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Table 1 Details of samples subjected to WGS

From: 5WBF: a low-cost and straightforward whole blood filtration method suitable for whole-genome sequencing of Plasmodium falciparum clinical isolates

Origin

Sample name

Enrichment method

% para

Blood volume (µL)

Blood:buffer dilution

Washing filter membranea

Volume of DNA elution buffer (µL)b

Mock (3D7)

M1

None

1.10

400

n.a

n.a

200

M1WGA

sWGA

1.10

400

n.a

n.a

200

M1-15F

5WBF

1.10

400

1:10, PBS 1×

2 mL PBS 1×

200

M1-25F

5WBF

1.10

400

1:10, PBS 1×

2 mL PBS 1×

200

M1-35F

5WBF

1.10

400

1:10, PBS 1×

2 mL PBS 1×

200

M2WGA

sWGA

0.23

400

n.a

n.a

200

M2-15F

5WBF

0.23

400

1:10, PBS 1×

2 mL PBS 1×

200

M2-25F

5WBF

0.23

400

1:10, PBS 1×

2 mL PBS 1×

200

M2-35F

5WBF

0.23

400

1:10, PBS 1×

2 mL PBS 1×

200

M3WGA

sWGA

0.022

400

n.a

n.a

200

M3-15F

5WBF

0.022

400

1:10, PBS 1×

2 mL PBS 1×

200

M3-25F

5WBF

0.022

400

1:10, PBS 1×

2 mL PBS 1×

200

M3-35F

5WBF

0.022

400

1:10, PBS 1×

2 mL PBS 1×

200

Patients

P15F-50

5WBF

0.04

50

1:30, RPMI 1640

n.d

200

P15F-200

5WBF

0.04

200

1:30, RPMI 1640

n.d

200

P25F-50

5WBF

0.08

50

1:30, RPMI 1640

n.d

200

P25F-200

5WBF

0.08

200

1:30, RPMI 1640

n.d

200

P35F-50

5WBF

0.25

50

1:30, RPMI 1640

n.d

200

P35F-200

5WBF

0.25

200

1:30, RPMI 1640

n.d

200

P45F-50

5WBF

0.40

50

1:30, RPMI 1640

n.d

200

P45F-200

5WBF

0.40

200

1:30, RPMI 1640

n.d

200

P55F-50

5WBF

5.50

50

1:30, RPMI 1640

n.d

200

P55F-200

5WBF

5.50

200

1:30, RPMI 1640

n.d

200

  1. % para: parasitaemia in percentage; n.a.: not applicable; n.d.: not done
  2. aRinsing the filter with 2 mL of buffer after blood filtration is optional: as skipping the rinsing step produced satisfactory WGS results, this step was not performed for the second part of this study on parasite isolates from patients in order to simplify the protocol
  3. bElution buffer refers to DNA extraction from the unfiltered/filtered blood samples