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Shum MHH, Lee Y, Tam L, Xia H, Chung OLW, Guo Z, Lam TTY. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput Struct Biotechnol J 2024; 23:759-770. [PMID: 38304547 PMCID: PMC10831124 DOI: 10.1016/j.csbj.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.
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Affiliation(s)
- Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Yang Lee
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leighton Tam
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Hui Xia
- Department of Chemistry, South University of Science and Technology of China, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Oscar Lung-Wa Chung
- Department of Chemistry, South University of Science and Technology of China, China
| | - Zhihong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
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2
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Liu X, Wong MKL, Zhang D, Chan DCL, Chan OSK, Chan GPL, Shum MHH, Peng Y, Lai CKC, Cowling BJ, Zhang T, Fukuda K, Lam TTY, Tun HM. Longitudinal monitoring reveals the emergence and spread of bla GES-5-harboring carbapenem-resistant Klebsiella quasipneumoniae in a Hong Kong hospital wastewater discharge line. Sci Total Environ 2023; 903:166255. [PMID: 37574056 DOI: 10.1016/j.scitotenv.2023.166255] [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: 05/18/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Testing hospital wastewater (HWW) is potentially an effective, long-term approach for monitoring trends in antimicrobial resistance (AMR) patterns in health care institutions. Over a year, we collected wastewater samples from the clinical and non-clinical sites of a tertiary hospital and from a downstream wastewater treatment plant (WWTP). We focused on the extent of carbapenem resistance among Enterobacteriaceae isolates given their clinical importance. Escherichia coli and Klebsiella spp. were the most frequently isolated Enterobacteriaceae species at all sampling sites. Additionally, a small number of isolates belonging to ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species), except K. pneumoniae, were detected. Of the 232 Klebsiella spp. isolates, 100 (43.1 %) were multi-drug resistant (MDR), with 46 being carbapenem-resistant. Most of these carbapenem-resistant isolates were K. quasipneumoniae (CRKQ) (n = 44). All CRKQ isolates were isolated from the wastewater of a clinical site that includes intensive care units, which also yielded significantly more multi-drug resistant isolates compared to all other sampling sites. Among the CRKQ isolates, blaGES-5 genes (n = 42) were the primary genetic determinant of carbapenem resistance. Notably, three different CRKQ isolates, collected within the same month in HWW and the influent and effluent flow of the WWTP, shared >99 % sequence similarity between their blaGES-5 genes and between their flanking regions and upstream integron-integrase region. The influent isolate was phylogenetically close to K. quasipnuemoniae isolates from wastewater collected in Japan. Its blaGES-5 gene and surrounding sequences were > 99 % identical to blaGES-24 genes found in the Japanese isolates. Our results suggest that testing samples from sites located closer to hospitals could support antibiotic stewardship programs compared to samples collected further downstream. Moreover, testing samples collected regularly from WWTPs may reflect the local and global spread of pathogens and their resistances.
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Affiliation(s)
- Xin Liu
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; Microbiota-I Center (MagIC), Hong Kong, China; System Microbiology and Antimicrobial Resistance (SMART) Lab, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew K L Wong
- Microbiota-I Center (MagIC), Hong Kong, China; System Microbiology and Antimicrobial Resistance (SMART) Lab, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Dengwei Zhang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Darren C L Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Olivia S K Chan
- System Microbiology and Antimicrobial Resistance (SMART) Lab, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China; School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Gary P L Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Marcus Ho-Hin Shum
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong, China
| | - Ye Peng
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; Microbiota-I Center (MagIC), Hong Kong, China; System Microbiology and Antimicrobial Resistance (SMART) Lab, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Christopher K C Lai
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Benjamin J Cowling
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 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, Hong Kong, China
| | - Keiji Fukuda
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tommy Tsam-Yuk Lam
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong, China
| | - Hein M Tun
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; Microbiota-I Center (MagIC), Hong Kong, China; System Microbiology and Antimicrobial Resistance (SMART) Lab, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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3
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Yin X, Chen X, Jiang XT, Yang Y, Li B, Shum MHH, Lam TTY, Leung GM, Rose J, Sanchez-Cid C, Vogel TM, Walsh F, Berendonk TU, Midega J, Uchea C, Frigon D, Wright GD, Bezuidenhout C, Picão RC, Ahammad SZ, Nielsen PH, Hugenholtz P, Ashbolt NJ, Corno G, Fatta-Kassinos D, Bürgmann H, Schmitt H, Cha CJ, Pruden A, Smalla K, Cytryn E, Zhang Y, Yang M, Zhu YG, Dechesne A, Smets BF, Graham DW, Gillings MR, Gaze WH, Manaia CM, van Loosdrecht MCM, Alvarez PJJ, Blaser MJ, Tiedje JM, Topp E, Zhang T. Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples. Environ Sci Technol 2023. [PMID: 37310875 DOI: 10.1021/acs.est.3c00159] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health" framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts.
