. 2015 May 1;10(5):e0125420. doi: 10.1371/journal.pone.0125420

Table 1. Primer sequences used in PCR to amplify LCL samples against EBV-1/ EBV-2.

Seq #	Primer Pair	Product size	Product coordinates	Genes covered-EBV1/ EBV-2
1	TTCTGGTGATGCTTGTGCTC	2076	540–2616	BNRF1
1	TGCTGGCGTCTCATAAACAG	2076	540–2616	BNRF1
2	CTGTTTATGAGACGCCAGCA	4764	597–7361	BNRF1
2	TTTTCGCTGCTTGTCCTTTT	4764	597–7361	BNRF1
3	CCTGTGTGACCCCTCACTTT	4567	5545–10112	BNFRF1, EBER1/2, BCRF1, EBNA1
3	TCCTTTTTCCTGCAGCTTGT	4567	5545–10112	BNFRF1, EBER1/2, BCRF1, EBNA1
4	AAAAGGACAAGCAGCGAAAA	4307	7342–11649	BSLF1, BSRF1, BSLF2
4	GTGCAGGAGGCTGTTTCTTC	4307	7342–11649	BSLF1, BSRF1, BSLF2
5	TTATGGTTCAGTGCGTCGAG	4007	10971–14978	EBNA1, EBNA3A, EBNA2
5	GAACTGAGGAGGGCATGAAG	4007	10971–14978	EBNA1, EBNA3A, EBNA2
6	ATGCCTACATTCTATCTTGCGTTAC	1439	36216–37655	EBNA2, EBNA3A, EBNA3B/C, EBNA-LP
6	TTACTGGATGGAGGGGCGAGGTCTT	1439	36216–37655	EBNA2, EBNA3A, EBNA3B/C, EBNA-LP
7	AGGGATGCCTGGACACAAGA	1412	36522–37934	EBNA2
7	AACATGGACTGGGAGTGGAG	1412	36522–37934	EBNA2
8	CTAGAGGTCCGCGAGATTTG	1251	40696–41947	BHRF1
8	AGAAGGCAAGCGAAAATTGA	1251	40696–41947	BHRF1
9	GCAGGCAGTACGAGATGTCA	2239	41700–43939	BHRF1
9	TCCCTTCACATCCCAGAGAC	2239	41700–43939	BHRF1
10	CGACATTGACAGCCTTCTCA AAACACGAATGCCAAGAACC	4312	43795–48107	BFLF1, BFRF1A, BFRF2
11	TGCTCCTGATGTTTCTGAGGTGGA	1776	47586–49362	BFRF3
11	AGGTAACTTCTTTGAGCCTCCCGA	1776	47586–49362	BFRF3
12	TTGCTCCATCTGTCAGCAAC	1759	49088–50847	BOLF1
12	CACAAGCCTCCTCTCAGGAC	1759	49088–50847	BOLF1
13	GGTGACCACTGAGGGAGTGT	1789	50045–51834	EBNA1
13	CTTTCGAGCCAGAGATGTCC	1789	50045–51834	EBNA1
14	CCGAAATAGGGCCTTGCCATCAAT	1046	51199–52245	EBNA1
14	ATTTCAGGACTACCTGCGCGACTT	1046	51199–52245	EBNA1
15	GGACATCTCTGGCTCGAAAG	4689	51815–56504	EBNA1, BOLF1, BPLF1
15	AGGAGGAGAACCCGAGGATA	4689	51815–56504	EBNA1, BOLF1, BPLF1
16	TCAGGAGGTCGTCAAAATCC	1720	56125–57845	EBNA1
16	AGTAATCCCCATCCCTCACC	1720	56125–57845	EBNA1
17	TCCAGGCTGTTGGAGAACACTTCA	1172	57133–58305	EBNA1
17	TTTCACATCCGACTCATTCCCTGC	1172	57133–58305	EBNA1
18	GGTGAGGGATGGGGATTACT	2035	57826–59861	EBNA1
18	ATCACAGTCACCCCCAGAAG	2035	57826–59861	EBNA1
19	GCTCATATACGCCACCGTCT	1768	59222–60990	EBNA1
19	GCTCATATACGCCACCGTCT	1768	59222–60990	EBNA1
20	CAGACGGTGGCGTATATGAG	4019	60970–64989	BOLF1, BORF1, BOLF2, EBNA1, BORF2
20	CAAAGAGCCCCGTAAAGATG	4019	60970–64989	BOLF1, BORF1, BOLF2, EBNA1, BORF2
21	AACAGGCGGGCGAATGTGTAAT	1272	60125–61397	EBNA1
21	ACCTTTCATCCGAACTCCTCAGGT	1272	60125–61397	EBNA1
