1
|
Brindle HE, Nadjm B, Choisy M, Christley R, Griffiths M, Baker S, Bryant JE, Campbell JI, Nguyen VVC, Nguyen TND, Vu TTH, Nguyen VH, Hoang BL, Le XL, Pham HM, Ta TDN, Ho DTN, Tran TN, Nguyen THN, Tran MP, Pham THP, Le VT, Nguyen DT, Hau TTT, Nguyen NV, Wertheim HFL, Thwaites GE, van Doorn HR. Aetiology and Potential Animal Exposure in Central Nervous System Infections in Vietnam. Ecohealth 2022; 19:463-474. [PMID: 36227390 PMCID: PMC9558024 DOI: 10.1007/s10393-022-01611-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 05/20/2022] [Indexed: 06/16/2023]
Abstract
An estimated 73% of emerging infections are zoonotic in origin, with animal contact and encroachment on their habitats increasing the risk of spill-over events. In Vietnam, close exposure to a wide range of animals and animal products can lead to acquisition of zoonotic pathogens, a number of which cause central nervous system (CNS) infections. However, studies show the aetiology of CNS infections remains unknown in around half of cases. We used samples and data from hospitalised patients with CNS infections, enrolled into the Vietnam Initiative on Zoonotic Infections multicentre study, to determine the association between aetiology and animal contact including those in whom the cause was unknown. Among 933 patients, a pathogen or an antibody response to it was identified in 291 (31.2%, 95% CI 28.3-34.3%). The most common pathogens were Streptococcus suis (n = 91 (9.8%, 8.0-11.9%)) and Japanese encephalitis virus (JEV) (n = 72 (7.7%, 6.1-9.7%)). Commonly reported animal contact included keeping, raising or handling (n = 364 (39.0%, 35.9-42.2%)) and handling, cooking or consuming raw meat, blood or viscera in the 2 weeks prior to symptom onset (n = 371 (39.8%, 36.6-43.0%)), with the latter most commonly from pigs (n = 343 (36.9%, 33.8-40.1%). There was no association between an unknown aetiology and exposure to animals in a multivariate logistic regression. Further testing for unknown or undetected pathogens may increase diagnostic yield, however, given the high proportion of zoonotic pathogens and the presence of risk factors, increasing public awareness about zoonoses and preventive measures can be considered.
Collapse
Affiliation(s)
- Hannah E Brindle
- Oxford University Clinical Research Unit, Hanoi, Vietnam.
- Institute of Infection and Global Health and National Institute, University of Liverpool, Liverpool, UK.
| | - Behzad Nadjm
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Serekunda, The Gambia
| | - Marc Choisy
- 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, UK.
| | - Rob Christley
- Institute of Infection and Global Health and National Institute, University of Liverpool, Liverpool, UK
| | - Michael Griffiths
- Institute of Infection and Global Health and National Institute, University of Liverpool, Liverpool, UK
| | - Stephen Baker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- The Global Fund to Fight AIDS, Tuberculosis and Malaria, Geneva, Switzerland
| | - James I Campbell
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Ty Thi Hang Vu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Bao Long Hoang
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Hanoi Medical University, Hanoi, Vietnam
| | - Xuan Luat Le
- National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Ha My Pham
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | | | | | | | - My Phuc Tran
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Van Tan Le
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Thi Thu Trang Hau
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Research Group 2, AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Heiman F L Wertheim
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- RadboudUMC, Nijmegen, The Netherlands
| | - Guy E 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, UK
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
2
|
Brindle HE, Nadjm B, Choisy M, Christley R, Griffiths M, Baker S, Bryant JE, Campbell JI, Nguyen VVC, Nguyen TND, Vu TTH, Nguyen VH, Hoang BL, Le XL, Pham HM, Ta TDN, Ho DTN, Tran TN, Nguyen THN, Tran MP, Pham THP, Le VT, Nguyen DT, Hau TTT, Nguyen NV, Wertheim HFL, Thwaites GE, van Doorn HR. Correction: Aetiology and Potential Animal Exposure in Central Nervous System Infections in Vietnam. Ecohealth 2022:10.1007/s10393-022-01618-3. [PMID: 36417035 DOI: 10.1007/s10393-022-01618-3] [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] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Hannah E Brindle
- Oxford University Clinical Research Unit, Hanoi, Vietnam.
- Institute of Infection and Global Health and National Institute, University of Liverpool, Liverpool, UK.
| | - Behzad Nadjm
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Serekunda, The Gambia
| | - Marc Choisy
- 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, UK.
| | - Rob Christley
- Institute of Infection and Global Health and National Institute, University of Liverpool, Liverpool, UK
| | - Michael Griffiths
- Institute of Infection and Global Health and National Institute, University of Liverpool, Liverpool, UK
| | - Stephen Baker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- The Global Fund to Fight AIDS, Tuberculosis and Malaria, Geneva, Switzerland
| | - James I Campbell
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Ty Thi Hang Vu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Bao Long Hoang
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Hanoi Medical University, Hanoi, Vietnam
| | - Xuan Luat Le
- National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Ha My Pham
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | | | | | | | - My Phuc Tran
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Van Tan Le
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Thi Thu Trang Hau
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Research Group 2, AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Heiman F L Wertheim
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- RadboudUMC, Nijmegen, The Netherlands
| | - Guy E 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, UK
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
3
|
Minh NNQ, Toi PV, Qui LM, Tinh LBB, Ngoc NT, Kim LTN, Uyen NH, Hang VTT, Chinh B’Krong NTT, Tham NT, Khoa TD, Khuong HD, Vi PQ, Phuc NNH, Vien LTM, Pouplin T, Khanh DV, Phuong PN, Lam PK, Wertheim HFL, Campbell JI, Baker S, Parry CM, Bryant JE, Schultsz C, Hung NT, de Jong MD, van Doorn HR. Antibiotic use and prescription and its effects on Enterobacteriaceae in the gut in children with mild respiratory infections in Ho Chi Minh City, Vietnam. A prospective observational outpatient study. PLoS One 2020; 15:e0241760. [PMID: 33147269 PMCID: PMC7641406 DOI: 10.1371/journal.pone.0241760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 10/10/2019] [Accepted: 10/20/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Treatment guidelines do not recommend antibiotic use for acute respiratory infections (ARI), except for streptococcal pharyngitis/tonsillitis and pneumonia. However, antibiotics are prescribed frequently for children with ARI, often in absence of evidence for bacterial infection. The objectives of this study were 1) to assess the appropriateness of antibiotic prescriptions for mild ARI in paediatric outpatients in relation to available guidelines and detected pathogens, 2) to assess antibiotic use on presentation using questionnaires and detection in urine 3) to assess the carriage rates and proportions of resistant intestinal Enterobacteriaceae before, during and after consultation. MATERIALS AND METHODS Patients were prospectively enrolled in Children's Hospital 1, Ho Chi Minh City, Vietnam and diagnoses, prescribed therapy and outcome were recorded on first visit and on follow-up after 7 days. Respiratory bacterial and viral pathogens were detected using molecular assays. Antibiotic use before presentation was assessed using questionnaires and urine HPLC. The impact of antibiotic usage on intestinal Enterobacteriaceae was assessed with semi-quantitative culture on agar with and without antibiotics on presentation and after 7 and 28 days. RESULTS A total of 563 patients were enrolled between February 2009 and February 2010. Antibiotics were prescribed for all except 2 of 563 patients. The majority were 2nd and 3rd generation oral cephalosporins and amoxicillin with or without clavulanic acid. Respiratory viruses were detected in respiratory specimens of 72.5% of patients. Antibiotic use was considered inappropriate in 90.1% and 67.5%, based on guidelines and detected pathogens, respectively. On presentation parents reported antibiotic use for 22% of patients, 41% of parents did not know and 37% denied antibiotic use. Among these three groups, six commonly used antibiotics were detected with HPLC in patients' urine in 49%, 40% and 14%, respectively. Temporary selection of 3rd generation cephalosporin resistant intestinal Enterobacteriaceae during antibiotic use was observed, with co-selection of resistance to aminoglycosides and fluoroquinolones. CONCLUSIONS We report overuse and overprescription of antibiotics for uncomplicated ARI with selection of resistant intestinal Enterobacteriaceae, posing a risk for community transmission and persistence in a setting of a highly granular healthcare system and unrestricted access to antibiotics through private pharmacies. REGISTRATION This study was registered at the International Standard Randomised Controlled Trials Number registry under number ISRCTN32862422: http://www.isrctn.com/ISRCTN32862422.
Collapse
Affiliation(s)
- Ngo Ngoc Quang Minh
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Children’s Hospital 1, Ho Chi Minh City, Vietnam
| | - Pham Van Toi
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Le Minh Qui
- Children’s Hospital 1, Ho Chi Minh City, Vietnam
| | | | | | | | - Nguyen Hanh Uyen
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Vu Thi Ty Hang
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | - Nguyen Thi Tham
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Thai Dang Khoa
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Huynh Duy Khuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Pham Quynh Vi
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Nguyen Ngoc Hong Phuc
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Le Thi Minh Vien
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Thomas Pouplin
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Doan Van Khanh
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Pham Nguyen Phuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Phung Khanh Lam
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Heiman F. L. Wertheim
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Henry Wellcome Building for Molecular Physiology, Old Road Campus, Headington, Oxford, United Kingdom
| | - James I. Campbell
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Christopher M. Parry
- Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Pl, Liverpool, United Kingdom
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Juliet E. Bryant
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Constance Schultsz
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Department of Global Health-Amsterdam, Institute of Global Health and Development, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Menno D. de Jong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Department of Medical Microbiology, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Henry Wellcome Building for Molecular Physiology, Old Road Campus, Headington, Oxford, United Kingdom
| |
Collapse
|
4
|
Hoa LNM, Sullivan SG, Mai LQ, Khvorov A, Phuong HVM, Hang NLK, Thai PQ, Thanh LT, Carolan L, Anh DD, Duong TN, Bryant JE, van Doorn HR, Wertheim HFL, Horby P, Fox A. Influenza A(H1N1)pdm09 but not A(H3N2) virus infection induces durable sero-protection: results from the Ha Nam Cohort. J Infect Dis 2020; 226:59-69. [PMID: 32484513 PMCID: PMC9373157 DOI: 10.1093/infdis/jiaa293] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 03/15/2020] [Accepted: 05/25/2020] [Indexed: 12/02/2022] Open
Abstract
Background The extent to which influenza recurrence depends upon waning immunity from prior infection is undefined. We used antibody titers of Ha-Nam cohort participants to estimate protection curves and decay trajectories. Methods Households (270) participated in influenza-like–illness (ILI) surveillance and provided blood at intervals spanning laboratory–confirmed virus transmission. Sera were tested in hemagglutination inhibition assay. Infection was defined as influenza virus-positive ILI and/or seroconversion. Median protective titers were estimated using scaled-logistic regression to model pretransmission titer against infection status in that season, limiting analysis to households with infection(s). Titers were modelled against month since infection using mixed-effects linear regression to estimate decay and when titers fell below protection thresholds. Results From December 2008–2012, 295 and 314 participants were infected with H1N1pdm09-like and A/Perth/16/09-like (H3N2Pe09) viruses, respectively. The proportion protected rose more steeply with titer for H1N1pdm09 than for H3N2Pe09, and estimated 50% protection titers were 19.6 and 37.3, respectively. Postinfection titers started higher against H3N2Pe09 but decayed more steeply than against H1N1pdm09. Seroprotection was estimated to be sustained against H1N1pdm09 but to wane by 8-months for H3N2Pe09. Conclusions Estimates indicate that infection induces durable seroprotection against H1N1pdm09 but not H3N2Pe09, which could in part account for the younger age of A(H1N1) versus A(H3N2) cases.
Collapse
Affiliation(s)
- Le Nguyen Minh Hoa
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Viet Nam
| | - Sheena G Sullivan
- The WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Doherty Department, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Fielding School of Public Health, University of California, Los Angeles, USA
| | - Le Quynh Mai
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Arseniy Khvorov
- Doherty Department, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | | | - Pham Quang Thai
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Le Thi Thanh
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Louise Carolan
- The WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Tran Nhu Duong
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Juliet E Bryant
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Viet Nam.,Center for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Viet Nam.,Center for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Heiman F L Wertheim
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Viet Nam.,Department of Medical Microbiology, Radboudumc, Nijmegen, Netherlands
| | - Peter Horby
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Viet Nam.,Center for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Annette Fox
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Viet Nam.,The WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| |
Collapse
|
5
|
Bryant JE, Azman AS, Ferrari MJ, Arnold BF, Boni MF, Boum Y, Hayford K, Luquero FJ, Mina MJ, Rodriguez-Barraquer I, Wu JT, Wade D, Vernet G, Leung DT. Serology for SARS-CoV-2: Apprehensions, opportunities, and the path forward. Sci Immunol 2020; 5:5/47/eabc6347. [PMID: 32430309 DOI: 10.1126/sciimmunol.abc6347] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/14/2020] [Indexed: 01/15/2023]
Abstract
Serological testing for SARS-CoV-2 has enormous potential to contribute to COVID-19 pandemic response efforts. However, the required performance characteristics of antibody tests will critically depend on the use case (individual-level vs. population-level).
Collapse
Affiliation(s)
- Juliet E Bryant
- Laboratory of Emerging Pathogens, Fondation Mérieux, Lyon, France
| | - Andrew S Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA.,Médecins Sans Frontières, Geneva, Switzerland
| | - Matthew J Ferrari
- Department Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Benjamin F Arnold
- Francis I Proctor Foundation, University of California San Francisco, CA, USA
| | - Maciej F Boni
- Department Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | | | - Kyla Hayford
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | | | - Michael J Mina
- Departments of Epidemiology and of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA USA
| | | | - Joseph T Wu
- WHO Collaborating Center for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Djibril Wade
- IRESSEF (Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation), Dakar, Senegal
| | - Guy Vernet
- Institut Pasteur de Bangui, Bangui, Central African Republic
| | - Daniel T Leung
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT, USA
| |
Collapse
|
6
|
Pouzol S, Tanmoy AM, Ahmed D, Khanam F, Brooks WA, Bhuyan GS, Fabre L, Bryant JE, Gustin MP, Vanhems P, Carman B, Weill FX, Qadri F, Saha S, Endtz H. Clinical Evaluation of a Multiplex PCR for the Detection of Salmonella enterica Serovars Typhi and Paratyphi A from Blood Specimens in a High-Endemic Setting. Am J Trop Med Hyg 2020; 101:513-520. [PMID: 31287048 PMCID: PMC6726943 DOI: 10.4269/ajtmh.18-0992] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Enteric fever is a major public health concern in endemic areas, particularly in infrastructure-limited countries where Salmonella Paratyphi A has emerged in increasing proportion of cases. We aimed to evaluate a method to detect Salmonella Typhi (S. Typhi) and Salmonella Paratyphi A (S. Paratyphi A) in febrile patients in Bangladesh. We conducted a prospective study enrolling patients with fever > 38°C admitted to two large urban hospitals and two outpatient clinics located in Dhaka, Bangladesh. We developed and evaluated a method combining short culture with a new molecular assay to simultaneously detect and differentiate S. Typhi and S. Paratyphi A from other Salmonella directly from 2 to 4 mL of whole blood in febrile patients (n = 680). A total of 680 cases were enrolled from the four participating sites. An increase in the detection rate (+38.8%) in S. Typhi and S. Paratyphi A was observed with a multiplex polymerase chain reaction (PCR) assay, and absence of non-typhoidal Salmonella detection was reported. All 45 healthy controls were culture and PCR negative, generating an estimated 92.9% of specificity on clinical samples. When clinical performance was assessed in the absence of blood volume prioritization for testing, a latent class model estimates clinical performance ≥ 95% in sensitivity and specificity with likelihood ratio (LR) LR+ > 10 and LR− < 0.1 for the multiplex PCR assay. The alternative method to blood culture we developed may be useful alone or in combination with culture or serological tests for epidemiological studies in high disease burden settings and should be considered as secondary endpoint test for future vaccine trials.
