1
|
Mekonen B, Dugassa S, Feleke SM, Dufera B, Gidisa B, Adamu A, Mandefro A, Tasew G, Golassa L. Widespread pfhrp2/3 deletions and HRP2-based false-negative results in southern Ethiopia. Malar J 2024; 23:108. [PMID: 38632640 PMCID: PMC11025231 DOI: 10.1186/s12936-024-04904-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Rapid diagnostic tests (RDTs) play a significant role in expanding case management in peripheral healthcare systems. Histidine-rich protein-2 (HRP2) antigen detection RDTs are predominantly used to diagnose Plasmodium falciparum infection. However, the evolution and spread of P. falciparum parasite strains with deleted hrp2/3 genes, causing false-negative results, have been reported. This study assessed the diagnostic performance of HRP2-detecting RDTs for P. falciparum cases and the prevalence of pfhrp2/3 deletions among symptomatic patients seeking malaria diagnosis at selected health facilities in southern Ethiopia. METHODS A multi-health facilities-based cross-sectional study was conducted on self-presenting febrile patients seeking treatment in southern Ethiopia from July to September 2022. A purposive sampling strategy was used to enroll patients with microscopically confirmed P. falciparum infections. A capillary blood sample was obtained to prepare a blood film for microscopy and a RDT using the SD Bioline™ Malaria Pf/Pv Test. Dried blood spot samples were collected for further molecular analysis. DNA was extracted using gene aid kits and amplification was performed using nested PCR assay. Exon 2 of hrp2 and hrp3, which are the main protein-coding regions, was used to confirm its deletion. The diagnostic performance of RDT was evaluated using PCR as the gold standard test for P. falciparum infections. RESULTS Of 279 P. falciparum PCR-confirmed samples, 249 (89.2%) had successful msp-2 amplification, which was then genotyped for hrp2/3 gene deletions. The study revealed that pfhrp2/3 deletions were common in all health centres, and it was estimated that 144 patients (57.8%) across all health facilities had pfhrp2/3 deletions, leading to false-negative PfHRP2 RDT results. Deletions spanning exon 2 of hrp2, exon 2 of hrp3, and double deletions (hrp2/3) accounted for 68 (27.3%), 76 (30.5%), and 33 (13.2%) of cases, respectively. The study findings revealed the prevalence of P. falciparum parasites lacking a single pfhrp2-/3-gene and that both genes varied across the study sites. This study also showed that the sensitivity of the SD Bioline PfHRP2-RDT test was 76.5% when PCR was used as the reference test. CONCLUSION This study confirmed the existence of widespread pfhrp2/3- gene deletions, and their magnitude exceeded the WHO-recommended threshold (> 5%). False-negative RDT results resulting from deletions in Pfhrp2/3- affect a country's attempts at malaria control and elimination. Therefore, the adoption of non-HRP2-based RDTs as an alternative measure is required to avoid the consequences associated with the continued use of HRP-2-based RDTs, in the study area in particular and in Ethiopia in general.
Collapse
Affiliation(s)
- Bacha Mekonen
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
- Malaria and NTDs Research Team, Bacterial, Parasitic, and Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
| | - Sisay Dugassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sindew Mekasha Feleke
- Malaria and NTDs Research Team, Bacterial, Parasitic, and Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Boja Dufera
- Malaria and NTDs Research Team, Bacterial, Parasitic, and Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Bedasa Gidisa
- Malaria and NTDs Research Team, Armeur Hansen Research Institute, Addis Ababa, Ethiopia
| | - Aderaw Adamu
- Department of Medical Laboratory Science, College of Medicine and Health Science, Wollo University, Dessie, Ethiopia
| | - Aynalem Mandefro
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Geremew Tasew
- Malaria and NTDs Research Team, Bacterial, Parasitic, and Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
| |
Collapse
|
2
|
Assefa A, Wamae K, Hennelly CM, Ngasala B, Muller M, Kalonji A, Phanzu F, Cunningham CH, Lin JT, Parr JB. Detection of P. malariae using a new rapid isothermal amplification lateral flow assay. Malar J 2024; 23:104. [PMID: 38609964 PMCID: PMC11015614 DOI: 10.1186/s12936-024-04928-9] [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: 10/03/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND While Plasmodium falciparum and Plasmodium vivax cause the majority of malaria cases and deaths, infection by Plasmodium malariae and other Plasmodium species also causes morbidity and mortality. Current understanding of these infections is limited in part by existing point-of-care diagnostics that fail to differentiate them and have poor sensitivity for low-density infections. Accurate diagnosis currently requires molecular assays performed in well-resourced laboratories. This report describes the development of a P. malariae diagnostic assay that uses rapid, isothermal recombinase polymerase amplification (RPA) and lateral-flow-strip detection. METHODS Multiple combinations of custom RPA primers and probes were designed using publicly available P. malariae genomic sequences, and by modifying published primer sets. Based on manufacturer RPA reaction conditions (TwistDx nfo kit), an isothermal assay was optimized targeting the multicopy P. malariae 18S rRNA gene with 39 °C incubation and 30-min run time. RPA product was visualized using lateral strips (FAM-labeled, biotinylated amplicon detected by a sandwich immunoassay, visualized using gold nanoparticles). Analytical sensitivity was evaluated using 18S rRNA plasmid DNA, and clinical sensitivity determined using qPCR-confirmed samples collected from Tanzania, Ethiopia, and the Democratic Republic of the Congo. RESULTS Using 18S rRNA plasmid DNA, the assay demonstrates a detection limit of 10 copies/µL (~ 1.7 genome equivalents) and 100% analytical specificity. Testing in field samples showed 95% clinical sensitivity and 88% specificity compared to qPCR. Total assay time was less than 40 min. CONCLUSION Combined with simplified DNA extraction methods, the assay has potential for future field-deployable, point-of-care use to detect P. malariae infection, which remains largely undiagnosed but a neglected cause of chronic malaria. The assay provides a rapid, simple readout on a lateral flow strip without the need for expensive laboratory equipment.
