Malaria and SARS-CoV-2 in Burkina Faso

Africa accounts for only 2.3% of the global coronavirus disease 2019 (COVID-19) cases and 4% of deaths, but this relative low incidence has been partly attributed to the limited testing capacity in most countries. In addition, the population in many African countries is also at high risk of infection with multiple diseases such as HIV, tuberculosis and malaria. It is therefore important to know the real spread of SARS-CoV-2 in Africa and its co-occurrence with other pathogens. The aim of this study is to determine the prevalence and circulation of SARS-CoV-2 variants, and the frequency of co-infection with the malaria parasite. For this purpose, we conducted serological point of care tests and microscopy examinations on 998 volunteers of different ages and sexes in a random and stratified population sample in Burkina-Faso. In addition, nasopharyngeal swab samples were taken for molecular detection of SARS-COV-2 by RT-qPCR and for whole viral genome sequencing. Our results show a 3.2% and a 2.5% of SARS-CoV-2 seroprevalence and PCR positivity, respectively; and 22% of malaria incidence over the sampling period (from August to November 2020). There were no significant differences in SARS-CoV-2 prevalence between male and female subjects, but we report marked differences linked to age. The age group most frequently infected by SARS-CoV-2 was people above 40 years (6.9%; 95% CI 3.7–10.1), whereas malaria was much more frequent in children aged below 12 years (42.2%; 95% CI 36.1–48.4). Importantly, we found 2 cases of confirmed co-infection (PCR positive) and 8 cases of suspected co-infection (seropositive/PCR negative) mostly in children and teenagers. Finally, we report the genome sequences of 13 SARS-CoV-2 isolates circulating in Burkina Faso at the time of analysis, which were assigned to lineages A.19, A.21, B.1.1.404, B.1.1.118, B.1 and grouped into clades; 19B, 20A and 20B. This is the first population-based study about SARS-CoV-2 and malaria prevalence and co-infection performed in Burkina Faso during the first wave of the pandemic. In addition, this study provides a relevant estimation of the real prevalence of SARS-CoV-2 and variants circulating in this Sub-Saharan African country. Besides, it highlights the low frequency of malaria co-infection in African communities.