Genetic diversity studies provide evidence of Plasmodium falciparum differentiation that could affect fitness and adaptation to drugs and target antigens for vaccine development. This study describes the genetic structure of P. falciparum populations in urban and rural sites from southwestern Nigeria.

Although Plasmodium falciparum continues to be the main target for malaria elimination, other Plasmodium species persist in Africa. Their clinical diagnosis is uncommon, whereas rapid diagnostic tests (RDTs), the most widely used malaria diagnostic tools, are only able to distinguish between P. falciparum and non-falciparum species, the latter as “pan-species.” Blood samples from health facilities were collected in southern Nigeria (Lagos and Calabar) in 2017 (October–December) and Calabar only in 2018 (October–November), and analyzed by several methods, namely, microscopy, quantitative real-time PCR (qPCR), and peptide serology targeting candidate antigens (Plasmodium malariae apical membrane antigen, P. malariae lactose dehydrogenase, and P. malariae circumsporozoite surface protein). Both microscopy and qPCR diagnostic approaches detected comparable proportions (∼80%) of all RDT-positive samples infected with the dominant P. falciparum malaria parasite. However, higher proportions of non-falciparum species were detected by qPCR than microscopy, 10% against 3% infections for P. malariae and 3% against 0% for Plasmodium ovale, respectively. No Plasmodium vivax infection was detected. Infection rates for P. malariae varied between age-groups, with the highest rates in individuals aged > 5 years. Plasmodium malariae–specific seroprevalence rates fluctuated in those aged < 10 years but generally reached the peak around 20 years of age for all peptides. The heterogeneity and rates of these non-falciparum species call for increased specific diagnosis and targeting by elimination strategies.

Background: Incidence of malaria and anaemia are of public health importance especially in pregnant women in endemic regions, due to the negative health consequences to the mother and fetus. This study aimed to assess the pattern of falciparum malaria infection and anaemia, based on malaria prevention methods practiced by participants. Methods: A semi-structured tool was used to capture information on demographic, socio-economic and malaria prevention practices from 113 pregnant women attending antenatal clinics in 2 peri-urban health facilities in Lagos, southwest Nigeria. Malaria microscopy was conducted and haematocrit was measured. Logistic regression analysis was performed on the data collated from the survey. Results: The prevalence of anaemia among pregnant women was 87.2%. The mean (± sd) packed cell volume (PCV) (%) of the 22 (19.5%) infected subjects (26.8 ± 6.6), was significantly lower (t = −2.60, P value = 0.007) than that of the 91 (80.5%) uninfected subjects (30.8 ± 6.0). The prevalence of infection was highest in the 3rd trimester (n = 40, 35.4%) at 27.5% (11/40) and among those in their first pregnancy (n = 32, 28.3%) at 25.0% (8/32). There was a significant difference (t = −2.23, P-value = 0.01) in the mean PCV % of pregnant women who consumed herbal teas in pregnancy (28.2 ± 5.2) compared to those who did not (30.8 ± 6.6). Regression analysis showed that first pregnancy, anti-malarial use and insecticide-treated nets use the night before study had increased odds of malaria infection in participants (OR = 1.35, P = 0.006, 95% CI 0.52−2.49; OR = 2.3, P = 0.005, 95% CI 0.14−0.41; OR = 1.92, P = 0.001, 95% CI 0.62−5.98) while intermittent preventive treatment (IPT) participation and formal education were strongly and significantly associated with lower risk of parasitaemia (OR = 0.95, P = 0.025, 95% CI 0.41−2.26; OR = 0.44, P = 0.005, 95% CI 0.34−10.50). Conclusion: Interventions that will reduce malaria and moderate to severe anaemia, especially in a first pregnancy, should include education on the correct use of long-lasting insecticide-treated bed nets (LLIN), IPT and the dangers of herbal teas in pregnancy.