Collapse
Affiliation(s)
- Ashenafi Assefa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
| | - Kevin Wamae
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Christopher M Hennelly
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Meredith Muller
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | | | - Clark H Cunningham
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jessica T Lin
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jonathan B Parr
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
| |
Collapse
|
3
|
Gartner V, Redelings BD, Gaither C, Parr JB, Kalonji A, Phanzu F, Brazeau NF, Juliano JJ, Wray GA. Genomic insights into Plasmodium vivax population structure and diversity in central Africa. Malar J 2024; 23:27. [PMID: 38238806 PMCID: PMC10797969 DOI: 10.1186/s12936-024-04852-y] [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: 07/27/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Though Plasmodium vivax is the second most common malaria species to infect humans, it has not traditionally been considered a major human health concern in central Africa given the high prevalence of the human Duffy-negative phenotype that is believed to prevent infection. Increasing reports of asymptomatic and symptomatic infections in Duffy-negative individuals throughout Africa raise the possibility that P. vivax is evolving to evade host resistance, but there are few parasite samples with genomic data available from this part of the world. METHODS Whole genome sequencing of one new P. vivax isolate from the Democratic Republic of the Congo (DRC) was performed and used in population genomics analyses to assess how this central African isolate fits into the global context of this species. RESULTS Plasmodium vivax from DRC is similar to other African populations and is not closely related to the non-human primate parasite P. vivax-like. Evidence is found for a duplication of the gene PvDBP and a single copy of PvDBP2. CONCLUSION These results suggest an endemic P. vivax population is present in central Africa. Intentional sampling of P. vivax across Africa would further contextualize this sample within African P. vivax diversity and shed light on the mechanisms of infection in Duffy negative individuals. These results are limited by the uncertainty of how representative this single sample is of the larger population of P. vivax in central Africa.
Collapse
Affiliation(s)
- Valerie Gartner
- Biology Department, Duke University, Durham, NC, 27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC, 27708, USA
| | - Benjamin D Redelings
- Biology Department, Duke University, Durham, NC, 27708, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
- Ronin Institute, Durham, NC, 27705, USA
| | | | | | - Albert Kalonji
- SANRU Asbl, 149 A/B, Boulevard du 30 Juin, Kinshasa, Gombe, Democratic Republic of Congo
| | - Fernandine Phanzu
- SANRU Asbl, 149 A/B, Boulevard du 30 Juin, Kinshasa, Gombe, Democratic Republic of Congo
| | | | | | - Gregory A Wray
- Biology Department, Duke University, Durham, NC, 27708, USA.
| |
Collapse
|
4
|
Watson OJ, Tran TNA, Zupko RJ, Symons T, Thomson R, Visser T, Rumisha S, Dzianach PA, Hathaway N, Kim I, Juliano JJ, Bailey JA, Slater H, Okell L, Gething P, Ghani A, Boni MF, Parr JB, Cunningham J. Global risk of selection and spread of Plasmodium falciparum histidine-rich protein 2 and 3 gene deletions. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.21.23297352. [PMID: 37905102 PMCID: PMC10615018 DOI: 10.1101/2023.10.21.23297352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In the thirteen years since the first report of pfhrp2-deleted parasites in 2010, the World Health Organization (WHO) has found that 40 of 47 countries surveyed worldwide have reported pfhrp2/3 gene deletions. Due to a high prevalence of pfhrp2/3 deletions causing false-negative HRP2 RDTs, in the last five years, Eritrea, Djibouti and Ethiopia have switched or started switching to using alternative RDTs, that target pan-specific-pLDH or P. falciparum specific-pLDH alone of in combination with HRP2. However, manufacturing of alternative RDTs has not been brought to scale and there are no WHO prequalified combination tests that use Pf-pLDH instead of HRP2 for P. falciparum detection. For these reasons, the continued spread of pfhrp2/3 deletions represents a growing public health crisis that threatens efforts to control and eliminate P. falciparum malaria. National malaria control programmes, their implementing partners and test developers desperately seek pfhrp2/3 deletion data that can inform their immediate and future resource allocation. In response, we use a mathematical modelling approach to evaluate the global risk posed by pfhrp2/3 deletions and explore scenarios for how deletions will continue to spread in Africa. We incorporate current best estimates of the prevalence of pfhrp2/3 deletions and conduct a literature review to estimate model parameters known to impact the selection of pfhrp2/3 deletions for each malaria endemic country. We identify 20 countries worldwide to prioritise for surveillance and future deployment of alternative RDT, based on quickly selecting for pfhrp2/3 deletions once established. In scenarios designed to explore the continued spread of deletions in Africa, we identify 10 high threat countries that are most at risk of deletions both spreading to and subsequently being rapidly selected for. If HRP2-based RDTs continue to be relied on for malaria case management, we predict that the major route for pfhrp2 deletions to spread is south out from the current hotspot in the Horn of Africa, moving through East Africa over the next 20 years. We explore the variation in modelled timelines through an extensive parameter sensitivity analysis and despite wide uncertainties, we identify three countries that have not yet switched RDTs (Senegal, Zambia and Kenya) that are robustly identified as high risk for pfhrp2/3 deletions. These results provide a refined and updated prediction model for the emergence of pfhrp2/3 deletions in an effort to help guide pfhrp2/3 policy and prioritise future surveillance efforts and innovation.
