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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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2
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Nelson CW, Poon LLM, Gu H. Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data. Nat Commun 2024; 15:3239. [PMID: 38627383 PMCID: PMC11021549 DOI: 10.1038/s41467-024-46262-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/21/2024] [Indexed: 04/19/2024] Open
Affiliation(s)
- Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
| | - 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.
| | - Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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3
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Chan RWY, Chan MCW, Agnihothram S, Chan LLY, Kuok DIT, Fong JHM, Guan Y, Poon LLM, Baric RS, Nicholls JM, Peiris JSM. Erratum for Chan et al., "Tropism of and Innate Immune Responses to the Novel Human Betacoronavirus Lineage C Virus in Human Ex Vivo Respiratory Organ Cultures". J Virol 2024; 98:e0037924. [PMID: 38497665 PMCID: PMC11019942 DOI: 10.1128/jvi.00379-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024] Open
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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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McNabb L, Durr PA, Lunt R, Barr J, Adams TE, Pearce L, Poon LLM, Perera RAM, Demissie GF, Bowden TR. Development and preliminary validation of a MERS-CoV ELISA for serological testing of camels and alpacas. J Virol Methods 2024; 327:114923. [PMID: 38561124 DOI: 10.1016/j.jviromet.2024.114923] [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: 12/08/2023] [Revised: 03/04/2024] [Accepted: 03/30/2024] [Indexed: 04/04/2024]
Abstract
This study describes the development and preliminary validation of a new serological assay using MERS-CoV S1 protein in an indirect enzyme-linked immunosorbent assay (ELISA) format. This assay has the advantage of being able to test MERS-CoV serum samples in a PC2 laboratory without the need for a high-level biocontainment laboratory (PC3 or PC4), which requires highly trained and skilled staff and a high level of resources and equipment. Furthermore, this MERS-CoV S1 ELISA enables a larger number of samples to be tested quickly, with results obtained in approximately five hours. The MERS-CoV S1 ELISA demonstrated high analytical specificity, with no cross-reactivity observed in serum of animals infected with other viruses, including different coronaviruses. We tested 166 positive and 40 negative camel serum samples and have estimated the diagnostic sensitivity (DSe) to be 99.4% (95% CI: 96.7 - 100.0%) and diagnostic specificity (DSp) to be 100% (95% CI: 97.2%-100.0%) relative to the assigned serology results (ppNT and VNT) using a S/P ratio cut-off value of >0.58. The findings of this study showed that our MERS-CoV S1 ELISA was more sensitive than the commercial EUROIMMUN ELISA (Se 99.4% vs 84.9%) and comparable to the ppNT assay, and therefore could be used as a diagnostic aid in countries in the Middle East where MERS-CoV is endemic in dromedary camels. The assay reagents and protocol were easily adapted and transferred from an Australian laboratory to a laboratory in the University of Hong Kong. Thus, the results described here show that the MERS-CoV S1 ELISA represents a cheap, rapid, robust, and reliable assay to support surveillance of MERS-CoV in camels in endemic regions.
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Affiliation(s)
- Leanne McNabb
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), East Geelong, Victoria, Australia.
| | - Peter A Durr
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), East Geelong, Victoria, Australia
| | - Ross Lunt
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), East Geelong, Victoria, Australia
| | - Jennifer Barr
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), East Geelong, Victoria, Australia
| | | | | | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, 999077, Hong Kong Special Administrative Region of China
| | - Ranawaka Ap M Perera
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, 999077, Hong Kong Special Administrative Region of China
| | - Getnet Fekadu Demissie
- College of Veterinary Medicine, Department of Veterinary Epidemiology, Microbiology and Public Health, Haramaya University, Haramaya, Ethiopia
| | - Timothy R Bowden
- Australian Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), East Geelong, Victoria, Australia
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6
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Peiris JSM, So RTY, Poon LLM, Chu KW, Mok CKP, Zhao J. Single amino acid substitution and inter-species transmission of MERS-coronavirus from camels to humans: abridged secondary publication. Hong Kong Med J 2024; 30 Suppl 1:9-15. [PMID: 38413205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Affiliation(s)
- J S M Peiris
- School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - R T Y So
- School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - L L M Poon
- School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - K W Chu
- School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - C K P Mok
- School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - J Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou, China
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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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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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9
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Xu X, Deng Y, Ding J, Shi X, Zheng X, Wang D, Yang Y, Liu L, Wang C, Li S, Gu H, Poon LLM, Zhang T. Refining detection methods for emerging SARS-CoV-2 mutants in wastewater: A case study on the Omicron variants. Sci Total Environ 2023; 904:166215. [PMID: 37591380 DOI: 10.1016/j.scitotenv.2023.166215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
COVID-19 is an ongoing public health threat worldwide driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Wastewater surveillance has emerged as a complementary tool to clinical surveillance to control the COVID-19 pandemic. With the emergence of new variants of SARS-CoV-2, accumulated mutations that occurred in the SARS-CoV-2 genome raise new challenges for RT-qPCR diagnosis used in wastewater surveillance. There is a pressing need to develop refined methods for modifying primer/probes to better detect these emerging variants in wastewater. Here, we exemplified this process by focusing on the Omicron variants, for which we have developed and validated a modified detection method. We first modified the primers/probe mismatches of three assays commonly used in wastewater surveillance according to in silico analysis results for the mutations of 882 sequences collected during the fifth-wave outbreak in Hong Kong, and then evaluated them alongside the seven original assays. The results showed that five of seven original assays had better sensitivity for detecting Omicron variants, with the limits of detection (LoDs) ranging from 1.53 to 2.76 copies/μL. UCDC-N1 and Charité-E sets had poor performances, having LoDs higher than 10 copies/μL and false-positive/false-negative results in wastewater testing, probably due to the mismatch and demonstrating the need for modification of primer/probe sequences. The modified assays exhibited higher sensitivity and specificity, along with better reproducibility in detecting 81 wastewater samples. In addition, the sequencing results of six wastewater samples by Illumina also validated the presence of mismatches in the primer/probe binding sites of the three assays. This study highlights the importance of re-configuration of the primer-probe sets and refinements for the sequences to ensure the diagnostic effectiveness of RT-qPCR detection.
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Affiliation(s)
- Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, 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 Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xianghui Shi
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Haogao Gu
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, 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
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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10
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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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11
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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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12
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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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13
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Xie R, Edwards KM, Wille M, Wei X, Wong SS, Zanin M, El-Shesheny R, Ducatez M, Poon LLM, Kayali G, Webby RJ, Dhanasekaran V. The episodic resurgence of highly pathogenic avian influenza H5 virus. Nature 2023; 622:810-817. [PMID: 37853121 DOI: 10.1038/s41586-023-06631-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023]
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 activity has intensified globally since 2021, increasingly causing mass mortality in wild birds and poultry and incidental infections in mammals1-3. However, the ecological and virological properties that underscore future mitigation strategies still remain unclear. Using epidemiological, spatial and genomic approaches, we demonstrate changes in the origins of resurgent HPAI H5 and reveal significant shifts in virus ecology and evolution. Outbreak data show key resurgent events in 2016-2017 and 2020-2021, contributing to the emergence and panzootic spread of H5N1 in 2021-2022. Genomic analysis reveals that the 2016-2017 epizootics originated in Asia, where HPAI H5 reservoirs are endemic. In 2020-2021, 2.3.4.4b H5N8 viruses emerged in African poultry, featuring mutations altering HA structure and receptor binding. In 2021-2022, a new H5N1 virus evolved through reassortment in wild birds in Europe, undergoing further reassortment with low-pathogenic avian influenza in wild and domestic birds during global dissemination. These results highlight a shift in the HPAI H5 epicentre beyond Asia and indicate that increasing persistence of HPAI H5 in wild birds is facilitating geographic and host range expansion, accelerating dispersion velocity and increasing reassortment potential. As earlier outbreaks of H5N1 and H5N8 were caused by more stable genomic constellations, these recent changes reflect adaptation across the domestic-bird-wild-bird interface. Elimination strategies in domestic birds therefore remain a high priority to limit future epizootics.
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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, 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, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Michelle Wille
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Xiaoman Wei
- School of Public Health, LKS 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 SAR, China
| | - Sook-San Wong
- School of Public Health, LKS 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 SAR, China
| | - Mark Zanin
- 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
| | - Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Mariette Ducatez
- IHAP, Université de Toulouse, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
| | - 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, 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
| | | | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Vijaykrishna Dhanasekaran
- School of Public Health, LKS 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 SAR, China.