The burden of falciparum malaria is especially high in sub-Saharan Africa. Differences in pressure from host immunity and antimalarial drugs lead to adaptive changes responsible for high level of genetic variations within and between the parasite populations. Population-specific genetic studies to survey for genes under positive or balancing selection resulting from drug pressure or host immunity will allow for refinement of interventions. We performed a pooled sequencing (pool-seq) of the genomes of 100 Plasmodium falciparum isolates from Nigeria. We explored allele-frequency based neutrality test (Tajima’s D) and integrated haplotype score (iHS) to identify genes under selection. Fourteen shared iHS regions that had at least 2 SNPs with a score > 2.5 were identified. These regions code for genes that were likely to have been under strong directional selection. Two of these genes were the chloroquine resistance transporter (CRT) on chromosome 7 and the multidrug resistance 1 (MDR1) on chromosome 5. There was a weak signature of selection in the dihydrofolate reductase (DHFR) gene on chromosome 4 and MDR5 genes on chromosome 13, with only 2 and 3 SNPs respectively identified within the iHS window. We observed strong selection pressure attributable to continued chloroquine and sulfadoxine-pyrimethamine use despite their official proscription for the treatment of uncomplicated malaria. There was also a major selective sweep on chromosome 6 which had 32 SNPs within the shared iHS region. Tajima’s D of circumsporozoite protein (CSP), erythrocyte-binding antigen (EBA-175), merozoite surface proteins - MSP3 and MSP7, merozoite surface protein duffy binding-like (MSPDBL2) and serine repeat antigen (SERA-5) were 1.38, 1.29, 0.73, 0.84 and 0.21, respectively. We have demonstrated the use of pool-seq to understand genomic patterns of selection and variability in P. falciparum from Nigeria, which bears the highest burden of infections. This investigation identified known genomic signatures of selection from drug pressure and host immunity. This is evidence that P. falciparum populations explore common adaptive strategies that can be targeted for the development of new interventions.

The decline in the efficacy of artemisinin-based combination treatment (ACT) in some endemic regions threatens the progress towards global elimination of malaria. Molecular surveillance of drug resistance in malaria-endemic regions is vital to detect the emergence and spread of mutant strains. We observed 89 malaria patients for the efficacy of artemether-lumefantrine for the treatment of uncomplicated Plasmodium falciparum infections in Lagos, Nigeria and determined the prevalence of drug resistant strains in the population. Parasite clearance rates were determined by microscopy and the highly sensitive var gene acidic terminal sequence (varATS) polymerase chain reaction for 65 patients with samples on days 0, 1, 3, 7, 14, 21 and 28 after commencement of treatment. The genomic finger print of parasite DNA from pre- and post-treatment samples were determined using 24 nuclear single nucleotide polymorphisms (SNP) barcode for P. falciparum. Drug resistance associated alleles in chloroquine resistance transporter gene (crt-76), multidrug resistance genes (mdr1–86 and mdr1–184), dihydropteroate synthase (dhps-540), dihydrofolate reductase (dhfr-108) and kelch domain (K-13580) were genotyped by high resolution melt analysis of polymerase chain reaction (PCR) fragments. By varATS qPCR, 12 (18.5%) of the participants had detectable parasite DNA in their blood three days after treatment, while eight (12.3%) individuals presented with genotypable day 28 parasitaemia. Complexity of infection (CoI) was 1.30 on day 0 and 1.34 on day 28, the mean expected heterozygosity (HE) values across all barcodes were 0.50 ± 0.05 and 0.56 ± 0.05 on days 0 and 28 respectively. Barcode (π) pairwise comparisons showed high genetic relatedness of day 0 and day 28 parasite isolates in three (37.5%) of the eight individuals who presented with re-appearing infections. Crt-76 mutant allele was present in 38 (58.5%) isolates. The mdr1–86 mutant allele was found in 56 (86.2%) isolates. No mutation in the K-13580 was observed. Persistence of DNA-detectable parasitaemia in more than 18% of cases after treatment and indications of genetic relatedness between pre- and post-treatment infections warrants further investigation of a larger population for signs of reduced ACT efficacy in Nigeria.

Background: Rampant chloroquine/hydroxychloroquine poisoning in Nigerian hospitals following suggestions of its possible efficacy in the treatment and prevention of the newly emerged COVID-19 disease informed this survey. Objectives: The aim of this study was to assess the knowledge, attitude and perception of the Nigerian populace on the use of chloroquine in the COVID-19 pandemic. Methods: This cross-sectional study was done by administering an electronic questionnaire created using Google Docs, through social media cascade methods including the WhatsApp application software to capture data on chloroquine use between April 20 and June 20, 2020. Results: Six hundred and twenty-eight people responded to the questionnaire (response rate 99.2%, mean age 41.05 ± 12.3) from the six geopolitical zones in Nigeria with 556 (88.5%) having tertiary level education. Only 21 (3.3%) of the respondents took chloroquine for treatment or prevention. Respondents from the North-west geopolitical zones used chloroquine 5.8 (95% CI: 1.55, 21.52, p=0.02) more times than other zones while the age group 20-29 were 8.8 times more likely to use chloroquine than any other age group (95% CI: 3.53, 21.70, p = 0.00). Female respondents were 2.3 times more likely to use chloroquinethan the males (OR 2.26 95% CI: 0.90-5.68; p=0.08) and those in the income bracket of N75,000-99,000, 2.5 times more than other income groups. Conclusion: Young adults, North-western geopolitical zone, and female gender should be target groups for education on rational chloroquine use. The danger of chloroquine overdose should be communicated to the general population in Nigeria. Keywords: COVID-19; Chloroquine/hydroxychloroquine; self-medication; rational drug use.