Table 4.
Genotyping of RT Position 103 Using Plasma Virus Samples and Cultured Virus Supernatants: Melt Curve Analysis of SS-DNA Generated from Asymmetric PCR of Reverse-Transcribed Extracted RNA
| Sample∗ | Subtype | Codon | Mismatches PS1-PS2-PS3† | ΔTm‡ |
|||
|---|---|---|---|---|---|---|---|
| PS1 | PS2 | PS3 | Mean | ||||
| 7908 | B | AAA | 2-1-3 | 0 (16.3) | 0 (7.9) | 0 (14.3) | 0 (12.8) |
| 26339 | B | AAA | 4-3-4 | — | 0 (17.0) | — | 0 (17.0) |
| 112986 | B | AAC | 1-1-3 | 0 (16.1) | 0 (16.4) | — | 0 (16.2) |
| 175042 | B | AAT | 1-0-2 | 0 (3.9) | 0 (1.6) | 0 (16.2) | 0 (7.2) |
| 175881 | B | AGC | 4-3-5 | 0 (16.8) | 0 (17.1) | 0 (6.0) | 0 (13.3) |
| 220161 | B | AGA | 2-1-3 | 0 (15.2) | 0 (15.0) | 0 (11.2) | 0 (13.5) |
| 175872 | A | AAA | 2-3-5 | 0 (14.5) | 0 (5.3) | — | 0 (9.9) |
| 139002 | C | AAA | 3-2-2 | 0 (5.6) | 0 (8.3) | 0 (8.2) | 0 (7.3) |
| 139189 | C | AAA | 3-2-4 | 0 (13.4) | 0 (15.4) | 0 (7.1) | 0 (12.0) |
| 175134 | C | AAC | 2-1-1 | 0 (16.3) | 0 (18.8) | 0 (18.9) | 0 (18.0) |
| 57384 | C | AAC | 3-2-2 | 0 (13.4) | 0 (15.2) | 0 (15.2) | 0 (14.6) |
| JX140670 | D | AAA | 4-3-5 | 0 (13.4) | 0 (14.7) | — | 0 (14.0) |
| 175289 | CRF01 | AAC | 0-1-3 | 0 (8.9) | 0 (7.1) | 0 (6.3) | 0 (7.8) |
| 220168 | CRF01 | AAG | 3-3-5 | 0 (4.3) | 0 (4.4) | — | 0 (4.3) |
| JX140646 | CRF02 | AAA | 2-2-4 | 0 (7.0) | 0 (5.9) | 0 (6.8) | 0 (6.6) |
PS, probe set; —, probe sets not hybridizing with the PCR product; ΔTm, change in melting temperature.
JX140670 and JX140646 were cultured virus supernatants from the Duke University External Quality Assurance Program Oversight Laboratory sample collection.
Number of mismatches in the flanking sequence for each of the three PSs in the plasma virus: PS1-PS2-PS3.
ΔTm is the difference between the Tm of the probe complementary to the codon in the third column and the Tm of the probe with the highest Tm (maximum Tm) for PS1, PS2, PS3, and the mean of PS1, PS2, and PS3. In all cases, ΔTm was 0°C because the Tm of the probe with the complementary codon was the highest within the probe set. The parentheses contain the ΔTm for the probe with the second lowest ΔTm (ie, the second-best match).