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Kenmoe S, Takuissu GR, Ebogo-Belobo JT, Kengne-Ndé C, Mbaga DS, Bowo-Ngandji A, Ondigui Ndzie JL, Kenfack-Momo R, Tchatchouang S, Lontuo Fogang R, Zeuko'o Menkem E, Kame-Ngasse GI, Magoudjou-Pekam JN, Puzelli S, Lucentini L, Veneri C, Mancini P, Bonanno Ferraro G, Iaconelli M, Del Giudice C, Brandtner D, Suffredini E, La Rosa G. A systematic review of influenza virus in water environments across human, poultry, and wild bird habitats. WATER RESEARCH X 2024; 22:100210. [PMID: 38298332 PMCID: PMC10825513 DOI: 10.1016/j.wroa.2023.100210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 02/02/2024]
Abstract
Influenza, a highly contagious acute respiratory disease, remains a major global health concern. This study aimed to comprehensively assess the prevalence of influenza virus in different aquatic environments. Using 43 articles from four databases, we thoroughly examined water matrices from wastewater treatment plants (WTPs) and other human environments, as well as poultry habitats and areas frequented by migratory wild birds. In WTP influents (10 studies), positivity rates for influenza A ranged from 0.0 % to 97.6 %. For influenza B (8 studies), most studies reported no positivity, except for three studies reporting detection in 0.8 %, 5.6 %, and 46.9 % of samples. Within poultry habitats (13 studies), the prevalence of influenza A ranged from 4.3 % to 76.4 %, while in environments frequented by migratory wild birds (11 studies), it ranged from 0.4 % to 69.8 %. Geographically, the studies were distributed as follows: 39.5 % from the Americas, 18.6 % from Europe, 2.3 % from South-East Asia and 39.5 % from the Western Pacific. Several influenza A subtypes were found in water matrices, including avian influenza (H3N6, H3N8, H4N1, H4N2, H4N6, H4N8, H5N1, H5N8, H6N2, H6N6, H7N9, H0N8, and H11N9) and seasonal human influenza (H1N1 and H3N2). The existing literature indicates a crucial requirement for more extensive future research on this topic. Specifically, it emphasizes the need for method harmonization and delves into areas deserving of in-depth research, such as water matrices pertaining to pig farming and prevalence studies in low-income countries.
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Affiliation(s)
- S Kenmoe
- Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
| | - GR Takuissu
- Centre for Food, Food Security and Nutrition Research, Institute of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon
| | - JT Ebogo-Belobo
- Medical Research Centre, Institute of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon
| | - C Kengne-Ndé
- Epidemiological Surveillance, Evaluation and Research Unit, National AIDS Control Committee, Douala, Cameroon
| | - DS Mbaga
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - A Bowo-Ngandji
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - JL Ondigui Ndzie
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - R Kenfack-Momo
- Department of Biochemistry, The University of Yaounde I, Yaounde, Cameroon
| | - S Tchatchouang
- Scientific Direction, Centre Pasteur du Cameroun, Yaounde, Cameroon
| | - R Lontuo Fogang
- Department of Animal Biology, University of Dschang, Dschang, Cameroon
| | - E Zeuko'o Menkem
- Department of Biomedical Sciences, University of Buea, Buea, Cameroon
| | - GI Kame-Ngasse
- Medical Research Centre, Institute of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon
| | - JN Magoudjou-Pekam
- Department of Biochemistry, The University of Yaounde I, Yaounde, Cameroon
| | - S Puzelli
- Department of Infectious Disease, Istituto Superiore di Sanità, Rome, Italy
| | - L Lucentini
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Rome, Italy
| | - C Veneri
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Rome, Italy
| | - P Mancini
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Rome, Italy
| | - G Bonanno Ferraro
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Rome, Italy
| | - C Del Giudice
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Rome, Italy
| | - D Brandtner
- Department of Infectious Disease, Istituto Superiore di Sanità, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary public health, Istituto Superiore di Sanità, Rome, Italy
| | - G La Rosa
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Rome, Italy
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2
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Islam A, Amin E, Munro S, Hossain ME, Islam S, Hassan MM, Al Mamun A, Samad MA, Shirin T, Rahman MZ, Epstein JH. Potential risk zones and climatic factors influencing the occurrence and persistence of avian influenza viruses in the environment of live bird markets in Bangladesh. One Health 2023; 17:100644. [PMID: 38024265 PMCID: PMC10665157 DOI: 10.1016/j.onehlt.2023.100644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Live bird markets (LBMs) are critical for poultry trade in many developing countries that are regarded as hotspots for the prevalence and contamination of avian influenza viruses (AIV). Therefore, we conducted weekly longitudinal environmental surveillance in LBMs to determine annual cyclic patterns of AIV subtypes, environmental risk zones, and the role of climatic factors on the AIV presence and persistence in the environment of LBM in Bangladesh. From January 2018 to March 2020, we collected weekly fecal and offal swab samples from each LBM and tested using rRT-PCR for the M gene and subtyped for H5, H7, and H9. We used Generalized Estimating Equations (GEE) approaches to account for repeated observations over time to correlate the AIV prevalence and potential risk factors and the negative binomial and Poisson model to investigate the role of climatic factors on environmental contamination of AIV at the LBM. Over the study period, 37.8% of samples tested AIV positive, 18.8% for A/H5, and A/H9 was, for 15.4%. We found the circulation of H5, H9, and co-circulation of H5 and H9 in the environmental surfaces year-round. The Generalized Estimating Equations (GEE) model reveals a distinct seasonal pattern in transmitting AIV and H5. Specifically, certain summer months exhibited a substantial reduction of risk up to 70-90% and 93-94% for AIV and H5 contamination, respectively. The slaughtering zone showed a significantly higher risk of contamination with H5, with a three-fold increase in risk compared to bird-holding zones. From the negative binomial model, we found that climatic factors like temperature and relative humidity were also significantly associated with weekly AIV circulation. An increase in temperature and relative humidity decreases the risk of AIV circulation. Our study underscores the significance of longitudinal environmental surveillance for identifying potential risk zones to detect H5 and H9 virus co-circulation and seasonal transmission, as well as the imperative for immediate interventions to reduce AIV at LBMs in Bangladesh. We recommend adopting a One Health approach to integrated AIV surveillance across animal, human, and environmental interfaces in order to prevent the epidemic and pandemic of AIV.
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Affiliation(s)
- Ariful Islam
- EcoHealth Alliance, New York, NY 10018, USA
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Emama Amin
- EcoHealth Alliance, New York, NY 10018, USA
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
| | | | - Mohammad Enayet Hossain
- One Health Laboratory, International Centre for Diarrheal Diseases Research, Bangladesh (ICDDR), Bangladesh
| | - Shariful Islam
- EcoHealth Alliance, New York, NY 10018, USA
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
| | - Mohammad Mahmudul Hassan
- Queensland Alliance for One Health Sciences, School of Veterinary Science, University of Queensland, QLD 4343, Australia
| | - Abdullah Al Mamun
- EcoHealth Alliance, New York, NY 10018, USA
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
| | - Mohammed Abdus Samad
- National Reference Laboratory for Avian Influenza, Bangladesh Livestock Research Institute (BLRI), Savar, Bangladesh
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh
| | - Mohammed Ziaur Rahman
- One Health Laboratory, International Centre for Diarrheal Diseases Research, Bangladesh (ICDDR), Bangladesh
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Horwood PF, Horm SV, Yann S, Tok S, Chan M, Suttie A, Y P, Rith S, Siegers JY, San S, Davun H, Tum S, Ly S, Tarantola A, Dussart P, Karlsson EA. Aerosol exposure of live bird market workers to viable influenza A/H5N1 and A/H9N2 viruses, Cambodia. Zoonoses Public Health 2023; 70:171-175. [PMID: 36409285 PMCID: PMC10098856 DOI: 10.1111/zph.13009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 11/23/2022]
Abstract
Live bird markets (LBMs) have been identified as key factors in the spread, persistence and evolution of avian influenza viruses (AIVs). In addition, these settings have been associated with human infections with AIVs of pandemic concern. Exposure to aerosolised AIVs by workers in a Cambodian LBM was assessed using aerosol impact samplers. LBM vendors were asked to wear an air sampler for 30 min per day for 1 week while continuing their usual activities in the LBM during a period of high AIV circulation (February) and a period of low circulation (May). During the period of high circulation, AIV RNA was detected from 100% of the air samplers using molecular methods and viable AIV (A/H5N1 and/or A/H9N2) was isolated from 50% of air samplers following inoculation into embryonated chicken eggs. In contrast, AIV was not detected by molecular methods or successfully isolated during the period of low circulation. This study demonstrates the increased risk of aerosol exposure of LBM workers to AIVs during periods of high circulation and highlights the need for interventions during these high-risk periods. Novel approaches, such as environmental sampling, should be further explored at key high-risk interfaces as a potentially cost-effective alternative for monitoring pandemic threats.
