Circulation and seasonality of influenza viruses in different transmission zones in Africa from 2013-2019

doi:10.21203/rs.3.rs-1451894/v1

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Circulation and seasonality of influenza viruses in different transmission zones in Africa from 2013-2019

https://doi.org/10.21203/rs.3.rs-1451894/v1

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Background: The Influenza Viruses are responsible for more than 5 million of severe cases and 290,000 to 650,000 deaths every year worldwide. Developing countries support 99% of deaths caused by Influenza in children under age of 5. This paper aims to determine the dynamics of influenza viruses in African transmission areas to identify regional seasonality for appropriate decision making and development of regional preparedness and response strategies.

Methods: We used data from the FluMart website collected by Influenza national programs for seven periods of transmission (2013-2019). We calculate the weekly proportions of positive influenza cases and follow the trend of the transmission in countries in the Africa continent to determine the seasonality.

Results: Over the period, Influenza A(H1N1) pdm 2009, A(H3N2), A(H5N1) viruses, as well as influenza B Victoria and Yamagata lineages identified circulated in the African regions. A(H1N1) pdm 2009 and A(H3N2) were highly circulated in northern and southern Africa. Influenza activity follows an annual and regional variation. In the tropical band, from the easter to the western via the middle, influenza activity is marked by the predominance of A subtypes despite the strong circulation of all B lineages. In the southern and northern Africa, only season has been identified for both regions. In the Eastern, four influenza seasons are differentiated and three for the Western part.

Conclusions: The circulating dynamic generates five periods of intense activity during the seasons, so five types of prevention zone. Particularly the tropical band, which is a mixing zone for all influenza viruses, seasons start in the Eastern to end in the Western. Health authorities from countries with same seasons, will need to implement concerted preparedness and control activities.

Influenza surveillance

Africa

circulation

seasonality

Influenza is an acute, common and contagious respiratory infection that infects humans and several animal species including birds and pigs. It occurs during the influenza seasons, particularly in winter in temperate regions and continuously or with one or two epidemic peaks in tropical regions. These annual epidemics are responsible for approximately 5 million of severe cases and 290,000 to 650,000 deaths (1) worldwide. Approximately 99% of deaths in children under 5 years of age from influenza-associated lower respiratory infections occur in developing countries (2, 3).

To protect the world from the threat of influenza, a global influenza surveillance system, the Global Influenza Surveillance and Response System (GISRS), coordinated by the WHO Influenza Programme, has been in place since 1965 (4). This system functions as a global surveillance, preparedness and response mechanism for seasonal, pandemic and zoonotic influenza, as a global platform for monitoring influenza epidemiology and disease, and as a global alert system for novel influenza viruses and other respiratory pathogens.

In addition, WHO recommends that countries develop a sentinel surveillance strategy for influenza-like illness (ILI) and severe acute respiratory infections (SARS) to better use surveillance data for decision-making at all levels of the health system (5). The purpose of this study is to determine the dynamics of influenza viruses in African transmission areas in order to identify regional seasonality for appropriate decision making and development of regional strategies.

Data Collection: Data are provided by Global Influenza Surveillance and Response System (GISRS) National Influenza Centers (NICs) and other national laboratories and are downloaded from WHO region databases. They are available online free of charge at the FluMart website: https://apps.who.int/flumart/Default?ReportNo=12. The data from African countries extracted for this study covers the period from 2013 to 2019 (3).

Data analysis: This is a descriptive cross-sectional study. The annual proportions of circulating influenza viruses by country and by transmission zone were described by means of pie charts.

The seasonal transmission dynamics per country and per transmission zone were also described through the definition of mean epidemic curves and alert thresholds. This method used the weekly proportions of positive influenza cases. First we identified the weeks with the highest proportions and determined the median peak week for the different years. Then the weeks with peaks were fitted to the median week. The average of the weekly proportions is the epidemiological curve with the lower bound being the standard deviation and the upper bound being the mean plus twice the standard deviation (1). Overlapping epidemic periods by country were grouped to identify seasons in new influenza transmission areas. Data analysis was performed with Stata MP 12 and Tableau Desktop®2020.3.3.

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).

