Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens
Abstract
:1. Introduction
2. Materials and Methods
2.1. Specimens Used in Assay Comparison
2.2. RNA Extractions and cDNA Synthesis
2.3. Pan-Coronavirus PCR Protocols Selected for Comparison
2.4. Statistical Analysis
3. Results
3.1. Clinical and Environmental Specimens Used in Evaluating the Assay
3.2. Comparative Analysis of Different Pan-CoV PCR Assays in Human Specimens
3.3. Comparative Analysis of Different Pan-CoV PCR Assays in Wastewater Specimens
3.4. Comparative Analysis of Different Pan-CoV PCR Assays in Bat Specimens
3.5. Comparative Analysis of Different Pan-CoV PCR Assays in Avian Specimens
3.6. Comparative Analysis of Different Pan-CoV PCR Assays in CoV Detection from Each Genus
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Virus Name | CoV Genus | Host/Source | Sample Type | Confirmed Assay | Number |
---|---|---|---|---|---|
HCoV-229E | α CoV | Human | NPS * | Real-time PCR | 5 |
HCoV-NL63 | α CoV | Human | NPS | Real-time PCR | 3 |
Bat Alphacoronavirus HKU10 | α CoV | Bat | Rectal swab | Q-CoV PCR and sequencing | 14 |
Bat Alphacoronavirus RsYN14 | α CoV | Bat | Rectal swab | Q-CoV PCR and sequencing | 2 |
HCoV- HKU1 | β CoV | Human | NPS | Real-time PCR | 1 |
HCoV-OC43 | β CoV | Human | NPS | Real-time PCR | 7 |
SARS-CoV-2 | β CoV | Human | NPS | Real-time PCR | 7 |
SARS-CoV-2 | β CoV | Hospital, aircraft | Wastewater | Real-time PCR | 27 |
Bat Sarbecovirus isolate Ra22QT77 | β CoV | Bat | Rectal swab | Q-CoV PCR and sequencing | 12 |
Anser fabalis coronavirus NCN2 | γ CoV | Avian | Oral swab Rectal swab | X-CoV PCR and sequencing | 3 |
Avian coronavirus Glaucous-winged gull CIR-66002 | γ CoV | Avian | Oral swab Rectal swab | X-CoV PCR and sequencing | 1 |
Avian coronavirus isolate CoV-9518-2016 | γ CoV | Avian | Oral swab Rectal swab | X-CoV PCR and sequencing | 2 |
Pigeon-dominant Coronavirus | γ CoV | Avian | Oral swab | X-CoV PCR and sequencing | 1 |
Night-heron coronavirus HKU19 | δ CoV | Avian | Rectal swab | X-CoV PCR and sequencing | 1 |
Magpie-robin coronavirus HKU18 | δ CoV | Avian | Oral swab Rectal swab | X-CoV PCR and sequencing | 2 |
unclassified Deltacoronavirus | δ CoV | Avian | Rectal swab | X-CoV PCR and sequencing | 7 |
Number of PCR Positive Samples Using Three PCR Assays in Four Sample Sources | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
CoV Genus | Human | Water | Bat | Avian | ||||||||
Q | W | X | Q | W | X | Q | W | X | Q | W | X | |
α | 6 | 4 | 8 | 7 | 2 | 2 | 16 | 16 | 16 | 0 | 0 | 0 |
β | 15 | 5 | 13 | 23 | 4 | 25 | 12 | 0 | 10 | 0 | 0 | 0 |
γ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 4 | 7 |
δ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 10 |
Negative no. | 29 | 41 | 29 | 16 | 40 | 19 | 0 | 12 | 2 | 16 | 13 | 0 |
Positive no. | 21 | 9 | 21 | 30 | 6 | 27 | 28 | 16 | 26 | 1 | 4 | 17 |
Total | 50 | 50 | 50 | 46 | 46 | 46 | 28 | 28 | 28 | 17 | 17 | 17 |
% positive | 42.00 | 18.00 | 42.00 | 65.22 | 13.04 | 58.70 | 100.00 | 57.14 | 92.86 | 5.88 | 23.53 | 100.00 |
95% CI | 79.79–100% | 19.18–59.08% | 79.79–100% | GS | 5.69–34.31% | 79.26–100% | GS | 38.83–75.47% | 83.32–100% | 0.00–17.07% | 3.34–43.69% | GS |
CoV Genus | Number (%) Positive/Negative Detected Using Three Assays | ||
---|---|---|---|
Q-CoV PCR | W-CoV PCR | X-CoV PCR | |
α | 29 (20.57) | 22 (15.60) | 26 (18.44) |
β | 50 (35.46) | 9 (6.38) | 48 (34.04) |
γ | 1 (0.71) | 4 (2.84) | 7 (4.96) |
δ | 0 (0.00) | 0 (0.00) | 10 (7.09) |
Negative | 61 (43.26) | 106 (2.84) | 50 (35.46) |
Total | 141 | 141 | 141 |
Positive | 80 | 35 | 91 |
% positive | 56.74 | 24.82 | 64.54 |
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Wacharapluesadee, S.; Thippamom, N.; Hirunpatrawong, P.; Rattanatumhi, K.; Sterling, S.L.; Khunnawutmanotham, W.; Noradechanon, K.; Maneeorn, P.; Buathong, R.; Paitoonpong, L.; et al. Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens. Viruses 2024, 16, 534. https://doi.org/10.3390/v16040534
Wacharapluesadee S, Thippamom N, Hirunpatrawong P, Rattanatumhi K, Sterling SL, Khunnawutmanotham W, Noradechanon K, Maneeorn P, Buathong R, Paitoonpong L, et al. Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens. Viruses. 2024; 16(4):534. https://doi.org/10.3390/v16040534
Chicago/Turabian StyleWacharapluesadee, Supaporn, Nattakarn Thippamom, Piyapha Hirunpatrawong, Khwankamon Rattanatumhi, Spencer L. Sterling, Wiparat Khunnawutmanotham, Kirana Noradechanon, Patarapol Maneeorn, Rome Buathong, Leilani Paitoonpong, and et al. 2024. "Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens" Viruses 16, no. 4: 534. https://doi.org/10.3390/v16040534
APA StyleWacharapluesadee, S., Thippamom, N., Hirunpatrawong, P., Rattanatumhi, K., Sterling, S. L., Khunnawutmanotham, W., Noradechanon, K., Maneeorn, P., Buathong, R., Paitoonpong, L., & Putcharoen, O. (2024). Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens. Viruses, 16(4), 534. https://doi.org/10.3390/v16040534