Background: Submicroscopic Plasmodium infections can be a source of persistent malaria transmission. The aim of this study was to assess their frequency, distribution, morbidity and associated factors in a pre-elimination malaria setting in sub-Saharan Africa, Guinea-Bissau, where the Plasmodium falciparum is the predominant Plasmodium species.

Methods: Dried fingerprick whole blood samples from 601 participants in the 2017 national, household-based, cross-sectional survey to estimate malaria prevalence were subjected to DNA extraction. The DNA was used in nested end-point PCR assays targeting genus- and species-specific regions of the Plasmodium 18S rRNA genes. Statistical analysis of socio-demographic, clinical and molecular data was carried out using the Statistical Package for the Social Sciences, version 29. Factors associated with submicroscopic P. falciparum infections and their magnitude were sought using Chi-square test and multiple logistic regression models, respectively. Statistically significant level was considered at P-value < 0.05.

Results: Nested PCR assays detected submicroscopic P. falciparum infections in 20.3% (95% CI = 16.8-23.8) of individuals microscopically negative for Plasmodium species in the general population and in 21.4% (95% CI = 9.9-36.5) of microscopically negative pregnant women. Submicroscopic Plasmodium malariae infections were also detected as co-infections in 3.0% individuals who were microscopically positive only for P. falciparum. Infections with other Plasmodium species were not detected. Submicroscopic P. falciparum infections were not associated with age, sex, or the presence of fever. A logistic regression model adjusted for ethnicity and health region showed that individuals from the Balanta and Bijagos ethnic groups, most of whom live in the low malaria-transmission areas of Quinara and Bissau, and the Bijagos archipelago, respectively, were less likely to have submicroscopic P. falciparum infections than individuals from the large Fula ethnic group, most of whom live in the high malaria-transmission area of Gabu. Submicroscopic P. falciparum infections were not associated with anaemia in children under 5 years of age.

Conclusion: The results obtained highlight the contribution of asymptomatic and submicroscopic P. falciparum infections to malaria transmission in high malaria-transmission areas and the need for molecular-based tools to detect submicroscopic Plasmodium species.