An expanded global inventory of allelic variation in the most extremely polymorphic region of Plasmodium falciparum merozoite surface protein 1 provided by short read sequence data

Table 1 Major allelic types of msp1 block 2 determined by alignment of short reads to a library of reference sequences

Region	Number	Number (and %) of each allelic sequence type detected
Region	Number	K1-like	MAD20-like	RO33-like	MR recombinant
Africa	2462	1119 (45.5)	618 (25.1)	610 (24.8)	115 (4.7)
Asia	1353	336 (24.8)	766 (56.6)	250 (18.5)	1 (0.1)
All	3815	1455 (38.1)	1384 (36.3)	860 (22.5)	116 (3.0)

Short read Illumina sequence data for 2400 P. falciparum infection isolates in the Pf3k project were aligned to a library of reference msp1 block 2 sequences to determine the presence of each allelic type. Overall, 3815 alleles were scored in 2385 of the isolates. MR recombinant alleles were detected by the presence of a specific MR identifier sequence, and in infections where MR recombinant alleles were detected, additional presence of MAD20-like and RO33-like alleles was checked for by searching aligned reads for the respective non-recombinant 3′ and 5′ sequences

ISSN: 1475-2875