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

Retrovirology

Table 2 Comparison of Recombination between methods at different consensus majority cutoffs in mixtures of BH10 WT and mutant transcript RNA

% Majority cutoff	Method/enzyme	Total sequences	% Sequences excluded^a	% Sequences remaining	% Remaining recombinants missed	% Error^b
50	uSGS	33,870	0.6	99.4	0.39	0.020
60		33,870	1.1	98.9	0.30	0.018
70	Kapa Hi Fi	33,870	2.6	97.4	0.20	0.015
80	Uracil+	33,870	5.8	94.2	0.13	0.014
90		33,870	28.4	71.6	0.12	0.010
100		33,870	43.9	56.1	0.12	0.009
50	LP-PCR-1	11,008	4.7	95.3	4.07	0.033
60		11,008	11.7	88.3	1.86	0.030
70	Taq Gold	11,008	27.3	72.7	0.34	0.020
80		11,008	45.0	55.0	0.20	0.014
90		11,008	77.3	22.7	<0.01	0.007
100		11,008	87.2	12.8	<0.06	0.006
50	LP-PCR-2	23,142	1.4	98.6	0.91	0.037
60		23,142	3.3	96.7	0.62	0.033
70	Kapa2G	23,142	10.5	89.5	0.30	0.024
80	Robust	23,142	25.4	74.6	0.14	0.020
90		23,142	63.5	36.5	0.09	0.013
100		23,142	85.7	14.3	0.15	0.009
50	LP-PCR-3	20,252	4.6	95.4	6.44	0.016
60		20,252	13.8	86.2	2.00	0.015
70	Platinum	20,252	23.4	76.6	0.35	0.013
80	Hi Fi Taq	20,252	34.8	65.3	0.15	0.011
90		20,252	71.7	28.3	<0.04	0.004
100		20,252	92.0	8.0	<0.07	0.004

^aConsensus sequences were excluded due to failure to achieve the required majority at each level of consensus at each nucleotide position, likely due to in vitro PCR recombination
^bIncorrect bases at non drug resistant sites

ISSN: 1742-4690