SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ohio Wastewater Network and the University of Toledo Campus Monitoring Network
2.2. Wastewater Sample Collection
2.3. RNA Extraction from the Wastewater
2.4. Quantitative RT-PCR Analyses of the SARS-CoV-2 Gene Copy Levels
2.5. SARS-CoV-2 Genome Amplification and Sequencing
2.6. Bioinformatic Analysis
2.7. Microbiome Analyses
3. Results and Discussion
3.1. Correlation between the Wastewater SARS-CoV-2 Viral Gene Copies and the Case Counts
3.2. Sequence Analysis of the Wastewater Samples
3.3. Potential Bacterial Biomarkers to Strengthen Wastewater SARS-CoV-2 Surveillance
4. 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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Sample Count | Gene | AA Pos | Ave Alt Freq | Med Alt Freq | Ref AA | Alt AA | Toledo | Lucas | Oregon | UT |
---|---|---|---|---|---|---|---|---|---|---|
4 | orf1ab | 265 | 100.0% | 100.0% | T | I | 0 | 1 | 3 | 0 |
4 | orf1ab | 314 | 100.0% | 100.0% | P | L | 2 | 2 | 0 | 0 |
3 | S | 614 | 100.0% | 100.0% | D | G | 1 | 2 | 0 | 0 |
4 | orf3a | 57 | 100.0% | 100.0% | Q | H | 3 | 1 | 0 | 0 |
4 | N | 199 | 97.6% | 99.8% | P | L | 1 | 3 | 0 | 0 |
1 | N | 203 | 99.9% | 99.9% | R | K | 0 | 0 | 1 | 0 |
1 | N | 204 | 100.0% | 100.0% | G | R | 0 | 0 | 1 | 0 |
1 | N | 205 | 9.1% | 9.1% | T | I | 0 | 1 | 0 | 0 |
1 | N | 235 | 99.9% | 99.9% | S | F | 0 | 0 | 1 | 0 |
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McGowan, J.; Borucki, M.; Omairi, H.; Varghese, M.; Vellani, S.; Chakravarty, S.; Fan, S.; Chattopadhyay, S.; Siddiquee, M.; Thissen, J.B.; et al. SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection. Viruses 2022, 14, 2032. https://doi.org/10.3390/v14092032
McGowan J, Borucki M, Omairi H, Varghese M, Vellani S, Chakravarty S, Fan S, Chattopadhyay S, Siddiquee M, Thissen JB, et al. SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection. Viruses. 2022; 14(9):2032. https://doi.org/10.3390/v14092032
Chicago/Turabian StyleMcGowan, Jenna, Monica Borucki, Hicham Omairi, Merina Varghese, Shahnaz Vellani, Sukanya Chakravarty, Shumin Fan, Srestha Chattopadhyay, Mashuk Siddiquee, James B. Thissen, and et al. 2022. "SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection" Viruses 14, no. 9: 2032. https://doi.org/10.3390/v14092032