. 2019 May 17;14(5):e0216944. doi: 10.1371/journal.pone.0216944

Table 1. 5’ copyback DVG genomes identified in viruses #1, #2 and #3 employing DVG-specific RT-PCR.

Virus rescue #	Predicted size of DVG (nt)	Break-point position	Reinitia-tion position	Loop size (nt)	Stem size (nt)	Detected by RT-PCR using primer pair ^b	Size of PCR fragment in bp ^c
1	2262	13811- 13812 ^a	14697- 14696 ^a	884- 886	688- 689	a/b5	776
	2226	13580	14964	1384	421	a/b1	1635 (1a1) ^d
	1941	13865	14964	1099	421	a/b1	1350 (1a1) ^d
	1261	14575	14934	359	451	a/b1	670 (1a2)
	997	14770	15004	234	381	a/b1	404 (1a3)
	792	14874	15104	230	281	a/b2	327 (1b1)
2	2598	13308	14864	1556	521	a/b4	860 (2d1)
	2526	13566- 13568 ^a	14678- 14676 ^a	1108–1112	707	a/b4	788 (2d2) ^d
	2490	13617	14663	1046	722	a/b4	751 (2d2) ^d
	2310	13316	15144	1828	241	a/b4	572 (2d3) ^d
	2300	13339	15131	1791	254	a/b4	563 (2d3) ^d
	2184	13347	15239	1892	146	a/b4	446 (2d4) ^d
	1905	13480	15064	1584	321	a/b4	488 (2d4) ^d
	1584 1125^e	13907–13909 ^a	15279–15277 ^a	1368–1372 909–913	108–106 108–106	a/b1 a/b2 a/b3 a/b3	993 (2a1) 1231(2b1) 1331 (2c1) 870 (2c2)^e
	1429	14456	14885	429	500	a/b1	838 (2a2) ^d
	1381 922^f	14223–14224 ^a	15166–15165 ^a	941–943 482–484	219–220 219–220	a/b1 a/b3	790 (2a2) ^d 668 (2c3)^f
	1320	14342	15108	766	277	a/b1	728 (2a3) ^d
	1278	14596	14896	300	489	a/b1	685 (2a3) ^d
	1092	14761	14917	156	468	a/b1	500 (2a4)
	1014	14730–14733 ^a	15026–15023 ^a	290–296	362–359	a/b1	423 (2a5)
	870	14868	15032	164	353	a/b2	407 (2b2)
	870	14856- 14863 ^a	15043- 15036 ^a	173- 187	349- 342	a/b3	615 (2c4)
	731	14861–14862 ^a	15178- 15177 ^a	317- 315	207- 208	a/b3	477 (2c5) ^d
	678	14947- 14950 ^a	15145- 15142 ^a	198- 192	240- 243	a/b4	426 (2c5) ^d
	708	14864	15198	333	187	a/b4	454 (2c5) ^d
	564	14934	15272	338	113	a/b3	310 (2c6)
3	1134	14706	14930	224	455	a/b1 a/b2	543 (3a1) 675 (3b1)
3	2878	12661	15231	2570	154	a/b2	2418 (3b2)^g

^a The exact nucleotide position of the breakpoint and the reinitiation site could not be determined due to inverse complementarity of a sequence of two to eight nucleotides at the DVG junctions.

^b Sequences of primers used are listed in S4 Table.

^c Numbers in parentheses indicate ethidium bromide stained PCR bands in agarose gels as depicted in Figs 8 and 9; an agarose gel depicting the RT-PCR result for primer pair a/b5 using RNA prepared from virus #1 is shown in S1 Fig.

^d more than one DVG was detected in the DNA extracted from agarose gel bands labeled 1a1, 2a2 and 2a3, 2d2, 2c5, 2d4.

^e and ^f These copyback DVGs displayed a deletion of 457 nt between positions 14585 and 15043 resulting in sizes of 1125 b or 992 b, respectively, and of PCR fragments of 870 bp or 668 bp length, respectively.

^g This 5’ copyback DVG was only identified by RT-PCR and not by DVG- profiler.