Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA

Boltz, Valerie F.; Rausch, Jason; Shao, Wei; Hattori, Junko; Luke, Brian; Maldarelli, Frank; Mellors, John W.; Kearney, Mary F.; Coffin, John M.

doi:10.1186/s12977-016-0321-6

Retrovirology

Table 6 Linkage of resistance mutations in donors failing anti-retroviral therapy as measured by uSGS

From: Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA

Patient/sample	Haplotypes Mutant codons in italics	Expected (%)	Observed (%)	P value
1/1	67N, 69T, 101E, 106I, 108V, 188Y, 190A, 215F, 219R	0.05	0.06	0.58
	67N, 69T, 101Q, 106V, 108I, 188Y, 190A, 215Y, 219R	0.002	0.13	0.0004
	67N, 69T, 101E,106V,108V,188Y,190A,215Y,219R	8.41	5.58	1.18*10⁻⁵
	67N,69T,101E,106V,108I,188Y,190A,215Y,219R	0.04	0.06	0.49
	67N,69T,101Q,106V,108V,188Y,190A,215Y,219R	0.36	3.04	1.0*10⁻²³⁷
	67N,69T,101Q,106V,108V,188Y,190G,215Y,219R	0.0002	0.06	0.004
	67N, 69T, 101E, 106I, 108I, 188Y, 190A, 215Y, 219R	0.44	0.25	0.18
	67N, 69T, 101E, 106I, 108V, 188Y, 190T, 215Y, 219R	0.11	0.13	0.52
	67N, 69T, 101E, 106I, 108V, 188Y, 190A,215Y, 219R	86.25	89.22	0.0003
	67N, 69T, 101E, 106I, 108V, 188Y, 190A, 215Y, 219K	0.05	0.06	0.58
	67N, 69T, 101K, 106I, 108V, 188Y, 190A, 215Y, 219R	0.34	0.38	0.46
	67N, 69T, 101Q, 106I, 108V, 188Y, 190A, 215Y, 219R	3.72	0.82	3.1*10⁻¹³
	67N, 69I, 101E, 106I, 108V, 188Y, 190A, 215Y, 219R	0.05	0.06	0.58
	67N, 69T, 101E, 106I, 108V, 188C, 190A, 215Y, 219R	0.05	0.06	0.58
	67N, 69T, 101Q, 106I, 108I, 188Y, 190A, 215Y, 219R	0.02	0.06	0.26
1/2	67N, 69T, 101E, 106I, 190A, 215Y, 219K	0.13	0.15	0.58
	67N, 69T, 101K, 106V, 190A, 215Y, 219R	0.02	0.15	0.15
	67D, 69T, 101E, 106V, 190A, 215Y, 219R	0.01	0.15	0.08
	67N, 69T, 101E, 106I, 190A, 215Y, 219R	87.42	90.25	0.01
	67N, 69T, 101Q, 106V, 190A, 215Y, 219R	0.33	3.10	5.1*10⁻¹⁴
	67N, 69T, 101K, 106I, 190A, 215Y, 219R	0.27	0.15	0.45
	67N, 69T, 101E, 106V, 190A, 215Y, 219R	8.04	5.02	0.001
	67N, 69A, 101E, 106I, 190A, 215Y, 219R	0.13	0.15	0.58
	67N, 69T, 101Q, 106I, 190A, 215Y, 219R	3.64	0.89	6.1*10⁻⁶
2/3	67N, 69T, 70Q, 74L, 101K, 106V, 108V, 184V, 190G, 215Y	1.05	1.07	0.51
	67N, 69T, 70K, 74L, 101R, 106V, 108V, 184V, 190G, 215Y	0.48	0.49	0.52
	67N, 69T, 70K, 74L, 101K, 106V, 108V, 184I, 190G, 215Y	0.16	0.16	0.57
	67D, 69T, 70K, 74L, 101K, 106V, 108V, 184V, 190G, 215Y	0.08	0.08	0.62
	67N.69T, 70K, 74L, 101K, 106I, 108V, 184V, 190G, 215Y	0.32	0.33	0.54
	67N, 69T, 70K, 74L, 101K, 106V, 108V, 184V, 190E, 215Y	0.08	0.08	0.62
	67N 69T, 70K, 74L, 101K, 106V, 108V, 184V, 190R, 215Y	0.08	0.08	0.62
	67N, 69T, 70K, 74I, 101K, 106V, 108V, 184V, 190G, 215Y	0.08	0.08	0.62
	67N 69A, 70K, 74L, 101K, 106V, 108V, 184V, 190G, 215Y	0.08	0.08	0.62
	67N, 69T, 70N, 74L, 101K, 106V, 108V, 184V, 190G, 215Y	0.08	0.08	0.63
	67N 69T, 70T, 74L, 101K, 106V, 108V, 184V, 190G, 215Y	1.21	1.23	0.51
	67N, 69T, 70K, 74L, 101Q, 106V, 108V184V, 190G, 215Y	0.08	0.08	0.62
	67N 69T, 70K, 74L101K, 106V, 108V, 184V, 190G, 215Y	95.76	95.64	0.44
	67N 69T, 70K, 74L, 101K, 106V, 108A, 184V, 190G, 215Y	0.08	0.08	0.62
	67N, 69T, 70K, 74L, 101K, 106V, 108I, 184V, 190G, 215Y	0.40	0.41	0.53

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