An economical Nanopore sequencing assay for human papillomavirus (HPV) genotyping

Chan, Wai Sing; Chan, Tsun Leung; Au, Chun Hang; Leung, Chin Pang; To, Man Yan; Ng, Man Kin; Leung, Sau Man; Chan, May Kwok Mei; Ma, Edmond Shiu Kwan; Tang, Bone Siu Fai

doi:10.1186/s13000-020-00964-6

Diagnostic Pathology

Table 7 Percentage of identity of Nanopore consensus sequences to HPV reference genomes

From: An economical Nanopore sequencing assay for human papillomavirus (HPV) genotyping

Patient	Nanopore results	Best BLAST hit		Second BLAST hit		Difference
Patient	Nanopore results	HPV type	% identity	HPV type	% identity	Difference
2	59	59	99%	18	77%	22%
2	^a90	90	97%	106	84%	15%
3	52	52	99%	58	80%	19%
3	55	55	100%	44	93%	7%
5	31	31	98%	35	80%	18%
	33	33	99%	58	86%	13%
	^a52	52	99%	58	80%	19%
	^a90	90	97%	106	85%	12%
7	31	31	95%	35	79%	16%
9	81	81	99%	62	85%	14%
10	18	18	99%	45	85%	14%
13	^a44	44	99%	55	92%	7%
	52	52	99%	58	80%	19%
	53	53	99%	30	85%	14%
	^a74	74	99%	55	83%	16%
	^a90	90	97%	106	85%	12%
16	52	52	99%	58	81%	18%
16	81	81	99%	62	85%	14%
17	52	52	99%	58	80%	19%
17	54	54	99%	45	74%	25%
18	11	11	99%	6	87%	12%
	52	52	99%	58	80%	19%
	59	59	99%	18	77%	22%
23	39	39	99%	70	81%	18%
	61	61	99%	mEV06c12b	83%	16%
	72	72	92%	mEV06c12b	89%	3%
	^a87	87	98%	86	85%	13%
24	66	66	98%	56	84%	14%
25	61	61	99%	mEV06c12b	83%	16%
26	^a90	90	97%	106	85%	12%
27	52	52	99%	58	80%	19%
27	^a87	87	98%	86	84%	14%
28	62	62	99%	81	84%	15%
30	35	35	98%	31	80%	18%
32	52	52	99%	58	81%	18%
34	51	51	99%	82	85%	14%
35	^a74	74	99%	55	84%	15%
37	51	51	99%	82	85%	14%
38	40	40	99%	7	88%	11%
	55	55	99%	44	93%	6%
	83	83	99%	102	84%	15%
40	^a52	52	99%	58	80%	19%
	53	53	98%	30	85%	13%
	55	55	100%	44	93%	7%
	58	58	99%	33	86%	13%
	62	62	99%	81	85%	14%
	^a74	74	98%	55	84%	14%
41	42	42	98%	32	83%	15%
	52	52	100%	58	81%	19%
	73	73	99%	34	85%	14%
43	16	16	100%	35	78%	22%
44	16	16	99%	35	78%	21%
45	59	59	99%	18	76%	23%
46	31	31	98%	35	80%	18%
46	58	58	99%	33	86%	13%
47	52	52	98%	58	80%	18%
	68	68	93%	39	81%	12%
	84	84	98%	87	84%	14%
	^a90	90	97%	106	85%	12%
48	^a44	44	99%	55	93%	6%
	66	66	98%	56	84%	14%
	84	84	99%	87	84%	15%
49	52	52	99%	58	80%	19%
50	40	40	98%	7	87%	11%
50	53	53	98%	30	85%	13%
51	11	11	100%	6	87%	13%
	^a43	43	95%	45	77%	18%
	52	52	99%	58	80%	19%
	81	81	99%	62	84%	15%
52	66	66	98%	56	83%	15%
53	^a43	43	95%	45	78%	17%
	51	51	99%	82	84%	15%
	^a90	90	97%	106	85%	12%
54	16	16	100%	35	78%	22%
	^a40	40	93%	7	85%	8%
	51	51	99%	82	84%	15%
	54	54	99%	45	73%	26%
	56	56	90%	66	76%	14%
	62	62	99%	81	84%	15%
	81	81	99%	62	85%	14%
55	53	53	99%	56	79%	20%
55	56	56	99%	66	84%	15%
57	54	54	87%	31	74%	13%
	55	55	100%	44	93%	7%
	66	66	98%	56	84%	14%
	81	81	99%	62	84%	15%
	^a90	90	97%	106	85%	12%
58	^a42	42	99%	32	84%	15%
	52	52	98%	58	80%	18%
	^a90	90	97%	106	85%	12%
