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).