Collapse
Affiliation(s)
- Oliver J Watson
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Thu Nguyen-Anh Tran
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Robert J Zupko
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Tasmin Symons
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | | | | | - Susan Rumisha
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Paulina A Dzianach
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Nicholas Hathaway
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Isaac Kim
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey A Bailey
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Warren Alpert Medical School, Brown University, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | | | - Lucy Okell
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Peter Gething
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
- Faculty of Health Sciences, Curtin University, Bentley, Australia
| | - Azra Ghani
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jonathan B Parr
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| |
Collapse
|
5
|
He W, Sendor R, Potlapalli VR, Kashamuka MM, Tshefu AK, Phanzu F, Kalonji A, Ngasala B, Thwai KL, Juliano JJ, Lin JT, Parr JB. A novel duplex qualitative real-time PCR assay for the detection and differentiation of Plasmodium ovale curtisi and Plasmodium ovale wallikeri malaria. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.31.23297819. [PMID: 37961397 PMCID: PMC10635243 DOI: 10.1101/2023.10.31.23297819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background P. ovale spp. infections are endemic across multiple African countries and are caused by two distinct non-recombining species, P. ovale curtisi (Poc) and P. ovale wallikeri (Pow). These species are thought to differ in clinical symptomatology and latency, but existing diagnostic assays have limited ability to detect and distinguish them. In this study, we developed a new duplex assay for the detection and differentiation of Poc and Pow that can be used to improve our understanding of these parasites. Methods Repetitive sequence motifs were identified in available Poc and Pow genomes and used for assay development and validation. We evaluated the analytical sensitivity and specificity of the best-performing assay using a panel of samples from Tanzania and the Democratic Republic of the Congo (DRC), then validated its performance using 55 P. ovale spp. samples and 40 non-ovale Plasmodium samples from the DRC. Poc and Pow prevalence among symptomatic individuals sampled across three provinces of the DRC were estimated. Results The best-performing Poc and Pow targets had 9 and 8 copies within the reference genomes, respectively. Our duplex assay had 100% specificity and 95% confidence lower limits of detection of 4.2 and 41.2 parasite genome equivalents/μl for Poc and Pow, respectively. Species was determined in 80% of all P. ovale spp.-positive field samples and 100% of those with >10 parasites/μl. Most P. ovale spp. field samples from the DRC were found to be Poc infections. Conclusions We identified promising multi-copy targets for molecular detection and differentiation of Poc and Pow and used them to develop a new duplex real-time PCR assay that performed well when applied to diverse field samples. Though low-density Pow infections are not reliably detected, the assay is highly specific and can be used for high-throughput studies of P. ovale spp. epidemiology among symptomatic cases in malaria-endemic countries like the DRC.
Collapse
Affiliation(s)
- Wenqiao He
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Rachel Sendor
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, United States
| | - Varun R. Potlapalli
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | | | | | | | - Billy Ngasala
- Muhimbili University of Health and Allied Sciences, Dar Es Salaam, Tanzania
| | - Kyaw Lay Thwai
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jonathan J. Juliano
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, United States
| | - Jessica T. Lin
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jonathan B. Parr
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| |
Collapse
|
6
|
Sendor R, Banek K, Kashamuka MM, Mvuama N, Bala JA, Nkalani M, Kihuma G, Atibu J, Thwai KL, Svec WM, Goel V, Nseka T, Lin JT, Bailey JA, Emch M, Carrel M, Juliano JJ, Tshefu A, Parr JB. Epidemiology of Plasmodium malariae and Plasmodium ovale spp. in Kinshasa Province, Democratic Republic of Congo. Nat Commun 2023; 14:6618. [PMID: 37857597 PMCID: PMC10587068 DOI: 10.1038/s41467-023-42190-w] [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: 04/06/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
Reports suggest non-falciparum species are an underappreciated cause of malaria in sub-Saharan Africa but their epidemiology is ill-defined, particularly in highly malaria-endemic regions. We estimated incidence and prevalence of PCR-confirmed non-falciparum and Plasmodium falciparum malaria infections within a longitudinal study conducted in Kinshasa, Democratic Republic of Congo (DRC) between 2015-2017. Children and adults were sampled at biannual household surveys and routine clinic visits. Among 9,089 samples from 1,565 participants, incidences of P. malariae, P. ovale spp., and P. falciparum infections by 1-year were 7.8% (95% CI: 6.4%-9.1%), 4.8% (95% CI: 3.7%-5.9%) and 57.5% (95% CI: 54.4%-60.5%), respectively. Non-falciparum prevalences were higher in school-age children, rural and peri-urban sites, and P. falciparum co-infections. P. falciparum remains the primary driver of malaria in the DRC, though non-falciparum species also pose an infection risk. As P. falciparum interventions gain traction in high-burden settings, continued surveillance and improved understanding of non-falciparum infections are warranted.