Collapse
Affiliation(s)
- Stephane Pouzol
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Arif Mohammad Tanmoy
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands.,Child Health Research Foundation (CHRF), Dhaka, Bangladesh
| | - Dilruba Ahmed
- International Centre for Diarrhoeal Disease Research (icddr,b), Dhaka, Bangladesh
| | - Farhana Khanam
- International Centre for Diarrhoeal Disease Research (icddr,b), Dhaka, Bangladesh
| | - W Abdullah Brooks
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Golam Sarower Bhuyan
- Institute for Developing Science and Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Laetitia Fabre
- Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France
| | - Juliet E Bryant
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Marie-Paule Gustin
- Department of Public Health, Institute of Pharmacy, University of Lyon 1, Lyon, France.,Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Philippe Vanhems
- Service d'Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France.,Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Bill Carman
- Fast Track Diagnostics, Esch sur alzette, Esch-sur-Alzette, Luxembourg
| | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research (icddr,b), Dhaka, Bangladesh
| | - Samir Saha
- Child Health Research Foundation (CHRF), Dhaka, Bangladesh
| | - Hubert Endtz
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands.,Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| |
Collapse
|
7
|
Trung NV, Hoi LT, Dien VM, Huong DT, Hoa TM, Lien VN, Van Luan P, Lewycka SO, Choisy M, Bryant JE, Nadjm B, Rogier van Doorn H, Richards AL, Van Kinh N. Clinical Manifestations and Molecular Diagnosis of Scrub Typhus and Murine Typhus, Vietnam, 2015-2017. Emerg Infect Dis 2019; 25. [PMID: 30882318 PMCID: PMC6433017 DOI: 10.3201/eid2504.180691] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Scrub typhus was the predominant rickettsial disease diagnosed among hospitalized patients with acute undifferentiated fever in northern Vietnam. Rickettsioses are endemic to Vietnam; however, only a limited number of clinical studies have been performed on these vectorborne bacteria. We conducted a prospective hospital-based study at 2 national referral hospitals in Hanoi to describe the clinical characteristics of scrub typhus and murine typhus in northern Vietnam and to assess the diagnostic applicability of quantitative real-time PCR assays to diagnose rickettsial diseases. We enrolled 302 patients with acute undifferentiated fever and clinically suspected rickettsiosis during March 2015–March 2017. We used a standardized case report form to collect clinical information and laboratory results at the time of admission and during treatment. We confirmed scrub typhus in 103 (34.1%) patients and murine typhus in 12 (3.3%) patients. These results highlight the need for increased emphasis on training for healthcare providers for earlier recognition, prevention, and treatment of rickettsial diseases in Vietnam.
Collapse
|
8
|
Genestet C, Tatai C, Berland JL, Claude JB, Westeel E, Hodille E, Fredenucci I, Rasigade JP, Ponsoda M, Jacomo V, Vachée A, Gaudart A, Gaillard JL, Roux AL, Ader F, Tararbit K, Terpant G, Bryant JE, Lina G, Dumitrescu O. Prospective Whole-Genome Sequencing in Tuberculosis Outbreak Investigation, France, 2017-2018. Emerg Infect Dis 2019; 25:589-592. [PMID: 30789329 PMCID: PMC6390740 DOI: 10.3201/eid2503.181124] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
During June 2017–April 2018, active tuberculosis with Beijing SIT1 isolates was diagnosed in 14 persons living in 4 distant cities in France. Whole-genome sequencing indicated that these patients belonged to a single transmission chain. Whole-genome sequencing–based laboratory investigations enabled prompt tracing of linked cases to improve tuberculosis control.
Collapse
|
9
|
Sealy JE, Fournie G, Trang PH, Dang NH, Sadeyen JR, Thanh TL, van Doorn HR, Bryant JE, Iqbal M. Poultry trading behaviours in Vietnamese live bird markets as risk factors for avian influenza infection in chickens. Transbound Emerg Dis 2019; 66:2507-2516. [PMID: 31357255 PMCID: PMC6899644 DOI: 10.1111/tbed.13308] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 06/18/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 01/16/2023]
Abstract
Vietnamese poultry are host to co‐circulating subtypes of avian influenza viruses, including H5N1 and H9N2, which pose a great risk to poultry productivity and to human health. AIVs circulate throughout the poultry trade network in Vietnam, with live bird markets being an integral component to this network. Traders at LBMs exhibit a variety of trading practices, which may influence the transmission of AIVs. We identified trading practices that impacted on AIV prevalence in chickens marketed in northern Vietnamese LBMs. We generated sequencing data for 31 H9N2 and two H5N6 viruses. Viruses isolated in the same LBM or from chickens sourced from the same province were genetically closer than viruses isolated in different LBMs or from chickens sourced in different provinces. The position of a vendor in the trading network impacted on their odds of having AIV‐infected chickens. Being a retailer and purchasing chickens from middlemen was associated with increased odds of infection, whereas odds decreased if vendors purchased chickens directly from large farms. Odds of infection were also higher for vendors having a greater volume of ducks unsold per day. These results indicate how the spread of AIVs is influenced by the structure of the live poultry trading network.
Collapse
Affiliation(s)
- Joshua E Sealy
- The Pirbright Institute, Pirbright, Woking, UK.,The Royal Veterinary College, London, UK
| | | | - Pham Hong Trang
- The National Centre for Veterinary Diagnostics, Hanoi, Vietnam
| | | | | | - To Long Thanh
- The National Centre for Veterinary Diagnostics, Hanoi, Vietnam.,The Department of Animal Health, Hanoi, Vietnam
| | | | - Juliet E Bryant
- Laboratory of Emerging Pathogens, Fondation Mérieux, Lyon, France
| | - Munir Iqbal
- The Pirbright Institute, Pirbright, Woking, UK
| |
Collapse
|
10
|
Genestet C, Hodille E, Westeel E, Ginevra C, Ader F, Venner S, Lina G, Bryant JE, Berland JL, Dumitrescu O. Subcultured Mycobacterium tuberculosis isolates on different growth media are fully representative of bacteria within clinical samples. Tuberculosis (Edinb) 2019; 116:61-66. [PMID: 31153520 DOI: 10.1016/j.tube.2019.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 11/16/2022]
Abstract
Mycobacterium tuberculosis (Mtb) whole genome sequencing (WGS) plays an increasingly important role in tuberculosis diagnosis and research. WGS is typically performed on biobanked isolates obtained by subculture during diagnosis. Genetic variation upon culturing is known to occur in other bacterial species. However, little is understood regarding the impact of different subculture media on genome-wide diversity and variant selection in Mtb. Here we compared WGS derived from direct sequencing of sputa samples to WGS sequences from isolates subcultured on 3 different media. Based on analysis of single nucleotide polymorphisms (SNPs), there was no evidence of variant selection caused by the different culture media used, indicating that subcultured clinical strains can be reliably used to explore genetic determinants of Mtb pathogenesis and epidemiological features.
Collapse
Affiliation(s)
- Charlotte Genestet
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université de Lyon, Lyon, France; Fondation Mérieux, Lyon, France.
| | - Elisabeth Hodille
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université de Lyon, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Lyon, France
| | - Emilie Westeel
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université de Lyon, Lyon, France; Fondation Mérieux, Lyon, France
| | - Christophe Ginevra
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université de Lyon, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Lyon, France
| | - Florence Ader
- Service des Maladies Infectieuses et Tropicales, Hôpital de la Croix Rousse, Hospices Civils de Lyon, Lyon, France
| | - Samuel Venner
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), CNRS UMR 5558, Université Lyon 1, Villeurbanne, France
| | - Gérard Lina
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université de Lyon, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Lyon, France
| | - Juliet E Bryant
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université de Lyon, Lyon, France; Fondation Mérieux, Lyon, France
| | - Jean-Luc Berland
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université de Lyon, Lyon, France; Fondation Mérieux, Lyon, France
| | - Oana Dumitrescu
- Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Université de Lyon, Lyon, France; Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Lyon, France
| | | |
Collapse
|
11
|
Do LAH, Pellet J, van Doorn HR, Tran AT, Nguyen BH, Tran TTL, Tran QH, Vo QB, Tran Dac NA, Trinh HN, Nguyen TTH, Le Binh BT, Nguyen HMK, Nguyen MT, Thai QT, Vo TV, Ngo NQM, Dang TKH, Cao NH, Tran TV, Ho LV, De Meulder B, Auffray C, Hofstra JJ, Farrar J, Bryant JE, de Jong M, Hibberd ML. Host Transcription Profile in Nasal Epithelium and Whole Blood of Hospitalized Children Under 2 Years of Age With Respiratory Syncytial Virus Infection. J Infect Dis 2019; 217:134-146. [PMID: 29029245 PMCID: PMC5853303 DOI: 10.1093/infdis/jix519] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 05/24/2017] [Accepted: 09/25/2017] [Indexed: 12/29/2022] Open
Abstract
Background Most insights into the cascade of immune events after acute respiratory syncytial virus (RSV) infection have been obtained from animal experiments or in vitro models. Methods In this study, we investigated host gene expression profiles in nasopharyngeal (NP) swabs and whole blood samples during natural RSV and rhinovirus (hRV) infection (acute versus early recovery phase) in 83 hospitalized patients <2 years old with lower respiratory tract infections. Results Respiratory syncytial virus infection induced strong and persistent innate immune responses including interferon signaling and pathways related to chemokine/cytokine signaling in both compartments. Interferon-α/β, NOTCH1 signaling pathways and potential biomarkers HIST1H4E, IL7R, ISG15 in NP samples, or BCL6, HIST2H2AC, CCNA1 in blood are leading pathways and hub genes that were associated with both RSV load and severity. The observed RSV-induced gene expression patterns did not differ significantly in NP swab and blood specimens. In contrast, hRV infection did not as strongly induce expression of innate immunity pathways, and significant differences were observed between NP swab and blood specimens. Conclusions We conclude that RSV induced strong and persistent innate immune responses and that RSV severity may be related to development of T follicular helper cells and antiviral inflammatory sequelae derived from high activation of BCL6.
Collapse
Affiliation(s)
- Lien Anh Ha Do
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Johann Pellet
- Murdoch Children's Research Institute, Melbourne, Australia
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | | | | | | | | | - Quoc Bao Vo
- Children Hospital 2, Ho Chi Minh City, Vietnam
| | | | | | | | | | | | | | | | - Thanh Vu Vo
- Children Hospital 1, Ho Chi Minh City, Vietnam
| | | | | | | | | | - Lu Viet Ho
- Children Hospital 2, Ho Chi Minh City, Vietnam
| | | | - Charles Auffray
- European Institute for Systems Biology and Medicine, Lyon, France
| | - Jorrit-Jan Hofstra
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, The Netherlands
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Menno de Jong
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, in partnership with the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom.,Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, The Netherlands
| | - Martin L Hibberd
- Genome Institute of Singapore.,London School of Hygiene & Tropical Medicine, United Kingdom
| |
Collapse
|
12
|
Lam HM, Wesolowski A, Hung NT, Nguyen TD, Nhat NTD, Todd S, Vinh DN, Vy NHT, Thao TTN, Thanh NTL, Tin PT, Minh NNQ, Bryant JE, Buckee CO, Ngoc TV, Chau NVV, Thwaites GE, Farrar J, Tam DTH, Vinh H, Boni MF. Nonannual seasonality of influenza-like illness in a tropical urban setting. Influenza Other Respir Viruses 2018; 12:742-754. [PMID: 30044029 PMCID: PMC6185894 DOI: 10.1111/irv.12595] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND In temperate and subtropical climates, respiratory diseases exhibit seasonal peaks in winter. In the tropics, with no winter, peak timings are irregular. METHODS To obtain a detailed picture of influenza-like illness (ILI) patterns in the tropics, we established an mHealth study in community clinics in Ho Chi Minh City (HCMC). During 2009-2015, clinics reported daily case numbers via SMS, with a subset performing molecular diagnostics for influenza virus. This real-time epidemiology network absorbs 6000 ILI reports annually, one or two orders of magnitude more than typical surveillance systems. A real-time online ILI indicator was developed to inform clinicians of the daily ILI activity in HCMC. RESULTS From August 2009 to December 2015, 63 clinics were enrolled and 36 920 SMS reports were received, covering approximately 1.7M outpatient visits. Approximately 10.6% of outpatients met the ILI case definition. ILI activity in HCMC exhibited strong nonannual dynamics with a dominant periodicity of 206 days. This was confirmed by time series decomposition, stepwise regression, and a forecasting exercise showing that median forecasting errors are 30%-40% lower when using a 206-day cycle. In ILI patients from whom nasopharyngeal swabs were taken, 31.2% were positive for influenza. There was no correlation between the ILI time series and the time series of influenza, influenza A, or influenza B (all P > 0.15). CONCLUSION This suggests, for the first time, that a nonannual cycle may be an essential driver of respiratory disease dynamics in the tropics. An immunological interference hypothesis is discussed as a potential underlying mechanism.
Collapse
Affiliation(s)
- Ha Minh Lam
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
| | - Amy Wesolowski
- Center for Communicable Disease DynamicsDepartment of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMassachusetts
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew Jersey
| | - Nguyen Thanh Hung
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
| | - Tran Dang Nguyen
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
| | - Nguyen Thi Duy Nhat
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
| | - Stacy Todd
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
- Liverpool School of Tropical MedicineLiverpoolUK
| | - Dao Nguyen Vinh
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
| | - Nguyen Ha Thao Vy
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
| | - Tran Thi Nhu Thao
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
| | - Nguyen Thi Le Thanh
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
| | | | - Ngo Ngoc Quang Minh
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
- Children's Hospital No. 1Ho Chi Minh CityVietnam
| | - Juliet E. Bryant
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
- Centre for Tropical Medicine and Global HealthNuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Caroline O. Buckee
- Center for Communicable Disease DynamicsDepartment of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMassachusetts
| | - Tran Van Ngoc
- Hospital for Tropical DiseasesHo Chi Minh CityVietnam
| | | | - Guy E. Thwaites
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
- Centre for Tropical Medicine and Global HealthNuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Jeremy Farrar
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
- Wellcome TrustLondonUK
| | - Dong Thi Hoai Tam
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
| | - Ha Vinh
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
- Hospital for Tropical DiseasesHo Chi Minh CityVietnam
- Department of Infectious DiseasesPham Ngoc Thach University of MedicineHo Chi Minh CityVietnam
| | - Maciej F. Boni
- Oxford University Clinical Research UnitWellcome Trust Major Overseas ProgrammeHo Chi Minh CityVietnam
- Centre for Tropical Medicine and Global HealthNuffield Department of MedicineUniversity of OxfordOxfordUK
- Center for Infectious Disease DynamicsDepartment of BiologyPennsylvania State UniversityUniversity ParkPennsylvania
| |
Collapse
|
13
|
Thi Nguyen D, Shepard SS, Burke DF, Jones J, Thor S, Nguyen LV, Nguyen TD, Balish A, Hoang DN, To TL, Iqbal M, Wentworth DE, Spackman E, van Doorn HR, Davis CT, Bryant JE. Antigenic characterization of highly pathogenic avian influenza A(H5N1) viruses with chicken and ferret antisera reveals clade-dependent variation in hemagglutination inhibition profiles. Emerg Microbes Infect 2018; 7:100. [PMID: 29855467 PMCID: PMC5981457 DOI: 10.1038/s41426-018-0100-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 01/04/2023]
Abstract
Highly pathogenic avian influenza (HPAI) A(H5N1) viruses pose a significant economic burden to the poultry industry worldwide and have pandemic potential. Poultry vaccination against HPAI A(H5N1) viruses has been an important component of HPAI control measures and has been performed in Vietnam since 2005. To systematically assess antigenic matching of current vaccines to circulating field variants, we produced a panel of chicken and ferret antisera raised against historical and contemporary Vietnamese reference viruses representing clade variants that were detected between 2001 and 2014. The antisera were used for hemagglutination inhibition (HI) assays to generate data sets for analysis by antigenic cartography, allowing for a direct comparison of results from chicken or ferret antisera. HI antigenic maps, developed with antisera from both hosts, revealed varying patterns of antigenic relationships and clustering of viruses that were dependent on the clade of viruses analyzed. Antigenic relationships between existing poultry vaccines and circulating field viruses were also aligned with in vivo protection profiles determined by previously reported vaccine challenge studies. Our results establish the feasibility and utility of HPAI A(H5N1) antigenic characterization using chicken antisera and support further experimental and modeling studies to investigate quantitative relationships between genetic variation, antigenic drift and correlates of poultry vaccine protection in vivo.
