Whole-Genome, Recombinant, and Phylogenetic Analysis of Porcine Epidemic Diarrhea Virus Strain CH/JSXZ/2015

Table 2

Primers for the amplification of the PEDV genomic fragments.

Primer name	Sequence (5^′to 3^′)	Product size (bp)
5UTR-F	ACTTAAAAAGATTTTCTATCTACGGATAG	291
5UTR-R	GCCGACAGTTACTGGTTTCA
ORF1a-1F	ACTAGACAAACAGCCTTCCTCCG	2005
ORF1a-1R	CCTCTCACAACGCAGCTGTAAGTTTTAT
ORF1a-2F	ATACCTGATTTTCCTATGCCTGTGGC	2127
ORF1a-2R	AACAAGGTCACTAAAGTCTCCTTGGT
ORF1a-3F	CTGTATTGGAGCCTGTTGTCAAACC	2083
ORF1a-3R	CAGAGACCCAAAATGCTAAGGATGTACA
ORF1a-4F	ACGCTACAAAGCTGTTAGACACTATG	2025
ORF1b-3R	CGCACTATTGTAACAAGTAGCAACCTTAC
ORF1b-4F	CTAATTTTTGTGTTGTGGGCTGGTG	2036
ORF1b-4R	TCACTGGCCTGAAGTTGCGGATAAA
ORF1b-5F	GCATTCTTAAATCGTTGGATTTGAGCG	3032
ORF1b-5R	CCGCCTAAAATTAGTGTTAGCTGAGC
S1-F	GAATGGTAAGTTGCTAGTGCG	1018
S1-R	ATTAAACCTCAGAGCCTCTGG
S2-F	CATGGTAAGGTGGTTTCCAACC	1045
S2-R	GGGACGTAAACTTAACACCACTACC
S3-F	GGACAGTAATTGCCCTTTCACCT	1035
S3-R	CCAAGGCCATTAGTAACCACT
S4-F	AATGTGCTGGGTGTTTCTGTG	1104
S4-R	ATCTGGGATTACTTCTGGTAGTT
S5-F	ACCAGGTGACTTTGTAAATGTT	800
S5-R	GCGTTTTGCTGTCATCTT
ORF3-F	GGTCCTAGACTTCAACCTTA	779
ORF3-R	AGCAGGAAAAAGAGTACGAA
EMN-F	GTCTTTTCGCAACATCAAATTGTTGGC	2100
EMN-R	ACAAGAAGCTCAACATTTGGATCAGAC
3UTR-F	ACCAAATGTTGCAGCATTGC	683
3UTR-R	GTGTATCCATATCAACACCGTCA