Analytical validation of quantitative SARS-CoV-2 subgenomic and viral load laboratory developed tests conducted on the Panther Fusion® (Hologic) with preliminary application to clinical samples.
<h4>Objective</h4>Validate the performance characteristics of two analyte specific, laboratory developed tests (LDTs) for the quantification of SARS-CoV-2 subgenomic RNA (sgRNA) and viral load on the Hologic Panther Fusion® using the Open Access functionality.<h4>Methods</h4>...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2023-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0287576 |
| _version_ | 1797788361150169088 |
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| author | Ines Lakhal-Naouar Holly R Hack Edgar Moradel Amie Jarra Hannah L Grove Rani M Ismael Steven Padilla Dante Coleman Jason Ouellette Janice Darden Casey Storme Kristina K Peachman Tara L Hall Mark E Huhtanen Paul T Scott Shilpa Hakre Linda L Jagodzinski Sheila A Peel |
| author_facet | Ines Lakhal-Naouar Holly R Hack Edgar Moradel Amie Jarra Hannah L Grove Rani M Ismael Steven Padilla Dante Coleman Jason Ouellette Janice Darden Casey Storme Kristina K Peachman Tara L Hall Mark E Huhtanen Paul T Scott Shilpa Hakre Linda L Jagodzinski Sheila A Peel |
| author_sort | Ines Lakhal-Naouar |
| collection | DOAJ |
| description | <h4>Objective</h4>Validate the performance characteristics of two analyte specific, laboratory developed tests (LDTs) for the quantification of SARS-CoV-2 subgenomic RNA (sgRNA) and viral load on the Hologic Panther Fusion® using the Open Access functionality.<h4>Methods</h4>Custom-designed primers/probe sets targeting the SARS-CoV-2 Envelope gene (E) and subgenomic E were optimized. A 20-day performance validation following laboratory developed test requirements was conducted to assess assay precision, accuracy, analytical sensitivity/specificity, lower limit of detection and reportable range.<h4>Results</h4>Quantitative SARS-CoV-2 sgRNA (LDT-Quant sgRNA) assay, which measures intermediates of replication, and viral load (LDT-Quant VLCoV) assay demonstrated acceptable performance. Both assays were linear with an R2 and slope equal to 0.99 and 1.00, respectively. Assay precision was evaluated between 4-6 Log10 with a maximum CV of 2.6% and 2.5% for LDT-Quant sgRNA and LDT-Quant VLCoV respectively. Using negative or positive SARS-CoV-2 human nasopharyngeal swab samples, both assays were accurate (kappa coefficient of 1.00 and 0.92). Common respiratory flora and other viral pathogens were not detected and did not interfere with the detection or quantification by either assay. Based on 95% detection, the assay LLODs were 729 and 1206 Copies/mL for the sgRNA and VL load LDTs, respectively.<h4>Conclusion</h4>The LDT-Quant sgRNA and LDT-Quant VLCoV demonstrated good analytical performance. These assays could be further investigated as alternative monitoring assays for viral replication; and thus, medical management in clinical settings which could inform isolation/quarantine requirements. |
| first_indexed | 2024-03-13T01:34:29Z |
| format | Article |
| id | doaj.art-f9ca43cf817f44cab7a4ef6f4b313754 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-03-13T01:34:29Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-f9ca43cf817f44cab7a4ef6f4b3137542023-07-04T05:31:56ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01186e028757610.1371/journal.pone.0287576Analytical validation of quantitative SARS-CoV-2 subgenomic and viral load laboratory developed tests conducted on the Panther Fusion® (Hologic) with preliminary application to clinical samples.Ines Lakhal-NaouarHolly R HackEdgar MoradelAmie JarraHannah L GroveRani M IsmaelSteven PadillaDante ColemanJason OuelletteJanice DardenCasey StormeKristina K PeachmanTara L HallMark E HuhtanenPaul T ScottShilpa HakreLinda L JagodzinskiSheila A Peel<h4>Objective</h4>Validate the performance characteristics of two analyte specific, laboratory developed tests (LDTs) for the quantification of SARS-CoV-2 subgenomic RNA (sgRNA) and viral load on the Hologic Panther Fusion® using the Open Access functionality.<h4>Methods</h4>Custom-designed primers/probe sets targeting the SARS-CoV-2 Envelope gene (E) and subgenomic E were optimized. A 20-day performance validation following laboratory developed test requirements was conducted to assess assay precision, accuracy, analytical sensitivity/specificity, lower limit of detection and reportable range.<h4>Results</h4>Quantitative SARS-CoV-2 sgRNA (LDT-Quant sgRNA) assay, which measures intermediates of replication, and viral load (LDT-Quant VLCoV) assay demonstrated acceptable performance. Both assays were linear with an R2 and slope equal to 0.99 and 1.00, respectively. Assay precision was evaluated between 4-6 Log10 with a maximum CV of 2.6% and 2.5% for LDT-Quant sgRNA and LDT-Quant VLCoV respectively. Using negative or positive SARS-CoV-2 human nasopharyngeal swab samples, both assays were accurate (kappa coefficient of 1.00 and 0.92). Common respiratory flora and other viral pathogens were not detected and did not interfere with the detection or quantification by either assay. Based on 95% detection, the assay LLODs were 729 and 1206 Copies/mL for the sgRNA and VL load LDTs, respectively.<h4>Conclusion</h4>The LDT-Quant sgRNA and LDT-Quant VLCoV demonstrated good analytical performance. These assays could be further investigated as alternative monitoring assays for viral replication; and thus, medical management in clinical settings which could inform isolation/quarantine requirements.https://doi.org/10.1371/journal.pone.0287576 |
| spellingShingle | Ines Lakhal-Naouar Holly R Hack Edgar Moradel Amie Jarra Hannah L Grove Rani M Ismael Steven Padilla Dante Coleman Jason Ouellette Janice Darden Casey Storme Kristina K Peachman Tara L Hall Mark E Huhtanen Paul T Scott Shilpa Hakre Linda L Jagodzinski Sheila A Peel Analytical validation of quantitative SARS-CoV-2 subgenomic and viral load laboratory developed tests conducted on the Panther Fusion® (Hologic) with preliminary application to clinical samples. PLoS ONE |
| title | Analytical validation of quantitative SARS-CoV-2 subgenomic and viral load laboratory developed tests conducted on the Panther Fusion® (Hologic) with preliminary application to clinical samples. |
| title_full | Analytical validation of quantitative SARS-CoV-2 subgenomic and viral load laboratory developed tests conducted on the Panther Fusion® (Hologic) with preliminary application to clinical samples. |
| title_fullStr | Analytical validation of quantitative SARS-CoV-2 subgenomic and viral load laboratory developed tests conducted on the Panther Fusion® (Hologic) with preliminary application to clinical samples. |
| title_full_unstemmed | Analytical validation of quantitative SARS-CoV-2 subgenomic and viral load laboratory developed tests conducted on the Panther Fusion® (Hologic) with preliminary application to clinical samples. |
| title_short | Analytical validation of quantitative SARS-CoV-2 subgenomic and viral load laboratory developed tests conducted on the Panther Fusion® (Hologic) with preliminary application to clinical samples. |
| title_sort | analytical validation of quantitative sars cov 2 subgenomic and viral load laboratory developed tests conducted on the panther fusion r hologic with preliminary application to clinical samples |
| url | https://doi.org/10.1371/journal.pone.0287576 |
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