Table 2 Genome-wide versus microhaplotype-based identity by descent (IBD) estimates in P. vivax infection pairs

From: Lineage-informative microhaplotypes for recurrence classification and spatio-temporal surveillance of Plasmodium vivax malaria parasites

Initial infection

Recurrent infection

Patient sampling framework

Site

Region

Year

No. days until recurrence

Genome-wide IBD fraction (*recurrence classification)

Microhaplotype IBD fraction (*recurrence classification)

VVX01694

VVX01695

Clinical survey: TQ vs PQ26

Oddar Meanchey, Cambodia

ESEA

2015

43

1.000 (clone)

1.000 (clone)

VVX01743

VVX01744

Clinical survey: TQ vs PQ26

Oddar Meanchey, Cambodia

ESEA

2015

169

1.000 (clone)

1.000 (clone)

VVX01078

VVX12129

Clinical survey: 7- vs 14-day PQ27

Dak O, Vietnam

ESEA

2015

332

0.997 (clone)

0.973 (clone)

VVX01026

VVX12145

Clinical survey: 7- vs 14-day PQ27

Krong Pa, Vietnam

ESEA

2015

130

0.070 (distant relative)

0.110 (distant relative)

VVX12151

VVX12078

Clinical survey: 7- vs 14-day PQ27

Krong Pa, Vietnam

ESEA

2016

53

1.000 (clone)

1.000 (clone)

VVX12078

VVX12150

Clinical survey: 7- vs 14-day PQ27

Krong Pa, Vietnam

ESEA

2016

49

1.000 (clone)

1.000 (clone)

VVX01303

VVX01304

Clinical survey: TQ vs PQ26

Bangkok, Thailand

WSEA

2014

61

0.999 (clone)

0.977 (clone)

PD0607-C

PD0623-C

Clinical survey: AS vs CQ vs CQ + PQ28

Tak, Thailand

WSEA

2001

136

1.000 (clone)

0.977 (clone)

PY0023-C

PY0023-CW

Clinical survey: CQ vs AM29

Sabah, Malaysia

MSEA

2014

12

1.000 (clone)

0.975 (clone)

PY0109-CWx

PY0109-Cx

Clinical survey: CQ vs AM29

Sabah, Malaysia

MSEA

2013

29

1.000 (clone)

0.937 (clone)

PY0081-C

PY0067-C

Clinical survey: CQ vs AM29

Sabah, Malaysia

MSEA

2014

29

1.000 (clone)

1.000 (clone)

PY0082-C

PY0072-C

Clinical survey: CQ vs AM29

Sabah, Malaysia

MSEA

2014

28

1.000 (clone)

1.000 (clone)

PJ0005-C

PJ0009-C

Returning travellers**

Papua Indonesia

OCE

2010

861

0.036 (stranger)

0.000 (stranger)

PJ0167-C

PJ0166-C

Returning travellers**

Papua Indonesia

OCE

2013

71

0.048 (stranger)

0.156 (distant relative)

  1. List of sample pairs evaluated for relatedness as a fraction of the genome IBD using genome-wide and microhaplotype-based data. Microhaplotype-based analyses were conducted using the High-diversity 100 microhaplotype panel. IBD fractions were determined using hmmIBD software, with microhaplotype variants analysed as biallelic SNPs. Clinical survey treatments; TQ (tafenoquine), PQ (primaquine), AS (artesunate), CQ (chloroquine), AM (artesunate-mefloquine). *Recurrence classification; clone (IBD ≥ 0.95), close relative (0.25 ≤ IBD < 0.95), distant relative (0.05 ≤ IBD < 0.25), stranger (IBD < 0.05). **Returning travellers presenting at the Royal Darwin Hospital, Darwin, Australia.
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