P. vivax Genome Variation

 

 

 

Started 2010

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

  • Brazil (BR)
  • Cambodia (KH)
  • China (CN)
  • India (IN)
  • Indonesia (ID)
  • Laos (LA)
  • Madagascar (MG)
  • Malaysia (MY)
  • Myanmar (MM)
  • Papua New Guinea (PG)
  • Sri Lanka (LK)
  • Thailand (TH)
  • Vietnam (VN)

Data

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

Current

21 Jun 2016

P. vivax Genome Variation May 2016 data release

Species: P. vivax

Sample information and genotypes for 228 samples from 13 countries

People

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

Prof Arjen Dondorp
Mahidol Oxford Tropical Medicine Research Unit (MORU), University of Oxford, Thailand
Chanaki Amaratunga
NIH National Institute of Allergy and Infectious Diseases (NIAID), USA
Dr Christiane Dolecek
Nuffield Department of Medicine, University of Oxford, UK
Dr Elizabeth Ashley
Mahidol Oxford Tropical Medicine Research Unit (MORU), University of Oxford, Thailand
Dr G L Abby Harrison
Postdoctoral Scientist
Walter and Eliza Hall Institute, Australia
Livingstone Tavul
Papua New Guinea Institute of Medical Research, PNG
Prof Maciej Boni
Head of Mathematical Modelling Group
Oxford University Clinical Research Unit (OUCRU), Vietnam
Associate Professor
Nuffield Department of Medicine, University of Oxford, UK
Dr Marcelo Ferreira
Professor of Parasitology
Universidade de São Paulo, Brazil
Dr Milijaona Randrianarivelojosia
Head of Malaria Research Unit
Institut Pasteur de Madagascar
Part-time lecturer
Universités d'Antananarivo et de Mahajanga, Madagascar
Prof Nadira Karunaweera
Chair, Head of Department and Senior Professor of Parasitology
University of Colombo, Sri Lanka
Visiting Scientist
School of Public Health, Harvard University, USA
Prof Nicholas J White
Professor of Tropical Medicine and Chair of Wellcome Trust SE Asian Tropical Medicine Research Programmes
Mahidol Oxford Tropical Medicine Research Unit (MORU), University of Oxford, Thailand
Dr Pharath Lim
NIH National Institute of Allergy and Infectious Diseases (NIAID), USA
Prof Ric N Price
Professor of Tropical Medicine
Centre for Tropical Medicine and Global Health, University of Oxford, UK
Professor of Global Health
Menzies School of Health Research, Darwin, Australia
Dr Thuy‐Nhien Nguyen
Senior Research Coordinator - Malaria
Oxford University Clinical Research Unit (OUCRU), Vietnam
Centre for Tropical Medicine and Global Health, Oxford University, UK