22	GCCTCTATGTCGCTCTGACC	4771	63737–68508	BARF1, BORF2, BMRF1
22	CGGAGGCGTGGTTAAATAAA	4771	63737–68508	BARF1, BORF2, BMRF1
23	GCGAGCCATAAAGCAGTTTC	4647	67334–71981	BMRF1, BMRF2, BSLF1, BMLF1
23	TCTCCCGAACTAGCAGCATT	4647	67334–71981	BMRF1, BMRF2, BSLF1, BMLF1
24	CTCGCGTGTTAGGAAGGAAG	5649	70814–76463	BSLF1/2, BMLF1, BSRF1, BLLF3
24	AGGCAAAGCTGGTCAAAGAA	5649	70814–76463	BSLF1/2, BMLF1, BSRF1, BLLF3
25	AGAAGCGCCGGTACTTGTTAAGGA	1495	75554–77049	BLLF3, BLRF1, BLRF2
25	TTGATTCTCGTGGTCGTGTTCCCT	1495	75554–77049	BLLF3, BLRF1, BLRF2
26	GCCTTCTTTGACCAGCTTTG	5215	76441–81656	BLRF1/2, BLLF1
26	GACGGGTTCTACTGGCATGT	5215	76441–81656	BLRF1/2, BLLF1
27	GGTGAAACGCGAGAAGAAAG	4797	81084–85881	EBNA3A, EBNA3B, EBNA3C
27	TTTAGCAGTTCCTCCGCACT	4797	81084–85881	EBNA3A, EBNA3B, EBNA3C
28	CCCCATCAGACACCTCAAGT	2138	85093–87231	EBNA3B/C
28	CACCTCCCGTTGCTAACATT	2138	85093–87231	EBNA3B/C
29	AGTGCGGAGGAACTGCTAAA	2917	85861–88778	EBNA3B/C
29	TGCAGAGGATGAGACCAGTG	2917	85861–88778	EBNA3B/C
30	CCCACCACGTCTTCAACTTT	2088	88730–90818	BZLF1
30	CCATACCAGGTGCCTTTTGT	2088	88730–90818	BZLF1
31	TCCAAGGTGACCCCTGTTAG	4859	89141–94000	BZLF2, EBNA3B, EBNA3C, BRLF1
31	TGATGCAGAGTCGCCTAATG	4859	89141–94000	BZLF2, EBNA3B, EBNA3C, BRLF1
32	ACTCCCGGCTGTAAATTCCT	4923	92774–97697	BRRF1, BRRF2, BRLF1, EBNA1
32	TGGCCAGAAATACACCAACA	4923	92774–97697	BRRF1, BRRF2, BRLF1, EBNA1
33	GTGATGAGGACGAGGATGGT	4100	95485–99585	BKRF2, BKRF3, BKRF4
33	TCGTGGATGCCCTAAAGAAC	4100	95485–99585	BKRF2, BKRF3, BKRF4
34	CCCATGTTGTCACGTCACTC	5281	97747–103028	BBLF4, BBRF1
34	CACCGTGTTGGAGACCTTTT	5281	97747–103028	BBLF4, BBRF1
34	ACAGACCATCTACGCCAACC	5392	102044–107436	BBRF1, BBRF2, BBRF3
34	CCACCACAAGAAGGTGTCCT	5392	102044–107436	BBRF1, BBRF2, BBRF3
36	TACGGGGCACTTAACCTGAC	4005	107002–111007	BBRF3, BGLF3, BGLF3.5, BGLF4, BGLF5, BBLF1
36	TGACGGAGCTGTATCACGAG	4005	107002–111007	BBRF3, BGLF3, BGLF3.5, BGLF4, BGLF5, BBLF1
37	GATGTTGCTGGGGCTAATGT	4358	110724–115082	BGLF4, BGLF5, BGLF3, BGLF3.5, BGRF1/BDRF1
37	AGAGAGGGAGTTTCGCTTCC	4358	110724–115082	BGLF4, BGLF5, BGLF3, BGLF3.5, BGRF1/BDRF1
38	GGCACCATAGCATGTCACAC	4571	113938–118509	BGRF1/BDRF1, BDLF3.5, BDLF4, BGLF1, BGLF4, BGLF2, BDLF1, BDLF3
38	AGTCCCAACAACTTCCAACG	4571	113938–118509
39	AACACCATCCAGCTCTCCTTCGAT	1526	117867–119393	BGRF1/BDRF1, BGLF3.5, BDLF1, BDLF2, BDLF3
39	ATGGGTGTCCGACCAATCCATTCT	1526	117867–119393	BGRF1/BDRF1, BGLF3.5, BDLF1, BDLF2, BDLF3
40	CGTTGGAAGTTGTTGGGACT CATTTTACCAGGGACGAGGA	4144	118490–122634	BDLF1, BDLF2, BDLF3, BcLF1
