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The implementation of a rapid sample preparation method for the detection of SARS-CoV-2 in a diagnostic laboratory in South Africa
The SARS-CoV-2 pandemic has resulted in shortages of both critical reagents for nucleic acid purification and highly trained staff as supply chains are strained by high demand, public health measures and frequent quarantining and isolation of staff. This created the need for alternate workflows with...
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| Format: | Thesis |
| Language: | English |
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Department of Clinical Laboratory Sciences
2023
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| _version_ | 1867613925415059456 |
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| access_status_str | Open Access |
| author | Marais, Gert J K |
| author2 | Hardie, Diana |
| author_browse | Hardie, Diana Marais, Gert J K |
| author_facet | Hardie, Diana Marais, Gert J K |
| author_sort | Marais, Gert J K |
| collection | Thesis |
| description | The SARS-CoV-2 pandemic has resulted in shortages of both critical reagents for nucleic acid purification and highly trained staff as supply chains are strained by high demand, public health measures and frequent quarantining and isolation of staff. This created the need for alternate workflows with limited reliance on specialised reagents, equipment and staff. We present here the validation and implementation of such a workflow for preparing samples for downstream SARS-CoV-2 RT-PCR using liquid handling robots. The rapid sample preparation and inactivation technique evaluated, which included sample centrifugation and heating prior to RT-PCR, showed a 97.37% (95% CI: 92.55-99.28%) positive percent agreement and 97.30% (95% CI: 90.67-99.52%) negative percent agreement compared to nucleic acid purification-based testing. A total of 195 samples were tested as part of the validation. This method was subsequently adopted as the primary sample preparation method in the Groote Schuur Hospital Virology Diagnostic Laboratory in Cape Town, South Africa. |
| format | Thesis |
| id | oai:open.uct.ac.za:11427/37618 |
| institution | University of Cape Town (South Africa) |
| language | eng |
| last_indexed | 2026-06-10T12:43:53.631Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UCTD — University of Cape Town Open Access Repository |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Department of Clinical Laboratory Sciences |
| publisherStr | Department of Clinical Laboratory Sciences |
| record_format | dspace |
| source_str | UCTD — University of Cape Town Open Access Repository |
| spelling | oai:open.uct.ac.za:11427/37618 The implementation of a rapid sample preparation method for the detection of SARS-CoV-2 in a diagnostic laboratory in South Africa Marais, Gert J K Hardie, Diana Virological Pathology The SARS-CoV-2 pandemic has resulted in shortages of both critical reagents for nucleic acid purification and highly trained staff as supply chains are strained by high demand, public health measures and frequent quarantining and isolation of staff. This created the need for alternate workflows with limited reliance on specialised reagents, equipment and staff. We present here the validation and implementation of such a workflow for preparing samples for downstream SARS-CoV-2 RT-PCR using liquid handling robots. The rapid sample preparation and inactivation technique evaluated, which included sample centrifugation and heating prior to RT-PCR, showed a 97.37% (95% CI: 92.55-99.28%) positive percent agreement and 97.30% (95% CI: 90.67-99.52%) negative percent agreement compared to nucleic acid purification-based testing. A total of 195 samples were tested as part of the validation. This method was subsequently adopted as the primary sample preparation method in the Groote Schuur Hospital Virology Diagnostic Laboratory in Cape Town, South Africa. 2023-03-31T08:39:41Z 2023-03-31T08:39:41Z 2022 2023-03-29T08:46:22Z Master Thesis Masters MMed http://hdl.handle.net/11427/37618 eng application/pdf Department of Clinical Laboratory Sciences Faculty of Health Sciences |
| spellingShingle | Virological Pathology Marais, Gert J K The implementation of a rapid sample preparation method for the detection of SARS-CoV-2 in a diagnostic laboratory in South Africa |
| thesis_degree_str | Master's |
| title | The implementation of a rapid sample preparation method for the detection of SARS-CoV-2 in a diagnostic laboratory in South Africa |
| title_full | The implementation of a rapid sample preparation method for the detection of SARS-CoV-2 in a diagnostic laboratory in South Africa |
| title_fullStr | The implementation of a rapid sample preparation method for the detection of SARS-CoV-2 in a diagnostic laboratory in South Africa |
| title_full_unstemmed | The implementation of a rapid sample preparation method for the detection of SARS-CoV-2 in a diagnostic laboratory in South Africa |
| title_short | The implementation of a rapid sample preparation method for the detection of SARS-CoV-2 in a diagnostic laboratory in South Africa |
| title_sort | implementation of a rapid sample preparation method for the detection of sars cov 2 in a diagnostic laboratory in south africa |
| topic | Virological Pathology |
| url | http://hdl.handle.net/11427/37618 |
| work_keys_str_mv | AT maraisgertjk theimplementationofarapidsamplepreparationmethodforthedetectionofsarscov2inadiagnosticlaboratoryinsouthafrica AT maraisgertjk implementationofarapidsamplepreparationmethodforthedetectionofsarscov2inadiagnosticlaboratoryinsouthafrica |