1
|
Krutz NL, Kimber I, Winget J, Nguyen MN, Limviphuvadh V, Maurer-Stroh S, Mahony C, Gerberick GF. Identification and semi-quantification of protein allergens in complex mixtures using proteomic and AllerCatPro 2.0 bioinformatic analyses: a proof-of-concept investigation. J Immunotoxicol 2024; 21:2305452. [PMID: 38291955 DOI: 10.1080/1547691x.2024.2305452] [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: 09/12/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
The demand for botanicals and natural substances in consumer products has increased in recent years. These substances usually contain proteins and these, in turn, can pose a risk for immunoglobulin E (IgE)-mediated sensitization and allergy. However, no method has yet been accepted or validated for assessment of potential allergenic hazards in such materials. In the studies here, a dual proteomic-bioinformatic approach is proposed to evaluate holistically allergenic hazards in complex mixtures of plants, insects, or animal proteins. Twelve commercial preparations of source materials (plant products, dust mite extract, and preparations of animal dander) known to contain allergenic proteins were analyzed by label-free proteomic analyses to identify and semi-quantify proteins. These were then evaluated by bioinformatics using AllerCatPro 2.0 (https://allercatpro.bii.a-star.edu.sg/) to predict no, weak, or strong evidence for allergenicity and similarity to source-specific allergens. In total, 4,586 protein sequences were identified in the 12 source materials combined. Of these, 1,665 sequences were predicted with weak or strong evidence for allergenic potential. This first-tier approach provided top-level information about the occurrence and abundance of proteins and potential allergens. With regards to source-specific allergens, 129 allergens were identified. The sum of the relative abundance of these allergens ranged from 0.8% (lamb's quarters) to 63% (olive pollen). It is proposed here that this dual proteomic-bioinformatic approach has the potential to provide detailed information on the presence and relative abundance of allergens, and can play an important role in identifying potential allergenic hazards in complex protein mixtures for the purposes of safety assessments.
Collapse
Affiliation(s)
- Nora L Krutz
- NV Procter & Gamble Services Company SA, Global Product Stewardship, Strombeek-Bever, Belgium
| | - Ian Kimber
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Minh N Nguyen
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute, Singapore, Singapore
| | - Vachiranee Limviphuvadh
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute, Singapore, Singapore
- Yong Loo Lin School of Medicine and Department of Biological Sciences, National University of Singapore (NUS), Singapore, Singapore
| | | | | |
Collapse
|
2
|
Goh YS, Fong SW, Tay MZ, Rouers A, Chang ZW, Chavatte JM, Hor PX, Loh CY, Huang Y, Tan YJ, Wang B, Ngoh EZX, Mohd Salleh SN, Lee RTC, Lim G, Maurer-Stroh S, Wang CI, Leo YS, Lin RTP, Lam MC, Lye DC, Young BE, Ng LFP, Renia L. Author Correction: Higher Delta variant-specific neutralizing antibodies prevented infection in close contacts vaccinated with ancestral mRNA vaccines during the SARS-CoV-2 Delta wave. Sci Rep 2024; 14:1492. [PMID: 38233454 PMCID: PMC10794195 DOI: 10.1038/s41598-024-51484-y] [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: 01/19/2024] Open
Affiliation(s)
- Yun Shan Goh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Matthew Zirui Tay
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Angeline Rouers
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Zi Wei Chang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Jean-Marc Chavatte
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Pei Xiang Hor
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Chiew Yee Loh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Yuling Huang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Yong Jie Tan
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Bei Wang
- Singapore Immunology Network, A*STAR, Singapore, Singapore
| | | | | | - Raphael Tze Chuen Lee
- Bioinformatics Institute, A*STAR, Singapore, Singapore
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
| | | | - Sebastian Maurer-Stroh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
- Bioinformatics Institute, A*STAR, Singapore, Singapore
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Cheng-I Wang
- Singapore Immunology Network, A*STAR, Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - David C Lye
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute of Health Research, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| |
Collapse
|
3
|
Karnaneedi S, Limviphuvadh V, Maurer-Stroh S, Lopata AL. De Novo Transcriptomic Analyses to Identify and Compare Allergens in Foods. Methods Mol Biol 2024; 2717:351-365. [PMID: 37737997 DOI: 10.1007/978-1-0716-3453-0_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Food allergens have been traditionally identified using biomolecular and immunological approaches. However, the techniques used in extracting proteins from the food source to be analyzed may hinder the availability of all proteins when assessing immunological allergenicity. Additionally, depending on the number and pool of patient sera used to detect the IgE antibody-binding allergens, some allergens may not be detected if not all the patients in the pool are sensitized to all the allergens. To overcome these limitations, we describe an additional approach before the in vitro approaches, by analyzing the transcriptome in silico for all putative allergens within the analyzed food source.
Collapse
Affiliation(s)
- Shaymaviswanathan Karnaneedi
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia.
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia.
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Melbourne, VIC, Australia.
| | - Vachiranee Limviphuvadh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
- IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
- IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Andreas L Lopata
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Tropical Futures Institute, James Cook University Singapore, Singapore, Singapore
| |
Collapse
|
4
|
Goh YS, Fong SW, Hor PX, Loh CY, Wang B, Salleh SNM, Ngoh EZX, Lee RTC, Poh XY, Rao S, Chia PY, Ong SWX, Lee TH, Lim C, Teo J, Pada S, Sun LJ, Ong DLS, Somani J, Lee ES, Maurer-Stroh S, Wang CI, Leo YS, Lye DC, Young BE, Ng LFP, Renia L. Variant-specific IgA protects against Omicron infection. J Infect Dis 2023:jiad525. [PMID: 37996071 DOI: 10.1093/infdis/jiad525] [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: 09/01/2023] [Revised: 10/25/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND The emergence of rapidly evolving SARS-CoV-2 variants, coupled with waning vaccine-induced immunity, has contributed to the rise of vaccine breakthrough infections. It is crucial to understand how vaccine-induced protection is mediated. METHODS We examined two prospective cohorts of mRNA-vaccinated-and-boosted individuals during the Omicron wave of infection in Singapore. RESULTS We found that, individuals, who remain uninfected over the follow-up period, had a higher variant-specific IgA, but not IgG, antibody response at 1-month post booster vaccination, compared with individuals who became infected. CONCLUSIONS We conclude that IgA may have a potential contributory role in protection against Omicron infection.
Collapse
Affiliation(s)
- Yun Shan Goh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Pei Xiang Hor
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chiew Yee Loh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Bei Wang
- Singapore Immunology Network, A*STAR, Singapore
| | | | | | - Raphael Tze Chuen Lee
- Bioinformatics Institute, A*STAR, Singapore
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
| | | | - Suma Rao
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
| | - Po Ying Chia
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Sean W X Ong
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
| | - Tau Hong Lee
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
| | - Clarissa Lim
- National Centre for Infectious Diseases, Singapore
| | - Jefanie Teo
- National Centre for Infectious Diseases, Singapore
| | | | | | | | - Jyoti Somani
- Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore
| | - Eng Sing Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- National Healthcare Group Polyclinics, Singapore
| | - Sebastian Maurer-Stroh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
- Bioinformatics Institute, A*STAR, Singapore
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
- National Public Health Laboratory, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - David C Lye
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool UK
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| |
Collapse
|
5
|
Goh YS, Fong SW, Tay MZ, Rouers A, Chang ZW, Chavatte JM, Hor PX, Loh CY, Huang Y, Tan YJ, Wang B, Ngoh EZX, Mohd Salleh SN, Lee RTC, Lim G, Maurer-Stroh S, Wang CI, Leo YS, Lin RTP, Lam MC, Lye DC, Young BE, Ng LFP, Renia L. Higher Delta variant-specific neutralizing antibodies prevented infection in close contacts vaccinated with ancestral mRNA vaccines during the SARS-CoV-2 Delta wave. Sci Rep 2023; 13:19331. [PMID: 37935965 PMCID: PMC10630438 DOI: 10.1038/s41598-023-46800-x] [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: 06/20/2023] [Accepted: 11/05/2023] [Indexed: 11/09/2023] Open
Abstract
Identification of the risk factors and the high-risk groups which are most vulnerable is critical in COVID-19 disease management at a population level. Evaluating the efficacy of vaccination against infections is necessary to determine booster vaccination strategies for better protection in high-risk groups. In this study, we recruited 158 mRNA-vaccinated individuals during the Delta wave of SARS-CoV-2 infections in Singapore and examined the antibody profiles of infected individuals. We found that, despite high exposure due to communal living conditions in proximity, 4% of individuals (6/158) had PCR-confirmed infections and 96% (152/158) remained uninfected. Time-course analysis of the antibody profile at the start and the end of quarantine period showed Delta-specific boosting of anti-spike antibody response in 57% of the uninfected individuals (86/152). In the remaining 43% of the uninfected individuals (66/152) with no Delta-specific antibody boost, we found a higher Delta-specific antibody response at the start of quarantine period, which correlated with higher Delta pseudovirus neutralizing capacity. Our findings indicate that a higher basal variant-specific antibody response in the mRNA-vaccinated individuals contributes to better protection against infections by the new emerging SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Yun Shan Goh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Matthew Zirui Tay
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Angeline Rouers
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Zi Wei Chang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Jean-Marc Chavatte
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Pei Xiang Hor
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Chiew Yee Loh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Yuling Huang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Yong Jie Tan
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Bei Wang
- Singapore Immunology Network, A*STAR, Singapore, Singapore
| | | | | | - Raphael Tze Chuen Lee
- Bioinformatics Institute, A*STAR, Singapore, Singapore
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
| | | | - Sebastian Maurer-Stroh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
- Bioinformatics Institute, A*STAR, Singapore, Singapore
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Cheng-I Wang
- Singapore Immunology Network, A*STAR, Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - David C Lye
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute of Health Research, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| |
Collapse
|
6
|
Krutz NL, Kimber I, Winget J, Nguyen MN, Limviphuvadh V, Maurer-Stroh S, Mahony C, Gerberick GF. Application of AllerCatPro 2.0 for protein safety assessments of consumer products. Front Allergy 2023; 4:1209495. [PMID: 37497076 PMCID: PMC10367106 DOI: 10.3389/falgy.2023.1209495] [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: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 07/28/2023] Open
Abstract
Foreign proteins are potentially immunogenic, and a proportion of these are able to induce immune responses that result in allergic sensitization. Subsequent exposure of sensitized subjects to the inducing protein can provoke a variety of allergic reactions that may be severe, or even fatal. It has therefore been recognized for some time that it is important to determine a priori whether a given protein has the potential to induce allergic responses in exposed subjects. For example, the need to assess whether transgene products expressed in genetically engineered crop plants have allergenic properties. This is not necessarily a straightforward exercise (as discussed elsewhere in this edition), but the task becomes even more challenging when there is a need to conduct an overall allergenicity safety assessment of complex mixtures of proteins in botanicals or other natural sources that are to be used in consumer products. This paper describes a new paradigm for the allergenicity safety assessment of proteins that is based on the use of AllerCatPro 2.0, a new version of a previously described web application model developed for the characterization of the allergenic potential of proteins. Operational aspects of AllerCatPro 2.0 are described with emphasis on the application of new features that provide improvements in the predictions of allergenic properties such as the identification of proteins with high allergenic concern. Furthermore, the paper provides a description of strategies of how AllerCatPro 2.0 can best be deployed as a screening tool for identifying suitable proteins as ingredients in consumer products as well as a tool, in conjunction with label-free proteomic analysis, for identifying and semiquantifying protein allergens in complex materials. Lastly, the paper discusses the steps that are recommended for formal allergenicity safety assessment of novel consumer products which contain proteins, including consideration and integration of predicted consumer exposure metrics. The article therefore provides a holistic perspective of the processes through which effective protein safety assessments can be made of potential allergenic hazards and risks associated with exposure to proteins in consumer products, with a particular focus on the use of AllerCatPro 2.0 for this purpose.
Collapse
Affiliation(s)
- Nora L. Krutz
- NV Procter & Gamble Services Company SA, Global Product Stewardship, Strombeek-Bever, Belgium
| | - Ian Kimber
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Jason Winget
- The Procter & Gamble Company, Mason, OH, United States
| | - Minh N. Nguyen
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Vachiranee Limviphuvadh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- YLL School of Medicine and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Catherine Mahony
- Procter & Gamble, Global Product Stewardship, Reading, United Kingdom
| | | |
Collapse
|
7
|
Dung NT, Hung LM, Hoa HTT, Nga LH, Hong NTT, Thuong TC, Ngoc NM, Ny NTH, Quy VT, Thoa VTK, Thanh NT, Tho PV, Toan LM, Quang VM, Man DNH, Phat NT, Phuong TTL, Tam TTT, Thoa PTN, Tam NH, Lan TTT, Thanh TT, Maurer-Stroh S, Khanh LTT, Yen LM, Hung NH, Thwaites G, Tung NLN, Thwaites L, Chau NVV, Anh NT, Van Tan L. Monkeypox Virus Infection in 2 Female Travelers Returning to Vietnam from Dubai, United Arab Emirates, 2022. Emerg Infect Dis 2023; 29:778-781. [PMID: 36696624 PMCID: PMC10045713 DOI: 10.3201/eid2904.221835] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Mpox was diagnosed in 2 women returning to Vietnam from the United Arab Emirates. The monkeypox viruses belonged to an emerging sublineage, A.2.1, distinct from B.1, which is responsible for the ongoing multicountry outbreak. Women could contribute to mpox transmission, and enhanced genomic surveillance is needed to clarify pathogen evolution.
Collapse
|
8
|
Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou X, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RTC, Freitas L, Maurer-Stroh S, Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nat Methods 2023; 20:512-522. [PMID: 36823332 PMCID: PMC10399614 DOI: 10.1038/s41592-023-01769-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 78.0] [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: 06/03/2022] [Accepted: 01/17/2023] [Indexed: 02/25/2023]
Abstract
In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info , a platform that currently tracks over 40 million combinations of Pango lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials and the general public. We describe the interpretable visualizations available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data and the server infrastructure that enables widespread data dissemination via a high-performance API that can be accessed using an R package. We show how outbreak.info can be used for genomic surveillance and as a hypothesis-generation tool to understand the ongoing pandemic at varying geographic and temporal scales.
Collapse
Affiliation(s)
- Karthik Gangavarapu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Alaa Abdel Latif
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Julia L Mullen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Manar Alkuzweny
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ginger Tsueng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Haag
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karina Zaiets
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marco Cano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Xinghua Zhou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Zhongchao Qian
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rachel Sattler
- Skaggs Graduate School of Biological and Chemical Sciences, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Raphael T C Lee
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Lucas Freitas
- GISAID Global Data Science Initiative, Munich, Germany
- Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Ministry of Health, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Chunlei Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew I Su
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, La Jolla, CA, USA
| | - Laura D Hughes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
9
|
Ng OT, Koh V, Chiew CJ, Marimuthu K, Thevasagayam NM, Mak TM, Chua JK, Hui Ong SS, Lim YK, Ferdous Z, Khairunnisa Bte Johari A, I-Cheng Chen M, Maurer-Stroh S, Cui L, Pin Lin RT, Tan KB, Cook AR, Leo PYS, Lee PVJM. Erratum to "Impact of delta variant and vaccination on SARS-CoV-2 secondary attack rate among household close contacts" [The Lancet Regional Health - Western Pacific 17 (2021) 100299]. Lancet Reg Health West Pac 2023; 33:100748. [PMID: 36945675 PMCID: PMC10022472 DOI: 10.1016/j.lanwpc.2023.100748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
[This corrects the article DOI: 10.1016/j.lanwpc.2021.100299.].