Collapse
Affiliation(s)
- Diep Thi Nguyen
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam. .,Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam. .,Oxford University Clinical Research Unit, Hanoi, Vietnam. .,Center for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
| | - Samuel S Shepard
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | | | - Joyce Jones
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Sharmi Thor
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Long Van Nguyen
- Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam
| | - Tho Dang Nguyen
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Amanda Balish
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Dang Nguyen Hoang
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Thanh Long To
- Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam
| | | | - David E Wentworth
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Erica Spackman
- United States Department of Agriculture, Southeast Poultry Research Laboratory, Athens, GA, USA
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam.,Center for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - C Todd Davis
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, Hanoi, Vietnam. .,Center for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
14
|
Van Nguyen D, Van Nguyen C, Bonsall D, Ngo TT, Carrique-Mas J, Pham AH, Bryant JE, Thwaites G, Baker S, Woolhouse M, Simmonds P. Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam. Viruses 2018; 10:v10030102. [PMID: 29495551 PMCID: PMC5869495 DOI: 10.3390/v10030102] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 01/20/2018] [Revised: 02/19/2018] [Accepted: 02/23/2018] [Indexed: 12/20/2022] Open
Abstract
Rodents and bats are now widely recognised as important sources of zoonotic virus infections in other mammals, including humans. Numerous surveys have expanded our knowledge of diverse viruses in a range of rodent and bat species, including their origins, evolution, and range of hosts. In this study of pegivirus and human hepatitis-related viruses, liver and serum samples from Vietnamese rodents and bats were examined by PCR and sequencing. Nucleic acids homologous to human hepatitis B, C, E viruses were detected in liver samples of 2 (1.3%) of 157 bats, 38 (8.1%), and 14 (3%) of 470 rodents, respectively. Hepacivirus-like viruses were frequently detected (42.7%) in the bamboo rat, Rhizomys pruinosus, while pegivirus RNA was only evident in 2 (0.3%) of 638 rodent serum samples. Complete or near-complete genome sequences of HBV, HEV and pegivirus homologues closely resembled those previously reported from rodents and bats. However, complete coding region sequences of the rodent hepacivirus-like viruses substantially diverged from all of the currently classified variants and potentially represent a new species in the Hepacivirus genus. Of the viruses identified, their routes of transmission and potential to establish zoonoses remain to be determined.
Collapse
MESH Headings
- Animals
- Chiroptera/virology
- Genome, Viral
- Hepatitis Viruses/classification
- Hepatitis Viruses/genetics
- Hepatitis, Viral, Animal/diagnosis
- Hepatitis, Viral, Animal/epidemiology
- Hepatitis, Viral, Animal/virology
- Hepatitis, Viral, Human/diagnosis
- Hepatitis, Viral, Human/epidemiology
- Hepatitis, Viral, Human/virology
- Humans
- Phylogeny
- Public Health Surveillance
- RNA, Viral
- Rodentia/virology
- Vietnam/epidemiology
- Zoonoses/epidemiology
- Zoonoses/virology
Collapse
Affiliation(s)
- Dung Van Nguyen
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK.
| | - Cuong Van Nguyen
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam.
| | - David Bonsall
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK.
| | - Tue Tri Ngo
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam.
| | - Juan Carrique-Mas
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, UK.
| | - Anh Hong Pham
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam.
| | - Juliet E Bryant
- Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), 69365 Lyon CEDEX 07, France.
| | - Guy Thwaites
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, UK.
| | - Stephen Baker
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, UK.
- The London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK.
| | - Mark Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK.
| |
Collapse
|
15
|
Chang P, Yao Y, Tang N, Sadeyen JR, Sealy J, Clements A, Bhat S, Munir M, Bryant JE, Iqbal M. The Application of NHEJ-CRISPR/Cas9 and Cre-Lox System in the Generation of Bivalent Duck Enteritis Virus Vaccine against Avian Influenza Virus. Viruses 2018; 10:E81. [PMID: 29438322 PMCID: PMC5850388 DOI: 10.3390/v10020081] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 01/02/2018] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 12/17/2022] Open
Abstract
Duck-targeted vaccines to protect against avian influenza are critically needed to aid in influenza disease control efforts in regions where ducks are endemic for highly pathogenic avian influenza (HPAI). Duck enteritis virus (DEV) is a promising candidate viral vector for development of vaccines targeting ducks, owing to its large genome and narrow host range. The clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 system is a versatile gene-editing tool that has proven beneficial for gene modification and construction of recombinant DNA viral vectored vaccines. Currently, there are two commonly used methods for gene insertion: non-homologous end-joining (NHEJ) and homology-directed repair (HDR). Owing to its advantages in efficiency and independence from molecular requirements of the homologous arms, we utilized NHEJ-dependent CRISPR/Cas9 to insert the influenza hemagglutinin (HA) antigen expression cassette into the DEV genome. The insert was initially tagged with reporter green fluorescence protein (GFP), and a Cre-Lox system was later used to remove the GFP gene insert. Furthermore, a universal donor plasmid system was established by introducing double bait sequences that were independent of the viral genome. In summary, we provide proof of principle for generating recombinant DEV viral vectored vaccines against the influenza virus using an integrated NHEJ-CRISPR/Cas9 and Cre-Lox system.
Collapse
Affiliation(s)
| | - Yongxiu Yao
- The Pirbright Institute, Pirbright, Woking GU24 0NF, UK.
| | - Na Tang
- Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou 256600, Shandong, China.
| | | | - Joshua Sealy
- The Pirbright Institute, Pirbright, Woking GU24 0NF, UK.
| | | | - Sushant Bhat
- The Pirbright Institute, Pirbright, Woking GU24 0NF, UK.
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Furness Building, Lancaster University, Bailrigg, Lancaster LA1 4YG, UK.
| | - Juliet E Bryant
- Laboratory of Emerging Pathogens, Fondation Mérieux, 69002 Lyon, France.
| | - Munir Iqbal
- The Pirbright Institute, Pirbright, Woking GU24 0NF, UK.
| |
Collapse
|
16
|
Sealy JE, Yaqub T, Peacock TP, Chang P, Ermetal B, Clements A, Sadeyen JR, Mehboob A, Shelton H, Bryant JE, Daniels RS, McCauley JW, Iqbal M. Association of Increased Receptor-Binding Avidity of Influenza A(H9N2) Viruses with Escape from Antibody-Based Immunity and Enhanced Zoonotic Potential. Emerg Infect Dis 2018; 25:63-72. [PMID: 30561311 PMCID: PMC6302589 DOI: 10.3201/eid2501.180616] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We characterized 55 influenza A(H9N2) viruses isolated in Pakistan during 2014-2016 and found that the hemagglutinin gene is of the G1 lineage and that internal genes have differentiated into a variety of novel genotypes. Some isolates had up to 4-fold reduction in hemagglutination inhibition titers compared with older viruses. Viruses with hemagglutinin A180T/V substitutions conveyed this antigenic diversity and also caused up to 3,500-fold greater binding to avian-like and >20-fold greater binding to human-like sialic acid receptor analogs. This enhanced binding avidity led to reduced virus replication in primary and continuous cell culture. We confirmed that altered receptor-binding avidity of H9N2 viruses, including enhanced binding to human-like receptors, results in antigenic variation in avian influenza viruses. Consequently, current vaccine formulations might not induce adequate protective immunity in poultry, and emergence of isolates with marked avidity for human-like receptors increases the zoonotic risk.
Collapse
|
17
|
Lu L, Van Dung N, Ivens A, Bogaardt C, O’Toole A, Bryant JE, Carrique-Mas J, Van Cuong N, Anh PH, Rabaa MA, Tue NT, Thwaites GE, Baker S, Simmonds P, Woolhouse ME. Genetic diversity and cross-species transmission of kobuviruses in Vietnam. Virus Evol 2018; 4:vey002. [PMID: 29449965 PMCID: PMC5810437 DOI: 10.1093/ve/vey002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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] [Indexed: 12/15/2022] Open
Abstract
Cross-species transmission of viruses poses a sustained threat to public health. Due to increased contact between humans and other animal species the possibility exists for cross-species transmissions and ensuing disease outbreaks. By using conventional PCR amplification and next generation sequencing, we obtained 130 partial or full genome kobuvirus sequences from humans in a sentinel cohort in Vietnam and various mammalian hosts including bats, rodents, pigs, cats, and civets. The evolution of kobuviruses in different hosts was analysed using Bayesian phylogenetic methods. We estimated and compared time of origin of kobuviruses in different host orders; we also examined the cross-species transmission of kobuviruses within the same host order and between different host orders. Our data provide new knowledge of rodent and bat kobuviruses, which are most closely related to human kobuviruses. The novel bat kobuviruses isolated from bat roosts in Southern Vietnam were genetically distinct from previously described bat kobuviruses, but closely related to kobuviruses found in rodents. We additionally found evidence of frequent cross-species transmissions of kobuviruses within rodents. Overall, our phylogenetic analyses reveal multiple cross-species transmissions both within and among mammalian species, which increases our understanding of kobuviruses genetic diversity and the complexity of their evolutionary history.
Collapse
Affiliation(s)
- Lu Lu
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Nguyen Van Dung
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Alasdair Ivens
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Carlijn Bogaardt
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Aine O’Toole
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Juliet E Bryant
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Juan Carrique-Mas
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Pham Hong Anh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Maia A Rabaa
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Ngo Tri Tue
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Guy E Thwaites
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
- The Department of Medicine, University of Cambridge, Hills Rd, Cambridge CB2 0SP, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Mark Ej Woolhouse
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | | |
Collapse
|
18
|
Puckett EE, Park J, Combs M, Blum MJ, Bryant JE, Caccone A, Costa F, Deinum EE, Esther A, Himsworth CG, Keightley PD, Ko A, Lundkvist Å, McElhinney LM, Morand S, Robins J, Russell J, Strand TM, Suarez O, Yon L, Munshi-South J. Global population divergence and admixture of the brown rat (Rattus norvegicus). Proc Biol Sci 2017; 283:rspb.2016.1762. [PMID: 27798305 DOI: 10.1098/rspb.2016.1762] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [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: 08/09/2016] [Accepted: 09/26/2016] [Indexed: 11/12/2022] Open
Abstract
Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Westward expansion resulted in the colonization of Europe from which subsequent rapid colonization of Africa, the Americas and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering between and within sampling sites underscored the extent to which urban heterogeneity shaped genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants, suggesting that recruitment into established populations is limited. Understanding the global population structure of R. norvegicus offers novel perspectives on the forces driving the spread of zoonotic disease, and aids in development of rat eradication programmes.
Collapse
Affiliation(s)
- Emily E Puckett
- Louis Calder Center, Biological Field Station, Fordham University, Armonk, NY 10504, USA
| | - Jane Park
- Louis Calder Center, Biological Field Station, Fordham University, Armonk, NY 10504, USA
| | - Matthew Combs
- Louis Calder Center, Biological Field Station, Fordham University, Armonk, NY 10504, USA
| | - Michael J Blum
- Xavier Center for Bioenvironmental Research, Tulane University, New Orleans, LA 70112, USA
| | | | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT 06520-8106, USA
| | - Federico Costa
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil
| | - Eva E Deinum
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.,Mathematical and Statistical Methods Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Alexandra Esther
- Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Vertebrate Research, Julius Kühn Institute, Münster, Germany
| | - Chelsea G Himsworth
- Animal Health Centre, British Columbia Ministry of Agriculture, 1767 Angus Campbell Road, Abbotsford, British Columbia, Canada V3G 2M3
| | - Peter D Keightley
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Albert Ko
- Laboratory of Epidemiology and Public Health, Yale University, New Haven, CT, USA
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Lorraine M McElhinney
- Wildlife Zoonoses and Vector Borne Disease Research Group, Animal and Plant Health Agency (APHA), Woodham Lane, New Haw Surrey, UK
| | - Serge Morand
- CNRS-CIRAD, Centre d'Infectiologie Christophe Mérieux du Laos, Vientiane, Lao PDR
| | - Judith Robins
- Department of Anthropology, University of Auckland, Private Bag 92019, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - James Russell
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.,Department of Statistics, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Tanja M Strand
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Olga Suarez
- Laboratorio de Ecologia de Roedores Urbanos, IEGEBA-CONICET, EGE-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires Pabellon II, Ciudad Universitaria (C1428EHA), Buenos Aires, Argentina
| | - Lisa Yon
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Jason Munshi-South
- Louis Calder Center, Biological Field Station, Fordham University, Armonk, NY 10504, USA
| |
Collapse
|
19
|
Trung NV, Hoi LT, Thuong NTH, Toan TK, Huong TTK, Hoa TM, Fox A, Kinh NV, van Doorn HR, Wertheim HFL, Bryant JE, Nadjm B. Seroprevalence of Scrub Typhus, Typhus, and Spotted Fever Among Rural and Urban Populations of Northern Vietnam. Am J Trop Med Hyg 2017; 96:1084-1087. [PMID: 28500808 PMCID: PMC5417199 DOI: 10.4269/ajtmh.16-0399] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Rickettsial infections are recognized as important causes of fever throughout southeast Asia. Herein, we determined the seroprevalence to rickettsioses within rural and urban populations of northern Vietnam. Prevalence of individuals with evidence of prior rickettsial infections (IgG positive) was surprisingly low, with 9.14% (83/908) testing positive to the three major rickettsial serogroups thought to circulate in the region. Prevalence of typhus group rickettsiae (TG)–specific antibodies (6.5%, 58/908) was significantly greater than scrub typhus group orientiae (STG)– or spotted fever group rickettsiae (SFG)–specific antibodies (P < 0.05). The majority of TG seropositives were observed among urban rather than rural residents (P < 0.05). In contrast, overall antibody prevalence to STG and SFG were both very low (1.1%, 10/908 for STG; 1.7%, 15/908 for SFG), with no significant differences between rural and urban residents. These results provide data on baseline population characteristics that may help inform development of Rickettsia serological testing criteria in future clinical studies.
Collapse
Affiliation(s)
| | - Le Thi Hoi
- National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Nguyen Thi Hong Thuong
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | | | - Tran Thi Kieu Huong
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Tran Mai Hoa
- National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Annette Fox
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | | | - H Rogier van Doorn
- Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.,Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Heiman F L Wertheim
- Department of Medical Microbiology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.,Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Juliet E Bryant
- Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.,Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Behzad Nadjm
- Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.,Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| |
Collapse
|
20
|
Hoa LNM, Tuan NA, My PH, Huong TTK, Chi NTY, Hau Thu TT, Carrique-Mas J, Duong MT, Tho ND, Hoang ND, Thanh TL, Diep NT, van Duong N, Toan TK, Tung TS, Mai LQ, Iqbal M, Wertheim H, van Doorn HR, Bryant JE. Assessing evidence for avian-to-human transmission of influenza A/H9N2 virus in rural farming communities in northern Vietnam. J Gen Virol 2017; 98:2011-2016. [PMID: 28771136 PMCID: PMC5656782 DOI: 10.1099/jgv.0.000877] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 03/30/2017] [Accepted: 06/28/2017] [Indexed: 12/22/2022] Open
Abstract
Rural farming communities in northern Vietnam do not routinely practice vaccination for influenza A viruses (IAV) for either humans or poultry, which enables us to study transmission intensity via seroepidemiology. Using samples from a longitudinal cohort of farming households, we determined the number of symptomatic and asymptomatic human infections for seasonal IAV and avian A/H9 over 2 years. As expected, we detected virologically confirmed acute cases of seasonal IAV in humans, as well as large numbers of subclinical seroconversions to A/H1pdm [55/265 (21 %)], A/H3 [95/265 (36 %)] and A/H9 [24/265 (9 %)]. Five of the A/H9 human seroconverters likely represented true infections rather than heterosubtypic immunity, because the individuals seroconverted solely to A/H9. Among co-located poultry, we found significantly higher seroprevalance for A/H5 compared to A/H9 in both chickens and ducks [for northern study sites overall, 337/1105 (30.5 %) seropositive for A/H5 and 123/1105 (11.1 %) seropositive for A/H9].
