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Table 2 UPDx (double digest) results obtained for clinical validation specimens confirmed positive for parasites by other diagnostic methods

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

Parasite in sample (specimen #) Reads assembled Total reads % Reads assembled % Similarity to sequence GB accession
Plasmodium falciparum (Specimen 1) 7457 15,861 47.01 100.0% similar to Plasmodium falciparum XR_002966654.1b
4820 15,861 30.39 100.0% similar to Plasmodium falciparum XR_002273081.2
239 15,861 1.51 99.4% similar to Plasmodium falciparum XR_002966654.1 b
Plasmodium vivax (Specimen 2) 6584 11,546 57.02 100.0% similar to Plasmodium vivax XR_003001206.1
2820 11,546 24.42 100.0% similar to Plasmodium vivax LT635616.1
208 11,546 1.80 100.0% similar to Plasmodium vivax U93234.1
Plasmodium ovale (Specimen 3) 11,617 15,295 76.00 100.0% similar to Plasmodium ovale wallikeri MG255222.1
122 15,295 0.798 100.0% similar to Plasmodium ovale wallikeri KY073344.1
Plasmodium malariae (Specimen 4) 8754 12,200 71.75 100.0% similar to Plasmodium malariae LT594631.1
Plasmodium knowlesi (Specimen 5) 10,119 11,999 84.33 100.0% similar to Plasmodium knowlesi MF370109.1
Babesia microti (Specimen 6) 9554 10,770 88.71 100.0% similar to Babesia microti LC314658.1
Babesia divergens (Specimen 7) 11,847 13,546 87.5 100.0% similar to Babesia sp. MG944238.1
Babesia duncani (Specimen 8) 11,011 12,591 87.5 100.0% similar to Babesia duncani HQ289870.1
Babesia divergens-like variant MO1 (Specimen 9) 10,842 12,323 88.0 100.0% similar to Babesia sp. MG944238.1
Trypanosoma cruzi (clinical–Specimen 10) 1882 18,229 10.32 100.0% similar to Demodex sp.a MH891494.1
111 18,229 0.609 99.4% similar to Demodex sp.a MH891494.1
Trypanosoma cruzi (HIV+ clinical–Specimen 11) 1824 14,897 12.24 100.0% similar to Trypanosoma cruzi AF288661.1
158 14,897 1.06 100.0% similar to Trypanosoma cruzi CP015675.1
Trypanosoma cruzi (culture–Specimen 12) 8852 15,471 57.2 100.0% similar to Trypanosoma cruzi CP015675.1
182 15,471 1.18 99.4% similar to Trypanosoma cruzi CP015675.1
Trypanosoma brucei (Specimen 13) 7928 18,334 43.24 100.0% similar to Trypanosoma brucei brucei XR_002989632.1
1361 18,334 7.42 99.4% similar to Trypanosoma brucei brucei XR_002989632.1
Leishmania infantum (Specimen 14) 11,735 17,418 67.373 100.0% similar to Leishmania sp. GQ332359.1
Leishmania donovani (Specimen 15) 11,781 14,653 80.400 100.0% similar to Leishmania sp. GQ332359.1
110 14,653 0.751 99.4% similar to Leishmania sp. GQ332359.1
Brugia malayi (Specimen 16) 1042 13,117 7.944 100.0% similar to Dirofilaria repens MG780293.1
Loa loa (Specimen 17) 2003 17,439 11.49 100.0% similar to Wuchereria bancrofti AY843436.1
Mansonella perstans (Sample 18) 180 15,196 1.18 100.0% similar to Filarioidea sp. KT907503.1
  1. Note: A 100% match to a sequence does not necessarily indicate that this is the species detected. The amplicon sequenced is sufficient for a species diagnosis for only some parasites. Please refer to Fig. 5 for details
  2. aDemodex are mites that commonly inhabit the pores in normal human skin and are considered non-pathogenic, we suspect that this represents potential contamination with skin debris from the venipuncture site. T. cruzi was not detected in this specimen
  3. bExamples where multiple hits to the same accession were observed. These are both shown because the percentage similarity to these accessions is different for these two haplotypes