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Affiliation(s)
- Paul F. Horwood
- Virology UnitInstitut Pasteur du Cambodge, Pasteur NetworkPhnom PenhCambodia
- College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Srey Viseth Horm
- Virology UnitInstitut Pasteur du Cambodge, Pasteur NetworkPhnom PenhCambodia
| | - Sokhoun Yann
- Virology UnitInstitut Pasteur du Cambodge, Pasteur NetworkPhnom PenhCambodia
| | - Songha Tok
- Virology UnitInstitut Pasteur du Cambodge, Pasteur NetworkPhnom PenhCambodia
| | - Malen Chan
- Epidemiology and Public Health Unit, Institut Pasteur du CambodgePasteur NetworkPhnom PenhCambodia
| | - Annika Suttie
- Virology UnitInstitut Pasteur du Cambodge, Pasteur NetworkPhnom PenhCambodia
- School of Applied and Biomedical SciencesFederation University AustraliaChurchillVictoriaAustralia
| | - Phalla Y
- Virology UnitInstitut Pasteur du Cambodge, Pasteur NetworkPhnom PenhCambodia
| | - Sareth Rith
- Virology UnitInstitut Pasteur du Cambodge, Pasteur NetworkPhnom PenhCambodia
| | - Jurre Y. Siegers
- Virology UnitInstitut Pasteur du Cambodge, Pasteur NetworkPhnom PenhCambodia
| | - Sorn San
- National Animal Health and Production Research Institute, Cambodian Ministry of Agriculture, Forestry and FisheriesPhnom PenhCambodia
| | - Holl Davun
- National Animal Health and Production Research Institute, Cambodian Ministry of Agriculture, Forestry and FisheriesPhnom PenhCambodia
| | - Sothyra Tum
- National Animal Health and Production Research Institute, Cambodian Ministry of Agriculture, Forestry and FisheriesPhnom PenhCambodia
| | - Sowath Ly
- Epidemiology and Public Health Unit, Institut Pasteur du CambodgePasteur NetworkPhnom PenhCambodia
| | - Arnaud Tarantola
- Epidemiology and Public Health Unit, Institut Pasteur du CambodgePasteur NetworkPhnom PenhCambodia
- Present address:
Regional Epidemiology UnitSanté Publique FranceParisFrance
| | - Philippe Dussart
- Virology UnitInstitut Pasteur du Cambodge, Pasteur NetworkPhnom PenhCambodia
- Present address:
Institut Pasteur de MadagascarPasteur NetworkAntananarivoMadagascar
| | - Erik A. Karlsson
- Virology UnitInstitut Pasteur du Cambodge, Pasteur NetworkPhnom PenhCambodia
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Siengsanan-Lamont J, Tum S, Kong L, Selleck PW, Gleeson LJ, Blacksell SD. Abattoir-based serological surveillance for transboundary and zoonotic diseases in cattle and swine in Cambodia: a pilot study in Phnom Penh province during 2019 and 2020. Trop Anim Health Prod 2022; 54:316. [PMID: 36149522 PMCID: PMC9508002 DOI: 10.1007/s11250-022-03309-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/31/2022] [Indexed: 12/04/2022]
Abstract
A pilot animal disease surveillance program was implemented at four abattoirs in Phnom Penh, Cambodia, between October 2019 and January 2020. A total of 1141 samples were collected from 477 cattle and 664 swine. Serological testing was performed using commercial antibody ELISA kits for zoonotic and high-impact animal diseases, namely brucellosis, Q fever, classical swine fever (CSF), porcine reproductive and respiratory syndrome (PRRS) and African swine fever (ASF). Only two samples tested positive for Brucella antibodies (0.2%, 95% CI 0.4-0.6, n = 1141). The seroprevalence of Q fever was 0.8% (95% CI 0.3-2.1, n = 477) in the cattle samples, while CSF, PRRS and ASF in pigs were 55.4% (95% CI 51.6-59.2, n = 655), 81.2% (95% CI 78.1-84.0, n = 655) and 2.6% (95% CI 1.6-4.1, n = 664), respectively. All 38 doubtful and 17 positive ASF antibody ELISA samples were negative when tested by real-time PCR. Univariate analyses demonstrated that the factor significantly associated with positive results of ASF was the abattoir location (p-value = 0.002). Based on logistic regression models, significant risk factors for CSF were province of origin (p-value = 1.7 × 10-6), abattoir (p-value = 3.6 × 10-11) and PRRS positivity (p-value = 0.004), and for PRRS were province of origin (p-value = 0.0004) and CSF positivity (p-value = 0.001). In conclusion, the seroprevalences of zoonotic diseases in this study were very low. The high prevalence of CSF and PRRS antibodies were most likely the result of vaccination. All ASF seropositive pigs, including those that gave equivocal results, originated from large-scale Cambodian-based commercial farms, as well as Thailand, which raises questions about possible illegal vaccination or low-pathogenicity ASF variants. The pilot abattoir serological surveillance program described here has the potential to provide a sentinel for incursions of novel and endemic pathogens, although further work is required to demonstrate its capacity to provide information on the longitudinal disease trends.
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Affiliation(s)
- Jarunee Siengsanan-Lamont
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sothyra Tum
- National Animal Health and Production Research Institute, Phnom Penh, Cambodia
| | - Lida Kong
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- National Animal Health and Production Research Institute, Phnom Penh, Cambodia
| | - Paul W Selleck
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Laurence J Gleeson
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Stuart D Blacksell
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Nuffield Department of Medicine, Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK.
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Mateus-Anzola J, Martínez-López B, Espinosa-García AC, Ojeda-Flores R. Global subtype diversity, spatial distribution patterns, and phylogenetic analysis of avian influenza virus in water. Transbound Emerg Dis 2021; 69:e344-e355. [PMID: 34464033 DOI: 10.1111/tbed.14307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 12/14/2022]
Abstract
The current COVID-19 pandemic highlights the need for zoonotic infectious disease surveillance. Avian influenza virus (AIV) poses a significant threat to animal and public health due to its pandemic potential. Virus-contaminated water has been suggested as an important AIV spread mechanism among multiple species. Nevertheless, few studies have characterized the global AIV subtype diversity and distribution in environmental water. Therefore, this study aims to provide an updated descriptive and phylogenetic analysis of AIVs isolated in water samples from high risk-sites for influenza outbreaks (i.e. live bird markets, poultry farms, and wild bird habitats) on a global scale. The descriptive analysis evidenced that 21 subtypes were reported from nine countries between 2003 and 2020. Fourteen AIV subtypes were solely reported from Asian countries. Most of the viral sequences were obtained in China and Bangladesh with 47.44% and 23.93%, respectively. Likewise, the greatest global AIV subtype diversity was observed in China with 12 subtypes. Live bird markets represented the main sampling site for AIV detection in water samples (64.1%), mostly from poultry cage water. Nevertheless, the highest subtype diversity was observed in water samples from wild bird habitats, especially from the Izumi plain and the Dongting Lake located in Japan and China, respectively. Water from drinking poultry troughs evidenced the greatest subtype diversity in live bird markets; meanwhile, environmental water used by ducks had the highest number of different subtypes in poultry farms. Maximum-likelihood phylogenetic trees of hemagglutinin (HA) and neuraminidase (NA) genes showed that some sequences were closely related among different poultry/wild bird-related environments from different geographic origins. Therefore, the results suggest that even though the availability of gene sequences in public-access databases varies greatly among countries, environmental AIV surveillance represents a useful tool to elucidate potential viral diversity in wild and domestic bird populations.
