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Panwar V, Bansal S, Chauhan C, Sinha A. Cost analyses for malaria molecular diagnosis for research planners in India and beyond. Expert Rev Mol Diagn 2024; 24:549-559. [PMID: 38768107 DOI: 10.1080/14737159.2024.2356172] [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: 07/17/2023] [Accepted: 03/23/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND Malaria elimination mandates early and accurate diagnosis of infection. Although malaria diagnosis is programmatically dependent on microscopy/RDTs, molecular diagnosis has much better diagnostic accuracy. Higher cost of molecular diagnoses is a recognized challenge for use at the point of care. Because funding is always a recognized constraint, we performed financial cost-analyses of available molecular platforms for better utilization of available budget. METHODS Two strategies were applied to deduce the cost per sample. Strategy 1 included recurring components (RC) in minimum pack size, and biologist's time whereas strategy 2 included only RC and non-recurring components and costs are calculated for sample sizes (1-1,000,000) to infer the sample size effect. RESULTS Spin column-based manual DNA extraction (US$ 3.93 per sample) is the lowest-cost method, followed by magnetic bead-based automated, semi-automated, and PCI-based manual method. Further, DNA extraction cost per sample via spin column-based manual method and semi-automated method decreases with an increase in sample size up to 10,000. Real-time PCRs are ~ 2-fold more economical than conventional PCR, regardless of sample size. CONCLUSIONS This study is the first for malaria to estimate systematic molecular diagnosis financial costs. Kit-based and automated methods may replace conventional DNA extraction and amplification methods for a frugal high-throughput diagnosis.
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Affiliation(s)
- Vandana Panwar
- Parasite host biology laboratory, ICMR-National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, India
| | - Shivani Bansal
- Parasite host biology laboratory, ICMR-National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, India
- Department of Cytopathology, ICMR-National Institute of Cancer Prevention and Research, Sector-39A, Noida, India
| | - Charu Chauhan
- Parasite host biology laboratory, ICMR-National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, India
| | - Abhinav Sinha
- Parasite host biology Laboratory, Scientist 'F', ICMR-National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, India
- Department of Life Sciences, Academy of Scientific and Innovative Research, Ghaziabad, UP, India
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Brokhattingen N, Matambisso G, da Silva C, Neubauer Vickers E, Pujol A, Mbeve H, Cisteró P, Maculuve S, Cuna B, Melembe C, Ndimande N, Palmer B, García-Ulloa M, Munguambe H, Montaña-Lopez J, Nhamussua L, Simone W, Chidimatembue A, Galatas B, Guinovart C, Rovira-Vallbona E, Saúte F, Aide P, Aranda-Díaz A, Greenhouse B, Macete E, Mayor A. Genomic malaria surveillance of antenatal care users detects reduced transmission following elimination interventions in Mozambique. Nat Commun 2024; 15:2402. [PMID: 38493162 PMCID: PMC10944499 DOI: 10.1038/s41467-024-46535-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: 11/02/2023] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
Routine sampling of pregnant women at first antenatal care (ANC) visits could make Plasmodium falciparum genomic surveillance more cost-efficient and convenient in sub-Saharan Africa. We compare the genetic structure of parasite populations sampled from 289 first ANC users and 93 children from the community in Mozambique between 2015 and 2019. Samples are amplicon sequenced targeting 165 microhaplotypes and 15 drug resistance genes. Metrics of genetic diversity and relatedness, as well as the prevalence of drug resistance markers, are consistent between the two populations. In an area targeted for elimination, intra-host genetic diversity declines in both populations (p = 0.002-0.007), while for the ANC population, population genetic diversity is also lower (p = 0.0004), and genetic relatedness between infections is higher (p = 0.002) than control areas, indicating a recent reduction in the parasite population size. These results highlight the added value of genomic surveillance at ANC clinics to inform about changes in transmission beyond epidemiological data.
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Affiliation(s)
| | - Glória Matambisso
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Clemente da Silva
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Eric Neubauer Vickers
- EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA
| | - Arnau Pujol
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Henriques Mbeve
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Pau Cisteró
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Sónia Maculuve
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Boaventura Cuna
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Cardoso Melembe
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Nelo Ndimande
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Brian Palmer
- EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA
| | | | | | | | - Lidia Nhamussua
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Wilson Simone
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | | | - Beatriz Galatas
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | | | | | - Francisco Saúte
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Pedro Aide
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Andrés Aranda-Díaz
- EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA
| | - Bryan Greenhouse
- EPPIcenter Research Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco, California, USA
| | - Eusébio Macete
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- National Directorate for Public Health, Ministry of Health, Maputo, Mozambique
| | - Alfredo Mayor
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.