Collapse
Affiliation(s)
- Oon Tek Ng
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Vanessa Koh
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
| | - Calvin J Chiew
- Communicable Diseases Division, Ministry of Health, Singapore
| | - Kalisvar Marimuthu
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | | | - Tze Minn Mak
- National Centre for Infectious Diseases, Singapore
| | | | | | | | - Zannatul Ferdous
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
| | | | - Mark I-Cheng Chen
- National Centre for Infectious Diseases, Singapore
- Communicable Diseases Division, Ministry of Health, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Sebastian Maurer-Stroh
- National Centre for Infectious Diseases, Singapore
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore
- Infectious Diseases Labs, Agency for Science Technology and Research, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore
| | - Raymond Tzer Pin Lin
- National Centre for Infectious Diseases, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Kelvin Bryan Tan
- Ministry of Health, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
- Centre for Regulatory Excellence, Duke-NUS Medical School
| | - Alex R Cook
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Prof Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Prof Vernon J M Lee
- Communicable Diseases Division, Ministry of Health, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| |
Collapse
|
10
|
Tay MZ, Goh YS, Fong SW, Chang ZW, Rouers A, Wong N, Torres-Ruesta A, Huang Y, Selvam SK, Hor PX, Loh CY, Wang B, Mohd Salleh SN, Ngoh EZX, Lee RTC, Neo V, Kam IKJ, Poh XY, Rao S, Chia PY, Ong SW, Lee TH, Lim C, Teo J, Maurer-Stroh S, Wang CI, Leo YS, Lin RTP, Lye DC, Young BE, Ng LF, Renia L. Heterologous mRNA vaccine boosters induce a stronger and longer-lasting antibody response against Omicron XBB variant. Lancet Reg Health West Pac 2023; 33:100732. [PMID: 37125085 PMCID: PMC9988436 DOI: 10.1016/j.lanwpc.2023.100732] [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] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 03/09/2023]
Affiliation(s)
- Matthew Zirui Tay
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Yun Shan Goh
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Siew-Wai Fong
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Zi Wei Chang
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Angeline Rouers
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Nathan Wong
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Anthony Torres-Ruesta
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Yuling Huang
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Sooriya Kannan Selvam
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Pei Xiang Hor
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Chiew Yee Loh
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Bei Wang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Siti Nazihah Mohd Salleh
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Eve Zi Xian Ngoh
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Raphael Tze Chuen Lee
- Bioinformatics Institute (BII), Agency of Science, Technology and Research (A∗STAR), Singapore, Singapore,GISAID Global Data Science Initiative (GISAID), Munich, Germany
| | - Vanessa Neo
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Isaac Kai Jie Kam
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Xuan Ying Poh
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Suma Rao
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Po Ying Chia
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sean W.X. Ong
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tau Hong Lee
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Clarissa Lim
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Jefanie Teo
- National Centre for Infectious Diseases, Singapore, Singapore
| | | | - PRIBIVAC Cohort Study Group
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Sebastian Maurer-Stroh
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore,Bioinformatics Institute (BII), Agency of Science, Technology and Research (A∗STAR), Singapore, Singapore,GISAID Global Data Science Initiative (GISAID), Munich, Germany,National Public Health Laboratory, Singapore, Singapore,Department of Biological Sciences, National University of Singapore, Singapore, Singapore,Human Potential Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Cheng-I Wang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Raymond Tzer Pin Lin
- National Centre for Infectious Diseases, Singapore, Singapore,National Public Health Laboratory, Singapore, Singapore,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - David C. Lye
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Lisa F.P. Ng
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore,National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK,Corresponding author. Lisa F.P. Ng, A∗STAR ID Labs, A∗STAR, 8A Biomedical Grove, Immunos #05-13, Singapore 138648, Singapore
| | - Laurent Renia
- A∗STAR Infectious Diseases Labs (A∗STAR ID Labs), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore,Corresponding author. Laurent Renia, A∗STAR ID Labs, A∗STAR, 8A Biomedical Grove, Immunos #05-13, Singapore 138648, Singapore
| |
Collapse
|
11
|
Cable J, Denison MR, Kielian M, Jackson WT, Bartenschlager R, Ahola T, Mukhopadhyay S, Fremont DH, Kuhn RJ, Shannon A, Frazier MN, Yuen KY, Coyne CB, Wolthers KC, Ming GL, Guenther CS, Moshiri J, Best SM, Schoggins JW, Jurado KA, Ebel GD, Schäfer A, Ng LFP, Kikkert M, Sette A, Harris E, Wing PAC, Eggenberger J, Krishnamurthy SR, Mah MG, Meganck RM, Chung D, Maurer-Stroh S, Andino R, Korber B, Perlman S, Shi PY, Bárcena M, Aicher SM, Vu MN, Kenney DJ, Lindenbach BD, Nishida Y, Rénia L, Williams EP. Positive-strand RNA viruses-a Keystone Symposia report. Ann N Y Acad Sci 2023; 1521:46-66. [PMID: 36697369 PMCID: PMC10347887 DOI: 10.1111/nyas.14957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Positive-strand RNA viruses have been the cause of several recent outbreaks and epidemics, including the Zika virus epidemic in 2015, the SARS outbreak in 2003, and the ongoing SARS-CoV-2 pandemic. On June 18-22, 2022, researchers focusing on positive-strand RNA viruses met for the Keystone Symposium "Positive-Strand RNA Viruses" to share the latest research in molecular and cell biology, virology, immunology, vaccinology, and antiviral drug development. This report presents concise summaries of the scientific discussions at the symposium.
Collapse
Affiliation(s)
| | - Mark R Denison
- Department of Pediatrics and Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; and Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, Tennessee, USA
| | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - William T Jackson
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University and German Cancer Research Center (DKFZ), Research Division Virus-associated Carcinogenesis, Heidelberg, Germany
| | - Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | | | - Daved H Fremont
- Department of Pathology & Immunology; Department of Molecular Microbiology; and Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Ashleigh Shannon
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix Marseille Université, Marseille, France
| | - Meredith N Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine and State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, People's Republic of China
| | - Carolyn B Coyne
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Katja C Wolthers
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam and Amsterdam Institute for Infection and Immunity, OrganoVIR Labs, Amsterdam, The Netherlands
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Jasmine Moshiri
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Sonja M Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kellie Ann Jurado
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory D Ebel
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lisa F P Ng
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR), Singapore City, Singapore
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Peter A C Wing
- Nuffield Department of Medicine and Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Julie Eggenberger
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology and NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Marcus G Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore City, Singapore
| | - Rita M Meganck
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Donghoon Chung
- Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, Texas, USA
| | - Sebastian Maurer-Stroh
- Yong Loo Lin School of Medicine and Department of Biological Sciences, National University of Singapore, Singapore City, Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore City, Singapore
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, and Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Montserrat Bárcena
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sophie-Marie Aicher
- Institut Pasteurgrid, Université de Paris Cité, Virus Sensing and Signaling Unit, Paris, France
| | - Michelle N Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Devin J Kenney
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yukiko Nishida
- Chugai Pharmaceutical, Co., Tokyo, Japan
- Lee Kong Chian School of Medicine and School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Laurent Rénia
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR), Singapore City, Singapore
| | - Evan P Williams
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, Tennessee, USA
| |
Collapse
|
12
|
Ngiam JN, Al-Mubaarak A, Maurer-Stroh S, Tambyah PA. Does the COVID-19 XBB Omicron subvariant signal the beginning of the end of the pandemic? Singapore Med J 2022; 0:367847. [PMID: 36648003 DOI: 10.4103/singaporemedj.smj-2022-180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
All pandemic viruses have eventually adapted to human hosts so that they become more transmissible and less virulent. The XBB Omicron subvariant is rapidly becoming the dominant strain of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Singapore from October 2022 and is one of several variants circulating globally with the potential to dominate autumn/winter waves in different countries. The XBB Omicron subvariant has demonstrated increased transmissibility through an apparent propensity for immune evasion. This is to be expected in the natural evolution of a virus in a population highly vaccinated with a vaccine targeting the spike protein of the original Wuhan strain of the virus. This review explores the important implications of the rising prevalence of the SARS-CoV-2 Omicron subvariant for public health in Singapore and beyond.
Collapse
Affiliation(s)
- Jinghao Nicholas Ngiam
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore
| | - Abdurrahmaan Al-Mubaarak
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute and Infectious Diseases Labs, Agency for Science Technology and Research; Department of Biological Sciences, Singapore
| | - Paul Anantharajah Tambyah
- Division of Infectious Diseases, Department of Medicine, National University Health System; Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| |
Collapse
|
13
|
Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Global disparities in SARS-CoV-2 genomic surveillance. Nat Commun 2022; 13:7003. [PMID: 36385137 PMCID: PMC9667854 DOI: 10.1038/s41467-022-33713-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [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: 01/29/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022] Open
Abstract
Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity.
Collapse
Affiliation(s)
- Anderson F Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Instituto Todos pela Saúde, São Paulo, SP, Brazil.
| | | | - Gytis Dudas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gabriel W Hassler
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale School of Medicine, Yale University, New Haven, CT, USA
| | | | - Joses Ho
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Charles N Agoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Lucy E Matkin
- Department of Biology, University of Oxford, Oxford, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | | | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Neta S Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Fernando R Spilki
- Feevale University, Institute of Health Sciences, Novo Hamburgo, RS, Brazil
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivan N Ivanov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivva Philipova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Christine V F Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nikita S D Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Ben Branda
- GISAID Global Data Science Initiative, Munich, Germany
| | - Céline Gurry
- GISAID Global Data Science Initiative, Munich, Germany
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Dhamari Naidoo
- Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India
| | - Karin J von Eije
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Mark D Perkins
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Maria van Kerkhove
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | | | - Ester C Sabino
- Instituto Todos pela Saúde, São Paulo, SP, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Royal Veterinary College, Hawkshead, UK
| | | | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Marc A Suchard
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R Faria
- Department of Biology, University of Oxford, Oxford, UK.
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK.
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
| |
Collapse
|
14
|
Goh YS, Rouers A, Fong SW, Zhuo NZ, Hor PX, Loh CY, Huang Y, Neo VK, Kam IKJ, Wang B, Ngoh EZX, Salleh SNM, Lee RTC, Pada S, Sun LJ, Ong DLS, Somani J, Lee ES, Maurer-Stroh S, Wang CI, Leo Y, Ren EC, Lye DC, Young BE, Ng LFP, Renia L. Waning of specific antibodies against Delta and Omicron variants five months after a third dose of BNT162b2 SARS-CoV-2 vaccine in elderly individuals. Front Immunol 2022; 13:1031852. [PMID: 36451833 PMCID: PMC9704817 DOI: 10.3389/fimmu.2022.1031852] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/21/2022] [Indexed: 07/30/2023] Open
Abstract
The emergence of new SARS-CoV-2 variants, such as the more transmissible Delta and Omicron variants, has raised concerns on efficacy of the COVID-19 vaccines. Here, we examined the waning of antibody responses against different variants following primary and booster vaccination. We found that antibody responses against variants were low following primary vaccination. The antibody response against Omicron was almost non-existent. Efficient boosting of antibody response against all variants, including Omicron, was observed following a third dose. The antibody response against the variants tested was significantly higher at one month following booster vaccination, compared with two months following primary vaccination, for all individuals, including the low antibody responders identified at two months following primary vaccination. The antibody response, for all variants tested, was significantly higher at four months post booster than at five months post primary vaccination, and the proportion of low responders remained low (6-11%). However, there was significant waning of antibody response in more than 95% of individuals at four months, compared to one month following booster. We also observed a robust memory B cell response following booster, which remained higher at four months post booster than prior to booster. However, the memory B cell responses were on the decline for 50% of individuals at four months following booster. Similarly, while the T cell response is sustained, at cohort level, at four months post booster, a substantial proportion of individuals (18.8 - 53.8%) exhibited T cell response at four months post booster that has waned to levels below their corresponding levels before booster. The findings show an efficient induction of immune response against SARS-CoV-2 variants following booster vaccination. However, the induced immunity by the third BNT162b2 vaccine dose was transient. The findings suggest that elderly individuals may require a fourth dose to provide protection against SARS-CoV-2.
Collapse
Affiliation(s)
- Yun Shan Goh
- ASTAR Infectious Diseases Labs (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Angeline Rouers
- ASTAR Infectious Diseases Labs (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Siew-Wai Fong
- ASTAR Infectious Diseases Labs (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Nicole Ziyi Zhuo
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Pei Xiang Hor
- ASTAR Infectious Diseases Labs (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Chiew Yee Loh
- ASTAR Infectious Diseases Labs (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Yuling Huang
- ASTAR Infectious Diseases Labs (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Vanessa Kexin Neo
- ASTAR Infectious Diseases Labs (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Isaac Kai Jie Kam
- ASTAR Infectious Diseases Labs (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Bei Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Eve Zi Xian Ngoh
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siti Nazihah Mohd Salleh
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Raphael Tze Chuen Lee
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Global Data Science Initiative (GISAID), Munich, Germany
| | - Surinder Pada
- Infectious Diseases, Ng Teng Fong General Hospital, Singapore, Singapore
| | - Louisa Jin Sun
- Infectious Diseases, Alexandra Hospital, Singapore, Singapore
| | | | - Jyoti Somani
- Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Eng Sing Lee
- Clinical Research Unit, National Healthcare Group Polyclincs, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | | | | | - Sebastian Maurer-Stroh
- ASTAR Infectious Diseases Labs (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Global Data Science Initiative (GISAID), Munich, Germany
- National Public Health Laboratory, National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Cheng-I Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yee‐Sin Leo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ee Chee Ren
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - David C. Lye
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Barnaby Edward Young
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Lisa F. P. Ng
- ASTAR Infectious Diseases Labs (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, United Kingdom
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Laurent Renia
- ASTAR Infectious Diseases Labs (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
15
|
Chan SH, Bylstra Y, Teo JX, Kuan JL, Bertin N, Gonzalez-Porta M, Hebrard M, Tirado-Magallanes R, Tan JHJ, Jeyakani J, Li Z, Chai JF, Chong YS, Davila S, Goh LL, Lee ES, Wong E, Wong TY, Prabhakar S, Liu J, Cheng CY, Eisenhaber B, Karnani N, Leong KP, Sim X, Yeo KK, Chambers JC, Tai ES, Tan P, Jamuar SS, Ngeow J, Lim WK, Gluckman PD, Goh DLM, Jain K, Kam S, Kassam I, Lakshmanan LN, Lee CG, Lee J, Lee SC, Lee YS, Li H, Lim CW, Lim TH, Loh M, Maurer-Stroh S, Mina TH, Mok SQ, Ng HK, Pua CJ, Riboli E, Rim TH, Sabanayagam C, Sim WC, Subramaniam T, Tan ES, Tan EK, Tantoso E, Tay D, Teo YY, Tham YC, Toh LXG, Tsai PK, van Dam RM, Veeravalli L, Khin-lin GW, Wilm A, Yang C, Yap F, Yew YW, Prabhakar S, Liu J, Cheng CY, Eisenhaber B, Karnani N, Leong KP, Sim X, Yeo KK, Chambers JC, Tai ES, Tan P, Jamuar SS, Ngeow J, Lim WK. Analysis of clinically relevant variants from ancestrally diverse Asian genomes. Nat Commun 2022; 13:6694. [PMID: 36335097 PMCID: PMC9637116 DOI: 10.1038/s41467-022-34116-9] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Asian populations are under-represented in human genomics research. Here, we characterize clinically significant genetic variation in 9051 genomes representing East Asian, South Asian, and severely under-represented Austronesian-speaking Southeast Asian ancestries. We observe disparate genetic risk burden attributable to ancestry-specific recurrent variants and identify individuals with variants specific to ancestries discordant to their self-reported ethnicity, mostly due to cryptic admixture. About 27% of severe recessive disorder genes with appreciable carrier frequencies in Asians are missed by carrier screening panels, and we estimate 0.5% Asian couples at-risk of having an affected child. Prevalence of medically-actionable variant carriers is 3.4% and a further 1.6% harbour variants with potential for pathogenic classification upon additional clinical/experimental evidence. We profile 23 pharmacogenes with high-confidence gene-drug associations and find 22.4% of Asians at-risk of Centers for Disease Control and Prevention Tier 1 genetic conditions concurrently harbour pharmacogenetic variants with actionable phenotypes, highlighting the benefits of pre-emptive pharmacogenomics. Our findings illuminate the diversity in genetic disease epidemiology and opportunities for precision medicine for a large, diverse Asian population.
