Browsing by Author "Pereus, Dativa"

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Genetic diversity of Plasmodium falciparum reticulocyte binding protein homologue-5, which is a potential malaria vaccine candidate: baseline data from areas of varying malaria endemicity in Mainland Tanzania
(BioMed Central, 2025-01-27) Kisambale, Angelina; Pereus, Dativa; Mandai, Salehe; Lyimo, Beatus; Bakari, Catherine; Chacha, Gervas; Mbwambo, Ruth; Moshi, Ramadhan; Petro, Daniel; Challe, Daniel; Seth, Misago; Madebe, Rashid; Budodo, Rule; Aaron, Sijenunu; Mbwambo, Daniel; Lusasi, Abdallah; Kajange, Stella; Lazaro, Samwel; Kapologwe, Ntuli; Mandara, Celine; Ishengoma, Deus
Background The limited efficacy of the two recently approved malaria vaccines, RTS,S/AS01 and R21/Matrix- M™, highlights the need for alternative vaccine candidate genes. Plasmodium falciparum Reticulocyte Binding Protein Homologue 5 (Pfrh5) is a promising malaria vaccine candidate, given its limited polymorphism, its essential role in parasite survival, a lack of immune selection pressure and higher efficacy against multiple parasites strains. This study evaluated the genetic diversity of Pfrh5 gene among parasites from regions with varying malaria transmission intensities in Mainland Tanzania, to generate baseline data for this potential malaria vaccine candidate. Methods This study utilized secondary data of 697 whole-genome sequences which were generated by the MalariaGEN Community Network. The samples which were sequenced to generated the data were collected between 2010 and 2015 from five districts within five regions of Mainland Tanzania, with varying endemicities (Morogoro-urban district in Morogoro region, Muheza in Tanga, Kigoma-Ujiji in Kigoma, Muleba in Kagera, and Nachingwea district in Lindi region). Wright's fixation index (FST), Wright’s inbreeding coefficient (Fws), Principal component analysis (PCA), nucleotide diversity (π), haplotype network, haplotype diversity (Hd), Tajima's D, and Linkage disequilibrium (LD) were used to assess the diversity of the gene. Results Of the sequences used in this study, 84.5% (n = 589/697) passed quality control and 313 (53.1%) were monoclonal (contained infections from a single strain of P. falciparum) and were used for haplotype diversity and haplotype network analysis. High within-host diversity (Fws < 0.95) was reported in Kigoma-Ujiji (60.7%), Morogoro-urban (53.1%), and Nachingwea (50.8%), while Muleba (53.9%) and Muheza (61.6%) had low within-host diversity (Fws ≥ 0.95). PCA did not show any population structure and the mean FST value was 0.015. Low nucleotide diversity values were observed across the study sites (mean π = 0.00056). A total of 27 haplotypes were observed among the 313 monoclonal samples and under-fives exhibited higher haplotype counts. The Pf3D7 was detected as Hap_1, which occurred in 16/313 (5.1%) monoclonal sequences. Negative Tajima's D values were observed among the parasite populations in all the study sites. Conclusion Low levels of polymorphism in the pfrh5 gene were observed based on low nucleotide and haplotype diversity, a lack of population structure and negative Tajima’s D values. This study provides essential data on the diversity of the Pfrh5 gene indicating that it can be considered in the development of the next generation malaria vaccines. Robust and intensive studies of this and other candidate genes are crucial to support the prioritization of the Pfrh5 gene for potential inclusion in a broadly cross-protective malaria vaccine
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
(Frontiers, 2022-07-13) Lyimo, Beatus; Popkin-Hall, Zachary; Giesbrecht, David; Mandara, Celine; Madebe, Rashid; Bakari, Catherine; Pereus, Dativa; Seth, Misago; Ngamba, Ramadhan; Mbwambo, Ruth; MacInnis, Bronwyn; Mbwambo, Daniel; Garimo, Issa; Chacky, Frank; Aaron, Sijenunu; Lusasi, Abdallah; Molteni, Fabrizio; Njau, Ritha; Cunningham, Jane; Lazaro, Samwel; Mohamed, Ally; Juliano, Jonathan; Bailey, Jeffrey; Ishengoma, Deus
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.