Collapse
MESH Headings
- Adolescent
- Adult
- Aged
- Agriculture
- Animals
- Antibodies, Viral/blood
- Chickens
- Child
- Child, Preschool
- Ducks
- Female
- Humans
- Infant
- Influenza A Virus, H9N2 Subtype/classification
- Influenza A Virus, H9N2 Subtype/genetics
- Influenza A Virus, H9N2 Subtype/immunology
- Influenza A Virus, H9N2 Subtype/isolation & purification
- Influenza in Birds/blood
- Influenza in Birds/epidemiology
- Influenza in Birds/transmission
- Influenza in Birds/virology
- Influenza, Human/blood
- Influenza, Human/epidemiology
- Influenza, Human/transmission
- Influenza, Human/virology
- Male
- Middle Aged
- Poultry Diseases/blood
- Poultry Diseases/epidemiology
- Poultry Diseases/transmission
- Poultry Diseases/virology
- Rural Population/statistics & numerical data
- Seroepidemiologic Studies
- Vietnam
- Young Adult
Collapse
Affiliation(s)
- Le Nguyen Minh Hoa
- Oxford University
Clinical Research Unit, Hospital for Tropical Diseases,
Vietnam
| | - Nguyen Anh Tuan
- Oxford University
Clinical Research Unit, Hospital for Tropical Diseases,
Vietnam
| | - Pham Ha My
- Oxford University
Clinical Research Unit, Hospital for Tropical Diseases,
Vietnam
| | - Tran Thi Kieu Huong
- Oxford University
Clinical Research Unit, Hospital for Tropical Diseases,
Vietnam
| | - Nguyen Thi Yen Chi
- Oxford University
Clinical Research Unit, Hospital for Tropical Diseases,
Vietnam
| | - Trang Thi Hau Thu
- Oxford University
Clinical Research Unit, Hospital for Tropical Diseases,
Vietnam
| | - Juan Carrique-Mas
- Oxford University
Clinical Research Unit, Hospital for Tropical Diseases,
Vietnam
| | - Mai Thuy Duong
- National Center for
Veterinary Diagnostics, Hanoi,
Vietnam
| | | | | | - To Long Thanh
- National Center for
Veterinary Diagnostics, Hanoi,
Vietnam
| | - Nguyen Thi Diep
- Department of Animal
Health, Epidemiology Division, Hanoi,
Vietnam
| | - Nguyen van Duong
- District Veterinary
Services, BaVi District, Subdepartment of Animal Health,
Hanoi province, Vietnam
| | | | - Trinh Son Tung
- Oxford University
Clinical Research Unit, Hospital for Tropical Diseases,
Vietnam
- National Institute
Hygiene and Epidemiology, Hanoi,
Vietnam
| | - Le Quynh Mai
- National Institute
Hygiene and Epidemiology, Hanoi,
Vietnam
| | | | - Heiman Wertheim
- Oxford University
Clinical Research Unit, Hospital for Tropical Diseases,
Vietnam
- Radboud
University, Nijmegen,
Netherlands
| | - H. Rogier van Doorn
- Oxford University
Clinical Research Unit, Hospital for Tropical Diseases,
Vietnam
- Nuffield Department
of Medicine, Centre for Tropical Medicine, University of
Oxford, Oxford,
UK
| | - Juliet E. Bryant
- Oxford University
Clinical Research Unit, Hospital for Tropical Diseases,
Vietnam
- Nuffield Department
of Medicine, Centre for Tropical Medicine, University of
Oxford, Oxford,
UK
| | - the VIZIONS consortium
- Oxford University
Clinical Research Unit, Hospital for Tropical Diseases,
Vietnam
- National Center for
Veterinary Diagnostics, Hanoi,
Vietnam
- Department of Animal
Health, Epidemiology Division, Hanoi,
Vietnam
- District Veterinary
Services, BaVi District, Subdepartment of Animal Health,
Hanoi province, Vietnam
- Hanoi Medical
University, Hanoi,
Vietnam
- National Institute
Hygiene and Epidemiology, Hanoi,
Vietnam
- The Pirbright
Insitute, UK
- Radboud
University, Nijmegen,
Netherlands
- Nuffield Department
of Medicine, Centre for Tropical Medicine, University of
Oxford, Oxford,
UK
| |
Collapse
|
21
|
Nguyen DT, Jang Y, Nguyen TD, Jones J, Shepard SS, Yang H, Gerloff N, Fabrizio T, Nguyen LV, Inui K, Yang G, Creanga A, Wang L, Mai DT, Thor S, Stevens J, To TL, Wentworth DE, Nguyen T, Pham DV, Bryant JE, Davis CT. Shifting Clade Distribution, Reassortment, and Emergence of New Subtypes of Highly Pathogenic Avian Influenza A(H5) Viruses Collected from Vietnamese Poultry from 2012 to 2015. J Virol 2017; 91:e01708-16. [PMID: 28003481 PMCID: PMC5309939 DOI: 10.1128/jvi.01708-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/28/2016] [Indexed: 11/20/2022] Open
Abstract
Whole-genome sequences of representative highly pathogenic avian influenza A(H5) viruses from Vietnam were generated, comprising samples from poultry outbreaks and active market surveillance collected from January 2012 to August 2015. Six hemagglutinin gene clades were characterized. Clade 1.1.2 was predominant in southern Mekong provinces throughout 2012 and 2013 but gradually disappeared and was not detected after April 2014. Clade 2.3.2.1c viruses spread rapidly during 2012 and were detected in the south and center of the country. A number of clade 1.1.2 and 2.3.2.1c interclade reassortant viruses were detected with different combinations of internal genes derived from 2.3.2.1a and 2.3.2.1b viruses, indicating extensive cocirculation. Although reassortment generated genetic diversity at the genotype level, there was relatively little genetic drift within the individual gene segments, suggesting genetic stasis over recent years. Antigenically, clade 1.1.2, 2.3.2.1a, 2.3.2.1b, and 2.3.2.1c viruses remained related to earlier viruses and WHO-recommended prepandemic vaccine strains representing these clades. Clade 7.2 viruses, although detected in only low numbers, were the exception, as indicated by introduction of a genetically and antigenically diverse strain in 2013. Clade 2.3.4.4 viruses (H5N1 and H5N6) were likely introduced in April 2014 and appeared to gain dominance across northern and central regions. Antigenic analyses of clade 2.3.4.4 viruses compared to existing clade 2.3.4 candidate vaccine viruses (CVV) indicated the need for an updated vaccine virus. A/Sichuan/26221/2014 (H5N6) virus was developed, and ferret antisera generated against this virus were demonstrated to inhibit some but not all clade 2.3.4.4 viruses, suggesting consideration of alternative clade 2.3.4.4 CVVs.IMPORTANCE Highly pathogenic avian influenza (HPAI) A(H5) viruses have circulated continuously in Vietnam since 2003, resulting in hundreds of poultry outbreaks and sporadic human infections. Despite a significant reduction in the number of human infections in recent years, poultry outbreaks continue to occur and the virus continues to diversify. Vaccination of poultry has been used as a means to control the spread and impact of the virus, but due to the diversity and changing distribution of antigenically distinct viruses, the utility of vaccines in the face of mismatched circulating strains remains questionable. This study assessed the putative amino acid changes in viruses leading to antigenic variability, underscoring the complexity of vaccine selection for both veterinary and public health purposes. Given the overlapping geographic distributions of multiple, antigenically distinct clades of HPAI A(H5) viruses in Vietnam, the vaccine efficacy of bivalent poultry vaccine formulations should be tested in the future.
Collapse
Affiliation(s)
- Diep T Nguyen
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
- Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
- Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Yunho Jang
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tho D Nguyen
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Joyce Jones
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Samuel S Shepard
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hua Yang
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nancy Gerloff
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Thomas Fabrizio
- St. Jude's Center for Excellence in Influenza Research and Surveillance, Memphis, Tennessee, USA
| | - Long V Nguyen
- Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam
| | - Ken Inui
- Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | - Genyan Yang
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Adrian Creanga
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Li Wang
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Duong T Mai
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Sharmi Thor
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - James Stevens
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Thanh L To
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - David E Wentworth
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tung Nguyen
- Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam
| | - Dong V Pham
- Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam
| | - Juliet E Bryant
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
- Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - C Todd Davis
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| |
Collapse
|
22
|
Phan MVT, Anh PH, Cuong NV, Munnink BBO, van der Hoek L, My PT, Tri TN, Bryant JE, Baker S, Thwaites G, Woolhouse M, Kellam P, Rabaa MA, Cotten M. Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection. Virus Evol 2016; 2:vew027. [PMID: 28748110 PMCID: PMC5522372 DOI: 10.1093/ve/vew027] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [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: 11/12/2022] Open
Abstract
Coordinated and synchronous surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus (RV) is an important cause of viral gastroenteritis in humans and animals. In this study, we document the RV diversity within co-located humans and animals sampled from the Mekong delta region of Vietnam using a primer-independent, agnostic, deep sequencing approach. A total of 296 stool samples (146 from diarrhoeal human patients and 150 from pigs living in the same geographical region) were directly sequenced, generating the genomic sequences of sixty human rotaviruses (all group A) and thirty-one porcine rotaviruses (thirteen group A, seven group B, six group C, and five group H). Phylogenetic analyses showed the co-circulation of multiple distinct RV group A (RVA) genotypes/strains, many of which were divergent from the strain components of licensed RVA vaccines, as well as considerable virus diversity in pigs including full genomes of rotaviruses in groups B, C, and H, none of which have been previously reported in Vietnam. Furthermore, the detection of an atypical RVA genotype constellation (G4-P[6]-I1-R1-C1-M1-A8-N1-T7-E1-H1) in a human patient and a pig from the same region provides some evidence for a zoonotic event.
Collapse
Affiliation(s)
- My V T Phan
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Pham Hong Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Bas B Oude Munnink
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Phuc Tran My
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tue Ngo Tri
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen Baker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,London School of Tropical Medicine and Hygiene, London, UK
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mark Woolhouse
- Centre for Immunity, Infection & Evolution, University of Edinburgh, Edinburgh, UK
| | - Paul Kellam
- Kymab Inc., Cambridge, UK.,Imperial College, London, UK
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew Cotten
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.,Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | |
Collapse
|
23
|
Do LAH, Bryant JE, Tran AT, Nguyen BH, Tran TTL, Tran QH, Vo QB, Tran Dac NA, Trinh HN, Nguyen TTH, Le Binh BT, Le K, Nguyen MT, Thai QT, Vo TV, Ngo NQM, Dang TKH, Cao NH, Tran TV, Ho LV, Farrar J, de Jong M, van Doorn HR. Respiratory Syncytial Virus and Other Viral Infections among Children under Two Years Old in Southern Vietnam 2009-2010: Clinical Characteristics and Disease Severity. PLoS One 2016; 11:e0160606. [PMID: 27500954 PMCID: PMC4976934 DOI: 10.1371/journal.pone.0160606] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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: 05/06/2016] [Accepted: 07/21/2016] [Indexed: 12/16/2022] Open
Abstract
Background Despite a high burden of respiratory syncytial virus (RSV) infections among children, data on demographic and clinical characteristics of RSV are scarce in low and middle income countries. This study aims to describe the viral etiologies, the demographic, epidemiological, and clinical characteristics of children under two years of age who were hospitalized with a lower respiratory tract infections (LRTI), focusing on RSV (prevalence, seasonality, subgroups, viral load) and its association with disease severity. Methods A prospective study among children under two years of age, hospitalized with LRTI was conducted in two referral pediatric hospitals in Ho Chi Minh City, Vietnam, from May 2009 to December 2010. Socio-demographic, clinical data and nasopharyngeal swabs were collected on enrolment and discharge. Multiplex real-time RT-PCR (13 viruses) and quantitative RSV RT-PCR were used to identify viral pathogens, RSV load and subgroups. Results Among 632 cases, 48% were RSV positive. RSV infections occurred at younger age than three other leading viral infections i.e rhinovirus (RV), metapneumovirus (MPV), parainfluenza virus (PIV-3) and were significantly more frequent in the first 6 months of life. Clinical severity score of RSV infection was significantly higher than PIV-3 but not for RV or MPV. In multivariate analysis, RV infection was significantly associated with severity while RSV infection was not. Among RSV infections, neither viral load nor viral co-infections were significantly associated with severity. Young age and having fever at admission were significantly associated with both RSV and LRTI severity. A shift in RSV subgroup predominance was observed during two consecutive rainy seasons but was not associated with severity. Conclusion We report etiologies, the epidemiological and clinical characteristics of LRTI among hospitalized children under two years of age and risk factors of RSV and LRTI severity.
Collapse
Affiliation(s)
- Lien Anh Ha Do
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
- Murdoch Children’s Research Institute, Melbourne, Australia
- * E-mail:
| | - Juliet E. Bryant
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Anh Tuan Tran
- Children Hospital 1, 341 Su Van Hanh, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Bach Hue Nguyen
- Children Hospital 1, 341 Su Van Hanh, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Thi Thu Loan Tran
- Children Hospital 2, 14 Ly Tu Trong, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Quynh Huong Tran
- Children Hospital 2, 14 Ly Tu Trong, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Quoc Bao Vo
- Children Hospital 2, 14 Ly Tu Trong, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Nguyen Anh Tran Dac
- Children Hospital 2, 14 Ly Tu Trong, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Hong Nhien Trinh
- Children Hospital 1, 341 Su Van Hanh, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Thi Thanh Hai Nguyen
- Children Hospital 1, 341 Su Van Hanh, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Bao Tinh Le Binh
- Children Hospital 1, 341 Su Van Hanh, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Khanh Le
- Children Hospital 1, 341 Su Van Hanh, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Minh Tien Nguyen
- Children Hospital 1, 341 Su Van Hanh, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Quang Tung Thai
- Children Hospital 1, 341 Su Van Hanh, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Thanh Vu Vo
- Children Hospital 1, 341 Su Van Hanh, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Ngoc Quang Minh Ngo
- Children Hospital 1, 341 Su Van Hanh, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Thi Kim Huyen Dang
- Children Hospital 2, 14 Ly Tu Trong, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Ngoc Huong Cao
- Children Hospital 2, 14 Ly Tu Trong, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Thu Van Tran
- Children Hospital 2, 14 Ly Tu Trong, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Lu Viet Ho
- Children Hospital 2, 14 Ly Tu Trong, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
| | - Menno de Jong
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
24
|
Nguyen DNT, Mai LQ, Bryant JE, Hang NLK, Hoa LNM, Nadjm B, Thai PQ, Duong TN, Anh DD, Horby P, van Doorn HR, Wertheim HFL, Fox A. Epidemiology and etiology of influenza-like-illness in households in Vietnam; it's not all about the kids! J Clin Virol 2016; 82:126-132. [PMID: 27479176 PMCID: PMC4994428 DOI: 10.1016/j.jcv.2016.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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: 05/18/2016] [Revised: 07/12/2016] [Accepted: 07/24/2016] [Indexed: 01/11/2023]
Abstract
BACKGROUND Household studies provide opportunities to understand influenza-like-illness (ILI) transmission, but data from (sub)tropical developing countries are scarce. OBJECTIVE To determine the viral etiology and epidemiology of ILI in households. STUDY DESIGN ILI was detected by active case finding amongst a cohort of 263 northern Vietnam households between 2008 and 2013. Health workers collected nose and throat swabs for virus detection by multiplex real-time RT-PCR. RESULTS ILI was detected at least once in 219 (23.7%) of 945 household members. 271 (62.3%) of 435 nose/throat swabs were positive for at least one of the 15 viruses tested. Six viruses predominated amongst positive swabs: Rhinovirus (28%), Influenza virus (17%), Coronavirus (8%), Enterovirus (5%), Respiratory syncytial virus (3%), Metapneumovirus virus (2.5%) and Parainfluenza virus 3 (1.8%). There was no clear seasonality, but 78% of episodes occurred in Winter/Spring for Influenza compared to 32% for Rhinovirus. Participants, on average, suffered 0.49 ILI, and 0.29 virus-positive ILI episodes, with no significant effects of gender, age, or household size. In contrast to US and Australian community studies, the frequency of ILI decreased as the number of household members aged below 5 years increased (p=0.006). CONCLUSION The findings indicate the need for tailored ILI control strategies, and for better understanding of how local childcare practices and seasonality may influence transmission and the role of children.
