Geographic genetic profiling of human Plasmodium malaria
Lead Research Organisation:
London School of Hygiene & Tropical Medicine
Department Name: Infectious and Tropical Diseases
Abstract
Malaria caused by Plasmodium falciparum kills about 600,000 people per year, and increased population mobility through international air travel carries further risks of re-introducing parasites to elimination areas and dispersing drug resistant parasites to new regions. A simple genetic marker that quickly and accurately identifies the geographic origin of infections would be a valuable tool for locating the source of outbreaks, and spotting the spread of drug resistant parasites from Asia into Africa. Genetic markers have proved extremely valuable in tracking and eradicating diseases, such as Polio. However, the previous candidates for malaria genetic barcodes have relied on identifying DNA markers found in the parasite nucleus, which shows too much genetic variation between individual parasites to be used accurately. Now, DNA sequences found outside the nucleus in organelles called the mitochondria and the apicoplast have been analysed. These are only inherited through maternal lines and therefore much more stable over generations than nuclear DNA sequences. The research outlined in this methodology proposal will create computational tools which will help to exploit use of mitochondria and the apicoplast sequences to create reliable genetic barcodes for tracking the geographical movement of malaria in an operational context.
Human malaria can be caused by one of 6 different Plasmodium species. We will develop genetic barcodes based on mitochondria and apicoplast sequences for each of the 6 species. We will develop new analytical approaches which can discriminate the different species even in mixed infections. We will also refine the exisiting barcoding methodology for discrimninating between infections originating from geographically distinct populations of the same species. Most crucially we will develop analytical software which can infer barcodes from complex mixed infections which are commonly found in malaria patients in many parts of the world.
We will create a publically available online resource to facilitate the widespread use of barcoding. It will be of practical use to malaria control agencies and research groups worldwide.
Human malaria can be caused by one of 6 different Plasmodium species. We will develop genetic barcodes based on mitochondria and apicoplast sequences for each of the 6 species. We will develop new analytical approaches which can discriminate the different species even in mixed infections. We will also refine the exisiting barcoding methodology for discrimninating between infections originating from geographically distinct populations of the same species. Most crucially we will develop analytical software which can infer barcodes from complex mixed infections which are commonly found in malaria patients in many parts of the world.
We will create a publically available online resource to facilitate the widespread use of barcoding. It will be of practical use to malaria control agencies and research groups worldwide.
Technical Summary
We propose to develop:
1. A library of apicoplast and mitochondrial genomic sequence variants across multiple human Plasmodium species P. falciparum, P. vivax, P. ovale curtisi, P. ovale wallikeri, P. malariae, and P. knowlesi using existing raw genomic sequence data generated by collaborating investigators with external funding.
2. A statistical algorithm to infer informative SNP haplotypes within and between species from complex mixed infections. The perfect linkage disequilibrium or "perfect phylogeny" across the co-inherited organelle SNPs leads to an opportunity to construct phylogenetic trees that represent the relationship between haplotypes. Crucially this allows modelling approaches to disaggregate complex mixed infections.
3. Prototype barcodes based on newly generated mt/apico sequences for Pv, Po, Pm, and Pk, in partnership with collaborators;
4. A proof of principle. In collaboration with overseas research colleagues who have raw genomic sequence data suspected to contain mixed species co-infection (e.g. P. falciparum + P. malariae in Kenya, P. falciparum+P. vivax in Thailand). Colleagues at the National Institute of Parasitic Diseases at the Chinese Center for Disease Control and Prevention in Shanghai, China are genotyping local and putative imported infections from archived bloodspot samples and we will reanalyse these using the published Pf barcoding methodology of 23 SNPs developed using a classification and regression tree (CART) algorithm (Preston et al Nature Communications in press).
5. An online resource, which summarises the library of mt/api genomic variants and barcode haplotypes, and facilitates the input of sequence data for the rapid identification of species and the potential geographic source of (imported) infections.
1. A library of apicoplast and mitochondrial genomic sequence variants across multiple human Plasmodium species P. falciparum, P. vivax, P. ovale curtisi, P. ovale wallikeri, P. malariae, and P. knowlesi using existing raw genomic sequence data generated by collaborating investigators with external funding.
2. A statistical algorithm to infer informative SNP haplotypes within and between species from complex mixed infections. The perfect linkage disequilibrium or "perfect phylogeny" across the co-inherited organelle SNPs leads to an opportunity to construct phylogenetic trees that represent the relationship between haplotypes. Crucially this allows modelling approaches to disaggregate complex mixed infections.