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14
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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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15
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Leung NHL, Cheng SMS, Cohen CA, Martín-Sánchez M, Au NYM, Luk LLH, Tsang LCH, Kwan KKH, Chaothai S, Fung LWC, Cheung AWL, Chan KCK, Li JKC, Ng YY, Kaewpreedee P, Jia JZ, Ip DKM, Poon LLM, Leung GM, Peiris JSM, Valkenburg SA, Cowling BJ. Comparative antibody and cell-mediated immune responses, reactogenicity, and efficacy of homologous and heterologous boosting with CoronaVac and BNT162b2 (Cobovax): an open-label, randomised trial. Lancet Microbe 2023; 4:e670-e682. [PMID: 37549680 PMCID: PMC10528748 DOI: 10.1016/s2666-5247(23)00216-1] [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] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Few trials have compared homologous and heterologous third doses of COVID-19 vaccination with inactivated vaccines and mRNA vaccines. The aim of this study was to assess immune responses, safety, and efficacy against SARS-CoV-2 infection following homologous or heterologous third-dose COVID-19 vaccination with either one dose of CoronaVac (Sinovac Biotech; inactivated vaccine) or BNT162b2 (Fosun Pharma-BioNTech; mRNA vaccine). METHODS This is an ongoing, randomised, allocation-concealed, open-label, comparator-controlled trial in adults aged 18 years or older enrolled from the community in Hong Kong, who had received two doses of CoronaVac or BNT162b2 at least 6 months earlier. Participants were randomly assigned, using a computer-generated sequence, in a 1:1 ratio with allocation concealment to receive a (third) dose of CoronaVac or BNT162b2 (ancestral virus strain), stratified by types of previous COVID-19 vaccination (homologous two doses of CoronaVac or BNT162b2). Participants were unmasked to group allocation after vaccination. The primary endpoint was serum neutralising antibodies against the ancestral virus at day 28 after vaccination in each group, measured as plaque reduction neutralisation test (PRNT50) geometric mean titre (GMT). Surrogate virus neutralisation test (sVNT) mean inhibition percentage and PRNT50 titres against omicron BA.1 and BA.2 subvariants were also measured. Secondary endpoints included geometric mean fold rise (GMFR) in antibody titres; incidence of solicited local and systemic adverse events; IFNγ+ CD4+ and IFNγ+ CD8+ T-cell responses at days 7 and 28; and incidence of COVID-19. Within-group comparisons of boost in immunogenicity from baseline and between-group comparisons were done according to intervention received (ie, per protocol) by paired and unpaired t test, respectively, and cumulative incidence of infection was compared using Kaplan-Meier curves and a proportional hazards model to estimate hazard ratio. The trial is registered with ClinicalTrials.gov, NCT05057169. FINDINGS We enrolled participants from Nov 12, 2021, to Jan 27, 2022. We vaccinated 219 participants who previously received two doses of CoronaVac, including 101 randomly assigned to receive CoronaVac (CC-C) and 118 randomly assigned to receive BNT162b2 (CC-B) as their third dose; and 232 participants who previously received two doses of BNT162b2, including 118 randomly assigned to receive CoronaVac (BB-C) and 114 randomly assigned to receive BNT162b2 (BB-B) as their third dose. The PRNT50 GMTs on day 28 against ancestral virus were 109, 905, 92, and 816; against omicron BA.1 were 9, 75, 8, and 86; and against omicron BA.2 were 6, 80, 6, and 67 in the CC-C, CC-B, BB-C, and BB-B groups, respectively. Mean sVNT inhibition percentages on day 28 against ancestral virus were 83%, 96%, 87%, and 96%; against omicron BA.1 were 15%, 58%, 19%, and 69%; and against omicron BA.2 were 43%, 85%, 50%, and 90%, in the CC-C, CC-B, BB-C, and BB-B groups, respectively. Participants who had previously received two doses of CoronaVac and a BNT162b2 third dose had a GMFR of 12 (p<0·0001) compared with those who received a CoronaVac third dose; similarly, those who had received two doses of BNT162b2 and a BNT162b2 third dose had a GMFR of 8 (p<0·0001). No differences in CD4+ and CD8+ T-cell responses were observed between groups. We did not identify any vaccination-related hospitalisation within 1 month after vaccination. We identified 58 infections when omicron BA.2 was predominantly circulating, with cumulative incidence of 15·3% and 15·4% in the CC-C and CC-B groups, respectively (p=0·93), and 16·7% and 14·0% in the BB-C and BB-B groups, respectively (p=0·56). INTERPRETATION Similar levels of incidence of, presumably, omicron BA.2 infections were observed in each group despite very weak antibody responses to BA.2 in the recipients of a CoronaVac third dose. Further research is warranted to identify appropriate correlates of protection for inactivated COVID-19 vaccines. FUNDING Health and Medical Research Fund, Hong Kong. TRANSLATION For the Chinese translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Nancy H L 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 Special Administrative Region, China; Takemi Program in International Health, Harvard T H Chan School of Public Health, Harvard University, Boston, MA, USA; Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Samuel M S Cheng
- 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
| | - Carolyn A Cohen
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Mario Martín-Sánchez
- 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
| | - Niki Y M Au
- 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
| | - Leo L H Luk
- 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
| | - Leo C H Tsang
- 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
| | - Kelvin K H Kwan
- 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
| | - Sara Chaothai
- 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
| | - Lison W C Fung
- 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
| | - Alan W L Cheung
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Karl C K Chan
- 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
| | - John K C Li
- 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
| | - Yvonne Y Ng
- 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
| | - Prathanporn Kaewpreedee
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Janice Z Jia
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, 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, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Leo L M Poon
- 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; HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Centre for Immunology and Infection, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, 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 Special Administrative Region, China; Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - J S 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; HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Centre for Immunology and Infection, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, 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 Special Administrative Region, China; Department of Microbiology and Immunology, Peter Doherty Institute of Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - 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, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.
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16
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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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de Sousa LLF, de Souza TL, Tibo LHS, Moura FBP, Junior FAS, de Oliveira-Filho EF, Ludwig-Begall LF, Cabral-Miranda G, Andreata-Santos R, Janini LMR, Poon LLM, Durães-Carvalho R. Rabies virus variants from bats closely related to variants found in marmosets (Callithrix jacchus), a neglected source of human rabies infection in Brazil. J Med Virol 2023; 95:e29046. [PMID: 37605969 DOI: 10.1002/jmv.29046] [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: 06/28/2023] [Revised: 07/25/2023] [Accepted: 08/09/2023] [Indexed: 08/23/2023]
Abstract
Rabies is a fatal viral zoonosis caused by rabies virus (RABV). RABV infects the central nervous system and triggers acute encephalomyelitis in both humans and animals. Endemic in the Brazilian Northeast region, RABV emergence in distinct wildlife species has been identified as a source of human rabies infection and as such, constitutes a public health concern. Here, we performed post-mortem RABV analyses of 144 encephalic tissues from bats sampled from January to July 2022, belonging to 15 different species. We identified phylogenetically distinct RABV from Phyllostomidae and Molossidae bats circulating in Northeastern Brazil. Phylogenetic clustering revealed the close evolutionary relationship between RABV viruses circulating in bats and variants hosted in white-tufted marmosets, commonly captured to be kept as pets and linked to human rabies cases and deaths in Brazil. Our findings underline the urgent need to implement a phylogenetic-scale epidemiological surveillance platform to track multiple RABV variants which may pose a threat to both humans and animals.
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Affiliation(s)
- Larissa L F de Sousa
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
- Rabies Diagnosis Laboratory, Central Laboratory of Public Health-LACEN, Fortaleza, Ceará, Brazil
| | - Tatiane L de Souza
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - Luiz H S Tibo
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | | | - Francisco A S Junior
- Rabies Diagnosis Laboratory, Central Laboratory of Public Health-LACEN, Fortaleza, Ceará, Brazil
| | | | - Louisa F Ludwig-Begall
- Department of Infectious and Parasitic Diseases, Veterinary Virology and Animal Viral Diseases, FARAH Research Centre, University of Liège, Liège, Belgium
| | - Gustavo Cabral-Miranda
- Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo, São Paulo, Brazil
| | - Robert Andreata-Santos
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - Luiz M R Janini
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - Leo L M Poon
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Ricardo Durães-Carvalho
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
- Department of Morphology and Genetics, UNIFESP, São Paulo, São Paulo, Brazil
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18
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Tan CW, Valkenburg SA, Poon LLM, Wang LF. Broad-spectrum pan-genus and pan-family virus vaccines. Cell Host Microbe 2023; 31:902-916. [PMID: 37321173 PMCID: PMC10265776 DOI: 10.1016/j.chom.2023.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 03/13/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023]
Abstract
Although the development and clinical application of SARS-CoV-2 vaccines during the COVID-19 pandemic demonstrated unprecedented vaccine success in a short time frame, it also revealed a limitation of current vaccines in their inability to provide broad-spectrum or universal protection against emerging variants. Broad-spectrum vaccines, therefore, remain a dream and challenge for vaccinology. This review will focus on current and future efforts in developing universal vaccines targeting different viruses at the genus and/or family levels, with a special focus on henipaviruses, influenza viruses, and coronaviruses. It is evident that strategies for developing broad-spectrum vaccines will be virus-genus or family specific, and it is almost impossible to adopt a universal approach for different viruses. On the other hand, efforts in developing broad-spectrum neutralizing monoclonal antibodies have been more successful and it is worth considering broad-spectrum antibody-mediated immunization, or "universal antibody vaccine," as an alternative approach for early intervention for future disease X outbreaks.
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Affiliation(s)
- Chee Wah Tan
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Sophie A Valkenburg
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 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 & Infection, Hong Kong Science Park, Hong Kong SAR, China.
| | - Lin-Fa Wang
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore; Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Singhealth Duke-NUS Global Health Institute, Singapore, Singapore.
