TABLE 1.
Subtype defined by phy of PRa | No. of PR sequences | Concordanceb with phy (%) for PR
|
No. of RT sequences | Concordanceb with phy (%) for RT
|
||||
---|---|---|---|---|---|---|---|---|
Stanford | NCBI | REGAc | Stanford | NCBI | REGAc | |||
A | 27 | 63 | 44.4 | 52 | 18 | 22.2 | 33.3 | 44.4 |
Bd | 2 | 100 | 100 | 50 | 7 | 100 | 100 | 71.4 |
C | 16 | 62.5 | 56.3 | 12.5 | 9 | 77.8 | 77.8 | 55.6 |
D | 5 | 100 | 80 | 20 | 2 | 100 | 100 | 0 |
F | 4 | 75 | 100 | 50 | 3 | 100 | 100 | 66.7 |
G | 32 | 87.5 | 72 | 37.5 | 20 | 80 | 65 | 25 |
H | 4 | 100 | 100 | 25 | 1 | 100 | 100 | 100 |
J | 1 | 0 | 100 | 0 | 0 | |||
CRF01_AE | 2 | 50 | 50 | 0 | 0 | |||
CRF02_AG | 141 | 97.2 | 99.3 | 18.4 | 81 | 92.5 | 96.3 | 32 |
CRF03_AB | 2 | 0 | 100 | 0 | 0 | |||
CRF06_cpx | 11 | 0 | 81.8 | 18.2 | 5 | 0 | 60 | 40 |
CRF10_CD | 2 | 0 | 0 | 0 | 3 | 0 | 0 | 0 |
CRF11_cpx | 5 | 0 | 100 | 40 | 4 | 0 | 75 | 50 |
CRF12_BF | 9 | 0 | 66.7 | 22.2 | 7 | 0 | 57.1 | 28.6 |
CRF13_cpx | 1 | 0 | 100 | 0 | 1 | 0 | 0 | 0 |
CRF14_BG | 13 | 0 | 100 | 0 | 10 | 0 | 100 | 0 |
Pure subtypes | 91 | 75.8 | 64.8 | 36.2 | 60 | 66.7 | 65 | 43.3 |
All CRFs | 186 | 74.2 | 95.1 | 17.5 | 111 | 67.6 | 85.6 | 28.8 |
CRFs without CRF02_AG | 45 | 2.2 | 82.2 | 13.3 | 30 | 0 | 56.7 | 20 |
Total | 277 | 74.7 | 85.2 | 23.5 | 171 | 67.2 | 78.4 | 33.9 |
Clade B controle | 33 | 100 | 100 | 90.9 | 33 | 100 | 100 | 90.9 |
Subtypes in the pol coding region are as follows: CRF01_AE, subtype A; CRF02_AG, subtypes A and G; CRF03_AB, subtypes A and B; CRF06_cpx, subtypes G, K, A, and J; CRF10_CD, clades C and D; CRF11_cpx, subtypes J, G, and A; CRF12_BF, subtypes F and B; CRF13_cpx, subtypes G and J; CRF14_BG, subtype G.
Italicized values indicate significant differences (P < 0.05) between Stanford and NCBI results.
Including all the sequences not assigned to a subtype by the REGA tool (194 PR and 95 RT sequences).
Specimens carrying non-B sequences at the pol coding region.
Specimens carrying clade B sequences at both PR and RT.