Profiling the occurance of sars-cov-2 variants in the municipal wastewaters of the Buffalo City Municipality, South Africa
1
Department of Biotechnology and Biological Sciences, University of Fort Hare, Alice, 5700, South Africa
2
SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, 5700, South Africa
3
DSTI/NRF SARChI Chair in Water Quality and Environmental Genomics,, University of Fort Hare, South Africa
Popul. Med. 2026;8(Supplement Supplement 1):A3852
ABSTRACT
BACKGROUND:
The inception of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants with remarkable infectivity and transmissibility caused a global health and economic calamity. Thus, this study’s aim was to profile spike protein mutations associated with the Delta (B.1.617.2) and Omicron (B.1.1.529) variants in wastewater from designated wastewater treatment plants (WWTPs) in the Buffalo City Metropolitan Municipality (BCM).
METHODS:
Wastewater samples were acquired for 46 surveillance weeks. Ribonucleic Acid (RNA) was extracted and purified, and the Quantitative Reverse Transcription Polymerase Chain Reaction (RT-qPCR) was employed to detect and enumerate SARS-CoV-2 genomes. Thereafter, TaqMan SARS-CoV-2 mutation panel genotyping-molecular-specific (GMS) RT-PCR assay, targeting single nucleotide polymorphism (SNP), was used for the rapid detection of mutations N501Y, L452R, P681R, K417N, P681H, E484K, and delH69V70. Results and
CONCLUSIONS:
Approximately 93 % of SARS-CoV-2 templates (n = 45) possessed the target mutations; 22% of SARS-CoV-2 templates possessed the N501Y, while only 3% possessed the E484K and K417N spike protein mutations, affirming the proliferation of variants of concern (VOC) in BCM. Mutations associated with VOC Delta and Omicron were observed in the metropolitan region, indicating the circulation of variants in BCM during the surveillance period. This Wastewater-Based Epidemiology approach advocates for the continuous surveillance of infectious pathogens in wastewater matrices as a valuable strategy for public health officials in monitoring and identifying the glaring and future pandemics at the population level.
The inception of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants with remarkable infectivity and transmissibility caused a global health and economic calamity. Thus, this study’s aim was to profile spike protein mutations associated with the Delta (B.1.617.2) and Omicron (B.1.1.529) variants in wastewater from designated wastewater treatment plants (WWTPs) in the Buffalo City Metropolitan Municipality (BCM).
METHODS:
Wastewater samples were acquired for 46 surveillance weeks. Ribonucleic Acid (RNA) was extracted and purified, and the Quantitative Reverse Transcription Polymerase Chain Reaction (RT-qPCR) was employed to detect and enumerate SARS-CoV-2 genomes. Thereafter, TaqMan SARS-CoV-2 mutation panel genotyping-molecular-specific (GMS) RT-PCR assay, targeting single nucleotide polymorphism (SNP), was used for the rapid detection of mutations N501Y, L452R, P681R, K417N, P681H, E484K, and delH69V70. Results and
CONCLUSIONS:
Approximately 93 % of SARS-CoV-2 templates (n = 45) possessed the target mutations; 22% of SARS-CoV-2 templates possessed the N501Y, while only 3% possessed the E484K and K417N spike protein mutations, affirming the proliferation of variants of concern (VOC) in BCM. Mutations associated with VOC Delta and Omicron were observed in the metropolitan region, indicating the circulation of variants in BCM during the surveillance period. This Wastewater-Based Epidemiology approach advocates for the continuous surveillance of infectious pathogens in wastewater matrices as a valuable strategy for public health officials in monitoring and identifying the glaring and future pandemics at the population level.
| eISSN: | 2654-1459 |
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