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19
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Wong CKH, Lau KTK, Au ICH, Lau EHY, Poon LLM, Hung IFN, Cowling BJ, Leung GM. Viral burden rebound in hospitalised patients with COVID-19 receiving oral antivirals in Hong Kong: a population-wide retrospective cohort study. Lancet Infect Dis 2023; 23:683-695. [PMID: 36796397 PMCID: PMC9949892 DOI: 10.1016/s1473-3099(22)00873-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/23/2022] [Accepted: 12/14/2022] [Indexed: 02/15/2023]
Abstract
BACKGROUND Viral rebound after nirmatrelvir-ritonavir treatment has implications for the clinical management and isolation of patients with COVID-19. We evaluated an unselected, population-wide cohort to identify the incidence of viral burden rebound and associated risk factors and clinical outcomes. METHODS We did a retrospective cohort study of hospitalised patients with a confirmed diagnosis of COVID-19 in Hong Kong, China, for an observation period from Feb 26 to July 3, 2022 (during the omicron BA.2.2 variant wave). Adult patients (age ≥18 years) admitted 3 days before or after a positive COVID-19 test were selected from medical records held by the Hospital Authority of Hong Kong. We included patients with non-oxygen-dependent COVID-19 at baseline receiving either molnupiravir (800 mg twice a day for 5 days), nirmatrelvir-ritonavir (nirmatrelvir 300 mg with ritonavir 100 mg twice a day for 5 days), or no oral antiviral treatment (control group). Viral burden rebound was defined as a reduction in cycle threshold (Ct) value (≥3) on quantitative RT-PCR test between two consecutive measurements, with such decrease sustained in an immediately subsequent Ct measurement (for those patients with ≥3 Ct measurements). Logistic regression models were used to identify prognostic factors for viral burden rebound, and to assess associations between viral burden rebound and a composite clinical outcome of mortality, intensive care unit admission, and invasive mechanical ventilation initiation, stratified by treatment group. FINDINGS We included 4592 hospitalised patients with non-oxygen-dependent COVID-19 (1998 [43·5%] women and 2594 [56·5%] men). During the omicron BA.2.2 wave, viral burden rebound occurred in 16 of 242 patients (6·6% [95% CI 4·1-10·5]) receiving nirmatrelvir-ritonavir, 27 of 563 (4·8% [3·3-6·9]) receiving molnupiravir, and 170 of 3787 (4·5% [3·9-5·2]) in the control group. The incidence of viral burden rebound did not differ significantly across the three groups. Immunocompromised status was associated with increased odds of viral burden rebound, regardless of antiviral treatment (nirmatrelvir-ritonavir: odds ratio [OR] 7·37 [95% CI 2·56-21·26], p=0·0002; molnupiravir: 3·05 [1·28-7·25], p=0·012; control: 2·21 [1·50-3·27], p<0·0001). Among patients receiving nirmatrelvir-ritonavir, the odds of viral burden rebound were higher in those aged 18-65 years (vs >65 years; 3·09 [1·00-9·53], p=0·050), those with high comorbidity burden (score >6 on the Charlson Comorbidity Index; 6·02 [2·09-17·38], p=0·0009), and those concomitantly taking corticosteroids (7·51 [1·67-33·82], p=0·0086); whereas the odds were lower in those who were not fully vaccinated (0·16 [0·04-0·67], p=0·012). In patients receiving molnupiravir, those aged 18-65 years (2·68 [1·09-6·58], p=0·032) or on concomitant corticosteroids (3·11 [1·23-7·82], p=0·016) had increased odds of viral burden rebound. We found no association between viral burden rebound and occurrence of the composite clinical outcome from day 5 of follow-up (nirmatrelvir-ritonavir: adjusted OR 1·90 [0·48-7·59], p=0·36; molnupiravir: 1·05 [0·39-2·84], p=0·92; control: 1·27 [0·89-1·80], p=0·18). INTERPRETATION Viral burden rebound rates are similar between patients with antiviral treatment and those without. Importantly, viral burden rebound was not associated with adverse clinical outcomes. FUNDING Health and Medical Research Fund, Health Bureau, The Government of the Hong Kong Special Administrative Region, China. TRANSLATION For the Chinese translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Carlos K H Wong
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Department of Family Medicine and Primary Care, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, China.
| | - Kristy T K Lau
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ivan C H Au
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric H Y Lau
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, 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 Special Administrative Region, China
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Centre for Immunology and Infection, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, 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 Special Administrative Region, China
| | - Benjamin J Cowling
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, 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 Special Administrative Region, China
| | - Gabriel M Leung
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Shatin, Hong Kong Special Administrative Region, 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 Special Administrative Region, China
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20
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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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21
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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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22
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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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23
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Zheng X, Wang M, Deng Y, Xu X, Lin D, Zhang Y, Li S, Ding J, Shi X, Yau CI, Poon LLM, Zhang T. A rapid, high-throughput, and sensitive PEG-precipitation method for SARS-CoV-2 wastewater surveillance. Water Res 2023; 230:119560. [PMID: 36623382 PMCID: PMC9803703 DOI: 10.1016/j.watres.2022.119560] [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] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
The effective application of wastewater surveillance is dependent on testing capacity and sensitivity to obtain high spatial resolution testing results for a timely targeted public health response. To achieve this purpose, the development of rapid, high-throughput, and sensitive virus concentration methods is urgently needed. Various protocols have been developed and implemented in wastewater surveillance networks so far, however, most of them lack the ability to scale up testing capacity or cannot achieve sufficient sensitivity for detecting SARS-CoV-2 RNA at low prevalence. In the present study, using positive raw wastewater in Hong Kong, a PEG precipitation-based three-step centrifugation method was developed, including low-speed centrifugation for large particles removal and the recovery of viral nucleic acid, and medium-speed centrifugation for the concentration of viral nucleic acid. This method could process over 100 samples by two persons per day to reach the process limit of detection (PLoD) of 3286 copies/L wastewater. Additionally, it was found that the testing capacity could be further increased by decreasing incubation and centrifugation time without significantly influencing the method sensitivity. The entire procedure uses ubiquitous reagents and instruments found in most laboratories to obtain robust testing results. This high-throughput, cost-effective, and sensitive tool will promote the establishment of nearly real-time wastewater surveillance networks for valuable public health information.
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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
| | - Mengying Wang
- 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
| | - 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
| | - Danxi Lin
- 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
| | - Yulin 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
| | - Shuxian Li
- 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
| | - Jiahui Ding
- 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
| | - Xianghui Shi
- 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
| | - Chung In Yau
- School of Public Health, Li Ka Shing Faculty of Medicine, 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
| | - 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; Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau SAR, China.
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24
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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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25
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Zheng X, Li S, Deng Y, Xu X, Ding J, Lau FTK, In Yau C, Poon LLM, Tun HM, Zhang T. Quantification of SARS-CoV-2 RNA in wastewater treatment plants mirrors the pandemic trend in Hong Kong. Sci Total Environ 2022; 844:157121. [PMID: 35787900 PMCID: PMC9249664 DOI: 10.1016/j.scitotenv.2022.157121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/12/2022] [Accepted: 06/28/2022] [Indexed: 05/09/2023]
Abstract
Wastewater-based epidemiology (WBE) for the SARS-CoV-2 virus in wastewater treatment plants (WWTPs) has emerged as a cost-effective and unbiased tool for population-level testing in the community. In the present study, we conducted a 6-month wastewater monitoring campaign from three WWTPs of different flow rates and catchment area characteristics, which serve 28 % (2.1 million people) of Hong Kong residents in total. Wastewater samples collected daily or every other day were concentrated using ultracentrifugation and the SARS-CoV-2 virus RNA in the supernatant was detected using the N1 and E primer sets. The results showed significant correlations between the virus concentration and the number of daily new cases in corresponding catchment areas of the three WWTPs when using 7-day moving average values (Kendall's tau-b value: 0.227-0.608, p < 0.001). SARS-CoV-2 virus concentration was normalized to a fecal indicator using PMMoV concentration and daily flow rates, but the normalization did not enhance the correlation. The key factors contributing to the correlation were also evaluated, including the sampling frequency, testing methods, and smoothing days. This study demonstrates the applicability of wastewater surveillance to monitor overall SARS-CoV-2 pandemic dynamics in a densely populated city like Hong Kong, and provides a large-scale longitudinal reference for the establishment of the long-term sentinel surveillance in WWTPs for WBE of pathogens which could be combined into a city-wide public health observatory.
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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
| | - Shuxian Li
- 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
| | - Jiahui Ding
- 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
| | - Frankie T K Lau
- Drainage Services Department, The Government of the Hong Kong Special Administrative Region of the People's Republic of China, Wanchai, Hong Kong, China
| | - Chung In Yau
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, 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
| | - Hein M Tun
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, 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.
