVac vaccinated individuals did not increase levels of non-synonymous mutations and did not change the direction of selection pressure. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 sequence diversification. Our findings suggest that vaccination does not increase exploration of SARS-CoV-2 protein sequence space and may not facilitate emergence of viral variants.
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Affiliation(s)
- Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ahmed Abdul Quadeer
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Pavithra Krishnan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Daisy Y M Ng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lydia D J Chang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Gigi Y Z Liu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Samuel M S Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tommy T Y Lam
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Matthew R McKay
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Electrical and Electronic Engineering, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China.
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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So RTY, Chu DKW, Hui KPY, Mok CKP, Sanyal S, Nicholls JM, Ho JCW, Cheung MC, Ng KC, Yeung HW, Chan MCW, Poon LLM, Zhao J, Peiris M. Mutation nsp6 L232F associated with MERS-CoV zoonotic transmission confers higher viral replication in human respiratory tract cultures ex-vivo. bioRxiv 2023:2023.03.27.534490. [PMID: 37034576 PMCID: PMC10081289 DOI: 10.1101/2023.03.27.534490] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) causes zoonotic disease. Dromedary camels are the source of zoonotic infection. We identified a mutation of amino acid leucine to phenylalanine in the codon 232 position of the non-structural protein 6 (nsp6) (nsp6 L232F) that is repeatedly associated with zoonotic transmission. We generated a pair of isogenic recombinant MERS-CoV with nsp6 232L and 232F residues, respectively, and showed that the nsp6 L232F mutation confers higher replication competence in ex-vivo culture of human nasal and bronchial tissues and in lungs of mice experimentally infected in-vivo. Mechanistically, the nsp6 L232F mutation appeared to modulate autophagy and was associated with higher exocytic virus egress, while innate immune responses and zippering activity of the endoplasmic reticulum remained unaffected. Our study suggests that MERS-CoV nsp6 may contribute to viral adaptation to humans. This highlights the importance of continued surveillance of MERS-CoV in both camels and humans.
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Affiliation(s)
- Ray TY So
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Daniel KW Chu
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- UK Health Security Agency, London, United Kingdom
| | - Kenrie PY Hui
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Chris KP Mok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, PR China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - John M Nicholls
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - John C. W. Ho
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Man-chun Cheung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Ka-chun Ng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Hin-Wo Yeung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Michael CW Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Leo LM Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
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Rodon J, Mykytyn AZ, Te N, Okba NMA, Lamers MM, Pailler-García L, Cantero G, Albulescu I, Bosch BJ, Peiris M, Bensaid A, Vergara-Alert J, Haagmans BL, Segalés J. Extended Viral Shedding of MERS-CoV Clade B Virus in Llamas Compared with African Clade C Strain. Emerg Infect Dis 2023; 29:585-589. [PMID: 36823022 PMCID: PMC9973703 DOI: 10.3201/eid2903.220986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) clade B viruses are found in camelids and humans in the Middle East, but clade C viruses are not. We provide experimental evidence for extended shedding of MERS-CoV clade B viruses in llamas, which might explain why they outcompete clade C strains in the Arabian Peninsula.
