Population structure and diversity of Plasmodium falciparum in children with asymptomatic malaria living in different ecological zones of Ghana

Plasmodium falciparum genetic diversity and multiplicity of infection based on msp-1, msp-2, glurp and microsatellite genetic markers in sub-Saharan Africa: a systematic review and meta-analysis

BACKGROUND

In sub-Saharan Africa (SSA), Plasmodium falciparum causes most of the malaria cases. Despite its crucial roles in disease severity and drug resistance, comprehensive data on Plasmodium falciparum genetic diversity and multiplicity of infection (MOI) are sparse in SSA. This study summarizes available information on genetic diversity and MOI, focusing on key markers (msp-1, msp-2, glurp, and microsatellites). The systematic review aimed to evaluate their influence on malaria transmission dynamics and offer insights for enhancing malaria control measures in SSA.

METHODS

The review was conducted following the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines. Two reviewers conducted article screening, assessed the risk of bias (RoB), and performed data abstraction. Meta-analysis was performed using the random-effects model in STATA version 17.

RESULTS

The review included 52 articles: 39 cross-sectional studies and 13 Randomized Controlled Trial (RCT)/cohort studies, involving 11,640 genotyped parasite isolates from 23 SSA countries. The overall pooled mean expected heterozygosity was 0.65 (95% CI: 0.51-0.78). Regionally, values varied: East (0.58), Central (0.84), Southern (0.74), and West Africa (0.69). Overall pooled allele frequencies of msp-1 alleles K1, MAD20, and RO33 were 61%, 44%, and 40%, respectively, while msp-2 I/C 3D7 and FC27 alleles were 61% and 55%. Central Africa reported higher frequencies (K1: 74%, MAD20: 51%, RO33: 48%) than East Africa (K1: 46%, MAD20: 42%, RO33: 31%). For msp-2, East Africa had 60% and 55% for I/C 3D7 and FC27 alleles, while West Africa had 62% and 50%, respectively. The pooled allele frequency for glurp was 66%. The overall pooled mean MOI was 2.09 (95% CI: 1.88-2.30), with regional variations: East (2.05), Central (2.37), Southern (2.16), and West Africa (1.96). The overall prevalence of polyclonal Plasmodium falciparum infections was 63% (95% CI: 56-70), with regional prevalences as follows: East (62%), West (61%), Central (65%), and South Africa (71%).

CONCLUSION

The study shows substantial regional variation in Plasmodium falciparum parasite genetic diversity and MOI in SSA. These findings suggest a need for malaria control strategies and surveillance efforts considering regional-specific factors underlying Plasmodium falciparum infection.

Effectiveness of artemether-lumefantrine for treating uncomplicated malaria in low- and high-transmission areas of Ghana

BACKGROUND

Artemisinin-based combination therapy (ACT) has been effective in the supervised treatment of uncomplicated malaria in Ghana. Since ACT usage is primarily unsupervised, this study aimed to determine the effectiveness of artemether-lumefantrine (AL) for treating malaria patients in two transmission settings in Ghana.

METHODS

Eighty-four individuals with uncomplicated Plasmodium falciparum malaria were recruited from Lekma Hospital (LH) in Accra (low-transmission area; N = 28), southern Ghana, and King's Medical Centre (KMC) in Kumbungu (high-transmission area; N = 56), northern Ghana. Participants were followed up for 28 days after unsupervised treatment with AL. The presence of asexual parasites was determined by microscopic examination of Giemsa-stained blood smears. Plasmodium species identification was confirmed using species-specific primers targeting the 18S rRNA gene. Parasite recrudescence or reinfection was determined by genotyping the Pfmsp 1 and Pfmsp 2 genes.

