Development and evaluation of a recombinase polymerase amplification assay for rapid detection of strawberry red stele pathogen

Munawar, Mustafa Ahmad; Toljamo, Anna; Martin, Frank; Oksanen, Elina; Kokko, Harri

doi:10.1186/s42483-020-00069-4

Table 3 Field validation results

From: Development and evaluation of a recombinase polymerase amplification assay for rapid detection of strawberry red stele pathogen

Rootlet sample No.	*P. fragariae-*specific RPA assay of this study	*P. fragariae-*specific SYBR Green PCR assay	*P. fragariae-*specific TaqMan PCR assay	Sanger’s sequencing results	Symptoms
98	Positive Onset at ~ 5 min	30.7 Ct	34.6 Ct	100% identical to JF771842	Wilting, stunting and red steles
99	Positive Onset at ~ 6 min	30.8 Ct	34.4 Ct	100% identical to JF771842	Wilting, stunting and red steles
101	Positive Onset at ~ 6 min	30.7 Ct	34.2 Ct	100% identical to JF771842	Wilting, stunting and red steles
102	Positive Onset at ~ 6 min	30.0 Ct	34.1 Ct	100% identical to JF771842	Wilting, stunting and red steles
105	Positive Onset at ~ 5 min	34.3 Ct	37.0 Ct	100% identical to JF771842	Wilting, stunting and red steles
106	Negative	No Ct	No Ct	No amplification	Stunting
107	Positive Onset at ~ 7 min	34.7 Ct	38.3 Ct	100% identical to JF771842	Wilting, stunting and red steles
108 (co-infected sample)	Positive Onset at ~ 6 min	33.1 Ct	37.2 Ct	100% identical to JF771842	Wilting, stunting, red steles, and typical crown rot
109	Negative	No Ct	No Ct	No amplification	Stunting
110	Negative	No Ct	No Ct	No amplification	Stunting
111	Positive Onset at ~ 7 min	32.5 Ct	36.5 Ct	100% identical to JF771842	Wilting, stunting and red steles
112	Negative	No Ct	No Ct	No amplification	Apparently healthy
114	Negative	No Ct	No Ct	No amplification	Wilting and typical crown rot
117	Positive Onset at ~ 6 min	29.2 Ct	32.7 Ct	100% identical to JF771842	Wilting and red steles
118	Negative	No Ct	No Ct	No amplification	Wilting and typical crown rot
119	Negative	No Ct	No Ct	No amplification	Wilting
120	Negative	No Ct	No Ct	No amplification	Wilting and typical crown rot
121	Negative	No Ct	No Ct	No amplification	Wilting and typical crown rot
122	Negative	No Ct	No Ct	No amplification	Stunting
123	Positive Onset at ~ 8 min	38.5 Ct	40.6 Ct	100% identical to JF771842	Minor wilting only (no red steles)
125	Negative	No Ct	No Ct	No amplification	Apparently healthy
127	Negative	No Ct	No Ct	No amplification	Apparently healthy

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