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Affiliation(s)
- Jessica Mateus-Anzola
- Laboratorio de Ecología de Enfermedades y Una Salud, Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Beatriz Martínez-López
- Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Ana Cecilia Espinosa-García
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rafael Ojeda-Flores
- Laboratorio de Ecología de Enfermedades y Una Salud, Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
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Hood G, Roche X, Brioudes A, von Dobschuetz S, Fasina FO, Kalpravidh W, Makonnen Y, Lubroth J, Sims L. A literature review of the use of environmental sampling in the surveillance of avian influenza viruses. Transbound Emerg Dis 2021; 68:110-126. [PMID: 32652790 PMCID: PMC8048529 DOI: 10.1111/tbed.13633] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 05/07/2020] [Accepted: 05/13/2020] [Indexed: 02/05/2023]
Abstract
This literature review provides an overview of use of environmental samples (ES) such as faeces, water, air, mud and swabs of surfaces in avian influenza (AI) surveillance programs, focussing on effectiveness, advantages and gaps in knowledge. ES have been used effectively for AI surveillance since the 1970s. Results from ES have enhanced understanding of the biology of AI viruses in wild birds and in markets, of links between human and avian influenza, provided early warning of viral incursions, allowed assessment of effectiveness of control and preventive measures, and assisted epidemiological studies in outbreaks, both avian and human. Variation exists in the methods and protocols used, and no internationally recognized guidelines exist on the use of ES and data management. Few studies have performed direct comparisons of ES versus live bird samples (LBS). Results reported so far demonstrate reliance on ES will not be sufficient to detect virus in all cases when it is present, especially when the prevalence of infection/contamination is low. Multiple sample types should be collected. In live bird markets, ES from processing/selling areas are more likely to test positive than samples from bird holding areas. When compared to LBS, ES is considered a cost-effective, simple, rapid, flexible, convenient and acceptable way of achieving surveillance objectives. As a non-invasive technique, it can minimize effects on animal welfare and trade in markets and reduce impacts on wild bird communities. Some limitations of environmental sampling methods have been identified, such as the loss of species-specific or information on the source of virus, and taxonomic-level analyses, unless additional methods are applied. Some studies employing ES have not provided detailed methods. In others, where ES and LBS are collected from the same site, positive results have not been assigned to specific sample types. These gaps should be remedied in future studies.
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Affiliation(s)
- Grace Hood
- Food and Agriculture Organization of the United NationsRomeItaly
| | - Xavier Roche
- Food and Agriculture Organization of the United NationsRomeItaly
| | - Aurélie Brioudes
- Food and Agriculture Organization of the United NationsRegional Office for Asia and the PacificBangkokThailand
| | | | | | | | - Yilma Makonnen
- Food and Agriculture Organization of the United Nations, Sub-Regional Office for Eastern AfricaAddis AbabaEthiopia
| | - Juan Lubroth
- Food and Agriculture Organization of the United NationsRomeItaly
| | - Leslie Sims
- Asia Pacific Veterinary Information ServicesMelbourneAustralia
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Frutos R, Lopez Roig M, Serra-Cobo J, Devaux CA. COVID-19: The Conjunction of Events Leading to the Coronavirus Pandemic and Lessons to Learn for Future Threats. Front Med (Lausanne) 2020; 7:223. [PMID: 32574324 PMCID: PMC7235412 DOI: 10.3389/fmed.2020.00223] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/01/2020] [Indexed: 12/27/2022] Open
Affiliation(s)
- Roger Frutos
- Cirad, UMR 17, Intertryp, Montpellier, France.,IES, UMR 5214 Univ. Montpellier-CNRS, Montpellier, France
| | - Marc Lopez Roig
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute, University of Barcelona, Barcelona, Spain
| | - Jordi Serra-Cobo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute, University of Barcelona, Barcelona, Spain
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Suttie A, Tok S, Yann S, Keo P, Horm SV, Roe M, Kaye M, Sorn S, Holl D, Tum S, Barr IG, Hurt AC, Greenhill AR, Karlsson EA, Vijaykrishna D, Deng YM, Dussart P, Horwood PF. The evolution and genetic diversity of avian influenza A(H9N2) viruses in Cambodia, 2015 - 2016. PLoS One 2019; 14:e0225428. [PMID: 31815945 PMCID: PMC6901181 DOI: 10.1371/journal.pone.0225428] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/04/2019] [Indexed: 11/18/2022] Open
Abstract
Low pathogenic A(H9N2) subtype avian influenza viruses (AIVs) were originally detected in Cambodian poultry in 2013, and now circulate endemically. We sequenced and characterised 64 A(H9N2) AIVs detected in Cambodian poultry (chickens and ducks) from January 2015 to May 2016. All A(H9) viruses collected in 2015 and 2016 belonged to a new BJ/94-like h9-4.2.5 sub-lineage that emerged in the region during or after 2013, and was distinct to previously detected Cambodian viruses. Overall, there was a reduction of genetic diversity of H9N2 since 2013, however two genotypes were detected in circulation, P and V, with extensive reassortment between the viruses. Phylogenetic analysis showed a close relationship between A(H9N2) AIVs detected in Cambodian and Vietnamese poultry, highlighting cross-border trade/movement of live, domestic poultry between the countries. Wild birds may also play a role in A(H9N2) transmission in the region. Some genes of the Cambodian isolates frequently clustered with zoonotic A(H7N9), A(H9N2) and A(H10N8) viruses, suggesting a common ecology. Molecular analysis showed 100% of viruses contained the hemagglutinin (HA) Q226L substitution, which favours mammalian receptor type binding. All viruses were susceptible to the neuraminidase inhibitor antivirals; however, 41% contained the matrix (M2) S31N substitution associated with resistance to adamantanes. Overall, Cambodian A(H9N2) viruses possessed factors known to increase zoonotic potential, and therefore their evolution should be continually monitored.
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Affiliation(s)
- Annika Suttie
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
- School of Health and Life Sciences, Federation University, Churchill, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Songha Tok
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Sokhoun Yann
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Ponnarath Keo
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Srey Viseth Horm
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Merryn Roe
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Matthew Kaye
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - San Sorn
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Cambodian Ministry of Agriculture, Forestry and Fisheries, Phnom Penh, Cambodia
| | - Davun Holl
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Cambodian Ministry of Agriculture, Forestry and Fisheries, Phnom Penh, Cambodia
| | - Sothyra Tum
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Cambodian Ministry of Agriculture, Forestry and Fisheries, Phnom Penh, Cambodia
| | - Ian G. Barr
- School of Health and Life Sciences, Federation University, Churchill, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Aeron C. Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Andrew R. Greenhill
- School of Health and Life Sciences, Federation University, Churchill, Australia
| | - Erik A. Karlsson
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Dhanasekaran Vijaykrishna
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria Australia
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
- * E-mail: (PH); (PD)
| | - Paul F. Horwood
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
- * E-mail: (PH); (PD)
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9
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Diversity of A(H5N1) clade 2.3.2.1c avian influenza viruses with evidence of reassortment in Cambodia, 2014-2016. PLoS One 2019; 14:e0226108. [PMID: 31815962 PMCID: PMC6901219 DOI: 10.1371/journal.pone.0226108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/18/2019] [Indexed: 11/19/2022] Open
Abstract
In Cambodia, highly pathogenic avian influenza A(H5N1) subtype viruses circulate endemically causing poultry outbreaks and zoonotic human cases. To investigate the genomic diversity and development of endemicity of the predominantly circulating clade 2.3.2.1c A(H5N1) viruses, we characterised 68 AIVs detected in poultry, the environment and from a single human A(H5N1) case from January 2014 to December 2016. Full genomes were generated for 42 A(H5N1) viruses. Phylogenetic analysis shows that five clade 2.3.2.1c genotypes, designated KH1 to KH5, were circulating in Cambodia during this period. The genotypes arose through multiple reassortment events with the neuraminidase (NA) and internal genes belonging to H5N1 clade 2.3.2.1a, clade 2.3.2.1b or A(H9N2) lineages. Phylogenies suggest that the Cambodian AIVs were derived from viruses circulating between Cambodian and Vietnamese poultry. Molecular analyses show that these viruses contained the hemagglutinin (HA) gene substitutions D94N, S133A, S155N, T156A, T188I and K189R known to increase binding to the human-type α2,6-linked sialic acid receptors. Two A(H5N1) viruses displayed the M2 gene S31N or A30T substitutions indicative of adamantane resistance, however, susceptibility testing towards neuraminidase inhibitors (oseltamivir, zanamivir, lananmivir and peramivir) of a subset of thirty clade 2.3.2.1c viruses showed susceptibility to all four drugs. This study shows that A(H5N1) viruses continue to reassort with other A(H5N1) and A(H9N2) viruses that are endemic in the region, highlighting the risk of introduction and emergence of novel A(H5N1) genotypes in Cambodia.