Collapse
Affiliation(s)
- Sock Hoai Chan
- grid.410724.40000 0004 0620 9745Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610 Singapore ,grid.428397.30000 0004 0385 0924Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857 Singapore ,grid.59025.3b0000 0001 2224 0361Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232 Singapore
| | - Yasmin Bylstra
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore
| | - Jing Xian Teo
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore
| | - Jyn Ling Kuan
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore
| | - Nicolas Bertin
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Mar Gonzalez-Porta
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Maxime Hebrard
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Roberto Tirado-Magallanes
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Joanna Hui Juan Tan
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Justin Jeyakani
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Zhihui Li
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Jin Fang Chai
- grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549 Singapore
| | - Yap Seng Chong
- grid.4280.e0000 0001 2180 6431Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore ,grid.452264.30000 0004 0530 269XSingapore Institute for Clinical Sciences, Singapore, 117609 Singapore
| | - Sonia Davila
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.428397.30000 0004 0385 0924Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore, 169857 Singapore ,grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Genomic Medicine Centre, Singapore, 168582 Singapore
| | - Liuh Ling Goh
- grid.240988.f0000 0001 0298 8161Personalized Medicine Service, Tan Tock Seng Hospital, Singapore, 308433 Singapore
| | - Eng Sing Lee
- grid.59025.3b0000 0001 2224 0361Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232 Singapore ,grid.466910.c0000 0004 0451 6215National Healthcare Group Polyclinics, Singapore, 138543 Singapore
| | - Eleanor Wong
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Tien Yin Wong
- grid.419272.b0000 0000 9960 1711Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 168751 Singapore
| | | | - Shyam Prabhakar
- grid.418377.e0000 0004 0620 715XLaboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Jianjun Liu
- grid.418377.e0000 0004 0620 715XHuman Genomics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore
| | - Ching-Yu Cheng
- grid.419272.b0000 0000 9960 1711Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 168751 Singapore ,grid.428397.30000 0004 0385 0924Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, 169857 Singapore
| | - Birgit Eisenhaber
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore ,grid.418325.90000 0000 9351 8132Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, 138671 Singapore
| | - Neerja Karnani
- grid.452264.30000 0004 0530 269XHuman Development, Singapore Institute for Clinical Sciences, Singapore, 117609 Singapore ,grid.418325.90000 0000 9351 8132Clinical Data Engagement, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, 138671 Singapore ,grid.4280.e0000 0001 2180 6431Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596 Singapore
| | - Khai Pang Leong
- grid.240988.f0000 0001 0298 8161Personalized Medicine Service, Tan Tock Seng Hospital, Singapore, 308433 Singapore ,grid.240988.f0000 0001 0298 8161Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore, 308433 Singapore
| | - Xueling Sim
- grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549 Singapore
| | - Khung Keong Yeo
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.419385.20000 0004 0620 9905Department of Cardiology, National Heart Centre Singapore, Singapore, 169609 Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, 169857 Singapore
| | - John C. Chambers
- grid.59025.3b0000 0001 2224 0361Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232 Singapore ,Precision Health Research Singapore (PRECISE), Singapore, 139234 Singapore ,grid.7445.20000 0001 2113 8111Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG UK
| | - E-Shyong Tai
- grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549 Singapore ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, 169857 Singapore ,Precision Health Research Singapore (PRECISE), Singapore, 139234 Singapore
| | - Patrick Tan
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore ,Precision Health Research Singapore (PRECISE), Singapore, 139234 Singapore ,grid.428397.30000 0004 0385 0924Cancer & Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857 Singapore ,grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599 Singapore
| | - Saumya S. Jamuar
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Genomic Medicine Centre, Singapore, 168582 Singapore ,grid.414963.d0000 0000 8958 3388Genetics Service, Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore, 229899 Singapore ,grid.428397.30000 0004 0385 0924Paediatric Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857 Singapore
| | - Joanne Ngeow
- grid.410724.40000 0004 0620 9745Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610 Singapore ,grid.428397.30000 0004 0385 0924Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857 Singapore ,grid.59025.3b0000 0001 2224 0361Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232 Singapore ,grid.185448.40000 0004 0637 0221Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore, 138673 Singapore
| | - Weng Khong Lim
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Genomic Medicine Centre, Singapore, 168582 Singapore ,grid.428397.30000 0004 0385 0924Cancer & Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857 Singapore
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Bose U, Broadbent JA, Juhász A, Karnaneedi S, Johnston EB, Stockwell S, Byrne K, Limviphuvadh V, Maurer-Stroh S, Lopata AL, Colgrave ML. Comparison of protein extraction protocols and allergen mapping from black soldier fly Hermetia illucens. J Proteomics 2022; 269:104724. [PMID: 36096435 DOI: 10.1016/j.jprot.2022.104724] [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: 03/26/2022] [Revised: 05/25/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022]
Abstract
Exploration of important insect proteins - including allergens - and proteomes can be limited by protein extraction buffer selection and the complexity of the proteome. Herein, LC-MS/MS-based proteomics experiments were used to assess the protein extraction efficiencies for a suite of extraction buffers and the effect of ingredient processing on proteome and allergen detection. Discovery proteomics revealed that SDS-based buffer yields the maximum number of protein groups from three types of BSF samples. Bioinformatic analysis revealed that buffer composition and ingredient processing could influence allergen detection. Upon applying multi-level filtering criteria, 33 putative allergens were detected by comparing the detected BSF proteins to sequences from public allergen protein databases. A targeted LC-MRM-MS assay was developed for the pan-allergen tropomyosin and used to assess the influence of buffer composition and ingredient processing using peptide abundance measurements. SIGNIFICANCE: We demonstrated that the selection of protein extraction buffer and the processing method could influence protein yield and cross-reactive allergen detection from processed and un-processed black soldier fly (BSF) samples. In total, 33 putative allergens were detected by comparing the detected BSF proteins to sequences from public allergen protein databases. An LC-MRM-MS assay was developed for tropomyosin, indicating the importance of buffer selection and processing conditions to reduce BSF samples' allergenicity.
Collapse
Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - James A Broadbent
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Shaymaviswanathan Karnaneedi
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Elecia B Johnston
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Sally Stockwell
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Vachiranee Limviphuvadh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore; IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore
| | - Sebastian Maurer-Stroh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore; IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore; Department of Biological Sciences, National University of Singapore, Singapore
| | - Andreas L Lopata
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia; Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore; Tropical Futures Institute, James Cook University-, Singapore, Singapore
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia.
| |
Collapse
|
17
|
Goh YS, Fong SW, Rouers A, Chang ZW, Tay MZ, Chavatte JM, Zhuo NZ, Hor PX, Loh CY, Huang Y, Wong JXE, Tan YJ, Lim DRX, Wang B, Ngoh EZX, Salleh SNM, Lee RTC, Pada S, Sun LJ, Ong DLS, Somani J, Lee ES, Maurer-Stroh S, Wang CI, Leo YS, Lin RT, Ren EC, Lye DC, Young BE, Lim PL, Ng LF, Renia L. Heterologous booster vaccination with CoronaVac following prime vaccination with mRNA vaccine. Clin Transl Immunology 2022; 11:e1403. [PMID: 36016852 PMCID: PMC9398778 DOI: 10.1002/cti2.1403] [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: 04/23/2022] [Revised: 06/07/2022] [Accepted: 06/21/2022] [Indexed: 12/03/2022] Open
Abstract
Objective Despite the high vaccine efficacy of mRNA COVID‐19 vaccines, there are individuals who developed excessive reactogenic and/or allergic responses after the first mRNA dose and were considered ineligible for further mRNA doses. CoronaVac, an inactivated SARS‐CoV‐2 vaccine, is recommended in Singapore as an alternative. Methods Individuals, ineligible for further mRNA vaccines (BNT162b2 or mRNA‐1273) because of excessive reactive responses to prime mRNA vaccination, were recruited and offered two doses of CoronaVac as booster vaccination 38–224 days post their mRNA vaccine dose. Individuals who did not develop any excessive reactive responses after the prime mRNA vaccination were also recruited and given another mRNA vaccine as booster vaccination. Blood samples were collected at days 0, 21 and 90 post first CoronaVac dose and mRNA dose, respectively, for analysis. Results We showed that two CoronaVac booster doses induced specific immunity in these mRNA vaccine‐primed individuals. Although the spike‐specific antibody response was lower, their memory B cell response against the receptor‐binding domain (RBD) of the spike protein was similar, compared with individuals who received two BNT162b2 injections. The spike‐specific memory T cell response also increased following CoronaVac booster doses. However, specific immunity against the Omicron variant was low, similar to individuals with two BNT162b2 doses. Conclusion Our findings showed that while mRNA vaccine‐primed individuals can opt for two subsequent doses of CoronaVac, an additional dose may be necessary to achieve protection, especially against newly emerging immune escape variants such as Omicron.
Collapse
Affiliation(s)
- Yun Shan Goh
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR) Singapore City Singapore
| | - Siew-Wai Fong
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR) Singapore City Singapore
| | - Angeline Rouers
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR) Singapore City Singapore
| | - Zi Wei Chang
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR) Singapore City Singapore
| | - Matthew Zirui Tay
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR) Singapore City Singapore
| | - Jean-Marc Chavatte
- National Public Health Laboratory National Centre for Infectious Diseases Singapore City Singapore
| | - Nicole Ziyi Zhuo
- Singapore Immunology Network, Agency for Science Technology and Research (ASTAR) Singapore City Singapore
| | - Pei Xiang Hor
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR) Singapore City Singapore
| | - Chiew Yee Loh
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR) Singapore City Singapore
| | - Yuling Huang
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR) Singapore City Singapore
| | - Joel Xu En Wong
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR) Singapore City Singapore
| | - Yong Jie Tan
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR) Singapore City Singapore
| | - Daniel Rui Xiang Lim
- National Public Health Laboratory National Centre for Infectious Diseases Singapore City Singapore
| | - Bei Wang
- Singapore Immunology Network, Agency for Science Technology and Research (ASTAR) Singapore City Singapore
| | - Eve Zi Xian Ngoh
- Singapore Immunology Network, Agency for Science Technology and Research (ASTAR) Singapore City Singapore
| | - Siti Nazihah Mohd Salleh
- Singapore Immunology Network, Agency for Science Technology and Research (ASTAR) Singapore City Singapore
| | - Raphael Tze Chuen Lee
- Bioinformatics Institute, ASTAR Singapore City Singapore.,GISAID Global Data Science Initiative (GISAID) Munich Germany
| | - Surinder Pada
- Ng Teng Fong General Hospital Singapore City Singapore
| | - Louisa Jin Sun
- Infectious Diseases Alexandra Hospital Singapore City Singapore
| | | | - Jyoti Somani
- Division of Infectious Diseases, Department of Medicine, National University Hospital National University Health System Singapore City Singapore
| | - Eng Sing Lee
- National Healthcare Group Polyclinics Singapore City Singapore.,Lee Kong Chian School of Medicine Nanyang Technological University Singapore City Singapore
| | | | | | - Sebastian Maurer-Stroh
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR) Singapore City Singapore.,National Public Health Laboratory National Centre for Infectious Diseases Singapore City Singapore.,Bioinformatics Institute, ASTAR Singapore City Singapore.,GISAID Global Data Science Initiative (GISAID) Munich Germany.,Department of Biological Sciences National University of Singapore Singapore City Singapore
| | - Cheng-I Wang
- Singapore Immunology Network, Agency for Science Technology and Research (ASTAR) Singapore City Singapore
| | - Yee-Sin Leo
- Lee Kong Chian School of Medicine Nanyang Technological University Singapore City Singapore.,National Centre for Infectious Diseases (NCID) Singapore City Singapore.,Department of Infectious Diseases Tan Tock Seng Hospital Singapore City Singapore.,Saw Swee Hock School of Public Health National University of Singapore Singapore City Singapore.,Yong Loo Lin School of Medicine National University of Singapore and National University Health System Singapore City Singapore
| | - Raymond Tp Lin
- National Public Health Laboratory National Centre for Infectious Diseases Singapore City Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine National University of Singapore Singapore City Singapore
| | - Ee Chee Ren
- Singapore Immunology Network, Agency for Science Technology and Research (ASTAR) Singapore City Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine National University of Singapore Singapore City Singapore
| | - David C Lye
- Lee Kong Chian School of Medicine Nanyang Technological University Singapore City Singapore.,National Centre for Infectious Diseases (NCID) Singapore City Singapore.,Department of Infectious Diseases Tan Tock Seng Hospital Singapore City Singapore.,Yong Loo Lin School of Medicine National University of Singapore and National University Health System Singapore City Singapore
| | - Barnaby Edward Young
- Lee Kong Chian School of Medicine Nanyang Technological University Singapore City Singapore.,National Centre for Infectious Diseases (NCID) Singapore City Singapore.,Department of Infectious Diseases Tan Tock Seng Hospital Singapore City Singapore
| | - Poh Lian Lim
- Lee Kong Chian School of Medicine Nanyang Technological University Singapore City Singapore.,National Centre for Infectious Diseases (NCID) Singapore City Singapore.,Department of Infectious Diseases Tan Tock Seng Hospital Singapore City Singapore.,Saw Swee Hock School of Public Health National University of Singapore Singapore City Singapore.,Yong Loo Lin School of Medicine National University of Singapore and National University Health System Singapore City Singapore
| | - Lisa Fp Ng
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR) Singapore City Singapore.,National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections University of Liverpool Liverpool UK.,Institute of Infection, Veterinary and Ecological Sciences University of Liverpool Liverpool UK
| | - Laurent Renia
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR) Singapore City Singapore.,Lee Kong Chian School of Medicine Nanyang Technological University Singapore City Singapore.,School of Biological Sciences Nanyang Technological University Singapore City Singapore
| |
Collapse
|
18
|
Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, Ndodo N, Ayansola O, Mboowa G, Bedford T, Neher RA, Roemer C, Hodcroft E, Tegally H, O’Toole Á, Rambaut A, Pybus O, Kraemer MUG, Wilkinson E, Isidro J, Borges V, Pinto M, Gomes JP, Freitas L, Resende PC, Lee RTC, Maurer-Stroh S, Baxter C, Lessells R, Ogwell AE, Kebede Y, Tessema SK, de Oliveira T. Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus. PLoS Biol 2022; 20:e3001769. [PMID: 35998195 PMCID: PMC9451062 DOI: 10.1371/journal.pbio.3001769] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/07/2022] [Indexed: 11/30/2022] Open
Abstract
The current nomenclature for monkeypox virus is stigmatising and misleading. This Perspective article proposes a practical and neutral system of nomenclature that will allow efficient communication without the risk of further misconceptions, discrimination and stigmatisation.
Collapse
Affiliation(s)
- Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University; Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- * E-mail: (CH); (TO)
| | | | - Placide Mbala
- Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of the Congo; University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Richard Njouom
- Virology Unit, Centre Pasteur of Cameroon, Yaoundé, Cameroon
| | | | - Anise Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University; Ede, Osun State, Nigeria
| | | | | | - Gerald Mboowa
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
| | - Richard A. Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Emma Hodcroft
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Geneva Center of Emerging Viral Diseases, HUG, University of Geneva, Geneva, Switzerland
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Áine O’Toole
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Oliver Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Moritz U. G. Kraemer
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Lucas Freitas
- GISAID at Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil
| | - Paola C. Resende
- GISAID at Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil
| | - Raphael T. C. Lee
- GISAID at Bioinformatics Institute and ID labs A*STAR, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Department of Biological Sciences and YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Ahmed E. Ogwell
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Yenew Kebede
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail: (CH); (TO)
| |
Collapse
|
19
|
Ng OT, Marimuthu K, Lim N, Lim ZQ, Thevasagayam NM, Koh V, Chiew CJ, Ma S, Koh M, Low PY, Tan SB, Ho J, Maurer-Stroh S, Lee VJM, Leo YS, Tan KB, Cook AR, Tan CC. Analysis of COVID-19 Incidence and Severity Among Adults Vaccinated With 2-Dose mRNA COVID-19 or Inactivated SARS-CoV-2 Vaccines With and Without Boosters in Singapore. JAMA Netw Open 2022; 5:e2228900. [PMID: 36018588 PMCID: PMC9419014 DOI: 10.1001/jamanetworkopen.2022.28900] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
IMPORTANCE Assessing booster effectiveness of COVID-19 mRNA vaccine and inactivated SARS-CoV-2 vaccine over longer time intervals and in response to any further SARS-CoV-2 variants is crucial in determining optimal COVID-19 vaccination strategies. OBJECTIVE To determine levels of protection against severe COVID-19 and confirmed SARS-CoV-2 infection by types and combinations of vaccine boosters in Singapore during the Omicron wave. DESIGN, SETTING, AND PARTICIPANTS This cohort study included Singapore residents aged 30 years or more vaccinated with either at least 2 doses of mRNA COVID-19 vaccines (ie, Pfizer-BioNTech BNT162b2 or Moderna mRNA-1273) or inactivated SARS-CoV-2 vaccines (Sinovac CoronaVac or Sinopharm BBIBP-CorV) as of March 10, 2022. Individuals with a known SARS-CoV-2 infection prior to December 27, 2021, an infection on or before the date of their second vaccine dose, or with reinfection cases were excluded. EXPOSURES Two or 3 doses of Pfizer-BioNTech BNT162b2, Moderna mRNA-1273, Sinovac CoronaVac, or Sinopharm BBIBP-CorV. MAIN OUTCOMES AND MEASURES Notified infections from December 27, 2021, to March 10, 2022, adjusted for age, sex, race, housing status, and calendar days. Estimated booster effectiveness, defined as the relative incidence-rate reduction of severe disease (supplemental oxygen, intensive care, or death) or confirmed infection following 3-dose vaccination compared with 5 months after second mRNA dose, was determined using binomial regression. RESULTS Among 2 441 581 eligible individuals (1 279 047 [52.4%] women, 846 110 (34.7%) aged 60 years and older), there were 319 943 (13.1%) confirmed SARS-CoV-2 infections, of which 1513 (0.4%) were severe COVID-19 cases. mRNA booster effectiveness against confirmed infection 15 to 60 days after boosting was estimated to range from 31.7% to 41.3% for the 4 boosting combinations (homologous BNT162b2, homologous mRNA-1273, 2-dose BNT162b2/mRNA-1273 booster, and 2-dose mRNA-1273/BNT162b2 booster). Five months and more after boosting, estimated booster effectiveness against confirmed infection waned, ranging from -2.8% to 14.6%. Against severe COVID-19, estimated mRNA booster effectiveness was 87.4% (95% CI, 83.3%-90.5%) 15 to 60 days after boosting and 87.2% (95% CI, 84.2%-89.7%) 5 to 6 months after boosting, with no significant difference comparing vaccine combinations. Booster effectiveness against severe COVID-19 15 days to 330 days after 3-dose inactivated COVID-19 vaccination, regardless of combination, was estimated to be 69.6% (95% CI, 48.7%-81.9%). CONCLUSIONS AND RELEVANCE Booster mRNA vaccine protection against severe COVID-19 was estimated to be durable over 6 months. Three-dose inactivated SARS-CoV-2 vaccination provided greater protection than 2-dose but weaker protection compared with 3-dose mRNA.
