Viral communities associated with porcine respiratory disease complex in intensive commercial farms in Sichuan province, China


Supplementary Table

 S1. Sequence information for the PCR primers used to detect the 17 different viruses in the 26 lung samples. 
*493 bp (for NADC30-like PRRSV); 797 bp (for HP-PRRSV); 887 bp (for Classical PRRSV) 

Virus

Primer sequence (5'→3') Product length (bp) 
PCV-2-F GCGAGGAGGGTAATGAGG PCV-2-R CTCTGCAACGGTCACCAG PRRSV(NSP2)-F GACACCTCCTTTGATTGG 493/797/887* PRRSV(NSP2)-R GAGAGGAIGCAGACAAATC PRV(gE)-F GCTCTGCGTGCTGTGCTCC PRV(gE)-R GGGTCCATTCGTCACTTCCG PPV-2-F AGCTCTGCGACAAGTGGG PPV-2-R GTCTACGGCCTGCAAGAA PPV-3-F CCACGCCAAATCAAAGTC PPV-3-R CTCCCACTCCCATCCACT PPV-4-F TATGTGGGCTGGGCAAGGAATGTC PPV-4-R GTTGCGGAATGCTATCAGGCTCTT PPV-5-F ACACCTCCTGCGGCTTAT PPV-5-R GTGTAGCGATGTCCTGGC PPV-6-F CTTTGGTGTAGAGGGCTTGA PPV-6-R CGGTTGTAGCAGGTCCAA PBoV-1-F GTTTGGTGGGAAGAAGCA PBoV-1-R TTATCACCGCCGCAAGAT PBoV-3-F CACAGGGGAAAGCATCGT PBoV-3-R CCACATTTGGTTCGGCAT PBoV-5-F CGACTGCCAGAGCAAACT PBoV-5-R CCACAGCGACAACAAGGT TTSuV-1a-F GGCTCAATTTGGCTCGCTTC TTSuV-1a-R CGATAGGCCCCTTGACTTC TTSuV-1b-F CACCATACCCTGCCCCTT TTSuV-1b-R TGTCCTGTGACATTGAGTGAG PCMV-F TGTGCGGTGAAGCAGTAT PCMV-R AGGCCTTACGGAGACCTT PKV-F ACAGGGTGGATGAAGAACG PKV-R GAAGTTTGGAGCGAACCC PAstV-F ACAGCAACCAAAGCCACA PAstV-R CACCACCACTCATTCACCTC PigSCV-F TGCGTGGGCTATGTATCAA PigSCV-R CTGCGAGGACGTGCGTAA

Table S2 .

 S2 Viruses detected by PCR in 74 serum samples from PRDC-affected piglets and clinically healthy controls from five farms. 


	Supplementary Farm A Asymptomatic samples Rate* A1 A2 A3 A4 A5 A6 A7 + + + + 4/7 + 2 + 2 + 3 3/7 0/7 + + + 3/7 0/7 0/7 0/7 + + + 3/7 0/7 0/7 0/7 TTSuV-1a Virus PCV-2 PRRSV PRV PPV-2 PPV-3 PPV-4 PPV-5 PPV-6 PBoV-1 PBoV-3 PBoV-5 0/7 TTSuV-1b + 1/7 PCMV 0/7 PKV + 1/7 PAstV + + + + + 5/7 Farm B Virus Asymptomatic samples Rate* A1 A2 A3 A4 A5 A6 A7 A8 PCV-2 + 1/8 PRRSV + 2 1/8 PRV 0/8 PPV-2 + + 2/8 PPV-3 0/8 PPV-4 0/8 PPV-5 0/7 PPV-6 + + 2/8 PBoV-1 0/8 PBoV-3 0/8 PBoV-5 0/8 TTSuV-1a 0/8 TTSuV-1b 0/8 PCMV 08 PKV + 1/8 PAstV + + + 3/8 Farm D Farm C Virus Asymptomatic samples Rate* A1 A2 A3 A4 A5 A6 A7 Virus Asymptomatic samples Rate* A1 A2 A3 A4 A5 A6 A7 PCV-2 + + + 3/7 PCV-2 + + + + + 5/7 PRRSV + 2 + 1,2 + 2 + 2,3 4/7 PRRSV + 1 1/7 PRV + 1/7 PRV 0/7 PPV-2 + + + + + + 6/7 PPV-2 + + + 3/7 PPV-3 + 1/7 PPV-3 + + 2/7 PPV-4 + 1/7 PPV-4 0/7 PPV-5 0/7 PPV-5 + 1/7 PPV-6 + + + + + 5/7 PPV-6 + 1/7 PBoV-1 0/7 PBoV-1 + + 2/7 PBoV-3 + + + 3/7 PBoV-3 0/7 PBoV-5 + 1/7 PBoV-5 0/7 TTSuV-1a + + + + 4/7 TTSuV-1a + + 2/7 TTSuV-1b + + + + 4/7 TTSuV-1b + + + 3/7 PCMV + + 2/7 PCMV 0/7 PKV 0/7 PKV + + + 3/7 PAstV + + + + + 5/7 PAstV + + + + + + 6/7 pigSCV 0/7 pigSCV + 1/7	Diseased samples B1 B2 B3 B4 B5 B6 B7 + + + + + + 1 + 2 + 1 + 1 + 1 + 1 + 1 7/7 Rate* 5/7 0/7 + + + + 4/7 + 1/7 0/7 0/7 + + + + + + 6/7 0/7 0/7 + 1/7 + + + 3/7 + + + 3/7 + + + 3/7 + + + 3/7 + + + + + + 6/7 Diseased samples Rate* B1 B2 B3 B4 B5 B6 B7 + + + + 4/7 + 2 + 3 + 2 3/7 0/7 + + + + + + + 7/7 + + + + + + 6/7 0/7 0/7 + + + + + + 6/7 0/7 0/7 + 1/7 + + + + + + 6/7 + + + + 4/7 0/7 0/7 + + + + + 5/7 Diseased samples Rate* Diseased samples Rate* B1 B2 B3 B4 B5 B6 B7 B1 B2 B3 B4 B5 B6 B7 + + + + + + + + + + + 7/7 4/7 + 2,3 + 2 + 2 + 2 + 1 + 1 + 1 + 2 4/7 + 2 + 2 6/7 + 0/7 1/7 + + + + + + + + + + + + + 6/7 7/7 + + + + + + + 5/7 1/7 0/7 0/7 + 1/7 0/7 + + + + + + + + + + 6/7 4/7 + + + + 4/7 0/7 + + 2/7 0/7 + 1/7 0/7 + + + + + + + + 5/7 3/7 + + + + + + + + 5/7 3/7 + + + + + 2/7 3/7 + + + 3/7 0/7 + + + + + + + + + + + + + 7/7 6/7 + + 2/7 + + 2/7
	pigSCV pigSCV	+	1/7 0/8	0/7 0/7

1: Highly pathogenic PRRSV; 2: NADC 30-like PRRSV; 3: Classical PRRSV *Detection rates of the 17 different viruses in serum samples. 

Farm E


Virus
Sinan Qin, Wenqiang Ruan, Hua Yue, Cheng Tang, Kelei Zhou, Bin Zhang
Viral communities associated with porcine respiratory disease complex in intensive commercial farms in Sichuan province, China