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10
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Karlsson EA, Horm SV, Tok S, Tum S, Kalpravidh W, Claes F, Osbjer K, Dussart P. Avian influenza virus detection, temporality and co-infection in poultry in Cambodian border provinces, 2017-2018. Emerg Microbes Infect 2019; 8:637-639. [PMID: 30999819 PMCID: PMC6493305 DOI: 10.1080/22221751.2019.1604085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Erik A Karlsson
- a Virology Unit , Institute Pasteur du Cambodge , Phnom Penh , Cambodia
| | - Srey Viseth Horm
- a Virology Unit , Institute Pasteur du Cambodge , Phnom Penh , Cambodia
| | - Songha Tok
- a Virology Unit , Institute Pasteur du Cambodge , Phnom Penh , Cambodia
| | - Sothyra Tum
- b National Animal Health and Production Research Institute, Cambodian Ministry of Agriculture, Forestry and Fisheries , Phnom Penh , Cambodia
| | - Wantanee Kalpravidh
- c Regional Office for Asia and the Pacific, Food and Agriculture Organization of the United Nations , Bangkok , Thailand
| | - Filip Claes
- c Regional Office for Asia and the Pacific, Food and Agriculture Organization of the United Nations , Bangkok , Thailand
| | - Kristina Osbjer
- d Emergency Centre for Transboundary Animal Diseases, Food and Agriculture Organization of the United Nations , Phnom Penh , Cambodia
| | - Philippe Dussart
- a Virology Unit , Institute Pasteur du Cambodge , Phnom Penh , Cambodia
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11
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Suttie A, Karlsson EA, Deng YM, Hurt AC, Greenhill AR, Barr IG, Dussart P, Horwood PF. Avian influenza in the Greater Mekong Subregion, 2003-2018. INFECTION GENETICS AND EVOLUTION 2019; 74:103920. [PMID: 31201870 DOI: 10.1016/j.meegid.2019.103920] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/20/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
Abstract
The persistent circulation of avian influenza viruses (AIVs) is an ongoing problem for many countries in South East Asia, causing large economic losses to both the agricultural and health sectors. This review analyses AIV diversity, evolution and the risk of AIV emergence in humans in countries of the Greater Mekong Subregion (GMS): Cambodia, Laos, Myanmar, Thailand and Vietnam (excluding China). The analysis was based on AIV sequencing data, serological studies, published journal articles and AIV outbreak reports available from January 2003 to December 2018. All countries of the GMS have suffered losses due repeated outbreaks of highly pathogenic (HP) H5N1 that has also caused human cases in all GMS countries. In Laos, Myanmar and Vietnam AIV outbreaks in domestic poultry have also been caused by clade 2.3.4.4 H5N6. A diverse range of low pathogenic AIVs (H1-H12) have been detected in poultry and wild bird species, though surveillance for and characterization of these subtypes is limited. Subtype H3, H4, H6 and H11 viruses have been detected over prolonged periods; whilst H1, H2, H7, H8, H10 and H12 viruses have only been detected transiently. H9 AIVs circulate endemically in Cambodia and Vietnam with seroprevalence data indicating human exposure to H9 AIVs in Cambodia, Thailand and Vietnam. As surveillance studies focus heavily on the detection of H5 AIVs in domestic poultry further research is needed to understand the true level of AIV diversity and the risk AIVs pose to humans in the GMS.
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Affiliation(s)
- Annika Suttie
- Virology Unit, Institute Pasteur in Cambodia, Phnom Penh, Cambodia; School of Applied and Biomedical Sciences, Federation University, Churchill, Australia; WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Erik A Karlsson
- Virology Unit, Institute Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Andrew R Greenhill
- School of Applied and Biomedical Sciences, Federation University, Churchill, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Philippe Dussart
- Virology Unit, Institute Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Paul F Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia.
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12
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Horwood PF, Horm SV, Suttie A, Thet S, Y P, Rith S, Sorn S, Holl D, Tum S, Ly S, Karlsson EA, Tarantola A, Dussart P. Co-circulation of Influenza A H5, H7, and H9 Viruses and Co-infected Poultry in Live Bird Markets, Cambodia. Emerg Infect Dis 2019; 24:352-355. [PMID: 29350140 PMCID: PMC5782910 DOI: 10.3201/eid2402.171360] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Longitudinal surveillance of 2 live bird markets in Cambodia revealed year-round, high co-circulation of H5, H7, and H9 influenza viruses. We detected influenza A viruses in 51.3% of ducks and 39.6% of chickens, and co-infections, mainly by H5 and H9 viruses, in 0.8% of ducks and 4.5% of chickens.
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13
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Suttie A, Karlsson EA, Deng YM, Horm SV, Yann S, Tok S, Sorn S, Holl D, Tum S, Hurt AC, Greenhill AR, Barr IG, Horwood PF, Dussart P. Influenza A(H5N1) viruses with A(H9N2) single gene (matrix or PB1) reassortment isolated from Cambodian live bird markets. Virology 2018; 523:22-26. [PMID: 30075357 DOI: 10.1016/j.virol.2018.07.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 01/31/2023]
Abstract
Live bird market surveillance for avian influenza viruses in Cambodia in 2015 has led to the detection of two 7:1 reassortant influenza A(H5N1) clade 2.3.2.1c viruses. These reassortant strains, designated A/duck/Cambodia/Z564W35M1/2015 and A/chicken/Cambodia/Z850W49M1/2015, both contained a single gene (PB1 and matrix gene, respectively) from concurrently circulating A(H9N2) influenza viruses. All other viral genes from both isolates clustered with A(H5N1) clade 2.3.2.1 viruses. Continued and prolonged co-circulation of influenza A(H5N1) and A(H9N2) viruses in Cambodian live bird markets may present a risk for the emergence of novel influenza reassortant viruses with negative agricultural and/or public health implications.
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Affiliation(s)
- Annika Suttie
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia; School of Applied and Biomedical Sciences, Federation University, Churchill, Australia; WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Erik A Karlsson
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Srey Viseth Horm
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Sokhoun Yann
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Songha Tok
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - San Sorn
- General Directorate for Animal Health and Production, Cambodian Ministry of Agriculture, Forestry and Fisheries, Phnom Penh, Cambodia
| | - Davun Holl
- General Directorate for Animal Health and Production, Cambodian Ministry of Agriculture, Forestry and Fisheries, Phnom Penh, Cambodia
| | - Sothyra Tum
- National Animal Health and Production Research Institute, Cambodian Ministry of Agriculture, Forestry and Fisheries, Phnom Penh, Cambodia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Andrew R Greenhill
- School of Applied and Biomedical Sciences, Federation University, Churchill, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Paul F Horwood
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia; Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, 4870, Australia.