3. Prototype barcodes based on newly generated mt/apico sequences for Pv, Po, Pm, and Pk, in partnership with collaborators;
4. A proof of principle. In collaboration with overseas research colleagues who have raw genomic sequence data suspected to contain mixed species co-infection (e.g. P. falciparum + P. malariae in Kenya, P. falciparum+P. vivax in Thailand). Colleagues at the National Institute of Parasitic Diseases at the Chinese Center for Disease Control and Prevention in Shanghai, China are genotyping local and putative imported infections from archived bloodspot samples and we will reanalyse these using the published Pf barcoding methodology of 23 SNPs developed using a classification and regression tree (CART) algorithm (Preston et al Nature Communications in press).
5. An online resource, which summarises the library of mt/api genomic variants and barcode haplotypes, and facilitates the input of sequence data for the rapid identification of species and the potential geographic source of (imported) infections.
Planned Impact
Malaria caused by Plasmodium falciparum kills about 600,000 people per year, and increased population mobility through international air travel carries further risks of re-introducing parasites to elimination areas and dispersing drug resistant parasites to new regions. A simple genetic marker that quickly and accurately identifies the geographic origin of infections would be a valuable tool for locating the source of outbreaks, and spotting the spread of drug resistant parasites from Asia into Africa. Genetic markers have proved extremely valuable in tracking and eradicating diseases, such as Polio. However, the previous candidates for malaria genetic barcodes have relied on identifying DNA markers found in the parasite nucleus, which shows too much genetic variation between individual parasites to be used accurately. DNA sequences found outside the nucleus in organelles called the mitochondria and the apicoplast are only inherited through maternal lines and therefore much more stable over generations than nuclear DNA sequences. The research outlined in this methodology proposal will create computational tools which will help to exploit use of mitochondria and the apicoplast sequences to create reliable genetic barcodes for tracking the geographical movement of malaria in an operational context. We aim to create an analytical framework which will support simple genetic barcoding for use by National Malaria Control Programmes who are engaged in malaria elimination. Other potential beneficiaries are all those engaged in malaria control and malaria treatment who's work will benefit from new knowledge about how malaria parasite populations are interconnected.
Organisations
- London School of Hygiene & Tropical Medicine (Lead Research Organisation)
- Universidade de São Paulo (Collaboration)
- University of Oklahoma (Collaboration)
- Oswaldo Cruz Foundation (Fiocruz) (Collaboration)
- LGC Ltd (Collaboration)
- Menzies School of Health Research (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
- Agency for Science, Technology and Research (A*STAR) (Collaboration)
People |
ORCID iD |
Taane Clark (Principal Investigator) | |
Cally Roper (Co-Investigator) |
Publications
Acford-Palmer H
(2023)
Identification of two insecticide resistance markers in Ethiopian Anopheles stephensi mosquitoes using a multiplex amplicon sequencing assay
in Scientific Reports
Ajawatanawong P
(2019)
A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages.
in Scientific reports
Andreu N
(2017)
Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis.
in Scientific reports
Ansari HR
(2016)
Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species.
in International journal for parasitology
Assefa S
(2015)
Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi.
in Proceedings of the National Academy of Sciences of the United States of America
Auburn S
(2018)
Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics.
in Nature communications
Benavente ED
(2018)
A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line.
in International journal for parasitology
Benavente ED
(2018)
Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development.
in Scientific reports
Benavente ED
(2021)
Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa.