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26
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Cowling BJ, Cheng SMS, Martín-Sánchez M, Au NYM, Chan KCK, Li JKC, Fung LWC, Luk LLH, Tsang LCH, Ip DKM, Poon LLM, Leung GM, Peiris JSM, Leung NHL. Slow Waning of Antibodies Following BNT162b2 as a Third Dose in Adults Who Had Previously Received 2 Doses of Inactivated Vaccine. J Infect Dis 2022; 227:251-255. [PMID: 36108092 PMCID: PMC9494487 DOI: 10.1093/infdis/jiac380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 01/14/2023] Open
Abstract
We administered BNT162b2 as a third dose to 314 adults aged ≥30 years who had previously received 2 doses of inactivated vaccine. We collected blood samples before the third dose and again after 1 month and 6 months, and found robust antibody responses to the ancestral strain at 6 months after receipt of BNT162b2. Antibody responses to Omicron BA.2 by live virus neutralization were weaker after the third dose and had declined to a low level by 6 months.
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Affiliation(s)
- Benjamin J Cowling
- Corresponding author: Benjamin Cowling, WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong; Hong Kong Special Administrative Region, China.
| | - Samuel M S Cheng
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Mario Martín-Sánchez
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Niki Y M Au
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Karl C K Chan
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - John K C Li
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Lison W C Fung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Leo L H Luk
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Leo C H Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Dennis K M Ip
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Leo L M Poon
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China,HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, Pokfulam, The University of Hong Kong; Hong Kong Special Administrative Region, China,Centre for Immunology and Infection; Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, 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, Pokfulam, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health; Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | | | - Nancy H L Leung
- Alternate corresponding author in the event that the corresponding author is unavailable: Nancy Leung,
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27
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Cowling BJ, Wong IOL, Shiu EYC, Lai AYT, Cheng SMS, Chaothai S, Kwan KKH, Martín-Sánchez M, Poon LLM, Ip DKM, Leung GM, Leung NHL, Peiris JSM. Strength and durability of antibody responses to BNT162b2 and CoronaVac. Vaccine 2022; 40:4312-4317. [PMID: 35701327 DOI: 10.1016/j.vaccine.2022.05.033] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/14/2022] [Accepted: 05/09/2022] [Indexed: 11/18/2022]
Abstract
We studied 2780 adults in Hong Kong who received CoronaVac inactivated virus vaccine (Sinovac) and BNT162b2 mRNA vaccine ("Comirnaty", BioNTech/Fosun Pharma). We compared rates of antibody waning over time using an enzyme-linked immunosorbent assay for spike receptor binding domain and a surrogate virus neutralization test. We found stronger and more durable antibody responses to two doses of the mRNA vaccine, and slightly stronger initial antibody responses to each vaccine in younger adults and women. The weaker and less durable responses following CoronaVac support earlier provision of third doses to persons who previously received two doses of this vaccine.
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Affiliation(s)
- Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region; Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region.
| | - Irene O L Wong
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Eunice Y C Shiu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Amber Y T Lai
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Samuel M S Cheng
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Sara Chaothai
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Kelvin K H Kwan
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Mario Martín-Sánchez
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Leo L M Poon
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region; HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region; Centre for Immunology and Infection, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region
| | - Dennis K M Ip
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - 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, Hong Kong Special Administrative Region; Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region
| | - Nancy H L Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region; Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region.
| | - J S Malik Peiris
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region; HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region; Centre for Immunology and Infection, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region
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28
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Xu X, Deng Y, Ding J, Zheng X, Li S, Liu L, Chui HK, Poon LLM, Zhang T. Real-time allelic assays of SARS-CoV-2 variants to enhance sewage surveillance. Water Res 2022; 220:118686. [PMID: 35679788 PMCID: PMC9148393 DOI: 10.1016/j.watres.2022.118686] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 01/19/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 05/21/2023]
Abstract
To effectively control the ongoing outbreaks of fast-spreading SARS-CoV-2 variants, there is an urgent need to add rapid variant detection and discrimination methods to the existing sewage surveillance systems established worldwide. We designed eight assays based on allele-specific RT-qPCR for real-time allelic discrimination of eight SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Omicron, Lambda, Mu, and Kappa) in sewage. In silico analysis of the designed assays for identifying SARS-CoV-2 variants using more than four million SARS-CoV-2 variant sequences yielded ∼100% specificity and >90% sensitivity. All assays could sensitively discriminate and quantify target variants at levels as low as 10 viral RNA copy/µL with minimal cross-reactivity to the corresponding nontarget genotypes, even for sewage samples containing mixtures of SARS-CoV-2 variants with differential abundances. Integration of this method into the routine sewage surveillance in Hong Kong successfully identified the Beta variant in a community sewage. Complete concordance was observed between the results of viral whole-genome sequencing and those of our novel assays in sewage samples that contained exclusively the Delta variant discharged by a clinically diagnosed COVID-19 patient living in a quarantine hotel. Our assays in this method also provided real-time discrimination of the newly emerging Omicron variant in sewage two days prior to clinical test results in another quarantine hotel in Hong Kong. These novel allelic discrimination assays offer a rapid, sensitive, and specific way for detecting multiple SARS-CoV-2 variants in sewage and can be directly integrated into the existing sewage surveillance systems.
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Affiliation(s)
- 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
| | - Jiahui Ding
- 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
| | - 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
| | - Shuxian Li
- 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
| | - Lei Liu
- 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
| | - Ho-Kwong Chui
- Environmental Protection Department, The Government of Hong Kong SAR, Tamar, 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
| | - 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.
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29
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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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30
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Xu X, Deng Y, Zheng X, Li S, Ding J, Yang Y, On HY, Yang R, Chui HK, Yau CI, Tun HM, Chin AWH, Poon LLM, Peiris M, Leung GM, Zhang T. Evaluation of RT-qPCR Primer-Probe Sets to Inform Public Health Interventions Based on COVID-19 Sewage Tests. Environ Sci Technol 2022; 56:8875-8884. [PMID: 35584232 PMCID: PMC9128008 DOI: 10.1021/acs.est.2c00974] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 05/02/2023]
Abstract
Sewage surveillance is increasingly employed as a supplementary tool for COVID-19 control. Experiences learnt from large-scale trials could guide better interpretation of the sewage data for public health interventions. Here, we compared the performance of seven commonly used primer-probe sets in RT-qPCR and evaluated the usefulness in the sewage surveillance program in Hong Kong. All selected primer-probe sets reliably detected SARS-CoV-2 in pure water at 7 copies per μL. Sewage matrix did not influence RT-qPCR determination of SARS-CoV-2 concentrated from a small-volume sewage (30 mL) but introduced inhibitory impacts on a large-volume sewage (920 mL) with a ΔCt of 0.2-10.8. Diagnostic performance evaluation in finding COVID-19 cases showed that N1 was the best single primer-probe set, while the ORF1ab set is not recommended. Sewage surveillance using the N1 set for over 3200 samples effectively caught the outbreak trend and, importantly, had a 56% sensitivity and a 96% specificity in uncovering the signal sources from new cases and/or convalescent patients in the community. Our study paves the way for selecting detection primer-probe sets in wider applications in responding to the COVID-19 pandemic.
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Affiliation(s)
- Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Hei Yin On
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
| | - Rong Yang
- Environmental Protection Department, The
Government of Hong Kong SAR, Tamar, Hong Kong SAR 999077,
China
| | - Ho-Kwong Chui
- Environmental Protection Department, The
Government of Hong Kong SAR, Tamar, Hong Kong SAR 999077,
China
| | - Chung In Yau
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
| | - Hein Min Tun
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
- HKU-Pasteur Research Pole,
Sassoon Road, Hong Kong SAR 999077, China
| | - Alex W. H. Chin
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, 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 999077, China
- HKU-Pasteur Research Pole,
Sassoon Road, Hong Kong SAR 999077, China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
- HKU-Pasteur Research Pole,
Sassoon Road, Hong Kong SAR 999077, China
| | - Gabriel M. Leung
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
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31
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Zheng X, Deng Y, Xu X, Li S, Zhang Y, Ding J, On HY, Lai JCC, In Yau C, Chin AWH, Poon LLM, Tun HM, Zhang T. Comparison of virus concentration methods and RNA extraction methods for SARS-CoV-2 wastewater surveillance. Sci Total Environ 2022; 824:153687. [PMID: 35134418 PMCID: PMC8816846 DOI: 10.1016/j.scitotenv.2022.153687] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [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: 11/15/2021] [Revised: 01/16/2022] [Accepted: 02/01/2022] [Indexed: 05/02/2023]
Abstract
Wastewater surveillance is a promising tool for population-level monitoring of the spread of infectious diseases, such as the coronavirus disease 2019 (COVID-19). Different from clinical specimens, viruses in community-scale wastewater samples need to be concentrated before detection because viral RNA is highly diluted. The present study evaluated eleven different virus concentration methods for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater. First, eight concentration methods of different principles were compared using spiked wastewater at a starting volume of 30 mL. Ultracentrifugation was the most effective method with a viral recovery efficiency of 25 ± 6%. The second-best option, AlCl3 precipitation method, yielded a lower recovery efficiency, only approximately half that of the ultracentrifugation method. Second, the potential of increasing method sensitivity was explored using three concentration methods starting with a larger volume of 1000 mL. Although ultracentrifugation using a large volume outperformed the other two large-volume methods, it only yielded a comparable method sensitivity as the ultracentrifugation using a small volume (30 mL). Thus, ultracentrifugation using less volume of wastewater is more preferable considering the sample processing throughput. Third, a comparison of two viral RNA extraction methods showed that the lysis-buffer-based extraction method resulted in higher viral recovery efficiencies, with cycle threshold (Ct) values 0.9-4.2 lower than those obtained for the acid-guanidinium-phenol-based method using spiked samples. These results were further confirmed by using positive wastewater samples concentrated by ultracentrifugation and extracted separately by the two viral RNA extraction methods. In summary, concentration using ultracentrifugation followed by the lysis buffer-based extraction method enables sensitive and robust detection of SARS-CoV-2 for wastewater surveillance.
