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. 2018 Aug 9;219(2):315–322. doi: 10.1093/infdis/jiy484

Table 4.

Genetic Differences Investigated by Genotyping and Whole-Genome Sequencing Between Parasites Collected From the Day of Initial Infection Identification (D0) and the Day of Recurrent Infection Identification (Dx), Ratanakiri, Cambodia, 2014

Relocation Status, Patient ID Dx Genotyping Whole-Genome Sequencing Potential Origin of Recurrent Parasitesc
Coverage, No. of Reads, D0 Coverage, No. of Reads, Dx New Allelesa Coverage, No. of Reads, D0 Coverage, No. of Reads, Dx New Allelesb
Relocated
 BL02 41 2184 1575 0/73 299 122 5437/21277399 Heterologous relapse (from related clones)
 BL03 60 2921 1425 0/87 313 Homologous relapse
 BL07 59 2472 403 5/51 271 7 Heterologous relapse
 BL08 36 2713 1572 1/96 171 Homologous relapse
 BL10 56 1546 1956 22/86 205 177 35400/21105486 Heterologous relapse
 BL11 48 3438 1797 1/96 431 146 4442/20705930 Heterologous relapse (from related clones)
 BL12 47 2292 1334 18/101 153 377 19930/21279386 Heterologous relapse
 BL18 58 2155 1145 6/82 374 163 3614/21299372 Heterologous relapse (from related clones)
Nonrelocated
 V04 53 1544 2645 14/102 131 182 20627/20313219 Heterologous relapse (or reinfection)
 V10 53 1958 357 181 37455/20167617 Heterologous relapse (or reinfection)
 V16 49 1330 2078 0/91 262 Homologous relapse
 V17 58 1650 1462 20/81 247 175 19743/21381922 Heterologous relapse (or reinfection)
 V27 62 1820 1208 0/64 217 Homologous relapse

Data are average sequence coverage (Cov) and number of new alleles detected in the recurrent infection obtained for each patient by genotyping and whole-genome sequencing, respectively.

Abbreviations: ID, identifier; SNP, single-nucleotide polymorphism.

aGenotyping of 128 SNPs was attempted; the number of SNPs successfully genotyped in both initial and recurrent infections is indicated as the denominator. The number of new alleles detected is further influenced by the polyclonality of the infections [26].

bThe number of nucleotides analyzed is indicated as the denominator. The number of new alleles detected is further influenced by the polyclonality of the infections [26].

cHeterologous relapses can be caused by relapse of clones unrelated to those present in the initial infections (leading to >15000 new alleles) or by sibling/recombinant clones (leading to only 3000–6000 new alleles detected by whole-genome sequencing and, typically, to only a handful of differences detected by genotyping).