PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

Table 1 Number of unique insertion sites (IS) identified via PCIP-seq

Sample name	Virus	Host	PVL	Template μg	Raw reads	Chimeric reads (%)	Pure host / pure viral reads	Insertion sites	Largest clone (%)
ATL2	HTLV-1	HSA	nd	4	81,219	68.21	0.0037 / 31.8	160	49.5
ATL100	HTLV-1	HSA	106	4	4838	64.14	9.16 / 26.7	13	89.624
233	BLV	OAR	78.3	7	524,698	53.4	0.04 / 46.53	5311	5.22
221 (022016)	BLV	OAR	63	4	180,276	67.14	3.59 / 29.27	8023	0.625
221 (032014)	BLV	OAR	16	4	32,266	68.69	0.11 / 31.20	5374	0.279
220	BLV	OAR	3.8	2	44,876	67.38	0 / 32.62	1352	3.55
1439	BLV	BosT	45	3	181,055	70.52	0.19 / 29.29	5773	1.17
560	BLV	BosT	0.644	1	6802	69.83	1.12 / 29.06	172	4.59
1053	BLV	BosT	23.5	6	367,454	72.13	0.04 / 27.83	17,903	0.353
HIV_U1	HIV-1	HSA	200	2	94,086	54.66	2.75 / 42.59	728	47.2
Jurkat U1–0.1	HIV-1	HSA	0.2	5	252,913	43.33	0.04 / 56.62	4	71.7
Jurkat U1–0.01	HIV-1	HSA	0.02	5	234,421	43.33	0.04 / 56.52	2	90.2
Jurkat neg	HIV-1	HSA	0	5	12,137	0	100 / 0	0	0
02006	HIV-1	HSA	0.46	12	240,641	51.63	1.10 / 47.27	158	7.82
06042	HIV-1	HSA	0.56	8	226,685	21.18	0.41 / 78.41	73	4.77
HPV18_PX	HPV18	HAS	nd	4	180,550	21.36	0.29 / 78.35	55	nd
HPV18_PY	HPV18	HAS	nd	4	82,807	0.09	0.05 / 99.86	19	nd

Chimeric reads reads containing host and viral DNA, cover the integration site, Pure host/pure viral reads reads containing either host or viral DNA, do not include the integration site, Largest clone % insertion site with highest number of reads in that sample, PVL proviral load. (Percentage cells carrying a single copy of integrated provirus or number proviral copies per 100 cells)

ISSN: 1474-760X