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How frequent was SARS-CoV-2 and malaria co-infection during the first wave of the pandemic?

In a recent study posted to the medRxiv* preprint server, researchers determined the prevalence of circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and the frequency of co-occurrence of coronavirus disease 2019 (COVID-19) and malaria in Burkina Faso, West Africa.

Study: Prevalence of SARS-CoV-2 and co-occurrence/co-infection with malaria during the first wave of the pandemic (the Burkina Faso case). Image Credit: Christoph Burgstedt/Shutterstock


SARS-CoV-2 transmission in Africa has been reported to have a lower incidence, comprising mostly asymptomatic cases, and lower associated death rates compared to developed nations. A greater proportion of youngsters and socioecological variability (i.e., low populace, warm weather, and trained immune responses against infectious disorders) and prompt enforcement of health measures such as government lockdowns can explain the lower incidence.

Studies have documented that the COVID-19 pandemic impacted some countries (such as Tunisia, Morocco, and South Africa) more prominently, indicative of region-specific SARS-CoV-2 spread; however, the findings could be due to low and disproportionate levels of diagnostic testing and surveillance measures.

Further, malaria is endemic to Africa, the cases of which have increased during the initial COVID-19 wave, which may have been due to disruptions in malaria campaigns, and diagnostic and testing capacities during the initial pandemic wave.

About the study

In the present population-based study, researchers evaluated the frequency of COVID-19 and malaria co-infections in the Burkina Faso nation in West Africa.

The study was conducted on 998 asymptomatic volunteers residing in different rural or urban regions across 11 villages in southern regions of Burkina Faso between 22 August and 19 November 2020. Blood samples were obtained from the participants and subjected to microscopic examination for the malaria parasite, Plasmodium falciparum detection (in the asexual and gametocyte stages), and rapid diagnostic tests for SARS-CoV-2 detection based on the presence of serum immunoglobulin G (IgG), A and M antibodies against SARS-CoV-2 nucleocapsid (N) protein.

SARS-CoV-2 seroprevalence was estimated as the fraction of participants with anti-SARS-CoV-2 N antibodies. In addition, nasopharyngeal swab specimens were obtained from the study participants for quantitative reverse transcription-polymerase chain reaction (RT-qPCR) analysis, and the cycle threshold (Ct) values were obtained. Further, SARS-CoV-2 ribonucleic acid (RNA) was extracted from seropositive individuals samples with Ct values ≤35 (n=19) and subjected to whole genome sequencing (WGS) analysis, following which genome libraries were constructed.

The sequences were also analyzed via comparative genomic and phylogenetic analyses, and the PANGOLIN (phylogenetic assignment of named global outbreak lineages) classification was used to identify SARS-CoV-2 lineages and clades. Demographical and clinical data obtained from the participants included sex, body temperature, and age.


Most participants (55%, n=549) were women, and the individuals were age-stratified into the following age groups: five years to 12 years, 13 years to 20 years, 21 years to 40 years, and above 40 years. The analysis showed a 3.2% SARS-CoV-2 seroprevalence (n=32), 2.5% SARS-CoV-2 RT-qPCR positivity, and 22% malaria incidence (n=219) with most co-infection cases detected among children aged <12 years (42%) with no significant sex-based differences.

The highest SARS-CoV-2 seropositivity (five percent) was reported for the Bobo-Dioulasso city in urban regions of West Africa and was significantly higher among individuals aged above 40 years (seven percent), followed by those aged 13 years to 20 years (three percent), five years to 12 years (two percent), and 21 years to 40 years (one percent). Significantly higher SARS-CoV-2 infection incidence rates (six percent) were observed in November 2020; however, no significant sex-based differences were observed in SARS-CoV-2 seroprevalence and PCR positivity.

The WGS analysis demonstrated 13 SARS-CoV-2 strains circulating in Burkina Faso during the study period, assigned to the A.19, A.21, B.1, B.1.1.118, and B.1.1.404 lineages clustered in the 19B, 20A and 20B clades. The circulating lineages found in Burkina Faso during the first wave of the pandemic were early clades derived from the Wuhan strain. Most of the reported lineages have been previously described in Burkina Faso or neighboring countries. However, we also identified two less frequent lineages (B.1.1.118 and B.1) that were probably imported to Burkina-Faso from the USA or Europe.

Of the SARS-CoV-2 seropositive/RT-qPCR-positive specimens (n=7), none showed malaria co-infection, whereas malaria and COVID-19 co-occurred in two (out of 17) seronegative/RT-qPCR-positive specimens. Out of the remaining seropositive/RT-qPCR-negative individuals (n=25), eight showed malaria co-infection. Therefore, two and eight cases of confirmed and suspected co-infections were detected, respectively, of which eight were aged <14 years and two were aged >40 years. Only one (out of two) RT-qPCR-positive co-infected samples was sequenced and assigned the A.21 lineage.

Most of the age groups most affected by the two diseases did not show overlapping; however, ten co-infection cases were observed among youngsters. The serology tests measured total antibody titers (IgG, A, and M) against SARS-CoV-2, making it difficult to delineate seropositive previous infection cases from current SARS-CoV-2 infections and, therefore, whether the data denoted a re-infection or a co-infection cannot be defined clearly.

Similar to the observed COVID-19 temporal trends, malaria cases increased significantly from five percent at study commencement to 29% by the end of the study period, indicative of a potential impact on malaria infection control due to the COVID-19 pandemic.


The study findings showed a low frequency of COVID-19 and malaria co-infections (1%) in Burkina Faso. The authors believe that the present study is the first of its kind and provides data for estimating the true prevalence and circulating variants of SARS-CoV-2 infections in Sub-Saharan Africa.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

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