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Affiliation(s)
- Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Laboratory, 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 Laboratory, 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 Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yulin Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Hei Yin On
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong, China; HKU-Pasteur Research Pole, Pokfulam Road, Hong Kong, China
| | - Jimmy C C Lai
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong, China; HKU-Pasteur Research Pole, Pokfulam Road, Hong Kong, China
| | - Chung In Yau
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Alex W H Chin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong, China; HKU-Pasteur Research Pole, Pokfulam Road, Hong Kong, China
| | - Hein M Tun
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong, China; HKU-Pasteur Research Pole, Pokfulam Road, Hong Kong, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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32
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Leung NHL, Cheng SMS, Martín-Sánchez M, Au NYM, Ng YY, Luk LLH, Chan KCK, Li JKC, Leung YWY, Tsang LCH, Chaothai S, Kwan KKH, Ip DKM, Poon LLM, Leung GM, Peiris JSM, Cowling BJ. Immunogenicity of a Third Dose of BNT162b2 to Ancestral Severe Acute Respiratory Syndrome Coronavirus 2 and the Omicron Variant in Adults Who Received 2 Doses of Inactivated Vaccine. Clin Infect Dis 2022; 76:e299-e307. [PMID: 35675370 PMCID: PMC9384189 DOI: 10.1093/cid/ciac458] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Limited data exist on antibody responses to mixed vaccination strategies that involve inactivated coronavirus disease 2019 (COVID-19) vaccines, particularly in the context of emerging variants. METHODS We conducted an open-label trial of a third vaccine dose of a messenger RNA (mRNA) vaccine (BNT162b2, Fosun Pharma/BioNTech) in adults aged ≥30 years who had previously received 2 doses of inactivated COVID-19 vaccine. We collected blood samples before administering the third dose and 28 days later and tested for antibodies to the ancestral virus using a binding assay (enzyme-linked immunosorbent assay [ELISA]), a surrogate virus neutralization test (sVNT), and a live virus plaque reduction neutralization test (PRNT). We also tested for antibodies against the Omicron variant using live-virus PRNT. RESULTS In 315 participants, a third dose of BNT162b2 substantially increased antibody titers on each assay. Mean ELISA levels increased from an optical density of 0.3 to 2.2 (P < .001), and mean sVNT levels increased from an inhibition of 17% to 96% (P < .001). In a random subset of 20 participants, the geometric mean PRNT50 titers rose substantially, by 45-fold from day 0 to day 28 against the ancestral virus (P < .001) and by 11-fold against the Omicron variant (P < .001). In daily monitoring, post-vaccination reactions subsided within 7 days for more than 99% of participants. CONCLUSIONS A third dose of COVID-19 vaccine with an mRNA vaccine substantially improved antibody levels against the ancestral virus and the Omicron variant with a well-tolerated safety profile in adults who had received 2 doses of inactivated vaccine 6 months earlier. CLINICAL TRIALS REGISTRATION NCT05057182.
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Affiliation(s)
- Nancy H L Leung
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Samuel M S Cheng
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Mario Martín-Sánchez
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Niki Y M Au
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yvonne Y Ng
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Leo L H Luk
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Karl C K Chan
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - John K C Li
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yonna W Y Leung
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Leo C H Tsang
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Sara Chaothai
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kelvin K H Kwan
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Dennis K M Ip
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Leo L M Poon
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China,Hong Kong University (HKU)-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China,Centre for Immunology and Infection, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Gabriel M Leung
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | | | - Benjamin J Cowling
- Correspondence: B. Cowling, WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, 1/F Patrick Manson Building, 7 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China ()
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33
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Hosseini M, Poon LLM, Chin AWH, Ducker WA. Effect of Surface Porosity on SARS-CoV-2 Fomite Infectivity. ACS Omega 2022; 7:18238-18246. [PMID: 35663285 PMCID: PMC9159070 DOI: 10.1021/acsomega.1c06880] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 03/18/2022] [Indexed: 05/06/2023]
Abstract
Previous reports indicated the low stability of severe actute respiratory syndrome coronovirus 2 (SARS-CoV-2) on various porous surfaces, but the role of porosity was unclear because there was no direct comparison between porous and nonporous solids of the same chemistry. Through comparing pairs of solids with very similar chemistry, we find that porosity is important: porous glass has a much lower infectivity than nonporous glass. However, porosity is not sufficient to lower infectivity; permeability, which is the ability of a liquid to move through a material, is the important parameter. We show this by comparing a pair of porous CuO coatings where the pores are accessible in one case and inaccessible in the other case. When the pores are inaccessible, the infectivity remains similar to that for nonporous solids. Thus, for both glass and CuO, it is the access to porosity that decreases the infectivity of extracted liquid droplets. Having established the importance of permeability, there is the open question of the mechanism of changing the infectivity of SARS-CoV-2. Several hypotheses are possible, such as increasing the difficulty of extracting the virus from the solid, changing the drying time, increasing the surface area of active ingredient, etc. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) measurements show that less viral DNA is extracted from a permeable surface, suggesting that the virus becomes trapped in the pores. Finally, we consider the effect of drying. We show that permeability and the water contact angle on the solid have effects on the drying time of a contaminated droplet, which may in turn affect infectivity.
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Affiliation(s)
- Mohsen Hosseini
- Deptartment
of Chemical Engineering and Center for Soft Matter and Biological
Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Leo L. M. Poon
- School
of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre
for Immunity and Infection, Hong Kong Science Park, Hong Kong, China
- HKU
Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong
Kong, China
| | - Alex W. H. Chin
- School
of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre
for Immunity and Infection, Hong Kong Science Park, Hong Kong, China
| | - William A. Ducker
- Deptartment
of Chemical Engineering and Center for Soft Matter and Biological
Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
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34
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Valkenburg SA, Poon LLM. Universal influenza vaccines are futile when benchmarked against seasonal influenza vaccines. Lancet Infect Dis 2022; 22:750-751. [PMID: 35305315 DOI: 10.1016/s1473-3099(21)00749-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Doherty Institute of Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | - 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 Special Administrative Region, China; Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
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35
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Hachim A, Gu H, Kavian O, Mori M, Kwan MYW, Chan WH, Yau YS, Chiu SS, Tsang OTY, Hui DSC, Mok CKP, Ma FNL, Lau EHY, Amarasinghe GK, Qavi AJ, Cheng SMS, Poon LLM, Peiris JSM, Valkenburg SA, Kavian N. SARS-CoV-2 accessory proteins reveal distinct serological signatures in children. Nat Commun 2022; 13:2951. [PMID: 35618731 PMCID: PMC9135746 DOI: 10.1038/s41467-022-30699-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/13/2022] [Indexed: 12/14/2022] Open
Abstract
The antibody response magnitude and kinetics may impact clinical severity, serological diagnosis and long-term protection of COVID-19, which may play a role in why children experience lower morbidity. We therefore tested samples from 122 children in Hong Kong with symptomatic (n = 78) and asymptomatic (n = 44) SARS-CoV-2 infections up to 200 days post infection, relative to 71 infected adults (symptomatic n = 61, and asymptomatic n = 10), and negative controls (n = 48). We assessed serum IgG antibodies to a 14-wide antigen panel of structural and accessory proteins by Luciferase Immuno-Precipitation System (LIPS) assay and circulating cytokines. Infected children have lower levels of Spike, Membrane, ORF3a, ORF7a, ORF7b antibodies, comparable ORF8 and elevated E-specific antibodies than adults. Combination of two unique antibody targets, ORF3d and ORF8, can accurately discriminate SARS-CoV-2 infection in children. Principal component analysis reveals distinct pediatric serological signatures, and the highest contribution to variance from adults are antibody responses to non-structural proteins ORF3d, NSP1, ORF3a and ORF8. From a diverse panel of cytokines that can modulate immune priming and relative inflammation, IL-8, MCP-1 and IL-6 correlate with the magnitude of pediatric antibody specificity and severity. Antibodies to SARS-CoV-2 internal proteins may become an important sero surveillance tool of infection with the roll-out of vaccines in the pediatric population. The antibody response of children to SARS-CoV-2 is less well studied than in adults. Here Hachim et al. show that children have reduced antibody levels to structural proteins and suggest that the predominance of antibody responses to non-structural proteins can be used to discriminate infection and vaccination.