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Lau JJ, Cheng SMS, Leung K, Lee CK, Hachim A, Tsang LCH, Yam KWH, Chaothai S, Kwan KKH, Chai ZYH, Lo THK, Mori M, Wu C, Valkenburg SA, Amarasinghe GK, Lau EHY, Hui DSC, Leung GM, Peiris M, Wu JT. Real-world COVID-19 vaccine effectiveness against the Omicron BA.2 variant in a SARS-CoV-2 infection-naive population. Nat Med 2023; 29:348-357. [PMID: 36652990 PMCID: PMC9941049 DOI: 10.1038/s41591-023-02219-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
The SARS-CoV-2 Omicron variant has demonstrated enhanced transmissibility and escape of vaccine-derived immunity. Although first-generation vaccines remain effective against severe disease and death, robust evidence on vaccine effectiveness (VE) against all Omicron infections, irrespective of symptoms, remains sparse. We used a community-wide serosurvey with 5,310 subjects to estimate how vaccination histories modulated risk of infection in infection-naive Hong Kong during a large wave of Omicron BA.2 epidemic in January-July 2022. We estimated that Omicron infected 45% (41-48%) of the local population. Three and four doses of BNT162b2 or CoronaVac were effective against Omicron infection 7 days after vaccination (VE of 48% (95% credible interval 34-64%) and 69% (46-98%) for three and four doses of BNT162b2, respectively; VE of 30% (1-66%) and 56% (6-97%) for three and four doses of CoronaVac, respectively). At 100 days after immunization, VE waned to 26% (7-41%) and 35% (10-71%) for three and four doses of BNT162b2, and to 6% (0-29%) and 11% (0-54%) for three and four doses of CoronaVac. The rapid waning of VE against infection conferred by first-generation vaccines and an increasingly complex viral evolutionary landscape highlight the necessity for rapidly deploying updated vaccines followed by vigilant monitoring of VE.
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Affiliation(s)
- Jonathan J Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Samuel M S Cheng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Cheuk Kwong Lee
- Hong Kong Red Cross Blood Transfusion Service, Hong Kong SAR, People's Republic of China
| | - Asmaa Hachim
- HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Leo C H Tsang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kenny W H Yam
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sara Chaothai
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kelvin K H Kwan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Zacary Y H Chai
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tiffany H K Lo
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Masashi Mori
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
| | - Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine at St. Louis, St. Louis, MO, USA
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine at St. Louis, St. Louis, MO, USA
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - David S C Hui
- Department of Medicine and Therapeutics and Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection, Hong Kong SAR, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China.
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, China.
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Leung D, Cohen CA, Mu X, Rosa Duque J, Cheng SMS, Wang X, Wang M, Zhang W, Zhang Y, Tam I, Lam JHY, Chan SM, Chaothai S, Kwan KKH, Chan KCK, Li J, Luk LLH, Tsang LCH, Chu N, Wong WHS, Mori M, Leung W, Valkenburg S, Peiris M, Tu W, Lau YL. Immunogenicity against wild-type and Omicron SARS-CoV-2 after a third dose of inactivated COVID-19 vaccine in healthy adolescents. Front Immunol 2023; 14:1106837. [PMID: 36949953 PMCID: PMC10026957 DOI: 10.3389/fimmu.2023.1106837] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Introduction Two doses of inactivated SARS-CoV-2 vaccine CoronaVac cannot elicit high efficacy against symptomatic COVID-19, especially against the Omicron variant, but that can be improved by a third dose in adults. The use of a third dose of CoronaVac in adolescents may be supported by immunobridging studies in the absence of efficacy data. Methods With an immunobridging design, our study (NCT04800133) tested the non-inferiority of the binding and neutralizing antibodies and T cell responses induced by a third dose of CoronaVac in healthy adolescents (N=94, median age 14.2 years, 56% male) compared to adults (N=153, median age 48.1 years, 44% male). Responses against wild-type (WT) and BA.1 SARS-CoV-2 were compared in adolescents. Safety and reactogenicity were also monitored. Results A homologous third dose of CoronaVac further enhanced antibody response in adolescents compared to just 2 doses. Adolescents mounted non-inferior antibody and T cell responses compared to adults. Although S IgG and neutralizing antibody responses to BA.1 were lower than to WT, they remained detectable in 96% and 86% of adolescents. T cell responses to peptide pools spanning only the mutations of BA.1 S, N and M in adolescents were preserved, increased, and halved compared to WT respectively. No safety concerns were identified. Discussion The primary vaccination series of inactivated SARS-CoV-2 vaccines for adolescents should include 3 doses for improved humoral immunogenicity.
