Table 1 The details of primers used by different PCR methods and their genotype detection limitation results for Acanthamoeba spp. by in Silico analysis.
Methods | Primers | Sequence (5′ → 3′) | Length (bp) | Un-detected genotype | References |
|---|---|---|---|---|---|
JDP-genotyping PCR (M1) | JDP 1 | GGC CCA GAT CGT TTA CCG TGA A | 440–550 | T9, T17, T18 | Schroeder et al.34 |
JDP 2 | TCT CAC AAG CTG CTA GGG GAG TCA | T7, T8, T9, T17, T18 | |||
Optimal modified genotyping nested PCR (M3) | ComFLA F (outer) | CGC GGT AAT TCC AGC TCC AAT AGC | 980–1090 | Nil | Coskun et al.35 |
ComFLA R (outer) | CAG GTT AAG GTC TCG TTC GTT AAC | Nil | |||
AcanF900 (inner) | CCC AGA TCG TTT ACC GTG AA | 440–550 | Nil | This study | |
JDP2-M (inner) | TCT CAC AAG CTG CTR GGG GAG TCA | Nil | |||
Genotyping nested PCR (M2) | ComFLA F (outer) | CGC GGT AAT TCC AGC TCC AAT AGC | 980–1090 | Nil | Coskun et al.35 |
ComFLA R (outer) | CAG GTT AAG GTC TCG TTC GTT AAC | Nil | |||
JDP 1 (inner) | GGC CCA GAT CGT TTA CCG TGA A | 440–550 | T9, T17, T18 | Schroeder et al.34 | |
JDP 2 (inner) | TCT CAC AAG CTG CTA GGG GAG TCA | T7, T8, T9, T17, T18 | |||
Scheikl genotyping nested PCR (M4) | JDP 1 (outer) | GGC CCA GAT CGT TTA CCG TGA A | 920–1030 | T9, T17, T18 | Scheikl et al.4 |
P3rev (outer) | CTA AGG GCA TCA CAG ACC TG | Nil | |||
P2fw (inner) | GAT CAG ATA CCG TCG TAG TC | 120–160 | T7, T8, T9, T17, T18 | ||
JDP 2 (inner) | TCT CAC AAG CTG CTA GGG GAG TCA | T7, T8, T9, T17, T18 | |||
Semi-nested PCR (M5) | JDP 1 (outer) | GGC CCA GAT CGT TTA CCG TGA A | 440–550 | T9, T17, T18 | Dhivya et al.23 |
JDP 2 (outer) | TCT CAC AAG CTG CTA GGG GAG TCA | T7, T8, T9, T17, T18 | |||
A1 (inner) | AAC GAT GCC GAC CAG CGA TTA | 120–160 | T7, T8, T9, T17, T18 | ||
JDP 2 (inner) | TCT CAC AAG CTG CTA GGG GAG TCA | T7, T8, T9, T17, T18 | |||
Real-time PCR (M6) | AcanF900 | CCC AGA TCG TTT ACC GTG AA | 180 | Nil | Qvarnstrom et al.36 |
AcanP1000 | FAM—CTG CCA CCG AAT ACA TTA GCA TGG—BHQ1 | Nil | |||
AcanR1100 | TAA ATA TTA ATG CCC CCA ACT ATC C | Nil |
