Detection of SARS-CoV-2 and Variants in Hospital Wastewater in a Developing Country
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection, Handling, and Storage of Wastewater Samples
2.2. Sample Preparation, Concentration, and RNA Extraction
2.3. Recovery Efficiency of the Ultrafiltration Method
2.4. Detection, Verification, and Confirmation of SARS-CoV-2 in Hospital Wastewater Samples
2.5. Quantification of the SARS-CoV-2 RNA Concentration in Hospital Wastewater Samples
2.6. Data Analysis and Cost-Efficiency Analysis
3. Results
3.1. Calculation of Recovery Efficiency of the Ultrafiltration Method
3.2. Detection and Quantification of SARS-CoV-2 RNA in Hospital Wastewater Samples
3.3. Cost-Efficiency Analysis for the Detection of SARS-CoV-2 in Wastewater
3.4. Mutation Sites of the SARS-CoV-2 Partial S Gene in Hospital Wastewater
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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PCR ID | Target Gene | Sequence (5′→3′) | Usage | Size, bp | Ref |
---|---|---|---|---|---|
PEDV_M | M gene | 5′ TGTCTACGGACGTGTTGGTC 3′ 5′ AGCTGAGTAGTCGCCGTGTT 3′ | RT-qPCR | 91 | [26] |
972 | S | 5′ ACCCTGACAAAGTTTTCAGATCCT 3′ 5′ GCTGAGAGACATATTCAAAAGTGCA 3′ | 1st cycle | 399–408 | [27] |
973 | S | 5′ TTCAACTCAGGACTTGTTCTTACC 3′ 5′ TCTGAACTCACTTTCCATCCAA 3′ | Nested | 319–327 |
Replicates | PEDV Concentration (log10 Copies of PEDV Recovered) | PEDV Copy Numbers per Reaction (5 µL Samples Were Added into Reactions) | % Recovery of PEDV | % Recovery of PEDV (Mean ± SD) |
---|---|---|---|---|
1 | 3.545 | 3.51 × 103 | 53.4 | 80.53 ± 23.526 |
2 | 3.794 | 6.23 × 103 | 94.8 | |
3 | 3.788 | 6.14 × 103 | 93.4 |
Procedures | Cost | Cost per Sample | Throughput per Day |
---|---|---|---|
Virus concentration | USD 358.98 | USD 14.96 | 48 |
RNA extraction | USD 131.03 | USD 4.09 | |
Detection of SARS-CoV-2 | USD 393.10 | USD 16.38 | |
Total cost | USD 35.43 per sample |
Tracking ID | Mutation Sites | NCBI Blast (Accession Number) |
---|---|---|
HW 8719 | H69del, V70del, Y144del | OP022966.1 |
HW 8723 | G142D | OX243730.1 |
HW 8765 | G142D | OX243730.1 |
HW 8778 | - | OX196900.1 |
HW 8916 | T95I | ON998987.1 |
HW 8603 | H69del, V70del, Y144del | ON909458.1 |
HW 9234 | - | OX243720.1 |
HW 9407 | - | OX243686.1 |
HW 9473 | - | OX243715.1 |
HW 9574 | G142D | OX243678.1 |
HW 9733 | - | ON800253.1 |
HW 9735 | - | OX243720.1 |
HW 8602 | H69del, V70del | OX243731.1 |
HW 8769 | G142D | OX243730.1 |
HW 8597 | T95I | OP022971.1 |
HW 9021 | T95I, G142D | OP012924.1 |
HW 9375 | - | OX243696.1 |
HW 8777 | - | OX243730.1 |
HW 8587 | H69del, V70del | OX243731.1 |
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Tiacharoen, V.; Denpetkul, T.; Kosoltanapiwat, N.; Maneekan, P.; Thippornchai, N.; Saeoueng, A.; Jittmittraphap, A.; Sattabongkot, J.; Leaungwutiwong, P. Detection of SARS-CoV-2 and Variants in Hospital Wastewater in a Developing Country. Water 2022, 14, 3798. https://doi.org/10.3390/w14233798
Tiacharoen V, Denpetkul T, Kosoltanapiwat N, Maneekan P, Thippornchai N, Saeoueng A, Jittmittraphap A, Sattabongkot J, Leaungwutiwong P. Detection of SARS-CoV-2 and Variants in Hospital Wastewater in a Developing Country. Water. 2022; 14(23):3798. https://doi.org/10.3390/w14233798
Chicago/Turabian StyleTiacharoen, Vichapon, Thammanitchpol Denpetkul, Nathamon Kosoltanapiwat, Pannamas Maneekan, Narin Thippornchai, Anon Saeoueng, Akanitt Jittmittraphap, Jetsumon Sattabongkot, and Pornsawan Leaungwutiwong. 2022. "Detection of SARS-CoV-2 and Variants in Hospital Wastewater in a Developing Country" Water 14, no. 23: 3798. https://doi.org/10.3390/w14233798
APA StyleTiacharoen, V., Denpetkul, T., Kosoltanapiwat, N., Maneekan, P., Thippornchai, N., Saeoueng, A., Jittmittraphap, A., Sattabongkot, J., & Leaungwutiwong, P. (2022). Detection of SARS-CoV-2 and Variants in Hospital Wastewater in a Developing Country. Water, 14(23), 3798. https://doi.org/10.3390/w14233798