Sequence variation can affect the performance of minor groove binder TaqMan probes in viral diagnostic assays.
A minor groove binder (MGB) TaqMan real-time PCR assay was developed for the detection of respiratory syncytial virus (RSV) in clinical specimens. Upon evaluation of the assay, notable differences were observed in the overall fluorescent response obtained from RSV positive specimens, with some linear amplification curves deviating only slightly from baseline fluorescence. Sequencing of the probes targets in these RSV strains revealed single base mismatches with the MGB TaqMan probe. Overall, these results highlight the usefulness of MGB TaqMan probes for the detection of mismatches, but suggest that MGB Taqman probes have limitations for routine screening for uncharacterised viral strains.
Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital & Health Service District, Herston Road, Herston, Qld 4029, Australia. d.whiley@uq.edu.au
David M
DM
Whiley
Theo P
TP
Sloots
D020137:Base Pair Mismatch; D001483:Base Sequence; D015342:DNA Probes / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods*; D018357:Respiratory Syncytial Virus Infections / Q000175:diagnosis* / Q000821:virology; D018113:Respiratory Syncytial Virus, Human / Q000235:genetics / Q000302:isolation & purification*; D019914:Taq Polymerase / Q000378:metabolism*
D015342:DNA Probes; D019914:Taq Polymerase