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Hubbard A, Hemming-Schroeder E, Machani MG, Afrane Y, Yan G, Lo E, Janies D. Implementing landscape genetics in molecular epidemiology to determine drivers of vector-borne disease: A malaria case study. Mol Ecol 2023; 32:1848-1859. [PMID: 36645165 PMCID: PMC10694861 DOI: 10.1111/mec.16846] [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: 09/08/2022] [Revised: 12/02/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
This study employs landscape genetics to investigate the environmental drivers of a deadly vector-borne disease, malaria caused by Plasmodium falciparum, in a more spatially comprehensive manner than any previous work. With 1804 samples from 44 sites collected in western Kenya in 2012 and 2013, we performed resistance surface analysis to show that Lake Victoria acts as a barrier to transmission between areas north and south of the Winam Gulf. In addition, Mantel correlograms clearly showed significant correlations between genetic and geographic distance over short distances (less than 70 km). In both cases, we used an identity-by-state measure of relatedness tailored to find highly related individual parasites in order to focus on recent gene flow that is more relevant to disease transmission. To supplement these results, we performed conventional population genetics analyses, including Bayesian clustering methods and spatial ordination techniques. These analyses revealed some differentiation on the basis of geography and elevation and a cluster of genetic similarity in the lowlands north of the Winam Gulf of Lake Victoria. Taken as a whole, these results indicate low overall genetic differentiation in the Lake Victoria region, but with some separation of parasite populations north and south of the Winam Gulf that is explained by the presence of the lake as a geographic barrier to gene flow. We recommend similar landscape genetics analyses in future molecular epidemiology studies of vector-borne diseases to extend and contextualize the results of traditional population genetics.
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Affiliation(s)
- Alfred Hubbard
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina, Charlotte, USA
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Elizabeth Hemming-Schroeder
- Department of Microbiology, Center for Vector-borne Infectious Diseases (CVID), Colorado State University, Fort Collins, Colorado, USA
| | | | - Yaw Afrane
- Department of Medical Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, California, USA
| | - Eugenia Lo
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), University of North Carolina at Charlotte, Charlotte, North Carolina, USA
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
- School of Data Science, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Daniel Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina, Charlotte, USA
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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Omondi CJ, Otambo WO, Odongo D, Ochwedo KO, Otieno A, Onyango SA, Orondo P, Ondeto BM, Lee MC, Zhong D, Kazura JW, Githeko AK, Yan G. Asymptomatic and submicroscopic Plasmodium infections in an area before and during integrated vector control in Homa Bay, western Kenya. Malar J 2022; 21:272. [PMID: 36153552 PMCID: PMC9509636 DOI: 10.1186/s12936-022-04288-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 09/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Long-lasting insecticidal nets (LLINs) have been the primary vector control strategy until indoor residual spraying (IRS) was added in Homa Bay and Migori Counties in western Kenya. The objective of this study was to evaluate the impact of LLINs integrated with IRS on the prevalence of asymptomatic and submicroscopic Plasmodium infections in Homa Bay County. METHODS A two-stage cluster sampling procedure was employed to enroll study participants aged ≥ 6 months old. Four consecutive community cross-sectional surveys for Plasmodium infection were conducted in residents of Homa Bay county, Kenya. Prior to the start of the study, all study households received LLINs, which were distributed between June 2017 and March 2018. The first (February 2018) and second (June 2018) surveys were conducted before and after the first round of IRS (Feb-Mar 2018), while the third (February 2019) and fourth (June 2019) surveys were conducted before and after the second application of IRS (February-March 2019). Finger-prick blood samples were obtained to prepare thick and thin smears for microscopic determination and qPCR diagnosis of Plasmodium genus. RESULTS Plasmodium spp. infection prevalence by microscopy was 18.5% (113/610) before IRS, 14.2% (105/737) and 3.3% (24/720) after the first round of IRS and 1.3% (11/849) after the second round of IRS (p < 0.0001). Submicroscopic (blood smear negative, qPCR positive) parasitaemia reduced from 18.9% (115/610) before IRS to 5.4% (46/849) after IRS (p < 0.0001). However, the proportion of PCR positive infections that were submicroscopic increased from 50.4% (115/228) to 80.7% (46/57) over the study period (p < 0.0001). Similarly, while the absolute number and proportions of microscopy positives which were asymptomatic decreased from 12% (73/610) to 1.2% (9/849) (p < 0.0001), the relative proportion increased. Geometric mean density of P. falciparum parasitaemia decreased over the 2-year study period (p < 0.0001). CONCLUSIONS These data suggest that two annual rounds of IRS integrated with LLINs significantly reduced the prevalence of Plasmodium parasitaemia, while the proportion of asymptomatic and submicroscopic infections increased. To reduce cryptic P. falciparum transmission and improve malaria control, strategies aimed at reducing the number of asymptomatic and submicroscopic infections should be considered.