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Affiliation(s)
- Daniel Leung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Carolyn A. Cohen
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Xiaofeng Mu
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jaime S. Rosa Duque
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Samuel M. S. Cheng
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Xiwei Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Manni Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Wenyue Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yanmei Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Issan Y. S. Tam
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jennifer H. Y. Lam
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Sau Man Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Sara Chaothai
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Kelvin K. H. Kwan
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Karl C. K. Chan
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - John K. C. Li
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Leo L. H. Luk
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Leo C. H. Tsang
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Nym Coco Chu
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Wilfred H. S. Wong
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Masashi Mori
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
| | - Wing Hang Leung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Sophie Valkenburg
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
- *Correspondence: Sophie Valkenburg, ; Malik Peiris, ; Wenwei Tu, ; Yu Lung Lau,
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection C2i, Hong Kong, Hong Kong SAR, China
- *Correspondence: Sophie Valkenburg, ; Malik Peiris, ; Wenwei Tu, ; Yu Lung Lau,
| | - Wenwei Tu
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- *Correspondence: Sophie Valkenburg, ; Malik Peiris, ; Wenwei Tu, ; Yu Lung Lau,
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- *Correspondence: Sophie Valkenburg, ; Malik Peiris, ; Wenwei Tu, ; Yu Lung Lau,
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Leong NKC, Gu H, Ng DYM, Chang LDJ, Krishnan P, Cheng SSM, Peiris M, Poon LLM. Development of multiplex RT-ddPCR assays for detection of SARS-CoV-2 and other common respiratory virus infections. Influenza Other Respir Viruses 2022; 17:e13084. [PMID: 36517993 PMCID: PMC9835441 DOI: 10.1111/irv.13084] [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: 09/29/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Measures for mitigation of Coronavirus Disease 2019 (COVID-19) were set to reduce the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 and other respiratory viruses share similar transmission routes and some common clinical manifestations. Co-circulation of SARS-CoV-2 and other common respiratory viruses is imminent. Therefore, development of multiplex assays for detecting these respiratory viruses is essential for being prepared for future outbreaks of respiratory viruses. METHODS A panel of three reverse transcription droplet digital PCR (RT-ddPCR) assays were developed to detect 15 different human respiratory viruses. Evaluations of its performance were demonstrated. A total of 100 local and 98 imported COVID-19 cases in Hong Kong were screened for co-infection with other common respiratory viruses. RESULTS All detected viral targets showed distinct signal clusters using the multiplex RT-ddPCR assays. These assays have a broad range of linearity and good intra-/inter-assay reproducibility for each target. The lower limits of quantification for all targets were ≤46 copies per reaction. Six imported cases of COVID-19 were found to be co-infected with other respiratory viruses, whereas no local case of co-infection was observed. CONCLUSIONS The multiplex RT-ddPCR assays were demonstrated to be useful for screening of respiratory virus co-infections. The strict preventive measures applied in Hong Kong may be effective in limiting the circulation of other human respiratory viruses. The multiplex assays developed in this study can achieve a robust detection method for clinical and research purposes.