Prevalence of subpatent Plasmodium falciparum infections in regions with varying transmission intensities and implications for malaria elimination in Mainland Tanzania
(PMC PubMed Central, 2025-03-26) Seth, Misago; Popkin-Hall, Zachary; Madebe, Rashid; Budodo, Rule; Bakari, Catherine; Lyimo, Beatus; Giesbrecht, David; Moshi, Ramadhani; Mbwambo, Ruth; Francis, Filbert; Pereus, Dativa; Mbata, Doris; Challe, Daniel; Mandai, Salehe; Chacha, Gervas A; Kisambale, Angelina; Mbwambo, Daniel; Aaron, Sijenunu; Lusasi, Abdallah; Lazaro, Samwel; Mandara, Celine; Bailey, Jeffrey; Juliano, Jonathan; Gutman, Julie; Ishengoma, Deus
Background Subpatent Plasmodium falciparum infections, defined as infections with parasite density below the detection limit of routine malaria diagnostic tests, contribute to infectious reservoirs, sustain transmission, and cause the failure of elimination strategies in target areas. This study assessed the prevalence of subpatent P. falci parum infections and associated risk factors in 14 regions of Mainland Tanzania. Methods The study used samples randomly selected from RDT‑negative dried blood spots (DBS) (n = 2685/10,101) collected in 2021 at 100 health facilities across 10 regions of Mainland Tanzania, and four communities in four addi tional regions. The regions were selected from four transmission strata; high (five regions), moderate (three regions), low (three regions), and very low (three regions). DNA was extracted by Tween‑Chelex method, and the Pf18S rRNA gene was amplified by quantitative polymerase chain reaction (qPCR). Logistic regression analysis was used to assess the associations between age groups, sex, fever status, and transmission strata with subpatent infection status, while linear regression analysis was used to assess the association between these factors and subpatent parasite density. Results Of the selected samples, 525/2685 (19.6%) were positive by qPCR for P. falciparum, and the positivity rates varied across different regions. Under‑fives (aOR: 1.4, 95% CI 1.04–1.88; p < 0.05) from health facilities had higher odds of subpatent infections compared to other groups, while those from community surveys (aOR: 0.33, 95% CI 0.15–0.72; p = 0.005) had lower odds. Participants from very low transmission stratum had significantly lower odds of subpatent infection compared to those from high transmission stratum (aOR = 0.53, 95% CI = 0.37–0.78; p < 0.01). The log‑trans formed median parasite density (interquartile range) was 6.9 (5.8–8.5) parasites/µL, with significantly higher parasitae mia in the low transmission stratum compared to a very low one (11.4 vs 7.0 parasites/µL, p < 0.001). Conclusion Even in very low transmission settings, the prevalence of subpatent infections was 13%, and in low trans mission settings it was even higher at 29.4%, suggesting a substantial reservoir that is likely to perpetuate transmis sion but can be missed by routine malaria case management strategies. Thus, control and elimination programmes may benefit from adoption of more sensitive detection methods to ensure that a higher proportion of subpatent infections are detected.
Trends of malaria prevalence among individuals from rural communities in three regions with varying transmission intensities in Mainland Tanzania; Data from 2021 - 2023 community cross-sectional surveys
(medRxiv, 2025-02-14) Challe, Daniel; Petro, Daniel; Francis, Filbert; Seth, Misago; Madebe, Rashid; Mandai, Salehe; Budodo, Rule; Kisambale, Angelina; Chacha, Gervas; Moshi, Ramadhan; Mbwambo, Ruth; Pereus, Dativa; Bakari, Catherine; Mbata, Doris; Lyimo, Beatus; Kanyankole, Grace; Aaron, Sijenunu; Mbwambo, Daniel; Kajange, Stella; Lazaro, Samwel; Kapologwe, Ntuli; Mandara, Celine; Makene, Vedastus; Deus S. Ishengoma
Background Recent reports showed the persistence of malaria transmission and disease burden in rural communities, which have limited the impact of ongoing control and elimination strategies. This study investigated the trends of malaria prevalence among community members from three regions of Mainland Tanzania with varying transmission intensities. Methods Community surveys were conducted from 2021 to 2023 and involved individuals aged ≥6 months in three regions Kigoma and Ruvuma (with high malaria transmission intensities) and Tanga (moderate transmission). Interviews were conducted using structured questionnaires, to collect anthropometric, clinical, parasitological (testing for malaria using rapid diagnostic tests (RDTs), type of house and socio-economic status (SES) data. Modified Poisson regression was used to identify factors associated with malaria infections and the results were presented as crude (cPR) and adjusted prevalence ratios (aPR). Results Malaria infections by RDTs were detected in 1,896 (23.2%, n=8,166) individuals, with significant variations across regions and years (22.9% in 2021, 20.6% in 2022, and 26.9% in 2023; p<0.001). The highest prevalence of malaria infections was in Kigoma in 2023 (35.6%) while the lowest was in Tanga in 2022 (10.5%). School children (5 – <15 years) had significantly higher prevalence (38.2% in 2021, 26.2% in 2022, and 34.4% in 2023 (p<0.001) as did males (26.7% in 2021, 25.4% in 2022 and 31.2% in 2023, p<0.001). Higher likelihood of malaria infections was in school children (aPR: 1.94, 95% CI: 1.67 – 2.25, p<0.001), males (aPR=1.24 95%CI: 1.14–1.34, p<0.001), individuals living in traditional houses (aPR=1.14, 95% CI: 1.01 – 1.28, p = 0.037), among individuals with moderate (aPR=1.27, 95% CI: 1.13 – 1.43, p<0.001) or low SES (aPR = 1.39, 95% CI: 1.24 – 1.55, p<0.001), and those with fever at presentation (axillary temperature ≥37.5°C; aPR = 1.34, 95% CI: 1.09 – 1.64, p = 0.005) or fever history within 48 hours before the survey (aPR = 3.55, 95% CI: 3.26–3.87, p<0.001). The likelihood of infections was also higher in Ruvuma (aPR=1.98, 95%CI: 1.77–2.21, p<0.001) and Kigoma (aPR=1.28, 95%CI: 1.15–1.42, p<0.001) regions compared to Tanga. The likelihood of malaria infections was similar among participants based on bed net ownership (aPR: 1.27, 95%CI: 0.80 – 2.01, p = 0.306) or use (aPR: 1.01, 95%CI: 0.64 – 1.50, p=0.920). Conclusion The study showed spatial and temporal variations of malaria prevalence, with the highest prevalence in 2023 and the lowest in 2022. Groups at higher risk of malaria infections included school children, males, participants with fever, low or moderate SES, and those who lived in traditional houses. Targeted interventions are urgently needed for areas with persistently high transmission and vulnerable groups, particularly in rural communities.