Collapse
Affiliation(s)
- Rachel Sendor
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Kristin Banek
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melchior M Kashamuka
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Nono Mvuama
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Joseph A Bala
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Marthe Nkalani
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Georges Kihuma
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Joseph Atibu
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Kyaw L Thwai
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - W Matthew Svec
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Varun Goel
- Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tommy Nseka
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Jessica T Lin
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Michael Emch
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Margaret Carrel
- Department of Geographical and Sustainability Sciences, University of Iowa, Iowa City, IA, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Antoinette Tshefu
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Jonathan B Parr
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
7
|
François R, Kashamuka MM, Banek K, Bala JA, Nkalani M, Kihuma G, Atibu J, Mahilu GE, Thwai KL, Assefa A, Bailey JA, Dinglasan RR, Juliano JJ, Tshefu AK, Parr JB. Plasmodium falciparum with pfhrp2/3 Deletion Not Detected in a 2018-2021 Malaria Longitudinal Cohort Study in Kinshasa Province, Democratic Republic of the Congo. Am J Trop Med Hyg 2023; 109:273-276. [PMID: 37339759 PMCID: PMC10397445 DOI: 10.4269/ajtmh.22-0715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/13/2023] [Indexed: 06/22/2023] Open
Abstract
Histidine-rich protein 2- (HRP2-) based rapid diagnostic tests (RDTs) are widely used to detect Plasmodium falciparum in sub-Saharan Africa. Reports of parasites with pfhrp2 and/or pfhrp3 (pfhrp2/3) gene deletions in Africa raise concerns about the long-term viability of HRP2-based RDTs. We evaluated changes in pfhrp2/3 deletion prevalence over time using a 2018-2021 longitudinal study of 1,635 enrolled individuals in Kinshasa Province, Democratic Republic of the Congo (DRC). Samples collected during biannual household visits with ≥ 100 parasites/µL by quantitative real-time polymerase chain reaction were genotyped using a multiplex real-time PCR assay. Among 2,726 P. falciparum PCR-positive samples collected from 993 participants during the study period, 1,267 (46.5%) were genotyped. No pfhrp2/3 deletions or mixed pfhrp2/3-intact and -deleted infections were identified in our study. Pfhrp2/3-deleted parasites were not detected in Kinshasa Province; ongoing use of HRP2-based RDTs is appropriate.
Collapse
Affiliation(s)
- Ruthly François
- Institute for Global Health and Infectious Diseases and Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Kristin Banek
- Institute for Global Health and Infectious Diseases and Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Joseph A. Bala
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Marthe Nkalani
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Georges Kihuma
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Joseph Atibu
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Georges E. Mahilu
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Kyaw L. Thwai
- Institute for Global Health and Infectious Diseases and Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ashenafi Assefa
- Institute for Global Health and Infectious Diseases and Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island
| | - Rhoel R. Dinglasan
- Department of Infectious Diseases & Immunology, University of Florida, Gainesville, Florida
| | - Jonathan J. Juliano
- Institute for Global Health and Infectious Diseases and Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Jonathan B. Parr
- Institute for Global Health and Infectious Diseases and Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| |
Collapse
|
8
|
Kojom Foko LP, Jakhan J, Narang G, Singh V. Global polymorphism of Plasmodium falciparum histidine rich proteins 2/3 and impact on malaria rapid diagnostic test detection: a systematic review and meta-analysis. Expert Rev Mol Diagn 2023; 23:925-943. [PMID: 37698448 DOI: 10.1080/14737159.2023.2255136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/18/2023] [Accepted: 08/10/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND This review presents an overview of field findings on sequence variation of Plasmodium falciparum histidine-rich proteins 2/3 (PfHRP2/3) for which reference types (1-24) have been identified, and its critical impact on PfHRP2-based rapid diagnostic test (RDT) detection. RESEARCH DESIGN AND METHODS This systematic review and meta-analysis was registered with PROSPERO, CRD42022316027, and conducted as per the PRISMA guidelines, and the methodological quality of studies was assessed. RESULTS Of the 2184 records identified, 34 studies were included mostly from Africa (47.1%) and Asia (35.3%). The reference PfHRP2 types 1, 2, 3, 6, and 7 are invariably found at proportions ≥ 80-100% in all areas with the exception of The Americas where their proportion is very low. The proteins exhibited high diversity of variants/unknown types, especially for types 1, 2, 4, and 7. Eleven major PfHRP2 epitopes were found at pooled proportion > 90%. The existing models to predict RDT detection are greatly limited by the impact of factors such as low (very low) parasitemia, RDT brand, and PfHRP3 cross-reactivity. PfHRP2 length and presence/number of a given reference repeat type/variant did not seem to impact RDT detection. CONCLUSIONS PfHRP2/3 are highly polymorphic and current findings are insufficient, conflicting and not convincing enough to conclude on the role of PfHRP2/3 sequence polymorphism in PfHRP2-based RDT detection.