Collapse
Affiliation(s)
- Diep Ngoc Thi Nguyen
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Vietnam
| | - Le Quynh Mai
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Juliet E Bryant
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Vietnam; Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | - Le Nguyen Minh Hoa
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Vietnam
| | - Behzad Nadjm
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Vietnam; Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Pham Quang Thai
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Tran Nhu Duong
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Peter Horby
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Vietnam; Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Vietnam; Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Heiman F L Wertheim
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Vietnam; Department of Medical Microbiology, Radboudumc, Nijmegen, Netherlands
| | - Annette Fox
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Vietnam; The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, Parkville, Victoria, Australia.
| |
Collapse
|
25
|
Do LAH, Wilm A, van Doorn HR, Lam HM, Sim S, Sukumaran R, Tran AT, Nguyen BH, Tran TTL, Tran QH, Vo QB, Dac NAT, Trinh HN, Nguyen TTH, Binh BTL, Le K, Nguyen MT, Thai QT, Vo TV, Ngo NQM, Dang TKH, Cao NH, Tran TV, Ho LV, Farrar J, de Jong M, Chen S, Nagarajan N, Bryant JE, Hibberd ML. Direct whole-genome deep-sequencing of human respiratory syncytial virus A and B from Vietnamese children identifies distinct patterns of inter- and intra-host evolution. J Gen Virol 2016; 96:3470-3483. [PMID: 26407694 DOI: 10.1099/jgv.0.000298] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infections in children ,2 years of age. Little is known about RSV intra-host genetic diversity over the course of infection or about the immune pressures that drive RSV molecular evolution. We performed whole-genome deep-sequencing on 53 RSV-positive samples (37 RSV subgroup A and 16 RSV subgroup B) collected from the upper airways of hospitalized children in southern Vietnam over two consecutive seasons. RSV A NA1 and RSV B BA9 were the predominant genotypes found in our samples, consistent with other reports on global RSV circulation during the same period. For both RSV A and B, the M gene was the most conserved, confirming its potential as a target for novel therapeutics. The G gene was the most variable and was the only gene under detectable positive selection. Further, positively selected sites inG were found in close proximity to and in some cases overlapped with predicted glycosylation motifs, suggesting that selection on amino acid glycosylation may drive viral genetic diversity. We further identified hotspots and coldspots of intra-host genetic diversity in the RSV genome, some of which may highlight previously unknown regions of functional importance.
Collapse
Affiliation(s)
- Lien Anh Ha Do
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
| | - Andreas Wilm
- Genome Institute of Singapore, Genome Building, 138672 Singapore
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Ha Minh Lam
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
| | - Shuzhen Sim
- Genome Institute of Singapore, Genome Building, 138672 Singapore
| | - Rashmi Sukumaran
- Genome Institute of Singapore, Genome Building, 138672 Singapore
| | - Anh Tuan Tran
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Bach Hue Nguyen
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Thi Thu Loan Tran
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Quynh Huong Tran
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Quoc Bao Vo
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | | | - Hong Nhien Trinh
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | | | - Bao Tinh Le Binh
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Khanh Le
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Minh Tien Nguyen
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Quang Tung Thai
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | - Thanh Vu Vo
- Children's Hospital 1, Ward 10, District 10, Ho Chi Minh City, Vietnam
| | | | - Thi Kim Huyen Dang
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Ngoc Huong Cao
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Thu Van Tran
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Lu Viet Ho
- Children's Hospital 2, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
| | - Menno de Jong
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Swaine Chen
- Genome Institute of Singapore, Genome Building, 138672 Singapore
| | | | - Juliet E Bryant
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Martin L Hibberd
- Genome Institute of Singapore, Genome Building, 138672 Singapore
| |
Collapse
|
26
|
Thuy DM, Peacock TP, Bich VTN, Fabrizio T, Hoang DN, Tho ND, Diep NT, Nguyen M, Hoa LNM, Trang HTT, Choisy M, Inui K, Newman S, Trung NV, van Doorn R, To TL, Iqbal M, Bryant JE. Prevalence and diversity of H9N2 avian influenza in chickens of Northern Vietnam, 2014. Infect Genet Evol 2016; 44:530-540. [PMID: 27340015 PMCID: PMC5036934 DOI: 10.1016/j.meegid.2016.06.038] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/17/2016] [Accepted: 06/19/2016] [Indexed: 12/23/2022]
Abstract
Despite their classification as low pathogenicity avian influenza viruses (LPAIV), A/H9N2 viruses cause significant losses in poultry in many countries throughout Asia, the Middle East and North Africa. To date, poultry surveillance in Vietnam has focused on detection of influenza H5 viruses, and there is limited understanding of influenza H9 epidemiology and transmission dynamics. We determined prevalence and diversity of influenza A viruses in chickens from live bird markets (LBM) of 7 northern Vietnamese provinces, using pooled oropharyngeal swabs collected from October to December 2014. Screening by real time RT-PCR revealed 1207/4900 (24.6%) of pooled swabs to be influenza A virus positive; overall prevalence estimates after accounting for pooling (5 swabs/pools) were 5.8% (CI 5.4–6.0). Subtyping was performed on 468 pooled swabs with M gene Ct < 26. No influenza H7 was detected; 422 (90.1%) were H9 positive; and 22 (4.7%) were H5 positive. There was no evidence was of interaction between H9 and H5 virus detection rates. We sequenced 17 whole genomes of A/H9N2, 2 of A/H5N6, and 11 partial genomes. All H9N2 viruses had internal genes that clustered with genotype 57 and were closely related to Chinese human isolates of A/H7N9 and A/H10N8. Using a nucleotide divergence cutoff of 98%, we identified 9 distinct H9 genotypes. Phylogenetic analysis suggested multiple introductions of H9 viruses to northern Vietnam rather than in-situ transmission. Further investigations of H9 prevalence and diversity in other regions of Vietnam are warranted to assess H9 endemicity elsewhere in the country. We report detection of highly pathogenic avian influenza (HPAI) from healthy chickens in Live Bird Markets of Vietnam. Because all breeds of domestic chickens are extremely susceptible to HPAI, we speculate that HPAI detections from market chickens may reflect infections that occur after arrival in the market. Alternatively, shedding of HPAI from healthy birds may reflect vaccine-induced protective immunity that mitigates disease but does not block viral infection. As many as 49% of all pooled surveillance swabs were positive for influenza A virus, corresponding to an overall Influenza A prevalence of 5.45% (95% Confidence Interval 5.4-6.0%). Low pathogenicity avian influenza (LPAI) H9N2 accounted for the vast majority of all influenza A detections in market chickens sampled from 9 northern provinces. To date there is no evidence to suggest an interaction effect between circulation of H5 and H9 viruses; however sampling strategies that involve pooling of surveillance swabs from multiple birds greatly complicates the assessment of co-infection rates or evaluation of epidemiological associations.
Collapse
Affiliation(s)
- Duong Mai Thuy
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Thomas P Peacock
- Avian Viral Diseases programme, The Pirbright Institute, Woking, UK; St Mary's Campus, Imperial College London, London, UK
| | - Vu Thi Ngoc Bich
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Thomas Fabrizio
- St Jude's Center for Excellence in Influenza Research and Surveillance, Memphis, TN, USA
| | - Dang Nguyen Hoang
- Division of Epidemiology, Department of Animal Health, Hanoi, Vietnam
| | - Nguyen Dang Tho
- MIVEGEC (UM1-UM2-CNRS 5290-IRD 224), Centre de Recherche IRD, Montpellier, France
| | - Nguyen Thi Diep
- Division of Epidemiology, Department of Animal Health, Hanoi, Vietnam
| | - Minh Nguyen
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Le Nguyen Minh Hoa
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Hau Thi Thu Trang
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Marc Choisy
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam; MIVEGEC (UM1-UM2-CNRS 5290-IRD 224), Centre de Recherche IRD, Montpellier, France
| | - Ken Inui
- Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | - Scott Newman
- Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | | | - Rogier van Doorn
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam; Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Thanh Long To
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Munir Iqbal
- Avian Viral Diseases programme, The Pirbright Institute, Woking, UK
| | - Juliet E Bryant
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam; Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
27
|
Anh PH, Van Cuong N, Son NT, Tue NT, Kosoy M, Woolhouse MEJ, Baker S, Bryant JE, Thwaites G, Carrique-Mas JJ, Rabaa MA. Diversity of Bartonella spp. in Bats, Southern Vietnam. Emerg Infect Dis 2016; 21:1266-7. [PMID: 26079810 PMCID: PMC4480386 DOI: 10.3201/eid2107.141760] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
28
|
Lu L, Van Dung N, Bryant JE, Carrique-Mas J, Van Cuong N, Anh PH, Rabaa MA, Baker S, Simmonds P, Woolhouse ME. Evolution and phylogeographic dissemination of endemic porcine picornaviruses in Vietnam. Virus Evol 2016; 2:vew001. [PMID: 27774295 PMCID: PMC4989877 DOI: 10.1093/ve/vew001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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
Members of the Picornaviridae are important and often zoonotic viruses responsible for a variety of human and animal diseases. However, the evolution and spatial dissemination of different picornaviruses circulating in domestic animals are not well studied. We examined the rate of evolution and time of origin of porcine enterovirus G (EV-G) and porcine kobuvirus species C lineages (PKV-C) circulating in pig farms in Vietnam and from other countries. We further explored the spatiotemporal spread of EV-G and PKV-C in Southwest Vietnam using phylogeographic models. Multiple types of EV-G are co-circulating in Vietnam. The two dominant EV-G types among isolates from Vietnam (G1 and G6) showed strong phylogenetic clustering. Three clades of PKV-C (PKV-C1-3) represent more recent introductions into Vietnam; PKV-C2 is closely related to PKV-C from Southwest China, indicating possible cross-border dissemination. In addition, high virus lineage migration rates were estimated within four districts in Dong Thap province in Vietnam for both EV-G types (G1, G6) and all PKV-C (C1-3) clades. We found that Chau Thanh district is a primary source of both EV-G and PKV-C clades, consistent with extensive pig trading in and out of the district. Understanding the evolution and spatial dissemination of endemic picornaviruses in pigs may inform future strategies for the surveillance and control of picornaviruses.
Collapse
Affiliation(s)
- Lu Lu
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Nguyen Van Dung
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam,; Nuffield Department of Medicine, Oxford University, Old Rd, Oxford OX3 7LF, UK and
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Pham Honh Anh
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, Dist. 5, Ho Chi Minh City, Vietnam,; Nuffield Department of Medicine, Oxford University, Old Rd, Oxford OX3 7LF, UK and; The London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT, UK
| | - Peter Simmonds
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK,; Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Mark E Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| |
Collapse
|
29
|
Carrique-Mas JJ, Tue NT, Bryant JE, Saylors K, Cuong NV, Hoa NT, An NN, Hien VB, Lao PV, Tu NC, Chuyen NK, Chuc NT, Tan DV, Duong HVV, Toan TK, Chi NT, Campbell J, Rabaa MA, Nadjm B, Woolhouse M, Wertheim H, Thwaites G, Baker S. The baseline characteristics and interim analyses of the high-risk sentinel cohort of the Vietnam Initiative on Zoonotic InfectiONS (VIZIONS). Sci Rep 2015; 5:17965. [PMID: 26659094 PMCID: PMC4674710 DOI: 10.1038/srep17965] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 10/26/2015] [Indexed: 11/08/2022] Open
Abstract
The Vietnam Initiative for Zoonotic Infections (VIZIONS) includes community-based 'high-risk sentinel cohort' (HRSC) studies investigating individuals at risk of zoonotic infection due to occupational or residential exposure to animals. A total of 852 HRSC members were recruited between March 2013 and August 2014 from three provinces (Ha Noi, Dak Lak, and Dong Thap). The most numerous group (72.8%) corresponded to individuals living on farms, followed by slaughterers (16.3%) and animal health workers (8.5%). Nasal/pharyngeal and rectal swabs were collected from HRSC members at recruitment and after notifying illness. Exposure to exotic animals (including wild pigs, porcupine, monkey, civet, bamboo rat and bat) was highest for the Dak Lak cohort (53.7%), followed by Ha Noi (13.7%) and Dong Thap (4.0%). A total of 26.8% of individuals reported consumption of raw blood over the previous year; 33.6% slaughterers reported no use of protective equipment at work. Over 686 person-years of observation, 213 episodes of suspect infectious disease were notified, equivalent of 0.35 reports per person-year. Responsive samples were collected from animals in the farm cohort. There was noticeable time and space clustering of disease episodes suggesting that the VIZIONS set up is also suitable for the formal epidemiological investigation of disease outbreaks.
Collapse
Affiliation(s)
- Juan J. Carrique-Mas
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7BN, United Kingdom
| | - Ngo T. Tue
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Global Viral, San Francisco, CA 94104 USA
| | - Juliet E. Bryant
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7BN, United Kingdom
- National Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ha Noi, Vietnam
| | | | - Nguyen V. Cuong
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ngo T. Hoa
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7BN, United Kingdom
| | - Nguyen N. An
- Preventive Medicine Centre Dong Thap Province, Cao Lanh, Vietnam
| | - Vo B. Hien
- Sub-Department of Animal Health Dong Thap Province, Cao Lanh, Vietnam
| | - Pham V. Lao
- Preventive Medicine Centre Dak Lak Province, Buon Ma Thuot, Vietnam
| | - Nguyen C. Tu
- Regional Animal Health Laboratory 5, Buon Ma Thuot, Vietnam
| | - Nguyen K. Chuyen
- Sub-Department of Animal Health Dak Lak Province, Buon Ma Thuot, Vietnam
| | | | - Dinh V. Tan
- Ba Vi District Health Centre, Ha Noi, Vietnam
| | | | | | - Nguyen T.Y. Chi
- National Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ha Noi, Vietnam
| | - James Campbell
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7BN, United Kingdom
| | - Maia A. Rabaa
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7BN, United Kingdom
| | - Behzad Nadjm
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7BN, United Kingdom
- National Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ha Noi, Vietnam
| | - Mark Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Heiman Wertheim
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7BN, United Kingdom
- National Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ha Noi, Vietnam
- Department of Medical Microbiology, Radboud University Medical Cente, Nijmegen 6500 HB, the Netherlands
| | - Guy Thwaites
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7BN, United Kingdom
| | - Stephen Baker
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford OX3 7BN, United Kingdom
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| |
Collapse
|
30
|
Van Dung N, Anh PH, Van Cuong N, Hoa NT, Carrique-Mas J, Hien VB, Sharp C, Rabaa M, Berto A, Campbell J, Baker S, Farrar J, Woolhouse ME, Bryant JE, Simmonds P. Large-scale screening and characterization of enteroviruses and kobuviruses infecting pigs in Vietnam. J Gen Virol 2015; 97:378-388. [PMID: 26653281 DOI: 10.1099/jgv.0.000366] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A recent survey of pigs in Dong Thap province, Vietnam identified a high frequency of enterovirus species G (EV-G) infection (144/198; 72.7%). Amongst these was a plethora of EV-G types (EV-G1, EV-G6 and four new types EV-G8-EV-G11). To better characterize the genetic diversity of EV-G and investigate the possible existence of further circulating types, we performed a larger-scale study on 484 pig and 45 farm-bred boar faecal samples collected in 2012 and 2014, respectively. All samples from the previous and current studies were also screened for kobuviruses. The overall EV infection frequency remained extremely high (395/484; 81.6%), but with comparable detection rates and viral loads between healthy and diarrhoeic pigs; this contrasted with less frequent detection of EV-G in boars (4/45; 8.9%). EV was most frequently detected in pigs ≤ 14 weeks old (∼ 95%) and declined in older pigs. Infections with EV-G1 and EV-G6 were most frequent, whilst less commonly detected types included EV-G3, EV-G4 and EV-G8-EV-G11, and five new types (EV-G12-EV-G16). In contrast, kobuvirus infection frequency was significantly higher in diarrhoeic pigs (40.9 versus 27.6%; P = 0.01). Kobuviruses also showed contrasting epizootiologies and age associations; a higher prevalence was found in boars (42%) compared with domestic pigs (29%), with the highest infection frequency amongst pigs >52 weeks old. Although genetically diverse, all kobuviruses identified belonged to the species Aichivirus C. In summary, this study confirms infection with EV-G was endemic in Vietnamese domestic pigs and exhibits high genetic diversity and extensive inter-type recombination.
