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Tambe LAM, Mathobo P, Matume ND, Munzhedzi M, Edokpayi JN, Viraragavan A, Glanzmann B, Tebit DM, Mavhandu-Ramarumo LG, Street R, Johnson R, Kinnear C, Bessong PO. Molecular epidemiology of SARS-CoV-2 in Northern South Africa: wastewater surveillance from January 2021 to May 2022. Front Public Health 2023; 11:1309869. [PMID: 38174083 PMCID: PMC10764116 DOI: 10.3389/fpubh.2023.1309869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 11/21/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction Wastewater-based genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) provides a comprehensive approach to characterize evolutionary patterns and distribution of viral types in a population. This study documents the molecular epidemiology of SARS-CoV-2, in Northern South Africa, from January 2021 to May 2022. Methodology A total of 487 wastewater samples were collected from the influent of eight wastewater treatment facilities and tested for SARS-CoV-2 RNA using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). SARS-CoV-2 positive samples with genome copies/mL ≥1,500 were subjected to allele-specific genotyping (ASG) targeting the Spike protein; 75 SARS-CoV-2 positive samples were subjected to whole genome sequencing (WGS) on the ATOPlex platform. Variants of concern (VoC) and lineages were assigned using the Nextclade and PangoLIN Software. Concordance for VoC between ASG and WGS analyses was determined. Sequence relationship was determined by phylogenetic analysis. Results Seventy-five percent (365/487) of the influent samples were positive for SARS-CoV-2 RNA. Delta and Omicron VoC were more predominant at a prevalence of 45 and 32%, respectively, and they were detected as early as January and February 2021, while Beta VoC was least detected at a prevalence of 5%. A total of 11/60 (18%) sequences were assigned lineages and clades only, but not a specific VoC name. Phylogenetic analysis was used to investigate the relationship of these sequences to other study sequences, and further characterize them. Concordance in variant assignment between ASG and WGS was seen in 51.2% of the study sequences. There was more intra-variant diversity among Beta VoC sequences; mutation E484K was absent. Three previously undescribed mutations (A361S, V327I, D427Y) were seen in Delta VoC. Discussion and Conclusion The detection of Delta and Omicron VoCs in study sites earlier in the outbreak than has been reported in other regions of South Africa highlights the importance of population-based approaches over individual sample-based approaches in genomic surveillance. Inclusion of non-Spike protein targets could improve the specificity of ASG, since all VoCs share similar Spike protein mutations. Finally, continuous molecular epidemiology with the application of sensitive technologies such as next generation sequencing (NGS) is necessary for the documentation of mutations whose implications when further investigated could enhance diagnostics, and vaccine development efforts.
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Affiliation(s)
- Lisa Arrah Mbang Tambe
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Phindulo Mathobo
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Nontokozo D. Matume
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Mukhethwa Munzhedzi
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Joshua Nosa Edokpayi
- Water and Environmental Management Research Group, University of Venda, Thohoyandou, South Africa
| | - Amsha Viraragavan
- South African Medical Research Council Genomics Platform, Tygerberg, South Africa
| | - Brigitte Glanzmann
- South African Medical Research Council Genomics Platform, Tygerberg, South Africa
| | - Denis M. Tebit
- Global Biomed Laboratories Inc., Lynchburg, VA, United States
| | - Lufuno Grace Mavhandu-Ramarumo
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Renee Street
- Environment and Health Research Unit, South African Medical Research Council, Johannesburg, South Africa
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa
- Division of Medical Physiology, Faculty of Medicine and Health Sciences, Centre for Cardiometabolic Research in Africa, Stellenbosch University, Stellenbosch, South Africa
| | - Craig Kinnear
- South African Medical Research Council Genomics Platform, Tygerberg, South Africa
| | - Pascal Obong Bessong
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
- Center for Global Health Equity, School of Medicine, University of Virginia, Charlottesville, VA, United States
- School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Jack BU, Mamushi M, Viraragavan A, Dias S, Pheiffer C. Comparing the effects of tumor necrosis factor alpha, lipopolysaccharide and palmitic acid on lipid metabolism and inflammation in murine 3T3-L1 adipocytes. Life Sci 2022; 297:120422. [DOI: 10.1016/j.lfs.2022.120422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 01/12/2023]