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Affiliation(s)
- Nathaniel K. C. Leong
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Haogao Gu
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Daisy Y. M. Ng
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Lydia D. J. Chang
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Pavithra Krishnan
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Samuel S. M. Cheng
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Malik Peiris
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong,Centre for Immunology and InfectionHong Kong Science and Technology ParkHong Kong,HKU‐Pasteur Research Pole, School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Leo L. M. Poon
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong,Centre for Immunology and InfectionHong Kong Science and Technology ParkHong Kong,HKU‐Pasteur Research Pole, School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
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40
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Cheng SS, Mok CK, Li JK, Ng SS, Lam BH, Jeevan T, Kandeil A, Pekosz A, Chan KC, Tsang LC, Ko FW, Chen C, Yiu K, Luk LL, Chan KK, Webby RJ, Poon LL, Hui DS, Peiris M. Plaque-neutralizing antibody to BA.2.12.1, BA.4 and BA.5 in individuals with three doses of BioNTech or CoronaVac vaccines, natural infection and breakthrough infection. J Clin Virol 2022; 156:105273. [PMID: 36081282 PMCID: PMC9428331 DOI: 10.1016/j.jcv.2022.105273] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND BA.2.12.1, BA.4 and BA.5 subvariants of SARS-CoV-2 variant-of-concern (VOC) Omicron (B.1.1.529) are spreading globally. They demonstrate higher transmissibility and immune escape. OBJECTIVES Determine BA.2.12.1, BA.4 and BA.5 virus plaque reduction neutralization test (PRNT) antibody titres in individuals recently vaccinated with BNT162b2 (n = 20) or CoronaVac (n = 20) vaccines or those convalescent from ancestral wild- type (WT) SARS-CoV-2 (n = 20) or BA.2 infections with (n = 17) or without (n = 7) prior vaccination. RESULTS Relative to neutralization of the WT virus, those vaccinated with BNT162b2 had 4.8, 3.4, 4.6, 11.3 and 15.5-fold reductions of geometric mean antibody titres (GMT) to BA.1, BA.2, BA.2.12.1, BA.4 and BA.5 viruses, respectively. Similarly, those vaccinated with CoronaVac had 8.0, 7.0, 11.8, 12.0 and 12.0 fold GMT reductions and those with two doses of CoronaVac boosted by BNT162b2 had 6.1, 6.7, 6,3, 13.0 and 21.2 fold GMT reductions to these viruses, respectively. Vaccinated individuals with BA.2 breakthrough infections had higher GMT antibody levels vs. BA.4 (36.9) and BA.5 (36.9) than unvaccinated individuals with BA.2 infections (BA.4 GMT 8.2; BA.5 GMT 11.0). CONCLUSIONS BA.4 and BA.5 subvariants were less susceptible to BNT162b2 or CoronaVac vaccine elicited antibody neutralization than subvariants BA.1, BA.2 and BA.2.12.1. Nevertheless, three doses BNT162b2 or booster of BNT162b2 following two doses of CoronaVac elicited detectable BA.4 and BA.5 neutralizing antibody responses while those vaccinated with three doses of CoronaVac largely fail to do so. BA.2 infections in vaccinated individuals led to higher levels of BA.4 or BA.5 neutralizing antibody compared to those who were vaccine-naive.
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Affiliation(s)
- Samuel Sm Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Chris Kp Mok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - John Kc Li
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Susanna S Ng
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Bosco Hs Lam
- Department of Pathology, North Lantau Hospital, Hong Kong SAR, China
| | - Trushar Jeevan
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ahmed Kandeil
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Karl Ck Chan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Leo Ch Tsang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Fanny W Ko
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chunke Chen
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Karen Yiu
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Leo Lh Luk
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ken Kp Chan
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Richard J Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Leo Lm Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - David Sc Hui
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Centre for Immunology and Infection, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
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Sit TH, Sun W, Tse AC, Brackman CJ, Cheng SM, Tang AWY, Cheung JT, Peiris M, Poon LL. Novel Zoonotic Avian Influenza A(H3N8) Virus in Chicken, Hong Kong, China. Emerg Infect Dis 2022; 28:2009-2015. [PMID: 36037827 PMCID: PMC9514342 DOI: 10.3201/eid2810.221067] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 12/13/2022] Open
Abstract
Zoonotic and pandemic influenza continue to pose threats to global public health. Pandemics arise when novel influenza A viruses, derived in whole or in part from animal or avian influenza viruses, adapt to transmit efficiently in a human population that has little population immunity to contain its onward transmission. Viruses of previous pandemic concern, such as influenza A(H7N9), arose from influenza A(H9N2) viruses established in domestic poultry acquiring a hemagglutinin and neuraminidase from influenza A viruses of aquatic waterfowl. We report a novel influenza A(H3N8) virus in chicken that has emerged in a similar manner and that has been recently reported to cause zoonotic disease. Although they are H3 subtype, these avian viruses are antigenically distant from contemporary human influenza A(H3N2) viruses, and there is little cross-reactive immunity in the human population. It is essential to heighten surveillance for these avian A(H3N8) viruses in poultry and in humans.
