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Mandai SS, Francis F, Challe DP, Seth MD, Madebe RA, Petro DA, Budodo R, Kisambale AJ, Chacha GA, Moshi R, Mbwambo RB, Pereus D, Bakari C, Aaron S, Mbwambo D, Lusasi A, Kajange S, Lazaro S, Kapologwe N, Mandara CI, Ishengoma DS. High prevalence and risk of malaria among asymptomatic individuals from villages with high prevalence of artemisinin partial resistance in Kyerwa district of Kagera region, north-western Tanzania. Malar J 2024; 23:197. [PMID: 38926854 PMCID: PMC11201325 DOI: 10.1186/s12936-024-05019-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Although Tanzania adopted and has been implementing effective interventions to control and eventually eliminate malaria, the disease is still a leading public health problem, and the country experiences heterogeneous transmission. Recent studies reported the emergence of parasites with artemisinin partial resistance (ART-R) in Kagera region with high prevalence (> 10.0%) in two districts of Karagwe and Kyerwa. This study assessed the prevalence and predictors/risk of malaria infections among asymptomatic individuals living in a hyperendemic area where ART-R has emerged in Kyerwa District of Kagera region, north-western Tanzania. METHODS This was a community-based cross-sectional survey which was conducted in July and August 2023 and involved individuals aged ≥ 6 months from five villages in Kyerwa district. Demographic, anthropometric, clinical, parasitological, type of house inhabited and socio-economic status (SES) data were collected using electronic capture tools run on Open Data Kit (ODK) software. Predictors/risks of malaria infections were determined by univariate and multivariate logistic regression, and the results were presented as crude (cORs) and adjusted odds ratios (aORs), with 95% confidence intervals (CIs). RESULTS Overall, 4454 individuals were tested using rapid diagnostic tests (RDTs), and 1979 (44.4%) had positive results. The prevalence of malaria infections ranged from 14.4% to 68.5% and varied significantly among the villages (p < 0.001). The prevalence and odds of infections were significantly higher in males (aOR = 1.28, 95% CI 1.08 -1.51, p = 0.003), school children (aged 5-≤10 years (aOR = 3.88, 95% CI 3.07-4.91, p < 0.001) and 10-≤15 years (aOR = 4.06, 95% CI 3.22-5.13, p < 0.001)) and among individuals who were not using bed nets (aOR = 1.22, 95% CI 1.03-1.46, p = 0.024). The odds of malaria infections were also higher in individuals with lower SES (aOR = 1.42, 95% CI 1.17-1.72, p < 0.001), and living in houses without windows (aOR = 2.08, 95% CI 1.46-2.96, p < 0.001), partially open (aOR = 1.33, 95% CI 1.11-1.58, p = 0.002) or fully open windows (aOR = 1.30, 95%CI 1.05-1.61, p = 0.015). CONCLUSION The five villages had a high prevalence of malaria infections and heterogeneity at micro-geographic levels. Groups with higher odds of malaria infections included school children, males, and individuals with low SES, living in poorly constructed houses or non-bed net users. These are important baseline data from an area with high prevalence of parasites with ART-R and will be useful in planning interventions for these groups, and in future studies to monitor the trends and potential spread of such parasites, and in designing a response to ART-R.
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Affiliation(s)
- Salehe S Mandai
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Filbert Francis
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | - Daniel P Challe
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | - Misago D Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rashid A Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Rule Budodo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Gervas A Chacha
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Ramadhan Moshi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Ruth B Mbwambo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | | | - Stella Kajange
- President's Office, Regional Administration and Local Government, Dodoma, Tanzania
| | - Samuel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ntuli Kapologwe
- Directorate of Preventive Services, Ministry of Health, Dodoma, Tanzania
| | - Celine I Mandara
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania.
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia.
- Harvard T.H Chan School of Public Health, Harvard University, Boston, MA, USA.
- Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania.