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia.
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14
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Ly S, Horwood P, Chan M, Rith S, Sorn S, Oeung K, Nguon K, Chan S, Y P, Parry A, Tsuyuoka R, Ly S, Richner B, Laurent D, Vong S, Dussart P, Buchy P, Tarantola A. Seroprevalence and Transmission of Human Influenza A(H5N1) Virus before and after Virus Reassortment, Cambodia, 2006-2014. Emerg Infect Dis 2018; 23:300-303. [PMID: 28098551 PMCID: PMC5324818 DOI: 10.3201/eid2302.161232] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Thirty-five human influenza A(H5N1) cases were reported in Cambodia during 2013–2014 after emergence of a clade 1.1.2 reassortant virus. We tested 881 villagers and found 2 cases of pauci- or asymptomatic infection. Seroprevalence after emergence of the reassortant strain (0.2%) was lower than the aggregate seroprevalence of 1.3% reported in earlier studies.
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15
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Biswas PK, Giasuddin M, Chowdhury P, Barua H, Debnath NC, Yamage M. Incidence of contamination of live bird markets in Bangladesh with influenza A virus and subtypes H5, H7 and H9. Transbound Emerg Dis 2017; 65:687-695. [PMID: 29226568 DOI: 10.1111/tbed.12788] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Indexed: 01/31/2023]
Abstract
In the absence of robust active surveillance of avian influenza viruses (AIV) affecting poultry in South Asian countries, monitoring of live bird markets (LBMs) can be an alternative. In a longitudinal study of 32 LBM, five environments were sampled as follows: market floor, stall floor, slaughter area, poultry holding cage and water used for meat processing. Samples were taken monthly for 5 months, September 2013-January 2014. Incidence rates (IRs) of LBM contamination with AIV and its subtypes H5, H7 and H9 were assessed. In 10 of the LBM selected, biosecurity measures had been implemented through FAO interventions: the other 22 were non-intervened. Standard procedures were applied to detect AIV and three subtypes in pooled samples (1:5). An LBM was considered positive for AIV or a subtype if at least one of the pooled samples tested positive. The incidence rates of LBM contamination with AIV, H5, H7 and H9 were 0.194 (95% confidence interval (CI) 0.136-0.276), 0.031 (95% CI 0.013-0.075), 0 and 0.175 (95% CI 0.12-0.253) per LBM-month at risk, respectively. The log IR ratio between the FAO-intervened and non-intervened LBM for contamination with AIV was -0.329 (95% CI -1.052 to -0.394, p = .372), 0.598 (95% CI -1.593 to 2.789, p = .593) with subtype H5 and -0.500 (95% CI -1.249 to 0.248, p = .190) with subtype H9, indicating no significant difference. The results obtained suggest that both H5 and H9 were circulating in LBM in Bangladesh in the second half of 2013. The incidence of contamination with H9 was much higher than with H5.
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Affiliation(s)
- P K Biswas
- Department of Microbiology and Veterinary Public Health, Chittagong Veterinary and Animal Sciences University, Chittagong, Bangladesh
| | - M Giasuddin
- National Reference Laboratories for Avian Influenza, Bangladesh Livestock Research Institute, Savar, Bangladesh
| | - P Chowdhury
- Department of Livestock Services, Chittagong, Bangladesh
| | - H Barua
- Department of Microbiology and Veterinary Public Health, Chittagong Veterinary and Animal Sciences University, Chittagong, Bangladesh
| | - N C Debnath
- Department of Microbiology and Veterinary Public Health, Chittagong Veterinary and Animal Sciences University, Chittagong, Bangladesh.,Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations, Dhaka, Bangladesh
| | - M Yamage
- Emergency Centre for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations, Dhaka, Bangladesh
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16
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Paul MC, Goutard FL, Roulleau F, Holl D, Thanapongtharm W, Roger FL, Tran A. Quantitative assessment of a spatial multicriteria model for highly pathogenic avian influenza H5N1 in Thailand, and application in Cambodia. Sci Rep 2016; 6:31096. [PMID: 27489997 PMCID: PMC4977984 DOI: 10.1038/srep31096] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/13/2016] [Indexed: 11/26/2022] Open
Abstract
The Highly Pathogenic Avian Influenza H5N1 (HPAI) virus is now considered endemic in several Asian countries. In Cambodia, the virus has been circulating in the poultry population since 2004, with a dramatic effect on farmers' livelihoods and public health. In Thailand, surveillance and control are still important to prevent any new H5N1 incursion. Risk mapping can contribute effectively to disease surveillance and control systems, but is a very challenging task in the absence of reliable disease data. In this work, we used spatial multicriteria decision analysis (MCDA) to produce risk maps for HPAI H5N1 in poultry. We aimed to i) evaluate the performance of the MCDA approach to predict areas suitable for H5N1 based on a dataset from Thailand, comparing the predictive capacities of two sources of a priori knowledge (literature and experts), and ii) apply the best method to produce a risk map for H5N1 in poultry in Cambodia. Our results showed that the expert-based model had a very high predictive capacity in Thailand (AUC = 0.97). Applied in Cambodia, MCDA mapping made it possible to identify hotspots suitable for HPAI H5N1 in the Tonlé Sap watershed, around the cities of Battambang and Kampong Cham, and along the Vietnamese border.
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Affiliation(s)
- Mathilde C. Paul
- CIRAD, UPR AGIRs, F-34398, Montpellier, France
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
- EPIA, INRA, 63122 Saint Genès Champanelle, France
| | - Flavie L. Goutard
- CIRAD, UPR AGIRs, F-34398, Montpellier, France
- CIRAD, UPR AGIRs, 10900 Bangkok, Thaïland
- Kasetsart University, 10900 Bangkok, Thailand
| | - Floriane Roulleau
- CIRAD, UPR AGIRs, F-34398, Montpellier, France
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
| | - Davun Holl
- National Veterinary Research Institute, Phnom Penh, Cambodia
| | | | - François L. Roger
- CIRAD, UPR AGIRs, F-34398, Montpellier, France
- CIRAD, UPR AGIRs, 10900 Bangkok, Thaïland
- Kasetsart University, 10900 Bangkok, Thailand
| | - Annelise Tran
- CIRAD, UPR AGIRs, F-34398, Montpellier, France
- CIRAD, UMR TETIS, F-34398, Montpellier, France
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17
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Osbjer K, Berg M, Sokerya S, Chheng K, San S, Davun H, Magnusson U, Olsen B, Zohari S. Influenza A Virus in Backyard Pigs and Poultry in Rural Cambodia. Transbound Emerg Dis 2016; 64:1557-1568. [PMID: 27484711 DOI: 10.1111/tbed.12547] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Indexed: 11/27/2022]
Abstract
Surveillance of influenza virus in humans and livestock is critical, given the worldwide public health threats and livestock production losses. Livestock farming involving close proximity between humans, pigs and poultry is often practised by smallholders in low-income countries and is considered an important driver of influenza virus evolution. This study determined the prevalence and genetic characteristics of influenza A virus (IAV) in backyard pigs and poultry in Cambodia. A total of 751 animals were tested by matrix gene-based rRT-PCR, and influenza virus was detected in 1.5% of sampled pigs, 1.4% of chickens and 1.0% of ducks, but not in pigeons. Full-length genome sequencing confirmed triple reassortant H3N2 in all IAV-positive pigs and various low pathogenic avian influenza subtypes in poultry. Phylogenetic analysis of the swine influenza viruses revealed that these had haemagglutinin and neuraminidase genes originating from human H3N2 viruses previously isolated in South-East Asia. Phylogenetic analysis also revealed that several of the avian influenza subtypes detected were closely related to internal viral genes from highly pathogenic H5N1 and H9N2 formerly sequenced in the region. High sequence homology was likewise found with influenza A viruses circulating in pigs, poultry and wild birds in China and Vietnam, suggesting transboundary introduction and cocirculation of the various influenza subtypes. In conclusion, highly pathogenic subtypes of influenza virus seem rare in backyard poultry, but virus reassortment, involving potentially zoonotic and pandemic subtypes, appears to occur frequently in smallholder pigs and poultry. Increased targeted surveillance and monitoring of influenza circulation on smallholdings would further improve understanding of the transmission dynamics and evolution of influenza viruses in humans, pigs and poultry in the Mekong subregion and could contribute to limit the influenza burden.
