Table 1.

Conserved RNA secondary structures (SS) in HCV genomes, along with their corresponding Rfam model IDs (if available)^46,47.

RNA SS	Genomic region	Alignment position		JFH-1 position		Rfam v12	Rfam v14.10
		S	E	S	E
SL I	$5^{\prime }$ UTR	13	28	5	19	RF00061	RF00061$_{}^{\circ }$
SL II	$5^{\prime }$ UTR	52	126	43	117	RF00061	RF00061$_{}^{\circ }$
SL III	$5^{\prime }$ UTR	133	334	124	322	RF00061	RF00061$_{}^{\circ }$
SL IV	$5^{\prime }$ UTR/C	346	360	334	348	RF00061	RF00061$_{}^{\circ }$
SL V	C	400	435	388	423	RF00620	RF00620$_{}^{\circ }$
SL VI	C	439	519	427	507	RF00620	RF00620$_{}^{\circ }$
SL 562	C	574	595	562	582
SL 588	C	601	678	588	665		RF04220
SL 669	C	684	761	671	748		RF04221
J 750	C	762	839	749	826		RF04219
SL 833	C	846	869	833	856		RF00***
SL 1412	E1	1430	1467	1414	1451		RF04305
SL 1850	E1	1881	2013	1850	1982
SL 2313	E1	2356	2433	2313	2390
SL 2531	E2	2 574	2591	2531	2548		RF04308
SL 2549	E2/p7	2592	2636	2549	2592		RF04308
SL 3308	NS2/NS3	3352	3644	3308	3600
SL 3844	NS3	3888	3952	3844	3908
SL 4005	NS3	4049	4099	4005	4056
SL 4214	NS3	4258	4223	4214	4279
SL 4527	NS3	4571	4591	4527	4547
SL 4621	NS3	4665	4725	4621	4681
SL 4691	NS3	4735	4788	4691	4744
SL 5016	NS3	5060	5125	5016	5081
SL 5128	NS3	5172	5249	5128	5205
SL 5357	NS4A	5401	5448	5357	5404
SL 5647	NS4B	5691	5777	5647	5733
SL 6027	NS4B	6071	6197	6027	6153
SL 6270	NS5A	6314	6410	6270	6366
SL 6371	NS5A	6415	6446	6371	6402
SL 6530	NS5A	6574	6689	6530	6645
SL 7516	NS5A	7584	7603	7516	7535
SL 7536	NS5A	7604	7702	7536	7634
SL 7816	NS5B	7893	7905	7816	7828
J 7880	NS5B	7959	8073	7882	7996		RF00***
SL 8001	NS5B	8077	8126	8000	8049		RF04306
SL 8075	NS5B	8152	8174	8075	8097
SL 8299	NS5B	8376	8396	8299	8334
SL 8670	NS5B	8722	8803	8645	8726		RF04307
5BSL1	NS5B	9194	9231	9117	9154		RF04218
5BSL2	NS5B	9276	9335	9198	9257	RF00468	RF00468$_{}^{\circ }$
5BSL3.1	NS5B	9361	9406	9283	9328	RF00260	RF00260$_{}^{\circ }$
5BSL3.2	NS5B	9410	9455	9332	9377	RF00260	RF00260$_{}^{\circ }$
5BSL3.3	NS5B	9467	9497	9389	9419	RF00260	RF00260$_{}^{\circ }$
SL IV	NS5B	9505	9533	9427	9452	RF00469	RF00260$_{}^{\circ }$
X-tail	$3^{\prime }$ UTR	9727	9826	9579	9678	RF00481	RF00481$_{}^{\circ }$

We updated and merged six Rfam models of v12 into five Rfam models (v14.10); confirmed the conservation of a total of 16 previously predicted RNA secondary structures throughout the phylogenetic tree (available in Rfam v14.10); and added further 23 novel conserved RNA families into Rfam (bold font). $\circ$ indicates that the existing Rfam model was updated with this publication. We named novel structures according to their position in the genome JFH-1 (S—Start; E—End). ***Rfam models will follow in the near future.