Plasmodium falciparum drug resistant genotypes - SUMUT study, North Sumatera, 2015 - Codebook

Permanent identifier

https://doi.org/10.17037/DATA.00002720

Description

A dataset produced as part of the SUMUT study, investigating plasmodium falciparum drug resistant genotypes. It consists of two tables:

A Full data table that contains individual-level information on 404 participants who were found to be positive, either by pfmdr1 nested PCR or 18S rDNA nested PCR;
A Cohort data table that contains individual-level information on 195 participants who were found to be positive by microscopy and randomised to receive either dihydroartemisinin-piperaquine (DP) or artemether-lumefantrine (AL).

Data was collected in Langkat, Batubara and South Nias Regencies by Dr Inke Nadia Lubis, as part of her PhD studies 2014-2018.

Data Creators

Colin Sutherland & Inke Nadia Luis

Keywords

Indonesia, antimalarial agents, drug resistance mechanisms

Codebook

AAC 2020 marker dataset – Full data table

The Full data table contains information recorded on 404 individuals positive either by pfmdr1 nested PCR or 18S rDNA nested PCR (Snounou's method) as shown in columns E, F (Snounou, Pfmdr1) where 1 = positive PCR by the method coded.

Variable name	Variable description	Answer code	Answer label
ID	Participant ID
Regency	Regency location
		1	Batubara
		2	Lankgat
		3	South Nias
Microscopy	Microscopy
		0	Negative blood film
		1	Positive blood film
Submicr	Submicroscopic persistence
		0	Both microscopy and at least one PCR test was positive, therefore not sub-microscopic
		1	Microscopy negative and at least one PCR test positive, therefore a sub-microscopic infection
Snounou	Snounou nested PCR	1	POSITIVE
Pfmdr1	Nested PCR for PFMDR1	1	POSITIVE
Pfcrt_CVMNK	Haplotypes at codons 72 - 76 of pfcrt are coded from qPCR results (see: https://doi.org/10.1128/AAC.02539-19)
Pfcrt_CVIET	Haplotypes at codons 72 - 76 of pfcrt are coded from qPCR results (see: https://doi.org/10.1128/AAC.02539-19)
Pfcrt_SVMNT	Haplotypes at codons 72 - 76 of pfcrt are coded from qPCR results (see: https://doi.org/10.1128/AAC.02539-19)
K13Mutant	Genotype
		0	Genotype absent
		1	Genotype present
		2	Mixed genotype – both mutant and wild-type present
K13_Summ	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13__G449	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13__N458	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13__T474	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13__M476	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13__A481	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13__Y493	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_T508	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_P527	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_G533	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_N537	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_R539	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_I543	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_P553	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_R561	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_V568	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_P574	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_C580	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_D584	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_E612	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_S623	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_Y456H	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_E461G	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_S521P	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_N523S	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_T535A	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_Y541H	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_C542R	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_V568A	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_T593A	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_N609S	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_Y616H	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_F628L	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_N642S	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
K13_P655S	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
Pfmdr1_86N	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
Pfmdr1_86Y	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
Pfmdr1_N86_86Y	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
Pfmdr1_86S	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
Pfmdr1_86F	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
Pfmdr1_184Y	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded
Pfmdr1_184F	Genotype	0 = genotype absent; 1= genotype present; NULL=no value recorded

AAC 2020 marker dataset – Cohort data table

The Cohort data table contains information on 195 individuals positive by microscopy and randomised to receive either DP or AL. In total, 90 individuals received AL and 105 individuals received DP. Methodology outlined in the following papers:

Plasmodium falciparum Isolates Carrying pfk13 Polymorphisms Harbor the SVMNT Allele of pfcrt in Northwestern Indonesia (https://doi.org/10.1128/AAC.02539-19)
Recurrence of Plasmodium malariae and P. falciparum Following Treatment of Uncomplicated Malaria in North Sumatera With Dihydroartemisinin-Piperaquine or Artemether-Lumefantrine (https://doi.org/10.1093/ofid/ofaa116)

For genotype columns, the digits 0 and 1 represent presence and absence of the variant genotype, except for columns 0 and P (day0_Pfmdr1_86, day0_Pfmdr1_184), where text is used; N86Y and Y184F denote mixed genotypes.