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Lyimo BM, Bakari C, Popkin-Hall ZR, Giesbrecht DJ, Seth MD, Pereus D, Shabani ZI, Moshi R, Boniface R, Mandara CI, Madebe R, Juliano JJ, Bailey JA, Ishengoma DS. Genetic polymorphism and evidence of signatures of selection in the Plasmodium falciparum circumsporozoite protein gene in Tanzanian regions with different malaria endemicity. Malar J 2024; 23:139. [PMID: 38720288 PMCID: PMC11080125 DOI: 10.1186/s12936-024-04974-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND In 2021 and 2023, the World Health Organization approved RTS,S/AS01 and R21/Matrix M malaria vaccines, respectively, for routine immunization of children in African countries with moderate to high transmission. These vaccines are made of Plasmodium falciparum circumsporozoite protein (PfCSP), but polymorphisms in the gene raise concerns regarding strain-specific responses and the long-term efficacy of these vaccines. This study assessed the Pfcsp genetic diversity, population structure and signatures of selection among parasites from areas of different malaria transmission intensities in Mainland Tanzania, to generate baseline data before the introduction of the malaria vaccines in the country. METHODS The analysis involved 589 whole genome sequences generated by and as part of the MalariaGEN Community Project. The samples were collected between 2013 and January 2015 from five regions of Mainland Tanzania: Morogoro and Tanga (Muheza) (moderate transmission areas), and Kagera (Muleba), Lindi (Nachingwea), and Kigoma (Ujiji) (high transmission areas). Wright's inbreeding coefficient (Fws), Wright's fixation index (FST), principal component analysis, nucleotide diversity, and Tajima's D were used to assess within-host parasite diversity, population structure and natural selection. RESULTS Based on Fws (< 0.95), there was high polyclonality (ranging from 69.23% in Nachingwea to 56.9% in Muheza). No population structure was detected in the Pfcsp gene in the five regions (mean FST = 0.0068). The average nucleotide diversity (π), nucleotide differentiation (K) and haplotype diversity (Hd) in the five regions were 4.19, 0.973 and 0.0035, respectively. The C-terminal region of Pfcsp showed high nucleotide diversity at Th2R and Th3R regions. Positive values for the Tajima's D were observed in the Th2R and Th3R regions consistent with balancing selection. The Pfcsp C-terminal sequences revealed 50 different haplotypes (H_1 to H_50), with only 2% of sequences matching the 3D7 strain haplotype (H_50). Conversely, with the NF54 strain, the Pfcsp C-terminal sequences revealed 49 different haplotypes (H_1 to H_49), with only 0.4% of the sequences matching the NF54 strain (Hap_49). CONCLUSIONS The findings demonstrate high diversity of the Pfcsp gene with limited population differentiation. The Pfcsp gene showed positive Tajima's D values, consistent with balancing selection for variants within Th2R and Th3R regions. The study observed differences between the intended haplotypes incorporated into the design of RTS,S and R21 vaccines and those present in natural parasite populations. Therefore, additional research is warranted, incorporating other regions and more recent data to comprehensively assess trends in genetic diversity within this important gene. Such insights will inform the choice of alleles to be included in the future vaccines.
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Affiliation(s)
- Beatus M Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania.
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | - Misago D Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Zulfa I Shabani
- Dar Es Salaam University College of Education, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Ramadhan Moshi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Ruth Boniface
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Celine I Mandara
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rashid Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | - Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia
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3
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Ngasala B, Chacky F, Mohamed A, Molteni F, Nyinondi S, Kabula B, Mkali H, Thwai K, Popkin-Hall ZR, Mitchell C, Parr JB, Juliano JJ, Lin JT. Evaluation of Malaria Rapid Diagnostic Test Performance and pfhrp2 Deletion in Tanzania School Surveys, 2017. Am J Trop Med Hyg 2024; 110:887-891. [PMID: 38507797 PMCID: PMC11066367 DOI: 10.4269/ajtmh.23-0771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/02/2024] [Indexed: 03/22/2024] Open
Abstract
As part of malaria nationwide monitoring and evaluation initiatives, there is an increasing trend of incorporating malaria rapid diagnostic tests (mRDTs) in surveys conducted within primary schools to detect malaria parasites. However, mRDTs based on the detection of histidine-rich protein 2 (HRP2) are known to yield false-positive results due to persistent antigenemia, and false-negative results may result from low parasitemia or Plasmodium falciparum hrp2/3 gene deletion. We evaluated diagnostic performance of an HRP2 and pan-parasite lactate dehydrogenase (HRP2/pLDH) mRDT against polymerase chain reaction (PCR) for detection of P. falciparum among 17,051 primary school-age children from eight regions of Tanzania in 2017. According to PCR, the prevalence of P. falciparum was 19.2% (95% CI: 18.6-19.8). Using PCR as reference, the sensitivity and specificity of mRDT was 76.2% (95% CI: 74.7-77.7) and 93.9% (95% CI: 93.5-94.3), respectively. Test agreement was lowest in low transmission areas, where true-positive mRDTs were outnumbered by false-negatives due to low parasitemia. Discordant samples (mRDT-negative but PCR-positive) were screened for pfhrp2/3 deletion by real-time PCR. Among those with a parasite density sufficient for analysis, pfhrp2 deletion was confirmed in 60 samples, whereas pfhrp3 deletion was confirmed in two samples; one sample had both pfhrp2 and pfhrp3 deletions. The majority of samples with gene deletions were detected in the high-transmission Kagera region. Compared with mRDTs, PCR and other molecular methods offer increased sensitivity and are not affected by pfhrp2/3 deletions, making them a useful supplement to mRDTs in schools and other epidemiological surveys.
