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Nhu LNT, Chambers M, Chantratita N, Cheah PY, Day NP, Dejnirattisai W, Dunachie SJ, Grifoni A, Hamers RL, Hill J, Jones EY, Klenerman P, Mongkolsapaya J, Screaton G, Sette A, Stuart DI, Tan CW, Thwaites G, Thanh VD, Wang LF, Tan LV. Southeast Asia initiative to combat SARS-CoV-2 variants (SEACOVARIANTS) consortium. Wellcome Open Res 2024; 9:181. [PMID: 39022321 PMCID: PMC11252647 DOI: 10.12688/wellcomeopenres.20742.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 07/20/2024] Open
Abstract
A strong and effective COVID-19 and future pandemic responses rely on global efforts to carry out surveillance of infections and emerging SARS-CoV-2 variants and to act accordingly in real time. Many countries in Southeast Asia lack capacity to determine the potential threat of new variants, or other emerging infections. Funded by Wellcome, the Southeast Asia initiative to combat SARS-CoV-2 variants (SEACOVARIANTS) consortium aims to develop and apply a multidisciplinary research platform in Southeast Asia (SEA) for rapid assessment of the biological significance of SARS-CoV-2 variants, thereby informing coordinated local, regional and global responses to the COVID-19 pandemic. Our proposal is delivered by the Vietnam and Thailand Wellcome Africa Asia Programmes, bringing together a multidisciplinary team in Indonesia, Thailand and Vietnam with partners in Singapore, the UK and the USA. Herein we outline five work packages to deliver strengthened regional scientific capacity that can be rapidly deployed for future outbreak responses.
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Affiliation(s)
| | - Mary Chambers
- Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Phaik Yeong Cheah
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicholas P.J. Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Wanwisa Dejnirattisai
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Susanna J. Dunachie
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Alba Grifoni
- La Jolla Institute for Immunology, San Diego, California, USA
| | - Raph L. Hamers
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
- Oxford University Clinical Research Unit Indonesia, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Jennifer Hill
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - E. Yvonne Jones
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Paul Klenerman
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Juthathip Mongkolsapaya
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, England, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Gavin Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, England, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | | | - David I. Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - Vu Duy Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
| | - SEACOVARIANTS Consortium
- Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
- La Jolla Institute for Immunology, San Diego, California, USA
- Oxford University Clinical Research Unit Indonesia, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, England, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
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Ting NI, Dang-Xuan S, Gilbert J, Nguyen NTT, Lam S, Nguyen-Viet H. A glance into traditional pig slaughtering practices in Vietnam and opportunities for zoonotic disease prevention. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2023.1101282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
IntroductionAfrican swine fever in Vietnam is contributing to existing concerns over zoonotic disease transmission from sick pigs to humans. While slaughterhouses are key sites of occupational hazards to workers and contamination of meat, the specific slaughtering practices contributing to zoonotic occupational and foodborne disease risks remain under-researched. Our objective is to identify and characterize aspects of pig slaughtering processes that contribute to such risks.MethodsWe draw on qualitative observations, photos, and videos from three mobile slaughterhouses and seven abattoirs in Hung Yen, Vietnam.ResultsBased on our analysis, areas likely leading to zoonotic disease risks include slaughtering procedures, personal hygiene of workers, equipment sanitation, and facility sanitation. Within the small-scale swine industry, slaughtering practices are long-standing and difficult to change.ConclusionOur study underscores the importance of hygiene training of workers, improvements to equipment and facilities, and awareness-building activities targeting consumers to reduce the burden of zoonotic disease risks in small-scale pig slaughter settings.
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Thi Kha Tu N, Thi Thu Hong N, Thi Han Ny N, My Phuc T, Thi Thanh Tam P, van Doorn HR, Dang Trung Nghia H, Thao Huong D, An Han D, Thi Thu Ha L, Deng X, Thwaites G, Delwart E, Virtala AMK, Vapalahti O, Baker S, Van Tan L. The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections. Viruses 2020; 12:E960. [PMID: 32872469 PMCID: PMC7552073 DOI: 10.3390/v12090960] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/11/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respiratory diseases. Fifteen virus RT-PCR-positive samples were included as controls, while the other 76 samples were RT-PCR negative for a wide panel of respiratory pathogens. Eukaryotic viruses detected by mNGS were then screened by PCR (using primers based on mNGS-derived contigs) in all samples to compare viral detection by mNGS versus PCR and assess the utility of mNGS in routine diagnostics. mNGS identified expected human rhinoviruses, enteroviruses, influenza A virus, coronavirus OC43, and respiratory syncytial virus (RSV) A in 13 of 15 (86.7%) positive control samples. Additionally, rotavirus, torque teno virus, human papillomavirus, human betaherpesvirus 7, cyclovirus, vientovirus, gemycircularvirus, and statovirus were identified through mNGS. Notably, complete genomes of novel cyclovirus, gemycircularvirus, and statovirus were genetically characterized. Using PCR screening, the novel cyclovirus was additionally detected in 5 and the novel gemycircularvirus in 12 of the remaining samples included for mNGS analysis. Our studies therefore provide pioneering data of the virome of acute-respiratory diseases from individuals at risk of zoonotic infections. The mNGS protocol/pipeline applied here is sensitive for the detection of a variety of viruses, including novel ones. More frequent detections of the novel viruses by PCR than by mNGS on the same samples suggests that PCR remains the most sensitive diagnostic test for viruses whose genomes are known. The detection of novel viruses expands our understanding of the respiratory virome of animal-exposed humans and warrant further studies.
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Affiliation(s)
- Nguyen Thi Kha Tu
- Doctoral School in Health Sciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
- Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam; (D.A.H.); (L.T.T.H.)
| | - Nguyen Thi Thu Hong
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Nguyen Thi Han Ny
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Tran My Phuc
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Pham Thi Thanh Tam
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Ha Noi 8000, Vietnam;
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Ho Dang Trung Nghia
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Dang Thao Huong
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Duong An Han
- Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam; (D.A.H.); (L.T.T.H.)
| | - Luu Thi Thu Ha
- Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam; (D.A.H.); (L.T.T.H.)
| | - Xutao Deng
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Eric Delwart
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Anna-Maija K. Virtala
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland;
| | - Olli Vapalahti
- Doctoral School in Health Sciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Virology and Immunology, HUSLAB, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK;
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
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