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Leung D, Mu X, Duque JSR, Cheng SMS, Wang M, Zhang W, Zhang Y, Tam IYS, Lee TSS, Lam JHY, Chan SM, Cheang CH, Chung Y, Wong HHW, Lee AMT, Li WY, Chaothai S, Tsang LCH, Chua GT, Cheong KN, Au EYL, Kwok JSY, Chan KW, Chong PCY, Lee PPW, Ho MHK, Lee TL, Tu W, Peiris M, Lau YL. Safety and immunogenicity of 3 doses of BNT162b2 and CoronaVac in children and adults with inborn errors of immunity. Front Immunol 2022; 13:982155. [PMID: 36203563 PMCID: PMC9530261 DOI: 10.3389/fimmu.2022.982155] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Abstract
Our study (NCT04800133) aimed to determine the safety and immunogenicity in patients with IEIs receiving a 3-dose primary series of mRNA vaccine BNT162b2 (age 12+) or inactivated whole-virion vaccine CoronaVac (age 3+) in Hong Kong, including Omicron BA.1 neutralization, in a nonrandomized manner. Intradermal vaccination was also studied. Thirty-nine patients were vaccinated, including 16 with homologous intramuscular 0.3ml BNT162b2 and 17 with homologous intramuscular 0.5ml CoronaVac. Two patients received 3 doses of intradermal 0.5ml CoronaVac, and 4 patients received 2 doses of intramuscular BNT162b2 and the third dose with intradermal BNT162b2. No safety concerns were identified. Inadequate S-RBD IgG and surrogate virus neutralization responses were found after 2 doses in patients with humoral immunodeficiencies and especially so against BA.1. Dose 3 of either vaccine increased S-RBD IgG response. T cell responses against SARS-CoV-2 antigens were detected in vaccinated IEI patients by intracellular cytokine staining on flow cytometry. Intradermal third dose vaccine led to high antibody response in 4 patients. The primary vaccination series of BNT162b2 and CoronaVac in adults and children with IEIs should include 3 doses for optimal immunogenicity.
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Affiliation(s)
- Daniel Leung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Xiaofeng Mu
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jaime S. Rosa Duque
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Samuel M. S. Cheng
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Manni Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Wenyue Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yanmei Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Issan Y. S. Tam
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Toby S. S. Lee
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jennifer H. Y. Lam
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Sau Man Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Cheuk Hei Cheang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yuet Chung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Howard H. W. Wong
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Amos M. T. Lee
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Wing Yan Li
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Sara Chaothai
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Leo C. H. Tsang
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Gilbert T. Chua
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Kai-Ning Cheong
- Hong Kong Children’s Hospital, Hong Kong, Hong Kong SAR, China
| | - Elaine Y. L. Au
- Division of Clinical Immunology, Department of Pathology, Queen Mary Hospital, Hong Kong, Hong Kong SAR, China
| | - Janette S. Y. Kwok
- Division of Transplantation and Immunogenetics, Department of Pathology, Queen Mary Hospital, Hong Kong, Hong Kong SAR, China
| | - Koon Wing Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | | | - Pamela P. W. Lee
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | | | - Tsz Leung Lee
- Hong Kong Children’s Hospital, Hong Kong, Hong Kong SAR, China
| | - Wenwei Tu
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- *Correspondence: Wenwei Tu, ; Malik Peiris, ; Yu Lung Lau,
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection C2i, Hong Kong, Hong Kong SAR, China
- *Correspondence: Wenwei Tu, ; Malik Peiris, ; Yu Lung Lau,
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- *Correspondence: Wenwei Tu, ; Malik Peiris, ; Yu Lung Lau,
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Cheung JTL, Lau EHY, Jin Z, Zhu H, Guan Y, Peiris M. Influenza A virus transmission in swine farms and during transport in the swine supply chain. Transbound Emerg Dis 2022; 69:e3101-e3110. [PMID: 35881331 PMCID: PMC9529857 DOI: 10.1111/tbed.14667] [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: 04/25/2022] [Revised: 06/25/2022] [Accepted: 07/23/2022] [Indexed: 11/30/2022]
Abstract