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Johnson R, Sharma JR, Ramharack P, Mangwana N, Kinnear C, Viraragavan A, Glanzmann B, Louw J, Abdelatif N, Reddy T, Surujlal-Naicker S, Nkambule S, Mahlangeni N, Webster C, Mdhluli M, Gray G, Mathee A, Preiser W, Muller C, Street R. Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiology. Sci Rep 2022; 12:1182. [PMID: 35064174 PMCID: PMC8783013 DOI: 10.1038/s41598-022-05110-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/31/2021] [Indexed: 12/13/2022] Open
Abstract
This study uses wastewater-based epidemiology (WBE) to rapidly and, through targeted surveillance, track the geographical distribution of SARS-CoV-2 variants of concern (Alpha, Beta and Delta) within 24 wastewater treatment plants (WWTPs) in the Western Cape of South Africa. Information obtained was used to identify the circulating variant of concern (VOC) within a population and retrospectively trace when the predominant variant was introduced. Genotyping analysis of SARS-CoV-2 showed that 50% of wastewater samples harbored signature mutations linked to the Beta variant before the third wave, with the Delta variant absent within the population. Over time, the prevalence of the beta variant decreased steadily. The onset of the third wave resulted in the Delta variant becoming the predominant variant, with a 100% prevalence supporting the theory that the Delta variant was driving the third wave. In silico molecular docking analysis showed that the signature mutations of the Delta variant increased binding to host proteins, suggesting a possible molecular mechanism that increased viral infectivity of the Delta variant.
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Affiliation(s)
- Rabia Johnson
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg, 7505, South Africa.
- Division of Medical Physiology, Faculty of Medicine and Health Sciences, Centre for Cardiometabolic Research in Africa, Stellenbosch University, Stellenbosch, South Africa.
| | - Jyoti R Sharma
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg, 7505, South Africa
| | - Pritika Ramharack
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg, 7505, South Africa
- Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Noluxabiso Mangwana
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg, 7505, South Africa
| | - Craig Kinnear
- Genomics Centre, South African Medical Research Council (SAMRC), Tygerberg, 7505, South Africa
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Amsha Viraragavan
- Genomics Centre, South African Medical Research Council (SAMRC), Tygerberg, 7505, South Africa
| | - Brigitte Glanzmann
- Genomics Centre, South African Medical Research Council (SAMRC), Tygerberg, 7505, South Africa
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Johan Louw
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg, 7505, South Africa
| | - Nada Abdelatif
- Biostatistics Research Unit, South African Medical Research Council (SAMRC), Durban, South Africa
| | - Tarylee Reddy
- Biostatistics Research Unit, South African Medical Research Council (SAMRC), Durban, South Africa
| | - Swastika Surujlal-Naicker
- Scientific Services, Water and Sanitation Department, City of Cape Town Metropolitan Municipality, Cape Town, South Africa
| | - Sizwe Nkambule
- Environment and Health Research Unit, South African Medical Research Council (SAMRC), Durban, South Africa
| | - Nomfundo Mahlangeni
- Environment and Health Research Unit, South African Medical Research Council (SAMRC), Durban, South Africa
| | - Candice Webster
- Environment and Health Research Unit, South African Medical Research Council (SAMRC), Johannesburg, South Africa
| | - Mongezi Mdhluli
- Office of the President, South African Medical Research Council, Tygerberg, 7050, South Africa
| | - Glenda Gray
- Office of the President, South African Medical Research Council, Tygerberg, 7050, South Africa
| | - Angela Mathee
- Environment and Health Research Unit, South African Medical Research Council (SAMRC), Johannesburg, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology at NHLS Tygerberg Hospital and Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Christo Muller
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg, 7505, South Africa
- Division of Medical Physiology, Faculty of Medicine and Health Sciences, Centre for Cardiometabolic Research in Africa, Stellenbosch University, Stellenbosch, South Africa
| | - Renee Street
- Environment and Health Research Unit, South African Medical Research Council (SAMRC), Durban, South Africa
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Abstract
