A new method for sequencing the hypervariable Plasmodium falciparum gene var2csa from clinical samples

Malaria Journal

Table 1 Comparison between reconstructed PacBio sequences and the respective reference var2csa alleles in 3D7 and HB3

Reference var2csa gene	Re-sequenced controls^a	Coverage depth	Sequence identity (%)	Reference length^b	PacBio length^c	Deletion length (bp)
PFL0030c	3D7_pacbio100_NumReads445	445	100	4843	4843	0
PFL0030c	3D7_pacbio70_NumReads119	119	99.94	4843	4840	3
PFL0030c	3D7_pacbio30_NumReads82	82	99.96	4843	4841	2
HB3var2csaA	HB3_pacbio100_NumReads101	101	99.98	4981	4980	1
HB3var2csaB	HB3_pacbio_100_NumReads100	100	99.98	4939	4938	1
HB3var2csaA	HB3_pacbio70_NumReads46	46	99.82	4981	4972	9
HB3var2csaB	HB3_pacbio70_NumReads59	59	99.94	4939	4936	3
HB3var2csaA	HB3_pacbio30_NumReads167	167	99.98	4981	4980	1
HB3var2csaB	HB3_pacbio30_NumReads70	70	99.94	4939	4936	3

^aThe type of control is indicated by the name of the consensus sequence: pacbio100: amplicon obtained from a single reference strain; pacbio30: amplicon obtained from a mix of reference strains in which the named strain was present at 30% of the DNA sample; pacbio70: similarly defined as pacbio30, with the named strain representing 70% of the DNA sample
^bLength of the reference var2csa allele
^cLength of the reconstructed var2csa coding sequence

ISSN: 1475-2875