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Affiliation(s)
- Billy Ngasala
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | | | - Kyaw Thwai
- Institute for Global health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Zachary R. Popkin-Hall
- Institute for Global health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Cedar Mitchell
- Institute for Global health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Jonathan B. Parr
- Institute for Global health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Jonathan J. Juliano
- Institute for Global health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Jessica T. Lin
- Institute for Global health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
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Bailey A, Prist PR. Landscape and Socioeconomic Factors Determine Malaria Incidence in Tropical Forest Countries. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2024; 21:576. [PMID: 38791790 PMCID: PMC11121048 DOI: 10.3390/ijerph21050576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/20/2024] [Accepted: 04/27/2024] [Indexed: 05/26/2024]
Abstract
Deforestation, landscape dynamics, and socioeconomic factors within the tropical Americas, Africa, and Asia may have different impacts on malaria incidence. To evaluate how these drivers affect malaria incidence at the global and regional scale, we collected malaria incidence rates from 2000 to 2019 from 67 tropical countries, along with forest loss, land use change types, and socioeconomic elements. LASSO regression, linear mixed effect modeling, and k-fold cross validation were used to create and evaluate the models. Regionality plays a role in the significance of varying risk factors. The Tropical Americas model had the highest coefficient of determination (marginal R2 = 0.369), while the Africa model showed the highest predictive accuracy with only a 17.4% error rate. Strong associations between tree cover loss (β = -4037.73, p < 0.001) and percentage forest area (β = 5373.18, p = 0.012) in Africa, and percent of key biodiversity areas under protection (β = 496.71, p < 0.001; β = 1679.20, p < 0.001) in the tropical Americas and Asia with malaria incidence indicates that malaria risk should be considered during conservation policy development, and recommends that individual approaches to policy and investment be considered when implementing malaria interventions on different spatial scales.
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Affiliation(s)
- Allison Bailey
- EcoHealth Alliance, 520 Eighth Ave., Ste. 1200, New York, NY 10018, USA;
| | - Paula R. Prist
- EcoHealth Alliance, 520 Eighth Ave., Ste. 1200, New York, NY 10018, USA;
- Future Earth, One Health, 413 Chukar Ct., Fort Collins, CO 80526, USA
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5
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Popkin-Hall ZR, Seth MD, Madebe RA, Budodo R, Bakari C, Francis F, Pereus D, Giesbrecht DJ, Mandara CI, Mbwambo D, Aaron S, Lusasi A, Lazaro S, Bailey JA, Juliano JJ, Ishengoma DS. Malaria Species Positivity Rates Among Symptomatic Individuals Across Regions of Differing Transmission Intensities in Mainland Tanzania. J Infect Dis 2024; 229:959-968. [PMID: 37992117 PMCID: PMC11011190 DOI: 10.1093/infdis/jiad522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Recent data indicate that non-Plasmodium falciparum species may be more prevalent than thought in sub-Saharan Africa. Although Plasmodium malariae, Plasmodium ovale spp., and Plasmodium vivax are less severe than P. falciparum, treatment and control are more challenging, and their geographic distributions are not well characterized. METHODS We randomly selected 3284 of 12 845 samples collected from cross-sectional surveys in 100 health facilities across 10 regions of Mainland Tanzania and performed quantitative real-time PCR to determine presence and parasitemia of each malaria species. RESULTS P. falciparum was most prevalent, but P. malariae and P. ovale were found in all but 1 region, with high levels (>5%) of P. ovale in 7 regions. The highest P. malariae positivity rate was 4.5% in Mara and 8 regions had positivity rates ≥1%. We only detected 3 P. vivax infections, all in Kilimanjaro. While most nonfalciparum malaria-positive samples were coinfected with P. falciparum, 23.6% (n = 13 of 55) of P. malariae and 14.7% (n = 24 of 163) of P. ovale spp. were monoinfections. CONCLUSIONS P. falciparum remains by far the largest threat, but our data indicate that malaria elimination efforts in Tanzania will require increased surveillance and improved understanding of the biology of nonfalciparum species.