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Affiliation(s)
- Xiaole Yin
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam, 99077 Hong Kong, China
| | - Xi Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam, 99077 Hong Kong, China
| | - Xiao-Tao Jiang
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, 2052 Sydney, Australia
| | - Ying Yang
- School of Marine Sciences, Sun Yat-sen University, 519082 Zhuhai, China
| | - Bing Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, F518055 Shenzhen, China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, 999077 Hong Kong, China
| | - Tommy T Y Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, 999077 Hong Kong, China
| | - Gabriel M Leung
- Laboratory of Data Discovery for Health, Hong Kong Science & Technology Parks, New Territories, 99077 Hong Kong, China
| | - Joan Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, 48824 Michigan, United States
| | - Concepcion Sanchez-Cid
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université Claude Bernard Lyon1, Université de Lyon, 69130 Écully, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université Claude Bernard Lyon1, Université de Lyon, 69130 Écully, France
| | - Fiona Walsh
- Department of Biology, Maynooth University, Maynooth, R51 Co. Kildare, Ireland
| | - Thomas U Berendonk
- Faculty of Environmental Sciences, Technische Universität Dresden, Institute for Hydrobiology, 01217 Dresden, Germany
| | | | | | - Dominic Frigon
- Department of Civil Engineering and Applied Mechanics, McGill University, 817 Sherbrooke St. West, Montreal, H3A 0C3 Quebec, Canada
| | - Gerard D Wright
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, L8N 3Z5 Ontario, Canada
| | - Carlos Bezuidenhout
- Unit for Environmental Sciences and Management (UESM)-Microbiology, North-West University, 2531 Potchefstroom, South Africa
| | - Renata C Picão
- Medical Microbiology Department, Paulo de Góes Microbiology Institute of the Federal University of Rio de Janeiro, 21941-902 Rio de Janeiro, Brazil
| | - Shaikh Z Ahammad
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, 110016 New Delhi, India
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9210 Aalborg, Denmark
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Nicholas J Ashbolt
- Faculty of Science and Engineering, Southern Cross University, Bilinga, 4225 Queensland, Australia
| | - Gianluca Corno
- Molecular Ecology Group (MEG), Water Research Institute, National Research Council of Italy (CNR-IRSA), 28922 Verbania, Italy
| | - Despo Fatta-Kassinos
- Department of Civil and Environmental Engineering and Nireas International Water Research Center, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Helmut Bürgmann
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Heike Schmitt
- Centre for Zoonoses and Environmental Microbiology-Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 Bilthoven, The Netherlands
- Department of Biotechnology, Delft University of Technology, 2628 Delft, the Netherlands
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, 17546 Anseong, Republic of Korea
| | - Amy Pruden
- The Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, 24060 Virginia, United States
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Eddie Cytryn
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agricultural Research Organization, 7528809 Rishon LeZion, Israel
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China
| | - Arnaud Dechesne
- Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Barth F Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - David W Graham
- School of Engineering, Newcastle University, NE1 7RU Newcastle Upon Tyne, U.K
| | - Michael R Gillings
- School of Natural Sciences and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, 2109 New South Wales, Australia
| | - William H Gaze
- University of Exeter Medical School, Environment and Sustainability Institute, University of Exeter, TR10 9FE Cornwall, U.K
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Escola Superior de Biotecnologia, 4169-005 Porto, Portugal
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, 77005 Texas, United States
| | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, 08854 New Jersey, United States
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, 48824 Michigan, United States
| | - Edward Topp
- London Research and Development Centre (LRDC), Agriculture and Agri-Food Canada, London, N5V 4T3 Ontario, Canada
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam, 99077 Hong Kong, China
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4
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Wu WG, Shum MHH, Wong ITF, Lu KK, Lee LK, Leung JSL, Lao HY, Lee AWT, Hau PT, Chan CTM, Wong HFT, Fung SKY, Wong SCY, Ng ICF, Ng TTL, Chow N, Ho AYM, Hung MF, Chow FWN, Wong MML, To WK, Lam TTY, Luk KS, Siu GKH. Probable Airborne Transmission of Burkholderia pseudomallei Causing an Urban Outbreak of Melioidosis during Typhoon Season in Hong Kong, China. Emerg Microbes Infect 2023; 12:2204155. [PMID: 37070526 PMCID: PMC10155638 DOI: 10.1080/22221751.2023.2204155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Between January 2015 and October 2022, 38 patients with culture-confirmed melioidosis were identified in the Kowloon West (KW) Region, Hong Kong. Notably, thirty of them were clustered in the Sham Shui Po (SSP) district, which covers an estimated area of 2.5 km2. Between August and October 2022, 18 patients were identified in this district after heavy rainfall and typhoons. The sudden upsurge in cases prompted an environmental investigation, which involved collecting 20 air samples and 72 soil samples from residential areas near the patients. A viable isolate of Burkholderia pseudomallei was obtained from an air sample collected at a building site five days after a typhoon. B. pseudomallei DNA was also detected in 21 soil samples collected from the building site and adjacent gardening areas using full-length 16S rRNA gene sequencing, suggesting that B. psuedomallei is widely distributed in the soil environment surrounding the district. Core genome-multilocus sequence typing showed that the air sample isolate was phylogenetically clustered with the outbreak isolates in KW Region. Multispectral satellite imagery revealed a continuous reduction in vegetation region in SSP district by 162,255 m2 from 2016 to 2022, supporting the hypothesis of inhalation of aerosols from the contaminated soil as the transmission route of melioidosis during extreme weather events. This is because the bacteria in unvegetated soil are more easily spread by winds. In consistent with inhalational melioidosis, 24 (63.2%) patients had pneumonia. Clinicians should be aware of melioidosis during typhoon season and initiate appropriate investigation and treatment for patients with compatible symptoms.
