Highly pathogenic avian influenza virus H5N1 in Africa: a comprehensive phylogenetic analysis and molecular characterization of isolates

09/Apr/09

Authors: Cattoli G, Monne I, Fusaro A, Joannis TM, Lombin LH, et al. 2009 Highly Pathogenic Avian Influenza Virus Subtype H5N1 in Africa: A Comprehensive Phylogenetic Analysis and Molecular Characterization of Isolates. PLoS ONE 4(3): e4842. doi:10.1371/journal.pone.0004842

This work follows the appearance of A(H5N1) viruses in birds in eleven African countries (Benin, Burkina Faso, Cameroon, Djibouti, Egypt, Ghana, Ivory Coast, Nigeria, Niger, Sudan, Togo) and the implications for the poultry sector and related public health issues. These include food security in low-income countries and the potential threat to human health from circulation of A(H5N1). To date there is only limited information on the molecular evolution and epidemiology of A(H5N1) in Africa. To fill this gap the authors applied molecular analysis tools to virus sequence data and combined the results with epidemiological data related to A(H5N1) viruses isolated between 2006 and early 2008. This included 494 full gene sequences from 67 African isolates and in addition molecular analysis tools were applied to a total of 1,152 A(H5N1) sequences obtained from viruses isolated in Africa along with Europe and the Middle East for comparison. Detailed phylogenetic analyses of the 8 gene viral segments confirmed that 3 distinct sub-lineages were introduced which have persisted and spread across the African countries.

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ECDC Comment (07-04-09): The authors note that despite phylogenetic analysis of all the gene segments of the A(H5N1) viruses in this study that did not allow them to pinpoint the origins of the different viruses. The epidemiological data here are rudimentary. It also remains unclear how, when and where the three distinct A(H5N1) sub-lineages entered the continent and spread. Resources for surveillance for avian influenza are considerably more plentiful than they were a decade ago but they still remain rudimentary compared to what is available in the European Union.
hat-tip Helblindi