Respiratory virus surveillance in the WHO African Region Epidemiological Week 40, September 29 to October 5 2025

During Epiweek 40, 12 countries in the WHO African region (WHO AFR) contributed virological data for analysis - Algeria, Cameroon, Central African Republic, Côte d’Ivoire, Ghana, Kenya, Madagascar, Mauritania, Senegal, South Africa, Togo, and United Republic of Tanzania (Figure 1). During week 40, 960 specimens were collected, and tested for influenza.

In Epiweek 40, 205 specimens tested positive for influenza virus (positivity of 21.4%), of which 197 specimens were Influenza A, and 8 specimens were Influenza B. The following influenza viruses were identified: Influenza A (H1N1)pdm09 (n = 53), Influenza A (H3) (n = 106), Influenza A (subtyping not performed) (n = 38), Influenza B (lineage not determined) (n = 2), and Influenza B (Victoria) (n = 6).

SARS-CoV-2
In Epiweek 40, of the 940 specimens processed by 11 laboratories in the African Region, a total of 10 specimens tested positive for SARS-CoV-2 (positivity of 1.1%).

Cumulatively from weeks 1 to 40, the WHO AFR influenza laboratory network has tested 63,259 sentinel surveillance specimens for SARS-CoV-2, of which 2,521 were positive for SARS-CoV-2 (cumulative positivity rate 4%).