Supplementary table 1 – Primers used for amplification and sequencing, of the OCFVPT genome.

Primer designation / Position1 / Orientation / Sequence (5’-3’)
AcFV1F / 8865-8888 / Forward / TGGTACATGTGGTTGGGATCGAGG
AcFV2R / 10208-10235 / Reverse / GACTCGGGGGAGCGGGKKCGTCAKGCC
AcFV3R / 8958-8984 / Reverse / ATAGTTGACTCCGATGCCTCCTACACC
AcFV4R / 7853-7878 / Reverse / CCGATGTCACACATRAAKGTGTCACA
AcFV5F / 5025-5051 / Forward / GYGASATGGCATCSAGGAAAAGSAAAG
AcFV6R / 10650-10674 / Reverse / GATADTCMAAACTCCCTAACGGTGG
AcFV7R / 5294-5320 / Reverse / GGATCCATGAARTGRCACTCATCCATG
AcFV8F / 1228-1249 / Forward / GCGGTTGGGGMACTGGSTGYTT
AcFV9R / 2864-2887 / Reverse / TCCATCCAAAACATSCCRTCAGTG
AcFV10F / 3559-3589 / Forward / TTGGACTDCCCAACWTDTTTTCATCKGTGGG
AcFV11F / 2627-2648 / Forward / GCCAACAAGTATTGTCTCTTGGTCGAC
AcFV12R / 3991-4016 / Reverse / CTATGCACAGTCCCGTCCTCCATCCG
AcFV13F / 4100-4120 / Forward / TCCGGGTGCGTCTGCGGCCATCGC
AcFV14F / 4953-4978 / Forward / CGATCTCTAGTTGTTCCAGTACCACG
AcFV15R / 8035-8059 / Reverse / CAATCCTGCCACCATACTTGTGCTG
AcFV16F / 5476-5599 / Forward / CAAGGTGGATTGGAGATGTGTCGG
AcFV18F / 6198-6224 / Forward / CTAGCCATCCAGTTCTACATGGGAAC
AcFV19F / 8769-8795 / Forward / CTAGCTGGTGATTGCAGAATGTGTGTG
AcFV20R / 9510-9533 / Reverse / CTGCACTCGTGATGGGAGGGATGG
AcFV21R / 5439-5465 / Reverse / CCGTGGAAACTGGAGGGCTTGCTCAGC
AcFV22F / 9562-9588 / Forward / CCCATCACTACCACCCAATGACTCTCC
AcFV23F / 9591-9612 / Forward / GACGGTCGGCGAATCATCGTTC
AcFV24F / 9664-9688 / Forward / GGTTGGTGACAATCGCAGATAGTGC
Flavi4F / 7671-7197 / Forward / GAYYTHGGNTGYGGVMGVGGNGGMTGG
SP52 / 1570-1595 / Reverse / CTGCACGATCTTGTCAAAGCCTCCG
SP53 / 1385-1410 / Reverse / GTGTTGTGGGTGCGTCAGGAACGAGC
SP54 / 633-657 / Reverse / AGTGCTTCGTGATAACCATTCCTGC
1NS5F / 8791-8809 / Forward / GCATCTAYAWCAYNATGGG
1NS5R / 9867-9884 / Reverse / CCANACNYNRTTCCANAC
2NS5F / 8859-8876 / Forward / GCNATNTGGTWYATGTGG
2NS5R
HANKF5
HANKR3 / 9841-9860
3-312
10.089-10.1182 / Reverse
Forward
Reverse / CATRTCTTCNGTNGTCATCC
GCACAGGTTGAGAGACCTTCTTCCCGACA
CTAAATCGTCCCATGCCACTCAGGAAATCC

1Unless indicated, the coordinates refer to those of the CFAV genome (accession number NC_001564).

2Coordinates indicated refer to those of the HANKV genome (accession number JQ268258).