The circulation of influenza viruses was analyzed by transmission zone over a 7-year period, i.e. from 2013 to 2019. Influenza A viruses, in particular A(H1N1) pdm 2009, A(H3N2), A(H5N1), as well as influenza B viruses with the Victoria and Yamagata lineages circulated in the African regions over this period. The influenza activity of the different viruses follows an annual and regional variation.
In 2013, influenza A viruses predominated in all African regions. But in terms of lineages and subtypes, the activity of B viruses with undetermined lineage was highest in eastern, middle, northern, and western Africa. In Southern and Northern Africa, the pandemic A(H1N1) pdm 2009 virus predominated, where they circulated in high proportions.
In 2014, influenza A viruses were supplanted by influenza B viruses in central Africa. But influenza A viruses predominated in the other transmission areas. In this context, A(H3N2) has supplanted the pandemic A(H1N1) pdm 2009 except in Northern Africa. In addition, the Victoria lineage B virus continued to circulate only in West Africa since 2013.
In 2015, influenza A viruses predominated over influenza B viruses. Pandemic A(H1N1) pdm 2009 viruses supplanted A(H3N2) in the 5 African transmission areas. Yamagata lineage B virus, which had been circulating only in West Africa since 2014, has reappeared for the first time in Southern and Eastern and Middle Africa.
In 2016, A(H3N2) and pandemic A(H1N1) pdm 2009 viruses were observed in high proportions in all regions. A(H3N2) was only supplanted by pandemic A(H1N1) pdm 2009 in Northern Africa. Victoria lineage B virus, which had been circulating only in West Africa since 2013, has reached for the first time Southern and Eastern Africa.
In 2017, A(H3N2) viruses predominated in southern and eastern Africa, while pandemic A(H1N1) pdm 2009 supplanted it in central, northern, and western Africa. In 2018, pandemic A(H1N1) pdm 2009 influenza activity continued to predominate in western and northern Africa. It also predominated A(H3N2) in southern and eastern Africa. A(H3N2) has high activity only in middle Africa. In 2019, there was proportional co-circulation of pandemic A(H1N1) pdm 2009 and A(H3N2) influenza viruses in eastern and central Africa. But in Middle Africa, Victoria lineage B virus predominated all viruses. (Figure 1).
In southern Africa the short influenza season runs from week 18 to week 37. In the Eastern part of the continent, four influenza seasons are differentiated. The first one occurring from week three to week 13 is observed in Ethiopia and Mauritius. The second influenza season starts from week 9 to week 15. Countries such as the Democratic Republic of Congo (DRC), Rwanda and Tanzania are subject to this variation. The third season begins in week 18 and ends in week 43 in Kenya, Mozambique, Uganda, and Zambia. The seasonality of influenza in Madagascar includes the first 3 seasons in the region, i.e. from week 3 to week 43. Central African countries including Cameroon and Central African Republic have a single influenza season starting from week 18 to week 39.
In Western Africa, three influenza seasons have also been observed. The first one runs from week 44 of the current year to week 20 of the following year. This season occurs in Burkina Faso and Niger. The second season in West Africa runs from week 25 to week 50 in Mali, Nigeria, Senegal and Togo. In Côte d'Ivoire and Ghana, influenza seasonality occurs between weeks 16 and 52 and between 1 and 34, respectively. The influenza seasons in these two countries are superimposable over weeks 16 to 34. In North Africa, only one influenza season is identified. It starts from week 32 of the current year to week 20 of the following year (Figure 2).
In Africa, five periods of high influenza activity are observed. From week 1 to week 52, influenza activity is continuous in countries such as Côte d'Ivoire and Ghana. From week 9 to 24, there is a period of high influenza activity in Tunisia, Niger, DRC, Rwanda and Tanzania. Cameroon, Kenya, Madagascar, South Africa, Uganda, Central African Republic and Zambia are the countries with high influenza activity during week 18 to 43. In the period from week 25 to 50, influenza epidemic peaks are detected in Nigeria, Mali, Senegal and Togo. The period from week 44 of the current year to week 12 of the following year, high influenza activity occurs in the following countries: Morocco, Algeria, Egypt, Ethiopia and Burkina Faso (Figure 3).