Evolutionary dynamics of multiple sublineages of H5N1 influenza viruses in Nigeria from 2006 to 2008

Abstract

Highly pathogenic A/H5N1 avian influenza (HPAI H5N1) viruses have seriously affected the Nigerian poultry industry since early 2006. Previous studies have identified multiple introductions of the virus into Nigeria and several reassortment events between cocirculating lineages. To determine the spatial, evolutionary, and population dynamics of the multiple H5N1 lineages cocirculating in Nigeria, we conducted a phylogenetic analysis of whole-genome sequences from 106 HPAI H5N1 viruses isolated between 2006 and 2008 and representing all 25 Nigerian states and the Federal Capital Territory (FCT) reporting outbreaks. We identified a major new subclade in Nigeria that is phylogenetically distinguishable from all previously identified sublineages, as well as two novel reassortment events. A detailed analysis of viral phylogeography identified two major source populations for the HPAI H5N1 virus in Nigeria, one in a major commercial poultry area (southwest region) and one in northern Nigeria, where contact between wild birds and backyard poultry is frequent. These findings suggested that migratory birds from Eastern Europe or Russia may serve an important role in the introduction of HPAI H5N1 viruses into Nigeria, although virus spread through the movement of poultry and poultry products cannot be excluded. Our study provides new insight into the genesis and evolution of H5N1 influenza viruses in Nigeria and has important implications for targeting surveillance efforts to rapidly identify the spread of the virus into and within Nigeria.

FIG. 1.

Maximum-likelihood (ML) phylogenetic tree for the HA gene segment of HPAI H5N1 viruses from Africa, Europe, the Middle East, and Asia. Sequences of Nigerian viruses analyzed in this study are highlighted in yellow. Sublineages and clades are colored as follows: clade 2.2.1 is in green, sublineage I is in orange, sublineage II is in pink, sublineage III is in red, and sublineage I/II-Nigeria is in yellow. The numbers at each branch point represent bootstrap values (black) and posterior probabilities (red). The numbers of substitutions that occur along the main branches appear in the blue boxes.

FIG. 2.

ML phylogenetic tree for the NA gene segment of HPAI H5N1 viruses from Africa, Europe, the Middle East, and Asia. The color scheme is the same as that used in Fig. 3.

FIG. 3.

Map showing Nigerian states. Regions identified in the migration analysis are highlighted with different colors.