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P. vivax Genome Variation

Started 2010

Parasite
 

Introduction

The P. vivax Genome Variation project aims to understand genome diversity of this parasite that, because it can remain dormant in the liver for years, is particularly hard to eliminate using conventional malaria control measures.

Objectives & Coordination

Plasmodium vivax is a major cause of illness in many tropical regions, particularly South America and much of Asia. The biology of P. vivax parasites complicates efforts to study its genome: the parasites don’t grow well in culture, hampering in vitro studies, and infections are characterised by a lower density of parasites in the blood, making it difficult to isolate sufficient parasite DNA for sequencing.

The P. vivax Genome Variation project is coordinated by the MalariaGEN Resource Centre and connects multiple research groups which are primarily concerned with understanding the population genetics and identifying the genetic causes of antimalarial drug resistance in P. vivax — a major public health concern.

Our work is focused on three related objectives:

Building a catalogue of P. vivax genome variation

We aim to create a genome-wide catalogue of P. vivax polymorphisms generated by sequencing clinical samples from endemic countries, which we will then use to construct a high-resolution map of genome variation and population genetics. This resource will provide a foundation for genomic surveillance of P. vivax to guide malaria elimination.

Providing researchers with standardised genotype data on their samples

Our sequence data analysis pipeline provides researchers with high-quality genotype calls on their samples in a standardised format which enables reliable comparisons to be made with data from other studies and geographical locations.

Publishing global analyses of genome variation, population genetics and evolutionary selection

The data resources generated through this project will be valuable in addressing a range of scientific questions in addition to drug resistance. Although P. vivax causes much less mortality than P. falciparum, there is growing recognition that it can sometimes cause severe complications, raising the question of whether there are parasite genetic factors that cause some strains of P. vivax to be more virulent than others. There is also much interest in whether there are genetic types of parasite that can overcome the resistance to P. vivax infection possessed by African populations due to the Duffy negative blood group.

Sampling locations

Afghanistan, Bhutan, Brazil, Cambodia, China, India, Indonesia, Iran, Laos, Madagascar, Malaysia, Myanmar, Papua New Guinea, Sri Lanka, Thailand, Vietnam.

Data

The following data have been released by the P. vivax Genome Variation project:

Current

11 Feb 2022 Pv4: An open dataset of Plasmodium vivax - v.4.0
Species: P. vivax

Sample information for 1,895 samples from 27 countries

ENA Accessions, Genotype data, Sample metadata, SNPs

Open access

21 Jun 2016 P. vivax Genome Variation May 2016 data release
Species: P. vivax

Sample information and genotypes for 228 samples from 13 countries

Open access

For partners

Resources for partners working on parasites

Partner studies

We work with investigators who are pursuing independent partner studies in a number of malaria-endemic countries. Click a link below to learn more about their work.

11 Nov 2015 1020 Measuring in vitro drug sensitivity in Vietnam

Partner study description Samples were collected in the southern province of Binh Phuoc, Vietnam, as part of a set of clinical studies initiated by Professor Tran Tinh Hien and Christiane Dolecek in 2009…

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11 Nov 2015 1044 Genomics of parasite clearance and recrudescence rates in Cambodia

Partner study description In field-based studies, Rick Fairhurst and colleagues investigated patient responses to artemisinin combination therapies (ACTs), in three Cambodian provinces, where artemisinin resistance is entrenched (Pursat), emerging (Preah Vihear), or uncommon…

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20 Nov 2015 1046 Developing the Plasmodium vivax Genome Variation project with partners in Brazil

Partner study description Marcelo Ferreira and colleagues contributed to the early stages of the MalariaGEN Plasmodium vivax Genome Variation project by providing samples that were not themselves the basis of a partner study,…

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20 Nov 2015 1047 Developing the Plasmodium vivax Genome Variation project with partners in Sri Lanka

Partner study description Nadira Karunaweera and colleagues contributed to the early stages of the MalariaGEN Plasmodium vivax Genome Variation project by providing samples that were not themselves the basis of a partner study,…

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20 Nov 2015 1049 Developing the Plasmodium vivax Genome Variation project with partners in Vietnam

Partner study description The Oxford University Clinical Research Unit in Vietnam contributed to the early stages of the MalariaGEN Plasmodium vivax Genome Variation project by providing samples that were not themselves the basis…

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20 Nov 2015 1050 Developing the Plasmodium vivax Genome Variation project with partners in Papua New Guinea