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Affiliation(s)
- Zachary R Popkin-Hall
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Misago D Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rashid A Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rule Budodo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Filbert Francis
- National Institute for Medical Research, Tanga Center, Tanga, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - David J Giesbrecht
- Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Celine I Mandara
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | | | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
| | - Jonathan J Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
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6
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Lyimo BM, Bakari C, Popkin-Hall ZR, Giesbrecht DJ, Seth MD, Pereus D, Moshi R, Boniface R, Mandara CI, Madebe R, Juliano JJ, Bailey JA, Ishengoma DS. Genetic polymorphism and evidence of signatures of selection in the Plasmodium falciparum circumsporozoite protein gene in Tanzanian regions with different malaria endemicity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.23.24301587. [PMID: 38343796 PMCID: PMC10854334 DOI: 10.1101/2024.01.23.24301587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Background In 2021 and 2023, the World Health Organization approved RTS, S/AS01 and R21/Matrix M malaria vaccines, respectively, for routine immunization of children in African countries with moderate to high transmission. These vaccines are made of Plasmodium falciparum circumsporozoite protein (Pfcsp) but polymorphisms in this gene raises concerns regarding strain-specific responses and the long-term efficacy of these vaccines. This study assessed the Pfcsp genetic diversity, population structure and signatures of selection among parasites from areas of different malaria transmission in mainland Tanzania, to generate baseline data before the introduction of the malaria vaccines in the country. Methods The analysis involved 589 whole genome sequences generated by and as part of the MalariaGEN Community Project. The samples were collected between 2013 and January 2015 from five regions of mainland Tanzania: Morogoro and Tanga (Muheza) (moderate transmission areas), and Kagera (Muleba), Lindi (Nachingwea), and Kigoma (Ujiji) (high transmission areas). Wright's inbreeding coefficient (Fws), Wright's fixation index (FST), principal component analysis, nucleotide diversity, and Tajima's D were used to assess within-host parasite diversity, population structure and natural selection. Results Based on Fws (< 0.95), there was high polyclonality (ranged from 69.23% in Nachingwea to 56.9% in Muheza). No population structure was detected in the Pfcsp gene in the five regions (mean FST= 0.0068). The average nucleotide diversity (π), nucleotide differentiation (K) and haplotype diversity (Hd) in the five regions were 4.19, 0.973 and 0.0035, respectively. The C-terminal region of Pfcsp showed high nucleotide diversity at Th2R and Th3R regions. Positive values for the Tajima's D were observed in the Th2R and Th3R regions consistent with balancing selection. The Pfcsp C-terminal sequences had 50 different haplotypes (H_1 to H_50) and only 2% of sequences matched the 3D7 strain haplotype (H_50). Conclusions The findings demonstrate high diversity of the Pfcsp gene with limited population differentiation. The Pfcsp gene showed positive Tajima's D values for parasite populations, consistent with balancing selection for variants within Th2R and Th3R regions. This data is consistent with other studies conducted across Africa and worldwide, which demonstrate low 3D7 haplotypes and little population structure. Therefore, additional research is warranted, incorporating other regions and more recent data to comprehensively assess trends in genetic diversity within this important gene. Such insights will inform the choice of alleles to be included in the future vaccines.