59	59	59	99%	18	77%	22%
60	59	59	99%	18	76%	23%
60	89	89	99%	81	78%	21%
61	^a43	43	96%	45	79%	17%
	56	56	97%	66	83%	14%
	82	82	99%	51	84%	15%
62	52	52	99%	58	80%	19%
63	33	33	99%	58	86%	13%
	^a44	44	99%	55	93%	6%
	51	51	99%	82	83%	16%
64	51	51	99%	82	84%	15%
65	16	16	100%	35	78%	22%
68	^a59	59	99%	18	77%	22%
69	^a87	87	99%	86	86%	13%
74	^a52	52	99%	58	81%	18%
	58	58	99%	33	86%	13%
	^a62	62	99%	81	85%	14%
75	58	58	99%	33	85%	14%
78	^a90	90	97%	106	85%	12%
79	^a44	44	99%	55	92%	7%
	56	56	96%	66	84%	12%
	70	70	99%	39	81%	18%
81	^a74	74	93%	55	81%	12%
82	42	42	95%	32	83%	12%
83	^a74	74	97%	55	83%	14%
85	82	82	99%	51	84%	15%
86	62	62	99%	81	85%	14%
91	52	52	99%	58	80%	19%
91	^a90	90	97%	106	84%	13%
92	^a42	42	93%	32	78%	15%
92	68	68	92%	39	80%	12%
96	52	52	99%	58	80%	19%
100	52	52	99%	58	80%	19%
104	62	62	98%	81	85%	13%
107	^a44	44	99%	55	93%	6%
	52	52	99%	58	81%	18%
	^a53	53	100%	30	86%	14%
	62	62	99%	81	85%	14%
112	16	16	98%	58	78%	20%
112	52	52	99%	58	81%	18%
114	^a26	26	100%	69	83%	17%
	55	55	100%	44	93%	7%
	^a59	59	99%	18	77%	22%
	^a62	62	99%	81	85%	14%
	89	89	99%	81	77%	22%
115	^a74	74	95%	55	83%	12%
118	6	6	99%	11	87%	12%
118	62	62	99%	81	84%	15%
124	81	81	99%	62	85%	14%
125	^a87	87	98%	86	85%	13%
126	^a90	90	97%	106	85%	12%
138	39	39	99%	68	81%	18%
143	^a40	40	99%	7	88%	11%
	^a74	74	98%	55	84%	14%
	81	81	99%	62	84%	15%
	^a87	87	97%	86	84%	13%
148	59	59	99%	18	77%	22%
152	62	62	98%	81	85%	13%
156	52	52	99%	58	81%	18%
156	54	54	95%	6	74%	21%
157	39	39	94%	70	81%	13%
	53	53	96%	30	84%	12%
	61	61	99%	mEV06c12b	83%	16%
161	62	62	98%	81	83%	15%
162	^a74	74	94%	55	85%	9%
163	62	62	99%	81	85%	14%
167	39	39	99%	70	81%	18%
170	66	66	98%	56	83%	15%
174	66	66	98%	56	83%	15%
175	54	54	99%	45	73%	26%
177	16	16	99%	35	80%	19%
	^a53	53	99%	30	84%	15%
	62	62	99%	81	85%	14%
181	51	51	99%	82	85%	14%
	66	66	98%	56	83%	15%
	^a68	68	98%	39	81%	17%
182	58	58	98%	33	87%	11%
182	61	61	100%	mEV06c12b	83%	17%
184	58	58	99%	33	85%	14%
185	58	58	99%	33	85%	14%
	70	70	99%	39	81%	18%
	89	89	99%	81	78%	21%
188	16	16	100%	35	78%	22%
191	56	56	99%	66	83%	16%
192	51	51	98%	82	84%	14%
193	62	62	99%	81	85%	14%
195	52	52	99%	58	81%	18%
195	59	59	99%	18	76%	23%
196	59	59	99%	18	77%	22%
197	52	52	100%	58	81%	19%
	59	59	99%	18	76%	23%
	70	70	99%	39	81%	18%
	^a90	90	97%	106	85%	12%
198	^a32	32	99%	42	84%	15%
	53	53	99%	30	86%	13%
	56	56	99%	66	84%	15%
	61	61	100%	mEV06c12b	83%	17%
	66	66	98%	56	83%	15%
	84	84	99%	87	84%	15%
200	53	53	98%	30	85%	13%
	54	54	99%	45	74%	25%
	81	81	99%	62	84%	15%
	83	83	95%	102	82%	13%
Average % identity of the best hit			98%	Average difference		15%

^a HPV types not detected by LA

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ISSN: 1746-1596

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