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Table 10 PCR Oligonucleotides Used for the Molecular Characterization of the Samples [7, 13, 62, 63]

From: Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessment

Pan-fungal PCR 1 (variable 18S rRNA gene region)
 Forward primer RTP_1 5′-ATT-GGA-GGG-CAA-GTC-TGG-TG-3′
 Reverse primer RTP_2 5′-CCG-ATC-CCT-AGT-CGG-CAT-AG-3′
 Probe 1 RTP_p1 5′-3FL-TTC-AAC-TAC-gAg-CTT-TTT-AAC-Tg-3′
 Probe 2 RTP_p2 5′-LC-Red640-AAC-AAC-TTT-AAT-ATA-CgC-TAT-Tgg A-3′
Pan-fungal PCR 2 (variable ITS-2 region of the fungal rRNA operon)
 Forward primer 5.8S 5′-GTG-AAT-CAT-CGA-RTC-TTT-GAA-C-3′
 Reverse primer 28S1-rev 5′-TAT-GCT-TAA-GTT-CAG-CGG-GTA-3′
Pan-fungal PCR 3 (variable 28S rRNA gene region)
 Forward primer 28S-10 5′-GAC-ATG-GGT-TAG-TCG-ATC-CTA-3′
 Reverse primer 28S-12-rev 5′-CCT-TAT-CTA-CAT-TRT-TCT-ATC-AAC-3′
Pan-fungal PCR 4 (variable ITS-2 region of the fungal rRNA operon)
 Forward primer ITS-3 5′-GCA-TCG-ATG-AAG-AAC-GCA-GC-3′
 Reverse primer ITS-4 5′-TCC-TCC-GCT-TAT-TGA-TAT-GC-3′
Pan fungal PCR 5 (variable ITS-1 region of the fungal rRNA operon)
 Forward primer ITS-1 5′-TCC-GTA-GGT-GAA-CCT-GCG-G-3′
 Reverse primer ITS-2 5′-GCT-GCG-TTC-TTC-ATC-GAT-GC-3′
Histoplasma capsulatum PCR (gene encoding the unique fungal 100-kDa-like protein)
 Forward primer 1 Hc I 5′-GCG-TTC-CGA-GCC-TTC-CAC-CTC-AAC-3’
 Forward primer 2 Hc III 5′-GAG-ATC-TAG-TCG-CGG-CCA-GGT-TCA-3’
 Reverse primer 1 Hc IV 5′-AGG-AGA-GAA-CTG-TAT-CGG-TGG-CTT-G-3’
 Reverse primer 3 Hc II 5′-ATG-TCC-CAT-CGG-GCG-CCG-TGT-AGT-3’
Mucorales PCR (18S rRNA gene)
 Forward primer ZM1 5′-ATT-ACC-ATG-AGC-AAA-TCA-GA-3’
 Reverse primer 1 ZM3 5′-CAA-TCC-AAG-AAT-TTC-ACC-TCT-AG-3‘
 Reverse primer 2 ZM2 5′-TCC-GTC-AAT-TCC-TTT-AAG-TTT-C-3’
Duplex PCR for Entamoeba histolytica and Entamoeba dispar (fragment of the ribosomal RNA gene located on an episomal plasmid)
 Forward primer Ehd-239F 5′-ATT-GTC-GTG-GCA-TCC-TAA-CTC-A-3′
 Reverse primer Ehd-88R 5′-GCG-GAC-GGC-TCA-TTA-TAA-CA-3′
 Probe 1 histolytica-96 T (specific for E. histolytica) 5′-JOE-TCA-TTG-AAT-GAA-TTG-GCC-ATT-T-BHQ1–3′
 Probe 2 dispar-96 T (specific for E. dispar) 5′-Cy5-TTA-CTT-ACA-TAA-ATT-GGC-CAC-TTT-G-BHQ2–3′
Inhibition control PCR (Phocid herpesvirus 1 (PhHV-1) 1 gB gene)
 Forward primer PhHV-267 s 5′-GGG-CGA-ATC-ACA-GAT-TGA-ATC-3′
 Reverse primer PhHV-337as 5′-GCG-GTT-CCA-AAC-GTA-CCA-A-3′
 Probe PhHV-305tq 5′-Cy55-TTT-TTA-TGT-GTC-CGC-CAC-CAT-CTG-GAT-C-BBQ-3′
Sample quality assessment PCR (human 18S rRNA gene)
 Forward primer 18S-f 5′-CTC-TTA-GCT-GAG-TGT-CCC-GC-3′
 Reverse primer 18S-r 5′-CTT-AAT-CAT-GGC-CTC-AGT-TCC-GA-3′
 Probe 18S-p 5′-FAM-CCG-AGC-CGC-CTG-GAT-ACC-GCA-GCT-A-TAMRA-3′