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Affiliation(s)
- K Osbjer
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - M Berg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - S Sokerya
- Centre for Livestock and Agriculture Development, Phnom Penh, Cambodia
| | - K Chheng
- National Institute of Public Health, Phnom Penh, Cambodia
| | - S San
- National Veterinary Research Institute, Phnom Penh, Cambodia
| | - H Davun
- National Veterinary Research Institute, Phnom Penh, Cambodia
| | - U Magnusson
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - B Olsen
- Infectious Diseases, Zoonosis Science Center, Department of Medical Sciences and IMBIM, Uppsala University (UU), Uppsala, Sweden
| | - S Zohari
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
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18
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Horm SV, Tarantola A, Rith S, Ly S, Gambaretti J, Duong V, Y P, Sorn S, Holl D, Allal L, Kalpravidh W, Dussart P, Horwood PF, Buchy P. Intense circulation of A/H5N1 and other avian influenza viruses in Cambodian live-bird markets with serological evidence of sub-clinical human infections. Emerg Microbes Infect 2016; 5:e70. [PMID: 27436362 PMCID: PMC5141262 DOI: 10.1038/emi.2016.69] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/13/2016] [Accepted: 04/25/2016] [Indexed: 01/05/2023]
Abstract
Surveillance for avian influenza viruses (AIVs) in poultry and environmental samples was conducted in four live-bird markets in Cambodia from January through November 2013. Through real-time RT-PCR testing, AIVs were detected in 45% of 1048 samples collected throughout the year. Detection rates ranged from 32% and 18% in duck and chicken swabs, respectively, to 75% in carcass wash water samples. Influenza A/H5N1 virus was detected in 79% of samples positive for influenza A virus and 35% of all samples collected. Sequence analysis of full-length haemagglutinin (HA) and neuraminidase (NA) genes from A/H5N1 viruses, and full-genome analysis of six representative isolates, revealed that the clade 1.1.2 reassortant virus associated with Cambodian human cases during 2013 was the only A/H5N1 virus detected during the year. However, multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of HA and NA genes revealed co-circulation of at least nine low pathogenic AIVs from HA1, HA2, HA3, HA4, HA6, HA7, HA9, HA10 and HA11 subtypes. Four repeated serological surveys were conducted throughout the year in a cohort of 125 poultry workers. Serological testing found an overall prevalence of 4.5% and 1.8% for antibodies to A/H5N1 and A/H9N2, respectively. Seroconversion rates of 3.7 and 0.9 cases per 1000 person-months participation were detected for A/H5N1 and A/H9N2, respectively. Peak AIV circulation was associated with the Lunar New Year festival. Knowledge of periods of increased circulation of avian influenza in markets should inform intervention measures such as market cleaning and closures to reduce risk of human infections and emergence of novel AIVs.
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Affiliation(s)
- Srey Viseth Horm
- Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh 12000, Cambodia
| | - Arnaud Tarantola
- Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh 12000, Cambodia
| | - Sareth Rith
- Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh 12000, Cambodia
| | - Sowath Ly
- Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh 12000, Cambodia
| | - Juliette Gambaretti
- Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh 12000, Cambodia
| | - Veasna Duong
- Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh 12000, Cambodia
| | - Phalla Y
- Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh 12000, Cambodia
| | - San Sorn
- National Veterinary Research Institute, Ministry of Agriculture, Forestry and Fisheries, Phnom Penh 12000, Cambodia
| | - Davun Holl
- National Veterinary Research Institute, Ministry of Agriculture, Forestry and Fisheries, Phnom Penh 12000, Cambodia
| | - Lotfi Allal
- Food and Agriculture Organization, Phnom Penh 12000, Cambodia
| | | | - Philippe Dussart
- Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh 12000, Cambodia
| | - Paul F Horwood
- Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh 12000, Cambodia
| | - Philippe Buchy
- Institute Pasteur in Cambodia, Institute Pasteur International Network, Phnom Penh 12000, Cambodia.,GlaxoSmithKline Pte Ltd, Singapore 189720, Singapore
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19
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Zeynalova S, Guliyev F, Vatani M, Abbasov B. Biosurveillance of avian influenza and Newcastle disease viruses in the Barda region of Azerbaijan using real time RT-PCR and hemagglutination inhibition. Front Microbiol 2015; 6:1128. [PMID: 26594200 PMCID: PMC4635216 DOI: 10.3389/fmicb.2015.01128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
The Azerbaijan State Veterinary Control Service (SVCS) has conducted active serological surveillance for avian influenza (AI) in poultry since 2006, when the first outbreak of AI H5N1 occurred in Azerbaijan. Samples are collected from September to May annually and tested using a hemagglutination inhibition (HI) assay to detect antibodies against H5 AI viruses. HI testing is also performed for Newcastle disease virus (NDV) upon request, but since this method cannot distinguish between natural infections and immune responses to vaccination, all positive results require follow-up epidemiological investigations. Furthermore, blood collection for the surveillance program is time-intensive and can be stressful to birds. In order to improve the national surveillance program, alternative sampling and testing methodologies were applied among a population of birds in the Barda region and compared with results of the national surveillance program. Tracheal and cloacal swabs were collected instead of blood. Rather than testing individual samples, RNA was pooled to conserve resources and time, and pools were tested by real-time reverse transcription polymerase chain reaction (rRT-PCR). Environmental sampling at a live bird market was also introduced as another surveillance mechanism. A total of 1,030 swabs were collected, comprising tracheal, and cloacal samples from 441 birds and 148 environmental surface samples from farms or the live bird market. During the same time, 3,890 blood samples were collected nationally for the surveillance program; 400 of these samples originated in the Barda region. Birds sampled for rRT-PCR were likely different than those tested as part of national surveillance. All swab samples tested negative by rRT-PCR for both AI and NDV. All blood samples tested negative for H5 by HI, while 6.2% of all samples and 5% of the Barda samples tested positive for exposure to NDV. Follow-up investigations found that positive samples were from birds vaccinated in the previous month. This study demonstrated that taking swabs was quicker and less invasive than blood collection. Results of rRT-PCR testing were similar to HI testing for H5 but also ruled out infection with all influenza type A viruses and not just H5. In addition, rRT-PCR testing was able to rule out active infections with NDV.
