RNA-seq of Plasmodium falciparum for comparative analysis of var genes expressed by parasites causing severe and uncomplicated malaria.. Plasmodium falciparum var genes transcribed in severe malaria

Genome wide transcriptome analyses could reveal whether P. falciparum parasites causing severe and uncomplicated malaria express different variant antigens, called PfEMP1s, that are encoded by members of the var multi-gene family. This knowledge could inform vaccine design targeting severe disease.Venous samples were collected from patients with severe (n=23) and uncomplicated (n=21) malaria in Timika, Papua Province, Indonesia. This area has unstable malaria transmission and symptomatic illness in all ages. Severe malaria was defined as peripheral parasitaemia with at least one modified World Health Organization (WHO) criterion of severity. Erythrocytes were immediately isolated from whole blood, solubilised in RNA preservative and frozen. Libraries were 100 bp paired end sequenced on a 2500-HT Hiseq (Illumina) using RapidRun chemistry (Illumina). Reads were filtered to remove reads that mapped to P. falciparum non-var gene sequences, human sequences and Plasmodium vivax sequences. The remaining reads were de novo assembled and the contigs queried by multiple approaches to identify var gene transcripts.