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Affiliation(s)
- Beatus M. Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ramadhan Moshi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Ruth Boniface
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Rashid Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | - Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia
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Mayor A, Ishengoma DS, Proctor JL, Verity R. Sampling for malaria molecular surveillance. Trends Parasitol 2023; 39:954-968. [PMID: 37730525 PMCID: PMC10580323 DOI: 10.1016/j.pt.2023.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/22/2023]
Abstract
Strategic use of Plasmodium falciparum genetic variation has great potential to inform public health actions for malaria control and elimination. Malaria molecular surveillance (MMS) begins with a strategy to identify and collect parasite samples, guided by public-health priorities. In this review we discuss sampling design practices for MMS and point out epidemiological, biological, and statistical factors that need to be considered. We present examples for different use cases, including detecting emergence and spread of rare variants, establishing transmission sources and inferring changes in malaria transmission intensity. This review will potentially guide the collection of samples and data, serve as a starting point for further methodological innovation, and enhance utilization of MMS to support malaria elimination.
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Affiliation(s)
- Alfredo Mayor
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; Department of Physiologic Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique.
| | - Deus S Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania; Faculty of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia; Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Joshua L Proctor
- Institute for Disease Modeling in Global Health, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, UK
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8
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Kioko M, Pance A, Mwangi S, Goulding D, Kemp A, Rono M, Ochola-Oyier LI, Bull PC, Bejon P, Rayner JC, Abdi AI. Extracellular vesicles could be a putative posttranscriptional regulatory mechanism that shapes intracellular RNA levels in Plasmodium falciparum. Nat Commun 2023; 14:6447. [PMID: 37833314 PMCID: PMC10575976 DOI: 10.1038/s41467-023-42103-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Plasmodium falciparum secretes extracellular vesicles (PfEVs) that contain parasite-derived RNA. However, the significance of the secreted RNA remains unexplored. Here, we compare secreted and intracellular RNA from asexual cultures of six P. falciparum lines. We find that secretion of RNA via extracellular vesicles is not only periodic throughout the asexual intraerythrocytic developmental cycle but is also highly conserved across P. falciparum isolates. We further demonstrate that the phases of RNA secreted via extracellular vesicles are discernibly shifted compared to those of the intracellular RNA within the secreting whole parasite. Finally, transcripts of genes with no known function during the asexual intraerythrocytic developmental cycle are enriched in PfEVs compared to the whole parasite. We conclude that the secretion of extracellular vesicles could be a putative posttranscriptional RNA regulation mechanism that is part of or synergise the classic RNA decay processes to maintain intracellular RNA levels in P. falciparum.
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Affiliation(s)
- Mwikali Kioko
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Open University, Milton Keynes, UK
| | - Alena Pance
- Pathogens and Microbes Programme, Wellcome Sanger Institute, Cambridge, UK
- School of Life and Medical Science, University of Hertfordshire, Hatfield, UK
| | - Shaban Mwangi
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - David Goulding
- Pathogens and Microbes Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Alison Kemp
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Martin Rono
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya
| | | | - Pete C Bull
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Philip Bejon
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Julian C Rayner
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Abdirahman I Abdi
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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9
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Sendor R, Mitchell CL, Chacky F, Mohamed A, Mhamilawa LE, Molteni F, Nyinondi S, Kabula B, Mkali H, Reaves EJ, Serbantez N, Kitojo C, Makene T, Kyaw T, Muller M, Mwanza A, Eckert EL, Parr JB, Lin JT, Juliano JJ, Ngasala B. Similar Prevalence of Plasmodium falciparum and Non-P. falciparum Malaria Infections among Schoolchildren, Tanzania 1. Emerg Infect Dis 2023; 29:1143-1153. [PMID: 37209670 DOI: 10.3201/eid2906.221016] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
Achieving malaria elimination requires considering both Plasmodium falciparum and non-P. falciparum infections. We determined prevalence and geographic distribution of 4 Plasmodium spp. by performing PCR on dried blood spots collected within 8 regions of Tanzania during 2017. Among 3,456 schoolchildren, 22% had P. falciparum, 24% had P. ovale spp., 4% had P. malariae, and 0.3% had P. vivax infections. Most (91%) schoolchildren with P. ovale infections had low parasite densities; 64% of P. ovale infections were single-species infections, and 35% of those were detected in low malaria endemic regions. P. malariae infections were predominantly (73%) co-infections with P. falciparum. P. vivax was detected mostly in northern and eastern regions. Co-infections with >1 non-P. falciparum species occurred in 43% of P. falciparum infections. A high prevalence of P. ovale infections exists among schoolchildren in Tanzania, underscoring the need for detection and treatment strategies that target non-P. falciparum species.
