Genetically Different Highly Pathogenic Avian Influenza A(H5N1) Viruses in West Africa, 2015

Tassoni, Luca; Fusaro, Alice; Milani, Adelaide; Lemey, Philippe; Awuni, Joseph A.; Sedor, V. B.; Dogbey, O.; Commey, Abraham Nii Okai; Meseko, Clement; Joannis, Tony M.; Minoungou, Germaine L.; Ouattara, Lassina; Haido, Abdoul Malick; Cisse-Aman, Diarra; Couacy‐Hymann, Emmanuel; Dauphin, Gwenae͏̈lle; Cattoli, Giovanni; Monne, Isabella

doi:10.3201/eid2212.160578

Cited by 20 publications

(24 citation statements)

References 10 publications

(12 reference statements)

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“…Our methodological pipeline was partially used only for the Nigerian outbreaks observed between 2006 and 2008 (Fusaro et al., ), while it has been never used for earlier or recent introductions in Nigeria and other West African countries. Most of the published literature on HPAI H5N1, upon which animal health agencies base their decision‐making process primarily, include numerical summaries of reported outbreaks in each country (Brown, ), risk mapping based purely on spatial and temporal distribution of the disease (Ekong et al., ), and traditional phylogenetic analysis of viral sequence isolates from these outbreaks (Asante et al., ; Ducatez et al., ; Tassoni et al., ). Our approach provides high‐resolution insights into HPAI dynamics impossible to achieve with traditional methods.…”

Section: Discussionmentioning

confidence: 99%

“…The IRD data do not always report all precise geographic coordinates, collection date and/or host species of accessions, so we consulted the metadata field of each sequence isolate to identify the approximate location and collection dates. Furthermore, when possible, we identified metadata for each sequence by cross‐referencing information with the corresponding publication (Cattoli et al., ; Chen & Holmes, ; Ducatez et al., , ; Ekong et al., ; FAO Empress, ; Fusaro et al., , ; Joannis et al., ; Monne et al., ; Paul, Assam, & Ndang, ; Scotch et al., ; Shittu et al., , Tassoni et al., ; Williams, Fasina, & Peterson, ). We converted the collection date for each sequence into fractional years to estimate divergence times.…”

Section: Methodsmentioning

confidence: 99%

“…The isolates are genetically related to H5N1 viruses collected in China and Canada in 2013 (Monne et al., ). Clade 2.3.2.1c was also isolated from the 2015 outbreaks in Ghana, Burkina Faso, Côte d'Ivoire and Niger (Asante et al., ; Tassoni et al., ). However, two cocirculating genetic groups (WA1 and WA2) within clade 2.3.2.1c were found.…”

Section: Introductionmentioning

confidence: 99%

“…However, two cocirculating genetic groups (WA1 and WA2) within clade 2.3.2.1c were found. WA1 comprises sequences collected from Nigeria, Ghana, Burkina Faso, Côte d'Ivoire and Niger while WA2 comprises sequences from Côte d'Ivoire and Niger suggesting the occurrence of at least two independent introductions of subtype H5N1 in West Africa in 2015 (Tassoni et al., ).…”

Section: Introductionmentioning

confidence: 99%

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Spatiotemporal evolutionary epidemiology of H5N1 highly pathogenic avian influenza in West Africa and Nigeria, 2006-2015