The last influenza pandemic in 2009 emerged from swine and surveillance of swine influenza is important for pandemic preparedness. Movement of swine during husbandry, trade or marketing for slaughter provide opportunities for transfer and genetic reassortment of swine influenza viruses. Over 90% of the swine slaughtered at the central swine abattoir in Hong Kong are imported from farms located in multiple provinces in mainland China. There is opportunity for virus cross-infection during this transport and slaughter process. Of the 26,980 swabs collected in the slaughterhouse in Hong Kong from 5 January 2012 to 15 December 2016, we analysed sequence data on influenza A (H3N2) virus isolates (n = 174) in conjunction with date of sampling and originating farm. Molecular epidemiology provided evidence of virus cross-infection between swine originating from different farms during transport. The findings are also suggestive of a virus lineage persisting in a swine farm for over 2 years, although the lack of information on management practices at farm-level means that alternative explanations cannot be excluded. We used virus serology and isolation data from 4226 pairs of linked serum and swabs collected from the same pig at slaughter from swine originating from Guangdong Province to compare the force of infection (FOI) during transport and within farms. The mean weekly FOI during transport was λt = 0.0286 (95% CI = 0.0211-0.0391) while the weekly FOI in farms was λf = 0.0089 (95% CI = 0.0084-0.0095), assuming a possible exposure duration in farm of 28 weeks, suggesting increased FOI during the transport process. Pigs sourced from farms with high seroprevalence were found to be a significant risk factor (adjusted OR = 2.24, p value = .015) for infection of imported pigs during transport by multivariable logistic regression analysis, whereas pigs with HAI titre of ≥1:40 were associated with a substantial reduction in infection risk by 67% (p value = 0.012). Transport may increase virus cross-infection rates and provide opportunities for virus reassortment potentially increasing zoonotic risk to those involved in the transportation and slaughtering processes.
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Affiliation(s)
| | - Eric HY Lau
- School of Public Health, The University of Hong Kong
| | - Ziying Jin
- School of Public Health, The University of Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases/Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (Shantou University and The University of Hong Kong), Shantou University, Shantou, P. R. China
| | - Huachen Zhu
- School of Public Health, The University of Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases/Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (Shantou University and The University of Hong Kong), Shantou University, Shantou, P. R. China
| | - Yi Guan
- School of Public Health, The University of Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
- Guangdong-Hong Kong Joint Laboratory of Emerging Infectious Diseases/Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (Shantou University and The University of Hong Kong), Shantou University, Shantou, P. R. China
| | - Malik Peiris
- School of Public Health, The University of Hong Kong
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Hui KP, Ng KC, Ho JC, Yeung HW, Ching RH, Gu H, Chung JC, Chow VL, Sit KY, Hsin MK, Au TW, Poon LL, Peiris M, Nicholls JM, Chan MC. Replication of SARS-CoV-2 Omicron BA.2 variant in ex vivo cultures of the human upper and lower respiratory tract. EBioMedicine 2022; 83:104232. [PMID: 35988466 PMCID: PMC9387351 DOI: 10.1016/j.ebiom.2022.104232] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 01/02/2023] Open
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Gu H, Quadeer AA, Krishnan P, Ng DY, Chang LD, Liu GY, Cheng SS, Lam TT, Peiris M, McKay MR, Poon LL. Within-host diversity of SARS-CoV-2 lineages and effect of vaccination. Res Sq 2022:rs.3.rs-1927944. [PMID: 35982671 PMCID: PMC9387541 DOI: 10.21203/rs.3.rs-1927944/v1] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Viral and host factors can shape SARS-CoV-2 within-host viral diversity and virus evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here we analysed deep sequencing data from 2,146 SARS-CoV-2 samples with different viral lineages to describe the patterns of within-host diversity in different conditions, including vaccine-breakthrough infections. Variant of Concern (VOC) Alpha, Delta, and Omicron samples were found to have higher within-host nucleotide diversity while being under weaker purifying selection at full genome level compared to non-VOC SARS-CoV-2 viruses. Breakthrough Delta and Omicron infections in Comirnaty and CoronaVac vaccinated individuals appeared to have higher within-host purifying selection at the full-genome and/or Spike gene levels. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 evolution. Our findings suggest that vaccination does not increase SARS-CoV-2 protein sequence space and may not facilitate emergence of more viral variants.
