Spatiotemporal circulation of influenza viruses in 5 African countries during 2008-2009: a collaborative study of the Institut Pasteur International Network

Abstract

Background: Although recent work has described the spatiotemporal diffusion of influenza viruses worldwide, comprehensive data on spatiotemporal patterns of influenza from the African continent and Madagascar are still lacking.

Methods: National Influenza Centers from 5 countries-Cameroon, Côte d'Ivoire, Madagascar, Niger, and Senegal--collected specimens from patients presenting with influenza-like illness who visited sentinel surveillance clinics during a 2-year period (2008-2009). Isolates were genetically and antigenically characterized.

Results: Overall, 8312 specimens were tested. Seasonal influenza A virus subtypes H1N1 and H3N2 and influenza B viruses were detected in 329, 689, and 148 specimens, respectively. In 2009, pandemic influenza A virus subtype H1N1 was detected in Madagascar most commonly (98.5% of cases). Influenza activity was either significant year-round or occurred during a specific period of the year in the African countries we evaluated.

Conclusions: Our results demonstrate that, from Madagascar to Senegal, the epidemiologic and virologic characteristics of influenza viruses are diverse in terms of spatiotemporal circulation of the different virus types, subtypes, and strains. Our data highlight the importance of country-specific surveillance and of data and virus sharing, and they provide a rational basis to aid policy makers to develop strategies, such as vaccination at the right moment and with the right formulation, aimed at reducing the disease burden in Africa and Madagascar.

Figure 1.

Incidence of the influenza virus detection from January 2008 through December 2009. Specimens from outpatients that consult for influenza-like illness were analyzed using real-time reverse-transcription polymerase chain reaction for influenza A virus subtypes H1N1 (A[H1N1]) and H3N2 (A[H3N2]), 2009 pandemic influenza A virus subtype H1N1 (A[H1N1]pdm09), and influenza B virus. Each panel shows the monthly incidence of influenza viruses in Senegal (A), Niger (B), Côte d’Ivoire (C), Cameroon (E), and Madagascar (F). Location of countries in the African sub-continent where specimens were collected is also represented (D). Bars represent the cumulative number of specimens that were positive for influenza (corresponding to the left y-axis). The curve shows the monthly proportion of influenza-positive specimens among tested specimens (corresponding to the right y-axis).

Figure 2.

Phylogenetic analysis of nucleotide sequences of the hemagglutinin 1 gene (nucleotide 886) of influenza A virus subtype H1N1 isolates from Cameroon, Côte d’Ivoire, Madagascar, Senegal, and Seychelles, as well as references viruses. The tree was constructed using an ML method. The scale bar shows the genetic distance expressed as nucleotide substitutions per site. Online, a specific color is used for isolates from each country (red for Cameroon, green for Madagascar, orange for Senegal, light blue for Seychelles, and dark blue for Côte d’Ivoire). The strains name includes the isolation date (year_month). Major genetic clades are indicated on the right.