Collapse
Affiliation(s)
- Oon Tek Ng
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Kalisvar Marimuthu
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Nigel Lim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Ze Qin Lim
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
| | | | - Vanessa Koh
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
| | - Calvin J. Chiew
- Communicable Diseases Division, Ministry of Health, Singapore
| | - Stefan Ma
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
- Public Health Group, Ministry of Health, Singapore
| | | | | | - Say Beng Tan
- National Medical Research Council, Ministry of Health, Singapore
- SingHealth, Singapore
- Duke-National University of Singapore Medical School, Singapore
| | - Joses Ho
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore
- GISAID Global Data Science Initiative, Munich, Germany
| | - Sebastian Maurer-Stroh
- National Centre for Infectious Diseases, Singapore
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore
- Infectious Diseases Labs, Agency for Science Technology and Research, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Vernon J. M. Lee
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
- Communicable Diseases Division, Ministry of Health, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Kelvin Bryan Tan
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
- Ministry of Health, Singapore
- Centre for Regulatory Excellence, Duke-National University of Singapore Medical School, Singapore
| | - Alex R. Cook
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Chorh Chuan Tan
- Office of Healthcare Transformation, Ministry of Health, Singapore
| |
Collapse
|
20
|
Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou J, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RTC, Freitas L, Maurer-Stroh S, Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Res Sq 2022:rs.3.rs-1723829. [PMID: 35794893 PMCID: PMC9258294 DOI: 10.21203/rs.3.rs-1723829/v1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The emergence of SARS-CoV-2 variants of concern has prompted the need for near real-time genomic surveillance to inform public health interventions. In response to this need, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info, a platform that currently tracks over 40 million combinations of PANGO lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials, and the general public. We describe the interpretable and opinionated visualizations in the variant and location focussed reports available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data, and the server infrastructure that enables widespread data dissemination via a high performance API that can be accessed using an R package. We present a case study that illustrates how outbreak.info can be used for genomic surveillance and as a hypothesis generation tool to understand the ongoing pandemic at varying geographic and temporal scales. With an emphasis on scalability, interactivity, interpretability, and reusability, outbreak.info provides a template to enable genomic surveillance at a global and localized scale.
Collapse
Affiliation(s)
- Karthik Gangavarapu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Alaa Abdel Latif
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Julia L. Mullen
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Manar Alkuzweny
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ginger Tsueng
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Emily Haag
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christine M. Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karina Zaiets
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marco Cano
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jerry Zhou
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Zhongchao Qian
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rachel Sattler
- Skaggs Graduate School of Biological and Chemical Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Raphael TC Lee
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore
| | - Lucas Freitas
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
- Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore
- National Centre for Infectious Diseases, Ministry of Health, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | - Marc A. Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Chunlei Wu
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew I. Su
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Laura D. Hughes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
21
|
Nguyen MN, Krutz NL, Limviphuvadh V, Lopata AL, Gerberick GF, Maurer-Stroh S. AllerCatPro 2.0: a web server for predicting protein allergenicity potential. Nucleic Acids Res 2022; 50:W36-W43. [PMID: 35640594 PMCID: PMC9252832 DOI: 10.1093/nar/gkac446] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/07/2022] [Accepted: 05/11/2022] [Indexed: 02/03/2023] Open
Abstract
Proteins in food and personal care products can pose a risk for an immediate immunoglobulin E (IgE)-mediated allergic response. Bioinformatic tools can assist to predict and investigate the allergenic potential of proteins. Here we present AllerCatPro 2.0, a web server that can be used to predict protein allergenicity potential with better accuracy than other computational methods and new features that help assessors making informed decisions. AllerCatPro 2.0 predicts the similarity between input proteins using both their amino acid sequences and predicted 3D structures towards the most comprehensive datasets of reliable proteins associated with allergenicity. These datasets currently include 4979 protein allergens, 162 low allergenic proteins, and 165 autoimmune allergens with manual expert curation from the databases of WHO/International Union of Immunological Societies (IUIS), Comprehensive Protein Allergen Resource (COMPARE), Food Allergy Research and Resource Program (FARRP), UniProtKB and Allergome. Various examples of profilins, autoimmune allergens, low allergenic proteins, very large proteins, and nucleotide input sequences showcase the utility of AllerCatPro 2.0 for predicting protein allergenicity potential. The AllerCatPro 2.0 web server is freely accessible at https://allercatpro.bii.a-star.edu.sg.
Collapse
Affiliation(s)
- Minh N Nguyen
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix 138671, Singapore.,IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore
| | - Nora L Krutz
- NV Procter & Gamble Services Company SA, Strombeek-Bever, Belgium
| | - Vachiranee Limviphuvadh
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix 138671, Singapore.,IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore
| | - Andreas L Lopata
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix 138671, Singapore.,Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia.,Tropical Futures Institute, James Cook University, Singapore
| | | | - Sebastian Maurer-Stroh
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix 138671, Singapore.,IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| |
Collapse
|
22
|
Pang J, Tan HN, Mak TM, Octavia S, Maurer-Stroh S, Sirota FL, Chan MPC, Leong IYO, Koh VTJ, Ooi PL, Vasoo S, Fisher D, Cui L, Rafman H, Cutter J, Lee VJ. Epidemiological, Clinical, and Phylogenetic Characteristics of the First SARS-CoV-2 Transmission in a Nursing Home of Singapore: A Prospective Observational Investigation. Front Med (Lausanne) 2022; 8:790177. [PMID: 35155470 PMCID: PMC8831716 DOI: 10.3389/fmed.2021.790177] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission has resulted in a significant burden among nursing home facilities globally. This prospective observational cohort study aims to define the potential sources of introduction and characteristics of SARS-CoV-2 transmission of the first nursing home facility in Singapore. An epidemiological serial point-prevalence survey of SARS-CoV-2 was conducted among 108 residents and 56 healthcare staff (HCS). In the current study, 14 (13%) residents and two (3.6%) HCS were diagnosed with coronavirus disease 2019 (COVID-19), with a case fatality rate (CFR) of 28.6% (4/14) among the residents. The median age of the infected residents was 86.5 [interquartile range (IQR) 78.5-88] and 85.7% were women. Five residents were symptomatic (35.7%) and the others were asymptomatic (64.3%). A higher proportion of residents who succumbed to COVID-19 had hypertension than those who recovered. The SARS-CoV-2 whole-genome sequencing showed lineage B.6 which is rare globally but common regionally during the early phase of the pandemic. Household transmission is a potential source of introduction into the nursing home, with at least six epidemiologically linked secondary cases. Male residents were less implicated due to the staff segregation plan by block. Among residents, a higher proportion of the non-survivors were asymptomatic and had hypertension compared with survivors.
Collapse
Affiliation(s)
- Junxiong Pang
- Ministry of Health, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Huei Nuo Tan
- Department of Geriatric Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tze Minn Mak
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Sophie Octavia
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Fernanda L. Sirota
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
- Genome Institute of Singapore and Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Mark Peng Chew Chan
- Department of Geriatric Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Ian Yi Onn Leong
- Division of Central Health, Tan Tock Seng Hospital, Singapore, Singapore
| | | | - Peng Lim Ooi
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore, Singapore
| | - Shawn Vasoo
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore, Singapore
| | - Dale Fisher
- Yong Loo Lin School of Medicine, National University Hospital and National University Health System, Singapore, Singapore
| | - Lin Cui
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Heidi Rafman
- Agency for Integrated Care, Singapore, Singapore
| | - Jeffery Cutter
- Ministry of Health, Singapore, Singapore
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore, Singapore
| | - Vernon J. Lee
- Ministry of Health, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| |
Collapse
|
23
|
Tay MZ, Rouers A, Fong SW, Goh YS, Chan YH, Chang ZW, Xu W, Tan CW, Chia WN, Torres-Ruesta A, Amrun SN, Huang Y, Hor PX, Loh CY, Yeo NKW, Wang B, Ngoh EZX, Salleh SNM, Chavatte JM, Lim AJ, Maurer-Stroh S, Wang LF, Lin RT, Wang CI, Tan SY, Young BE, Leo YS, Lye DC, Renia L, Ng LFP. Decreased memory B cells frequencies in COVID-19 Delta variant vaccine breakthrough infection. EMBO Mol Med 2022; 14:e15227. [PMID: 34994081 PMCID: PMC8899913 DOI: 10.15252/emmm.202115227] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 11/09/2022] Open
Abstract
The SARS‐CoV‐2 Delta (B.1.617.2) variant is capable of infecting vaccinated persons. An open question remains as to whether deficiencies in specific vaccine‐elicited immune responses result in susceptibility to vaccine breakthrough infection. We investigated 55 vaccine breakthrough infection cases (mostly Delta) in Singapore, comparing them against 86 vaccinated close contacts who did not contract infection. Vaccine breakthrough cases showed lower memory B cell frequencies against SARS‐CoV‐2 receptor‐binding domain (RBD). Compared to plasma antibodies, antibodies secreted by memory B cells retained a higher fraction of neutralizing properties against the Delta variant. Inflammatory cytokines including IL‐1β and TNF were lower in vaccine breakthrough infections than primary infection of similar disease severity, underscoring the usefulness of vaccination in preventing inflammation. This report highlights the importance of memory B cells against vaccine breakthrough and suggests that lower memory B cell levels may be a correlate of risk for Delta vaccine breakthrough infection.
Collapse
Affiliation(s)
- Matthew Zirui Tay
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore.,These authors contributed equally, Matthew Zirui Tay Angeline Rouers
| | - Angeline Rouers
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore.,These authors contributed equally, Matthew Zirui Tay Angeline Rouers
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yun Shan Goh
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yi-Hao Chan
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Zi Wei Chang
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Weili Xu
- Singapore Immunology Network, A*STAR, Singapore
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Anthony Torres-Ruesta
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Siti Naqiah Amrun
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yuling Huang
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Pei Xiang Hor
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chiew Yee Loh
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Nicholas Kim-Wah Yeo
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Bei Wang
- Singapore Immunology Network, A*STAR, Singapore
| | | | | | | | - Alicia Jieling Lim
- National Centre for Infectious Diseases, Singapore.,National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | | | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.,SingHealth Duke-NUS Global Health Institute, Singapore, Singapore
| | - Raymond Tp Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Seow-Yen Tan
- Department of Infectious Diseases, Changi General Hospital, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore
| | - David C Lye
- National Centre for Infectious Diseases, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore
| | - Laurent Renia
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore.,Singapore Immunology Network, A*STAR, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| |
Collapse
|
24
|
Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MU, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Global disparities in SARS-CoV-2 genomic surveillance. medRxiv 2021:2021.08.21.21262393. [PMID: 34462754 PMCID: PMC8404891 DOI: 10.1101/2021.08.21.21262393] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genomic sequencing provides critical information to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments and vaccines, and guide public health responses. To investigate the spatiotemporal heterogeneity in the global SARS-CoV-2 genomic surveillance, we estimated the impact of sequencing intensity and turnaround times (TAT) on variant detection in 167 countries. Most countries submit genomes >21 days after sample collection, and 77% of low and middle income countries sequenced <0.5% of their cases. We found that sequencing at least 0.5% of the cases, with a TAT <21 days, could be a benchmark for SARS-CoV-2 genomic surveillance efforts. Socioeconomic inequalities substantially impact our ability to quickly detect SARS-CoV-2 variants, and undermine the global pandemic preparedness.
Collapse
Affiliation(s)
- Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Instituto Todos pela Saúde, São Paulo, São Paulo, Brazil
| | - Elizaveta Semenova
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Mathematics, Imperial College London, London, UK
| | - Gytis Dudas
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Gabriel W. Hassler
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | | | - Joses Ho
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Houriiyah Tegally
- KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kenya
| | | | - Lucy E. Matkin
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom
| | | | | | | | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales 2145, Australia
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, Michigan, USA
| | - Tulio de Oliveira
- KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | | | | | | | - Fernando R. Spilki
- Feevale University, Institute of Health Sciences, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D’Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivan N. Ivanov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivva Philipova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Christine V. F. Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nikita S. D. Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Céline Gurry
- GISAID Global Data Science Initiative, Munich, Germany
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore
| | - Dhamari Naidoo
- Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India
| | - Karin J von Eije
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Mark D. Perkins
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Maria van Kerkhove
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | | | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Royal Veterinary College, Hawkshead, United Kingdom
| | - Christopher Dye
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Marc A. Suchard
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R. Faria
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
25
|
Khare S, Gurry C, Freitas L, Schultz MB, Bach G, Diallo A, Akite N, Ho J, Lee RT, Yeo W, Curation Team GC, Maurer-Stroh S. GISAID's Role in Pandemic Response. China CDC Wkly 2021; 3:1049-1051. [PMID: 34934514 PMCID: PMC8668406 DOI: 10.46234/ccdcw2021.255] [Citation(s) in RCA: 422] [Impact Index Per Article: 140.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Shruti Khare
- GISAID Global Data Science Initiative (GISAID), Munich, Germany.,Bioinformatics Institute, Agency for Science Technology and Research, Singapore
| | - Céline Gurry
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
| | - Lucas Freitas
- GISAID Global Data Science Initiative (GISAID), Munich, Germany.,Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Mark B Schultz
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
| | - Gunter Bach
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
| | - Amadou Diallo
- GISAID Global Data Science Initiative (GISAID), Munich, Germany.,Institut Pasteur de Dakar, Dakar, Senegal
| | - Nancy Akite
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
| | - Joses Ho
- GISAID Global Data Science Initiative (GISAID), Munich, Germany.,Bioinformatics Institute, Agency for Science Technology and Research, Singapore
| | - Raphael Tc Lee
- GISAID Global Data Science Initiative (GISAID), Munich, Germany.,Bioinformatics Institute, Agency for Science Technology and Research, Singapore
| | - Winston Yeo
- GISAID Global Data Science Initiative (GISAID), Munich, Germany.,Bioinformatics Institute, Agency for Science Technology and Research, Singapore
| | - Gisaid Core Curation Team
- GISAID Global Data Science Initiative (GISAID), Munich, Germany.,Bioinformatics Institute, Agency for Science Technology and Research, Singapore.,Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil.,National Institutes of Biotechnology Malaysia, Selangor, Malaysia.,Smorodintsev Research Institute of Influenza, St. Petersburg, Russia.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore.,China National GeneBank, Shenzhen, China
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative (GISAID), Munich, Germany.,Bioinformatics Institute, Agency for Science Technology and Research, Singapore.,ASTAR Infectious Disease Labs (ID Labs), Singapore.,National Public Health Laboratory, National Centre for Infectious Diseases, Ministry of Health, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| |
Collapse
|
26
|
Ng OT, Koh V, Chiew CJ, Marimuthu K, Thevasagayam NM, Mak TM, Chua JK, Ong SSH, Lim YK, Ferdous Z, Johari AKB, Chen MIC, Maurer-Stroh S, Cui L, Lin RTP, Tan KB, Cook AR, Leo PYS, Lee PVJM. Impact of Delta Variant and Vaccination on SARS-CoV-2 Secondary Attack Rate Among Household Close Contacts. Lancet Reg Health West Pac 2021; 17:100299. [PMID: 34746899 PMCID: PMC8560026 DOI: 10.1016/j.lanwpc.2021.100299] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND Impact of the Delta variant and vaccination on SARS-CoV-2 transmission remains unclear. In Singapore, quarantine of all close contacts, including entry and exit PCR testing, provided the opportunity to determine risk of infection by the Delta variant compared to other variants, vaccine efficacy against SARS-CoV-2 acquisition, symptomatic or severe COVID-19, and risk factors associated with SARS-CoV-2 acquisition and symptomatic disease. METHODS This retrospective cohort study included all close contacts between September 1, 2020 and May 31, 2021. Regardless of symptoms, all were quarantined for 14 days with entry and exit PCR testing. Household contacts were defined as individuals who shared a residence with a Covid-19 index case. Secondary attack rates among household close contacts of Delta variant-infected indexes and other variant-infected indexes were derived from prevalence of diagnosed cases among contacts. Relative risk ratios and bootstrapping at the cluster level was used to determine risk of infection by the Delta variant compared to other variants and vaccine efficacy against SARS-CoV-2 acquisition, symptomatic or severe COVID-19. Logistic regression using generalized estimating equations was used to determine risk factors associated with SARS-CoV-2 acquisition and symptomatic disease. FINDINGS Of 1024 household contacts linked to 301 PCR-confirmed index cases, 753 (73.5%) were linked to Delta-infected indexes and 248 (24.2%) were exposed to indexes with other variants. Household secondary attack rate among unvaccinated Delta-exposed contacts was 25.8% (95% boostrap confidence interval [BCI] 20.6-31.5%) compared with 12.9% (95%BCI 7.0-20.0%) among other variant-exposed contacts. Unvaccinated Delta-exposed contacts were more likely to be infected than those exposed to other variants (Relative risk 2.01, 95%CI 1.24-3.84). Among Delta-exposed contacts, complete vaccination had a vaccine effectiveness of 56.4% (95%BCI 32.6-75.8%) against acquisition, 64.1% (95%BCI 37.8-85.4%) against symptomatic disease and 100% against severe disease. Among Delta-exposed contacts, vaccination status (adjusted odds ratio [aOR] 0.33, 95% robust confidence interval [RCI] 0.17-0.63) and older age of the index (aOR 1.20 per decade, 95%RCI 1.03-1.39) was associated with increased risk of SARS-CoV-2 acquisition by the contact. Vaccination status of the index was not associated with a statistically-significant difference for contact SARS-CoV-2 acquisition (aOR 0.73, 95%RCI 0.38-1.40). INTERPRETATION Increased risk of SARS-CoV-2 Delta acquisition compared with other variants was reduced with vaccination. Close-contacts of vaccinated Delta-infected indexes did not have statistically significant reduced risk of acquisition compared with unvaccinated Delta-infected indexes.
