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Sanogo IN, Guinat C, Dellicour S, Diakité MA, Niang M, Koita OA, Camus C, Ducatez M. Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa. Virus Evol 2024; 10:veae011. [PMID: 38435712 PMCID: PMC10908551 DOI: 10.1093/ve/veae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/18/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
Avian influenza viruses (AIVs) of the H9N2 subtype have become widespread in Western Africa since their first detection in 2017 in Burkina Faso. However, the genetic characteristics and diffusion patterns of the H9N2 virus remain poorly understood in Western Africa, mainly due to limited surveillance activities. In addition, Mali, a country considered to play an important role in the epidemiology of AIVs in the region, lacks more comprehensive data on the genetic characteristics of these viruses, especially the H9N2 subtype. To better understand the genetic characteristics and spatio-temporal dynamics of H9N2 virus within this region, we carried out a comprehensive genetic characterization of H9N2 viruses collected through active surveillance in live bird markets in Mali between 2021 and 2022. We also performed a continuous phylogeographic analysis to unravel the dispersal history of H9N2 lineages between Northern and Western Africa. The identified Malian H9N2 virus belonged to the G1 lineage, similar to viruses circulating in both Western and Northern Africa, and possessed multiple molecular markers associated with an increased potential for zoonotic transmission and virulence. Notably, some Malian strains carried the R-S-N-R motif at their cleavage site, mainly observed in H9N2 strains in Asia. Our continuous phylogeographic analysis revealed a single and significant long-distance lineage dispersal event of the H9N2 virus to Western Africa, likely to have originated from Morocco in 2015, shaping the westward diffusion of the H9N2 virus. Our study highlights the need for long-term surveillance of H9N2 viruses in poultry populations in Western Africa, which is crucial for a better understanding of virus evolution and effective management against potential zoonotic AIV strain emergence.
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Affiliation(s)
- Idrissa Nonmon Sanogo
- Interactions Hôtes-Agents Pathogènes (IHAP), UMR 1225, Université de Toulouse, INRAE, ENVT, Toulouse 31076, France
- Faculté d’Agronomie et de Médecine Animale (FAMA), Université de Ségou, Ségou BP 24, Mali
| | - Claire Guinat
- Interactions Hôtes-Agents Pathogènes (IHAP), UMR 1225, Université de Toulouse, INRAE, ENVT, Toulouse 31076, France
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels B-1050, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven BE-3000, Belgium
| | - Mohamed Adama Diakité
- Service diagnostic et recherche Laboratoire Central Vétérinaire, Bamako BP 2295, Mali
| | - Mamadou Niang
- Food and Agriculture Organization of the United Nations (FAO-UN), Emergency Centre for Transboundary Animal Diseases (ECTAD), Regional Office for Africa (RAF), Accra BP 1628, Ghana
| | - Ousmane A Koita
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques (FAST), University of Sciences, Techniques and Technologies of Bamako (USTTB), Mali Université de Bamako, Bamako E 3206, Mali
| | - Christelle Camus
- Interactions Hôtes-Agents Pathogènes (IHAP), UMR 1225, Université de Toulouse, INRAE, ENVT, Toulouse 31076, France
| | - Mariette Ducatez
- Interactions Hôtes-Agents Pathogènes (IHAP), UMR 1225, Université de Toulouse, INRAE, ENVT, Toulouse 31076, France
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Kalonda A, Saasa N, Nkhoma P, Kajihara M, Sawa H, Takada A, Simulundu E. Avian Influenza Viruses Detected in Birds in Sub-Saharan Africa: A Systematic Review. Viruses 2020; 12:v12090993. [PMID: 32906666 PMCID: PMC7552061 DOI: 10.3390/v12090993] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/03/2020] [Accepted: 09/05/2020] [Indexed: 12/20/2022] Open
Abstract
In the recent past, sub-Saharan Africa has not escaped the devastating effects of avian influenza virus (AIV) in poultry and wild birds. This systematic review describes the prevalence, spatiotemporal distribution, and virus subtypes detected in domestic and wild birds for the past two decades (2000–2019). We collected data from three electronic databases, PubMed, SpringerLink electronic journals and African Journals Online, using the Preferred Reporting Items for Systematic reviews and Meta-Analyses protocol. A total of 1656 articles were reviewed, from which 68 were selected. An overall prevalence of 3.0% AIV in birds was observed. The prevalence varied between regions and ranged from 1.1% to 7.1%. The Kruskal–Wallis and Wilcoxon signed-rank sum test showed no significant difference in the prevalence of AIV across regions, χ2(3) = 5.237, p = 0.1553 and seasons, T = 820, z = −1.244, p = 0.2136. Nineteen hemagglutinin/neuraminidase subtype combinations were detected during the reviewed period, with southern Africa recording more diverse AIV subtypes than other regions. The most detected subtype was H5N1, followed by H9N2, H5N2, H5N8 and H6N2. Whilst these predominant subtypes were mostly detected in domestic poultry, H1N6, H3N6, H4N6, H4N8, H9N1 and H11N9 were exclusively detected in wild birds. Meanwhile, H5N1, H5N2 and H5N8 were detected in both wild and domestic birds suggesting circulation of these subtypes among wild and domestic birds. Our findings provide critical information on the eco-epidemiology of AIVs that can be used to improve surveillance strategies for the prevention and control of avian influenza in sub-Saharan Africa.
