TABLE 2.
Comparison of standard genotype and single-genome sequencing
| Patientd | No. of resistance mutationsa
|
Resistance mutations found only by SGSb
|
||||
|---|---|---|---|---|---|---|
| PRe
|
RTc
|
|||||
| Bulk | SGS | Bulk | SGS | PR | RT | |
| 1N | 4 | 4 | 0, 0 | 7, 5 | A98S (33), K101E (33), V179A (7), Y181C (33), G190A (33), L210W (33), T215Y (33) | |
| 2N | 8 | 8 | 4, 0 | 6, 1 | A62V (12), K103N (3) | |
| 3N | 8 | 10 | 11, 0 | 17, 1 | D30G (3), I93V (3) | M41L (3), A62V (3), V75A (15), K103N (3), V106T (3), V108F (3), Y115D (3) |
| 4N | 2 | 5 | 5, 0 | 8, 0 | M36I (9), M46I (2), V82G (2) | D67N (2), M184K (2), T215D (2) |
| 5N | 6 | 10 | 1, 0 | 5, 0 | L10V (2), L24F (2), G73S (5), V82I (2) | A62T (2), K103E (2), F116C (2), V118I (2) |
| 6 | 4 | 5 | 2, 0 | 6, 0 | M46L (5) | E44K (2), A62T (2), D67N (2), K70R (2) |
| 7 | 5 | 5 | 1, 0 | 2, 0 | E44A (2) | |
| 8 | 1 | 3 | 2, 0 | 4, 0 | I47V (2), 184K (2) | V118D (2), L210M (2) |
| 9 | 8 | 9 | 5, 0 | 9, 1 | I93L (7) | F77L (2), K103N (2), V106I (2), V108G (2) |
| 10 | 3 | 3 | 1, 0 | 5, 0 | T69P (3), V106I (36), M184I (11), K219N (3) | |
| 11 | 5 | 6 | 3, 0 | 6, 0 | M36V (3) | M41L (3), V118I (3), T215F (5) |
| 12 | 8 | 11 | 6, 0 | 7, 0 | M46I (9), I54V (5), I84G (5) | V118I (5) |
| 13 | 2 | 4 | 1, 0 | 4, 1 | M36I (6), A71V (3) | E44K (3), L100I (3), P225L (3) |
| 14 | 2 | 7 | 5, 0 | 5, 0 | L10I (4), M46I (13), M46L (13), V82A (4), N88D (4) | |
| 15N | 1 | 2 | 0, 0 | 0, 0 | V77I (5) | |
| 16N | 1 | 2 | 0, 0 | 0, 0 | L10I (5) | |
| 17N | 6 | 8 | 6, 0 | 11, 1 | M36I (22), A71I (4) | T69N (4), K101E (30), K103E (4), K103R (4), F116S (4) |
| 18N | 8 | 11 | 6, 2 | 8, 3 | G73A (5), G73T (9), V82I (5) | L74V (5), Y181C (14) |
| 19N | 5 | 5 | 3, 1 | 4, 1 | D67N (30) | |
| 20 | 6 | 7 | 4, 1 | 7, 3 | M36I (10) | L74V (15), L100I (25), V108I (15) |
| 21N | 7 | 10 | 6, 1 | 6, 1 | M36I (10), G73S (5), L90M (5) | K101R (5) |
| 22N | 6 | 12 | 10, 2 | 14, 2 | L10V (20), M36V (5), M46I (15), I84V (15), L90M (15), 193L (15) | T69A (10), K101R (15), V179I (5), P225H (10) |
| 23N | 8 | 10 | 10, 3 | 10, 3 | K20T (7), L63S (7) | |
| 24N | 9 | 9 | 10, 2 | 10, 2 | ||
| 25N | 12 | 15 | 7, 2 | 13, 2 | K20I (13), K20T (7), I84L (7) | E44D (13), D67N (20), K70A (7), V75L (7), K103E (7), K103I (7) |
| 26N | 9 | 12 | 7, 2 | 12, 2 | L10I (6), L33I (3), L63T (3) | T69I (16), V75I (19), M184V (3), K219T (19), K219Q (3) |
a
Mutations in retroviral codons associated with drug resistance as designated by the Stanford database (24).
b
Mutations in boldface type are considered drug resistance mutations as designated by the Stanford database; parentheses show percentages of genomes containing mutations. NNRTI resistance mutations are underlined.
c
Numbers of NNRTI resistance mutations are underlined; numbers of NRTI mutations are not underlined.
d
All patients but one had failed a treatment regimen containing at least one PI and at least two NRTIs. Patients indicated by an N had also been treated with at least one NNRTI. Patient 20 was untreated but was infected with a multidrug-resistant strain.
e
PR, protease.