Collapse
Affiliation(s)
- Oon Tek Ng
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Vanessa Koh
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
| | - Calvin J Chiew
- Communicable Diseases Division, Ministry of Health, Singapore
| | - Kalisvar Marimuthu
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | | | - Tze Minn Mak
- National Centre for Infectious Diseases, Singapore
| | | | | | | | - Zannatul Ferdous
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
| | | | - Mark I-Cheng Chen
- National Centre for Infectious Diseases, Singapore
- Communicable Diseases Division, Ministry of Health, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Sebastian Maurer-Stroh
- National Centre for Infectious Diseases, Singapore
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore
- Infectious Diseases Labs, Agency for Science Technology and Research, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore
| | - Raymond Tzer Pin Lin
- National Centre for Infectious Diseases, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Kelvin Bryan Tan
- Ministry of Health, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
- Centre for Regulatory Excellence, Duke-NUS Medical School
| | - Alex R Cook
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Prof. Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Prof. Vernon JM Lee
- Communicable Diseases Division, Ministry of Health, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| |
Collapse
|
27
|
Wang B, Goh YS, Prince T, Ngoh EZX, Salleh SNM, Hor PX, Loh CY, Fong SW, Hartley C, Tan SY, Young BE, Leo YS, Lye DC, Maurer-Stroh S, Ng LFP, Hiscox JA, Renia L, Wang CI. Resistance of SARS-CoV-2 variants to neutralization by convalescent plasma from early COVID-19 outbreak in Singapore. NPJ Vaccines 2021; 6:125. [PMID: 34697298 PMCID: PMC8546091 DOI: 10.1038/s41541-021-00389-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/01/2021] [Indexed: 12/22/2022] Open
Abstract
The rapid spreading of SARS-CoV-2 variants B.1.1.7 originated from the United Kingdom and B.1.351 from South Africa has contributed to the second wave of COVID-19 cases in the respective countries and also around the world. In this study, we employed advanced biochemical and virological methodologies to evaluate the impact of Spike mutations of these strains on the degree of protection afforded by humoral immune responses following natural infection of the ancestral SARS-CoV-2 strain during the early stages of the outbreak. We found that antibody-mediated neutralization activity was partially reduced for B.1.1.7 variant and significantly attenuated for the B.1.351 strain. We also found that mutations outside the receptor-binding domain (RBD) can strongly influence antibody binding and neutralization, cautioning the use of solely RBD mutations in evaluating vaccine efficacy. These findings highlight an urgent need to develop new SARS-CoV-2 vaccines that are not based exclusively on the ancestral SARS-CoV-2 Spike gene sequence.
Collapse
Affiliation(s)
- Bei Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yun Shan Goh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Tessa Prince
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Eve Zi Xian Ngoh
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siti Nazihah Mohd Salleh
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Pei Xiang Hor
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chiew Yee Loh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siew Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Catherine Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Seow-Yen Tan
- Department of Infectious Diseases, Changi General Hospital, Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - David C Lye
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Julian A Hiscox
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Cheng-I Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| |
Collapse
|
28
|
Wang B, Goh YS, Fong SW, Young BE, Ngoh EZX, Chavatte JM, Salleh SNM, Yeo NKW, Amrun SN, Hor PX, Loh CY, Lee CY, Chan YH, Chang ZW, Tay MZ, Rouers A, Torres-Ruesta A, Carissimo G, Soh MK, Lee RTC, Xu Y, Pada S, Lin RTP, Leo YS, Lye DC, Maurer-Stroh S, Ng LFP, Renia L, Wang CI. Resistance of SARS-CoV-2 Delta variant to neutralization by BNT162b2-elicited antibodies in Asians. Lancet Reg Health West Pac 2021; 15:100276. [PMID: 34568853 PMCID: PMC8450274 DOI: 10.1016/j.lanwpc.2021.100276] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/12/2021] [Accepted: 08/26/2021] [Indexed: 12/04/2022]
Affiliation(s)
- Bei Wang
- Singapore Immunology Network, ASTAR, Singapore
| | - Yun Shan Goh
- ASTAR Infectious Diseases Labs, A*STAR, Singapore
| | | | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | | | | | | | | | | | | | | | - Yi-Hao Chan
- ASTAR Infectious Diseases Labs, A*STAR, Singapore
| | - Zi Wei Chang
- ASTAR Infectious Diseases Labs, A*STAR, Singapore
| | | | | | | | | | | | | | - Yani Xu
- Bioinformatics Institute, ASTAR, Singapore
| | - Surinder Pada
- Division of Infectious Diseases, Ng Teng Fong General Hospital, Singapore
| | - Raymond Tzer Pin Lin
- National Centre for Infectious Diseases, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - David C Lye
- National Centre for Infectious Diseases, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Sebastian Maurer-Stroh
- ASTAR Infectious Diseases Labs, A*STAR, Singapore.,Bioinformatics Institute, ASTAR, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Lisa F P Ng
- ASTAR Infectious Diseases Labs, A*STAR, Singapore.,Department of Biochemistry, National University of Singapore, Singapore.,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Laurent Renia
- ASTAR Infectious Diseases Labs, A*STAR, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
| | | |
Collapse
|
29
|
Ong SWX, Chiew CJ, Ang LW, Mak TM, Cui L, Toh MPHS, Lim YD, Lee PH, Lee TH, Chia PY, Maurer-Stroh S, Lin RTP, Leo YS, Lee VJ, Lye DC, Young BE. Clinical and Virological Features of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants of Concern: A Retrospective Cohort Study Comparing B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta). Clin Infect Dis 2021; 75:e1128-e1136. [PMID: 34423834 PMCID: PMC8522361 DOI: 10.1093/cid/ciab721] [Citation(s) in RCA: 228] [Impact Index Per Article: 76.0] [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: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The impact of SARS-CoV-2 variants of concern (VOCs) on disease severity is unclear. In this retrospective study, we compared the outcomes of patients infected with B.1.1.7, B.1.351, and B.1.617.2 with wild-type strains from early 2020. METHODS National surveillance data from January to May 2021 were obtained and outcomes in relation to VOCs were explored. Detailed patient-level data from all patients with VOC infection admitted to our center between December 2020 and May 2021 were analyzed. Clinical outcomes were compared with a cohort of 846 patients admitted from January to April 2020. RESULTS A total of 829 patients in Singapore in the study period were infected with these 3 VOCs. After adjusting for age and sex, B.1.617.2 was associated with higher odds of oxygen requirement, intensive care unit admission, or death (adjusted odds ratio [aOR], 4.90; 95% confidence interval [CI]: 1.43-30.78). Of these patients, 157 were admitted to our center. After adjusting for age, sex, comorbidities, and vaccination, the aOR for pneumonia with B.1.617.2 was 1.88 (95% CI: .95-3.76) compared with wild-type. These differences were not seen with B.1.1.7 and B.1.351. Vaccination status was associated with decreased severity. B.1.617.2 was associated with significantly lower polymerase chain reaction cycle threshold (Ct) values and longer duration of Ct value ≤30 (median duration 18 days for B.1.617.2, 13 days for wild-type). CONCLUSIONS B.1.617.2 was associated with increased severity of illness, and with lower Ct values and longer viral shedding. These findings provide impetus for the rapid implementation of vaccination programs.
Collapse
Affiliation(s)
- Sean Wei Xiang Ong
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Calvin J Chiew
- National Centre for Infectious Diseases, Singapore, Singapore,Ministry of Health, Singapore, Singapore
| | - Li Wei Ang
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Tze Minn Mak
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Matthias Paul H S Toh
- National Centre for Infectious Diseases, Singapore, Singapore,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | | | - Pei Hua Lee
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tau Hong Lee
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Po Ying Chia
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore,A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore,Department of Biological Sciences, National University of Singapore, Singapore
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yee Sin Leo
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vernon J Lee
- Ministry of Health, Singapore, Singapore,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Barnaby Edward Young
- Correspondence: Barnaby Young, National Centre for Infectious Diseases, 16 Jln Tan Tock Seng, Singapore 308442 ()
| |
Collapse
|
30
|
Sirota FL, Maurer-Stroh S, Li Z, Eisenhaber F, Eisenhaber B. Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications. Front Bioeng Biotechnol 2021; 9:701120. [PMID: 34409021 PMCID: PMC8366029 DOI: 10.3389/fbioe.2021.701120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Large enzyme families such as the groups of zinc-dependent alcohol dehydrogenases (ADHs), long chain alcohol oxidases (AOxs) or amine dehydrogenases (AmDHs) with, sometimes, more than one million sequences in the non-redundant protein database and hundreds of experimentally characterized enzymes are excellent cases for protein engineering efforts aimed at refining and modifying substrate specificity. Yet, the backside of this wealth of information is that it becomes technically difficult to rationally select optimal sequence targets as well as sequence positions for mutagenesis studies. In all three cases, we approach the problem by starting with a group of experimentally well studied family members (including those with available 3D structures) and creating a structure-guided multiple sequence alignment and a modified phylogenetic tree (aka binding site tree) based just on a selection of potential substrate binding residue positions derived from experimental information (not from the full-length sequence alignment). Hereupon, the remaining, mostly uncharacterized enzyme sequences can be mapped; as a trend, sequence grouping in the tree branches follows substrate specificity. We show that this information can be used in the target selection for protein engineering work to narrow down to single suitable sequences and just a few relevant candidate positions for directed evolution towards activity for desired organic compound substrates. We also demonstrate how to find the closest thermophile example in the dataset if the engineering is aimed at achieving most robust enzymes.
Collapse
Affiliation(s)
- Fernanda L Sirota
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore.,Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science Technology and Research (ASTAR), Singapore, Singapore.,Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| |
Collapse
|
31
|
Konings F, Perkins MD, Kuhn JH, Pallen MJ, Alm EJ, Archer BN, Barakat A, Bedford T, Bhiman JN, Caly L, Carter LL, Cullinane A, de Oliveira T, Druce J, El Masry I, Evans R, Gao GF, Gorbalenya AE, Hamblion E, Herring BL, Hodcroft E, Holmes EC, Kakkar M, Khare S, Koopmans MPG, Korber B, Leite J, MacCannell D, Marklewitz M, Maurer-Stroh S, Rico JAM, Munster VJ, Neher R, Munnink BO, Pavlin BI, Peiris M, Poon L, Pybus O, Rambaut A, Resende P, Subissi L, Thiel V, Tong S, van der Werf S, von Gottberg A, Ziebuhr J, Van Kerkhove MD. SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse. Nat Microbiol 2021; 6:821-823. [PMID: 34108654 DOI: 10.1038/s41564-021-00932-w] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [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)
| | | | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Mark J Pallen
- Quadram Institute Bioscience, University of East Anglia, Norwich, UK
| | - Erik J Alm
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | | | | | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jinal N Bhiman
- National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne, Victoria, Australia
| | | | - Anne Cullinane
- Faculty of Science and Engineering, University of Limerick, Limerick, Ireland
| | | | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne, Victoria, Australia
| | - Ihab El Masry
- Emergency Centre for Transboundary Animal Disease, Food and Agriculture Organization of the United Nations (FAO), Cairo, Egypt
| | - Roger Evans
- World Health Organization, Geneva, Switzerland
| | - George F Gao
- Chinese Center for Disease Control and Prevention, Beijing, P.R. China
| | - Alexander E Gorbalenya
- Leiden University Medical Center, Leiden, The Netherlands.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | | | | | | | - Edward C Holmes
- The University of Sydney, Sydney, New South Wales, Australia
| | | | | | | | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | - Duncan MacCannell
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Sebastian Maurer-Stroh
- The Global Initiative on Sharing All Influenza Data (GISAID), Munich, Germany.,Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Vincent J Munster
- Virus Ecology Unit, National Institute of Allergy and Infectious Diseases, Rockville, MA, USA
| | - Richard Neher
- Biozentrum, University of Basel, Switzerland Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | | | | | - Leo Poon
- The University of Hong Kong, Hong Kong, China
| | | | - Andrew Rambaut
- Institute for Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Paola Resende
- Laboratory of Respiratory Viruses and Measles (LVRS), Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | | | - Volker Thiel
- University of Bern, Bern, Switzerland.,Institute of Virology and Immunology, Mittelhäusern, Switzerland
| | - Suxiang Tong
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Anne von Gottberg
- National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | | |
Collapse
|
32
|
Wong HH, Seet SH, Maier M, Gurel A, Traspas RM, Lee C, Zhang S, Talim B, Loh AY, Chia CY, Teoh TS, Sng D, Rensvold J, Unal S, Shishkova E, Cepni E, Nathan FM, Sirota FL, Liang C, Yarali N, Simsek-Kiper PO, Mitani T, Ceylaner S, Arman-Bilir O, Mbarek H, Gumruk F, Efthymiou S, Çïmen DU, Georgiadou D, Sotiropoulou K, Houlden H, Paul F, Pehlivan D, Lainé C, Chai G, Ali NA, Choo SC, Keng SS, Boisson B, Yılmaz E, Xue S, Coon JJ, Nguyen Ly TT, Gilani N, Hasbini D, Kayserili H, Zaki MS, Isfort RJ, Ordonez N, Tripolszki K, Bauer P, Rezaei N, Seyedpour S, Khotaei GT, Bascom CC, Maroofian R, Chaabouni M, Alsubhi A, Eyaid W, Işıkay S, Gleeson JG, Lupski JR, Casanova JL, Pagliarini DJ, Akarsu NA, Maurer-Stroh S, Cetinkaya A, Bertoli-Avella A, Mathuru AS, Ho L, Bard FA, Reversade B. Loss of C2orf69 defines a fatal autoinflammatory syndrome in humans and zebrafish that evokes a glycogen-storage-associated mitochondriopathy. Am J Hum Genet 2021; 108:1356. [PMID: 34214448 DOI: 10.1016/j.ajhg.2021.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
|
33
|
Wong HH, Seet SH, Maier M, Gurel A, Traspas RM, Lee C, Zhang S, Talim B, Loh AYT, Chia CY, Teoh TS, Sng D, Rensvold J, Unal S, Shishkova E, Cepni E, Nathan FM, Sirota FL, Liang C, Yarali N, Simsek-Kiper PO, Mitani T, Ceylaner S, Arman-Bilir O, Mbarek H, Gumruk F, Efthymiou S, Uğurlu Çi Men D, Georgiadou D, Sotiropoulou K, Houlden H, Paul F, Pehlivan D, Lainé C, Chai G, Ali NA, Choo SC, Keng SS, Boisson B, Yılmaz E, Xue S, Coon JJ, Ly TTN, Gilani N, Hasbini D, Kayserili H, Zaki MS, Isfort RJ, Ordonez N, Tripolszki K, Bauer P, Rezaei N, Seyedpour S, Khotaei GT, Bascom CC, Maroofian R, Chaabouni M, Alsubhi A, Eyaid W, Işıkay S, Gleeson JG, Lupski JR, Casanova JL, Pagliarini DJ, Akarsu NA, Maurer-Stroh S, Cetinkaya A, Bertoli-Avella A, Mathuru AS, Ho L, Bard FA, Reversade B. Loss of C2orf69 defines a fatal autoinflammatory syndrome in humans and zebrafish that evokes a glycogen-storage-associated mitochondriopathy. Am J Hum Genet 2021; 108:1301-1317. [PMID: 34038740 PMCID: PMC8322802 DOI: 10.1016/j.ajhg.2021.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 03/19/2021] [Accepted: 05/07/2021] [Indexed: 12/20/2022] Open
Abstract
Human C2orf69 is an evolutionarily conserved gene whose function is unknown. Here, we report eight unrelated families from which 20 children presented with a fatal syndrome consisting of severe autoinflammation and progredient leukoencephalopathy with recurrent seizures; 12 of these subjects, whose DNA was available, segregated homozygous loss-of-function C2orf69 variants. C2ORF69 bears homology to esterase enzymes, and orthologs can be found in most eukaryotic genomes, including that of unicellular phytoplankton. We found that endogenous C2ORF69 (1) is loosely bound to mitochondria, (2) affects mitochondrial membrane potential and oxidative respiration in cultured neurons, and (3) controls the levels of the glycogen branching enzyme 1 (GBE1) consistent with a glycogen-storage-associated mitochondriopathy. We show that CRISPR-Cas9-mediated inactivation of zebrafish C2orf69 results in lethality by 8 months of age due to spontaneous epileptic seizures, which is preceded by persistent brain inflammation. Collectively, our results delineate an autoinflammatory Mendelian disorder of C2orf69 deficiency that disrupts the development/homeostasis of the immune and central nervous systems.