Collapse
Affiliation(s)
- Nguyen Van Dung
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Pham Hong Anh
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.,Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Vo Be Hien
- Subdepartment of Animal Health, Dong Thap Province, Vietnam
| | - C Sharp
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - M Rabaa
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - A Berto
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - James Campbell
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.,Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK.,London School of Hygiene and Tropical Medicine, Keppel Street, Bloomsbury, London WC1E 7HT, UK
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam
| | - Mark E Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1, District 5, Ho Chi Minh City, Vietnam.,Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK
| | - Peter Simmonds
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK.,Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| |
Collapse
|
31
|
Rabaa MA, Tue NT, Phuc TM, Carrique-Mas J, Saylors K, Cotten M, Bryant JE, Nghia HDT, Cuong NV, Pham HA, Berto A, Phat VV, Dung TTN, Bao LH, Hoa NT, Wertheim H, Nadjm B, Monagin C, van Doorn HR, Rahman M, Tra MPV, Campbell JI, Boni MF, Tam PTT, van der Hoek L, Simmonds P, Rambaut A, Toan TK, Van Vinh Chau N, Hien TT, Wolfe N, Farrar JJ, Thwaites G, Kellam P, Woolhouse MEJ, Baker S. The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases. Ecohealth 2015; 12:726-35. [PMID: 26403795 PMCID: PMC4700077 DOI: 10.1007/s10393-015-1061-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 05/20/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
The effect of newly emerging or re-emerging infectious diseases of zoonotic origin in human populations can be potentially catastrophic, and large-scale investigations of such diseases are highly challenging. The monitoring of emergence events is subject to ascertainment bias, whether at the level of species discovery, emerging disease events, or disease outbreaks in human populations. Disease surveillance is generally performed post hoc, driven by a response to recent events and by the availability of detection and identification technologies. Additionally, the inventory of pathogens that exist in mammalian and other reservoirs is incomplete, and identifying those with the potential to cause disease in humans is rarely possible in advance. A major step in understanding the burden and diversity of zoonotic infections, the local behavioral and demographic risks of infection, and the risk of emergence of these pathogens in human populations is to establish surveillance networks in populations that maintain regular contact with diverse animal populations, and to simultaneously characterize pathogen diversity in human and animal populations. Vietnam has been an epicenter of disease emergence over the last decade, and practices at the human/animal interface may facilitate the likelihood of spillover of zoonotic pathogens into humans. To tackle the scientific issues surrounding the origins and emergence of zoonotic infections in Vietnam, we have established The Vietnam Initiative on Zoonotic Infections (VIZIONS). This countrywide project, in which several international institutions collaborate with Vietnamese organizations, is combining clinical data, epidemiology, high-throughput sequencing, and social sciences to address relevant one-health questions. Here, we describe the primary aims of the project, the infrastructure established to address our scientific questions, and the current status of the project. Our principal objective is to develop an integrated approach to the surveillance of pathogens circulating in both human and animal populations and assess how frequently they are exchanged. This infrastructure will facilitate systematic investigations of pathogen ecology and evolution, enhance understanding of viral cross-species transmission events, and identify relevant risk factors and drivers of zoonotic disease emergence.
Collapse
Affiliation(s)
- Maia A Rabaa
- Centre for Immunity, Infection & Evolution, The University of Edinburgh, Edinburgh, UK
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Ngo Tri Tue
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Tran My Phuc
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | | | | | - Juliet E Bryant
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Ho Dang Trung Nghia
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- The Hospital for Tropical Diseases, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Hong Anh Pham
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Alessandra Berto
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Voong Vinh Phat
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Tran Thi Ngoc Dung
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Long Hoang Bao
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Heiman Wertheim
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Behzad Nadjm
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | | | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Motiur Rahman
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | | | - James I Campbell
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Maciej F Boni
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Pham Thi Thanh Tam
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Simmonds
- Centre for Immunity, Infection & Evolution, The University of Edinburgh, Edinburgh, UK
| | - Andrew Rambaut
- Centre for Immunity, Infection & Evolution, The University of Edinburgh, Edinburgh, UK
| | | | - Nguyen Van Vinh Chau
- The Hospital for Tropical Diseases, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | | | - Jeremy J Farrar
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Paul Kellam
- The Wellcome Trust Sanger Institute, Cambridge, UK
| | - Mark E J Woolhouse
- Centre for Immunity, Infection & Evolution, The University of Edinburgh, Edinburgh, UK
| | - Stephen Baker
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam.
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.
- The Hospital for Tropical Diseases, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.
- The London School of Hygiene and Tropical Medicine, London, UK.
| |
Collapse
|
32
|
Loan HK, Van Cuong N, Takhampunya R, Kiet BT, Campbell J, Them LN, Bryant JE, Tippayachai B, Van Hoang N, Morand S, Hien VB, Carrique-Mas JJ. How important are rats as vectors of leptospirosis in the Mekong Delta of Vietnam? Vector Borne Zoonotic Dis 2015; 15:56-64. [PMID: 25629781 PMCID: PMC4307199 DOI: 10.1089/vbz.2014.1613] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [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: 11/12/2022] Open
Abstract
Leptospirosis is a zoonosis known to be endemic in the Mekong Delta of Vietnam, even though clinical reports are uncommon. We investigated leptospira infection in rats purchased in food markets during the rainy season (October) (n=150), as well as those trapped during the dry season (February–March) (n=125) in the region using RT-PCR for the lipL32 gene, confirmed by 16S rRNA, as well as by the microscopic agglutination test (MAT). Results were compared with the serovar distribution of human cases referred from Ho Chi Minh City hospitals (2004–2012) confirmed by MAT (n=45). The MAT seroprevalence among rats was 18.3%. The highest MAT seroprevalence corresponded, in decreasing order, to: Rattus norvegicus (33.0%), Bandicota indica (26.5%), Rattus tanezumi (24.6%), Rattus exulans (14.3%), and Rattus argentiventer (7.1%). The most prevalent serovars were, in descending order: Javanica (4.6% rats), Lousiana (4.2%), Copenageni (4.2%), Cynopterie (3.7%), Pomona (2.9%), and Icterohaemorrhagiae (2.5%). A total of 16 rats (5.8%) tested positive by RT-PCR. Overall, larger rats tended to have a higher prevalence of detection. There was considerable agreement between MAT and PCR (kappa=0.28 [0.07–0.49]), although significantly more rats were positive by MAT (McNemar 29.9 (p<0.001). MAT prevalence was higher among rats during the rainy season compared with rats in the dry season. There are no current available data on leptospira serovars in humans in the Mekong Delta, although existing studies suggest limited overlapping between human and rat serovars. Further studies should take into account a wider range of potential reservoirs (i.e., dogs, pigs) as well as perform geographically linked co-sampling of humans and animals to establish the main sources of leptospirosis in the region.
Collapse
|
33
|
Le Viet T, Choisy M, Bryant JE, Vu Trong D, Pham Quang T, Horby P, Nguyen Tran H, Tran Thi Kieu H, Nguyen Vu T, Nguyen Van K, Le Quynh M, Wertheim HFL. A dengue outbreak on a floating village at Cat Ba Island in Vietnam. BMC Public Health 2015; 15:940. [PMID: 26395076 PMCID: PMC4579793 DOI: 10.1186/s12889-015-2235-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/07/2015] [Indexed: 01/26/2023] Open
Abstract
Background A dengue outbreak in an ecotourism destination spot in Vietnam, from September to November 2013, impacted a floating village of fishermen on the coastal island of Cat Ba. The outbreak raises questions about how tourism may impact disease spread in rural areas. Methods Epidemiological data were obtained from the Hai Phong Preventive Medical Center (PMC), including case histories and residential location from all notified dengue cases from this outbreak. All household addresses were geo-located. Knox test, a spatio-temporal analysis that enables inference dengue clustering constrained by space and time, was performed on the geocoded locations. From the plasma available from two patients, positive for Dengue serotype 3 virus (DENV3), the Envelope (E) gene was sequenced, and their genetic relationships compared to other E sequences in the region. Results Of 192 dengue cases, the odds ratio of contracting dengue infections for people living in the floating villages compared to those living on the island was 4.9 (95 % CI: 3.6-6.7). The space-time analyses on 111 geocoded dengue residences found the risk of dengue infection to be the highest within 4 days and a radius of 20 m of a given case. Of the total of ten detected clusters with an excess risk greater than 2, the cluster with the highest number of cases was in the floating village area (24 patients for a total duration of 31 days). Phylogenetic analysis revealed a high homology of the two DENV3 strains (genotype III) from Cat Ba with DENV3 viruses circulating in Hanoi in the same year (99.1 %). Conclusions Our study showed that dengue transmission is unlikely to be sustained on Cat Ba Island and that the 2013 epidemic likely originated through introduction of viruses from the mainland, potentially Hanoi. These findings suggest that prevention efforts should be focused on mainland rather than on the island. Electronic supplementary material The online version of this article (doi:10.1186/s12889-015-2235-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Thanh Le Viet
- Oxford University Clinical Research Unit Hanoi, Hanoi, Vietnam.
| | - Marc Choisy
- Oxford University Clinical Research Unit Hanoi, Hanoi, Vietnam. .,MIVEGEC (University of Montpellier, CNRS 5290, IRD 224), Montpellier, France.
| | - Juliet E Bryant
- Oxford University Clinical Research Unit Hanoi, Hanoi, Vietnam. .,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom.
| | - Duoc Vu Trong
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
| | - Thai Pham Quang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
| | - Peter Horby
- Oxford University Clinical Research Unit Hanoi, Hanoi, Vietnam. .,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom.
| | | | | | | | | | - Mai Le Quynh
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
| | - Heiman F L Wertheim
- Oxford University Clinical Research Unit Hanoi, Hanoi, Vietnam. .,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom. .,Radboudumc, Nijmegen, Netherlands.
| |
Collapse
|
34
|
Huong VTL, Hoa NT, Horby P, Bryant JE, Van Kinh N, Toan TK, Wertheim HFL. Raw pig blood consumption and potential risk for Streptococcus suis infection, Vietnam. Emerg Infect Dis 2015; 20:1895-8. [PMID: 25340391 PMCID: PMC4214319 DOI: 10.3201/eid2011.140915] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We assessed consumption of raw pig blood, which is a risk factor for Streptococcus suis infection in Vietnam, by using a mix-method design. Factors associated with consumption included rural residency, age, sex, occupation, income, and marital status. We identified risk groups and practices and perceptions that should be targeted by communication programs.
Collapse
|
35
|
Nhung NT, Cuong NV, Campbell J, Hoa NT, Bryant JE, Truc VNT, Kiet BT, Jombart T, Trung NV, Hien VB, Thwaites G, Baker S, Carrique-Mas J. High levels of antimicrobial resistance among escherichia coli isolates from livestock farms and synanthropic rats and shrews in the Mekong Delta of Vietnam. Appl Environ Microbiol 2015; 81:812-20. [PMID: 25398864 PMCID: PMC4292488 DOI: 10.1128/aem.03366-14] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [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: 10/12/2014] [Accepted: 11/07/2014] [Indexed: 01/21/2023] Open
Abstract
In Mekong Delta farms (Vietnam), antimicrobials are extensively used, but limited data are available on levels of antimicrobial resistance (AMR) among Escherichia coli isolates. We performed a structured survey of AMR in E. coli isolates (n = 434) from 90 pig, chicken, and duck farms. The results were compared with AMR among E. coli isolates (n = 234) from 66 small wild animals (rats and shrews) trapped on farms and in forests and rice fields. The isolates were susceptibility tested against eight antimicrobials. E. coli isolates from farmed animals were resistant to a median of 4 (interquartile range [IQR], 3 to 6) antimicrobials versus 1 (IQR, 1 to 2) among wild mammal isolates (P < 0.001). The prevalences of AMR among farmed species isolates (versus wild animals) were as follows: tetracycline, 84.7% (versus 25.6%); ampicillin, 78.9% (versus 85.9%); trimethoprim-sulfamethoxazole, 52.1% (versus 18.8%); chloramphenicol, 39.9% (versus 22.5%); amoxicillin-clavulanic acid, 36.6% (versus 34.5%); and ciprofloxacin, 24.9% (versus 7.3%). The prevalence of multidrug resistance (MDR) (resistance against three or more antimicrobial classes) among pig isolates was 86.7% compared to 66.9 to 72.7% among poultry isolates. After adjusting for host species, MDR was ∼8 times greater among isolates from wild mammals trapped on farms than among those trapped in forests/rice fields (P < 0.001). Isolates were assigned to unique profiles representing their combinations of susceptibility results. Multivariable analysis of variance indicated that AMR profiles from wild mammals trapped on farms and those from domestic animals were more alike (R(2) range, 0.14 to 0.30) than E. coli isolates from domestic animals and mammals trapped in the wild (R(2) range, 0.25 to 0.45). The results strongly suggest that AMR on farms is a key driver of environmental AMR in the Mekong Delta.
Collapse
Affiliation(s)
- N T Nhung
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - N V Cuong
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - J Campbell
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - N T Hoa
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - J E Bryant
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - V N T Truc
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - B T Kiet
- Sub-Department of Animal Health, Dong Thap Province, Cao Lanh, Vietnam
| | - T Jombart
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, United Kingdom
| | - N V Trung
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - V B Hien
- Sub-Department of Animal Health, Dong Thap Province, Cao Lanh, Vietnam
| | - G Thwaites
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - S Baker
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - J Carrique-Mas
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| |
Collapse
|
36
|
Van Cuong N, Carrique-Mas J, Vo Be H, An NN, Tue NT, Anh NL, Anh PH, Phuc NT, Baker S, Voutilainen L, Jääskeläinen A, Huhtamo E, Utriainen M, Sironen T, Vaheri A, Henttonen H, Vapalahti O, Chaval Y, Morand S, Bryant JE. Rodents and risk in the Mekong Delta of Vietnam: seroprevalence of selected zoonotic viruses in rodents and humans. Vector Borne Zoonotic Dis 2015; 15:65-72. [PMID: 25629782 PMCID: PMC4676424 DOI: 10.1089/vbz.2014.1603] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 11/13/2022] Open
Abstract
In the Mekong Delta in southern Vietnam, rats are commonly traded in wet markets and sold live for food consumption. We investigated seroprevalence to selected groups of rodent-borne viruses among human populations with high levels of animal exposure and among co-located rodent populations. The indirect fluorescence antibody test (IFAT) was used to determine seropositivity to representative reference strains of hantaviruses (Dobrava virus [DOBV], Seoul virus [SEOV]), cowpox virus, arenaviruses (lymphocytic choriomeningitis virus [LCMV]), flaviviruses (tick-borne encephalitis virus [TBEV]), and rodent parechoviruses (Ljungan virus), using sera from 245 humans living in Dong Thap Province and 275 rodents representing the five common rodent species sold in wet markets and present in peridomestic and farm settings. Combined seropositivity to DOBV and SEOV among the rodents and humans was 6.9% (19/275) and 3.7% (9/245), respectively; 1.1% (3/275) and 4.5% (11/245) to cowpox virus; 5.4% (15/275) and 47.3% (116/245) for TBEV; and exposure to Ljungan virus was 18.8% (46/245) in humans, but 0% in rodents. Very little seroreactivity was observed to LCMV in either rodents (1/275, 0.4%) or humans (2/245, 0.8%). Molecular screening of rodent liver tissues using consensus primers for flaviviruses did not yield any amplicons, whereas molecular screening of rodent lung tissues for hantavirus yielded one hantavirus sequence (SEOV). In summary, these results indicate low to moderate levels of endemic hantavirus circulation, possible circulation of a flavivirus in rodent reservoirs, and the first available data on human exposures to parechoviruses in Vietnam. Although the current evidence suggests only limited exposure of humans to known rodent-borne diseases, further research is warranted to assess public health implications of the rodent trade.
