Study site
This study is part of an ongoing program initiated in the villages of Dielmo and Ndiop (Fatick region, Senegal) in 1990 and 1993 respectively. The project consists of long-term investigations on host-parasite relationships and the study of the mechanisms of protective immunity against malaria [29]. Ndiop is located 280 km from the capital Dakar and about 15 km north of the Gambian border. At the beginning of the study, Ndiop was a mesoendemic area with a moderate seasonal malaria transmission [30]. Vector control was implemented in July 2008 and long-lasting insecticide-treated nets (LLINs) were provided to each household [31]. The EIR was estimated to 20 infective bites/person/year in 1993 [32], 79 in 2000 and 4.6 in 2010 [33]. Microscopic parasite prevalence followed the same trend as EIR with 50%, 7% [33], 0.27% and 0% [34] in 2000, 2010, 2014 and 2015 respectively. From 2014, parasite prevalence in Ndiop has become predominantly submicroscopic with community-based prevalence estimated by qPCR to 12.5 % and 6.4 % in 2014 and 2015, respectively. The majority of these infections (95.5 %) were due to P. falciparum [34].
Ethical consideration
The Dielmo/Ndiop project was approved by the Senegalese Ministry of Health and National Ethics Committee for Health Research of Senegal [35]. Informed written consent was initially obtained from individuals, parents or guardians of children and was regularly renewed.
Sample collection and study design
The samples used in this study were collected during a cross-sectional survey conducted at the village level in June 2016 (just before the malaria transmission season) in Ndiop. A venous blood sample was taken from each participant, and thick and thin blood smears were prepared for malaria diagnosis by microscopy. Plasma and blood pellets were separated and stored at -20°C for serological and molecular analysis respectively.
The study involved 353 venous samples from individuals over 5 years of age. Children less than 5 years, whose blood was collected on capillary tubes, were excluded because DNA extraction required 200 µl globular pellet. The microscopic parasite prevalence was determined by examination of thick and thin blood smears stained with Giemsa. The submicroscopic parasite prevalence was determined by real-time PCR (qPCR). In order to compare parasite prevalence and IgG seroprevalence, all 353 samples were tested for IgG against the crude schizont antigen of a local P. falciparum strain using the ELISA technique. A first set of 45 qPCR positive samples were genotyped at the msp-2 locus to investigate parasite genetic diversity. A second set of age-matched cohort of 110 individuals between qPCR positive (N=55) and qPCR negative (N=55) samples was used to analyze the impact of submicroscopic carriage of Plasmodium on the antibody responses. An age-stratified analysis was done with three age groups: under 10 years, 10-15 years and over 15 years old.
Microscopic examination
Thick and thin smears were stained with 10% Giemsa for 25 minutes and microscopically examined for determination of parasite density and identification of Plasmodium species. The number of parasites per 200 white blood cells in thick films was recorded and parasite density was estimated by counting the number of leucocytes by field examined and by arbitrarily considering that 8,000 leucocytes were present in 1µl of blood. At least two hundred thick-film fields were examined before a slide was declared negative. Each slide was read by two experienced microscopists and in the case of a discrepancy, a third microscopist examined the slide. A slide was considered positive after two concordant readings.
Molecular detection and characterization of Plasmodium species
The detection of Plasmodium spp was carried out by qPCR following genomic DNA isolation of Plasmodium parasites using QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. Extraction was performed from 200 μl of packed red blood cells, and. the DNA was recovered in 50 μl of elution buffer provided with the kit into a properly labelled 1.5 ml Eppendorf tube and was stored at - 20°C until used.
Parasite diagnostic by qPCR was based on melt curve comparison against negative and positive controls using “screening real-time PCR” with genus-specific primers targeting the Plasmodium cytochrome b gene [34]. Briefly, a 20 μl mix was prepared with 4 μl of 5X Evagreen qPCR Master Mix (Solis Biodyne), 0.3 μl of each primer (10 μM), 5 μl of genomic DNA and 10.4 μl distilled water. Primers and running programs were as described by Carnier et al. [36].
Identification of Plasmodium species was carried out using a nested PCR technique with primers targeting the Plasmodium spp. 18S small sub-unit ribosomal RNA (18S ssrRNA) gene. A volume of 5 µl from the primary PCR amplification with Plasmodium genus-specific rPLU 5 and rPLU6 primers pairs is used as a template for the second PCR. The primer pairs: rFAL1 and rFAL2 for P. falciparum, rVIV1 and rVIV2 for P. vivax, rOVA1 and rOVA2 for P. ovale and rMAL1 and rMAL2 for P. malariae were synthesized from TIB MOLbIOL (Germany). The PCR conditions were described by Zhou et al. 2014 [37]. The expected sizes for the different species were: 120 bp for P. vivax, 144 bp for P. malariae, 205 bp for P. falciparum, 375 bp for P. ovale.
