Table 1 List of oligonucleotides

Probe_norf1_fw

GTAATACGACTCACTATAGGGAGACCATCGACTATTCTTCAGTACTGTTTAC

Amplification of probe template norf1 (168 nt) for in vitro-transcription (T7 promoter is underlined)

Probe_norf1_rev

TTGAGATGCTACAGGACCTTATGC

Pnorf1_fw

taccggtGCCTAGGGGATACCTCTCCCC

Amplification of putative norf1 promoter for ligation into pILA reporter plasmid

Pnorf1_rev

tggccggcCTCCGTCCCAATGGGGGAAAC

nsiR6_probe_fw

GTAATACGACTCACTATAGGGAGATTACCGATCGCCGCTTCATC

Amplification of probe template nsiR6 (166 nt) for in vitro-transcription (T7 promoter is underlined)

nsiR6_probe_rev

TGTGTGGCGTCACCATTGAAAATG

hliR1_probe_fw

GTAATACGACTCACTATAGGGAGACTCGGGAAGATTAAGACTGGTTTTG

Amplification of probe template hliR1 (135 nt) for in vitro-transcription (T7 promoter is underlined)

hliR1_probe_rev

ATGTCTAATTTGATTGCTGTTGCTTTC

norf4_probe_fw

GTAATACGACTCACTATAGGGAGACCCCCTTTAGCAAAACTACCCATC

Amplification of probe template norf4 (116 nt) for in vitro-transcription (T7 promoter is underlined)

norf4_probe_rev

ATGACCGCCGATCAACTGTTG

nsiR6_fw

gccaagaagtATGAGTGTTTTCCCCGCAGA

Amplification of nsiR6 generating overlaps with PpetE and 3xFLAG::3′UTR norf1::Toop

nsiR6_rev

tataatccatGTCGTAATAATCCCGGCTGG

PpetE::hliR1_fw

gccaagaagtATGTCTAATTTGATTGCTGTTG

Amplification of hliR1 generating overlaps with PpetE and 3xFLAG::3′UTR norf1::Toop

3xFlag_hliR1_rev

tataatccatCTCGGGAAGATTAAGACTGG

PpetE::ssr1169_fw

gccaagaagtATGGATATTGTTAAGATCATTTGTGCGATTC

Amplification of ssr1169 generating overlaps with PpetE and 3xFLAG::3′UTR norf1::Toop

3xFlag_ssr1169_rev

tataatccatACGTTCCCTGGCAATGACCC

PpetE::Norf4_fw

gccaagaagtATGACCGCCGATCAACTGTT

Amplification of n orf4 generating overlaps with PpetE and 3xFLAG::3′UTR n orf1::Toop

3xFlag_Norf4_rev

tataatccatACCCCCTTTAGCAAAACTAC

pUC19-XbaI_PpetE_fw

gctcggtacccggggatcctctagaCTGGGCCTACTGGGCTATTC

Amplification of PpetE introducing XbaI site (underlined) + creating overlaps with pUC19 and nsiR1, hliR 1, ssr1169 or n orf4

nsiR6::PpetE_rev

aaacactcatACTTCTTGGCGATTGTATCTATAGG

hliR1::PpetE_rev

aattagacatACTTCTTGGCGATTGTATCTATAGG

ssr1169::PpetE_rev

caatatccatACTTCTTGGCGATTGTATCTATAGG

Norf4::PpetE_rev

gatcggcggtcatACTTCTTGGCGATTGTATCTATAGG

3xFlag_PstI-pUC19_rev

gccaagcttgcatgcctgcagAATAAAAAACGCCCGGCGGC

Amplification of 3xFLAG::3′UTR norf1::Toop introducing PstI site (underlined) + creating overlaps with pUC19 and nsiR1, hlirR, ssr1169 or norf4 or amplification of particular CDS associated with 3xFLAG__3′UTR norf1::Toop introducing PstI site (underlined) + creating overlaps with pUC19 and respective promoter sequence

nsiR6_3xFlag_fw

ttattacgacATGGATTATAAAGATCATGATGGCGATTATAAAG

hliR1_3xFlag_fw

tcttcccgagATGGATTATAAAGATCATGATGGCGATTATAAAG

ssr1169_3xFlag_fw

cagggaacgtATGGATTATAAAGATCATGATGGCGATTATAAAG

Norf4_3xFlag_fw

taaagggggtATGGATTATAAAGATCATGATGGCGATTATAAAG

CDSnsiR6::PnsiR6_fw

ataaatactcATGAGTGTTTTCCCCGCAGAAAC

CDShliR1::PhliR1_fw

aaattaactaaATGTCTAATTTGATTGCTGTTGCTTTCTG

CDSNorf4::PNorf4_fw

aatttttaccATGACCGCCGATCAACTGTTG

CDSssr1169::Pssr1169_fw

gagtgaactaATGGATATTGTTAAGATCATTTGTGCGATTC

pUC19::PnsiR6_fw

gctcggtacccggggatcctctagaATCGCCGTATTACACCTCTG

Amplification of PnsiR6 introducing XbaI site (underlined) + generating overlaps with pUC19 and nsiR6.

PnsiR6::CDSnsiR6_rev

aaacactcatGAGTATTTATTCCTAGTGAATGAATTAGAAG

pUC19::PhliR1_fw

gctcggtacccggggatcctctagaGGAGTTTACAGCGAGATTTG

Amplification of PhliR1 introducing XbaI site (underlined) + generating overlaps with pUC19 and hliR1.

PhliR::CDShliR1_rev

aattagacatTTAGTTAATTTTTGTAACGGGAG

pUC19::PNorf4_fw

gctcggtacccggggatcctctagaAGGTGATGATTATGAGCCGTC

Amplification of Pnorf4 introducing XbaI site (underlined) + generating overlaps with pUC19 and norf4.

PNorf4::CDSNorf4_rev

gatcggcggtcatGGTAAAAATTCCACTAATTCAAAAAAC

pUC19::Pssr1169_fw

gctcggtacccggggatcctctagaCGAGTAGCCAGCCAAAGCAG

Amplification of Pssr1169 introducing XbaI site (underlined) + generating overlaps with pUC19 and ssr1169.

Pssr1169::CDSssr1169_rev

caatatccatTAGTTCACTCCAATATGTCGGGATAATTAG