Collapse
Affiliation(s)
- Loick P Kojom Foko
- Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, India
| | - Jahnvi Jakhan
- Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, India
| | - Geetika Narang
- Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, India
| | - Vineeta Singh
- Parasite and Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, India
| |
Collapse
|
9
|
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.
Collapse
|
10
|
Sendor R, Banek K, Kashamuka MM, Mvuama N, Bala JA, Nkalani M, Kihuma G, Atibu J, Thwai KL, Svec WM, Goel V, Nseka T, Lin JT, Bailey JA, Emch M, Carrel M, Juliano JJ, Tshefu A, Parr JB. Epidemiology of Plasmodium malariae and Plasmodium ovale spp. in a highly malaria-endemic country: a longitudinal cohort study in Kinshasa Province, Democratic Republic of Congo. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.20.23288826. [PMID: 37790376 PMCID: PMC10543032 DOI: 10.1101/2023.04.20.23288826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background Increasing reports suggest that non-falciparum species are an underappreciated cause of malaria in sub-Saharan Africa, but their epidemiology is not well-defined. This is particularly true in regions of high P. falciparum endemicity such as the Democratic Republic of Congo (DRC), where 12% of the world's malaria cases and 13% of deaths occur. Methods and Findings The cumulative incidence and prevalence of P. malariae and P. ovale spp. infection detected by real-time PCR were estimated among children and adults within a longitudinal study conducted in seven rural, peri-urban, and urban sites from 2015-2017 in Kinshasa Province, DRC. Participants were sampled at biannual household survey visits (asymptomatic) and during routine health facility visits (symptomatic). Participant-level characteristics associated with non-falciparum infections were estimated for single- and mixed-species infections. Among 9,089 samples collected from 1,565 participants over a 3-year period, the incidence of P. malariae and P. ovale spp. infection was 11% (95% CI: 9%-12%) and 7% (95% CI: 5%-8%) by one year, respectively, compared to a 67% (95% CI: 64%-70%) one-year cumulative incidence of P. falciparum infection. Incidence continued to rise in the second year of follow-up, reaching 26% and 15% in school-age children (5-14yo) for P. malariae and P. ovale spp., respectively. Prevalence of P. malariae, P. ovale spp., and P. falciparum infections during household visits were 3% (95% CI: 3%-4%), 1% (95% CI: 1%-2%), and 35% (95% CI: 33%-36%), respectively. Non-falciparum malaria was more prevalent in rural and peri-urban vs. urban sites, in school-age children, and among those with P. falciparum co-infection. A crude association was detected between P. malariae and any anemia in the symptomatic clinic population, although this association did not hold when stratified by anemia severity. No crude associations were detected between non-falciparum infection and fever prevalence. Conclusions P. falciparum remains the primary driver of malaria morbidity and mortality in the DRC. However, non-falciparum species also pose an infection risk across sites of varying urbanicity and malaria endemicity within Kinshasa, DRC, particularly among children under 15 years of age. As P. falciparum interventions gain traction in high-burden settings like the DRC, continued surveillance and improved understanding of non-falciparum infections are warranted.
Collapse
Affiliation(s)
- Rachel Sendor
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kristin Banek
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Nono Mvuama
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Joseph A. Bala
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Marthe Nkalani
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Georges Kihuma
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Joseph Atibu
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Kyaw L. Thwai
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - W. Matthew Svec
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Varun Goel
- Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tommy Nseka
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Jessica T. Lin
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Michael Emch
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Margaret Carrel
- Department of Geographical and Sustainability Sciences, University of Iowa, Iowa City, Iowa, United States of America
| | - Jonathan J. Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Antoinette Tshefu
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Jonathan B. Parr
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| |
Collapse
|
11
|
Assefa A, Wamae KK, Hennelly CM, Ngasala B, Muller M, Kalonji A, Phanzu F, Cunningham CH, Lin JT, Parr JB. Detection of P. malariae using a new rapid isothermal amplification lateral flow assay. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.26.23286371. [PMID: 37790493 PMCID: PMC10543045 DOI: 10.1101/2023.02.26.23286371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
P. malariae is found worldwide and causes chronic parasitism in its human hosts. We developed a P. malariae (Pm) diagnostic assay that uses rapid, isothermal recombinase polymerase amplification (RPA) and lateral-flow-strip detection. Using 18S rRNA plasmid DNA, the assay demonstrates a detection limit of 10 copies /μL (~1.7 genome equivalents) and 100% analytical specificity. Testing in field samples showed 95% clinical sensitivity and 88% specificity compared to qPCR. Total assay time was 35 minutes. Combined with simplified DNA extraction methods, the assay has potential for future field-deployable point-of-care use to detect a parasite species that remains largely undiagnosed.