in Nature communications
Description | NIH Research grant |
Amount | $2,100,000 (USD) |
Funding ID | 2R01AI103629 - 04A1 |
Organisation | National Institutes of Health (NIH) |
Sector | Public |
Country | United States |
Start | 08/2017 |
End | 08/2021 |
Description | Newton Institutional Links Grant |
Amount | £279,000 (GBP) |
Funding ID | 261868591 |
Organisation | British Council |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 04/2017 |
End | 04/2019 |
Description | Newton Researcher Links Workshop Grants (Infectious Disease 'Omics (Philippines) ) |
Amount | £60,000 (GBP) |
Funding ID | 2017-RLWK8-10671 |
Organisation | Newton Fund |
Sector | Public |
Country | United Kingdom |
Start | 01/2018 |
End | 12/2018 |
Description | Newton Researcher Links Workshop Grants (Infectious Disease 'Omics (Philippines) ) |
Amount | £60,000 (GBP) |
Funding ID | Ref. 2017-RLWK9-110970 |
Organisation | Newton Fund |
Sector | Public |
Country | United Kingdom |
Start | 04/2018 |
End | 12/2018 |
Title | Molecular barcode for Plasmodia |
Description | A software tool to call malaria parasite species from whole genome sequencing data. Ongoing work is developing a molecular assay for a field setting. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2018 |
Provided To Others? | No |
Impact | It will have impact. A manuscript is under review, and a molecular assay is under development. |
Title | New barcode for Plasmodium vivax |
Description | We have now developed a molecular barcode for Plasmodium vivax, and an informatics tool to translate sequence data into a geographical and transmission profile. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | There is no impact as yet. |
Title | Sequence data analysis pipelines |
Description | We have established bioinformatic pipelines to process large numbers of sample sequences, and identify informative genomic variants. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2015 |
Provided To Others? | Yes |
Impact | More rapid and accurate analysis by ourselves and collaborators, leading to new research insights. We propose to publish our methods and make them available to the research community. |
Title | Malaria sequencing database |
Description | We have processed sequences for over 2000 malaria samples, and all genomic variants detected have been assembled in a database. |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
Impact | It has allowed our collaborators to investigate their genes of interest. We plan to make the database accessible to the research community after further testing and confirmation of variants. |
Title | Neglected malaria sequence data |
Description | To fill in gaps in Plasmodium genomics, and to improve our geographical and species barcodes, we have sequenced >500 P. vivax, P. malaria and P. ovale parasites. |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | No |
Impact | We have a new molecular barcode for malaria speciation, geographical source and drug resistance. This has been implemented within a new software tool ("Malaria_Profiler"), which we will release in the next few months via a manuscript in preparation. |
Description | Brazil Falciparum & Vivax - Simone Santos Silva Oliveira |
Organisation | Oswaldo Cruz Foundation (Fiocruz) |
Country | Brazil |
Sector | Public |
PI Contribution | Analysis of genetic data. |
Collaborator Contribution | Contributing malaria samples to sequence. |
Impact | Sequence data is being generated. |
Start Year | 2015 |
Description | Brazil Falciparum and Vivax - Claudio Marinho |
Organisation | Universidade de São Paulo |
Department | Department of Parasitology |
Country | Brazil |
Sector | Academic/University |
PI Contribution | Supported visitor that came to work in the laboratory. |
Collaborator Contribution | DNA Samples. A technician visited to work on samples. |
Impact | A draft manuscript. Samples genotyped. |
Start Year | 2016 |
Description | Brazil Vivax - Marcelo Urbano Ferreira |
Organisation | Universidade de São Paulo |
Country | Brazil |
Sector | Academic/University |
PI Contribution | Analysis of P.vivax sequence data for the collaborator. |
Collaborator Contribution | Contributing P.vivax sequence data to the MRC funded barcoding project. |
Impact | A manuscript describing P.vivax diversity is in preparation. |
Start Year | 2016 |
Description | Cambodia Vivax - Rich Fairhurst |
Organisation | National Institutes of Health (NIH) |
Country | United States |
Sector | Public |
PI Contribution | Sequencing of malaria samples |
Collaborator Contribution | Malaria samples to sequence. |
Impact | Samples are being prepared. |
Start Year | 2015 |
Description | Malaria genotyping - Jonathan Curry |
Organisation | LGC Ltd |
Country | Global |
Sector | Private |
PI Contribution | Samples provided for genotyping |
Collaborator Contribution | Genotyping of 200 samples |
Impact | Genotyping data, currently being written up for a publication. |
Start Year | 2016 |
Description | Malaysia - Knowlesi |
Organisation | Menzies School of Health Research |
Country | Australia |
Sector | Academic/University |
PI Contribution | Sequencing of malaria samples. |
Collaborator Contribution | Malaria samples for sequencing. |
Impact | Samples have been sent. |
Start Year | 2015 |
Description | Pakistan Vivax - Nazma Habib Khan |
Organisation | University of Oklahoma |
Department | Department of Zoology |
Country | United States |
Sector | Academic/University |
PI Contribution | Sequencing of P.vivax samples |
Collaborator Contribution | Contributed P.vivax samples. |
Impact | Malaria samples are about to be sequenced. |
Start Year | 2016 |
Description | Sequencing - GIS |
Organisation | Agency for Science, Technology and Research (A*STAR) |
Department | Genome Institute of Singapore |
Country | Singapore |
Sector | Academic/University |
PI Contribution | Samples for pacino sequencing |
Collaborator Contribution | Sequencing data. |
Impact | Sequence data, and scientific publications. |
Start Year | 2016 |
Description | Capacity building workshop in LSHTM |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Study participants or study members |
Results and Impact | 35 participants (including collaborators and partners) attended a genomic data workshop where malaria data (including generated by the project) was analysed. Future projects were discussed. |
Year(s) Of Engagement Activity | 2017,2018 |