Collapse
Affiliation(s)
- Hui Hui Wong
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore 138673, Singapore
| | - Sze Hwee Seet
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore 138673, Singapore
| | - Michael Maier
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Biopolis, Singapore 138672, Singapore
| | - Ayse Gurel
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey
| | - Ricardo Moreno Traspas
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Biopolis, Singapore 138672, Singapore
| | - Cheryl Lee
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore 138673, Singapore; Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Shan Zhang
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey
| | - Beril Talim
- Pediatric Pathology Unit, Department of Pediatrics, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey
| | - Abigail Y T Loh
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore 138673, Singapore
| | - Crystal Y Chia
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Biopolis, Singapore 138672, Singapore
| | - Tze Shin Teoh
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Biopolis, Singapore 138672, Singapore
| | - Danielle Sng
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Biopolis, Singapore 138672, Singapore
| | - Jarred Rensvold
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| | - Sule Unal
- Pediatric Hematology Unit, Department of Pediatrics, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey; Research Center of Fanconi Anemia and Other Inherited Bone Marrow Failure Syndromes, Hacettepe University, Ankara 06230, Turkey
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53562, USA
| | - Ece Cepni
- Institute of Health Sciences, Koç University, 34010 Istanbul, Turkey
| | - Fatima M Nathan
- Yale-NUS College, 12 College Avenue West, Singapore 138610, Singapore
| | - Fernanda L Sirota
- Bioinformatics Institute, A(∗)STAR, Biopolis, Singapore 138671, Singapore
| | - Chao Liang
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey
| | - Nese Yarali
- Ankara Child Health and Diseases Hematology Oncology Training and Research Hospital, Ankara 06110, Turkey
| | - Pelin O Simsek-Kiper
- Pediatric Genetics Unit, Department of Pediatrics, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Ozlem Arman-Bilir
- Ankara Child Health and Diseases Hematology Oncology Training and Research Hospital, Ankara 06110, Turkey
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Fatma Gumruk
- Pediatric Hematology Unit, Department of Pediatrics, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey; Research Center of Fanconi Anemia and Other Inherited Bone Marrow Failure Syndromes, Hacettepe University, Ankara 06230, Turkey
| | - Stephanie Efthymiou
- Molecular and Clinical Sciences Institute, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Deniz Uğurlu Çi Men
- Medical Genetics Department, Koç University School of Medicine, 34010 Istanbul, Turkey
| | - Danai Georgiadou
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Biopolis, Singapore 138672, Singapore
| | - Kortessa Sotiropoulou
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore 138673, Singapore
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Franziska Paul
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore 138673, Singapore
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Candice Lainé
- Paris University, Imagine Institute, Paris 75015, France; Laboratory of Human Genetics of Infectious Disease, Necker Branch, INSERM U1163, Paris, France
| | - Guoliang Chai
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nur Ain Ali
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Biopolis, Singapore 138672, Singapore
| | - Siew Chin Choo
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Biopolis, Singapore 138672, Singapore
| | - Soh Sok Keng
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore 138673, Singapore
| | - Bertrand Boisson
- Paris University, Imagine Institute, Paris 75015, France; Laboratory of Human Genetics of Infectious Disease, Necker Branch, INSERM U1163, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Elanur Yılmaz
- Medical Genetics Department, Koç University School of Medicine, 34010 Istanbul, Turkey
| | - Shifeng Xue
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI 53715, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53562, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53562, USA
| | - Thanh Thao Nguyen Ly
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | | | - Dana Hasbini
- Chief Division Pediatric Neurology, Department of Pediatrics, Rafic Hariri University Hospital, Beirut, Lebanon
| | - Hulya Kayserili
- Medical Genetics Department, Koç University School of Medicine, 34010 Istanbul, Turkey
| | - Maha S Zaki
- Clinical Genetics Department, National Research Centre, Cairo 12622, Egypt
| | - Robert J Isfort
- Corporate Research, The Procter and Gamble Company, Cincinnati, OH 45040, USA
| | | | | | - Peter Bauer
- Genomic Research, CENTOGENE GmbH, 18055 Rostock, Germany
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran 14194, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity, Universal Scientific Education and Research Network, Tehran 14197, Iran
| | - Simin Seyedpour
- Laboratoire d'analyses spécialisé en Génétique, Tunis 1082, Tunisia
| | - Ghamar Taj Khotaei
- Department of Pediatric Infectious Diseases, Children's Medical Center, Tehran University of Medical Sciences, Tehran 14194, Iran
| | - Charles C Bascom
- Corporate Research, The Procter and Gamble Company, Cincinnati, OH 45040, USA
| | - Reza Maroofian
- Molecular and Clinical Sciences Institute, St. George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Myriam Chaabouni
- Laboratoire d'analyses spécialisé en Génétique, Tunis 1082, Tunisia
| | - Afaf Alsubhi
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh 14611, Saudi Arabia; King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, MNGHA, Riyadh 11481, Saudi Arabia
| | - Wafaa Eyaid
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh 14611, Saudi Arabia; King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, MNGHA, Riyadh 11481, Saudi Arabia
| | - Sedat Işıkay
- Department of Pediatrics, Division of Neurology, University of Gaziantep, School of Medicine, Gaziantep 27310, Turkey
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jean-Laurent Casanova
- Paris University, Imagine Institute, Paris 75015, France; Laboratory of Human Genetics of Infectious Disease, Necker Branch, INSERM U1163, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Pediatric Immunology-Hematology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris 75015, France; Howard Hughes Medical Institute, New York, NY 10065, USA
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Morgridge Institute for Research, Madison, WI 53715, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nurten A Akarsu
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey
| | | | - Arda Cetinkaya
- Department of Medical Genetics, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey
| | | | - Ajay S Mathuru
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore 138673, Singapore; Yale-NUS College, 12 College Avenue West, Singapore 138610, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Lena Ho
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore 138673, Singapore; Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Frederic A Bard
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore 138673, Singapore.
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore 138673, Singapore; Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Biopolis, Singapore 138672, Singapore; Medical Genetics Department, Koç University School of Medicine, 34010 Istanbul, Turkey; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore.
| |
Collapse
|
34
|
Chong CS, Limviphuvadh V, Maurer-Stroh S. Global spectrum of population-specific common missense variation in cytochrome P450 pharmacogenes. Hum Mutat 2021; 42:1107-1123. [PMID: 34153149 DOI: 10.1002/humu.24243] [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: 10/09/2020] [Revised: 04/12/2021] [Accepted: 06/08/2021] [Indexed: 11/06/2022]
Abstract
Next-generation sequencing technology has afforded the discovery of many novel variants that are of significance to inheritable pharmacogenomics (PGx) traits but a large proportion of them have unknown consequences. These include missense variants resulting in single amino acid substitutions in cytochrome P450 (CYP) proteins that can impair enzyme function, leading to altered drug efficacy and toxicity. While most unknown variants are rare, an overlooked minority are variants that are collectively rare but enriched in specific populations. Here, we analyzed sequence variation data in 141,456 individuals from across eight study populations in gnomAD for 38 CYP genes to identify such variants in addition to common variants. By further comparison with data from two PGx-specific databases (PharmVar and PharmGKB) and ClinVar, we identified 234 missense variants in 35 CYP genes, of which 107 were unknown to these databases. Most unknown variants (n = 83) were population-specific common variants and several (n = 7) were found in important CYP pharmacogenes (CYP2D6, CYP4F2, and CYP2C19). Overall, 29% (n = 31) of 107 unknown variants were predicted to affect CYP enzyme function although further biochemical characterization is necessary. These variants may elucidate part of the unexplained interpopulation differences observed in drug response.
Collapse
Affiliation(s)
- Cheng-Shoong Chong
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Innovations in Food and Chemical Safety Programme (IFCS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National University of Singapore Graduate School for Integrative Sciences and Engineering (NGS), National University of Singapore, Singapore, Singapore
| | - Vachiranee Limviphuvadh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Innovations in Food and Chemical Safety Programme (IFCS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Innovations in Food and Chemical Safety Programme (IFCS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National University of Singapore Graduate School for Integrative Sciences and Engineering (NGS), National University of Singapore, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| |
Collapse
|
35
|
Asarnow D, Wang B, Lee WH, Hu Y, Huang CW, Faust B, Ng PML, Ngoh EZX, Bohn M, Bulkley D, Pizzorno A, Ary B, Tan HC, Lee CY, Minhat RA, Terrier O, Soh MK, Teo FJ, Yeap YYC, Seah SGK, Chan CEZ, Connelly E, Young NJ, Maurer-Stroh S, Renia L, Hanson BJ, Rosa-Calatrava M, Manglik A, Cheng Y, Craik CS, Wang CI. Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia. Cell 2021; 184:3192-3204.e16. [PMID: 33974910 PMCID: PMC8064868 DOI: 10.1016/j.cell.2021.04.033] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 11/18/2020] [Revised: 02/19/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022]
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by binding of the viral Spike protein to host receptor angiotensin-converting enzyme 2 (ACE2), followed by fusion of viral and host membranes. Although antibodies that block this interaction are in emergency use as early coronavirus disease 2019 (COVID-19) therapies, the precise determinants of neutralization potency remain unknown. We discovered a series of antibodies that potently block ACE2 binding but exhibit divergent neutralization efficacy against the live virus. Strikingly, these neutralizing antibodies can inhibit or enhance Spike-mediated membrane fusion and formation of syncytia, which are associated with chronic tissue damage in individuals with COVID-19. As revealed by cryoelectron microscopy, multiple structures of Spike-antibody complexes have distinct binding modes that not only block ACE2 binding but also alter the Spike protein conformational cycle triggered by ACE2 binding. We show that stabilization of different Spike conformations leads to modulation of Spike-mediated membrane fusion with profound implications for COVID-19 pathology and immunity.
Collapse
Affiliation(s)
- Daniel Asarnow
- Department of Biochemistry and Biophysics, University of California, San Francisco (UCSF) School of Medicine, San Francisco, CA, USA; QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
| | - Bei Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Wen-Hsin Lee
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Yuanyu Hu
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Ching-Wen Huang
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Bryan Faust
- Department of Biochemistry and Biophysics, University of California, San Francisco (UCSF) School of Medicine, San Francisco, CA, USA; QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
| | - Patricia Miang Lon Ng
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Eve Zi Xian Ngoh
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Markus Bohn
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - David Bulkley
- Department of Biochemistry and Biophysics, University of California, San Francisco (UCSF) School of Medicine, San Francisco, CA, USA; QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
| | - Andrés Pizzorno
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Beatrice Ary
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Hwee Ching Tan
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Chia Yin Lee
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Rabiatul Adawiyah Minhat
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Mun Kuen Soh
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Frannie Jiuyi Teo
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Yvonne Yee Chin Yeap
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Shirley Gek Kheng Seah
- Biological Defence Program, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore
| | - Conrad En Zuo Chan
- Biological Defence Program, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore
| | - Emily Connelly
- Department of Pharmaceutical Chemistry, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Nicholas J Young
- Department of Pharmaceutical Chemistry, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research (A(∗)STAR), 30 Biopolis Street, Matrix, Singapore 138671, Singapore; Infectious Diseases Laboratories (ID Labs), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore; Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117558, Singapore
| | - Laurent Renia
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore; Infectious Diseases Laboratories (ID Labs), Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Brendon John Hanson
- Biological Defence Program, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore
| | - Manuel Rosa-Calatrava
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007 Lyon, France; VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Aashish Manglik
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco (UCSF), San Francisco, CA, USA; Department of Anesthesia and Perioperative Care, UCSF, San Francisco, CA, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco (UCSF) School of Medicine, San Francisco, CA, USA; QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA; Howard Hughes Medical Institute, UCSF, San Francisco, CA, USA.
| | - Charles S Craik
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco (UCSF), San Francisco, CA, USA.
| | - Cheng-I Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Singapore.
| |
Collapse
|
36
|
Young TL, Whisenhunt KN, Jin J, LaMartina SM, Martin SM, Souma T, Limviphuvadh V, Suri F, Souzeau E, Zhang X, Dan Y, Anagnos E, Carmona S, Jody NM, Stangel N, Higuchi EC, Huang SJ, Siggs OM, Simões MJ, Lawson BM, Martin JS, Elahi E, Narooie-Nejad M, Motlagh BF, Quaggin SE, Potter HD, Silva ED, Craig JE, Egas C, Maroofian R, Maurer-Stroh S, Bradfield YS, Tompson SW. SVEP1 as a Genetic Modifier of TEK-Related Primary Congenital Glaucoma. Invest Ophthalmol Vis Sci 2021; 61:6. [PMID: 33027505 PMCID: PMC7545080 DOI: 10.1167/iovs.61.12.6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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] [Indexed: 12/15/2022] Open
Abstract
Purpose Affecting children by age 3, primary congenital glaucoma (PCG) can cause debilitating vision loss by the developmental impairment of aqueous drainage resulting in high intraocular pressure (IOP), globe enlargement, and optic neuropathy. TEK haploinsufficiency accounts for 5% of PCG in diverse populations, with low penetrance explained by variable dysgenesis of Schlemm's canal (SC) in mice. We report eight families with TEK-related PCG, and provide evidence for SVEP1 as a disease modifier in family 8 with a higher penetrance and severity. Methods Exome sequencing identified coding/splice site variants with an allele frequency less than 0.0001 (gnomAD). TEK variant effects were assayed in construct-transfected HEK293 cells via detection of autophosphorylated (active) TEK protein. An enucleated eye from an affected member of family 8 was examined via histology. SVEP1 expression in developing outflow tissues was detected by immunofluorescent staining of 7-day mouse anterior segments. SVEP1 stimulation of TEK expression in human umbilical vascular endothelial cells (HUVECs) was measured by TaqMan quantitative PCR. Results Heterozygous TEK loss-of-function alleles were identified in eight PCG families, with parent–child disease transmission observed in two pedigrees. Family 8 exhibited greater disease penetrance and severity, histology revealed absence of SC in one eye, and SVEP1:p.R997C was identified in four of the five affected individuals. During SC development, SVEP1 is secreted by surrounding tissues. SVEP1:p.R997C abrogates stimulation of TEK expression by HUVECs. Conclusions We provide further evidence for PCG caused by TEK haploinsufficiency, affirm autosomal dominant inheritance in two pedigrees, and propose SVEP1 as a modifier of TEK expression during SC development, affecting disease penetrance and severity.
Collapse
Affiliation(s)
- Terri L Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Kristina N Whisenhunt
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Jing Jin
- Feinberg Cardiovascular Research Institute and Division of Nephrology/Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
| | - Sarah M LaMartina
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Sean M Martin
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Tomokazu Souma
- Feinberg Cardiovascular Research Institute and Division of Nephrology/Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
| | - Vachiranee Limviphuvadh
- Bioinformatics Institute (BII), Agency for Science Technology and Research (A*STAR), Singapore.,Innovations in Food & Chemical Safety Programme (IFCS), A*STAR, Singapore
| | - Fatemeh Suri
- Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - Xue Zhang
- Feinberg Cardiovascular Research Institute and Division of Nephrology/Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
| | - Yongwook Dan
- Feinberg Cardiovascular Research Institute and Division of Nephrology/Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
| | - Evie Anagnos
- Feinberg Cardiovascular Research Institute and Division of Nephrology/Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
| | - Susana Carmona
- Biocant, Transfer Technology Association, Cantanhede, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Nicole M Jody
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Nickie Stangel
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Emily C Higuchi
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Samuel J Huang
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Owen M Siggs
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, South Australia, Australia
| | | | - Brendan M Lawson
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Jacob S Martin
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Elahe Elahi
- School of Biology, University College of Science, University of Tehran, Tehran, Iran
| | - Mehrnaz Narooie-Nejad
- Genetics of Non-communicable Disease Research Center, Zahedan University of Medical Science, Zahedan, Iran
| | | | - Susan E Quaggin
- Feinberg Cardiovascular Research Institute and Division of Nephrology/Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
| | - Heather D Potter
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Eduardo D Silva
- Faculty of Medicine, Institute for Biomedical Imaging and Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - Conceição Egas
- Biocant, Transfer Technology Association, Cantanhede, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Reza Maroofian
- Genetics Research Center, Molecular and Clinical Sciences Institute, St George's, University of London, Cranmer Terrace, London, United Kingdom
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science Technology and Research (A*STAR), Singapore.,Innovations in Food & Chemical Safety Programme (IFCS), A*STAR, Singapore.,Department of Biological Sciences, National University of Singapore (NUS), Singapore
| | - Yasmin S Bradfield
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Stuart W Tompson
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| |
Collapse
|
37
|
Young BE, Wei WE, Fong SW, Mak TM, Anderson DE, Chan YH, Pung R, Heng CS, Ang LW, Zheng AKE, Lee B, Kalimuddin S, Pada S, Tambyah PA, Parthasarathy P, Tan SY, Sun L, Smith GJ, Lin RTP, Leo YS, Renia L, Wang LF, Ng LF, Maurer-Stroh S, Lye DC, Lee VJ. Association of SARS-CoV-2 clades with clinical, inflammatory and virologic outcomes: An observational study. EBioMedicine 2021; 66:103319. [PMID: 33840632 PMCID: PMC8027908 DOI: 10.1016/j.ebiom.2021.103319] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Host determinants of severe coronavirus disease 2019 include advanced age, comorbidities and male sex. Virologic factors may also be important in determining clinical outcome and transmission rates, but limited patient-level data is available. METHODS We conducted an observational cohort study at seven public hospitals in Singapore. Clinical and laboratory data were collected and compared between individuals infected with different SARS-CoV-2 clades. Firth's logistic regression was used to examine the association between SARS-CoV-2 clade and development of hypoxia, and quasi-Poisson regression to compare transmission rates. Plasma samples were tested for immune mediator levels and the kinetics of viral replication in cell culture were compared. FINDINGS 319 patients with PCR-confirmed SARS-CoV-2 infection had clinical and virologic data available for analysis. 29 (9%) were infected with clade S, 90 (28%) with clade L/V, 96 (30%) with clade G (containing D614G variant), and 104 (33%) with other clades 'O' were assigned to lineage B.6. After adjusting for age and other covariates, infections with clade S (adjusted odds ratio (aOR) 0·030 (95% confidence intervals (CI): 0·0002-0·29)) or clade O (B·6) (aOR 0·26 (95% CI 0·064-0·93)) were associated with lower odds of developing hypoxia requiring supplemental oxygen compared with clade L/V. Patients infected with clade L/V had more pronounced systemic inflammation with higher concentrations of pro-inflammatory cytokines, chemokines and growth factors. No significant difference in the severity of clade G infections was observed (aOR 0·95 (95% CI: 0·35-2·52). Though viral loads were significantly higher, there was no evidence of increased transmissibility of clade G, and replicative fitness in cell culture was similar for all clades. INTERPRETATION Infection with clades L/V was associated with increased severity and more systemic release of pro-inflammatory cytokines. Infection with clade G was not associated with changes in severity, and despite higher viral loads there was no evidence of increased transmissibility.