Collapse
Affiliation(s)
- Nguyen Van Cuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Hien Vo Be
- Sub-Department of Animal Health, Dong Thap Province, Cao Lanh, Vietnam
| | - Nguyen Ngoc An
- Department of Preventive Medicine, Dong Thap Province, Cao Lanh, Vietnam
| | - Ngo Tri Tue
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Nguyet Lam Anh
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Pham Hong Anh
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Nguyen The Phuc
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | - Anne Jääskeläinen
- Haartman Institute, University of Helsinki, Helsinki, Finland
- HUSLAB, Department of Virology and Immunology, Helsinki University Central Hospital, Helsinki, Finland
| | - Eili Huhtamo
- Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Mira Utriainen
- Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Antti Vaheri
- Haartman Institute, University of Helsinki, Helsinki, Finland
- HUSLAB, Department of Virology and Immunology, Helsinki University Central Hospital, Helsinki, Finland
| | | | - Olli Vapalahti
- Haartman Institute, University of Helsinki, Helsinki, Finland
- HUSLAB, Department of Virology and Immunology, Helsinki University Central Hospital, Helsinki, Finland
- Faculty of Veterinary Medicine, Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | | | - Juliet E. Bryant
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| |
Collapse
|
37
|
My PVT, Rabaa MA, Donato C, Cowley D, Phat VV, Dung TTN, Anh PH, Vinh H, Bryant JE, Kellam P, Thwaites G, Woolhouse MEJ, Kirkwood CD, Baker S. Novel porcine-like human G26P[19] rotavirus identified in hospitalized paediatric diarrhoea patients in Ho Chi Minh City, Vietnam. J Gen Virol 2014; 95:2727-2733. [PMID: 25121549 PMCID: PMC4233630 DOI: 10.1099/vir.0.068403-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 12/17/2022] Open
Abstract
During a hospital-based diarrhoeal disease study conducted in Ho Chi Minh City, Vietnam from 2009 to 2010, we identified four symptomatic children infected with G26P[19] rotavirus (RV) – an atypical variant that has not previously been reported in human gastroenteritis. To determine the genetic structure and investigate the origin of this G26P[19] strain, the whole genome of a representative example was characterized, revealing a novel genome constellation: G26–P[19]–I5–R1–C1–M1–A8–N1–T1–E1–H1. The genome segments were most closely related to porcine (VP7, VP4, VP6 and NSP1) and Wa-like porcine RVs (VP1–3 and NSP2–5). We proposed that this G26P[19] strain was the product of zoonotic transmission coupled with one or more reassortment events occurring in human and/or animal reservoirs. The identification of such strains has potential implications for vaccine efficacy in south-east Asia, and outlines the utility of whole-genome sequencing for studying RV diversity and zoonotic potential during disease surveillance.
Collapse
Affiliation(s)
- Phan Vu Tra My
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Maia A Rabaa
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Celeste Donato
- La Trobe University, Melbourne, Australia.,Murdoch Childrens Research Institute, Melbourne, Australia
| | - Daniel Cowley
- Murdoch Childrens Research Institute, Melbourne, Australia
| | - Voong Vinh Phat
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran Thi Ngoc Dung
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Pham Hong Anh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ha Vinh
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Juliet E Bryant
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - Paul Kellam
- Division of Infection and Immunity, University College London, London, United Kingdom.,The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Guy Thwaites
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Mark E J Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Carl D Kirkwood
- La Trobe University, Melbourne, Australia.,Murdoch Childrens Research Institute, Melbourne, Australia
| | - Stephen Baker
- The London School of Hygiene and Tropical Medicine, London, UK.,Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| |
Collapse
|
38
|
Nguyen DT, Bryant JE, Davis CT, Nguyen LV, Pham LT, Loth L, Inui K, Nguyen T, Jang Y, To TL, Nguyen TD, Hoang DT, Do HT, Nguyen TT, Newman S, Siembieda J, Pham DV. Prevalence and Distribution of Avian Influenza A(H5N1) Virus Clade Variants in Live Bird Markets of Vietnam, 2011–2013. Avian Dis 2014; 58:599-608. [DOI: 10.1637/10814-030814-reg] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Diep T. Nguyen
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Juliet E. Bryant
- Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - C. Todd Davis
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30333 USA
| | - Long V. Nguyen
- Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam
| | - Long T. Pham
- Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam
| | - Leo Loth
- Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | - Ken Inui
- Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | - Tung Nguyen
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Yunho Jang
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30333 USA
| | - Thanh L. To
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Tho D. Nguyen
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Diep T. Hoang
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Hoa T. Do
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Trang T. Nguyen
- National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - Scott Newman
- Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | | | - Dong V. Pham
- Department of Animal Health, Ministry of Agriculture and Rural Development of Vietnam, Hanoi, Vietnam
| |
Collapse
|
39
|
Pham HA, Carrique-Mas JJ, Nguyen VC, Ngo TH, Nguyet LA, Do TD, Vo BH, Phan VTM, Rabaa MA, Farrar J, Baker S, Bryant JE. The prevalence and genetic diversity of group A rotaviruses on pig farms in the Mekong Delta region of Vietnam. Vet Microbiol 2014; 170:258-65. [PMID: 24679960 PMCID: PMC4003349 DOI: 10.1016/j.vetmic.2014.02.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [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: 10/15/2013] [Revised: 02/10/2014] [Accepted: 02/17/2014] [Indexed: 12/15/2022]
Abstract
Group A rotaviruses (ARoVs) are a common cause of severe diarrhea among children worldwide and the cause of approximately 45% of pediatric hospitalizations for acute diarrhea in Vietnam. ARoVs are known to cause significant economic losses to livestock producers by reducing growth performance and production efficiencies, however little is known about the implications of asymptomatic endemic circulation of ARoV. We aimed to determine the prevalence and predominant circulating genotypes of ARoVs on pig farms in a southern province of Vietnam. We found overall animal-level and farm-level prevalence of 32.7% (239/730) and 74% (77/104), respectively, and identified six different G types and 4 P types in various combinations (G2, G3, G4, G5, G9, G11 and P[6], P[13], P[23], and P[34]). There was no significant association between ARoV infection and clinical disease in pigs, suggesting that endemic asymptomatic circulation of ARoV may complicate rotavirus disease attribution during outbreaks of diarrhea in swine. Sequence analysis of the detected ARoVs suggested homology to recent human clinical cases and extensive genetic diversity. The epidemiological relevance of these findings for veterinary practitioners and to ongoing pediatric ARoV vaccine initiatives in Vietnam merits further study.
Collapse
Affiliation(s)
- Hong Anh Pham
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam
| | - Juan J Carrique-Mas
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam
| | - Van Cuong Nguyen
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam
| | - Thi Hoa Ngo
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam
| | - Lam Anh Nguyet
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam
| | | | - Be Hien Vo
- Sub-Department of Animal Health, Dong Thap, Viet Nam
| | - Vu Tra My Phan
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam; University of Edinburgh, London, United Kingdom
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam; Centre for Tropical Medicine, Nuffield Department of Medicine, Oxford University, London, United Kingdom
| | - Stephen Baker
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam; Centre for Tropical Medicine, Nuffield Department of Medicine, Oxford University, London, United Kingdom; The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Juliet E Bryant
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Viet Nam; Centre for Tropical Medicine, Nuffield Department of Medicine, Oxford University, London, United Kingdom.
| |
Collapse
|
40
|
Le VT, de Jong MD, Nguyen VK, Nguyen VT, Taylor W, Wertheim HFL, van der Ende A, van der Hoek L, Canuti M, Crusat M, Sona S, Nguyen HU, Giri A, Nguyen TTCB, Ho DTN, Farrar J, Bryant JE, Tran TH, Nguyen VVC, van Doorn HR. Limited geographic distribution of the novel cyclovirus CyCV-VN. Sci Rep 2014; 4:3967. [PMID: 24495921 PMCID: PMC3913916 DOI: 10.1038/srep03967] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 09/05/2013] [Accepted: 01/17/2014] [Indexed: 01/03/2023] Open
Abstract
A novel cyclovirus, CyCV-VN, was recently identified in cerebrospinal fluid (CSF) from patients with central nervous system (CNS) infections in central and southern Vietnam. To explore the geographic distribution of this novel virus, more than 600 CSF specimens from patients with suspected CNS infections in northern Vietnam, Cambodia, Nepal and The Netherlands were screened for the presence of CyCV-VN but all were negative. Sequence comparison and phylogenetic analysis between CyCV-VN and another novel cyclovirus recently identified in CSF from Malawian patients indicated that these represent distinct cycloviral species, albeit phylogenetically closely related. The data suggest that CyCV-VN has a limited geographic distribution within southern and central Vietnam. Further research is needed to determine the global distribution and diversity of cycloviruses and importantly their possible association with human disease.
Collapse
Affiliation(s)
- Van Tan Le
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Menno D de Jong
- 1] Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam [2] Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Van Kinh Nguyen
- 1] National Hospital for Tropical Diseases, Hanoi, Vietnam [2] Hanoi Medical University, Hanoi, Vietnam
| | - Vu Trung Nguyen
- 1] National Hospital for Tropical Diseases, Hanoi, Vietnam [2] Hanoi Medical University, Hanoi, Vietnam
| | - Walter Taylor
- 1] Oxford University Clinical Research Unit, Hanoi, Vietnam [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heiman F L Wertheim
- 1] Oxford University Clinical Research Unit, Hanoi, Vietnam [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Arie van der Ende
- 1] Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands [2] The Netherlands National Reference Laboratory for Bacterial Meningitis, Amsterdam, the Netherlands
| | - Lia van der Hoek
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Marta Canuti
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Martin Crusat
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Soeng Sona
- Angkor Hospital for Children, Siem Reap, Kingdom of Cambodia
| | - Hanh Uyen Nguyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Abhishek Giri
- Oxford University Clinical Research Unit, Patan Hospital, Kathmandu, Nepal
| | | | - Dang Trung Nghia Ho
- 1] Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam [2] Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam [3] Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Jeremy Farrar
- 1] Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Juliet E Bryant
- 1] Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tinh Hien Tran
- 1] Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - H Rogier van Doorn
- 1] Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
41
|
Van Dung N, Anh PH, Van Cuong N, Hoa NT, Carrique-Mas J, Hien VB, Campbell J, Baker S, Farrar J, Woolhouse ME, Bryant JE, Simmonds P. Prevalence, genetic diversity and recombination of species G enteroviruses infecting pigs in Vietnam. J Gen Virol 2013; 95:549-556. [PMID: 24323635 DOI: 10.1099/vir.0.061978-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Picornaviruses infecting pigs, described for many years as 'porcine enteroviruses', have recently been recognized as distinct viruses within three distinct genera (Teschovirus, Sapelovirus and Enterovirus). To better characterize the epidemiology and genetic diversity of members of the Enterovirus genus, faecal samples from pigs from four provinces in Vietnam were screened by PCR using conserved enterovirus (EV)-specific primers from the 5' untranslated region (5' UTR). High rates of infection were recorded in pigs on all farms, with detection frequencies of approximately 90% in recently weaned pigs but declining to 40% in those aged over 1 year. No differences in EV detection rates were observed between pigs with and without diarrhoea [74% (n = 70) compared with 72% (n = 128)]. Genetic analysis of consensus VP4/VP2 and VP1 sequences amplified from a subset of EV-infected pigs identified species G EVs in all samples. Among these, VP1 sequence comparisons identified six type 1 and seven type 6 variants, while four further VP1 sequences failed to group with any previously identified EV-G types. These have now been formally assigned as EV-G types 8-11 by the Picornavirus Study Group. Comparison of VP1, VP4/VP2, 3D(pol) and 5' UTRs of study samples and those available on public databases showed frequent, bootstrap-supported differences in their phylogenies indicative of extensive within-species recombination between genome regions. In summary, we identified extremely high frequencies of infection with EV-G in pigs in Vietnam, substantial genetic diversity and recombination within the species, and evidence for a much larger number of circulating EV-G types than currently described.
Collapse
Affiliation(s)
- Nguyen Van Dung
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Pham Hong Anh
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1 Quan 5, Ho Chi Minh City, Vietnam
| | - Nguyen Van Cuong
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1 Quan 5, Ho Chi Minh City, Vietnam
| | - Ngo Thi Hoa
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.,Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1 Quan 5, Ho Chi Minh City, Vietnam
| | - Juan Carrique-Mas
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1 Quan 5, Ho Chi Minh City, Vietnam
| | - Vo Be Hien
- Subdepartment of Animal Health, Dong Thap Province, Vietnam
| | - James Campbell
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1 Quan 5, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT, UK.,Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.,Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1 Quan 5, Ho Chi Minh City, Vietnam
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1 Quan 5, Ho Chi Minh City, Vietnam
| | - Mark E Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| | - Juliet E Bryant
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.,Oxford University Clinical Research Unit, 764 Vo Van Kiet, W.1 Quan 5, Ho Chi Minh City, Vietnam
| | - Peter Simmonds
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK.,Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| |
Collapse
|
42
|
Carrique-Mas JJ, Bryant JE. A review of foodborne bacterial and parasitic zoonoses in Vietnam. Ecohealth 2013; 10:465-89. [PMID: 24162798 PMCID: PMC3938847 DOI: 10.1007/s10393-013-0884-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 06/10/2013] [Accepted: 09/24/2013] [Indexed: 06/02/2023]
Abstract
Vietnam has experienced unprecedented economic and social development in recent years, and the livestock sector is undergoing significant transformations. Although food animal production is still dominated by small-scale 'backyard' enterprises with mixed crop-livestock or livestock-aquatic systems, there is a trend towards more intensive and vertically integrated operations. Changes in animal production, processing and distribution networks for meat and animal products, and the shift from wet markets to supermarkets will undoubtedly impact food safety risks in Vietnam in unforeseen and complex ways. Here, we review the available published literature on bacterial and parasitic foodborne zoonoses (FBZ) in Vietnam. We report on clinical disease burden and pathogen prevalence in animal reservoirs for a number of important FBZ, and outline opportunities for future research.
