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Table 2 PCR primers and cycling protocols to amplify target sequences from Cryptosporidium, Cyclospora, Giardia and Entamoeba

From: Molecular characterisation of protist parasites in human-habituated mountain gorillas (Gorilla beringei beringei), humans and livestock, from Bwindi Impenetrable National Park, Uganda

Parasite PCR target Size (bp) Primer Reference Cycling protocol Reference
Cyclospora SSU 1000 ExCycF (forward: 5′-AATGTAAAACCCTTCCAGAGTAAC-3′) [90] 94 °C/ 5 min, followed by 35 cycles of 94 °C/ 45 s, 55 °C/ 45 s and 72 °C/ 1 min, with a final extension of 72 °C/ 10 min [91]
    ExCycR (reverse: 5′-GCAATAATCTATCCCCATCACG-3′)
   500 NesCycF (forward: 5′-AATTCCAGCTCCAATAGTGTAT-3′) Secondary amplification was achieved employing identical PCR conditions to those used in the primary PCR
    NesCycR (reverse: 5′-CAGGAGAAGCCAAGGTAGGCRTTT-3′)
Cryptosporidium SSU 824–864 XF2 (forward: 5′-GGAAGGGTTGTATTTATTAGATAAAG-3′) [92] 94 °C/ 5 min, followed by 35 cycles of 94 °C/ 45 s, 60 °C/ 45 s and 72 °C/ 1 min, with a final extension of 72 °C/ 10 min [92]
    XR2 (reverse: 5′-AAGGAGTAAGGAACAACCTCCA-3′)
   298 18SiF (forward: 5′-AGTGACAAGAAATAACAATACAGG-3′) [93] 94 °C/ 5 min, followed by 35 cycles of 94 °C/ 45 s, 50 °C/ 45 s and 72 °C/ 1 min, with a final extension of 72 °C/ 10 min [93]
    18SiR (reverse: 5′-CCTGCTTTAAGCACTCTAATTTTC-3′)
  gp60 1000 AL3531 (forward: 5′-ATAGTCTCCGCTGTATTC-3′) [94] 94 °C/ 5 min, followed by 35 cycles of 94 °C/ 45 s, 50 °C/ 45 s and 72 °C/ 1 min, with a final extension of 72 °C/ 10 min [95]
    AL3535 (reverse: 5′-GGAAGGAACGATGTATCT-3′) [96]
   457 AL3532 (forward: 5′-TCCGCTGTATTCTCAGCC-3′) [94] Secondary amplification was achieved employing identical PCR conditions to those used in the primary PCR
    AL3533 (reverse: 5′-GAGATATATCTTGGTGCG-3′)
Giardia tpi 605 AL3543 (forward: 5′-AAATTATGCCTGCTCGTCG-3′) [84] 94 °C/ 5 min, followed by 35 cycles of 94 °C/ 45 s, 50 °C/ 45 s and 72 °C/ 1 min, with a final extension of 72 °C/ 10 min [84]
    AL3546 (reverse: 5′-CAAACCTTTTCCGCAAACC-3′)
   530 AL3544 (forward: 5′-CCCTTCATCGGTGGTAACTT-3′) Secondary amplification was achieved employing identical PCR conditions to those used in the primary PCR
    AL3545 (reverse: 5′-GTGGCCACCACTCCCGTGCC-3′)
  bg 753 G7 (forward: 5′-AAGCCCGACGACCTCACCCGCAGTGC-3′) [63] 94 °C/ 5 min, followed by 35 cycles of 94 °C/ 30 s, 65 °C/ 30 s and 72 °C/ 1 min, with a final extension of 72 °C/ 7 min [63]
    G759 (reverse: 5′-GAGGCCGCCCTGGATCTTCGAGACGAC-3′)
   511 bgiF (forward: 5′-GAACGAACGAGATCGAGGTCCG-3′) [97] 95 °C/ 15 min, followed by 35 cycles of 95 °C/ 30 s, 55 °C/ 30 s and 72 °C/ 1 min, with a final extension of 72 °C/ 7 min [97]
    bgiR (reverse: 5′-CTCGACGAGCTTCGTGTT-3′)
  gdh 786 Ghd1 (forward: 5′-TTCCGTRTYCAGTACAACTC-3′) [53] 94 °C/ 2 min, followed by 35 cycles of 94 °C/ 30 s, 50 °C/ 30 s and 72 °C/ 1 min, with a final extension of 72 °C/ 7 min [53]
    Gdh2 (reverse: 5′-ACCTCGTTCTGRGTGGCGCA-3′)
   530 Gdh3 (forward: 5′-ATGACYGAGCTYCAGAGGCACGT-3′) Secondary amplification was achieved employing identical PCR conditions to those used in the primary PCR
    Gdh4 (reverse: 5′-GTGGCGCARGGCATGATGCA-3′)
  SSU 497 Gia2029 (forward: 5′-AAGTGTGGTGCAGACGGACTC-3′) [98] 94 °C/ 4 min, followed by 35 cycles of 96 °C/ 45 s, 55 °C/ 30 s and 72 °C/ 45 s, with a final extension of 72 °C/ 4 min [98]
    Gia2150c (reverse: 5′-CTGCTGCCGTCCTTGGATGT-3′)  
   292 RH11 (forward: 5′-CATCCGGTCGATCCTGCC-3′) [99] 94 °C/ 4 min, followed by 35 cycles of 96 °C/ 45 s, 59 °C/ 30 s and 72 °C/ 45 s, with a final extension of 72 °C/ 4 min
    RH4 (reverse: 5′-AGTCGAACCCTGATTCTCCGCCAGG-3′)  
Entamoeba SSU   JVC (forward: 5′-GTTGATCCTGCCAGTATTATATG-3′) [100] 95 °C/ 5 min, followed by 40 cycles of 95 °C/ 30 s, 57 °C/ 30 s and 72 °C/ 1 min, with a final extension of 72 °C/ 4 min [100]
    DSPR2 (reverse: 5′-CACTATTGGAGCTGGAATTAC-3′)