RESULTS

After AL treatment, 3.6% (2/56) of the patients from KMC were parasitaemic on day 3 compared to none from the LH patients. One patient from KMC with delayed parasite clearance on day 3 remained parasite-positive by microscopy on day 7 but was parasite-free by day 14. While none of the patients from LH experienced parasite recurrence during the 28-day follow-up, three and two patients from KMC had recurrent parasitaemia on days 21 and 28, respectively. Percentage reduction in parasite densities from day 1, 2, and 3 for participants from the KMC was 63.2%, 89.5%, and 84.5%. Parasite densities for participants from the LH reduced from 98.2%, 99.8% on day 1, and 2 to 100% on day 3. The 28-day cumulative incidence rate of treatment failure for KMC was 12.8% (95% confidence interval: 1.9-23.7%), while the per-protocol effectiveness of AL in KMC was 89.47%. All recurrent cases were assigned to recrudescence after parasite genotyping by Pfmsp 1 and Pfmsp 2.

CONCLUSION

While AL is efficacious in treating uncomplicated malaria in Ghana, when taken under unsupervised conditions, it showed an 89.4% PCR-corrected cure rate in northern Ghana, which is slightly below the WHO-defined threshold.

Molecular speciation of Plasmodium and multiplicity of P. falciparum infection in the Central region of Ghana

Malaria is endemic in the Central region of Ghana, however, the ecological and the seasonal variations of Plasmodium population structure and the intensity of malaria transmission in multiple sites in the region have not been explored. In this cross-sectional study, five districts in the region were involved. The districts were Agona Swedru, Assin Central and Gomoa East (representing the forest zone) and Abura-Asebu-Kwamankese and Cape Coast representing the coastal zone. Systematically, blood samples were collected from patients with malaria. The malaria status was screened with a rapid diagnostic test (RDT) kit (CareStart manufactured by Access Bio in Somerset, USA) and the positive ones confirmed microscopically. Approximately, 200 μL of blood was used to prepare four dried blood spots of 50μL from each microscopy positive sample. The Plasmodium genome was sequenced at the Malaria Genome Laboratory (MGL) of Wellcome Sanger Institute (WSI), Hinxton, UK. The single nucleotide polymorphisms (SNPs) in the parasite mitochondria (PfMIT:270) core genome aided the species identification of Plasmodium. Subsequently, the complexity of infection (COI) was determined using the complexity of infection likelihood (COIL) computational analysis. In all, 566 microscopy positive samples were sequenced. Of this number, Plasmodium genome was detected in 522 (92.2%). However, whole genome sequencing was successful in 409/522 (72.3%) samples. In total, 516/522 (98.8%) of the samples contained P. falciparum mono-infection while the rest (1.2%) were either P. falciparum/P. ovale (Pf/Po) (n = 4, 0.8%) or P. falciparum/P. malariae/P. vivax (Pf/Pm/Pv) mixed-infection (n = 2, 0.4%). All the four Pf/Po infections were identified in samples from the Assin Central municipality whilst the two Pf/Pm/Pv triple infections were identified in Abura-Asebu-Kwamankese district and Cape Coast metropolis. Analysis of the 409 successfully sequenced genome yielded between 1-6 P. falciparum clones per individual infection. The overall mean COI was 1.78±0.92 (95% CI: 1.55-2.00). Among the study districts, the differences in the mean COI between ecological zones (p = 0.0681) and seasons (p = 0.8034) were not significant. However, regression analysis indicated that the transmission of malaria was more than twice among study participants aged 15-19 years (OR = 2.16, p = 0.017) and almost twice among participants aged over 60 years (OR = 1.91, p = 0.021) compared to participants between 20-59 years. Between genders, mean COI was similar except in Gomoa East where females recorded higher values. In conclusion, the study reported, for the first time, P. vivax in Ghana. Additionally, intense malaria transmission was found to be higher in the 15-19 and > 60 years, compared to other age groups. Therefore, active surveillance for P. vivax in Ghana and enhanced malaria control measures in the 15-19 year group years and those over 60 years are recommended.

Amplicon deep sequencing of five highly polymorphic markers of Plasmodium falciparum reveals high parasite genetic diversity and moderate population structure in Ethiopia

BACKGROUND

Plasmodium falciparum genetic diversity can add information on transmission intensity and can be used to track control and elimination interventions.

METHODS

Dried blood spots (DBS) were collected from patients who were recruited for a P. falciparum malaria therapeutic efficacy trial in three malaria endemic sites in Ethiopia from October to December 2015, and November to December 2019. qPCR-confirmed infections were subject to amplicon sequencing of polymorphic markers ama1-D3, csp, cpp, cpmp, msp7. Genetic diversity, the proportion of multiclonal infections, multiplicity of infection, and population structure were analysed.