Collapse
Affiliation(s)
- Juan J Carrique-Mas
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, W.1, Dist.5, Ho Chi Minh City, Vietnam,
| | | |
Collapse
|
43
|
Hoa NT, Chieu TTB, Do Dung S, Long NT, Hieu TQ, Luc NT, Nhuong PT, Huong VTL, Trinh DT, Wertheim HFL, Van Kinh N, Campbell JI, Farrar J, Chau NVV, Baker S, Bryant JE. Streptococcus suis and porcine reproductive and respiratory syndrome, Vietnam. Emerg Infect Dis 2013; 19:331-3. [PMID: 23343623 PMCID: PMC3559037 DOI: 10.3201/eid1902.120470] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
|
44
|
Nguyen NM, Thi Hue Kien D, Tuan TV, Quyen NTH, Tran CNB, Vo Thi L, Thi DL, Nguyen HL, Farrar JJ, Holmes EC, Rabaa MA, Bryant JE, Nguyen TT, Nguyen HTC, Nguyen LTH, Pham MP, Nguyen HT, Luong TTH, Wills B, Nguyen CVV, Wolbers M, Simmons CP. Host and viral features of human dengue cases shape the population of infected and infectious Aedes aegypti mosquitoes. Proc Natl Acad Sci U S A 2013; 110:9072-7. [PMID: 23674683 PMCID: PMC3670336 DOI: 10.1073/pnas.1303395110] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [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: 11/18/2022] Open
Abstract
Dengue is the most prevalent arboviral disease of humans. The host and virus variables associated with dengue virus (DENV) transmission from symptomatic dengue cases (n = 208) to Aedes aegypti mosquitoes during 407 independent exposure events was defined. The 50% mosquito infectious dose for each of DENV-1-4 ranged from 6.29 to 7.52 log10 RNA copies/mL of plasma. Increasing day of illness, declining viremia, and rising antibody titers were independently associated with reduced risk of DENV transmission. High early DENV plasma viremia levels in patients were a marker of the duration of human infectiousness, and blood meals containing high concentrations of DENV were positively associated with the prevalence of infectious mosquitoes 14 d after blood feeding. Ambulatory dengue cases had lower viremia levels compared with hospitalized dengue cases but nonetheless at levels predicted to be infectious to mosquitoes. These data define serotype-specific viremia levels that vaccines or drugs must inhibit to prevent DENV transmission.
Collapse
Affiliation(s)
- Nguyet Minh Nguyen
- Oxford University Clinical Research Unit, District 5, Ho Chi Minh City, Vietnam
| | - Duong Thi Hue Kien
- Oxford University Clinical Research Unit, District 5, Ho Chi Minh City, Vietnam
| | - Trung Vu Tuan
- Oxford University Clinical Research Unit, District 5, Ho Chi Minh City, Vietnam
| | | | - Chau N. B. Tran
- Oxford University Clinical Research Unit, District 5, Ho Chi Minh City, Vietnam
| | - Long Vo Thi
- Oxford University Clinical Research Unit, District 5, Ho Chi Minh City, Vietnam
| | - Dui Le Thi
- Oxford University Clinical Research Unit, District 5, Ho Chi Minh City, Vietnam
| | - Hoa Lan Nguyen
- Oxford University Clinical Research Unit, District 5, Ho Chi Minh City, Vietnam
| | - Jeremy J. Farrar
- Oxford University Clinical Research Unit, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Edward C. Holmes
- Sydney Emerging Infections and Biosecurity Institute, School of Biological Sciences and Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892;
| | - Maia A. Rabaa
- Oxford University Clinical Research Unit, District 5, Ho Chi Minh City, Vietnam
| | - Juliet E. Bryant
- Oxford University Clinical Research Unit, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford OX1 2JD, United Kingdom
| | | | | | | | - Mai Phuong Pham
- Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam; and
| | - Hung The Nguyen
- Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam; and
| | - Tai Thi Hue Luong
- Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam; and
| | - Bridget Wills
- Oxford University Clinical Research Unit, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford OX1 2JD, United Kingdom
| | | | - Marcel Wolbers
- Oxford University Clinical Research Unit, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Cameron P. Simmons
- Oxford University Clinical Research Unit, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford OX1 2JD, United Kingdom
- Nossal Institute for Global Health, University of Melbourne, VIC 3010, Australia
| |
Collapse
|
45
|
Aine CJ, Sanfratello L, Ranken D, Best E, MacArthur JA, Wallace T, Gilliam K, Donahue CH, Montaño R, Bryant JE, Scott A, Stephen JM. MEG-SIM: a web portal for testing MEG analysis methods using realistic simulated and empirical data. Neuroinformatics 2012; 10:141-58. [PMID: 22068921 DOI: 10.1007/s12021-011-9132-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MEG and EEG measure electrophysiological activity in the brain with exquisite temporal resolution. Because of this unique strength relative to noninvasive hemodynamic-based measures (fMRI, PET), the complementary nature of hemodynamic and electrophysiological techniques is becoming more widely recognized (e.g., Human Connectome Project). However, the available analysis methods for solving the inverse problem for MEG and EEG have not been compared and standardized to the extent that they have for fMRI/PET. A number of factors, including the non-uniqueness of the solution to the inverse problem for MEG/EEG, have led to multiple analysis techniques which have not been tested on consistent datasets, making direct comparisons of techniques challenging (or impossible). Since each of the methods is known to have their own set of strengths and weaknesses, it would be beneficial to quantify them. Toward this end, we are announcing the establishment of a website containing an extensive series of realistic simulated data for testing purposes ( http://cobre.mrn.org/megsim/ ). Here, we present: 1) a brief overview of the basic types of inverse procedures; 2) the rationale and description of the testbed created; and 3) cases emphasizing functional connectivity (e.g., oscillatory activity) suitable for a wide assortment of analyses including independent component analysis (ICA), Granger Causality/Directed transfer function, and single-trial analysis.
Collapse
Affiliation(s)
- C J Aine
- Department of Radiology, MSC10 5530, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Do LAH, van Doorn HR, Bryant JE, Nghiem MN, Nguyen Van VC, Vo CK, Nguyen MD, Tran TH, Farrar J, de Jong MD. A sensitive real-time PCR for detection and subgrouping of human respiratory syncytial virus. J Virol Methods 2011; 179:250-5. [PMID: 22119628 PMCID: PMC3405522 DOI: 10.1016/j.jviromet.2011.11.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [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: 01/07/2011] [Revised: 11/08/2011] [Accepted: 11/10/2011] [Indexed: 12/01/2022]
Abstract
Improved diagnostic tools for rapid detection, quantitation, and subgrouping of human respiratory syncytial virus (RSV) are needed to aid the development and evaluation of novel intervention strategies. A quantitative real-time RT-PCR using specific locked nucleic acid (LNA) probes was developed to identify RSV and to distinguish RSV subgroups A and B (RSV LNA assay). RSV subgroup diversity and the relationship between viral load and disease severity in confirmed RSV infections were also explored. 264 archived respiratory specimens from pediatric patients were tested in parallel using the commercial multiplex Seeplex™ RV detection kit (Seegene) and the novel RSV LNA assay. The LNA assay demonstrated a significantly higher sensitivity than Seeplex, improving overall detection rates from 24% (64/264) to 32% (84/264). Detection limits of 9.0 × 101 and 6.0 × 102 copies/mL were observed for RSV A and B, respectively. RSV A was detected in 53/84 (63%) cases, and 31/84 (37%) were positive for RSV B. This novel method offers a rapid, quantitative, highly specific and sensitive approach to laboratory diagnosis of RSV.
Collapse
Affiliation(s)
- Lien Anh Ha Do
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Viet Nam.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Long NT, Thanh TT, van Doorn HR, Vu PP, Dung PT, Dung TTK, Tien TN, Thao DTT, Hung P, Quang NV, Hoa NT, Bryant JE, Boni MF. Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. Transbound Emerg Dis 2011; 58:537-43. [PMID: 21586098 PMCID: PMC3258422 DOI: 10.1111/j.1865-1682.2011.01229.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We report 15 new avian influenza virus A/H5N1 haemagglutinin (HA) sequences sampled from visibly sick domestic poultry in southern Vietnam, between 1 January 2010 and 6 March 2010. These HA sequences form a new sub-clade of the clade 1 H5N1 viruses that have been circulating in Vietnam since 2003/2004. The viruses are characterized by a change from isoleucine to valine at position 514 (I514V) and are 1.8% divergent at the nucleotide level from HA sequences sampled in Vietnam in 2007. Five new amino acid changes were observed at previously identified antigenic sites, and three were located within structural elements of the receptor-binding domain. One new mutation removed a potential N-linked glycosylation site, and a methionine insertion was observed in one virus at the polybasic cleavage site. Five of these viruses were sampled from farms where poultry were vaccinated against H5N1, but there was no association between observed amino acid changes and flock vaccination status. Despite the current lack of evidence for antigenic drift or immune escape in Vietnamese H5N1 viruses, continued surveillance remains a high priority.
Collapse
Affiliation(s)
- N T Long
- Regional Animal Health Office No. 6, Ho Chi Minh City, Vietnam
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Do AHL, van Doorn HR, Nghiem MN, Bryant JE, Hoang THT, Do QH, Van TL, Tran TT, Wills B, Nguyen VCV, Vo MH, Vo CK, Nguyen MD, Farrar J, Tran TH, de Jong MD. Viral etiologies of acute respiratory infections among hospitalized Vietnamese children in Ho Chi Minh City, 2004-2008. PLoS One 2011; 6:e18176. [PMID: 21455313 PMCID: PMC3063798 DOI: 10.1371/journal.pone.0018176] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 02/27/2011] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The dominant viral etiologies responsible for acute respiratory infections (ARIs) are poorly understood, particularly among hospitalized children in resource-limited tropical countries where morbidity and mortality caused by ARIs are highest. Improved etiological insight is needed to improve clinical management and prevention. OBJECTIVES We conducted a three-year prospective descriptive study of severe respiratory illness among children from 2 months to 13 years of age within the largest referral hospital for infectious diseases in southern Vietnam. METHODS Molecular detection for 15 viral species and subtypes was performed on three types of respiratory specimens (nose, throat swabs and nasopharyngeal aspirates) using a multiplex RT-PCR kit (Seeplex™ RV detection, Seegene) and additional monoplex real-time RT-PCRs. RESULTS A total of 309 children were enrolled from November 2004 to January 2008. Viruses were identified in 72% (222/309) of cases, including respiratory syncytial virus (24%), influenza virus A and B (17%), human bocavirus (16%), enterovirus (9%), human coronavirus (8%), human metapneumovirus (7%), parainfluenza virus 1-3 (6%), adenovirus (5%), and human rhinovirus A (4%). Co-infections with multiple viruses were detected in 20% (62/309) of patients. When combined, diagnostic yields in nose and throat swabs were similar to nasopharyngeal aspirates. CONCLUSION Similar to other parts in the world, RSV and influenza were the predominant viral pathogens detected in Vietnamese hospitalized children. Combined nasal and throat swabs are the specimens of choice for sensitive molecular detection of a broad panel of viral agents. Further research is required to better understand the clinical significance of single versus multiple viral coinfections and to address the role of bacterial (co-)infections involved in severe respiratory illness.
Collapse
Affiliation(s)
- Anh Ha Lien Do
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Hiscox A, Winter CH, Vongphrachanh P, Sisouk T, Somoulay V, Phompida S, Kaul S, Sananikhom P, Nguyen TY, Paul RE, Brey P, Bryant JE. Serological investigations of flavivirus prevalence in Khammouane Province, Lao People's Democratic Republic, 2007-2008. Am J Trop Med Hyg 2010; 83:1166-9. [PMID: 21036856 PMCID: PMC2963988 DOI: 10.4269/ajtmh.2010.09-0480] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [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: 12/02/2022] Open
Abstract
A large-scale cross-sectional seroprevalence study of dengue (DEN) and Japanese encephalitis (JE) was conducted in Khammouane province, Lao PDR, as part of the initial baseline health impact assessment of the Nam Theun 2 hydroelectric dam construction project. Health surveys were performed between May 2007 and February 2008 with serum samples collected from healthy individuals involved in the resettlement program of 16 villages (total surveyed population 4,369). Hemagglutination inhibition assay using flavivirus antigens (DENV1, DENV3, and JEV) performed on 1,708 plasma specimens revealed 30.4% (519) cross-reactive positives, and 10% (172) and 1.3% (22) positives to JEV or DENV, respectively. Entomological surveys conducted during the rainy season of 2008 indicated the presence of competent flavivirus vectors (Culex vishnui group and Aedes albopictus), although Aedes aegypti was not found. Continued surveillance and investigation is warranted to assess the clinical disease burden of flaviviruses in this area that is undergoing rapid ecological and demographic change.
Collapse
|
50
|
Hien TT, Boni MF, Bryant JE, Ngan TT, Wolbers M, Nguyen TD, Truong NT, Dung NT, Ha DQ, Hien VM, Thanh TT, Nhu LNT, Uyen LTT, Nhien PT, Chinh NT, Chau NVV, Farrar J, van Doorn HR. Early pandemic influenza (2009 H1N1) in Ho Chi Minh City, Vietnam: a clinical virological and epidemiological analysis. PLoS Med 2010; 7:e1000277. [PMID: 20502525 PMCID: PMC2872648 DOI: 10.1371/journal.pmed.1000277] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [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: 11/04/2009] [Accepted: 04/08/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND To date, little is known about the initial spread and response to the 2009 pandemic of novel influenza A ("2009 H1N1") in tropical countries. Here, we analyse the early progression of the epidemic from 26 May 2009 until the establishment of community transmission in the second half of July 2009 in Ho Chi Minh City (HCMC), Vietnam. In addition, we present detailed systematic viral clearance data on 292 isolated and treated patients and the first three cases of selection of resistant virus during treatment in Vietnam. METHODS AND FINDINGS Data sources included all available health reports from the Ministry of Health and relevant health authorities as well as clinical and laboratory data from the first confirmed cases isolated at the Hospital for Tropical Diseases in HCMC. Extensive reverse transcription (RT)-PCR diagnostics on serial samples, viral culture, neuraminidase-inhibition testing, and sequencing were performed on a subset of 2009 H1N1 confirmed cases. Virological (PCR status, shedding) and epidemiological (incidence, isolation, discharge) data were combined to reconstruct the initial outbreak and the establishment of community transmission. From 27 April to 24 July 2009, approximately 760,000 passengers who entered HCMC on international flights were screened at the airport by a body temperature scan and symptom questionnaire. Approximately 0.15% of incoming passengers were intercepted, 200 of whom tested positive for 2009 H1N1 by RT-PCR. An additional 121 out of 169 nontravelers tested positive after self-reporting or contact tracing. These 321 patients spent 79% of their PCR-positive days in isolation; 60% of PCR-positive days were spent treated and in isolation. Influenza-like illness was noted in 61% of patients and no patients experienced pneumonia or severe outcomes. Viral clearance times were similar among patient groups with differing time intervals from illness onset to treatment, with estimated median clearance times between 2.6 and 2.8 d post-treatment for illness-to-treatment intervals of 1-4 d, and 2.0 d (95% confidence interval 1.5-2.5) when treatment was started on the first day of illness. CONCLUSIONS The patients described here represent a cross-section of infected individuals that were identified by temperature screening and symptom questionnaires at the airport, as well as mildly symptomatic to moderately ill patients who self-reported to hospitals. Data are observational and, although they are suggestive, it is not possible to be certain whether the containment efforts delayed community transmission in Vietnam. Viral clearance data assessed by RT-PCR showed a rapid therapeutic response to oseltamivir.
Collapse
Affiliation(s)
- Tran Tinh Hien
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Southeast Asian Infectious Diseases Clinical Research Network (SEAICRN, Jakarta, Indonesia
| | - Maciej F. Boni
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Centre for Clinical Vaccinology and Tropical Medicine, Oxford, United Kingdom
| | - Juliet E. Bryant
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Centre for Clinical Vaccinology and Tropical Medicine, Oxford, United Kingdom
| | - Tran Thuy Ngan
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Southeast Asian Infectious Diseases Clinical Research Network (SEAICRN, Jakarta, Indonesia
| | - Marcel Wolbers
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Centre for Clinical Vaccinology and Tropical Medicine, Oxford, United Kingdom
| | - Tran Dang Nguyen
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | | | - Do Quang Ha
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Vo Minh Hien
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Tran Tan Thanh
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Le Nguyen Truc Nhu
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Le Thi Tam Uyen
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Pham Thi Nhien
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | | | - Jeremy Farrar
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Southeast Asian Infectious Diseases Clinical Research Network (SEAICRN, Jakarta, Indonesia
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Centre for Clinical Vaccinology and Tropical Medicine, Oxford, United Kingdom
| | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Program, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Southeast Asian Infectious Diseases Clinical Research Network (SEAICRN, Jakarta, Indonesia
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Centre for Clinical Vaccinology and Tropical Medicine, Oxford, United Kingdom
| |
Collapse
|