Direct whole-genome sequencing of Plasmodium falciparum specimens from dried erythrocyte spots

Malaria Journal
Sidsel NagFrank M Aarestrup

Abstract

Plasmodium falciparum malaria remains a major health burden and genomic research represents one of the necessary approaches for continued progress towards malaria control and elimination. Sample acquisition for this purpose is troublesome, with the majority of malaria-infected individuals living in rural areas, away from main infrastructure and the electrical grid. The aim of this study was to describe a low-tech procedure to sample P. falciparum specimens for direct whole genome sequencing (WGS), without use of electricity and cold-chain. Venous blood samples were collected from malaria patients in Bandim, Guinea-Bissau and leukocyte-depleted using Plasmodipur filters, the enriched parasite sample was spotted on Whatman paper and dried. The samples were stored at ambient temperatures and subsequently used for DNA-extraction. Ratios of parasite:human content of the extracted DNA was assessed by qPCR, and five samples with varying parasitaemia, were sequenced. Sequencing data were used to analyse the sample content, as well as sample coverage and depth as compared to the 3d7 reference genome. qPCR revealed that 73% of the 199 samples were applicable for WGS, as defined by a minimum ratio of parasite:human DNA of 2:1. WGS reveale...Continue Reading

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Citations

Nov 14, 2019·Expert Review of Anti-infective Therapy·James CheaveauDylan R Pillai
Sep 3, 2019·Current Pharmaceutical Design·Brijesh S YadavNinoslav Marina
Dec 11, 2019·Tropical Medicine and Infectious Disease·Christian Nsanzabana

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Software Mentioned

BWA
sWGA
MGmapper
Assimpler
SAMtools
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