Detection of Human Adenovirus and Rotavirus in Wastewater in Lusaka, Zambia: Demonstrating the Utility of Environmental Surveillance for the Community
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Design
2.2. Sample Collection
2.3. Viral Concentration
2.3.1. Skimmed Milk Flocculation
2.3.2. Bag-Mediated Filtration System (BMFS)
Secondary Concentration Procedure
2.3.3. Polyethylene Glycol-Based (PEG) Concentration
2.4. Nucleic Acid Extraction
2.5. Genomic Screening for Adenovirus and Rotavirus
2.5.1. Detection of Adenovirus and Rotavirus on PCR
2.5.2. Conventional PCR and Sequencing of Adenovirus
2.6. Statistical Analysis
3. Results
3.1. Detection of Adenovirus and Rotavirus
3.2. Comparison of Viral Concentration Methods
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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Site | Sewer Catchment Area |
---|---|
Chelstone pumping station | Chelstone Zambia Airways, Waterfalls mall |
Kaunda Square stabilization ponds | PHI, Nyumba Yanga, Ibex Hills, Chamba Valley, Chainama, Kaunda Square Stage 1, Kaunda Square stage 2, Mtendere East, Salama Park, Mtendere, part of Kabulonga, part of Woodlands, Helen Kaunda, part of Kalingalinga, East Park mall, part of Handsworth |
Mass Media pumping station | University of Zambia, part of Showgrounds, part of Longacres, Mass Media, Arcades mall up to National Assembly |
Manchichi sewage treatment plant and Garden stabilization ponds | Part of Woodlands, Chilenje, Libala, Villa Elizabetha, Kabwata, Northmead, Parts of Emmasdale, part of Rhodes Park, Mass Media, part of Central Business district, Thorn Park, Part of the Light Industrial Area bordered by Great North Road, Sheki Road, Lumumba Road, and Kalambo Road. |
No. | Name | Sequence | Tm (°C) | Reference |
---|---|---|---|---|
1 | JTVXF_18895Fw | 5′-GGACGCCTCGGAGTACCTGAG-3′ | [26] | |
2 | JTVXR_18990Rv | 5′-ACIGTGGGGGTTTCTGAACTTGTT-3′ | 60 | |
3 | Probe JTVXP_18923Fw | 5′-CTGGTGCAGTTCGCCCGTGCCA-3′ | ||
4 | Hex1DegFw(1) | 5′-GCCSCARTGGKCWTACATGCACATC-3′ | 54 | [23] |
5 | Hex2DegRv(1) | 5′-CAGCACSCCICGRATGTCAAA-3′ | ||
6 | Adeno Cap 17467Fw(2) | 5′-CTGTAGGTTCCGTTCCCGTT-3′ | 54 | |
7 | Adeno Hex 18185Rv (2) | 5′-CGGTGCCTGAGCAAAGGTAT-3′ | ||
8 | RotaA-NSP3Fw | 5′-ACCATCTWCACRTRACCCTCTATGAG-3′ | [27] | |
9 | RotaA-NSP3Rv | 5′-GGTCACATAACGCCCCTATAGC-3′ | 60 | |
10 | Probe RotaA-NSP3Pr | 5′-AGTTAAAAGCTAACACTGTCAAA-3′ |
Site | qPCR HAdV | cPCR HAdV | qPCR RVA |
---|---|---|---|
Chelstone | 3/5 | 3/5 | 3/5 |
Mass Media | 5/5 | 3/5 | 4/5 |
Kaunda Square | 5/5 | 5/5 | 4/5 |
Manchichi | 5/5 | 5/5 | 3/5 |
Total | 18/20 (90%) | 16/20 (80%) | 14/20 (70%) |
Sample ID | Sampling Site | Week of Collection | RVA qPCR | HAdV qPCR | HAdV cPCR | GenBank Accession no. (HAdV) | % Nucleotide Identity |
---|---|---|---|---|---|---|---|
1 | CB | 1 | Negative | Negative | Negative | ||
2 | MMP | 1 | POSITIVE | POSITIVE | POSITIVE | PP341455 | 99.30 |
3 | KSP | 1 | POSITIVE | POSITIVE | POSITIVE | ||
4 | MP | 1 | POSITIVE | POSITIVE | POSITIVE | PP341456 | 98.31 |
5 | CB | 2 | Negative | Negative | Negative | ||
6 | MMP | 2 | Negative | POSITIVE | POSITIVE | PP341457 | 98.92 |
7 | KSP | 2 | POSITIVE | POSITIVE | POSITIVE | PP341458 | 98.85 |
8 | MP | 2 | Negative | POSITIVE | POSITIVE | ||
9 | CB | 3 | POSITIVE | POSITIVE | POSITIVE | PP341459 | 99.01 |
10 | MMP | 3 | POSITIVE | POSITIVE | POSITIVE | PP341460 | 98.62 |
11 | KSP | 3 | POSITIVE | POSITIVE | POSITIVE | PP341461 | 99.53 |
12 | MP | 3 | POSITIVE | POSITIVE | POSITIVE | ||
13 | CB | 4 | POSITIVE | POSITIVE | POSITIVE | ||
14 | MMP | 4 | POSITIVE | POSITIVE | POSITIVE | PP341462 | 98.48 |
15 | KSP | 4 | POSITIVE | POSITIVE | POSITIVE | PP341463 | 99.03 |
16 | MP | 4 | Negative | POSITIVE | POSITIVE | ||
17 | CB | 5 | POSITIVE | POSITIVE | POSITIVE | ||
18 | MMP | 5 | POSITIVE | POSITIVE | POSITIVE | PP341464 | 99.03 |
19 | KSP | 5 | Negative | POSITIVE | POSITIVE | PP341465 | 98.68 |
20 | MS | 5 | POSITIVE | POSITIVE | POSITIVE |
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Saasa, N.; M’kandawire, E.; Ndebe, J.; Mwenda, M.; Chimpukutu, F.; Mukubesa, A.N.; Njobvu, F.; Shempela, D.M.; Sikalima, J.; Chiyesu, C.; et al. Detection of Human Adenovirus and Rotavirus in Wastewater in Lusaka, Zambia: Demonstrating the Utility of Environmental Surveillance for the Community. Pathogens 2024, 13, 486. https://doi.org/10.3390/pathogens13060486
Saasa N, M’kandawire E, Ndebe J, Mwenda M, Chimpukutu F, Mukubesa AN, Njobvu F, Shempela DM, Sikalima J, Chiyesu C, et al. Detection of Human Adenovirus and Rotavirus in Wastewater in Lusaka, Zambia: Demonstrating the Utility of Environmental Surveillance for the Community. Pathogens. 2024; 13(6):486. https://doi.org/10.3390/pathogens13060486
Chicago/Turabian StyleSaasa, Ngonda, Ethel M’kandawire, Joseph Ndebe, Mulenga Mwenda, Fred Chimpukutu, Andrew Nalishuwa Mukubesa, Fred Njobvu, Doreen Mainza Shempela, Jay Sikalima, Carol Chiyesu, and et al. 2024. "Detection of Human Adenovirus and Rotavirus in Wastewater in Lusaka, Zambia: Demonstrating the Utility of Environmental Surveillance for the Community" Pathogens 13, no. 6: 486. https://doi.org/10.3390/pathogens13060486