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Affiliation(s)
- Collince J Omondi
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya.
- Sub-Saharan International Center of Excellence for Malaria Research, Homa Bay, Kenya.
| | - Wilfred O Otambo
- Sub-Saharan International Center of Excellence for Malaria Research, Homa Bay, Kenya
- Department of Zoology, Maseno University, Kisumu, Kenya
| | - David Odongo
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
| | - Kevin O Ochwedo
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
- Sub-Saharan International Center of Excellence for Malaria Research, Homa Bay, Kenya
| | - Antony Otieno
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
| | - Shirley A Onyango
- Sub-Saharan International Center of Excellence for Malaria Research, Homa Bay, Kenya
- Department of Zoological Sciences, School of Science and Technology, Kenyatta University, Nairobi, Kenya
| | - Pauline Orondo
- Sub-Saharan International Center of Excellence for Malaria Research, Homa Bay, Kenya
| | - Benyl M Ondeto
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
- Sub-Saharan International Center of Excellence for Malaria Research, Homa Bay, Kenya
| | - Ming-Chieh Lee
- Sub-Saharan International Center of Excellence for Malaria Research, Homa Bay, Kenya
- Program in Public Health, College of Health Sciences, University of California, Irvine, CA, 92697, USA
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California, Irvine, CA, 92697, USA
| | - James W Kazura
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Andrew K Githeko
- Sub-Saharan International Center of Excellence for Malaria Research, Homa Bay, Kenya
- Climate and Human Health Research Unit, Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California, Irvine, CA, 92697, USA
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Malaria epidemic and transmission foci in highland of Kisii, western Kenya. Parasite Epidemiol Control 2022; 18:e00263. [PMID: 35880192 PMCID: PMC9307932 DOI: 10.1016/j.parepi.2022.e00263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/07/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
Background The vulnerable population within the malaria epidemic zone remains at risk of increased burden and fatality. This is because of unpreparedness and overstretching of healthcare capacity in the event of a full-fledged epidemic. The purpose of this study was to determine the prevalence of microscopic and submicroscopic infections, as well as map specific Plasmodium transmission foci, in the malaria epidemic-prone zone of Kisii highland. Methodology Patients seeking malaria treatment at Eramba health facility in the epidemic-prone zone of Kisii highland were enrolled in the study. Malaria outpatient data for the entire month of May were also included in the analysis. Patients' finger prick blood smears were examined for microscopic infections, while a real-time polymerase chain reaction targeting the Plasmodium species 18S rRNA gene was used to detect the presence of submicroscopic infections on DNA extracted from dry blood spots. Results Based on outpatient data, the malaria positivity rate was 20.7% (231/1115, 95% CI, 0.18–0.23). The positivity rate varied significantly by age group (χ2 = 75.05, df 2, p < 0.0001). Children under the age of five had the highest positivity rate (27.8%, 78/281), followed by children aged 5–15 years (19.4%, 69/356), and individuals aged 15 years and above (17.6%, 84/478). Out of the 102 patients recruited, the positivity rate by microscopy was 57.8% (59/102) and 72.5% (74/102) by RT-PCR. Most of the microscopic infections (40.7%, 24/59) were from Morara and Nyabikondo villages in Rioma and Kiomooncha sublocations, respectively. The submicroscopic prevalence was 14.7% (15/102) and was observed only in patients from high-infection villages in Rioma (15.8%, 9/57) and Kiomooncha (16.2%, 6/37) sublocations. Across gender and age groups, females (19.7%, 12/61) and patients aged 15 years and above (21.1%, 8/38) had high levels of submicroscopic infections. There were two mixed infections of P. falciparum/P. malariae and P. falciparum/P. ovale, both from patients residing in Kiomooncha sublocation. Conclusion Plasmodium falciparum infections remained relatively high in the Marani subcounty. Infections were concentrated in two villages, which could serve as a target for future public health intervention, particularly during a malaria epidemic.
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Lyimo BM, Popkin-Hall ZR, Giesbrecht DJ, Mandara CI, Madebe RA, Bakari C, Pereus D, Seth MD, Ngamba RM, Mbwambo RB, MacInnis B, Mbwambo D, Garimo I, Chacky F, Aaron S, Lusasi A, Molteni F, Njau R, Cunningham JA, Lazaro S, Mohamed A, Juliano JJ, Bailey J, Ishengoma DS. 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. Front Cell Infect Microbiol 2022; 12:757844. [PMID: 35909968 PMCID: PMC9326448 DOI: 10.3389/fcimb.2022.757844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
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.
