title: Increased sensitivity for various rotavirus genotypes in stool specimens by amending three mismatched nucleotides in the forward primer of a real-time RT-PCR assay.
abstract: The real-time TaqMan RT-PCR assay (Pang et al., 2004) did not detect 14 clinical samples with rotavirus G2 genotype. Three to five nucleotides (nt) were found to be mismatched between the published forward primer when compared to G2P[4], G2P[8], G3P[4], G9P[4], G8 and G12 sequences. An additional forward primer was designed and included in a modified assay to test the 14 clinical samples and 12 samples with known rotavirus G and P genotypes. The modified assay has improved significantly the sensitivity for specific rotavirus strains without affecting the detection of other genotypes, creating a molecular assay with broad detection of various genotypes of group A rotaviruses.
authors.affiliation: Provincial Public Health Laboratory, Edmonton, Alberta, Canada. x.pang@provlab.ab.ca
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Pang
authors.forename: Min
authors.initials: M
authors.lastname: Cao
authors.forename: Min
authors.initials: M
authors.lastname: Zhang
authors.forename: Bonita
authors.initials: B
authors.lastname: Lee
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D017931:DNA Primers; D005243:Feces / Q000821:virology*; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012401:Rotavirus / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology*; D012400:Rotavirus Infections / Q000175:diagnosis* / Q000821:virology*; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017361:Viral Nonstructural Proteins / Q000235:genetics
chemical_list: D017931:DNA Primers; C082740:NSP3 protein, Rotavirus; D017361:Viral Nonstructural Proteins