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Affiliation(s)
- Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ahmed Abdul Quadeer
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Pavithra Krishnan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Daisy Y.M. Ng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lydia D.J Chang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Gigi Y.Z. Liu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Samuel S.M. Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tommy T.Y. Lam
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Matthew R. McKay
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Electrical and Electronic Engineering, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Leo L.M. Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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46
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Mok CKP, Hui DS, Peiris M. Reply to Mungmunpuntipantip and Wiwanitkit: CoronaVac or BNT162b2 Vaccine as a Third Dose. Am J Respir Crit Care Med 2022; 206:361-362. [PMID: 35561327 PMCID: PMC9890265 DOI: 10.1164/rccm.202201-0221le] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
| | - David S. Hui
- The Chinese University of Hong KongHong Kong, China
| | - Malik Peiris
- The University of Hong KongHong Kong, China,Corresponding author (e-mail: )
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Abstract
As of April 2022, the Omicron BA.1 variant of concern of SARS-CoV-2 was spreading quickly around the world and outcompeting other circulating strains. We examined its stability on various surfaces and found that this Omicron variant is more stable than its ancestral strain on smooth and porous surfaces.
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48
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Sun W, Cheng SSM, Lam KNT, Kwan TC, Wong RWK, Lau LHK, Liu GYZ, Luk LLH, Li JKC, Gu H, Peiris M, Poon LLM. Natural Reassortment of Eurasian Avian-Like Swine H1N1 and Avian H9N2 Influenza Viruses in Pigs, China. Emerg Infect Dis 2022; 28:1509-1512. [PMID: 35731193 PMCID: PMC9239857 DOI: 10.3201/eid2807.220642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Several zoonotic influenza A viruses detected in humans contain genes derived from avian H9N2 subtypes. We uncovered a Eurasian avian-like H1N1 swine influenza virus with polymerase basic 1 and matrix gene segments derived from the H9N2 subtype, suggesting that H9N2 viruses are infecting pigs and reassorting with swine influenza viruses in China.