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Affiliation(s)
- Annie Kalonda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (A.K.); (P.N.)
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Africa Centre of Excellence for Infectious Disease of Humans and Animals, School of Veterinary Medicine, Lusaka 10101, Zambia
| | - Ngonda Saasa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
| | - Panji Nkhoma
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (A.K.); (P.N.)
| | - Masahiro Kajihara
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
| | - Hirofumi Sawa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
| | - Ayato Takada
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University Kita-ku, Sapporo 001-0020, Japan
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Macha Research Trust, Choma 20100, Zambia
- Correspondence: ; Tel.: +260-977469479
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Oluwayelu DO, Omolanwa A, Adebiyi AI, Aiki-Raji OC. FLOCK-BASED SURVEILLANCE FOR LOW PATHOGENIC AVIAN INFLUENZA VIRUS IN COMMERCIAL BREEDERS AND LAYERS, SOUTHWEST NIGERIA. Afr J Infect Dis 2016. [PMID: 28337492 PMCID: PMC5349764 DOI: 10.21010/ajid.v11i1.5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background: Flock surveillance systems for avian influenza (AI) virus play a critical role in countries where vaccination is not practiced so as to establish the epidemiological characteristics of AI needed for the development of prevention and control strategies in such countries. Materials and Methods: As part of routine AI monitoring in southwest Nigeria, a competitive ELISA was used for detecting influenza A virus antibodies in the sera of 461 commercial breeder and layer birds obtained from different flocks in Oyo State, Nigeria while haemagglutination inhibiting antibodies against low pathogenic AI viruses (LPAIVs) were detected using H5N2, H7N7 and H9N2 subtype-specific antigens. Suspensions prepared from cloacal swabs were tested for AI virus RNA using reverse transcriptase-polymerase chain reaction. Results: Results showed that influenza A virus antibody prevalence was 12.8% and 9.3% for breeders and layers, respectively while HI assay revealed 22.0%, 2.0% and 78.0% prevalence of LPAIV H5N2, H7N7 and H9N2 antibodies respectively. All cloacal swab suspensions were negative for AIV RNA. Conclusion: Since LPAI infections result in decreased or complete cessation of egg production in breeder and layer birds, increased infection severity due to co-infection with other poultry viruses have occasionally been transmitted to humans, the detection of LPAIV H5N2, H7N7 and H9N2 antibodies in these birds is of both economic and public health significance. These findings underscore the need for continuous flock monitoring as part of early warning measure to facilitate rapid detection and sustainable control of AI in Nigerian poultry.
