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

BACKGROUND

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.

METHODS

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.

RESULTS

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 revealed an even distribution of sequence data across the 3d7 reference genome, regardless of parasitaemia. The acquired read depths varied from 16 to 99×, and coverage varied from 87.5 to 98.9% of the 3d7 reference genome. SNP-analysis of six genes, for which amplicon sequencing has been performed previously, confirmed the reliability of the WGS-data.

CONCLUSION

This study describes a simple filter paper based protocol for sampling P. falciparum from malaria patients for subsequent direct WGS, enabling acquisition of samples in remote settings with no access to electricity.

Biochemical and cellular changes in leukocyte-depleted red blood cells stored for transfusion

BACKGROUND

To evaluate biochemical and cellular changes associated with the storage of leukocyte-depleted red blood cells (RBCs).

METHODS

We investigated 10 leukocyte-depleted RBC units, randomly chosen from volunteer donors. Every week an aliquot was collected for laboratorial evaluation, which included complete cell blood count, glucose-6-phosphate dehydrogenase (G6PD) activity, extracellular sodium, potassium and pH, membrane-bound hemoglobin (MBH), band 3 profile, and quantification of RBC membrane proteins composition.

RESULTS

We observed an increase in mean cell volume (from 91.86 ± 4.65 fl to 98.10 ± 5.80 fl, day 0 vs. day 21; p < 0.05), red cell distribution width, percentage of macrocytic RBCs, reticulocyte hemoglobin content and a decreased percentage of microcytic RBCs, mean cell volume concentration and G6PD activity. The extracellular concentration of sodium decreased, and that of potassium increased significantly over time. RBC membrane composition revealed an increase in spectrin/ankyrin ratio after 21 days (from 4.84 ± 0.99 to 5.27 ± 0.94, day 0 vs. day 21; p < 0.05). At day 35, a decrease in ankyrin (from 6.44 ± 1.70% to 5.49 ± 1.96%, day 0 vs. day 35; p < 0.05), in protein 4.1/band 3, protein 4.2/band 3, and ankyrin/band 3 ratios and in band 5 was observed.

CONCLUSIONS

Our data show that leukocyte-depleted RBCs present changes in the RBC morphology, membrane protein composition, enzymatic activity, and extracellular electrolyte concentration and pH.