Regency: 1=Batubara, 2=Lankgat, 3=South Nias.

Row H (P_vivax): Presence of P. vivax as seen by microscopists. Protocol allowed recruitment of mixed species infections where both P. falciparum and P. vivax were present.

Row N (PCR_Species_call): PCR investigations conducted post hoc found a much more complex mix of parasie species in these 195 individuals (see https://doi.org/10.1093/ofid/ofaa116).

Columns T, U, V (Pfcrt_d0_CVMNK, Pfcrt_d0_CVIET, Pfcrt_d0_SVMNT): Haplotypes at codons 72 - 76 of pfcrt are coded from qPCR results (see https://doi.org/10.1128/AAC.02539-19).

Variable name	Variable description	Answer code	Answer label
ID	Participant ID	SUMUT-
Regency	Regency location
		1	Batubara
		2	Lankgat
		3	South Nias
Age_months	Participant age in months
Sex	Participant sex
		Female	Female
		Male	Male
Wt_kg	Weight in kilograms
Ht_cm	Height in centimetres
Treatment	Treatment type
		AL	artemether-lumefantrine
		DP	dihydroartemisinin-piperaquine
P_vivax	Presence of P. vivax as seen by microscopists. Protocol allowed recruitment of mixed species infections where both P. falciparum and P. vivax were present
		0	No
		1	Yes
Pf_asex_d0	P. falciparum asexual parasites per mL peripheral blood by microscopy
Pf_sex_d0	P. falciparum gametocytes per mL peripheral blood by microscopy
Pv_asex_d0	P. vivax asexual parasites per mL peripheral blood by microscopy
Pv_sex_d0	P. vivax gametocytes per mL peripheral blood by microscopy
Asexual_d0	Repeat of column I – can be deleted?
PCR_Species_call	PCR investigations conducted post hoc found a much more complex mix of parasite species in these 195 individuals (see https://doi.org/10.1093/ofid/ofaa116)
		Pf	Plasmodium falciparum
		Pk	Plasmodium knowlesi
		Pm	Plasmodium malariae
		Pv	Plasmodium vivax
day0_Pfmdr1_86
		86S	codon 86 Ser
		86Y	Codon 86 Tyr
		N86	Codon 86 Asn
		N86Y	Mixed genotypes
day0_Pfmdr1_184
		184F	Codon 184 Phe
		Y184	Codon 184 Tyr
day0_Pfmdr1_1034	Genotype
		0	Variant genotype absent
		1	Variant genotype present
		NULL	Not recorded
day0_Pfmdr1_1042	Genotype
		0	Variant genotype absent
		1	Variant genotype present
		NULL	Not recorded
day0_Pfmdr1_1246	Genotype
		0	Variant genotype absent
		1	Variant genotype present
		NULL	Not recorded
Pfcrt_d0_CVMNK	Haplotypes at codons 72 - 76 of pfcrt are coded from qPCR results (see: https://doi.org/10.1128/AAC.02539-19
		0	CVMNK genotype absent
		1	CVMNK genotype present
		NULL	Not recorded
Pfcrt_d0_CVIET	Haplotypes at codons 72 - 76 of pfcrt are coded from qPCR results (see: https://doi.org/10.1128/AAC.02539-19
		0	CVIET genotype absent
		1	CVIET genotype present
		NULL	Not recorded
Pfcrt_d0_SVMNT	Haplotypes at codons 72 - 76 of pfcrt are coded from qPCR results (see: https://doi.org/10.1128/AAC.02539-19
		0	SVMNT genotype absent
		1	SVMNT genotype present
		NULL	Not recorded
K13_d0_wild-type	Genotype
K13_d0_T474A	Genotype
		0	Variant genotype absent
		1	Variant genotype present
		NULL	Not recorded