Journal Article Ppublish
PubMed: 42525447 DOI: 10.1099/mgen.0.001776
Benchmarking of real-time, field-deployable whole-genome sequencing of Plasmodium falciparum using Nanopore technology.
Microb Genom 12(7)
Authors: Zahra Razook, Somya Mehra, Myo T Naung, Brittany Gilchrist, Sachintha Wijegunasekara, Digjaya Utama, Dulcie Lautu-Gumal, Abebe A Fola, Didier Menard, James Kazura, Moses Laman, Ivo Mueller, Leanne J Robinson, Melanie Bahlo, Alyssa E Barry
Affiliations
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
- 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), School of Medicine, Deakin University, Geelong, Victoria, Australia.
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia. Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
- 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), School of Medicine, Deakin University, Geelong, Victoria, Australia.
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia. 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), School of Medicine, Deakin University, Geelong, Victoria, Australia. Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia. Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Madang Province, Papua New Guinea.
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Parasites and Insect Vectors, Institut Pasteur Paris, Paris, France.
- INSERM U1201, Paris, France.
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, USA.
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Madang Province, Papua New Guinea.
Abstract
Malaria parasite genomes have been generated predominantly using Illumina short-read sequencing that requires expensive equipment, is time-consuming with complex protocols, and does not adequately interrogate complex genomic regions that harbour important malaria virulence determinants. The portable Oxford Nanopore Technologies MinION platform generates long reads in real time and may overcome these limitations. We present compelling evidence that Nanopore sequencing delivers valuable additional information for malaria parasites with similar data fidelity for single nucleotide variant (SNV) calls compared to standard Illumina whole-genome sequencing. We demonstrate this through sequencing of pure Plasmodium falciparum DNA, mock infections and natural isolates from low-density, asymptomatic infections. Nanopore has low error rates for haploid SNV genotyping and identifies structural variants not detected with short reads. Nanopore genomes can be directly compared to publicly available genomes and produce high-quality end-to-end chromosome assemblies including complex, previously difficult-to-access regions. Nanopore sequencing could expedite whole-genome surveillance of malaria and provide new insights into parasite genome biology.
MeSH
Malaria, Genomics, Whole Genome Sequencing, Genome, Parasites, Benchmarking, Infections, Nanopores, Drug Resistance