Increased visceral adipose tissue (VAT) is associated with metabolic dysfunction, while subcutaneous adipose tissue (SAT) is considered protective. The mechanisms underlying these differences are not fully elucidated. This study aimed to investigate molecular differences in VAT and SAT of male Wistar rats fed a cafeteria diet (CD) or a standard rodent diet (STD) for three months. The expression of fatty acid metabolism genes was analysed by quantitative real-time PCR. Global and gene-specific DNA methylation was quantified using the Imprint® Methylated DNA Quantification Kit and pyrosequencing, respectively. Bodyweight, retroperitoneal fat mass, insulin resistance, leptin and triglyceride concentrations and adipocyte hypertrophy were higher in CD- compared to STD-fed rats. The expression of solute carrier family 27 member 3 (Slc27a3), a fatty acid transporter, was 9.6-fold higher in VAT and 6.3-fold lower in SAT of CD- versus STD-fed rats. Taqman probes confirmed increased Slc27a3 expression, while pyrosequencing showed Slc27a3 hypomethylation in VAT of CD- compared to STD-fed rats. The CD decreased global methylation in both VAT and SAT, although no depot differences were observed. Dysregulated fatty acid influx in VAT, in response to a CD, provides insight into the mechanisms underlying depot-differences in adipose tissue expansion during obesity and metabolic disease. Abbreviations: CD: cafeteria diet; E2F1: E2F Transcription Factor 1; EMSA: electrophoretic mobility shift assay; EGFR: epidermal growth factor receptor; GCF: GC-Rich Sequence DNA-Binding Factor; HOMA-IR: Homeostasis model for insulin resistance; NKX2-1: NK2 homeobox 1; PCR: Polymerase chain reaction; qRT-PCR: quantitative real-time PCR; RF: retroperitoneal fat; SAT: subcutaneous adipose tissue; Slc27a3: solute carrier family 27 member 3; STD: standard diet; TNFα: tumour necrosis factor alpha; TTS: transcriptional start site; T2D: Type 2 Diabetes; VAT: visceral adipose tissue; WT1 I: Wilms’ tumour protein 1
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Affiliation(s)
- Amsha Viraragavan
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa
| | - Tarryn Willmer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Oelfah Patel
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Medicine and Health Sciences, University of Stellenbosch, Tygerberg, South Africa
| | - Albertus Basson
- Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
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Viraragavan A, Hlengwa N, de Beer D, Riedel S, Miller N, Bowles S, Walczak B, Muller C, Joubert E. Model development for predicting in vitro bio-capacity of green rooibos extract based on composition for application as screening tool in quality control. Food Funct 2020; 11:3084-3094. [PMID: 32195502 DOI: 10.1039/c9fo02480h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Mounting evidence of the ability of aspalathin to target underlying metabolic dysfunction relevant to the development or progression of obesity and type 2 diabetes created a market for green rooibos extract as a functional food ingredient. Aspalathin is the obvious choice as a chemical marker for extract standardisation and quality control, however, often the concentration of a single constituent of a complex mixture such as a plant extract is not directly related to its bio-capacity, i.e. the level of in vitro bioactivity effected in a cell system at a fixed concentration. Three solvents (hot water and two EtOH-water mixtures), previously shown to produce bioactive green rooibos extracts, were selected for extraction of different batches of rooibos plant material (n = 10). Bio-capacity of the extracts, tested at 10 μg ml-1, was evaluated in terms of glucose uptake by C2C12 and C3A cells and lipid accumulation in 3T3-L1 cells. The different solvents and inter-batch plant variation delivered extracts ranging in aspalathin content from 54.1 to 213.8 g kg-1. The extracts were further characterised in terms of other major flavonoids (n = 10) and an enolic phenylpyruvic acid glucoside, using HPLC-DAD. The 80% EtOH-water extracts, with the highest mean aspalathin content (170.9 g kg-1), had the highest mean bio-capacity in the respective assays. Despite this, no significant (P≥ 0.05) correlation existed between aspalathin content and bio-capacity, while the orientin, isoorientin and vitexin content correlated moderately (r≥ 0.487; P < 0.05) with increased glucose uptake by C2C12 cells. Various multivariate analysis methods were then applied with Evolution Program-Partial Least Squares (EP-PLS) resulting in models with the best predictive power. These EP-PLS models, based on all quantified compounds, predicted the bio-capacity of the extracts for the respective cell types with RMSECV values ≤ 11.5, confirming that a complement of compounds, and not aspalathin content alone, is needed to predict the in vitro bio-capacity of green rooibos extracts. Additionally, the composition of hot water infusions of different production batches of green rooibos (n = 29) at 'cup-of-tea' equivalence was determined to relate dietary supplementation with the extract to intake in the form of herbal tea.
