Table 2.

Data of the positive results for RT-PCR and sequencing obtained from clinical samples in Vietnam.

Index	Day of fever	NS1a	bCt Value (qPCR)	RT-PCRc	Flongle	Minion	dNumber of reads
							DENV1	DENV2	DENV3	DENV4	Other flaviviruses	Other viruses
i01-i20	4	+	−	+	DENV2	Not tested	3	44	0	0	0	0
i03-i15	6	+	−	−	−	DENV1	12	0	0	0	0	0
i06-i15	2	+	−	−	−	DENV4	0	0	0	16	0	0
i06-i18	3	+	39	−	−	−	0	0	0	0	0	0
i06-i19	1	+	28.2	+	DENV1	Not tested	179	0	0	0	0	0
i06-i20	4	+	41.5	−	−	DENV1	187	0	0	0	0	0
i06-i21	2	+	35.8	−	−	−	0	0	0	0	0	0
i06-i22	3	+	34	−	−	DENV1	107	0	0	0	0	0
i06-i23	2	+	32.5	+	DENV1	Not tested	43	0	0	0	0	0
i08-i20	1	−	Not tested	−		DENV1	60	0	0	0	0	0

Viral RNA was extracted from 114 serum sample, then subjected to pan-flavivirus RT-PCR and sequencing. First-round of sequencing was carried out using a Flongle flowcell. Positive samples were then excluded from the second-round sequencing (using a MinION flowcell).

^aAs a comparison, the samples were also screened with the NS1 antigen test.

^bSamples positive for NS1 were also subjected to the CDC based DENV-1-4 Real-Time RT-PCR Multiplex Assay.

^cPrior to sequencing, 1 µL of PCR product were visualized on agarose, alongside 100 bp DNA ladder (Supplementary Fig. S5).

^dReads meeting the criteria were counted at the end of analysis and presented here.