Collapse
Affiliation(s)
- Ashenafi Assefa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - Kevin K. Wamae
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - Chris M. Hennelly
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Meredith Muller
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | | | | | - Clark H. Cunningham
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - Jessica T. Lin
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - Jonathan B. Parr
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| |
Collapse
|
12
|
Rogier E, McCaffery JN, Mohamed MA, Herman C, Nace D, Daniels R, Lucchi N, Jones S, Goldman I, Aidoo M, Cheng Q, Kemenang EA, Udhayakumar V, Cunningham J. Plasmodium falciparum pfhrp2 and pfhrp3 Gene Deletions and Relatedness to Other Global Isolates, Djibouti, 2019-2020. Emerg Infect Dis 2022; 28:2043-2050. [PMID: 36148905 PMCID: PMC9514350 DOI: 10.3201/eid2810.220695] [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] [Indexed: 12/13/2022] Open
Abstract
Deletions of pfhrp2 and paralogue pfhrp3 (pfhrp2/3) genes threaten Plasmodium falciparum diagnosis by rapid diagnostic test. We examined 1,002 samples from suspected malaria patients in Djibouti City, Djibouti, to investigate pfhrp2/3 deletions. We performed assays for Plasmodium antigen carriage, pfhrp2/3 genotyping, and sequencing for 7 neutral microsatellites to assess relatedness. By PCR assay, 311 (31.0%) samples tested positive for P. falciparum infection, and 296 (95.2%) were successfully genotyped; 37 (12.5%) samples were pfhrp2+/pfhrp3+, 51 (17.2%) were pfhrp2+/pfhrp3-, 5 (1.7%) were pfhrp2-/pfhrp3+, and 203 (68.6%) were pfhrp2-/pfhrp3-. Histidine-rich protein 2/3 antigen concentrations were reduced with corresponding gene deletions. Djibouti P. falciparum is closely related to Ethiopia and Eritrea parasites (pairwise GST 0.68 [Ethiopia] and 0.77 [Eritrea]). P. falciparum with deletions in pfhrp2/3 genes were highly prevalent in Djibouti City in 2019-2020; they appear to have arisen de novo within the Horn of Africa and have not been imported.
Collapse
|
13
|
Martiáñez-Vendrell X, Skjefte M, Sikka R, Gupta H. Factors Affecting the Performance of HRP2-Based Malaria Rapid Diagnostic Tests. Trop Med Infect Dis 2022; 7:tropicalmed7100265. [PMID: 36288006 PMCID: PMC9611031 DOI: 10.3390/tropicalmed7100265] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
The recent COVID-19 pandemic has profoundly impacted global malaria elimination programs, resulting in a sharp increase in malaria morbidity and mortality. To reduce this impact, unmet needs in malaria diagnostics must be addressed while resuming malaria elimination activities. Rapid diagnostic tests (RDTs), the unsung hero in malaria diagnosis, work to eliminate the prevalence of Plasmodium falciparum malaria through their efficient, cost-effective, and user-friendly qualities in detecting the antigen HRP2 (histidine-rich protein 2), among other proteins. However, the testing mechanism and management of malaria with RDTs presents a variety of limitations. This paper discusses the numerous factors (including parasitic, host, and environmental) that limit the performance of RDTs. Additionally, the paper explores outside factors that can hinder RDT performance. By understanding these factors that affect the performance of HRP2-based RDTs in the field, researchers can work toward creating and implementing more effective and accurate HRP2-based diagnostic tools. Further research is required to understand the extent of these factors, as the rapidly changing interplay between parasite and host directly hinders the effectiveness of the tool.
Collapse
Affiliation(s)
- Xavier Martiáñez-Vendrell
- Molecular Virology Laboratory, Department of Medical Microbiology, LUMC Center for Infectious Diseases (LU-CID), Leiden University Medical Center, 2333 ZA Leiden, The Netherlands or
| | - Malia Skjefte
- Department of Global Health and Population, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Ruhi Sikka
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura 281406, UP, India
| | - Himanshu Gupta
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura 281406, UP, India
- Correspondence: or
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Beshir KB, Parr JB, Cunningham J, Cheng Q, Rogier E. Screening strategies and laboratory assays to support Plasmodium falciparum histidine-rich protein deletion surveillance: where we are and what is needed. Malar J 2022; 21:201. [PMID: 35751070 PMCID: PMC9233320 DOI: 10.1186/s12936-022-04226-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/17/2022] [Indexed: 11/10/2022] Open
Abstract
Rapid diagnostic tests (RDTs) detecting Plasmodium falciparum histidine-rich protein 2 (HRP2) have been an important tool for malaria diagnosis, especially in resource-limited settings lacking quality microscopy. Plasmodium falciparum parasites with deletion of the pfhrp2 gene encoding this antigen have now been identified in dozens of countries across Asia, Africa, and South America, with new reports revealing a high prevalence of deletions in some selected regions. To determine whether HRP2-based RDTs are appropriate for continued use in a locality, focused surveys and/or surveillance activities of the endemic P. falciparum population are needed. Various survey and laboratory methods have been used to determine parasite HRP2 phenotype and pfhrp2 genotype, and the data collected by these different methods need to be interpreted in the appropriate context of survey and assay utilized. Expression of the HRP2 antigen can be evaluated using point-of-care RDTs or laboratory-based immunoassays, but confirmation of a deletion (or mutation) of pfhrp2 requires more intensive laboratory molecular assays, and new tools and strategies for rigorous but practical data collection are particularly needed for large surveys. Because malaria diagnostic strategies are typically developed at the national level, nationally representative surveys and/or surveillance that encompass broad geographical areas and large populations may be required. Here is discussed contemporary assays for the phenotypic and genotypic evaluation of P. falciparum HRP2 status, consider their strengths and weaknesses, and highlight key concepts relevant to timely and resource-conscious workflows required for efficient diagnostic policy decision making.