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Affiliation(s)
- Asmaa Hachim
- 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
| | - Otared Kavian
- Department of Mathematics, Université de Versailles Saint-Quentin, Versailles, France
| | - Masashi Mori
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Mike Y W Kwan
- Department of Pediatric and Adolescent Medicine, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Wai Hung Chan
- Department of Pediatrics, Queen Elizabeth Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Yat Sun Yau
- Department of Pediatrics, Queen Elizabeth Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Susan S Chiu
- Department of Pediatric and Adolescent Medicine, The University of Hong Kong and Queen Mary Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Owen T Y Tsang
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - David S C Hui
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese 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
| | - Fionn N L Ma
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - 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
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Abraham J Qavi
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Samuel M S Cheng
- 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
| | - 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
| | - J S Malik Peiris
- 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
| | - 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. .,Doherty Institute of Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Australia.
| | - Niloufar Kavian
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.,Faculté de Médecine Université Paris Descartes, Sorbonne Paris Cité, Assistance Publique-Hôpitaux de Paris, Hôpital Universitaire Paris Centre, Centre Hospitalier Universitaire Cochin, Service d'Immunologie Biologique, Paris, France.,Institut Cochin, INSERM U1016, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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36
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Deng Y, Xu X, Zheng X, Ding J, Li S, Chui HK, Wong TK, Poon LLM, Zhang T. Use of sewage surveillance for COVID-19 to guide public health response: A case study in Hong Kong. Sci Total Environ 2022; 821:153250. [PMID: 35065122 PMCID: PMC8769675 DOI: 10.1016/j.scitotenv.2022.153250] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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: 12/01/2021] [Revised: 01/14/2022] [Accepted: 01/14/2022] [Indexed: 05/10/2023]
Abstract
Sewage surveillance could help develop proactive response to the Coronavirus Disease 2019 (COVID-19) pandemic, but currently there are limited reports about examples in practical exercises. Here, we report a use case of intensified sewage surveillance to initiate public health action to thwart a looming Delta variant outbreak in Hong Kong. On 21 June 2021, albeit under basically contained COVID-19 situation in Hong Kong, routine sewage surveillance identified a high viral load of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a sewage sample from one site covering over 33,000 population, suggesting infected cases living in the respective sewershed. The use of a newly developed method based on allele-specific real-time quantitative polymerase chain reaction (AS RT-qPCR) served to alert the first documentation of the Delta variant in local community sewage three days before the case was confirmed to be a Delta variant carrier. Intensified sewage surveillance was triggered. Targeted upstream sampling at sub-sewershed areas pinpointed the source of positive viral signal across spatial scales from sewershed to building level, and assisted in determining the specific area for issuing a compulsory testing order for individuals on 23 June 2021. A person who lived in a building with the positive result of sewage testing was confirmed to be infected with COVID-19 on 24 June 2021. Viral genome sequences determined from the sewage sample were compared to those from the clinic specimens of the matched patient, and confirmed that the person was the source of the positive SARS-CoV-2 signal in the sewage sample. This study could help build confidences for public health agencies in using the sewage surveillance in their own communities.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - Jiahui Ding
- 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
| | - Shuxian Li
- 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
| | - Ho-Kwong Chui
- Environmental Protection Department, The Government of the Hong Kong SAR, Tamar, Hong Kong SAR, China
| | - Tsz-Kin Wong
- Drainage Services Department, The Government of the Hong Kong SAR, Wanchai, 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
| | - 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.
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Bull MB, Gu H, Ma FNL, Perera LP, Poon LLM, Valkenburg SA. Next-generation T cell-activating vaccination increases influenza virus mutation prevalence. Sci Adv 2022; 8:eabl5209. [PMID: 35385318 PMCID: PMC8986104 DOI: 10.1126/sciadv.abl5209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
To determine the potential for viral adaptation to T cell responses, we probed the full influenza virus genome by next-generation sequencing directly ex vivo from infected mice, in the context of an experimental T cell-based vaccine, an H5N1-based viral vectored vaccinia vaccine Wyeth/IL-15/5Flu, versus the current standard-of-care, seasonal inactivated influenza vaccine (IIV) and unvaccinated conditions. Wyeth/IL-15/5Flu vaccination was coincident with increased mutation incidence and frequency across the influenza genome; however, mutations were not enriched within T cell epitope regions, but high allele frequency mutations within conserved hemagglutinin stem regions and PB2 mammalian adaptive mutations arose. Depletion of CD4+ and CD8+ T cell subsets led to reduced frequency of mutants in vaccinated mice; therefore, vaccine-mediated T cell responses were important drivers of virus diversification. Our findings suggest that Wyeth/IL-15/5Flu does not generate T cell escape mutants but increases stochastic events for virus adaptation by stringent bottlenecks.
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Affiliation(s)
- Maireid B. Bull
- 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
| | - Fionn N. L. Ma
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Liyanage P. Perera
- Metabolism Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1374, USA
| | - 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
| | - 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, at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
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Gu H, Ng DYM, Liu GYZ, Cheng SSM, Krishnan P, Chang LDJ, Cheuk SSY, Hui MMY, Lam TTY, Peiris M, Poon LLM. Recombinant BA.1/BA.2 SARS-CoV-2 Virus in Arriving Travelers, Hong Kong, February 2022. Emerg Infect Dis 2022; 28:1276-1278. [PMID: 35394420 PMCID: PMC9155883 DOI: 10.3201/eid2806.220523] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We studied SARS-CoV-2 genomes from travelers arriving in Hong Kong during November 2021-February 2022. In addition to Omicron and Delta variants, we detected a BA.1/BA.2 recombinant with a breakpoint near the 5' end of the spike gene in 2 epidemiologically linked case-patients. Continued surveillance for SARS-CoV-2 recombinants is needed.
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Liu LT, Chin AWH, Yu P, Poon LLM, Huang MX. Anti-pathogen stainless steel combating COVID-19. Chem Eng J 2022; 433:133783. [PMID: 34853550 PMCID: PMC8613009 DOI: 10.1016/j.cej.2021.133783] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/05/2021] [Accepted: 11/19/2021] [Indexed: 05/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibits strong stability on conventional stainless steel (SS) surface, with infectious virus detected even after two days, posing a high risk of virus transmission via surface touching in public areas. In order to mitigate the surface toughing transmission, the present study develops the first SS with excellent anti-pathogen properties against SARS-COV-2. The stabilities of SARS-CoV-2, H1N1 influenza A virus (H1N1), and Escherichia coli (E.coli) on the surfaces of Cu-contained SS, pure Cu, Ag-contained SS, and pure Ag were investigated. It is discovered that pure Ag and Ag-contained SS surfaces do not display apparent inhibitory effects on SARS-CoV-2 and H1N1. In comparison, both pure Cu and Cu-contained SS with a high Cu content exhibit significant antiviral properties. Significantly, the developed anti-pathogen SS with 20 wt% Cu can distinctly reduce 99.75% and 99.99% of viable SARS-CoV-2 on its surface within 3 and 6 h, respectively. In addition, the present anti-pathogen SS also exhibits an excellent inactivation ability for H1N1 influenza A virus (H1N1), and Escherichia coli (E.coli). Interestingly, the Cu ion concentration released from the anti-pathogen SS with 10 wt% and 20 wt% Cu was notably higher than the Ag ion concentration released from Ag and the Ag-contained SS. Lift buttons made of the present anti-pathogen SS are produced using mature powder metallurgy technique, demonstrating its potential applications in public areas and fighting the transmission of SARS-CoV-2 and other pathogens via surface touching.
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Affiliation(s)
- L T Liu
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, PR China
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518000, PR China
| | - A W H Chin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong, PR China
- Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, PR China
| | - P Yu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518000, PR China
| | - L L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong, PR China
- Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, PR China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, PR China
| | - M X Huang
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, PR China
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Yen HL, Sit THC, Brackman CJ, Chuk SSY, Gu H, Tam KWS, Law PYT, Leung GM, Peiris M, Poon LLM. Transmission of SARS-CoV-2 delta variant (AY.127) from pet hamsters to humans, leading to onward human-to-human transmission: a case study. Lancet 2022; 399:1070-1078. [PMID: 35279259 PMCID: PMC8912929 DOI: 10.1016/s0140-6736(22)00326-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND Transmission of SARS-CoV-2 from humans to other mammals, including pet animals, has been reported. However, with the exception of farmed mink, there is no previous evidence that these infected animals can infect humans, resulting in sustained human-to-human transmission. Following a confirmed SARS-CoV-2 infection of a pet shop worker, animals in the shop and the warehouse supplying it were tested for evidence of SARS-CoV-2 infection. METHODS In this case study, viral swabs and blood samples were collected from animals in a pet shop and its corresponding warehouse in Hong Kong. Nasal swab or saliva samples from human COVID-19 patients epidemiologically linked to the pet shop and from subsequent local cases confirmed to be infected by SARS-CoV-2 delta variant were collected. Oral swabs were tested by quantitative RT-PCR (RT-qPCR) for SARS-CoV-2 and blood samples were serologically tested by a surrogate virus neutralisation test and plaque reduction neutralisation test. The SARS-CoV-2 RT-qPCR positive samples were sequenced by next generation viral full genome sequencing using the ISeq sequencing platform (Illumina), and the viral genomes were phylogenetically analysed. FINDINGS Eight (50%) of 16 individually tested Syrian hamsters in the pet shop and seven (58%) of 12 Syrian hamsters in the corresponding warehouse were positive for SARS-CoV-2 infection in RT-qPCR or serological tests. None of the dwarf hamsters (n=75), rabbits (n=246), guinea pigs (n=66), chinchillas (n=116), and mice (n=2) were confirmed positive for SARS-CoV-2 in RT-qPCR tests. SARS-CoV-2 viral genomes deduced from human and hamster cases in this incident all belong to the delta variant of concern (AY.127) that had not been circulating locally before this outbreak. The viral genomes obtained from hamsters were phylogenetically related with some sequence heterogeneity. Phylogenetic dating suggests infection in these hamsters occurred around Oct 14, 2021 (95% CI Sept 15 to Nov 9, 2021). Multiple zoonotic transmission events to humans were detected, leading to onward human-to-human transmission. INTERPRETATION Pet hamsters can be naturally infected with SARS-CoV-2. The virus can circulate among hamsters and lead to human infections. Both genetic and epidemiological results strongly suggest that there was more than one hamster-to-human transmission event in this study. This incident also led to onward human transmission. Importation of SARS-CoV-2-infected hamsters was a likely source of this outbreak. FUNDING US National Institutes of Health, Research Grants Council of Hong Kong, Food and Health Bureau, and InnoHK.
