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Singh L, Anyaneji UJ, Ndifon W, Turok N, Mattison SA, Lessells R, Sinayskiy I, San EJ, Tegally H, Barnett S, Lorimer T, Petruccione F, de Oliveira T. Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing. Sci Rep 2021; 11:17793. [PMID: 34493744 PMCID: PMC8423848 DOI: 10.1038/s41598-021-96934-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 04/26/2021] [Accepted: 08/18/2021] [Indexed: 12/21/2022] Open
Abstract
The rapid identification and isolation of infected individuals remains a key strategy for controlling the spread of SARS-CoV-2. Frequent testing of populations to detect infection early in asymptomatic or presymptomatic individuals can be a powerful tool for intercepting transmission, especially when the viral prevalence is low. However, RT-PCR testing-the gold standard of SARS-CoV-2 diagnosis-is expensive, making regular testing of every individual unfeasible. Sample pooling is one approach to lowering costs. By combining samples and testing them in groups the number of tests required is reduced, substantially lowering costs. Here we report on the implementation of pooling strategies using 3-d and 4-d hypercubes to test a professional sports team in South Africa. We have shown that infected samples can be reliably detected in groups of 27 and 81, with minimal loss of assay sensitivity for samples with individual Ct values of up to 32. We report on the automation of sample pooling, using a liquid-handling robot and an automated web interface to identify positive samples. We conclude that hypercube pooling allows for the reliable RT-PCR detection of SARS-CoV-2 infection, at significantly lower costs than lateral flow antigen (LFA) tests.
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Affiliation(s)
- Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Ugochukwu J Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Wilfred Ndifon
- African Institute for Mathematical Sciences, The Next Einstein Initiative, Kigali, Rwanda.
| | - Neil Turok
- Higgs Centre for Theoretical Physics, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Stacey A Mattison
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ilya Sinayskiy
- School of Chemistry and Physics, University of Kwa-Zulu Natal, Westville, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), KwaZulu-Natal, South Africa
| | - Emmanuel J San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Shaun Barnett
- Discipline of Electrical, Electronic and Computer Engineering, University of KwaZulu-Natal, Durban, South Africa
| | - Trevor Lorimer
- Discipline of Electrical, Electronic and Computer Engineering, University of KwaZulu-Natal, Durban, South Africa
| | - Francesco Petruccione
- School of Chemistry and Physics, University of Kwa-Zulu Natal, Westville, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), KwaZulu-Natal, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
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Mattison SA, Blatch GL, Edkins AL. HOP expression is regulated by p53 and RAS and characteristic of a cancer gene signature. Cell Stress Chaperones 2017; 22:213-223. [PMID: 27987076 PMCID: PMC5352595 DOI: 10.1007/s12192-016-0755-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/21/2016] [Accepted: 12/07/2016] [Indexed: 01/01/2023] Open
Abstract
The Hsp70/Hsp90 organising protein (HOP) is a co-chaperone essential for client protein transfer from Hsp70 to Hsp90 within the Hsp90 chaperone machine. Although HOP is upregulated in various cancers, there is limited information from in vitro studies on how HOP expression is regulated in cancer. The main objective of this study was to identify the HOP promoter and investigate its activity in cancerous cells. Bioinformatic analysis of the -2500 to +16 bp region of the HOP gene identified a large CpG island and a range of putative cis-elements. Many of the cis-elements were potentially bound by transcription factors which are activated by oncogenic pathways. Luciferase reporter assays demonstrated that the upstream region of the HOP gene contains an active promoter in vitro. Truncation of this region suggested that the core HOP promoter region was -855 to +16 bp. HOP promoter activity was highest in Hs578T, HEK293T and SV40- transformed MEF1 cell lines which expressed mutant or inactive p53. In a mutant p53 background, expression of wild-type p53 led to a reduction in promoter activity, while inhibition of wild-type p53 in HeLa cells increased HOP promoter activity. Additionally, in Hs578T and HEK293T cell lines containing inactive p53, expression of HRAS increased HOP promoter activity. However, HRAS activation of the HOP promoter was inhibited by p53 overexpression. These findings suggest for the first time that HOP expression in cancer may be regulated by both RAS activation and p53 inhibition. Taken together, these data suggest that HOP may be part of the cancer gene signature induced by a combination of mutant p53 and mutated RAS that is associated with cellular transformation.
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Affiliation(s)
- Stacey A Mattison
- Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Gregory L Blatch
- Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
- Centre for Chronic Disease, College of Health and Biomedicine, Victoria University, Melbourne, Australia
| | - Adrienne L Edkins
- Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa.
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