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Affiliation(s)
- Shalala Zeynalova
- Virology Department, Republican Veterinary Laboratory Baku, Azerbaijan
| | - Fizuli Guliyev
- Virology Department, Republican Veterinary Laboratory Baku, Azerbaijan
| | - Mahira Vatani
- Virology Department, Republican Veterinary Laboratory Baku, Azerbaijan
| | - Bahruz Abbasov
- Virology Department, Barda Zonal Veterinary Laboratory Baku, Azerbaijan
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Surveillance of Avian H7N9 Virus in Various Environments of Zhejiang Province, China before and after Live Poultry Markets Were Closed in 2013-2014. PLoS One 2015; 10:e0135718. [PMID: 26308215 PMCID: PMC4550274 DOI: 10.1371/journal.pone.0135718] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 07/24/2015] [Indexed: 11/19/2022] Open
Abstract
Background To date, there have been a total of 637 laboratory-confirmed cases of human infection with avian influenza A (H7N9) virus across mainland China, with 28% (179/637) of these reported in Zhejiang Province. Surveillance of avian H7N9 virus was conducted to investigate environmental contamination during H7N9 outbreaks. We sought to evaluate the prevalence of H7N9 in the environment, and the effects of poultry market closures on the incidence of human H7N9 cases. Methods We collected 6740 environmental samples from 751 sampling sites across 11 cities of Zhejiang Province (China) between January 2013 and March 2014. The presence of H7N9 was determined by reverse transcription polymerase chain reaction, with prevalence compared between sites and over time. The relationship between environmental contamination and human cases of H7N9 infection were analyzed using Spearman’s ranked correlation coefficient. Results Of the 6740 samples, 10.09% (680/6740) were H7N9-positive. The virus was found to circulate seasonally, and peaked during the spring and winter of 2013–2014. The prevalence of the virus decreased from the north to the southeast of the province, coinciding with the geographical distribution of human H7N9 cases. Compared with other sampling sites, live poultry markets (LPMs) had the highest prevalence of H7N9 virus at 13.94% (667/4784). Of the various sample types analyzed, virus prevalence was highest for chopping board swabs at 15.49% (110/710). The prevalence of the virus in the environment positively correlated with the incidence of human H7N9 cases (r2 = 0.498; P < 0.01). Cities with a higher incidence of human H7N9 cases also had a higher prevalence of H7N9 among samples and at sampling sites. Following the closure of LPMs at the end of January 2014, the prevalence of H7N9 decreased from 19.18% (487/2539) to 6.92% (79/1141). This corresponded with a decrease in the number of human H7N9 cases reported. Conclusions The prevalence of H7N9 virus in environmental samples oscillated seasonally, regardless of whether LPMs were open. The presence of H7N9 in environmental samples positively correlated with the number of human H7N9 cases, indicating that eradication of the virus from the environment is essential in reducing the numbers of H7N9 cases and halting the spread of the virus.
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Kang M, He J, Song T, Rutherford S, Wu J, Lin J, Huang G, Tan X, Zhong H. Environmental Sampling for Avian Influenza A(H7N9) in Live-Poultry Markets in Guangdong, China. PLoS One 2015; 10:e0126335. [PMID: 25933138 PMCID: PMC4416787 DOI: 10.1371/journal.pone.0126335] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 04/01/2015] [Indexed: 12/03/2022] Open
Abstract
Background To provide an increased understanding of avian influenza A(H7N9) activity in live-poultry market in space and time and hence improve H7N9 epidemic control, an ongoing environmental sampling program in multiple live-poultry markets across Guangdong, China was conducted during March 2013–June 2014. Methods A total of 625 live-poultry markets throughout 21 prefecture areas took part in the study. A total of 10 environmental sites in markets for sampling were identified to represent 4 different poultry-related activity areas. At least 10 environmental samples were collected from each market every month. The real time RT-PCR was performed to detect the avian influenza A(H7N9) virus. Field survey was conducted to investigate the sanitation status of live-poultry markets. Results There were 109 human infections with H7N9 avian influenza in Guangdong, of which 37 (34%) died. A total of 18741 environmental swabs were collected and subjected to real-time RT-PCR test, of which 905(4.83%) were found positive for H7N9 virus. There were 201 (32.16%) markets affected by H7N9 in 16 prefecture areas. The detection of H7N9 virus in markets spiked in winter months. 63.33% markets (38/60) had no physical segregation for poultry holding, slaughter or sale zones. Closing live-poultry market significantly decreased the H7N9 detection rate from 14.83% (112/755) to 1.67% (5/300). Conclusions This study indicates the importance of live-poultry market surveillance based on environmental sampling for H7N9 Avian Influenza control. Improving live-poultry market management and sanitation and changing consumer practices are critical to reduce the risk of H7N9 infection.
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Affiliation(s)
- Min Kang
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, People’s Republic of China
| | - Jianfeng He
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, People’s Republic of China
| | - Tie Song
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, People’s Republic of China
| | - Shannon Rutherford
- Centre for Environment and Population Health, School of Environment, Griffith University, Brisbane, Australia
| | - Jie Wu
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, People’s Republic of China
| | - Jinyan Lin
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, People’s Republic of China
| | - Guofeng Huang
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, People’s Republic of China
| | - Xiaohua Tan
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, People’s Republic of China
| | - Haojie Zhong
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, People’s Republic of China
- * E-mail:
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Goutard FL, Binot A, Duboz R, Rasamoelina-Andriamanivo H, Pedrono M, Holl D, Peyre MI, Cappelle J, Chevalier V, Figuié M, Molia S, Roger FL. How to reach the poor? Surveillance in low-income countries, lessons from experiences in Cambodia and Madagascar. Prev Vet Med 2015; 120:12-26. [PMID: 25842000 DOI: 10.1016/j.prevetmed.2015.02.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 02/16/2015] [Accepted: 02/16/2015] [Indexed: 10/24/2022]
Abstract
Surveillance of animal diseases in developing countries faces many constraints. Innovative tools and methods to enhance surveillance in remote and neglected areas should be defined, assessed and applied in close connection with local farmers, national stakeholders and international agencies. The authors performed a narrative synthesis of their own publications about surveillance in Madagascar and Cambodia. They analysed the data in light of their fieldwork experiences in the two countries' very challenging environments. The burden of animal and zoonotic diseases (e.g. avian influenza, African swine fever, Newcastle disease, Rift Valley fever) is huge in both countries which are among the poorest in the world. Being poor countries implies a lack of human and financial means to ensure effective surveillance of emerging and endemic diseases. Several recent projects have shown that new approaches can be proposed and tested in the field. Several advanced participatory approaches are promising and could be part of an innovative method for improving the dialogue among different actors in a surveillance system. Thus, participatory modelling, developed for natural resources management involving local stakeholders, could be applied to health management, including surveillance. Data transmission could benefit from the large mobile-phone coverage in these countries. Ecological studies and advances in the field of livestock surveillance should guide methods for enhancing wildlife monitoring and surveillance. Under the umbrella of the One Health paradigm, and in the framework of a risk-based surveillance concept, a combination of participatory methods and modern technologies could help to overcome the constraints present in low-income countries. These unconventional approaches should be merged in order to optimise surveillance of emerging and endemic diseases in challenging environments.
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Affiliation(s)
- F L Goutard
- Cirad, AGIRs Research Unit, Montpellier, France; Kasetsart University, Bangkok, Thailand.
| | - A Binot
- Cirad, AGIRs Research Unit, Montpellier, France; Kasetsart University, Bangkok, Thailand
| | - R Duboz
- Cirad, AGIRs Research Unit, Montpellier, France; AIT, Bangkok, Thailand
| | | | - M Pedrono
- Cirad, AGIRs Research Unit, Montpellier, France; FOFIFA, Antananarivo, Madagascar
| | - D Holl
- NaVRI, Phnom Penh, Cambodia
| | - M I Peyre
- Cirad, AGIRs Research Unit, Montpellier, France; NIVR, Hanoi, Viet Nam
| | - J Cappelle
- Cirad, AGIRs Research Unit, Montpellier, France; Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - V Chevalier
- Cirad, AGIRs Research Unit, Montpellier, France
| | - M Figuié
- Cirad, MOISA Research Unit, Montpellier, France
| | - S Molia
- Cirad, AGIRs Research Unit, Montpellier, France; Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - F L Roger
- Cirad, AGIRs Research Unit, Montpellier, France; Kasetsart University, Bangkok, Thailand
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Bui C, Bethmont A, Chughtai AA, Gardner L, Sarkar S, Hassan S, Seale H, MacIntyre CR. A Systematic Review of the Comparative Epidemiology of Avian and Human Influenza A H5N1 and H7N9 - Lessons and Unanswered Questions. Transbound Emerg Dis 2015; 63:602-620. [DOI: 10.1111/tbed.12327] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Indexed: 11/29/2022]
Affiliation(s)
- C. Bui
- School of Public Health and Community Medicine; University of New South Wales; Sydney NSW Australia
| | - A. Bethmont
- School of Public Health and Community Medicine; University of New South Wales; Sydney NSW Australia
| | - A. A. Chughtai
- School of Public Health and Community Medicine; University of New South Wales; Sydney NSW Australia
| | - L. Gardner
- School of Civil and Environmental Engineering; University of New South Wales; Sydney NSW Australia
| | - S. Sarkar
- Section of Integrative Biology; University of Texas at Austin; Austin TX USA
| | - S. Hassan
- School of Public Health and Community Medicine; University of New South Wales; Sydney NSW Australia
| | - H. Seale
- School of Public Health and Community Medicine; University of New South Wales; Sydney NSW Australia
| | - C. R. MacIntyre
- School of Public Health and Community Medicine; University of New South Wales; Sydney NSW Australia
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Abstract
The last few decades have been marked by a rapid expansion in the world?s population, along with an increasingly dynamic mobility of individuals. This accelerated global inter-connectedness enabled microorganisms to reach virtually any location worldwide more rapidly and efficiently than ever before, reshaping the global dynamics of pathogens. As a result, a local infectious disease outbreak anywhere in the world may almost instantaneously assume global dimensions, and should therefore be considered a global priority. The history of several infectious diseases illustrates that in addition to prophylactic and therapeutic medical interventions, the interplay of social, economic, and political factors makes a fundamental contribution to the outcome of infectious disease outbreaks. Furthermore, this multi- and cross-disciplinary interconnectedness is a key determinant of the outcome of efforts to eradicate vaccine-preventable infectious diseases. A combined framework that incorporates teachings provided by previous outbreaks, and integrates medical and biomedical interventions with contributions made by social, economic, and political factors, emerges as vital requirement of successful global public health initiatives.