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Affiliation(s)
- Hui-Ling Yen
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Thomas H C Sit
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong Special Administrative Region, China
| | - Christopher J Brackman
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong Special Administrative Region, China
| | - Shirley S Y Chuk
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong Special Administrative Region, China
| | - Haogao Gu
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Karina W S Tam
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong Special Administrative Region, China
| | - Pierra Y T Law
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong Special Administrative Region, China
| | - Gabriel M Leung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; WHO Collaborating Centre for Infectious Disease Epidemiology and Control, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Laboratory of Data Discovery for Health, Hong Kong Science Park, Shatin, Hong Kong Special Administrative Region, China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Centre for Immunology and Infection, Hong Kong Science Park, Shatin, Hong Kong Special Administrative Region, China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Centre for Immunology and Infection, Hong Kong Science Park, Shatin, Hong Kong Special Administrative Region, China.
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41
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Cheng SMS, Mok CKP, Leung YWY, Ng SS, Chan KCK, Ko FW, Chen C, Yiu K, Lam BHS, Lau EHY, Chan KKP, Luk LLH, Li JKC, Tsang LCH, Poon LLM, Hui DSC, Peiris M. Neutralizing antibodies against the SARS-CoV-2 Omicron variant BA.1 following homologous and heterologous CoronaVac or BNT162b2 vaccination. Nat Med 2022; 28:486-489. [PMID: 35051989 PMCID: PMC8940714 DOI: 10.1038/s41591-022-01704-7] [Citation(s) in RCA: 241] [Impact Index Per Article: 120.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/18/2022] [Indexed: 11/09/2022]
Abstract
The Omicron variant is rapidly becoming the dominant SARS-CoV-2 virus circulating globally. It is important to define reductions in virus neutralizing activity in the serum of convalescent or vaccinated individuals to understand potential loss of protection against infection by Omicron. We previously established that a 50% plaque reduction neutralization antibody titer (PRNT50) ≥25.6 in our live virus assay corresponded to the threshold for 50% protection from infection against wild-type (WT) SARS-CoV-2. Here we show markedly reduced serum antibody titers against the Omicron variant (geometric mean titer (GMT) < 10) compared to WT virus 3-5 weeks after two doses of BNT162b2 (GMT = 218.8) or CoronaVac vaccine (GMT = 32.5). A BNT162b2 booster dose elicited Omicron PRNT50 titers ≥25.6 in 88% of individuals (22 of 25) who previously received 2 doses of BNT162b2 and 80% of individuals (24 of 30) who previously received CoronaVac. However, few (3%) previously infected individuals (1 of 30) or those vaccinated with three doses of CoronaVac (1 of 30) met this threshold. Our findings suggest that countries primarily using CoronaVac vaccines should consider messenger RNA vaccine boosters in response to the spread of Omicron. Studies evaluating the effectiveness of different vaccines against the Omicron variant are urgently needed.
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Affiliation(s)
- Samuel M S Cheng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Chris Ka Pun Mok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, P. R. China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, P. R. China
| | - Yonna W Y Leung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Susanna S Ng
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong, Kong, Hong Kong, P. R. China
| | - Karl C K Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Fanny W Ko
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong, Kong, Hong Kong, P. R. China
| | - Chunke Chen
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, P. R. China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, P. R. China
| | - Karen Yiu
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong, Kong, Hong Kong, P. R. China
| | - Bosco H S Lam
- Department of Pathology, North Lantau Hospital, Hong Kong, P. R. China
| | - Eric H Y Lau
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
- Laboratory of Data Discovery for Health Limited, Hong Kong Science Park, Hong Kong, P. R. China
| | - Ken K P Chan
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong, Kong, Hong Kong, P. R. China
| | - Leo L H Luk
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - John K C Li
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Leo C H Tsang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong, P. R. China
| | - David S C Hui
- Department of Medicine & Therapeutics, Faculty of Medicine, The Chinese University of Hong, Kong, Hong Kong, P. R. China.
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, P. R. China.
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China.
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong, P. R. China.
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Hosseini M, Chin AWH, Williams MD, Behzadinasab S, Falkinham JO, Poon LLM, Ducker WA. Transparent Anti-SARS-CoV-2 and Antibacterial Silver Oxide Coatings. ACS Appl Mater Interfaces 2022; 14:8718-8727. [PMID: 35138100 PMCID: PMC8848512 DOI: 10.1021/acsami.1c20872] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 10/29/2021] [Accepted: 01/14/2022] [Indexed: 05/17/2023]
Abstract
Transparent antimicrobial coatings can maintain the aesthetic appeal of surfaces and the functionality of a touch-screen while adding the benefit of reducing disease transmission. We fabricated an antimicrobial coating of silver oxide particles in a silicate matrix on glass. The matrix was grown by a modified Stöber sol-gel process with vapor-phase water and ammonia. A coating on glass with 2.4 mg of Ag2O per mm2 caused a reduction of 99.3% of SARS-CoV-2 and >99.5% of Pseudomonas aeruginosa, Staphylococcus aureus, and methicillin-resistant Staphylococcus aureus compared to the uncoated glass after 1 h. We envisage that screen protectors with transparent antimicrobial coatings will find particular application to communal touch-screens, such as in supermarkets and other check-out or check-in facilities where a number of individuals utilize the same touch-screen in a short interval.
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Affiliation(s)
- Mohsen Hosseini
- Dept. of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia, 24061, USA
| | - Alex W. H. Chin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
- Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, Hong Kong, China
| | - Myra D. Williams
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA
| | - Saeed Behzadinasab
- Dept. of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia, 24061, USA
| | - Joseph O. Falkinham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, 24061, USA
| | - Leo L. M. Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
- Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, Hong Kong, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - William A. Ducker
- Dept. of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia, 24061, USA
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43
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Valkenburg SA, Poon LLM. Exploring the landscape of immune responses to influenza infection and vaccination. Nat Med 2022; 28:239-240. [PMID: 35177856 DOI: 10.1038/s41591-021-01656-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- 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
| | - 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 & Infection, Hong Kong Science Park, Hong Kong SAR, China.
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44
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Ma Z, Li X, Fan RLY, Yang KY, Ng CSH, Lau RWH, Wong RHL, Ng KK, Wang CC, Ye P, Fu Z, Chin AWH, Lai MYA, Huang Y, Tian XY, Poon LLM, Lui KO. A human pluripotent stem cell-based model of SARS-CoV-2 infection reveals an ACE2-independent inflammatory activation of vascular endothelial cells through TLR4. Stem Cell Reports 2022; 17:538-555. [PMID: 35180397 PMCID: PMC8851885 DOI: 10.1016/j.stemcr.2022.01.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 08/12/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 12/15/2022] Open
Abstract
To date, the direct causative mechanism of SARS-CoV-2-induced endotheliitis remains unclear. Here, we report that human ECs barely express surface ACE2, and ECs express less intracellular ACE2 than non-ECs of the lungs. We ectopically expressed ACE2 in hESC-ECs to model SARS-CoV-2 infection. ACE2-deficient ECs are resistant to the infection but are more activated than ACE2-expressing ones. The virus directly induces endothelial activation by increasing monocyte adhesion, NO production, and enhanced phosphorylation of p38 mitogen-associated protein kinase (MAPK), NF-κB, and eNOS in ACE2-expressing and -deficient ECs. ACE2-deficient ECs respond to SARS-CoV-2 through TLR4 as treatment with its antagonist inhibits p38 MAPK/NF-κB/ interleukin-1β (IL-1β) activation after viral exposure. Genome-wide, single-cell RNA-seq analyses further confirm activation of the TLR4/MAPK14/RELA/IL-1β axis in circulating ECs of mild and severe COVID-19 patients. Circulating ECs could serve as biomarkers for indicating patients with endotheliitis. Together, our findings support a direct role for SARS-CoV-2 in mediating endothelial inflammation in an ACE2-dependent or -independent manner. The majority of adult and fetal ECs rarely express surface ACE2 ACE2 is dispensable for SARS-CoV-2-mediated endothelial activation SARS-CoV-2 directly induces endothelial inflammation through TLR4 activation ScRNA-seq reveals TLR4 pathway activation in circulating ECs of COVID-19 patients
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Affiliation(s)
- Zhangjing Ma
- Department of Chemical Pathology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Xisheng Li
- Department of Chemical Pathology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Rebecca L Y Fan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kevin Y Yang
- Department of Chemical Pathology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Calvin S H Ng
- Department of Surgery, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Rainbow W H Lau
- Department of Surgery, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Randolph H L Wong
- Department of Surgery, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Kevin K Ng
- Department of Surgery, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi Chiu Wang
- Department of Obstetrics & Gynaecology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China; School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Peng Ye
- Department of Chemical Pathology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Zelong Fu
- Department of Chemical Pathology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Alex W H Chin
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - M Y Alison Lai
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yu Huang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Xiao Yu Tian
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Kathy O Lui
- Department of Chemical Pathology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
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45
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Gu H, Cheng SSM, Krishnan P, Ng DYM, Chang LDJ, Liu GYZ, Cheuk SSY, Hui MMY, Fan MCY, Wan JHL, Lau LHK, Chu DKW, Dhanasekaran V, Peiris M, Poon LLM. Monitoring International Travelers Arriving in Hong Kong for Genomic Surveillance of SARS-CoV-2. Emerg Infect Dis 2022; 28:247-250. [PMID: 34932453 PMCID: PMC8714226 DOI: 10.3201/eid2801.211804] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 01/02/2023] Open
Abstract
We sequenced ≈50% of coronavirus disease cases imported to Hong Kong during March-July 2021 and identified 70 cases caused by Delta variants of severe acute respiratory syndrome coronavirus 2. The genomic diversity detected in Hong Kong was similar to global diversity, suggesting travel hubs can play a substantial role in surveillance.