Collapse
Affiliation(s)
- Khalid B Beshir
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Diseases, Keppel Street, London, WC1E 7HT, UK
| | - Jonathan B Parr
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Qin Cheng
- Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Eric Rogier
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, 30029, USA.
| |
Collapse
|
16
|
Nundu SS, Arima H, Simpson SV, Chitama BYA, Munyeku YB, Muyembe JJ, Mita T, Ahuka S, Culleton R, Yamamoto T. Low prevalence of Plasmodium falciparum parasites lacking pfhrp2/3 genes among asymptomatic and symptomatic school-age children in Kinshasa, Democratic Republic of Congo. Malar J 2022; 21:126. [PMID: 35439987 PMCID: PMC9020024 DOI: 10.1186/s12936-022-04153-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
Background Loss of efficacy of diagnostic tests may lead to untreated or mistreated malaria cases, compromising case management and control. There is an increasing reliance on rapid diagnostic tests (RDTs) for malaria diagnosis, with the most widely used of these targeting the Plasmodium falciparum histidine-rich protein 2 (PfHRP2). There are numerous reports of the deletion of this gene in P. falciparum parasites in some populations, rendering them undetectable by PfHRP2 RDTs. The aim of this study was to identify P. falciparum parasites lacking the P. falciparum histidine rich protein 2 and 3 genes (pfhrp2/3) isolated from asymptomatic and symptomatic school-age children in Kinshasa, Democratic Republic of Congo. Methods The performance of PfHRP2-based RDTs in comparison to microscopy and PCR was assessed using blood samples collected and spotted on Whatman 903™ filter papers between October and November 2019 from school-age children aged 6–14 years. PCR was then used to identify parasite isolates lacking pfhrp2/3 genes. Results Among asymptomatic malaria carriers (N = 266), 49%, 65%, and 70% were microscopy, PfHRP2_RDT, and pfldh-qPCR positive, respectively. The sensitivity and specificity of RDTs compared to PCR were 80% and 70% while the sensitivity and specificity of RDTs compared to microscopy were 92% and 60%, respectively. Among symptomatic malaria carriers (N = 196), 62%, 67%, and 87% were microscopy, PfHRP2-based RDT, pfldh-qPCR and positive, respectively. The sensitivity and specificity of RDTs compared to PCR were 75% and 88%, whereas the sensitivity and specificity of RDTs compared to microscopy were 93% and 77%, respectively. Of 173 samples with sufficient DNA for PCR amplification of pfhrp2/3, deletions of pfhrp2 and pfhrp3 were identified in 2% and 1%, respectively. Three (4%) of samples harboured deletions of the pfhrp2 gene in asymptomatic parasite carriers and one (1%) isolate lacked the pfhrp3 gene among symptomatic parasite carriers in the RDT positive subgroup. No parasites lacking the pfhrp2/3 genes were found in the RDT negative subgroup. Conclusion Plasmodium falciparum histidine-rich protein 2/3 gene deletions are uncommon in the surveyed population, and do not result in diagnostic failure. The use of rigorous PCR methods to identify pfhrp2/3 gene deletions is encouraged in order to minimize the overestimation of their prevalence. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04153-2.
Collapse
Affiliation(s)
- Sabin S Nundu
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan. .,Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan. .,Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo.
| | - Hiroaki Arima
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Shirley V Simpson
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Ben-Yeddy Abel Chitama
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Yannick Bazitama Munyeku
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Jean-Jacques Muyembe
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
| | - Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Steve Ahuka
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
| | - Richard Culleton
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan. .,Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Ehime, Japan.
| | - Taro Yamamoto
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| |
Collapse
|
17
|
Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions among patients in the DRC enrolled from 2017 to 2018. Sci Rep 2021; 11:22979. [PMID: 34837020 PMCID: PMC8626453 DOI: 10.1038/s41598-021-02452-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/15/2021] [Indexed: 11/08/2022] Open
Abstract
Rapid diagnostic tests (RDTs) detecting histidine-rich protein 2 (HRP2) and HRP3 are widely used throughout sub-Saharan Africa (SSA) to diagnose Plasmodium falciparum malaria. However, multiple SSA countries have reported pfhrp2 and pfhrp3 (pfhrp2/3) gene deletions. Blood samples (n = 1109) collected from patients with P. falciparum infection from six health facilities throughout the Democratic Republic of the Congo (DRC) from March 2017 to January 2018 were evaluated for pfhrp2/3 deletions. Samples were assayed for HRP2, pan-Plasmodium LDH (pLDH) and aldolase (pAldolase) antigens by bead-based multiplex antigen assay. Samples with low HRP2 concentration compared to pLDH and pAldolase antigens were selected for further pfhrp2/3 genotyping PCRs. The majority of blood samples (93.3%, 1035/1109) had high concentrations of the HRP2 antigen. Single deletions of pfhrp2 were identified in 0.27% (3/1109) of screened samples, with one sample from each of the Kapolowe, Mikalayi, and Rutshuru study sites. A pfhrp3 single deletion (0.09%, 1/1109) was found in the Kapolowe site. Dual pfhrp2 and pfhrp3 deletions were not observed. Due to, the low numbers of pfhrp2 deletions and the sporadic locations of these deletions, the use of HRP2-based RDTs appears to still be appropriate for these locations in DRC.