- Spanish Consortium for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain.
- Department of Physiological Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique.
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Ruybal-Pesántez S, McCann K, Vibin J, Siegel S, Auburn S, Barry AE. Molecular markers for malaria genetic epidemiology: progress and pitfalls. Trends Parasitol 2024; 40:147-163. [PMID: 38129280 DOI: 10.1016/j.pt.2023.11.006] [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: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Over recent years, progress in molecular markers for genotyping malaria parasites has enabled informative studies of epidemiology and transmission dynamics. Results have highlighted the value of these tools for surveillance to support malaria control and elimination strategies. There are many different types and panels of markers available for malaria parasite genotyping, and for end users, the nuances of these markers with respect to 'use case', resolution, and accuracy, are not well defined. This review clarifies issues surrounding different molecular markers and their application to malaria control and elimination. We describe available marker panels, use cases, implications for different transmission settings, limitations, access, cost, and data accuracy. The information provided can be used as a guide for molecular epidemiology and surveillance of malaria.
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Affiliation(s)
- Shazia Ruybal-Pesántez
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - Kirsty McCann
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Jessy Vibin
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia
| | | | - Sarah Auburn
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Alyssa E Barry
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia.
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Hamilton WL, Ishengoma DS, Parr JB, Bridges DJ, Barry AE. Nanopore sequencing for malaria molecular surveillance: opportunities and challenges. Trends Parasitol 2023; 39:996-1000. [PMID: 37865609 DOI: 10.1016/j.pt.2023.09.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/23/2023]
Abstract
Nanopore-based sequencing platforms offer the potential for affordable malaria molecular surveillance (MMS) in resource-limited settings to track and ultimately counteract emerging threats, such as drug resistance and diagnostic escape. Here, we discuss opportunities and challenges to implementing MMS using nanopore sequencing, highlighting priority areas for technical development and innovation.
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Affiliation(s)
- William L Hamilton
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1RQ, UK; University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK; Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK.
| | - 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, VIC, Australia
| | - Jonathan B Parr
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel J Bridges
- PATH, National Malaria Elimination Center, Chainama Hospital Grounds, Great East Road, Lusaka, Zambia
| | - Alyssa E Barry
- Centre for Innovation in Infectious Disease and Immunology Research, IMPACT, School of Medicine, Deakin University, Geelong, VIC 3220, Australia; Burnet Institute, Melbourne, VIC 3000, Australia.
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Mayor A, Brokhattingen N, Matambisso G, da Silva C, Vickers EN, Pujol A, Mbeve H, Cistero P, Maculuve S, Cuna B, Melembe C, Ndimande N, Palmer B, García M, Munguambe H, Lopez JM, Nhamussa L, Simone W, Chidimatembue A, Galatas B, Guinovart C, Rovira-Vallbona E, Saute F, Aide P, Aranda-Díaz A, Greenhouse B, Macete E. Genomic malaria surveillance of antenatal care users detects reduced transmission following elimination interventions in Mozambique. RESEARCH SQUARE 2023:rs.3.rs-3545903. [PMID: 38014035 PMCID: PMC10680916 DOI: 10.21203/rs.3.rs-3545903/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Routine sampling of pregnant women at first antenatal care (ANC) visits could make Plasmodium falciparum genomic surveillance more cost-efficient and convenient in sub-Saharan Africa. We compared the genetic structure of parasite populations sampled from 289 first ANC attendees and 93 children from the community in Mozambique between 2015 and 2019. Samples were amplicon sequenced targeting 165 microhaplotypes and 15 drug resistance genes. Metrics of genetic diversity and relatedness, as well as the prevalence of drug resistance markers, were consistent between the two populations. In an area targeted for elimination, intra-host genetic diversity declined in both populations (p=0.002-0.007), while for the ANC population, population genetic diversity was also lower (p=0.0004), and genetic relatedness between infections were higher (p=0.002) than control areas, indicating a recent reduction in the parasite population size. These results highlight the added value of genomic surveillance at ANC clinics to inform about changes in transmission beyond epidemiological data.
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Affiliation(s)
- Alfredo Mayor
- Barcelona Institute for Global Health / Manhiça Health Research Centre
| | | | | | | | | | - Arnau Pujol
- ISGlobal, Barcelona Center for International Health Research (CRESIB), Hospital Clínic - Universitat de Barcelona / Centro de Investigação em Saúde da Manhiça
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Beatriz Galatas
- ISGlobal, Barcelona Center for International Health Research (CRESIB), Hospital Clínic - Universitat de Barcelona / Centro de Investigação em Saúde da Manhiça
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