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Affiliation(s)
- R A Stein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
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Minodier L, Arena C, Heuze G, Ruello M, Amoros JP, Souty C, Varesi L, Falchi A. Epidemiology and viral etiology of the influenza-like illness in corsica during the 2012-2013 Winter: an analysis of several sentinel surveillance systems. PLoS One 2014; 9:e100388. [PMID: 24959929 PMCID: PMC4069071 DOI: 10.1371/journal.pone.0100388] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 05/26/2014] [Indexed: 11/19/2022] Open
Abstract
Influenza-like illness (ILI) surveillance is important to identify circulating and emerging/reemerging strains and unusual epidemiological trends. The present study aimed to give an accurate picture of the 2012-2013 ILI outbreak in Corsica by combining data from several surveillance systems: general practice, emergency general practice, hospital emergency units, intensive care units, and nursing homes. Twenty-eight respiratory viruses were retrospectively investigated from patients in general practice with ILI. Sequence analysis of the genetic changes in the hemagglutinin gene of influenza viruses (A(H1N1)pdm2009, A(H3N2) and B) was performed. The trends in ILI/influenza consultation rates and the relative illness ratios (RIRs) of having an ILI consultation were estimated by age group for the different surveillance systems analyzed. Of the 182 ILI patients enrolled by general practitioners, 57.7% tested positive for influenza viruses. Phylogenetic analyses suggested a genetic drift for influenza B and A(H3N2) viruses. The ILI/influenza surveillance systems showed similar trends and were well correlated. In accordance with virological data, the RIRs of having an ILI consultation were highest among the young (<15 years old) and decreased with age. No clusters of acute respiratory illness were declared by the sentinel nursing homes. This study is noteworthy in that it is the first extensive description of the 2012-2013 ILI outbreak in Corsica as monitored through several surveillance systems. To improve ILI surveillance in Corsica, a consortium that links together the complementary regional surveillance ILI systems described here is being implemented.
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Affiliation(s)
- Laëtitia Minodier
- EA7310, Laboratoire de Virologie, Université de Corse, Institut national de la Santé et de la Recherche Médicale, Corte, France
| | - Christophe Arena
- EA7310, Laboratoire de Virologie, Université de Corse, Institut national de la Santé et de la Recherche Médicale, Corte, France
- Observatoire régional de la Santé de Corse, Ajaccio, France
| | - Guillaume Heuze
- Cellule de l'Institut national de Veille Sanitaire en région, Ajaccio, France
| | - Marc Ruello
- Cellule de l'Institut national de Veille Sanitaire en région, Ajaccio, France
| | - Jean Pierre Amoros
- EA7310, Laboratoire de Virologie, Université de Corse, Institut national de la Santé et de la Recherche Médicale, Corte, France
| | - Cécile Souty
- Sorbonne Universités Pierre et Marie Curie, Paris 06, UMRS 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
- Institut national de la Santé et de la Recherche Médicale, UMRS 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Laurent Varesi
- EA7310, Laboratoire de Virologie, Université de Corse, Institut national de la Santé et de la Recherche Médicale, Corte, France
| | - Alessandra Falchi
- EA7310, Laboratoire de Virologie, Université de Corse, Institut national de la Santé et de la Recherche Médicale, Corte, France
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Little evidence of subclinical avian influenza virus infections among rural villagers in Cambodia. PLoS One 2014; 9:e97097. [PMID: 24819948 PMCID: PMC4018260 DOI: 10.1371/journal.pone.0097097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 04/14/2014] [Indexed: 11/19/2022] Open
Abstract
In 2008, 800 adults living within rural Kampong Cham Province, Cambodia were enrolled in a prospective cohort study of zoonotic influenza transmission. After enrollment, participants were contacted weekly for 24 months to identify acute influenza-like illnesses (ILI). Follow-up sera were collected at 12 and 24 months. A transmission substudy was also conducted among the family contacts of cohort members reporting ILI who were influenza A positive. Samples were assessed using serological or molecular techniques looking for evidence of infection with human and avian influenza viruses. Over 24 months, 438 ILI investigations among 284 cohort members were conducted. One cohort member was hospitalized with a H5N1 highly pathogenic avian influenza (HPAI) virus infection and withdrew from the study. Ninety-seven ILI cases (22.1%) were identified as influenza A virus infections by real-time RT-PCR; none yielded evidence for AIV. During the 2 years of follow-up, 21 participants (3.0%) had detectable antibody titers (≥1∶10) against the studied AIVs: 1 against an avian-like A/Migratory duck/Hong Kong/MPS180/2003(H4N6), 3 against an avian-like A/Teal/Hong Kong/w312/97(H6N1), 9 (3 of which had detectible antibody titers at both 12- and 24-month follow-up) against an avian-like A/Hong Kong/1073/1999(H9N2), 6 (1 detected at both 12- and 24-month follow-up) against an avian-like A/Duck/Memphis/546/74(H11N9), and 2 against an avian-like A/Duck/Alberta/60/76(H12N5). With the exception of the one hospitalized cohort member with H5N1 infection, no other symptomatic avian influenza infections were detected among the cohort. Serological evidence for subclinical infections was sparse with only one subject showing a 4-fold rise in microneutralization titer over time against AvH12N5. In summary, despite conducting this closely monitored cohort study in a region enzootic for H5N1 HPAI, we were unable to detect subclinical avian influenza infections, suggesting either that these infections are rare or that our assays are insensitive at detecting them.
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Wang C, Wang J, Su W, Gao S, Luo J, Zhang M, Xie L, Liu S, Liu X, Chen Y, Jia Y, Zhang H, Ding H, He H. Relationship between domestic and wild birds in live poultry market and a novel human H7N9 virus in China. J Infect Dis 2013; 209:34-7. [PMID: 23990569 DOI: 10.1093/infdis/jit478] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To trace the source of the avian H7N9 viruses, we collected 99 samples from 4 live poultry markets and the family farms of 3 patients in Hangzhou city of Zhejiang province, China. We found that almost all positive samples came from chickens and ducks in live poultry markets. These results strongly suggest that the live poultry markets are the major source of recent human infections with H7N9 in Hangzhou city, Zhejiang province of China. Therefore, control measures are needed, not only in the domestic bird population, but also in the live poultry markets to reduce human H7N9 infection risk.
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Affiliation(s)
- Chengmin Wang
- National Research Center For Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences
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