Influenza virus activity in Africa has followed the global trend. These viruses are the same ones that have been circulating everywhere else in the world over the same period. These include 2009 pandemic A(H1N1), A(H3N2), A(H5N1) and influenza B viruses of the Victoria and Yamagata lineage (3, 4). Indeed, after the 2009 influenza pandemic, only these four influenza viruses continued to circulate worldwide (5–7). Our work has shown that their influenza activity follows an annual and regional variation. The period was mainly marked by a high activity of the A(H1N1) pdm 2009 and A(H3N2) viruses in the temperate zones of North and South Africa while influenza B viruses showed a high activity in the African tropical band. Our results were confirmed by other studies. These revealed high proportions of seasonal influenza A activity in temperate countries versus high rates of influenza B in the sub-Saharan region (8, 9). In addition to the fact that influenza seasons have always been dominated in the temperate zone of southern Africa by the A(H1N1) pdm 2009 or A(H3N2) and in the north by A(H1N1) pdm 2009, our work has shown that in the tropical African band (East, West and Central), the B viruses that were in high circulation in 2013 have been progressively replaced by A(H3N2) and then a few times by A(H1N1) pdm 2009 from 2014. However, the B Victoria virus, isolated in the 2014 season in West Africa, has continued to grow in proportion in Central Africa until it predominates all others in the 2019 season. For this reason, some authors have stated that the influenza activity of type B viruses is relatively strong in the tropics, but it has often been predominated by that of type A viruses, which is more intense and longer lasting (5, 7, 9, 10).

The data from the study show that in southern Africa, the influenza epidemic seasons occur during the southern winter, particularly from May to August. In the tropical part of the continent, the influenza seasons start in the East and extend to the West, lasting almost the whole year. One or even four epidemic peaks can be identified depending on the area of transmission. However, exceptions are observed in West Africa where the Sahelian zone (Group 1) follows a seasonality similar to that observed in temperate northern countries. In fact, in North Africa, the impact of the cold Mediterranean climate results in an influenza season that extends from August to April. This seasonality observed in temperate and tropical Africa are the effect of certain climatic factors including temperature for cold regions and rain, humidity and drought for tropical regions (5, 11–13).

Globally, in Africa five influenza seasons are identifiable in the five transmission zones. The influenza season, which runs from March to October, extends from the southern African transmission zone to the central and eastern African transmission zones. At these times, influenza activity is strongly influenced by climatic effects (14). However, exceptionally for Madagascar, the season is spread over the whole year. This study corroborates the conclusions of Alonso et al. that in this country-continent influenza activity is irregular and not influenced by the climate (15).

In the transmission areas of North and West Africa, especially near the coast, the influenza seasons occur somewhat later and are spread throughout the year. These late winter activities of influenza viruses in these transmission areas sometimes coincide with climatic phenomena such as cold, el-niño and la niña (5, 12, 16, 17).

Prevention, preparedness and response measures should be implemented prior to the influenza seasons in each transmission area, including January to December for West Africa, February to December for East Africa, February to October for Central and Southern Africa and November to March for North Africa.

Our study is limited by the inclusion of data exclusively from the WHO FluMart. Despite the relevance and quality of this free and open access data, it may be different in different countries. But this could not influence the quality of our work thanks to the multitude of data from included countries.

Seven years of data from the GISRS network have shown that the influenza viruses circulating in the five transmission zones in Africa are similar to those isolated elsewhere in the world. Their activity generates different epidemic periods each year in the transmission zones. In southern Africa, a single epidemic season extends from May to August, while in the northern zone, which straddles two years, it extends from August to April. It has also been shown that in the tropical band of the continent, the influenza seasons start in the East and end in the West. They generate three main epidemic peaks in the East, one in the Center and three in the West. Health authorities in different transmission areas will need to implement concerted preparedness and control activities before the epidemic periods. Despite the lack of surveillance in some countries, the synchronization of preparedness and control activities should include all countries from transmission zones to limit the impact of influenza on their populations.

WHO: World Health Organization; GISRS: WHO Global Influenza Surveillance and Response System; NIC: National Influenza Center; pH1: A(H1N1) pdm09; H3: A(H3N2); Ans: Influenza A not subtyped; Byam : Influenza B Yamagata; Bvic : Influenza B Victoria; Bind : Influenza B with undetermined lineage; DRC: Democratic Republic of Congo.

Ethics approval and consent to participate: Public data freely accessible on WHO website. They use by the authors do not need approval by an appropriate ethics committee none by WHO. All methods were performed in accordance with the relevant guidelines and regulations.

Consent for publication: Not applicable

Availability of data and materials: The datasets generated and/or analyzed during the current study are available in the GISRS repository, [https://apps.who.int/flumart/Default?ReportNo=10]

Competing interest: The authors declare that they have no competing interests

Funding: This study does not benefit of any funding source

Authors' contributions: MRDB and AKN have made substantial contributions to the conception, the design of the study, the analysis, interpretation of data as well as the draft of the work. BW has contributed to the design and the interpretation of data. CR has reviewed the manuscript. EN, BL and FB substantively revised the manuscript and provide inputs to improve the discussions. All the authors have reviewed the final version approved the submitted version.

Acknowledgements: to the World Health Organization Regional Office for Africa for the general support we received.

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No competing interests reported.

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Circulation and seasonality of influenza viruses in different transmission zones in Africa from 2013-2019

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