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Table 2 Genotyping of Pepino mosaic virus isolates with reverse transcription loop-mediated isothermal amplification (RT-LAMP) and its validation with genotype-specific RT-PCR

From: Pepino mosaic virus genotype shift in North America and development of a loop-mediated isothermal amplification for rapid genotype identification

Country of origin Isolate name ELISAa EU US1 CH2
RT-PCR/RT-LAMP RT-PCR/RT-LAMP RT-PCR/RT-LAMP
USA VFTX12-01 (++++) (−)/(+)b −/− +/+
VFTX12-02 (++++) (−)/(+)b −/− +/+
VFTX12-03 (++++) (−)/(+)b −/− +/+
VFTX12-04 (++++) −/− −/− +/+
VFTX12-05 (++++) +/+ −/− +/+
VFTX12-06 (++++) +/+ −/− +/+
VFTX12-07 (++++) +/+ −/− +/+
VFTX12-08 (++++) +/+ −/− +/+
VFTX12-09 (+++) +/+ −/− +/+
VFTX12-10 (++++) +/+ −/− +/+
VFTX12-11 (++++) −/− −/− +/+
VFTX12-12 (++++) −/− −/− +/+
VFTX12-13 (+++) +/+ −/− +/+
VFTX12-14 (+++) +/+ −/− +/+
VFTX12-15 (+++) +/+ −/− +/+
VFTX12-16 (+++) −/− −/− +/+
VFTX12-18 (+++) −/− −/− +/+
VFTX12-19 (+++) −/− −/− +/+
VFTX12-20 (+++) −/− −/− +/+
VFTX12-21 (+) +/+ −/− +/+
VFTX12-22 (+++) −/− −/− +/+
VFTX12-23 (+) −/− −/− +/+
VFTX12-24 (+++) −/− −/− +/+
VFTX12-25 (+++) −/− −/− +/+
Mexico BNMX12-01 (+++) −/− +/+ −/−
BNMX12-02 (+++) −/− +/+ −/−
BNMX12-03 (+++) −/− +/+ −/−
BNMX12-04 (+++) −/− +/+ −/−
BNMX12-05 (+++) −/− +/+ −/−
BNMX12-06 (+++) −/− +/+ −/−
BNMX12-07 (+++) −/− +/+ −/−
BNMX12-08 (+++) −/− +/+ −/−
BNMX12-09 (+++) −/− +/+ −/−
BNMX12-10 (+++) −/− +/+ −/−
BNMX12-11 (+++) −/− +/+ −/−
BNMX12-12 (+++) −/− +/+ −/−
BNMX12-13 (+++) −/− +/+ +/+
BNMX12-14 (+++) −/− +/+ −/−
BNMX12-15 (++) −/− +/+ −/−
BNMX12-16 (++) −/− +/+ +/+
Canada VFBC12-01 (+++) −/− (−)/(+)b +/+
VFBC12-02 (++++) −/− (−)/(+)b +/+
VFBC12-03 (+++) −/− (−)/(+)b +/+
VFBC12-04 (−) −/− −/− +/+
VFBC12-05 (+++) −/− −/− +/+
VFBC12-06 (++) −/− −/− +/+
VFBC12-07 (+) −/− −/− +/+
VFBC12-08 (++++) −/− −/− +/+
VFBC12-09 (+) −/− −/− +/+
VFBC12-10 (+++) −/− −/− (+)/+c
Positive   (+++) +/+ +/+ +/+
Negative   (−) −/− −/− −/−
  1. a ELISA ratings: (−) <0.100; (+): 0.101-0.500; (++): 0.501-1.000; (+++): 1.001-2.000; (++++) >2.001.
  2. b A discrepancy was observed in these isolates with a negative (−) RT-PCR, but a positive (+) RT-LAMP. A confirmation test through sequencing of cloned RT-LAMP products was performed to determine the authenticity of their viral origin.
  3. c The result for a positive (+) RT-PCR was not consistent from one experiment to another while RT-LAMP was consistently positive.