Multiyear persistence of 2 pandemic A/H1N1 influenza virus lineages in West Africa

Abstract

Our understanding of the global ecology of influenza viruses is impeded by historically low levels of viral surveillance in Africa. Increased genetic sequencing of African A/H1N1 pandemic influenza viruses during 2009-2013 revealed multiyear persistence of 2 viral lineages within West Africa, raising questions about the roles of reduced air traffic and the asynchrony of seasonal influenza epidemics among West African countries in the evolution of independent lineages. The potential for novel influenza virus lineages to evolve within Africa warrants intensified influenza surveillance in Africa and other understudied areas.

Figure 1.

Phylogenetic relationships of H1 sequences from 1643 pandemic A/H1N1 influenza viruses collected globally during 2009–2013, estimated using a maximum likelihood method. West African clades I and II, the main global clade of 2012–2013 viruses, and the cluster of Kenyan viruses are labeled. Bootstrap values >70% are provided for West African clades I and II and the main 2012–2013 clade. The full phylogeny, including tip labels, is provided in Supplementary Figure 2.