41	ATGCACCTCAAAGGTTACCG	4589	121912–126501	BcLF1, BcRF1
41	TTGCAAACTCGCATCTTCAC	4589	121912–126501	BcLF1, BcRF1
42	CCCGTTCACCAAAACAGTCT	4445	122398–126843	BcRF1
42	AACCAGGACACGTTGAGACC	4445	122398–126843	BcRF1
43	GGTCTCAACGTGTCCTGGTT	4287	126824–131111	BTRF1, BXLF1, BXLF2
43	GTGAAGGTATGTGCCGGTCT	4287	126824–131111	BTRF1, BXLF1, BXLF2
44	ACCTCCCATAGCAACACCAG	4195	130704–134899	BXLF1, BXLF2, BXRF1
44	CCCGTGCGATGAGTTTATTT	4195	130704–134899	BXLF1, BXLF2, BXRF1
45	CCTGAGAACGCTCCAGGTAG	4136	133032–137168	BXRF1, BVRF1, BVLF1, BVRF2
45	CCTGGTGAGAAGTTGGTGGT	4136	133032–137168	BXRF1, BVRF1, BVLF1, BVRF2
46	CCAGACATACCCCAAACCAC	4360	136001–140361	BdRF1, BILF2, RPMS1
46	CTCCAGAGGGCAGACGTTAG	4360	136001–140361	BdRF1, BILF2, RPMS1
47	GCCCGTTGGGTTACATTAAGGTGT	1437	143534–144971	LF3, Repeat region IR4
47	CATGCAGTGGTGTCAGACAGGAAA	1437	143534–144971	LF3, Repeat region IR4
48	TTTGGGATGCATCACTTTGA	3279	144203–147482	Repeat region “DR”
48	CCTCAAAGGTGTGGTCGTTT	3279	144203–147482	Repeat region “DR”
49	CTTTGGGTTCCATTGTGTGCCCTT	2838	147061–149899	“RPMS1”
49	ACCTGGTACATTGTGCCCATCAGA	2838	147061–149899	“RPMS1”
50	TCGTGGCTCGTACAGACGATTGTT	3411	147344–150755	“RPMS1”
50	TTTGCGCCTTCTCCTGGTTTATGC	3411	147344–150755	“RPMS1”
51	CCCACACCTTCACTCCTTGT	4112	148290–152402	BILF1, LF1, LF2, BALF5
51	CAGAGCCAGGCACATCTACA	4112	148290–152402	BILF1, LF1, LF2, BALF5
52	CCCACACCTTCACTCCTTGT	4002	151117–155119	A73
52	CAGAGCCAGGCACATCTACA	4002	151117–155119	A73
53	TAGTAGCGGGCAACGAGAGA	4030	151842–155872	A73
53	CGTGTGTGTGAACGTGTTTG	4030	151842–155872	A73
54	TGGAAGAAGGCGTAGAGCAT	4181	155195–159376	A73
54	CTTGTTTACCCAGACCCTGA	4181	155195–159376	A73
55	ACGCCGAGTCATCTCTCATTTGGA	1080	158854–159934	A73, BALF3, BALF4
55	GCAAGGCTGACTCACCTGTTTGA	1080	158854–159934	A73, BALF3, BALF4
56	GCTCAGGGTCTGGGTAAACA	2368	159355–161723	BARF0, BALF2
56	CGTGACTACCCCCACGTACT	2368	159355–161723	BARF0, BALF2
57	AGGTTGCACACCACATCAAA	3871	161261–165132	BALF2, BALF1, BARF1
57	GACTCGCTCACCCAAGAAAG	3871	161261–165132	BALF2, BALF1, BARF1
58	GTGCAGAGCCTTGACATTGA	4183	164101–168284	BALF1, LMP1
58	TGAACACCACCACGATGACT	4183	164101–168284	BALF1, LMP1
59	CACGGGGTTTATGTTTCTGG	4002	165676–169678	BRF1, LMP1
59	CCCCCTCCACTTTTTCCA	4002	165676–169678	BRF1, LMP1

Note that although most primer sets targeted single gene regions, there is overlap of some genes, and multiple genes covered by single primer sets. Also note that the same primer pairs covered different regions of EBV-1 and EBV-2 in some cases.