Supplementary Table 2

RT-PCR and nested PCR primers for the detection of porcine sapelovirus (PSV), porcine kobuvirus (PKV), porcine enterovirus (PEV), porcine teschovirus (PTV), porcine enteric caliciviruses (porcine sapovirus [PSaV] and porcine norovirus [PNoV]), groups A, B and C porcine rotaviruses (PRVA-C), transmissible gastroenteritis coronavirus (TGEV) and porcine epidemic diarrhea coronavirus (PEDV) in the fecal samples of pigs

Target viruses / Target genesa / Primer names / Primer sequence, 5’ to 3’b / Region (nt) / Size (bp) / Source of reference
PSV / VP1 / PSVVP1F / F: AGG ATG TGG TGC AAG CAA GCA T / 2282-2303 / 636 / In this study
PSVVP1R / R: AGG CAG CAC CGT TCT GGT CAA / 2897-2917
PSVVP1nF / nF: GTG CAA GCA AGC ATA AAC ACC A / 2290-2311 / 542 / In this study
PSVVP1nR / nR: GAG GCT GGG CAG TTC CCT AC / 2812-2831
PKV / VP1 / PK-VP1-2898F / F: TGG TAT CCA AGC TCC TGG AT / 2898-2917 / 875 / Okitsu et al., 2012
PK-VP1-3753R / R: TGT ACG TCA TGC GCT GGA CC / 3753-3772
PK-VP1-2916F / nF: GAT TCC AAA TCC AGG CCG CT / 2916-2915 / 781 / In this study
PK-VP1-3697R / nR: TGG CAT TGA CGT ACA ACG GG / 3697-3696
PEV / 5’UTR / F: GTA CCT TTG TAC GCC TGT TTT A / 66-87 / 491 / Palmquist et al. 2002
R: ACC CAA AGT AGT CGG TTC CGC / 536-556
nF: CAA GCA CTT CTG TTT CCC CGG / 167-187 / 313
nR: GTT AGG ATT AGC CGC ATT CA / 460-479
PTV / RdRp / F: CAA AGA CTG GTC CTT CAT TG / 6068-6086 / 884 / Kaku et al. 2001
R: ATA CGC CGA GCG CGG AAG AT / 6932-6951
PT-RdRp-6203F / nF: CGC GTC ATA GAT GTG GCA GG / 6203-6222 / 716 / In this study
PT-RdRp-6899R / nR: GCA ATG GAC AGC AAC TTG GC / 6899-6918
PSaV and PNoV / RdRp / P289c / F: GAT TAC TCC AGT GGA CTT CCA / 4568-4590 / 319 / Farkas et al., 2004
P290 / R: TGA CGA TTT CAT CAT CACCCA GTA / 4865-4886 / 331
PRVA / VP6 / F: AAA GAT GCT AGG GAC AAA ATT G / 57-77 / 309 / Elschner et al. 2002
R: TTC AGA TTG TGG AGC TAT TCC A / 344-365
nF: GAC AAA ATT GTC GAA GGC ACA TTA TA / 69-94 / 121
nR: TCG GTA GAT TAC CAA TTC CTC CAG / 166-189
PRVB / NSP2 / F: CTA TTC AGT GTG TCG TGA GAG G / 14-35 / 433 / Gouvea et al. 1991
R: CGA AGC GGG CTA GCT TGT CTG C / 425-446
PRVC / VP6 / F: CTC GAT GCT ACT ACA GAA TCA G / 994-1018 / 359 / Gouvea et al. 1991
R: AGC CAC ATA GTT CAC ATT TCA TCC / 1339-1352
nF: CTC GAT GCT ACT ACA GAA TCA G / 997-1018 / 327
nR: GGG ATC ATC CAC GTC ATG CGT / 1300-1320
TGEV / ORF1b
Spike / F: GGG TAA GTT GCT CAT TAG AAA TAA TGG / 20300-20326 / 1006 / Kim et al. 2000
R: CTT CTT CAA AGC TAG GGA CTG / 21285-21305
nF: TTG TGG TYT TGG TYG TAA TKC C / 20379-20400 / 873
nR: GGC TGT TTG GTA ACT AAT TTR CCA / 21228-21251
PEDV / N / F: TTG GCA TTT CTA CTA CCT CGG A / 251-272 / 1306 / Kubota et al. 1999
R: AGA TGA AAA GGT ACT GCG TTC C / 1535-1556
nF: AGG AAC GTG ACC TCA AAG ACA TCC C / 847-871 / 540
nR: CCA GGA TAA GCC GGT CTA ACA TTG / 1363-1386

a VP1: viral protein 1; RdRp: RNA dependent RNA polymerase; 5’UTR: 5’untranslated region; VP6: viral protein 6; NSP2: non-structural protein 2; ORF1: open reading frame 1b; N; nucleocapsid

b F: upstream primer for RT-PCR; R: downstream primer for RT-PCR; nF: upstream primer for nested PCR; nR: downstream primer for nested PCR

c A primer pair p289/290 designed to detect both noroviruses and sapoviruses by RT-PCR (norovirus; 319 bp sapovirus; 331 bp)

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