Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing

Flaherty, Briana R.; Barratt, Joel; Lane, Meredith; Talundzic, Eldin; Bradbury, Richard S.

doi:10.1186/s40168-020-00939-1

Table 3 Positive detection of multiple parasites in a single specimen using UPDx

From: Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing

Sample name	Spiked analytes	% Similarity to reference sequences	Parasite abbreviation: accession # (% reads assembled^a)	Total % reads assembled
Mix 1	*P. falciparum*	100.0% similar to Plasmodium falciparum	Pf: XR_002966654.1 (2.3%), XR_002273081.2 (2.1%)	4.4
Mix 1	*P. vivax*	100.0% similar to Plasmodium vivax	Pv: LT635616.1 (15.8%), XR_003001206.1 (43.9%)	59.7
Mix 2	*P. ovale*	100.0% similar to Plasmodium ovale wallikeri	Po: MG255222.1 (34.1%), KY073344.1 (1.5%)	35.6
Mix 2	*P. falciparum*	100.0% similar to Plasmodium falciparum	Pf: XR_002966654.1 (13.9%), XR_002273081.2 (9.3%)	23.2
Mix 3	*P. falciparum*	100.0% similar to Plasmodium falciparum	Pf: XR_002966654.1 (23.1%), XR_002273081.2 (15.1%)	38.2
Mix 3	*P. malariae*	100%% similar to Plasmodium malariae	Pm: LT594631.1 (15.9%)	15.9
Mix 4	*P. falciparum*	100.0% similar to Plasmodium falciparum	Pf: XR_002966654.1 (5.6%), XR_002273081.2 (4.5%)	10.1
Mix 4	*P. knowlesi*	100.0% similar to Plasmodium knowlesi	Pk: MF370109.1 (55.0)	55.0
Mix 5	*P. falciparum*	100.0% similar to Plasmodium falciparum	Pf: XR_002966654.1 (1.5%), XR_002273081.2 (1.3%)	2.8
	*P. vivax*	100.0% similar to Plasmodium vivax	Pv: LT635616.1 (10.0%), XR_003001206.1 (27.2%), U93234.1 (0.6%)	37.8
	*P. ovale*	100.0% similar to Plasmodium ovale wallikeri	Po: MG255222.1 (5.4%)	5.4
	*P. malariae*	100.0% similar to Plasmodium malariae	Pm: LT594631.1 (1.6%)	1.6
	*P. knowlesi*	100.0% similar to Plasmodium knowlesi	Pk: MF370109.1 (16.8)	16.8
Mix 6	*P. falciparum*	100.0% similar to Plasmodium falciparum	Pf: XR_002966654.1 (22.4%), XR_002273081.2 (12.5%)	34.9
Mix 6	*T. cruzi*	100.0% similar to Trypanosoma cruzi	Tc: CP015675.1 (20.5%), AF288661.1 (1.2%)	21.7
Mix 7	*P. vivax*	100.0% similar to Plasmodium vivax	Pv: LT635616.1 (17.4%), XR_003001206.1 (43.8%)	61.2
Mix 7	*T. cruzi*	100.0% similar to Trypanosoma cruzi	Tc: CP015675.1 (2.5%)	2.5
Mix 8	*P. falciparum*	100.0% similar to Plasmodium falciparum	Pf: XR_002966654.1 (27.0%), XR_002273081.2 (15.0%)	42.0
Mix 8	*T. brucei*	100.0% similar to Trypanosoma brucei brucei	Tb: XR_002989632.1 (10.3%)	10.3
Mix 9	*P. falciparum*	100.0% similar to Plasmodium falciparum	Pf: XR_002966654.1 (27.0%), XR_002273081.2 (15.0%)	52.2
Mix 9	*L. loa*	100.0% similar to Loa loa and Wuchereria bancrofti^b	Ll: AY843436.1 (0.91%)	0.91
Mix 10	*P. falciparum*	100.0% similar to Plasmodium falciparum	Pf: XR_002966654.1 (34.6%), XR_002273081.2 (18.4%)	49.2
Mix 10	*B. malayi*	100.0% similar to filarial nematode sequences^c	Bm: MG780293.1 (0.55%)	0.55
Natural mixed infection	N/A	100.0% similar to Plasmodium falciparum	Pf: XR_002966654.1 (0.80%), XR_002273081.2 (0.80%)	1.60
Natural mixed infection	N/A	100.0% similar to Plasmodium malariae	Pm: LT594631.1 (2.2%)	2.2

^aPercentage of reads assembled to produce a haplotype that obtained a 100% similarity BLASTN hit to the sequence associated with the accession numbers provided
^bThe sequence generated cannot distinguish between Loa loa and Wuchereria bancrofti
^cThe sequence generated from this amplicon cannot differentiate between several filarial nematodes. For example, our reference database included a sequence from Dirofilaria repens though it is important to note that the nucleotide sequence is identical to Brugia malayi at the 18S rDNA region captured by UPDx

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