RESULTS

Among 198 samples selected for sequencing, data was obtained for 181 samples. Mean MOI was 1.38 (95% CI 1.24-1.53) and 17% (31/181) of infections were polyclonal. Mean He across all markers was 0.730. Population structure was moderate; populations from Metema and Metehara 2015 were very similar to each other, but distinct from Wondogent 2015 and Metehara 2019.

CONCLUSION

The high level of parasite genetic diversity and moderate population structure in this study suggests frequent gene flow of parasites among sites. The results obtained can be used as a baseline for additional parasite genetic diversity and structure studies, aiding in the formulation of appropriate control strategies in Ethiopia.

Modelling the relative cost-effectiveness of the RTS,S/AS01 malaria vaccine compared to investment in vector control or chemoprophylaxis

BACKGROUND

The World Health Organization has recommended a 4-dose schedule of the RTS,S/AS01 (RTS,S) vaccine for children in regions of moderate to high P. falciparum transmission. Faced with limited supply and finite resources, global funders and domestic malaria control programs will need to examine the relative cost-effectiveness of RTS,S and identify target areas for vaccine implementation relative to scale-up of existing interventions.

METHODS

Using an individual-based mathematical model of P. falciparum, we modelled the cost-effectiveness of RTS,S across a range of settings in sub-Saharan Africa, incorporating various rainfall patterns, insecticide-treated net (ITN) use, treatment coverage, and parasite prevalence bands. We compare age-based and seasonal RTS,S administration to increasing ITN usage, switching to next generation ITNs in settings experiencing insecticide-resistance, and introduction of seasonal malaria chemoprevention (SMC) in areas of seasonal transmission.

RESULTS

For RTS,S to be the most cost-effective intervention option considered, the maximum cost per dose was less than $9.30 USD in 90.9% of scenarios. Nearly all (89.8%) values at or above $9.30 USD per dose were in settings with 60% established bed net use and / or with established SMC, and 76.3% were in the highest PfPR_2-10 band modelled (40%). Addition of RTS,S to strategies involving 60% ITN use, increased ITN usage or a switch to PBO nets, and SMC, if eligible, still led to significant marginal case reductions, with a median of 2,653 (IQR: 1,741 to 3,966) cases averted per 100,000 people annually, and 82,270 (IQR: 54,034 to 123,105) cases averted per 100,000 fully vaccinated children (receiving at least three doses).

CONCLUSIONS

Use of RTS,S results in reductions in malaria cases and deaths even when layered upon existing interventions. When comparing relative cost-effectiveness, scale up of ITNs, introduction of SMC, and switching to new technology nets should be prioritized in eligible settings.

Genetic diversity and natural selection of rif gene (PF3D7_1254800) in the Plasmodium falciparum global populations

To reveal the genetic characteristics of one member of the Plasmodium falciparum repetitive interspersed family (rif), we sequenced the rif gene (PF3D7_1254800) in 53 field isolates collected from Ghana-imported cases into China and compared them with 350 publicly available P. falciparum rif sequences from global populations. In the Ghana-imported population, the nucleotide diversities were 0.05714 and 0.06616 for the full length and variable region of rif gene, respectively. Meanwhile, 22 and 20 haplotypes were identified for the full length and variable region of rif gene (Hd = 0.843 and 0.838, respectively). Diversity of rif gene in Ghana-imported population was higher than that observed in Cambodia, Thailand, Vietnam, Myanmar, Mali, Ghana, and Senegal populations. In this analysis, we found high genetic diversity of rif gene in global P. falciparum populations and identified 158 haplotypes. Tajima's D-test shows that there are large differences in the direction of selection between the conserved and variable region of rif gene. Tajima's D value for the variable region was 0.20074, indicating that balancing selection existed in this region. We found that the variable region was the main target of selection for positive diversification, and most mutation sites were located in this region. The population structure suggested optimized cluster values of K = 6. The five groups in Ghana-imported population included a unique subpopulation. Our results reveal the dynamics of the rif gene (PF3D7_1254800) in P. falciparum populations, which can aid in the rational design of P. falciparum rif-based vaccines.

Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa

Recent developments in molecular biology and genomics have revolutionized biology and medicine mainly in the developed world. The application of next generation sequencing (NGS) and CRISPR-Cas tools is now poised to support endemic countries in the detection, monitoring and control of endemic diseases and future epidemics, as well as with emerging and re-emerging pathogens. Most low and middle income countries (LMICs) with the highest burden of infectious diseases still largely lack the capacity to generate and perform bioinformatic analysis of genomic data. These countries have also not deployed tools based on CRISPR-Cas technologies. For LMICs including Tanzania, it is critical to focus not only on the process of generation and analysis of data generated using such tools, but also on the utilization of the findings for policy and decision making. Here we discuss the promise and challenges of NGS and CRISPR-Cas in the context of malaria as Africa moves towards malaria elimination. These innovative tools are urgently needed to strengthen the current diagnostic and surveillance systems. We discuss ongoing efforts to deploy these tools for malaria detection and molecular surveillance highlighting potential opportunities presented by these innovative technologies as well as challenges in adopting them. Their deployment will also offer an opportunity to broadly build in-country capacity in pathogen genomics and bioinformatics, and to effectively engage with multiple stakeholders as well as policy makers, overcoming current workforce and infrastructure challenges. Overall, these ongoing initiatives will build the malaria molecular surveillance capacity of African researchers and their institutions, and allow them to generate genomics data and perform bioinformatics analysis in-country in order to provide critical information that will be used for real-time policy and decision-making to support malaria elimination on the continent.

Ecological and seasonal variations and other factors associated with clinical malaria in the Central Region of Ghana: A cross-sectional study

BACKGROUND

This study investigated malaria transmission under various contrasting settings in the Central Region, a malaria endemic region in Ghana.

METHODS

This cross-sectional study was carried out in five randomly selected districts in the Central Region of Ghana. Three of the districts were forested, while the rest was coastal. Study participants were selected to coincide with either the regular rainy or dry season. From each study site, hospital attendees were randomly selected with prior consent. Consciously, study participants were selected in both rainy (September and October, 2020) and dry (November and December, 2020) seasons. Clinical data for each patient was checked for clinical malaria suspicion and microscopic confirmation of malaria. Using SPSS Version 24 (Chicago, IL, USA), bivariate analysis was done to determine the association of independent variables (ecological and seasonal variations) with malaria status. When the overall analysis did not yield significant association, further statistical analysis was performed after stratification of variables (into age and gender) to determine whether any or both of them would significantly associate with the dependent variable.

RESULTS

Of the 3993 study participants, 62.5% were suspected of malaria whereas 38.2% were confirmed to have clinical falciparum malaria. Data analysis revealed that in both rainy and dry seasons, malaria cases were significantly higher in forested districts ) than coastal districts (x2 = 217.9 vs x2 = 50.9; p < 0.001). Taken together, the risk of malaria was significantly higher in the dry season (COR = 1.471, p < 0.001) and lower in coastal zones (COR = 0.826, p = 0.007). There was significant reduced risk of participants aged over 39 years of malaria (COR=0.657, p < 0.001). Whereas, in general patients between 10 and 19 years were insignificantly less likely to have malaria (COR = 0.911, p = 0.518) compared to participants aged less than< 10 years, the reverse was observed in coastal districts where patients less than 10 years of age in coastal districts were less likely to have malaria (COR=2.440, p = 0.003). In general, gender did not associate with malaria, but when stratified by study district, the risk of female gender to malaria was significantly higher in Agona Swedru (COR = 5.605, p < 0.001), Assin central (COR = 2.172, p < 0.001), Awutu Senya (COR = 2.410, p < 0.001) and Cape Coast (COR = 3.939, p < 0.001) compared to Abura-Asebu-Kwamankese.

CONCLUSION

This study demonstrated that the predictors of malaria differ from one endemic area to another. Therefore, malaria control interventions such as distribution of long-lasting insecticide treated bed nets, residual spraying with insecticide and mass distribution of antimalaria prophylaxis must be intensified in forested districts in all seasons with particular attention on females.