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Affiliation(s)
- Amsha Viraragavan
- Biomedical Research and Innovation Platform, South African Medical Research Council, P.O. Box 19070, Tygerberg 7505, South Africa.
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Dludla PV, Jack B, Viraragavan A, Pheiffer C, Johnson R, Louw J, Muller CJF. A dose-dependent effect of dimethyl sulfoxide on lipid content, cell viability and oxidative stress in 3T3-L1 adipocytes. Toxicol Rep 2018; 5:1014-1020. [PMID: 30364542 PMCID: PMC6197677 DOI: 10.1016/j.toxrep.2018.10.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/03/2018] [Accepted: 10/02/2018] [Indexed: 12/23/2022] Open
Abstract
Depending on the concentration, dimethyl sulfoxide (DMSO) can be toxic to cells. 3T3-L1 adipocytes are a well-established model to study anti-obesity properties. DMSO doses ≥1% reduced cell viability and promoted cell damage in 3T3-L1 adipocytes.
Dimethyl sulfoxide (DMSO) is an effective solvent and cytoprotectant agent that can induce diverse actions in experimental settings, ranging from metabolic stress to cytotoxic effects depending on the concentration used. Therefore, for the quality of experiments and reproducibility of results it is essential to establish a precise and non-toxic dose of DMSO within a specific cell system. 3T3-L1 adipocytes, represent a well-established in vitro cell model used to assess the anti-obesity potential of extracts and compounds. Although DMSO is commonly used as a solvent for these experiments, there is limited data available on the compounding effects of using DMSO. The purpose of this study was to assess a concentration-dependent effect of DMSO on lipid content, cell viability and oxidative damage in 3T3-L1 adipocytes. Results showed that DMSO at doses ≥ 0.1% increased mitochondrial membrane potential as measured by JC-1 fluorescent staining, while doses ≥ 10% reduced the lipid content in matured adipocytes. Consistently, higher doses significantly reduced cell viability, elevated reactive oxygen species levels, depleted intracellular glutathione levels, and accelerated apoptosis and cell necrosis. An interesting finding was that a DMSO dose of 0.01% improved glutathione content of 3T3-L1 adipocytes and had minimal effects on cell viability, apoptosis or and necrosis, supporting its antioxidant effect. Therefore, this study provides compelling evidence that precaution should be taken when assessing compounds dissolved in DMSO, particularly doses ≥1% that were shown to induce oxidative stress in 3T3-L1 adipocytes.
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Key Words
- 3T3-L1 adipocytes
- Apoptosis
- Cell viability
- DCFH-DA, 2′, 7′-dichlorofluorescein diacetate
- DMEM, Dulbecco’s Modified Eagle’s Medium
- DMSO, dimethyl sulfoxide
- DPBS, Dulbecco’s Phosphate Buffered Saline
- Dimethyl sulfoxide
- Dimethyl sulfoxide (PubChem CID: 679)
- FBS, fetal bovine serum
- HBSS, Hank’s Balanced Salt Solution
- IBMX, 3-isobutyl-1-methylxanthine
- JC-1, 5,5′,6,6′-tetrachloro-1,1′,3,3-tetraethylbenzimidazolyl-carbocyanineiodide
- MTT, 3-(4,5-Dimethylthiazol-2-yl)-2,5-DiphenyltetrazoliumBromide)
- ORO, oil red O
- Oxidative stress
- ROS, reactive oxygen species
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Affiliation(s)
- Phiwayinkosi V Dludla
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
| | - Babalwa Jack
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
| | - Amsha Viraragavan
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa.,Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa.,Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa.,Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Johan Louw
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa.,Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Christo J F Muller
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa.,Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa.,Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
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