Ekong

Fountain-Jones

Alkhamis

2017

Transbound Emerg Dis

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SummaryH5N1 highly pathogenic avian influenza virus (HPAIV) was first observed in Nigeria in early 2006 and has now spread to more than 17 African countries having severe economic and public health implications. Here, we explore the spatiotemporal patterns of viral dispersal both among West African countries and within Nigeria using sequence data from hemagglutinin (HA) gene region of the virus. Analyses were performed within a statistical Bayesian framework using phylodynamic models on data sets comprising of all publically available HA sequence data collected from seven West African countries and Egypt between 2006 and 2015. Our regional-level analyses indicated that H5N1 in West Africa originated in Nigeria in three geopolitical regions, specifically north central and north-east, where backyard poultry and wild birds are in frequent contact, as well as south-west, a major commercial poultry area, then dispersed to West African countries. We inferred significant virus dispersal routes between Niger and Nigeria on one side and Burkina Faso, Ivory Coast, Ghana and Egypt on the other. Furthermore, south-west Nigeria identified as a primary source for virus dispersal within Nigeria as well as to Niger in 2006 and2008. Niger was an important epicentre for the virus spread into other West African countries in 2015. Egyptian introductions from West Africa were sporadic and resulted most likely from poultry trade with Nigeria rather than contact with infected wild birds. Our inferred viral dispersal routes reflected the large-scale unrestricted movements of infected poultry in the region. Our study illustrates the ability of phylodynamic models to trace important HPAIV dispersal routes at a regional and national level. Our results have clear implications for the control and prevention of this pathogen across scales and will help improve molecular surveillance of transboundary HPAIVs. K E Y W O R D Savian influenza, Bayesian phylodynamics, dispersal routes, Phylogeography, poultry | INTRODUCTIONThe continuous spread of H5N1 highly pathogenic avian influenza (HPAI) in West and Central Africa has caused large-scale economic losses and threatens farmer's livelihoods, poultry production and trade. Furthermore, there is added concern of the disease becoming endemic in the region which also threatens public health Tables S1 and S2).The IRD data do not always report all precise geographic coordinates, collection date and/or host species of accessions, so we consulted the metadata field of each sequence isolate to identify the approximate location and collection dates. Furthermore, when possible, we identified metadata for each sequence by cross-referencing information with the corresponding publication Chen & Holmes, 2006; Ducatez et al., 2006 Ducatez et al., , 2007Ekong et al., 2012; FAO Empress, 2015;Fusaro et al., 2009Fusaro et al., , 2010Joannis et al., 2006;Monne et al., 2008;Paul, Assam, & Ndang, 2013;Scotch et al., 2013;Shittu et al., 2017, Tassoni et al., 2016Williams, Fasina, & Peterson, 2008). We converted the ...

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Spatiotemporal evolutionary epidemiology of H5N1 highly pathogenic avian influenza in West Africa and Nigeria, 2006-2015

Ekong

Fountain-Jones

Alkhamis

2017

Transbound Emerg Dis

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“…In addition, viruses of this clade have caused major outbreaks among poultry in several Western African countries with ongoing virus circulation to date [16]. Interestingly, 2.3.2.1c viruses have not (yet) been reported from Egypt.…”

Section: Introductionmentioning

confidence: 99%

Novel real-time PCR-based patho- and phylotyping of potentially zoonotic avian influenza A subtype H5 viruses at risk of incursion into Europe in 2017

et al. 2017

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Since November 2016, Europe witnesses another wave of incursion of highly pathogenic avian influenza (HPAI) A(H5) viruses of the Asian origin goose/Guangdong (gs/GD) lineage. Infections with H5 viruses of clade 2.3.4.4b affect wild bird and poultry populations. H5 viruses of clades 2.2, 2.3.1.2c and 2.3.4.4a were detected previously in Europe in 2006, 2010 and 2014. Clades 2.2.1.2 and 2.3.2.1.c are endemic in Egypt and Western Africa, respectively and have caused human fatalities. Evidence exists of their co-circulation in the Middle East. Subtype H5 viruses of low pathogenicity (LPAI) are endemic in migratory wild bird populations. They potentially mutate into highly pathogenic phenotypes following transmission into poultry holdings. However, to date only the gs/GD H5 lineage had an impact on human health. Rapid and specific diagnosis marks the cornerstone for control and eradication of HPAI virus incursions. We present the development and validation of five real-time RT-PCR assays (RT-qPCR) that allow sequencing-independent pathotype and clade-specific distinction of major gs/GD HPAI H5 virus clades and of Eurasian LPAI viruses currently circulating. Together with an influenza A virus-generic RT-qPCR, the assays significantly speed up time-to-diagnosis and reduce reaction times in a OneHealth approach of curbing the spread of gs/GD HPAI viruses.

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Avian Influenza

Meseko¹,

Oluwayelu²

2019

Transboundary Animal Diseases in Sahelian Africa and Connected Regions

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Genetically Different Highly Pathogenic Avian Influenza A(H5N1) Viruses in West Africa, 2015

Cited by 20 publications

References 10 publications

Spatiotemporal evolutionary epidemiology of H5N1 highly pathogenic avian influenza in West Africa and Nigeria, 2006-2015

Spatiotemporal evolutionary epidemiology of H5N1 highly pathogenic avian influenza in West Africa and Nigeria, 2006-2015

Novel real-time PCR-based patho- and phylotyping of potentially zoonotic avian influenza A subtype H5 viruses at risk of incursion into Europe in 2017

Avian Influenza

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