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Affiliation(s)
| | - Ayoyimika Omolanwa
- Department of Veterinary Microbiology and Parasitology, University of Ibadan, Ibadan, Nigeria
| | - Adebowale Idris Adebiyi
- Department of Veterinary Microbiology and Parasitology, University of Ibadan, Ibadan, Nigeria
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Oluwayelu DO, Omolanwa A, Adebiyi AI, Aiki-Raji OC. FLOCK-BASED SURVEILLANCE FOR LOW PATHOGENIC AVIAN INFLUENZA VIRUS IN COMMERCIAL BREEDERS AND LAYERS, SOUTHWEST NIGERIA. Afr J Infect Dis 2016; 11:44-49. [PMID: 28337492 PMCID: PMC5349764 DOI: 10.4314/ajid.v11i1.4538] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Flock surveillance systems for avian influenza (AI) virus play a critical role in countries where vaccination is not practiced so as to establish the epidemiological characteristics of AI needed for the development of prevention and control strategies in such countries. MATERIALS AND METHODS As part of routine AI monitoring in southwest Nigeria, a competitive ELISA was used for detecting influenza A virus antibodies in the sera of 461 commercial breeder and layer birds obtained from different flocks in Oyo State, Nigeria while haemagglutination inhibiting antibodies against low pathogenic AI viruses (LPAIVs) were detected using H5N2, H7N7 and H9N2 subtype-specific antigens. Suspensions prepared from cloacal swabs were tested for AI virus RNA using reverse transcriptase-polymerase chain reaction. RESULTS Results showed that influenza A virus antibody prevalence was 12.8% and 9.3% for breeders and layers, respectively while HI assay revealed 22.0%, 2.0% and 78.0% prevalence of LPAIV H5N2, H7N7 and H9N2 antibodies respectively. All cloacal swab suspensions were negative for AIV RNA. CONCLUSION Since LPAI infections result in decreased or complete cessation of egg production in breeder and layer birds, increased infection severity due to co-infection with other poultry viruses have occasionally been transmitted to humans, the detection of LPAIV H5N2, H7N7 and H9N2 antibodies in these birds is of both economic and public health significance. These findings underscore the need for continuous flock monitoring as part of early warning measure to facilitate rapid detection and sustainable control of AI in Nigerian poultry.
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Affiliation(s)
| | - Ayoyimika Omolanwa
- Department of Veterinary Microbiology and Parasitology, University of Ibadan, Ibadan, Nigeria
| | - Adebowale Idris Adebiyi
- Department of Veterinary Microbiology and Parasitology, University of Ibadan, Ibadan, Nigeria
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Munyua PM, Githinji JW, Waiboci LW, Njagi LM, Arunga G, Mwasi L, Murithi Mbabu R, Macharia JM, Breiman RF, Kariuki Njenga M, Katz MA. Detection of influenza A virus in live bird markets in Kenya, 2009-2011. Influenza Other Respir Viruses 2012; 7:113-9. [PMID: 22515746 PMCID: PMC5780755 DOI: 10.1111/j.1750-2659.2012.00365.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Please cite this paper as: Munyua et al. (2013) Detection of influenza A virus in live bird markets in Kenya, 2009–2011. Influenza and Other Respiratory Viruses 7(2), 113–119. Background Surveillance for influenza viruses within live bird markets (LBMs) has been recognized as an effective tool for detecting circulating avian influenza viruses (AIVs). In Sub‐Saharan Africa, limited data exist on AIVs in animal hosts, and in Kenya the presence of influenza virus in animal hosts has not been described. Objectives This surveillance project aimed to detect influenza A virus in poultry traded in five LBMs in Kenya. Methods We visited each market monthly and collected oropharyngeal and cloacal specimens from poultry and environmental specimens for virological testing for influenza A by real time RT‐PCR. On each visit, we collected information on the number and types of birds in each market, health status of the birds, and market practices. Results During March 24, 2009–February 28, 2011, we collected 5221 cloacal and oropharyngeal swabs. Of the 5199 (99·6%) specimens tested, influenza A virus was detected in 42 (0·8%), including 35/4166 (0·8%) specimens from chickens, 3/381 (0·8%) from turkeys, and 4/335 (1·2%) from geese. None of the 317 duck specimens were positive. Influenza was more commonly detected in oropharyngeal [33 (1·3%)] than in cloacal [9 (0·4%)] specimens. None of the 485 environmental specimens were positive. Virus was detected in all five markets during most (14/22) of the months. Ducks and geese were kept longer at the market (median 30 days) than chickens (median 2 days). Conclusions Influenza A was detected in a small percentage of poultry traded in LBMs in Kenya. Efforts should be made to promote practices that could limit the maintenance and transmission of AIVs in LBMs.