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Affiliation(s)
- Wing-Gi Wu
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ivan Tak-Fai Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Kelvin Keru Lu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Annie Wing-Tung Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Pak-Ting Hau
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Harmen Fung-Tin Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Sharon Ka-Yee Fung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Sally Choi-Ying Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Iain Chi-Fung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Ning Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Alex Yat-Man Ho
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Mei Fan Hung
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Maureen Mo-Lin Wong
- Department of Medicine and Geriatrics/Intensive Care Unit, Caritas Medical Centre, Hong Kong Special Administrative Region, China
| | - Wing-Kin To
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kristine Shik Luk
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
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5
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Lam TTY, Jia N, Zhang YW, Shum MHH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WYM, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 2020; 583:282-285. [PMID: 32218527 DOI: 10.1101/2020.02.13.945485] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [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: 02/07/2020] [Accepted: 03/17/2020] [Indexed: 05/24/2023]
Abstract
The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-21. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection2. Although bats are probable reservoir hosts for SARS-CoV-2, the identity of any intermediate host that may have facilitated transfer to humans is unknown. Here we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses, including one that exhibits strong similarity in the receptor-binding domain to SARS-CoV-2. The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of new coronaviruses and should be removed from wet markets to prevent zoonotic transmission.
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Affiliation(s)
- Tommy Tsan-Yuk Lam
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ya-Wei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Hua-Chen Zhu
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Yi-Gang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Yong-Xia Shi
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Xue-Bing Ni
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Yun-Shi Liao
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Wen-Juan Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Wei Wei
- Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China
| | - Ting-Ting Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Kui Zheng
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Guang-Qian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Xin Qiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - William Yiu-Man Cheung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Lian-Feng Li
- School of Information and Management, Guangxi Medical University, Nanning, P. R. China
| | - Fang-Fang Sun
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Si Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ji-Cheng Huang
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Gabriel M Leung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Yan-Ling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China.
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, P. R. China.
| | - Yi Guan
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China.
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China.
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.
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Lam TTY, Jia N, Zhang YW, Shum MHH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WYM, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 2020. [DOI: 10.1038/s41586-020-2169-0 10.1101/2020.02.13.945485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Lam TTY, Jia N, Zhang YW, Shum MHH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WYM, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 2020; 583:282-285. [PMID: 32218527 DOI: 10.1038/s41586-020-2169-0] [Citation(s) in RCA: 1121] [Impact Index Per Article: 280.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/17/2020] [Indexed: 11/09/2022]
Abstract
The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-21. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection2. Although bats are probable reservoir hosts for SARS-CoV-2, the identity of any intermediate host that may have facilitated transfer to humans is unknown. Here we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses, including one that exhibits strong similarity in the receptor-binding domain to SARS-CoV-2. The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of new coronaviruses and should be removed from wet markets to prevent zoonotic transmission.
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Affiliation(s)
- Tommy Tsan-Yuk Lam
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China.,State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ya-Wei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Hua-Chen Zhu
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China.,State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Yi-Gang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Yong-Xia Shi
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Xue-Bing Ni
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Yun-Shi Liao
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Wen-Juan Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Wei Wei
- Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China
| | - Ting-Ting Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Kui Zheng
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Guang-Qian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Xin Qiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - William Yiu-Man Cheung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Lian-Feng Li
- School of Information and Management, Guangxi Medical University, Nanning, P. R. China
| | - Fang-Fang Sun
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Si Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China
| | - Ji-Cheng Huang
- Guangzhou Customs Technology Center, Guangzhou, P. R. China
| | - Gabriel M Leung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Yan-Ling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China. .,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, P. R. China.
| | - Yi Guan
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China. .,State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China.
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.
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