Collapse
Affiliation(s)
- Barnaby E Young
- National Centre for Infectious Diseases, Singapore; Deaprtment of Infectious Diseases, Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Wycliffe E Wei
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore; Singapore Ministry of Health, Singapore
| | - Siew-Wai Fong
- A*STAR ID Labs, Agency for Science, Technology and Research (A*STAR), Singapore; Singapore Immunology Network, A*STAR, Singapore; Department of Biological Science, National University of Singapore, Singapore
| | - Tze-Minn Mak
- National Centre for Infectious Diseases, Singapore
| | | | - Yi-Hao Chan
- Singapore Immunology Network, A*STAR, Singapore; Singapore Immunology Network, A*STAR, Singapore
| | - Rachael Pung
- Singapore Ministry of Health, Singapore; London School of Hygiene and Tropical Medicine, London, UK
| | | | - Li Wei Ang
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore
| | | | - Bernett Lee
- Singapore Immunology Network, A*STAR, Singapore
| | - Shirin Kalimuddin
- Duke NUS Medical School, Singapore; Singapore General Hospital of Singapore, Singapore
| | | | - Paul A Tambyah
- National University Health System, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | | | | | | | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore; Deaprtment of Infectious Diseases, Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Laurent Renia
- Singapore Immunology Network, A*STAR, Singapore; Singapore Immunology Network, A*STAR, Singapore
| | | | - Lisa Fp Ng
- Singapore Immunology Network, A*STAR, Singapore; Singapore Immunology Network, A*STAR, Singapore
| | | | - David Chien Lye
- National Centre for Infectious Diseases, Singapore; Deaprtment of Infectious Diseases, Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vernon J Lee
- Singapore Ministry of Health, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
| |
Collapse
|
38
|
Ooi KH, Liu MM, Tay JWD, Teo SY, Kaewsapsak P, Jin S, Lee CK, Hou J, Maurer-Stroh S, Lin W, Yan B, Yan G, Gao YG, Tan MH. An engineered CRISPR-Cas12a variant and DNA-RNA hybrid guides enable robust and rapid COVID-19 testing. Nat Commun 2021; 12:1739. [PMID: 33741959 PMCID: PMC7979722 DOI: 10.1038/s41467-021-21996-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
Extensive testing is essential to break the transmission of SARS-CoV-2, which causes the ongoing COVID-19 pandemic. Here, we present a CRISPR-based diagnostic assay that is robust to viral genome mutations and temperature, produces results fast, can be applied directly on nasopharyngeal (NP) specimens without RNA purification, and incorporates a human internal control within the same reaction. Specifically, we show that the use of an engineered AsCas12a enzyme enables detection of wildtype and mutated SARS-CoV-2 and allows us to perform the detection step with loop-mediated isothermal amplification (LAMP) at 60-65 °C. We also find that the use of hybrid DNA-RNA guides increases the rate of reaction, enabling our test to be completed within 30 minutes. Utilizing clinical samples from 72 patients with COVID-19 infection and 57 healthy individuals, we demonstrate that our test exhibits a specificity and positive predictive value of 100% with a sensitivity of 50 and 1000 copies per reaction (or 2 and 40 copies per microliter) for purified RNA samples and unpurified NP specimens respectively.
Collapse
Affiliation(s)
- Kean Hean Ooi
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Mengying Mandy Liu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Jie Wen Douglas Tay
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Seok Yee Teo
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Pornchai Kaewsapsak
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Shengyang Jin
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chun Kiat Lee
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Jingwen Hou
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, Singapore
| | - Weisi Lin
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Benedict Yan
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Gabriel Yan
- Division of Infectious Diseases, Department of Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Meng How Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore.
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.
| |
Collapse
|
39
|
Chua AQ, Al Knawy B, Grant B, Legido-Quigley H, Lee WC, Leung GM, Looi MK, Maurer-Stroh S. How the lessons of previous epidemics helped successful countries fight covid-19. BMJ 2021; 372:n486. [PMID: 33707174 DOI: 10.1136/bmj.n486] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Alvin Qijia Chua
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Bandar Al Knawy
- Ministry of National Guard Health Affairs, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | | | | | - Wui-Chiang Lee
- Department of Medical Affairs and Planning, Taipei Veterans General Hospital, Taiwan
- National Yang-Ming University Institute of Hospital and Health Care Administration, Taiwan
| | | | | | | |
Collapse
|
40
|
Min N, Ong YHB, Han AX, Ho SX, Yen EWP, Ban KHK, Maurer-Stroh S, Chong CY, Chu JJH. An epidemiological surveillance of hand foot and mouth disease in paediatric patients and in community: A Singapore retrospective cohort study, 2013-2018. PLoS Negl Trop Dis 2021; 15:e0008885. [PMID: 33566802 PMCID: PMC7901731 DOI: 10.1371/journal.pntd.0008885] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 02/23/2021] [Accepted: 10/13/2020] [Indexed: 11/30/2022] Open
Abstract
Background While hand, foot and mouth disease (HFMD) is primarily self-resolving—soaring incidence rate of symptomatic HFMD effectuates economic burden in the Asia-Pacific region. Singapore has seen a conspicuous rise in the number of HFMD cases from 2010s. Here, we aims to identify the serology and genotypes responsible for such outbreaks in hospitals and childcare facilities. Methods We studied symptomatic paediatric HFMD cases from 2013 to 2018 in Singapore. Surveillance for subclinical enterovirus infections was also performed in childcares at the same time period. Results Genotyping 101 symptomatic HFMD samples revealed CV-A6 as the major etiological agent for recent outbreaks. We detected infections with CV-A6 (41.0%), EV-A71 (7%), CV-A16 (3.0%), coxsackievirus A2, CV-A2 (1.0%) and coxsackievirus A10, CV-A10 (1.0%). Phylogenetic analysis of local CV-A6 strains revealed a high level of heterogeneity compared against others worldwide, dissimilar to other HFMD causative enteroviruses for which the dominant strains and genotypes are highly region specific. We detected sub-clinical enterovirus infections in childcare centres; 17.1% (n = 245) tested positive for enterovirus in saliva, without HFMD indicative symptoms at the point of sample collection. Conclusions CV-A6 remained as the dominant HFMD causative strain in Singapore. Silent subclinical enteroviral infections were detected and warrant further investigations. In most cases, Hand Foot and Mouth Disease or HFMD typically manifest in mild fever along with sore throat and rashes on the body. From 2010 onwards, Singapore has seen a steady increase in the case number of HFMD reaching tens of thousands in recent years. HFMD is caused by intestinal viruses and in this study, we established with molecular surveillance methods that one of the causative serotypes, CV-A6 is the major etiological agent for HFMD in Singapore for the current decade. We discovered that circulating enterovirus, CV-A6 in Singapore share similarities in genetic make-up to those currently circulating strains found worldwide and found to be especially close to the ones in neighbouring countries. HFMD spreads from person to person, especially in high-risk areas such as childcare centers where children congregate. Therefore, we conducted saliva collections routinely from childcare centers across Singapore and found that subclinical enterovirus infections have also been prevailing in clusters, occurring silently and unnoticed.
Collapse
Affiliation(s)
- Nyo Min
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yasmin Hui Binn Ong
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Alvin X. Han
- Protein Sequence Analysis Group, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Si Xian Ho
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Emmerie Wong Phaik Yen
- Infectious Disease Service, Department of Pediatrics, KK Women’s and Children’s Hospital, Singapore, Singapore
| | - Kenneth Hon Kim Ban
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Protein Sequence Analysis Group, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore, Singapore, Singapore
| | - Chia Yin Chong
- Infectious Disease Service, Department of Pediatrics, KK Women’s and Children’s Hospital, Singapore, Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Collaborative and Translation Unit for HFMD, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- * E-mail:
| |
Collapse
|
41
|
Bauer DC, Metke-Jimenez A, Maurer-Stroh S, Tiruvayipati S, Wilson LOW, Jain Y, Perrin A, Ebrill K, Hansen DP, Vasan SS. Interoperable medical data: The missing link for understanding COVID-19. Transbound Emerg Dis 2021; 68:1753-1760. [PMID: 33095970 PMCID: PMC8359419 DOI: 10.1111/tbed.13892] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/14/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022]
Abstract
Being able to link clinical outcomes to SARS‐CoV‐2 virus strains is a critical component of understanding COVID‐19. Here, we discuss how current processes hamper sustainable data collection to enable meaningful analysis and insights. Following the ‘Fast Healthcare Interoperable Resource’ (FHIR) implementation guide, we introduce an ontology‐based standard questionnaire to overcome these shortcomings and describe patient 'journeys' in coordination with the World Health Organization's recommendations. We identify steps in the clinical health data acquisition cycle and workflows that likely have the biggest impact in the data‐driven understanding of this virus. Specifically, we recommend detailed symptoms and medical history using the FHIR standards. We have taken the first steps towards this by making patient status mandatory in GISAID (‘Global Initiative on Sharing All Influenza Data’), immediately resulting in a measurable increase in the fraction of cases with useful patient information. The main remaining limitation is the lack of controlled vocabulary or a medical ontology.
Collapse
Affiliation(s)
- Denis C Bauer
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Geelong, Australia, Australia.,Department of Biomedical Sciences, Macquarie University, Macquarie Park, NSW, Australia
| | - Alejandro Metke-Jimenez
- Commonwealth Scientific and Industrial Research Organisation, Australian e-Health Research Centre, Herston, QLD, Australia
| | - Sebastian Maurer-Stroh
- Agency for Science Technology and Research, Bioinformatics Institute, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,National Public Health Laboratory, National Centre for Infectious Diseases, Ministry of Health, Singapore, Singapore.,Global Initiative on Sharing All Influenza Data (GISAID), Munich, Germany
| | - Suma Tiruvayipati
- Global Initiative on Sharing All Influenza Data (GISAID), Munich, Germany.,Infectious Diseases Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Bacterial Genomics Laboratory, Genome Institute of Singapore, Singapore, Singapore
| | - Laurence O W Wilson
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Geelong, Australia, Australia
| | - Yatish Jain
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Geelong, Australia, Australia
| | - Amandine Perrin
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France.,Microbial Evolutionary Genomics, Institut Pasteur, UMR 3525 CNRS, Paris, France.,Collège doctoral, Sorbonne Université, Paris, France
| | - Kate Ebrill
- Commonwealth Scientific and Industrial Research Organisation, Australian e-Health Research Centre, Herston, QLD, Australia
| | - David P Hansen
- Commonwealth Scientific and Industrial Research Organisation, Australian e-Health Research Centre, Herston, QLD, Australia
| | - Seshadri S Vasan
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia.,Department of Health Sciences, University of York, York, UK
| |
Collapse
|
42
|
Bose U, Broadbent JA, Juhász A, Karnaneedi S, Johnston EB, Stockwell S, Byrne K, Limviphuvadh V, Maurer-Stroh S, Lopata AL, Colgrave ML. Protein extraction protocols for optimal proteome measurement and arginine kinase quantitation from cricket Acheta domesticus for food safety assessment. Food Chem 2021; 348:129110. [PMID: 33508605 DOI: 10.1016/j.foodchem.2021.129110] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 12/10/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/20/2022]
Abstract
Insects have been consumed by people for millennia and have recently been proposed as a complementary, sustainable source of protein to feed the world's growing population. Insects and crustaceans both belong to the arthropod family. Crustacean (shellfish) allergies are common and potentially severe; hence, the cross-reactivity of the immune system with insect proteins is a potential health concern. Herein, LC-MS/MS was used to explore the proteome of whole, roasted whole and roasted powdered cricket products. Eight protein extraction protocols were compared using the total number of protein and distinct peptide identifications. Within these data, 20 putative allergens were identified, of which three were arginine kinase (AK) proteoforms. Subsequently, a multiple reaction monitoring MS assay was developed for the AK proteoforms and applied to a subset of extracts. This targeted assay demonstrated that allergen abundance/detectability varies according to the extraction method as well as the food processing method.
Collapse
Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - James A Broadbent
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Shaymaviswanathan Karnaneedi
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Elecia B Johnston
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Sally Stockwell
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Keren Byrne
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Vachiranee Limviphuvadh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore; IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore
| | - Sebastian Maurer-Stroh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore; IFCS Programme, Singapore Institute for Food and Biotechnology Innovation, Agency for Science, Technology and Research, Singapore; Department of Biological Sciences, National University of Singapore, Singapore
| | - Andreas L Lopata
- Molecular Allergy Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia.
| |
Collapse
|
43
|
Koel BF, Vigeveno RM, Pater M, Koekkoek SM, Han AX, Tuan HM, Anh TTN, Hung NT, Thinh LQ, Hai LT, Ngoc HTB, Chau NVV, Ngoc NM, Chokephaibulkit K, Puthavathana P, Kinh NV, Trinh T, Lee RTC, Maurer-Stroh S, Eggink D, Thanh TT, Tan LV, van Doorn HR, de Jong MD. Longitudinal sampling is required to maximize detection of intrahost A/H3N2 virus variants. Virus Evol 2020; 6:veaa088. [PMID: 33343927 PMCID: PMC7733607 DOI: 10.1093/ve/veaa088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Seasonal human influenza viruses continually change antigenically to escape from neutralizing antibodies. It remains unclear how genetic variation in the intrahost virus population and selection at the level of individual hosts translates to the fast-paced evolution observed at the global level because emerging intrahost antigenic variants are rarely detected. We tracked intrahost variants in the hemagglutinin and neuraminidase surface proteins using longitudinally collected samples from 52 patients infected by A/H3N2 influenza virus, mostly young children, who received oseltamivir treatment. We identified emerging putative antigenic variants and oseltamivir-resistant variants, most of which remained detectable in samples collected at subsequent days, and identified variants that emerged intrahost immediately prior to increases in global rates. In contrast to most putative antigenic variants, oseltamivir-resistant variants rapidly increased to high frequencies in the virus population. Importantly, the majority of putative antigenic variants and oseltamivir-resistant variants were first detectable four or more days after onset of symptoms or start of treatment, respectively. Our observations demonstrate that de novo variants emerge, and may be positively selected, during the course of infection. Additionally, based on the 4–7 days post-treatment delay in emergence of oseltamivir-resistant variants in six out of the eight individuals with such variants, we find that limiting sample collection for routine surveillance and diagnostic testing to early timepoints after onset of symptoms can potentially preclude detection of emerging, positively selected variants.
Collapse
Affiliation(s)
- B F Koel
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - R M Vigeveno
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - M Pater
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - S M Koekkoek
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - A X Han
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | - N T Hung
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - L Q Thinh
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - L T Hai
- Vietnam National Children's Hospital, Hanoi, Vietnam
| | - H T B Ngoc
- Vietnam National Children's Hospital, Hanoi, Vietnam
| | - N V V Chau
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - N M Ngoc
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | | | - N V Kinh
- National Hospital of Tropical Diseases, Hanoi, Vietnam
| | - T Trinh
- National Hospital of Tropical Diseases, Hanoi, Vietnam
| | - R T C Lee
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore 138671 Singapore
| | - S Maurer-Stroh
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore 138671 Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.,National Public Health Laboratory, National Centre for Infectious Diseases, Ministry of Health, Singapore 308442, Singapore
| | - D Eggink
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - T T Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - L V Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - H R van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - M D de Jong
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
44
|
Hochreiter B, Chong CS, Hartig A, Maurer-Stroh S, Berger J, Schmid JA, Kunze M. A Novel FRET Approach Quantifies the Interaction Strength of Peroxisomal Targeting Signals and Their Receptor in Living Cells. Cells 2020; 9:cells9112381. [PMID: 33143123 PMCID: PMC7693011 DOI: 10.3390/cells9112381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 02/02/2023] Open
Abstract
Measuring Förster–resonance–energy–transfer (FRET) efficiency allows the investigation of protein–protein interactions (PPI), but extracting quantitative measures of affinity necessitates highly advanced technical equipment or isolated proteins. We demonstrate the validity of a recently suggested novel approach to quantitatively analyze FRET-based experiments in living mammalian cells using standard equipment using the interaction between different type-1 peroxisomal targeting signals (PTS1) and their soluble receptor peroxin 5 (PEX5) as a model system. Large data sets were obtained by flow cytometry coupled FRET measurements of cells expressing PTS1-tagged EGFP together with mCherry fused to the PTS1-binding domain of PEX5, and were subjected to a fitting algorithm extracting a quantitative measure of the interaction strength. This measure correlates with results obtained by in vitro techniques and a two-hybrid assay, but is unaffected by the distance between the fluorophores. Moreover, we introduce a live cell competition assay based on this approach, capable of depicting dose- and affinity-dependent modulation of the PPI. Using this system, we demonstrate the relevance of a sequence element next to the core tripeptide in PTS1 motifs for the interaction strength between PTS1 and PEX5, which is supported by a structure-based computational prediction of the binding energy indicating a direct involvement of this sequence in the interaction.