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Affiliation(s)
- Beatus M. Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania
- School of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | - David J. Giesbrecht
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | | | - Rashid A. Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Ruth B. Mbwambo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Bronwyn MacInnis
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute, Boston, MA, United States
| | | | - Issa Garimo
- National Malaria Control Programme, Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | - Ritha Njau
- World Health Organization, Country Office, Dar es Salaam, Tanzania
| | - Jane A. Cunningham
- Global Malaria Programme, World Health Organization, Headquarters, Geneva, Switzerland
| | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Programme, Dodoma, Tanzania
| | - Jonathan J. Juliano
- School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Jeffrey A. Bailey
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | - Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
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Ochwedo KO, Ariri FO, Otambo WO, Magomere EO, Debrah I, Onyango SA, Orondo PW, Atieli HE, Ogolla SO, Otieno ACA, Mukabana WR, Githeko AK, Lee MC, Yan G, Zhong D, Kazura JW. Rare Alleles and Signatures of Selection on the Immunodominant Domains of Pfs230 and Pfs48/45 in Malaria Parasites From Western Kenya. Front Genet 2022; 13:867906. [PMID: 35656326 PMCID: PMC9152164 DOI: 10.3389/fgene.2022.867906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/25/2022] [Indexed: 01/27/2023] Open
Abstract
Background: Malaria elimination and eradication efforts can be advanced by including transmission-blocking or reducing vaccines (TBVs) alongside existing interventions. Key transmission-blocking vaccine candidates, such as Pfs230 domain one and Pfs48/45 domain 3, should be genetically stable to avoid developing ineffective vaccines due to antigenic polymorphisms. We evaluated genetic polymorphism and temporal stability of Pfs230 domain one and Pfs48/45 domain three in Plasmodium falciparum parasites from western Kenya. Methods: Dry blood spots on filter paper were collected from febrile malaria patients reporting to community health facilities in endemic areas of Homa Bay and Kisumu Counties and an epidemic-prone area of Kisii County in 2018 and 2019. Plasmodium speciation was performed using eluted DNA and real-time PCR. Amplification of the target domains of the two Pfs genes was performed on P. falciparum positive samples. We sequenced Pfs230 domain one on 156 clinical isolates and Pfs48/45 domain three on 118 clinical isolates to infer the levels of genetic variability, signatures of selection, genetic diversity indices and perform other evolutionary analyses. Results: Pfs230 domain one had low nucleotide diversity (π = 0.15 × 10-2) with slight variation per study site. Six polymorphic sites with nonsynonymous mutations and eight haplotypes were discovered. I539T was a novel variant, whereas G605S was nearing fixation. Pfs48/45 domain three had a low π (0.063 × 10-2), high conservation index, and three segregating sites, resulting in nonsynonymous mutation and four haplotypes. Some loci of Pfs230 D1 were in positive or negative linkage disequilibrium, had negative or positive selection signatures, and others (1813, 1955) and (1813, 1983) had a history of recombination. Mutated loci pairs in Pfs48/45 domain three had negative linkage disequilibrium, and some had negative and positive Tajima's D values with no history of recombination events. Conclusion: The two transmission blocking vaccine candidates have low nucleotide diversity, a small number of zone-specific variants, high nucleotide conservation index, and high frequency of rare alleles. With the near fixation a polymorphic site and the proximity of mutated codons to antibody binding epitopes, it will be necessary to continue monitoring sequence modifications of these domains when designing TBVs that include Pfs230 and Pfs48/45 antigens.
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Affiliation(s)
- Kevin O. Ochwedo
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya,Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Fredrick O. Ariri
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,Department of Zoology, School of Physical and Biological Sciences, Maseno University, Kisumu, Kenya
| | - Wilfred O. Otambo
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,Department of Zoology, School of Physical and Biological Sciences, Maseno University, Kisumu, Kenya
| | - Edwin O. Magomere
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,Department of Biochemistry, Egerton University, Nakuru, Kenya
| | - Isaiah Debrah
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,West Africa Centre for Cell Biology of Infectious Pathogen, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Shirley A. Onyango
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,School of Zoological Sciences, Kenyatta University, Nairobi, Kenya
| | - Pauline W. Orondo
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Harrysone E. Atieli
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Sidney O. Ogolla
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Antony C. A. Otieno
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
| | - Wolfgang R. Mukabana
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya,Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Andrew K. Githeko
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Ming-Chieh Lee
- Program in Public Health, College of Health Sciences, University of California, Irvine, Irvine, CA, United States
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California, Irvine, Irvine, CA, United States
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California, Irvine, Irvine, CA, United States,*Correspondence: Daibin Zhong,
| | - James W. Kazura
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, United States
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