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Molia S, Samaké K, Diarra A, Sidibé MS, Doumbia L, Camara S, Kanté S, Kamissoko B, Diakité A, Gil P, Hammoumi S, de Almeida RS, Albina E, Grosboisa V. Avian influenza and Newcastle disease in three risk areas for H5N1 highly pathogenic avian influenza in Mali, 2007-2008. Avian Dis 2012; 55:650-8. [PMID: 22312986 DOI: 10.1637/9775-050911-reg.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Our survey aimed to investigate avian influenza (AI) and Newcastle disease (ND) prevalence and risk factors in three areas of Mali at risk for occurrence of H5N1 highly pathogenic avian influenza. Blood samples and cloacal and oropharyngeal swabs were collected from 1470 birds between February 2007 and May 2008 and were tested by commercial enzyme-linked immunosorbent assay to detect antibodies and real-time reverse-transcription (rRT)-PCR to detect virus. Risk factors associated with seropositivity or positive rRT-PCR were identified by random effect logistic regression. AI seroprevalence was significantly lower in birds from commercial farms (0%) than in village backyard birds (3.1%). For backyard birds, no individual risk factors (species, age, sex) were identified, but birds in the Mopti area in the Sahelian zone, where millions of wild birds migrate, were more seropositive than in the Sikasso area in the Sudano-Guinean zone (odds ratio [OR] = 2.0, P = 0.051). Among backyard birds nonvaccinated against ND, ND seroprevalence was 58.4%, and the odds of seropositivity was 2.0 higher in chickens than in ducks, 1.7 higher in females than in males, 3.1 higher in adults than in young birds, and 3.0 higher in poultry from the Sikasso area than from the Mopti area (P < 0.01 in all cases). Prevalence established by rRT-PCR was low for both AI virus (1.1%) and ND virus (2.6%) and was associated with no risk factors for AI but was higher in chickens than in ducks (OR = 5.3, P = 0.05) and in the Sikasso area than in the Mopti area (OR = 3.4, P = 0.027) for ND. For AI and ND, prevalence assessed by serology or rRT-PCR varied over time, although seasonal and interannual variation could not be clearly distinguished. The intracluster correlation coefficient for serologic data was low for AI (0.014) and higher for ND (0.222). These results are useful to optimize surveillance and control strategy for notifiable avian diseases in African countries with similar agroecological and resource-limited contexts.
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Affiliation(s)
- S Molia
- CIRAD, UPR AGIRs, Campus International de Baillarguet, F-34398 Montpellier, France.
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Cappelle J, Gaidet N, Iverson SA, Takekawa JY, Newman SH, Fofana B, Gilbert M. Characterizing the interface between wild ducks and poultry to evaluate the potential of transmission of avian pathogens. Int J Health Geogr 2011; 10:60. [PMID: 22085837 PMCID: PMC3280937 DOI: 10.1186/1476-072x-10-60] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 11/15/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Characterizing the interface between wild and domestic animal populations is increasingly recognized as essential in the context of emerging infectious diseases (EIDs) that are transmitted by wildlife. More specifically, the spatial and temporal distribution of contact rates between wild and domestic hosts is a key parameter for modeling EIDs transmission dynamics. We integrated satellite telemetry, remote sensing and ground-based surveys to evaluate the spatio-temporal dynamics of indirect contacts between wild and domestic birds to estimate the risk that avian pathogens such as avian influenza and Newcastle viruses will be transmitted between wildlife to poultry. We monitored comb ducks (Sarkidiornis melanotos melanotos) with satellite transmitters for seven months in an extensive Afro-tropical wetland (the Inner Niger Delta) in Mali and characterise the spatial distribution of backyard poultry in villages. We modelled the spatial distribution of wild ducks using 250-meter spatial resolution and 8-days temporal resolution remotely-sensed environmental indicators based on a Maxent niche modelling method. RESULTS Our results show a strong seasonal variation in potential contact rate between wild ducks and poultry. We found that the exposure of poultry to wild birds was greatest at the end of the dry season and the beginning of the rainy season, when comb ducks disperse from natural water bodies to irrigated areas near villages. CONCLUSIONS Our study provides at a local scale a quantitative evidence of the seasonal variability of contact rate between wild and domestic bird populations. It illustrates a GIS-based methodology for estimating epidemiological contact rates at the wildlife and livestock interface integrating high-resolution satellite telemetry and remote sensing data.
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Affiliation(s)
- Julien Cappelle
- CIRAD ES, UR Animal et Gestion Intégrée des Risques, Montpellier, France.
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Sabarinath A, Sabarinath GP, Tiwari KP, Kumthekar SM, Thomas D, Sharma RN. Virological and Serological Surveillance of Avian Influenza Virus in the Birds of Grenada. ACTA ACUST UNITED AC 2011. [DOI: 10.3923/ijps.2011.579.582] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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