Collapse
Affiliation(s)
- Bernhard Hochreiter
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, 1090 Vienna, Austria;
| | - Cheng-Shoong Chong
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore; (C.-S.C.); (S.M.-S.)
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore
| | - Andreas Hartig
- Department of Biochemistry and Cell Biology, Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria;
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore; (C.-S.C.); (S.M.-S.)
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Johannes Berger
- Center for Brain Research, Department of Pathobiology of the Nervous System, Medical University of Vienna, 1090 Vienna, Austria;
| | - Johannes A. Schmid
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, 1090 Vienna, Austria;
- Correspondence: (J.A.S.); (M.K.)
| | - Markus Kunze
- Center for Brain Research, Department of Pathobiology of the Nervous System, Medical University of Vienna, 1090 Vienna, Austria;
- Correspondence: (J.A.S.); (M.K.)
| |
Collapse
|
45
|
Jaladanki CK, He Y, Zhao LN, Maurer-Stroh S, Loo LH, Song H, Fan H. Virtual screening of potentially endocrine-disrupting chemicals against nuclear receptors and its application to identify PPARγ-bound fatty acids. Arch Toxicol 2020; 95:355-374. [PMID: 32909075 PMCID: PMC7811525 DOI: 10.1007/s00204-020-02897-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 07/02/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022]
Abstract
Nuclear receptors (NRs) are key regulators of energy homeostasis, body development, and sexual reproduction. Xenobiotics binding to NRs may disrupt natural hormonal systems and induce undesired adverse effects in the body. However, many chemicals of concerns have limited or no experimental data on their potential or lack-of-potential endocrine-disrupting effects. Here, we propose a virtual screening method based on molecular docking for predicting potential endocrine-disrupting chemicals (EDCs) that bind to NRs. For 12 NRs, we systematically analyzed how multiple crystal structures can be used to distinguish actives and inactives found in previous high-throughput experiments. Our method is based on (i) consensus docking scores from multiple structures at a single functional state (agonist-bound or antagonist-bound), (ii) multiple functional states (agonist-bound and antagonist-bound), and (iii) multiple pockets (orthosteric site and alternative sites) of these NRs. We found that the consensus enrichment from multiple structures is better than or comparable to the best enrichment from a single structure. The discriminating power of this consensus strategy was further enhanced by a chemical similarity-weighted scoring scheme, yielding better or comparable enrichment for all studied NRs. Applying this optimized method, we screened 252 fatty acids against peroxisome proliferator-activated receptor gamma (PPARγ) and successfully identified 3 previously unknown fatty acids with Kd = 100-250 μM including two furan fatty acids: furannonanoic acid (FNA) and furanundecanoic acid (FUA), and one cyclopropane fatty acid: phytomonic acid (PTA). These results suggested that the proposed method can be used to rapidly screen and prioritize potential EDCs for further experimental evaluations.
Collapse
Affiliation(s)
- Chaitanya K Jaladanki
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore
- Toxicity Mode-of-Action Discovery (ToxMAD) Platform, Innovations in Food and Chemical Safety Programme, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Yang He
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Li Na Zhao
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore
- Toxicity Mode-of-Action Discovery (ToxMAD) Platform, Innovations in Food and Chemical Safety Programme, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Lit-Hsin Loo
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore
- Toxicity Mode-of-Action Discovery (ToxMAD) Platform, Innovations in Food and Chemical Safety Programme, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Haiwei Song
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore.
| | - Hao Fan
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore.
| |
Collapse
|
46
|
Young BE, Fong SW, Chan YH, Mak TM, Ang LW, Anderson DE, Lee CYP, Amrun SN, Lee B, Goh YS, Su YCF, Wei WE, Kalimuddin S, Chai LYA, Pada S, Tan SY, Sun L, Parthasarathy P, Chen YYC, Barkham T, Lin RTP, Maurer-Stroh S, Leo YS, Wang LF, Renia L, Lee VJ, Smith GJD, Lye DC, Ng LFP. Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study. Lancet 2020; 396:603-611. [PMID: 32822564 PMCID: PMC7434477 DOI: 10.1016/s0140-6736(20)31757-8] [Citation(s) in RCA: 305] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with a 382-nucleotide deletion (∆382) in the open reading frame 8 (ORF8) region of the genome have been detected in Singapore and other countries. We investigated the effect of this deletion on the clinical features of infection. METHODS We retrospectively identified patients who had been screened for the ∆382 variant and recruited to the PROTECT study-a prospective observational cohort study conducted at seven public hospitals in Singapore. We collected clinical, laboratory, and radiological data from patients' electronic medical records and serial blood and respiratory samples taken during hospitalisation and after discharge. Individuals infected with the ∆382 variant were compared with those infected with wild-type SARS-CoV-2. Exact logistic regression was used to examine the association between the infection groups and the development of hypoxia requiring supplemental oxygen (an indicator of severe COVID-19, the primary endpoint). Follow-up for the study's primary endpoint is completed. FINDINGS Between Jan 22 and March 21, 2020, 278 patients with PCR-confirmed SARS-CoV-2 infection were screened for the ∆382 deletion and 131 were enrolled onto the study, of whom 92 (70%) were infected with the wild-type virus, ten (8%) had a mix of wild-type and ∆382-variant viruses, and 29 (22%) had only the ∆382 variant. Development of hypoxia requiring supplemental oxygen was less frequent in the ∆382 variant group (0 [0%] of 29 patients) than in the wild-type only group (26 [28%] of 92; absolute difference 28% [95% CI 14-28]). After adjusting for age and presence of comorbidities, infection with the ∆382 variant only was associated with lower odds of developing hypoxia requiring supplemental oxygen (adjusted odds ratio 0·07 [95% CI 0·00-0·48]) compared with infection with wild-type virus only. INTERPRETATION The ∆382 variant of SARS-CoV-2 seems to be associated with a milder infection. The observed clinical effects of deletions in ORF8 could have implications for the development of treatments and vaccines. FUNDING National Medical Research Council Singapore.
Collapse
Affiliation(s)
- Barnaby E Young
- National Centre for Infectious Diseases, Singapore; Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Siew-Wai Fong
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore; Department of Biological Sciences, National University of Singapore, Singapore
| | - Yi-Hao Chan
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore
| | | | - Li Wei Ang
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore
| | | | - Cheryl Yi-Pin Lee
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore
| | - Siti Naqiah Amrun
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore
| | - Yun Shan Goh
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore
| | - Yvonne C F Su
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Wycliffe E Wei
- National Public Health and Epidemiology Unit, National Centre for Infectious Diseases, Singapore
| | - Shirin Kalimuddin
- Duke-NUS Medical School, National University of Singapore, Singapore; Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Louis Yi Ann Chai
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Medicine, National University Health System, Singapore
| | - Surinder Pada
- Department of Medicine, Infectious Diseases Service, Ng Teng Fong General Hospital, Singapore
| | - Seow Yen Tan
- Department of Infectious Diseases, Changi General Hospital, Singapore
| | | | | | | | - Timothy Barkham
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Sebastian Maurer-Stroh
- National Centre for Infectious Diseases, Singapore; Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore; Department of Biological Sciences, National University of Singapore, Singapore; Global Initiative on Sharing All Influenza Data, Munich, Germany
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore; Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Lin-Fa Wang
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Laurent Renia
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore
| | - Vernon J Lee
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Ministry of Health, Singapore
| | - Gavin J D Smith
- Duke-NUS Medical School, National University of Singapore, Singapore.
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore; Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lisa F P Ng
- Infectious Diseases Horizontal Technology Centre, Agency for Science, Technology, and Research, Singapore; Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore.
| |
Collapse
|
47
|
Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, Melidou A, Neher RA, O'Toole Á, Pereyaslov D. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. ACTA ACUST UNITED AC 2020; 25. [PMID: 32794443 PMCID: PMC7427299 DOI: 10.2807/1560-7917.es.2020.25.32.2001410] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.
Collapse
Affiliation(s)
- Erik Alm
- The European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Eeva K Broberg
- The European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Thomas Connor
- Cardiff University School of Biosciences, Cardiff, United Kingdom.,Public Health Wales Microbiology, Cardiff, United Kingdom
| | | | - Andrey B Komissarov
- Smorodintsev Research Institute of Influenza, Saint Petersburg, Russian Federation
| | - Sebastian Maurer-Stroh
- Global Initiative on Sharing All Influenza Data (GISAID), Munich, Germany.,National Public Health Laboratory, National Centre for Infectious Diseases, Ministry of Health, Singapore, Singapore.,Bioinformatics Institute, Agency for Science Technology and Research, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Angeliki Melidou
- The European Centre for Disease Prevention and Control, Stockholm, Sweden
| | | | - Áine O'Toole
- University of Edinburgh, Edinburgh, United Kingdom
| | - Dmitriy Pereyaslov
- Health Emergency Programme, WHO Regional Office for Europe, Copenhagen, Denmark
| | -
- The members of the working group are listed in the Investigator tab
| | | |
Collapse
|
48
|
Krutz NL, Kimber I, Maurer-Stroh S, Gerberick GF. Determination of the relative allergenic potency of proteins: hurdles and opportunities. Crit Rev Toxicol 2020; 50:521-530. [DOI: 10.1080/10408444.2020.1793895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Nora L. Krutz
- Procter & Gamble Services Company SA, Strombeek-Bever, Belgium
| | - Ian Kimber
- University of Manchester, Faculty of Biology, Medicine and Health, Manchester, UK
| | - Sebastian Maurer-Stroh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | | |
Collapse
|
49
|
Zheng Z, Monteil VM, Maurer-Stroh S, Yew CW, Leong C, Mohd-Ismail NK, Cheyyatraivendran Arularasu S, Chow VTK, Lin RTP, Mirazimi A, Hong W, Tan YJ. Monoclonal antibodies for the S2 subunit of spike of SARS-CoV-1 cross-react with the newly-emerged SARS-CoV-2. ACTA ACUST UNITED AC 2020; 25. [PMID: 32700671 PMCID: PMC7376845 DOI: 10.2807/1560-7917.es.2020.25.28.2000291] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background A novel coronavirus, SARS-CoV-2, which emerged at the end of 2019 and causes COVID-19, has resulted in worldwide human infections. While genetically distinct, SARS-CoV-1, the aetiological agent responsible for an outbreak of severe acute respiratory syndrome (SARS) in 2002–2003, utilises the same host cell receptor as SARS-CoV-2 for entry: angiotensin-converting enzyme 2 (ACE2). Parts of the SARS-CoV-1 spike glycoprotein (S protein), which interacts with ACE2, appear conserved in SARS-CoV-2. Aim The cross-reactivity with SARS-CoV-2 of monoclonal antibodies (mAbs) previously generated against the S protein of SARS-CoV-1 was assessed. Methods The SARS-CoV-2 S protein sequence was aligned to those of SARS-CoV-1, Middle East respiratory syndrome (MERS) and common-cold coronaviruses. Abilities of mAbs generated against SARS-CoV-1 S protein to bind SARS-CoV-2 or its S protein were tested with SARS-CoV-2 infected cells as well as cells expressing either the full length protein or a fragment of its S2 subunit. Quantitative ELISA was also performed to compare binding of mAbs to recombinant S protein. Results An immunogenic domain in the S2 subunit of SARS-CoV-1 S protein is highly conserved in SARS-CoV-2 but not in MERS and human common-cold coronaviruses. Four murine mAbs raised against this immunogenic fragment could recognise SARS-CoV-2 S protein expressed in mammalian cell lines. In particular, mAb 1A9 was demonstrated to detect S protein in SARS-CoV-2-infected cells and is suitable for use in a sandwich ELISA format. Conclusion The cross-reactive mAbs may serve as useful tools for SARS-CoV-2 research and for the development of diagnostic assays for COVID-19.
Collapse
Affiliation(s)
- Zhiqiang Zheng
- Immunology programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore.,Infectious Diseases programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore
| | - Vanessa Marthe Monteil
- Public Health Agency of Sweden, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden
| | - Sebastian Maurer-Stroh
- National Public Health Laboratory (NPHL), National Centre for Infectious Diseases (NCID), Singapore.,Department of Biological Sciences (DBS), National University of Singapore, Singapore.,Bioinformatics Institute (BII), A*STAR (Agency for Science, Technology and Research), Singapore
| | - Chow Wenn Yew
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore
| | - Carol Leong
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore
| | - Nur Khairiah Mohd-Ismail
- Immunology programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore.,Infectious Diseases programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore
| | - Suganya Cheyyatraivendran Arularasu
- Immunology programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore.,Infectious Diseases programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore
| | - Vincent Tak Kwong Chow
- Infectious Diseases programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore
| | - Raymond Tzer Pin Lin
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore.,National Public Health Laboratory (NPHL), National Centre for Infectious Diseases (NCID), Singapore
| | - Ali Mirazimi
- National Veterinary Institute, Uppsala, Sweden.,Public Health Agency of Sweden, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden
| | - Wanjin Hong
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore
| | - Yee-Joo Tan
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore.,Immunology programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore.,Infectious Diseases programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore
| |
Collapse
|
50
|
Su YCF, Anderson DE, Young BE, Linster M, Zhu F, Jayakumar J, Zhuang Y, Kalimuddin S, Low JGH, Tan CW, Chia WN, Mak TM, Octavia S, Chavatte JM, Lee RTC, Pada S, Tan SY, Sun L, Yan GZ, Maurer-Stroh S, Mendenhall IH, Leo YS, Lye DC, Wang LF, Smith GJD. Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2. mBio 2020; 11:e01610-20. [PMID: 32694143 PMCID: PMC7374062 DOI: 10.1128/mbio.01610-20] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/23/2020] [Indexed: 12/27/2022] Open
Abstract
To date, limited genetic changes in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome have been described. Here, we report a 382-nucleotide (nt) deletion in SARS-CoV-2 that truncates open reading frame 7b (ORF7b) and ORF8, removing the ORF8 transcription regulatory sequence (TRS) and eliminating ORF8 transcription. The earliest 382-nt deletion variant was detected in Singapore on 29 January 2020, with the deletion viruses circulating in the country and accounting for 23.6% (45/191) of SARS-CoV-2 samples screened in this study. SARS-CoV-2 with the same deletion has since been detected in Taiwan, and other ORF7b/8 deletions of various lengths, ranging from 62 nt to 345 nt, have been observed in other geographic locations, including Australia, Bangladesh, and Spain. Mutations or deletions in ORF8 of SARS-CoV have been associated with reduced replicative fitness and virus attenuation. In contrast, the SARS-CoV-2 382-nt deletion viruses showed significantly higher replicative fitness in vitro than the wild type, while no difference was observed in patient viral load, indicating that the deletion variant viruses retained their replicative fitness. A robust antibody response to ORF8 has been observed in SARS-CoV-2 infection, suggesting that the emergence of ORF8 deletions may be due to immune-driven selection and that further deletion variants may emerge during the sustained transmission of SARS-CoV-2 in humans.IMPORTANCE During the SARS epidemic in 2003/2004, a number of deletions were observed in ORF8 of SARS-CoV, and eventually deletion variants became predominant, leading to the hypothesis that ORF8 was an evolutionary hot spot for adaptation of SARS-CoV to humans. However, due to the successful control of the SARS epidemic, the importance of these deletions for the epidemiological fitness of SARS-CoV in humans could not be established. The emergence of multiple SARS-CoV-2 strains with ORF8 deletions, combined with evidence of a robust immune response to ORF8, suggests that the lack of ORF8 may assist with host immune evasion. In addition to providing a key insight into the evolutionary behavior of SARS-CoV-2 as the virus adapts to its new human hosts, the emergence of ORF8 deletion variants may also impact vaccination strategies.
Collapse
Affiliation(s)
- Yvonne C F Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Barnaby E Young
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
| | - Martin Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jayanthi Jayakumar
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yan Zhuang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Shirin Kalimuddin
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Singapore General Hospital, Singapore
| | - Jenny G H Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Singapore General Hospital, Singapore
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Tze Minn Mak
- National Centre for Infectious Diseases, Singapore
| | | | | | - Raphael T C Lee
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | | | | | | | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore
- Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
- Duke Global Health Institute, Duke University, North Carolina, USA
| | - Gavin J D Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore
- Duke Global Health Institute, Duke University, North Carolina, USA
| |
Collapse
|