Partner study description Ivo Mueller and colleagues contributed to the early stages of the MalariaGEN Plasmodium vivax Genome Variation project by providing samples that were not themselves the basis of a partner study,…

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21 Nov 2015 1052 Tracking Resistance to Artemisinin Collaboration (TRAC)

Partner study description TRAC is investigating the scope and spread of parasite resistance to artemisinin-based therapies at sites across Asia and Africa. The first TRAC study has been completed. This multi-centre, open-label randomised…

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21 Nov 2015 1062 Understanding malaria parasite populations and outbreaks in Papua New Guinea

Partner study description Microsatellite analysis has previously demonstrated that Plasmodium falciparum populations on the north coast of PNG are organised into distinct subpopulations. If this pattern is observed throughout PNG, maps of population…

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1098 The prevalence of asymptomatic carriage; emergence of parasite mutations conferring anti-malaria drug resistance; and G6PD deficiency in the human population, as possible impediments to malaria elimination in Ethiopia

Partner study description Since 2004, Ethiopia has adopted a species-specific treatment policy for malaria: artemether-lumefantrine (AL) for the treatment of uncomplicated Plasmodium falciparum malaria and chloroquine (CQ) for Plasmodium vivax infections. P. falciparum…

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21 Nov 2015 1102 Genotyping Plasmodium falciparum and Plasmodium vivax in Madagascar

Partner study description The island of Madagascar is geographically situated in the south western region of the Indian Ocean and amongst malaria-endemic countries, its situation is unique: historically, human migration has occurred from…

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1128 A global survey of P. vivax genome variation in samples from two GSK phase 3 clinical trials of tafenoquine in Pv relapse/reinfection (trial names DETECTIVE and GATHER)

Partner study description As a service to the P. vivax genomics scientific community, GSK made DNA from the DETECTIVE and GATHER trials available for whole genome sequencing and analysis. The whole genome sequence…

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23 Nov 2015 1154 Characterisation of drug resistance in P. falciparum and P. vivax populations from Indonesia and Thailand

Partner study description Ric Price, Rintis Noviyanti and Francois Nosten are the principal investigators in a genome-wide study that aims to characterise the molecular profile of drug resistance-conferring variants in Thai and Indonesian…

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23 Nov 2015 1157 P. vivax SNP barcode for mapping parasite transmission and spread within and across borders: a vivaxGEN initiative

Partner study description This project describes the genomic component within the broader vivaxGEN initiative. The vivaxGEN network comprises researchers and other key stakeholders from across the globe with a shared aim to develop…

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1269 Pan-African Malaria Genetic Epidemiology Network (PAMGEN) Plasmodium vivax samples

Partner study description The Plasmodium vivax samples due to be collected from Ethiopia and Madagascar will contribute to the Pan-African Malaria Genetic Epidemiology Network (PAMGEN) project. The aim of PAMGEN is to create…

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Publications

User guide

1,895 samples

from

27 countries

Project contact

People

Investigators involved in the P. vivax Genome Variation project include:

Updates

19 Apr 2022

Data release (v4.0)

We’ve released the P. vivax Genome Variation project data (v4.0). This major release includes 4.5M SNPs based on an analysis of 1,895 samples from 14 studies. Details of the release can be found in the key publication MalariaGEN et al, Wellcome Open Research 2022, 7:136 https://doi.org/10.12688/wellcomeopenres.17795.1.

16 Dec 2016

Partner data release (v3.0)

We’ve released the P. vivax Genome Variation project data (v3.0) to partners. This major release includes 1.2M SNPs and 0.3M indels based on an analysis of 733 samples from 15 partner studies. Partners with data in this release should receive an email and can login to access data on their samples.

21 Mar 2016

Partner data release (v2.0)

We’ve released the P. vivax Genome Variation project data (v2.0) to partners. This major release includes 514,477 high-quality SNPs based on an analysis of 641 samples from 14 partner studies. Partners with data in this release should receive an email and can login to access data on their samples.

26 Nov 2015

Partner data release (v1.0)

We’ve released the P. vivax Genome Variation project data (v1.0) to partners. This major release includes includes 303,616 high-quality SNPs based on an analysis of 228 samples from 12 partner studies. Partners with data in this release should receive an email and can login to access data on their samples.

8 May 2013

Initial data release to partners (v0.1)

We’ve released initial genotype data (v0.1) to partners. Partners with data in this release will have received an email, and can login to access data on their samples.