Table 2.
PANDAA improves sensitivity to detect single nucleotide changes in HIV-1 compared to conventional qPCR.
| Allele | Probe-binding site | qPCR median Cq (IQR) | PANDAA median Cq (IQR) | ∆Cq (PANDAA - qPCR) |
|---|---|---|---|---|
| Probe | AAAAAGAA C AAATCAGC | |||
| 001 | …………….. | 22.9 (22.6–23.0) | 22.6 (22.5–22.6) | −0.3 |
| 002 | ………..G….. | 29.5 (29.4–29.5) | 23.0 (23.0–23.0) | −6.5 |
| 003 | ..G………….. | 31.9 (31.9–32.0) | 26.2 (26.1–26.2) | −5.7 |
| 004 | ……….G…… | n.d. | 22.7 (22.4–22.8) | – |
| 005 | …C…………. | 26.2 (26.1–26.2) | 23.4 (23.4–23.6) | −2.7 |
| 006 | ……………A. | 24.1 (24.0–24.1) | 22.5 (22.5–22.5) | −1.6 |
| 007 | ….G………… | 25.1 (25.0 - 25.1) | 23.6 (23.5–23.7) | −1.5 |
| 008 | …….G……… | n.d. | 24.9 (24.8–25.0) | – |
| 009 | .G…………… | 23.9 (23.8–24.0) | 23.7 (23.5–23.9) | −0.2 |
| 010 | …………..T.. | 25.4 (24.9–25.4) | 22.8 (22.8–22.9) | −2.6 |
| 011 | ..G..A……….. | n.d. | 32.6 (32.5–32.6) | – |
| 012 | …………..C.. | 24.7 (24.3–24.8) | 22.9 (22.9–23.1) | −1.8 |
| 013 | …………..G.. | 41.2 (40.3–41.4) | 22.6 (22.6–22.7) | −18.6 |
| 014 | ..G……..G….. | n.d. | 23.1 (23.0–23.1) | – |
| 015 | .C…………… | 34.1 (34.1–34.1) | 24.6 (24.3–24.8) | −9.5 |
| 016 | ..C………….. | 39.8 (39.6–40.1) | 25.8 (25.7–25.8) | −14.0 |
| 017 | …….G…….A. | n.d. | 26.2 (26.2–26.3) | – |
| 018 | …C……G…… | n.d. | 23.2 (22.9–23.3) | – |
| 019 | ..G…………A. | n.d. | 33.1 (33.0–33.1) | – |
n.d. not detected.