msp-2 genotyping
DNA from 45 qPCR P. falciparum positive samples was genotyped by nested PCR amplification of the highly polymorphic region of msp-2 gene (block 3) as described previously [38, 39]. All primers used were synthesized from Tib Molbiol (Germany). In the primary reaction, the primers used span the entire msp-2 block 3. The initial amplification was followed by individual nested PCR reactions using primers specific for FC27 and 3D7 allelic families of msp-2. In the first PCR, 5 μl of DNA was amplified with 12.5 μl of 2×GMM (Go Taq Green Master Mix, Catalogue no M7113 Promega), 1 μl of each primer (10 μM) and sterile ultrapure water to a final volume of 25 μl. For the second PCR, 5 μl of product from the first PCR was amplified using 12.5 μl of 2× GMM (Go Taq Green Master Mix, M7113 Promega), 1 μl of each primer (10 μM) and sterile ultrapure water to a final volume of 25 μl. Positive and negative controls were included in each set of reactions. After amplification, 10 μl of each PCR product were separated by electrophoresis on a 1.5% agarose gel that was stained with ethidium bromide. The size of the PCR products was estimated using a DNA ladder (1 kb Plus DNA ladder, Invitrogen). Amplified DNA was visualized by ultraviolet trans-illumination using an E-GEL IMAGER (Life Technologies). Gel photographs were re-scored by visual comparison of DNA fragments and genotypes were identified according to band sizes for each individual sample. The size polymorphism for each allelic family was analyzed assuming that one band represented one amplified PCR fragment derived from a single copy of P. falciparum msp-2 gene.
Antigen preparation and ELISA assay
Crude schizont antigens from P. falciparum 0703 field-adapted strain [40] were prepared from in vitro continuous culture on O+ erythrocytes in RPMI medium containing 0.5 % Albumax [41]. The parasites were incubated in an atmosphere of 5% CO2, 5% O2, and 90% N2 generated with an adjustable gas-mixing device [42]. Schizonts stage parasites were harvested and lysed in three volumes of sterile distilled water and stored into aliquotes in liquid nitrogen [43]. The MSP3 antigen (clone T9/96) was an E. coli-expressed DG-210 purified protein 28 (kind gift from Dr C. Oeuvray) [44].The ELISA assay was performed as previously described [33, 44]. The 0703 crude extract was set to 1/3000 dilution by a dose-effect assay using positive control sera. Maxisorp plates (Nunc, Roskilde, Denmark) were coated with 100 μl of diluted crude extracts antigen in phosphate-buffered saline (PBS, pH 7.4). Non-infected red blood cell extracts were also tested for non-specific binding. MSP3 antigen was diluted to 1 μg/ml in PBS and 100 μl was used for coating the Immulon 4HBX plates (Thermo Fisher Scientific). All plates were incubated overnight at 4 °C and then washed four times with 200 μl/well of washing buffer (PBS containing 0.05% Tween 20). The wells were then blocked with 150 μl of blocking buffer (3% skimmed milk in washing buffer) for 1 hour. Plasma samples were diluted at 1/200 in a dilution buffer (1 % skimmed milk in PBS with 0.05 % Tween and 0.03% sodium azide) and 100μl of diluted sera were distributed in triplicate in the wells. Positive (a pool of 25 sera from clinically immune adults living in Dielmo) and negative (a pool of non‐immune Europeans) controls were included on each plate. Following incubation with sera and washing, polyclonal goat anti-human IgG (Life Technologies, USA) or goat anti-human IgM (Life technologies, USA) conjugated to peroxidase were added at a dilution of 1/6000 and 1/3000 in the dilution buffer (1 % skimmed milk in PBS-Tween 0.05 %) respectively. Bound peroxidase was detected with 100 μl of substrate solution (TMB Solution; Thermo Fisher Scientific Inc.) for 30 min and the enzymatic reaction stopped by addition of 50 μl of 0.2 mM sulfuric acid. The optical density (OD) at 450 nm was read in a BIO-RAD Microplate Reader (iMark).
Parameters definition and statistical analysis
Genetic parameters
The frequency of allelic families was expressed as the percentage of fragments assigned to one allelic family or combination of allelic families out of the total number of fragments detected for msp-2 gene. The complexity of infection (COI), also referred as the multiplicity of infection (MOI) or number of genotypes per infection was calculated by dividing the total number of fragments detected in msp-1 or msp-2 by the number of samples positive for the same marker. Multiple infections (MI) or polyclonal infections corresponded to the proportion of isolates with more than one amplified PCR fragment. Expected heterozygosity (HE) was defined as the probability of being infected by two parasites with different alleles at a given locus. Result of HE ranging from 0 to 1 was calculated by using the following formula: HE=[n/(n−1)][(1−∑pi2)], where n is the number of isolates sampled and pi is the allele frequency at a given locus.
Immunological parameters
Results were expressed as optical density (OD) ratio calculated as follow: mean OD sample/mean OD naive serum pool. Sera with an OD ratio > 2 were considered as positive response for prevalence calculations [44] (Mbengue, B et al., 2019). Variations between tests for positive controls should not exceed 20 %. The Plate to plate reproducibility was considered satisfactory with coefficients of variation not exceeding 4 % using two positive controls, two negative controls and the same antigen for each plate.
Statistical analysis
Association between the prevalence of sub-microscopic P. falciparum carriage (qPCR+) and seroprevalence (IgG+ against crude schizont extract of strain 0703) was analyzed using the chi-square test. Mean OD ratio differences between qPCR positive and qPCR negative groups were calculated using Student's t-test. Differences were considered significant when p-value was less than 0.05. All analyses were performed using R software (version 3.6.1).