Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants
Abstract
:1. Introduction
2. Methods
2.1. Plasmids and Virus Strains
2.2. Sample Collection and Processing
2.3. MeltArray Assay
2.4. Analytical Evaluation of MeltArray Assay
2.5. NGS
2.6. ddPCR Assays for XBB.1.16 and XBB.1.9
2.7. Statistical Analysis
3. Results
3.1. MeltArray Assay Design
3.2. Analytical Performance of MeltArray Assay
3.3. Clinical Evaluation of MeltArray Assay
3.4. Local Epidemic Surveillance during the Omicron Outbreak
3.5. Potential for Estimation of Variant Abundance via MeltArray Assay
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Target | Codon Change | Channel | Tm (℃) | CV (%) | Limit of Detection |
---|---|---|---|---|---|
(Mean ± 3SD) | (Copies/Reaction) | ||||
T19I | ACA > ATA | ROX | 66.02 ± 0.24 | 0.12 | 50 |
Q183E | CAG > GAG | Cy5 | 82.69 ± 0.21 | 0.08 | 50 |
I210V | ATT > GTT | HEX | 81.76 ± 0.24 | 0.10 | 50 |
V213G | GTG > GGG | FAM | 80.53 ± 0.23 | 0.10 | 50 |
G252V | GGT > GTT | Cy5 | 71.87 ± 0.22 | 0.10 | 50 |
G257S | GGT > AGT | FAM | 73.40 ± 0.21 | 0.10 | 50 |
R346T | AGA > ACA | HEX | 71.51 ± 0.22 | 0.10 | 50 |
K444T | AAG > ACG | Cy5 | 67.98 ± 0.16 | 0.08 | 50 |
L452R | CTG > CGG | ROX | 81.55 ± 0.24 | 0.10 | 50 |
F486V | TTT > GTT | Cy5 | 77.63 ± 0.23 | 0.10 | 50 |
F486P | TTT > CCT | ROX | 71.22 ± 0.24 | 0.11 | 50 |
N658S | AAC > AGC | HEX | 66.71 ± 0.18 | 0.09 | 50 |
G1819S | GGT > AGT | Quasar 705 | 70.90 ± 0.23 | 0.11 | 50 |
L3829F | CTC > TTC | Atto 425 | 70.98 ± 0.30 | 0.14 | 50 |
Variant | MeltArray Assay/NGS | Sensitivity% (95% CI) | Specificity% (95% CI) | PPV% (95% CI) | NPV% (95% CI) | Accuracy% (95% CI) | Kappa | |||
---|---|---|---|---|---|---|---|---|---|---|
+/+ | +/− | −/+ | −/− | |||||||
BA.5.2* | 117 | 5 | 6 | 104 | 95.12 (89.77–97.75) | 95.41 (89.71–98.02) | 95.90 (90.76–98.24) | 94.55 (88.61–97.48) | 95.26 (91.71–97.33) | 0.90 (0.78–1.03) |
BF.7 | 44 | 9 | 0 | 179 | 100 (91.97–100) | 95.21 (91.15–97.46) | 83.02 (70.77–90.80) | 100 (97.90–100) | 96.12 (92.79–97.95) | 0.88 (0.76–1.01) |
BN.1 | 11 | 1 | 0 | 220 | 100 (74.12–100) | 99.55 (97.48–99.92) | 91.67 (64.61–98.51) | 100 (98.28–100) | 99.57 (97.60–99.92) | 0.95 (0.83–1.08) |
BQ.1* | 10 | 0 | 0 | 222 | 100 (72.25–100) | 100 (98.30–100) | 100 (72.25–100) | 100 (98.30–100) | 100 (98.37–100) | 1 (0.87–1.13) |
BQ.1.1 | 10 | 0 | 0 | 222 | 100 (72.25–100) | 100 (98.30–100) | 100 (72.25–100) | 100 (98.30–100) | 100 (98.37–100) | 1 (0.87–1.13) |
XBB.1* | 10 | 0 | 0 | 222 | 100 (72.25–100) | 100 (98.30–100) | 100 (72.25–100) | 100 (98.30–100) | 100 (98.37–100) | 1 (0.87–1.13) |
BA.2* | 4 | 0 | 0 | 228 | 100 (51.01–100) | 100 (98.34–100) | 100 (51.01–100) | 100 (98.34–100) | 100 (98.37–100) | 1 (0.87–1.13) |
BA.2.75* | 3 | 0 | 0 | 229 | 100 (43.85–100) | 100 (98.35–100) | 100 (43.85–100) | 100 (98.35–100) | 100 (98.37–100) | 1 (0.87–1.13) |
XBB.1.5 | 1 | 0 | 0 | 231 | 100 (20.65–100) | 100 (98.36–100) | 100 (20.65–100) | 100 (98.36–100) | 100 (98.37–100) | 1 (0.87–1.13) |
BR.2 | 1 | 0 | 0 | 231 | 100 (20.65–100) | 100 (98.36–100) | 100 (20.65–100) | 100 (98.36–100) | 100 (98.37–100) | 1 (0.87–1.13) |
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Yan, T.; Zheng, R.; Li, Y.; Sun, S.; Zeng, X.; Yue, Z.; Liao, Y.; Hu, Q.; Xu, Y.; Li, Q. Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants. Viruses 2023, 15, 2397. https://doi.org/10.3390/v15122397
Yan T, Zheng R, Li Y, Sun S, Zeng X, Yue Z, Liao Y, Hu Q, Xu Y, Li Q. Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants. Viruses. 2023; 15(12):2397. https://doi.org/10.3390/v15122397
Chicago/Turabian StyleYan, Ting, Rongrong Zheng, Yinghui Li, Siyang Sun, Xiaohong Zeng, Zhijiao Yue, Yiqun Liao, Qinghua Hu, Ye Xu, and Qingge Li. 2023. "Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants" Viruses 15, no. 12: 2397. https://doi.org/10.3390/v15122397
APA StyleYan, T., Zheng, R., Li, Y., Sun, S., Zeng, X., Yue, Z., Liao, Y., Hu, Q., Xu, Y., & Li, Q. (2023). Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants. Viruses, 15(12), 2397. https://doi.org/10.3390/v15122397