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Katile A, Sagara I, Cissoko M, Bationo CS, Dolo M, Thera I, Traore S, Kone M, Dembele P, Bocoum D, Sidibe I, Simaga I, Sissoko MS, Landier J, Gaudart J. Spatio-Temporal Variability of Malaria Incidence in the Health District of Kati, Mali, 2015-2019. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:14361. [PMID: 36361240 PMCID: PMC9656757 DOI: 10.3390/ijerph192114361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
INTRODUCTION Despite the implementation of control strategies at the national scale, the malaria burden remains high in Mali, with more than 2.8 million cases reported in 2019. In this context, a new approach is needed, which accounts for the spatio-temporal variability of malaria transmission at the local scale. This study aimed to describe the spatio-temporal variability of malaria incidence and the associated meteorological and environmental factors in the health district of Kati, Mali. METHODS Daily malaria cases were collected from the consultation records of the 35 health areas of Kati's health district, for the period 2015-2019. Data on rainfall, relative humidity, temperature, wind speed, the normalized difference vegetation index, air pressure, and land use-land cover were extracted from open-access remote sensing sources, while data on the Niger River's height and flow were obtained from the National Department of Hydraulics. To reduce the dimension and account for collinearity, strongly correlated meteorological and environmental variables were combined into synthetic indicators (SI), using a principal component analysis. A generalized additive model was built to determine the lag and the relationship between the main SIs and malaria incidence. The transmission periods were determined using a change-point analysis. High-risk clusters (hotspots) were detected using the SatScan method and were ranked according to risk level, using a classification and regression tree analysis. RESULTS The peak of the malaria incidence generally occurred in October. Peak incidence decreased from 60 cases per 1000 person-weeks in 2015, to 27 cases per 1000 person-weeks in 2019. The relationship between the first SI (river flow and height, relative humidity, and rainfall) and malaria incidence was positive and almost linear. A non-linear relationship was found between the second SI (air pressure and temperature) and malaria incidence. Two transmission periods were determined per year: a low transmission period from January to July-corresponding to a persisting transmission during the dry season-and a high transmission period from July to December. The spatial distribution of malaria hotspots varied according to the transmission period. DISCUSSION Our study confirmed the important variability of malaria incidence and found malaria transmission to be associated with several meteorological and environmental factors in the Kati district. The persistence of malaria during the dry season and the spatio-temporal variability of malaria hotspots reinforce the need for innovative and targeted strategies.
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Affiliation(s)
- Abdoulaye Katile
- INSERM, IRD, SESSTIM, ISSPAM, UMR1252, Faculty of Medicine, Aix Marseille University, 13005 Marseille, France
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Issaka Sagara
- INSERM, IRD, SESSTIM, ISSPAM, UMR1252, Faculty of Medicine, Aix Marseille University, 13005 Marseille, France
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Mady Cissoko
- INSERM, IRD, SESSTIM, ISSPAM, UMR1252, Faculty of Medicine, Aix Marseille University, 13005 Marseille, France
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Cedric Stephane Bationo
- INSERM, IRD, SESSTIM, ISSPAM, UMR1252, Faculty of Medicine, Aix Marseille University, 13005 Marseille, France
| | - Mathias Dolo
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Ismaila Thera
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Siriman Traore
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Mamady Kone
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Pascal Dembele
- Programme National de Lutte Contre le Paludisme, Bamako BP 233, Mali
| | - Djoouro Bocoum
- Direction Nationale de L’Hydraulique, Bamako BP 66, Mali
| | | | - Ismael Simaga
- Centre de Santé de Référence du District Sanitaire de Kati, Région de Koulikoro, Kati BP 594, Mali
| | - Mahamadou Soumana Sissoko
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Jordi Landier
- INSERM, IRD, SESSTIM, ISSPAM, UMR1252, Faculty of Medicine, Aix Marseille University, 13005 Marseille, France
| | - Jean Gaudart
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
- APHM, INSERM, IRD, SESSTIM, ISSPAM, UMR1252, Hop Timone, BioSTIC, Biostatistic & ICT, Faculty of Medicine, Aix Marseille University, 13005 Marseille, France
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