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Lakhal-Naouar I, Hack HR, Moradel E, Jarra A, Grove HL, Ismael RM, Padilla S, Coleman D, Ouellette J, Darden J, Storme C, Peachman KK, Hall TL, Huhtanen ME, Scott PT, Hakre S, Jagodzinski LL, Peel SA. 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 2023; 18:e0287576. [PMID: 37384714 PMCID: PMC10309597 DOI: 10.1371/journal.pone.0287576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023] Open
Abstract
OBJECTIVE 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. METHODS 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. RESULTS 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. CONCLUSION 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.
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Affiliation(s)
- Ines Lakhal-Naouar
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Holly R. Hack
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Edgar Moradel
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Amie Jarra
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Hannah L. Grove
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Rani M. Ismael
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Steven Padilla
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Dante Coleman
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Jason Ouellette
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Janice Darden
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Casey Storme
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Kristina K. Peachman
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Tara L. Hall
- Moncrief Army Health Clinic, Fort Jackson, South Carolina, United States of America
| | - Mark E. Huhtanen
- Moncrief Army Health Clinic, Fort Jackson, South Carolina, United States of America
| | - Paul T. Scott
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Shilpa Hakre
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Linda L. Jagodzinski
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Sheila A. Peel
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
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Hakre S, Lakhal-Naouar I, King DB, Burns JL, Jackson KN, Krauss SW, Chandrasekaran P, McCauley MD, Ober Shepherd BL, McHenry S, Bianchi EJ, Ouellette J, Darden JM, Sanborn AD, Daye SP, Kwon PO, Stubbs J, Brigantti CL, Hall TL, Beagle MH, Pieri JA, Frambes TR, O’Connell RJ, Modjarrad K, Murray CK, Jagodzinski LL, Scott PT, Peel SA. Virological and Serological Assessment of US Army Trainees Isolated for Coronavirus Disease 2019. J Infect Dis 2022; 226:1743-1752. [PMID: 35543272 PMCID: PMC9129211 DOI: 10.1093/infdis/jiac198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/09/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Laboratory screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key mitigation measure to avoid the spread of infection among recruits starting basic combat training in a congregate setting. Because viral nucleic acid can be detected persistently after recovery, we evaluated other laboratory markers to distinguish recruits who could proceed with training from those who were infected. METHODS Recruits isolated for coronavirus disease 2019 (COVID-19) were serially tested for SARS-CoV-2 subgenomic ribonucleic acid (sgRNA), and viral load (VL) by reverse-transcriptase polymerase chain reaction (RT-PCR), and for anti- SARS-CoV-2. Cluster and quadratic discriminant analyses of results were performed. RESULTS Among 229 recruits isolated for COVID-19, those with a RT-PCR cycle threshold >30.49 (sensitivity 95%, specificity 96%) or having sgRNA log10 RNA copies/mL <3.09 (sensitivity and specificity 96%) at entry into isolation were likely SARS-CoV-2 uninfected. Viral load >4.58 log10 RNA copies/mL or anti-SARS-CoV-2 signal-to-cutoff ratio <1.38 (VL: sensitivity and specificity 93%; anti-SARS-CoV-2: sensitivity 83%, specificity 79%) had comparatively lower sensitivity and specificity when used alone for discrimination of infected from uninfected. CONCLUSIONS Orthogonal laboratory assays used in combination with RT-PCR may have utility in determining SARS-CoV-2 infection status for decisions regarding isolation.
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Affiliation(s)
- Shilpa Hakre
- Correspondence: Shilpa Hakre, DrPH MPH, Emerging Infectious Diseases Branch, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720-A Rockledge Drive, Suite 400, Bethesda, MD 20817 ()
| | - Ines Lakhal-Naouar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA,Walter Reed Army Institute of Research, Diagnostics and Countermeasures Branch, Silver Spring, Maryland, USA
| | - David B King
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA
| | - Jennifer L Burns
- Walter Reed Army Institute of Research, Pilot Bioproduction Facility, Silver Spring, Maryland, USA
| | - Kenya N Jackson
- Walter Reed Army Institute of Research, Experimental Therapeutics, Silver Spring, Maryland, USA
| | - Stephen W Krauss
- Walter Reed Army Institute of Research, Center for Military Psychiatry and Neuroscience, Silver Spring, Maryland, USA
| | - Prabha Chandrasekaran
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA,Walter Reed Army Institute of Research, Diagnostics and Countermeasures Branch, Silver Spring, Maryland, USA
| | - Melanie D McCauley
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA
| | - Brittany L Ober Shepherd
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA
| | - Samantha McHenry
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA
| | - Elizabeth J Bianchi
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA
| | - Jason Ouellette
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA,Walter Reed Army Institute of Research, Diagnostics and Countermeasures Branch, Silver Spring, Maryland, USA
| | - Janice M Darden
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MarylandUSA,Walter Reed Army Institute of Research, Diagnostics and Countermeasures Branch, Silver Spring, Maryland, USA
| | - Aaron D Sanborn
- Walter Reed Army Institute of Research, Clinical Trials Center, Silver Spring, Maryland, USA
| | - Sharon P Daye
- Walter Reed Army Institute of Research, One Health Branch, Silver Spring, Maryland, USA
| | - Paul O Kwon
- Program Executive Office for Simulation, Training and Instrumentation, Orlando, Florida, USA
| | | | - Crystal L Brigantti
- DiLorenzo Pentagon Health Clinic, Optometry, Washington, District of Columbia, USA
| | - Tara L Hall
- Moncrief Army Health Clinic, Fort Jackson, South Carolina, USA
| | | | - Jason A Pieri
- United States Army Training Center, Fort Jackson, South Carolina, USA
| | - Timothy R Frambes
- United States Army Training Center, Fort Jackson, South Carolina, USA
| | | | - Kayvon Modjarrad
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, USA
| | | | - Linda L Jagodzinski
- Walter Reed Army Institute of Research, Diagnostics and Countermeasures Branch, Silver Spring, Maryland, USA
| | - Paul T Scott
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, USA
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