Highly Pathogenic Avian Influenza Virus Subtype H5N1 in Africa: A Comprehensive Phylogenetic Analysis and Molecular Characterization of Isolates

Abstract

Highly pathogenic avian influenza virus A/H5N1 was first officially reported in Africa in early 2006. Since the first outbreak in Nigeria, this virus spread rapidly to other African countries. From its emergence to early 2008, 11 African countries experienced A/H5N1 outbreaks in poultry and human cases were also reported in three of these countries. At present, little is known of the epidemiology and molecular evolution of A/H5N1 viruses in Africa. We have generated 494 full gene sequences from 67 African isolates and applied molecular analysis tools to a total of 1,152 A/H5N1 sequences obtained from viruses isolated in Africa, Europe and the Middle East between 2006 and early 2008. Detailed phylogenetic analyses of the 8 gene viral segments confirmed that 3 distinct sublineages were introduced, which have persisted and spread across the continent over this 2-year period. Additionally, our molecular epidemiological studies highlighted the association between genetic clustering and area of origin in a majority of cases. Molecular signatures unique to strains isolated in selected areas also gave us a clearer picture of the spread of A/H5N1 viruses across the continent. Mutations described as typical of human influenza viruses in the genes coding for internal proteins or associated with host adaptation and increased resistance to antiviral drugs have also been detected in the genes coding for transmembrane proteins. These findings raise concern for the possible human health risk presented by viruses with these genetic properties and highlight the need for increased efforts to monitor the evolution of A/H5N1 viruses across the African continent. They further stress how imperative it is to implement sustainable control strategies to improve animal and public health at a global level.

Evolutionary Dynamics of Multiple Sublineages of H5N1 Influenza Viruses in Nigeria from 2006 to 2008

“…This area also sustains a large backyard poultry population and the highest concentration of domestic ducks, reared under free-range conditions, providing opportunities for contact between wild birds and backyard poultry (3). It has been suggested that migratory birds may play a role in the introduction of HPAI H5N1 virus into Nigeria (2,3,15,27). In fact, the migration paths ending in the Hadejia-Nuguru wetlands intersect with areas in Eastern Europe where HPAI H5N1 virus has been circulating since autumn of 2005 (3).…”

“…It is also possible that stochastic effects may have a greater impact on the population structure of HPAI H5N1 virus than selective pressures. Interestingly, sublineage I also appears to have circulated in poultry populations for only short durations in other African countries, including Ivory Coast (10 months), Burkina Faso (2 months), Sudan (7 months), and Ghana (4 months) (2). A similar situations was reported in Thailand, where one reassortant H5N1 strain emerged and replaced the two parental lineages (PC168-like and PC170-like) of clade 1 (29) Additional influenza virus sequence data from other African countries are greatly needed to further understand the evolutionary dynamics of the multiple sublineages circulating in Nigeria and other parts of Africa.…”

“…The nucleotide sequences obtained in this study are available from GenBank under accession numbers CY047976 to CY048647, CY016276 to CY016283, CY017179 to CY017186, CY016284 to CY016291, CY016907 to CY016954, and EU148356 to EU148451 or from the GISAID public database under accession numbers EPI161701 to EPI161708. (2,9,10,13,22). Sublineages I and III and clade 2.2.1 were defined by high bootstrap (Ͼ70%) or posterior probability (Ͼ90%) values and long branches in all the phylogenetic trees (with the exception of the phylogenetic tree for the M gene), while sublineage II had poor bootstrap and posterior probability support ( Fig.…”

Identification of risk factors associated with highly pathogenic avian influenza H5N1 virus infection in poultry farms, in Nigeria during the epidemic of 2006–2007

“…In Africa, despite reports on the genetic/biological constituents/properties of HPAI H5N1 viruses of African origin (Ducatez et al, 2006(Ducatez et al, , 2007Njouom et al, 2008;Couacy-Hymann et al, 2008;Cattoli et al, 2009;Fasina et al, 2009), the epidemiologic aspects of HPAI H5N1 virus infection in poultry have not been investigated. Although previous studies have provided an epidemiologic framework for investigation of risk factors for HPAI H5N1 virus in poultry (Henzler et al, 2003;Thomas et al, 2005;Bouma et al, 2009;Busani et al, 2009), study findings and proposed prevention strategies may not apply to the conditions of Nigeria in view of variations in climatic conditions, poultry practices, and the socioeconomic and cultural orientations of agricultural populations in this geographic region.…”

Persistence of Low Pathogenic Avian Influenza Virus in Waterfowl in a Southern African Ecosystem

“…A relation between environmental determinants, host community ecology and virus ecology is presented with potential for a predictive approach. These observations are particularly relevant for animal and public health at the wildlife/domestic/human interface in two contexts: (a) in Africa, where HPAI H5N1 is recurring in domestic poultry production systems (Ducatez et al 2007;Cattoli et al 2009) (providing opportunities for recombination with local LPAI), veterinary/public health sectors may be weak, and the wild/domestic bird interface is rarely monitored or controlled despite a predicted risk (Kilpatrick et al 2006);and (b) in Eurasia, since the spring migration of paleartic birds can theoretically expose Eurasian ecosystems to LPAI strains from Africa (although thus far, with little information available, no genes of African origin have been detected in the Eurasian viral pool) (Abolnik et al 2006;Abolnik 2007). Table 2: Prevalence (prev; in percent), sample size (n) for the entire birds sampled (All birds) and only the ducks sampled (Ducks Only) compared between sessions when paleartics birds are present in the ecosystem (September to March) and absent (May to July).…”