Comparative evaluation of Taqman real-time PCR and semi-nested VP1 PCR for detection of enteroviruses in clinical specimens.
BACKGROUND
Molecular diagnostic tests to detect enterovirus in clinical specimens usually target highly conserved sites in the 5'-non-translated region, allowing detection of all members of the genus. The sequences in the 5'-NTR do not correlate with serotype, but PCR and sequencing of the VP1 region can be used for typing; this system has largely replaced traditional antigenic typing.


OBJECTIVE
To investigate the relative performance of two common enterovirus assays.


METHODS
We compared the relative sensitivities of Taqman real-time RT-PCR (rRT-PCR) and a VP1 semi-nested PCR (RT-snPCR) assay in which sequencing the VP1 amplicon also provides typing information.


RESULTS
There was 89% concordance between the two methods among the 371 clinical specimens tested (74 positive in both assays and 257 negative in both assays). Twenty-seven rRT-PCR-negative/VP1-positive specimens were confirmed positive by sequencing; 13 specimens were rRT-PCR-positive/VP1-negative.


CONCLUSIONS
The results suggest that either assay can produce satisfactory results, but that using both assays in parallel should provide the highest sensitivity for clinical diagnostic testing.
Oberste
M Steven
MS
Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA. soberste@cdc.gov
Peñaranda
Silvia
S
Rogers
Shannon L
SL
Henderson
Elizabeth
E
Nix
W Allan
WA
D036022:Capsid Proteins / Q000235:genetics*; D002555:Cerebrospinal Fluid / Q000821:virology; D004770:Enterovirus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D004769:Enterovirus Infections / Q000097:blood* / Q000134:cerebrospinal fluid* / Q000175:diagnosis / Q000821:virology; D005243:Feces / Q000821:virology; D006801:Humans; D009305:Nasopharynx / Q000821:virology; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000032:analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity
D036022:Capsid Proteins; D012367:RNA, Viral