title: New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali.
abstract: Encoded by the var gene family, highly variable Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) proteins mediate tissue-specific cytoadherence of infected erythrocytes, resulting in immune evasion and severe malaria disease. Sequencing and assembling the 40-60 var gene complement for individual infections has been notoriously difficult, impeding molecular epidemiological studies and the assessment of particular var elements as subunit vaccine candidates.
  
  
  
  We developed and validated a novel algorithm, Exon-Targeted Hybrid Assembly (ETHA), to perform targeted assembly of var gene sequences, based on a combination of Pacific Biosciences and Illumina data.
  
  
  
  Using ETHA, we characterized the repertoire of var genes in 12 samples from uncomplicated malaria infections in children from a single Malian village and showed them to be as genetically diverse as vars from isolates from around the globe. The gene var2csa, a member of the var family associated with placental malaria pathogenesis, was present in each genome, as were vars previously associated with severe malaria.
  
  
  
  ETHA, a tool to discover novel var sequences from clinical samples, will aid the understanding of malaria pathogenesis and inform the design of malaria vaccines based on PfEMP1. ETHA is available at: https://sourceforge.net/projects/etha/ .
authors.affiliation: Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
authors.forename: Antoine
authors.initials: A
authors.lastname: Dara
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
authors.forename: Elliott F
authors.initials: EF
authors.lastname: Drábek
authors.affiliation: Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Travassos
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
authors.forename: Kara A
authors.initials: KA
authors.lastname: Moser
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
authors.forename: Arthur L
authors.initials: AL
authors.lastname: Delcher
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
authors.forename: Qi
authors.initials: Q
authors.lastname: Su
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
authors.forename: Timothy
authors.initials: T
authors.lastname: Hostelley
authors.affiliation: Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali.
authors.forename: Drissa
authors.initials: D
authors.lastname: Coulibaly
authors.affiliation: Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali.
authors.forename: Modibo
authors.initials: M
authors.lastname: Daou
authors.affiliation: Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali.
authors.forename: Ahmadou
authors.initials: A
authors.lastname: Dembele
authors.affiliation: Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali.
authors.forename: Issa
authors.initials: I
authors.lastname: Diarra
authors.affiliation: Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali.
authors.forename: Abdoulaye K
authors.initials: AK
authors.lastname: Kone
authors.affiliation: Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali.
authors.forename: Bourema
authors.initials: B
authors.lastname: Kouriba
authors.affiliation: Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Laurens
authors.affiliation: Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali.
authors.forename: Amadou
authors.initials: A
authors.lastname: Niangaly
authors.affiliation: Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali.
authors.forename: Karim
authors.initials: K
authors.lastname: Traore
authors.affiliation: Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali.
authors.forename: Youssouf
authors.initials: Y
authors.lastname: Tolo
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.|Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.|Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
authors.forename: Claire M
authors.initials: CM
authors.lastname: Fraser
authors.affiliation: Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali.
authors.forename: Mahamadou A
authors.initials: MA
authors.lastname: Thera
authors.affiliation: Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali.
authors.forename: Abdoulaye A
authors.initials: AA
authors.lastname: Djimde
authors.affiliation: Malaria Research and Training Center, University of Science, Techniques and Technologies, Bamako, Mali.
authors.forename: Ogobara K
authors.initials: OK
authors.lastname: Doumbo
authors.affiliation: Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
authors.forename: Christopher V
authors.initials: CV
authors.lastname: Plowe
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA. jcsilva@som.umaryland.edu.|Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA. jcsilva@som.umaryland.edu.
authors.forename: Joana C
authors.initials: JC
authors.lastname: Silva
mesh_terms: D000465:Algorithms; D002648:Child; D014644:Genetic Variation; D006801:Humans; D016778:Malaria, Falciparum / Q000235:genetics / Q000378:metabolism; D008302:Mali; D010963:Plasmodium falciparum / Q000235:genetics / Q000378:metabolism*; D015800:Protozoan Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D015800:Protozoan Proteins; C085731:erythrocyte membrane protein 1, Plasmodium falciparum
keywords: ETHA; Malaria; Mali; PfEMP1; Plasmodium falciparum; Plasmodium falciparum erythrocyte membrane protein-1; var; var2csa