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46
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Dhanasekaran V, Edwards KM, Xie R, Gu H, Adam DC, Chang LDJ, Cheuk SSY, Gurung S, Krishnan P, Ng DYM, Liu GYZ, Wan CKC, Cheng SSM, Tsang DNC, Cowling BJ, Peiris M, Poon LLM. Air travel-related outbreak of multiple SARS-CoV-2 variants. J Travel Med 2021; 28:6372544. [PMID: 34542623 PMCID: PMC8522424 DOI: 10.1093/jtm/taab149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/20/2021] [Accepted: 09/05/2021] [Indexed: 01/12/2023]
Abstract
BACKGROUND A large cluster of 59 cases were linked to a single flight with 146 passengers from New Delhi to Hong Kong in April 2021. This outbreak coincided with early reports of exponential pandemic growth in New Delhi, which reached a peak of > 400 000 newly confirmed cases on 7 May 2021. METHODS Epidemiological information including date of symptom onset, date of positive-sample detection and travel and contact history for individual cases from this flight were collected. Whole genome sequencing was performed, and sequences were classified based on the dynamic Pango nomenclature system. Maximum-likelihood phylogenetic analysis compared sequences from this flight alongside other cases imported from India to Hong Kong on 26 flights between June 2020 and April 2021, as well as sequences from India or associated with India-related travel from February to April 2021 and 1217 reference sequences. RESULTS Sequence analysis identified six lineages of SARS-CoV-2 belonging to two variants of concern (Alpha and Delta) and one variant of public health interest (Kappa) involved in this outbreak. Phylogenetic analysis confirmed at least three independent sub-lineages of Alpha with limited onward transmission, a superspreading event comprising 37 cases of Kappa and transmission of Delta to only one passenger. Additional analysis of another 26 flights from India to Hong Kong confirmed widespread circulation of all three variants in India since early March 2021. CONCLUSIONS The broad spectrum of disease severity and long incubation period of SARS-CoV-2 pose a challenge for surveillance and control. As illustrated by this particular outbreak, opportunistic infections of SARS-CoV-2 can occur irrespective of variant lineage, and requiring a nucleic acid test within 72 hours of departure may be insufficient to prevent importation or in-flight transmission.
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Affiliation(s)
- Vijaykrishna Dhanasekaran
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kimberly M Edwards
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ruopeng Xie
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Dillon C Adam
- 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
| | - Sammi S Y Cheuk
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Shreya Gurung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, 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
| | - Gigi Y Z Liu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Carrie K C Wan
- 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
| | - Dominic N C Tsang
- Centre for Health Protection, Department of Health, The Government of Hong Kong Special Administrative Region, Hong Kong, China
| | - Benjamin J Cowling
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, 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.,HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Immunology and Infection, Hong Kong Science and Technology Park, Hong Kong, China
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Immunology and Infection, Hong Kong Science and Technology Park, Hong Kong, China
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47
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Gu H, Krishnan P, Ng DYM, Chang LDJ, Liu GYZ, Cheng SSM, Hui MMY, Fan MCY, Wan JHL, Lau LHK, Cowling BJ, Peiris M, Poon LLM. Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China, November 2021. Emerg Infect Dis 2021; 28:460-462. [PMID: 34860154 PMCID: PMC8798678 DOI: 10.3201/eid2802.212422] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We report detection of severe acute respiratory syndrome coronavirus 2 Omicron variant (B.1.1.529) in an asymptomatic, fully vaccinated traveler in a quarantine hotel in Hong Kong, China. The Omicron variant was also detected in a fully vaccinated traveler staying in a room across the corridor from the index patient, suggesting transmission despite strict quarantine precautions.
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48
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Behzadinasab S, Chin AWH, Hosseini M, Poon LLM, Ducker WA. SARS-CoV-2 virus transfers to skin through contact with contaminated solids. Sci Rep 2021; 11:22868. [PMID: 34819522 PMCID: PMC8613237 DOI: 10.1038/s41598-021-00843-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/06/2021] [Indexed: 12/20/2022] Open
Abstract
Transfer of SARS-CoV-2 from solids to fingers is one step in infection via contaminated solids, and the possibility of infection from this route has driven calls for increased frequency of handwashing during the COVID-19 pandemic. To analyze this route of infection, we measured the percentage of SARS-CoV-2 that was transferred from a solid to an artificial finger. A droplet of SARS-CoV-2 suspension (1 µL) was placed on a solid, and then artificial skin was briefly pressed against the solid with a light force (3 N). Transfer from a variety of solids was detected, and transfer from the non-porous solids, glass, stainless steel, and Teflon, was substantial when the droplet was still wet. The viral titer for the finger was 13-16% or 0.8-0.9 log less than for the input droplet. Transfer still occurred after the droplet evaporated, but was smaller, 3-9%. We found a lower level of transfer from porous solids but did not find a significant effect of solid wettability for non-porous solids.
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Affiliation(s)
- Saeed Behzadinasab
- Department of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Alex W H Chin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Mohsen Hosseini
- Department of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - William A Ducker
- Department of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, USA.
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49
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Behzadinasab S, Williams MD, Hosseini M, Poon LLM, Chin AWH, Falkinham JO, Ducker WA. Transparent and Sprayable Surface Coatings that Kill Drug-Resistant Bacteria Within Minutes and Inactivate SARS-CoV-2 Virus. ACS Appl Mater Interfaces 2021; 13:54706-54714. [PMID: 34766745 PMCID: PMC8609913 DOI: 10.1021/acsami.1c15505] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/27/2021] [Indexed: 05/05/2023]
Abstract
Antimicrobial coatings are one method to reduce the spread of microbial diseases. Transparent coatings preserve the visual properties of surfaces and are strictly necessary for applications such as antimicrobial cell phone screens. This work describes transparent coatings that inactivate microbes within minutes. The coatings are based on a polydopamine (PDA) adhesive, which has the useful property that the monomer can be sprayed, and then the monomer polymerizes in a conformal film at room temperature. Two coatings are described (1) a coating where PDA is deposited first and then a thin layer of copper is grown on the PDA by electroless deposition (PDA/Cu) and (2) a coating where a suspension of Cu2O particles in a PDA solution is deposited in a single step (PDA/Cu2O). In the second coating, PDA menisci bind Cu2O particles to the solid surface. Both coatings are transparent and are highly efficient in inactivating microbes. PDA/Cu kills >99.99% of Pseudomonas aeruginosa and 99.18% of methicillin-resistant Staphylococcus aureus (MRSA) in only 10 min and inactivates 99.98% of SARS-CoV-2 virus in 1 h. PDA/Cu2O kills 99.94% of P. aeruginosa and 96.82% of MRSA within 10 min and inactivates 99.88% of SARS-CoV-2 in 1 h.
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Affiliation(s)
- Saeed Behzadinasab
- Department of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Myra D Williams
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Mohsen Hosseini
- Department of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Alex W H Chin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, China
| | - Joseph O Falkinham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - William A Ducker
- Department of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
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50
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Abstract
We developed antimicrobial coatings from ZnO particles that reduce the infectivity of SARS-CoV-2 suspensions by >99.9% in 1 h. The advantage of a coating is that it can be applied to a variety of objects, e.g., hand rails and door knobs, to hinder the spread of disease. Two porous coatings were prepared: one from submicrometer zinc oxide particles bound with silica menisci and the other from zinc oxide tetrapods bound with polyurethane. Experiments on glass coatings show that infectivity depends on porosity for hydrophilic materials, wherein aqueous droplets are imbibed into the pores.
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Affiliation(s)
- Mohsen Hosseini
- Department of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Saeed Behzadinasab
- Department of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Alex W H Chin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, China
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, China.,HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - William A Ducker
- Department of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
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