Pandemic influenza A/H1N1 virus incursion into Africa: countries, hosts and phylogenetic analysis

Abstract

Swine origin influenza A/H1N1 virus was first detected in Mexico in April 2009. It thereafter spread to over a hundred countries in five continents including Africa and was declared a pandemic by the WHO. The disease was estimated to have caused 18,500 laboratory - confirmed deaths worldwide among millions of infected people within the first year. Though Africa was late in detecting and reporting pandemic H1N1, information on the incursion of the virus into Africa and its molecular features are important for planning control measures between countries and to understand inter-host and genetic relationship of influenza viruses detected in Africa. We studied time and events of the detection of 2009 pandemic Influenza A/HIN1 virus in Africa and selected viral HA and NA gene sequences from the GenBank and GISAID data bases . Nucleotide sequence alignment and construction of phylogenetic trees were carried out with MEGA version 5 bioinformatics software and the neighbor-joining ClustalW method with 1000 bootstrap replicates. Earliest human cases of pandemic H1N1 in Africa were detected  by June 2009 in Egypt, Morocco, South Africa and later cases in Ghana, Nigeria and Cameroon, with varying phylogenetic clusters. Following cases of Influenza A/H1N1 pandemic in humans, infections in pigs earlier reported in America, Europe and Asia were also observed in Cameroon, Nigeria, Togo and Kenya, apparently transmitted from humans by reverse zoonoses. Adoption of an integrated, cross-sectoral and transboundary approach to zoonotic diseases surveillance and management in the context of One-Health in Africa is advocated. Africa particularly needs to be better prepared to prevent or mitigate outbreaks and spread of emerging diseases.

Keywords: Influenza virus incursion, Pandemic, Africa, Phylogeny, One-Health