Impact of a six-month COVID-19 travel moratorium on Plasmodium falciparum malaria prevalence on Bioko Island, Equatorial Guinea (preprint)

Importation of malaria infections has long been suspected as a driver of sustained malaria prevalence on areas of Bioko Island, Equatorial Guinea. However, quantifying the impact of imported infections is difficult because of the dynamic nature of the disease and the complexity of designing a randomized trial. Here, we leverage a six-month travel moratorium in and out of Bioko Island during the initial COVID-19 pandemic response to evaluate the contribution of imported infections to Pf prevalence on Bioko Island. Using a difference in differences design and data from island wide household surveys conducted before (2019) and after (2020) the travel moratorium, we compared the change in prevalence between areas of low historical travel to those with high historical travel. We found that prevalence increased in low travel areas after the moratorium compared to before, while prevalence decreased in high travel areas. In the absence of a travel moratorium, the prevalence of infection in high travel areas was expected to be 5% higher than what was observed. The observed decrease in prevalence can be directly attributed to the lack of imported cases, highlighting the importance of control measures that target these types of infections.

Circulation of SARS-CoV-2 and co-infection with Plasmodium falciparum in Equatorial Guinea (preprint)

The impact of COVID-19 in Africa has been a big concern since the beginning of the pandemic. However, low incidence of COVID-19 case severity and mortality has been reported in many African countries, although data are highly heterogeneous and, in some regions, like Sub-Saharan Africa, very scarce. Many of these regions are also the cradle of endemic infectious diseases like malaria. The aim of this study was to determine the prevalence of SARS-CoV-2, the diversity and origin of circulating variants as well as the frequency of co-infections with malaria in Equatorial Guinea. For this purpose, we conducted antigen diagnostic tests for SARS-CoV-2, and microscopy examinations for malaria of 1,556 volunteers at six health centres in Bioko and Bata from June to October 2021. Nasopharyngeal swab samples were also taken for molecular detection of SARS-CoV-2 by RT-qPCR and whole genome viral sequencing. We report 3.0% of SARS-CoV-2 and 24.4% of malaria prevalence over the sampling in Equatorial Guinea. SARS-CoV-2 cases were found at a similar frequency in all age groups, whereas the age groups most frequently affected by malaria were children (36.8% [95% CI 30.9-42.7]) and teenagers (34.7% [95% CI 29.5-39.9]). We found six cases of confirmed co-infection of malaria and SARS-CoV-2 distributed among all age groups, representing a 0.4% frequency of co-infection in the whole sampled population. Interestingly, the majority of malaria and SARS-CoV-2 co-infections were mild. We obtained the genome sequences of 43 SARS-CoV-2 isolates, most of which belong to the lineage Delta (AY.43) and that according to our pandemic-scale phylogenies were introduced from Europe in multiple occasions (7 transmission groups and 17 unique introductions). This study is relevant in providing first-time estimates of the actual prevalence of SARS-CoV-2 in this malaria-endemic country, with the identification of circulating variants, their origin, and the occurrence of SARS-CoV-2 and malaria co-infection.