TABLE 2.

Primer and probe oligonucleotides used for real-time quantitative RT-PCR

GenogroupPrimer or probeSequence (5′ → 3′)aPolaritybLocation
GIPrimer COG1FCGYTGGATGCGNTTYCATGA+5291e
Primer COG1RCTTAGACGCCATCATCATTYAC5375e
Probec RING1(a)-TPFAM-AGATYGCGATCYCCTGTCCA-TAMRAd5340e
RING1(b)-TPFAM-AGATCGCGGTCTCCTGTCCA-TAMRA5340e
GIIPrimer COG2FCARGARBCNATGTTYAGRTGGATGAG+5003f
Primer COG2RTCGACGCCATCTTCATTCACA5100f
Probe RING2-TPFAM-TGGGAGGGCGATCGCAATCT-TAMRA+5048f
  • a Mixed bases in degenerate primers and probes are as follows: Y, C or T; R, A or G; B, not A; N, any.

  • b +, virus sense; −, anti-virus sense.

  • c Mixed probes are used for the GI NLVs.

  • d 6-Carboxyfluorescein (FAM) as the reporter dye is coupled in the 5′ end of the oligonucleotide, and 6-carboxy-tetramethylrhodamine (TAMRA) as the quencher dye is coupled in the 3′ end of the oligonucleotide.

  • e Corresponding nucleotide position of Norwalk/68 virus (accession no. M87661) of the 5′ end.

  • f Corresponding nucleotide position of Camberwell virus (accession no. AF145896) of the 5′ end.