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49
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Su W, Choy KT, Gu H, Sia SF, Cheng KM, Nizami SIN, Krishnan P, Ng YM, Chang LDJ, Liu Y, Cheng SM, Peiris M, Poon LL, Nicholls JM, Yen HL. Omicron BA.1 and BA.2 sub-lineages show reduced pathogenicity and transmission potential than the early SARS-CoV-2 D614G variant in Syrian hamsters. J Infect Dis 2022; 227:1143-1152. [PMID: 35776136 PMCID: PMC9278237 DOI: 10.1093/infdis/jiac276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 03/20/2022] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Background The epidemiological advantage of Omicron variant is evidenced by its rapid spread and the ability to outcompete prior variants. Among Omicron sub-lineages, early outbreaks were dominated by BA.1 while BA.2 has gained dominance since February 2022. The relative pathogenicity and transmissibility of BA.1 and BA.2 have not been fully defined. Methods We compared viral loads and clinical signs in Syrian hamsters after infection with BA.1, BA.2, or D614G variant. A competitive transmission model and next generation sequencing were used to compare the relative transmission potential of BA.1 and BA.2. Results BA.1 and BA.2 caused no apparent clinical signs while D614G caused more than 10% weight loss. Higher viral loads were detected from the nasal washes, nasal turbinate and lungs of BA.1 than BA.2 inoculated hamsters. No aerosol transmission was observed for BA.1 or BA.2 under the experimental condition that D614G transmitted efficiently. BA.1 and BA.2 were able to transmit among hamsters via direct contact; however, BA.1 transmitted more efficiently than BA.2 under the competitive transmission model. No recombination was detected from direct contacts exposed simultaneously to BA.1 and BA.2. Conclusions Omicron BA.1 and BA.2 demonstrated attenuated pathogenicity and reduced transmission potential in hamsters when compared to early SARS-CoV-2 strains.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - John M Nicholls
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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50
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Tso WWY, Kwan MYW, Wang YL, Leung LK, Leung D, Chua GT, Ip P, Fong DYT, Wong WHS, Chan SHS, Chan JFW, Peiris M, Lau YL, Rosa Duque JS. Severity of SARS-CoV-2 Omicron BA.2 infection in unvaccinated hospitalized children: Comparison to influenza and parainfluenza infections. Emerg Microbes Infect 2022; 11:1742-1750. [PMID: 35730665 PMCID: PMC9258055 DOI: 10.1080/22221751.2022.2093135] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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] [Indexed: 02/06/2023]
Abstract
There has been a rapid surge of hospitalization due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants globally. The severity of Omicron BA.2 in unexposed, unvaccinated, hospitalized children is unknown. We investigated the severity and clinical outcomes of COVID-19 infection during the Omicron wave in uninfected, unvaccinated hospitalized children and in comparison with influenza and parainfluenza viral infections. This population-based study retrieved data from the HK territory-wide CDARS database of hospitalisations in all public hospitals and compared severe outcomes for the Omicron BA.2-dominant fifth wave (5–28 February 2022, n = 1144), and influenza and parainfluenza viruses (1 January 2015–31 December 2019, n = 32212 and n = 16423, respectively) in children 0–11 years old. Two deaths (0.2%) out of 1144 cases during the initial Omicron wave were recorded. Twenty-one (1.8%) required PICU admission, and the relative risk was higher for Omicron than influenza virus (n = 254, 0.8%, adjusted RR = 2.1, 95%CI 1.3–3.3, p = 0.001). The proportion with neurological complications was 15.0% (n = 171) for Omicron, which was higher than influenza and parainfluenza viruses (n = 2707, 8.4%, adjusted RR = 1.6, 95%CI 1.4–1.9 and n = 1258, 7.7%, adjusted RR = 1.9, 95%CI 1.6–2.2, p < 0.001 for both, respectively). Croup occurred for Omicron (n = 61, 5.3%) more than influenza virus (n = 601, 1.9%, adjusted RR = 2.0, 95%CI 1.5–2.6, p < 0.001) but not parainfluenza virus (n = 889, 5.4%). Our findings showed that for hospitalized children who had no past COVID-19 or vaccination, Omicron BA.2 was not mild. Omicron BA.2 appeared to be more neuropathogenic than influenza and parainfluenza viruses. It targeted the upper airways more than influenza virus.
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Affiliation(s)
- Winnie W Y Tso
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, China
| | - Mike Y W Kwan
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Yu Liang Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Lok Kan Leung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Daniel Leung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Gilbert T Chua
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Patrick Ip
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Daniel Y T Fong
- School of Nursing, The University of Hong Kong, Hong Kong, China
| | - Wilfred H S Wong
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Sophelia H S Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jasper F W Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jaime S Rosa Duque
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
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