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Table S2. Primers and PCR cycling parameters for amplifying and sequencing.
RT and PCR reactions Sequencing
Primer Primer sequence PCR Product Primer Primer sequence
namea(5′→3′)parametersblength (bp) namea(5′→3′)
RT_AmpR ACTTCTCCCAGGCAACAGCTT Annealing: 1415 RT_SeqF1 ATTAACCCAACGCGTAAAGC
RT_AmpF GCAATCTTCCGTTCGCTACAC 68 ºC, 1 min RT_SeqF2 CGCAGTATAGTACCGATGAGG
Extension: RT_SeqF3 CGGCTTAGTTATACCACGTTC
72 ºC, 2 min RT_SeqR1 GAGAGAGTTACGCGAAGATGC
RT_SeqR2 GTCGCATCAAGGTCAATATAA
RT_SeqR3 TCGGTACTATACTGCGTGAAC
ßsub_AmpF1 CCGATGGCGTGATAGTTG Annealing: 1887 ßsub_SeqF1 GTGCCATACCGTTTGACTTC
ßsub_AmpR1 TCGTGCCCTGGAAGACC 65 ºC, 1 min ßsub_SeqF2 CTCGGGCTTTGAAGTATGTTTTAG
Extension: ßsub_SeqF3 GGAAGTTTTTAAGTATGTTGGTTT
72 ºC, 2 min ßsub_SeqR1 CCGTAGGGTGCCAGAAC
ßsub_SeqR2 AAACCAACATACTTAAAAACTTCC
ßsub_SeqR3 CTGATATCGAAATGTGTAGAAGC
ßsub_AmpF2 GCGGCAAGCACTACTATTCT Annealing: 655 ßsub_SeqF4 ACCTCTTCTCGCGTTGTCTCT
ßsub_AmpR2 GATCCCCCTCTCACTCGT 62 ºC, 1 min
Extension:
72 ºC, 1 min
aThe RT primers were used for the mutation reporter and the ßsub primers were used for the Qß replicase.
bThe remaining parameters were as specified by the PfuTurbo DNA polymerase manufacturer’s instructions. In all cases, the second
segment of the PCR was cycled 35 times.