Collapse
|
18
|
Cunningham CH, Hennelly CM, Lin JT, Ubalee R, Boyce RM, Mulogo EM, Hathaway N, Thwai KL, Phanzu F, Kalonji A, Mwandagalirwa K, Tshefu A, Juliano JJ, Parr JB. A novel CRISPR-based malaria diagnostic capable of Plasmodium detection, species differentiation, and drug-resistance genotyping. EBioMedicine 2021; 68:103415. [PMID: 34139428 PMCID: PMC8213918 DOI: 10.1016/j.ebiom.2021.103415] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022] Open
Abstract
Background CRISPR-based diagnostics are a new class of highly sensitive and specific assays with multiple applications in infectious disease diagnosis. SHERLOCK, or Specific High-Sensitivity Enzymatic Reporter UnLOCKing, is one such CRISPR-based diagnostic that combines recombinase polymerase pre-amplification, CRISPR-RNA base-pairing, and LwCas13a activity for nucleic acid detection. Methods We developed SHERLOCK assays capable of detecting all Plasmodium species known to cause human malaria and species-specific detection of P. vivax and P. falciparum, the species responsible for the majority of malaria cases worldwide. We further tested these assays using a diverse panel of clinical samples from the Democratic Republic of the Congo, Uganda, and Thailand and pools of Anopheles mosquitoes from Thailand. In addition, we developed a prototype SHERLOCK assay capable of detecting the dihydropteroate synthetase (dhps) single nucleotide variant A581G associated with P. falciparum sulfadoxine resistance. Findings The suite of Plasmodium assays achieved analytical sensitivities ranging from 2•5-18•8 parasites per reaction when tested against laboratory strain genomic DNA. When compared to real-time PCR, the P. falciparum assay achieved 94% sensitivity and 94% specificity during testing of 123 clinical samples. Compared to amplicon-based deep sequencing, the dhps SHERLOCK assay achieved 73% sensitivity and 100% specificity when applied to a panel of 43 clinical samples, with false-negative calls only at lower parasite densities. Interpretation These novel SHERLOCK assays demonstrate the versatility of CRISPR-based diagnostics and their potential as a new generation of molecular tools for malaria diagnosis and surveillance. Funding National Institutes of Health (T32GM007092, R21AI148579, K24AI134990, R01AI121558, UL1TR002489, P30CA016086)
Collapse
Affiliation(s)
- Clark H Cunningham
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | - Jessica T Lin
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ratawan Ubalee
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Ross M Boyce
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Mbarara University of Science and Technology, Mbarara, Uganda
| | - Edgar M Mulogo
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Nicholas Hathaway
- University of Massachusetts School of Medicine, Worcester, MA, United States
| | - Kyaw L Thwai
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Fernandine Phanzu
- SANRU ASBL (Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Albert Kalonji
- SANRU ASBL (Global Fund), Kinshasa, Democratic Republic of the Congo
| | | | - Antoinette Tshefu
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Jonathan J Juliano
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jonathan B Parr
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
| |
Collapse
|
19
|
Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia. Nat Microbiol 2021; 6:1289-1299. [PMID: 34580442 PMCID: PMC8478644 DOI: 10.1038/s41564-021-00962-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/16/2021] [Indexed: 02/07/2023]
Abstract
In Africa, most rapid diagnostic tests (RDTs) for falciparum malaria recognize histidine-rich protein 2 antigen. Plasmodium falciparum parasites lacking histidine-rich protein 2 (pfhrp2) and 3 (pfhrp3) genes escape detection by these RDTs, but it is not known whether these deletions confer sufficient selective advantage to drive rapid population expansion. By studying blood samples from a cohort of 12,572 participants enroled in a prospective, cross-sectional survey along Ethiopia's borders with Eritrea, Sudan and South Sudan using RDTs, PCR, an ultrasensitive bead-based immunoassay for antigen detection and next-generation sequencing, we estimate that histidine-rich protein 2-based RDTs would miss 9.7% (95% confidence interval 8.5-11.1) of P. falciparum malaria cases owing to pfhrp2 deletion. We applied a molecular inversion probe-targeted deep sequencing approach to identify distinct subtelomeric deletion patterns and well-established pfhrp3 deletions and to uncover recent expansion of a singular pfhrp2 deletion in all regions sampled. We propose a model in which pfhrp3 deletions have arisen independently multiple times, followed by strong positive selection for pfhrp2 deletion owing to RDT-based test-and-treatment. Existing diagnostic strategies need to be urgently reconsidered in Ethiopia, and improved surveillance for pfhrp2 deletion is needed throughout the Horn of Africa.
Collapse
|