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Theel ES, Kirby JE, Pollock NR. Testing for SARS-CoV-2: lessons learned and current use cases. Clin Microbiol Rev 2024; 37:e0007223. [PMID: 38488364 PMCID: PMC11237512 DOI: 10.1128/cmr.00072-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
SUMMARYThe emergence and worldwide dissemination of SARS-CoV-2 required both urgent development of new diagnostic tests and expansion of diagnostic testing capacity on an unprecedented scale. The rapid evolution of technologies that allowed testing to move out of traditional laboratories and into point-of-care testing centers and the home transformed the diagnostic landscape. Four years later, with the end of the formal public health emergency but continued global circulation of the virus, it is important to take a fresh look at available SARS-CoV-2 testing technologies and consider how they should be used going forward. This review considers current use case scenarios for SARS-CoV-2 antigen, nucleic acid amplification, and immunologic tests, incorporating the latest evidence for analytical/clinical performance characteristics and advantages/limitations for each test type to inform current debates about how tests should or should not be used.
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Affiliation(s)
- Elitza S. Theel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - James E. Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Nira R. Pollock
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
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Ngetsa C, Osoti V, Okanda D, Marura F, Shah K, Karanja H, Mugo D, Gitonga J, Mutunga M, Lewa C, Orindi B, Bejon P, Ochola-Oyier LI. Validation of saline, PBS and a locally produced VTM at varying storage conditions to detect the SARS-CoV-2 virus by qRT-PCR. PLoS One 2023; 18:e0280685. [PMID: 36780469 PMCID: PMC9924993 DOI: 10.1371/journal.pone.0280685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/05/2023] [Indexed: 02/15/2023] Open
Abstract
Coronavirus Disease-2019 tests require a Nasopharyngeal (NP) and/or Oropharyngeal (OP) specimen from the upper airway, from which virus RNA is extracted and detected through quantitative reverse transcription-Polymerase Chain Reaction (qRT-PCR). The viability of the virus is maintained after collection by storing the NP/OP swabs in Viral Transport Media (VTM). We evaluated the performance of four transport media: locally manufactured ("REVITAL") Viral Transport Media (RVTM), Standard Universal Transport Media (SUTM), PBS and 0.9% (w/v) NaCl (normal saline). We used laboratory cultured virus to evaluate: i) viral recovery and maintaining integrity at different time periods and temperatures; ii) stability in yielding detectable RNA consistently for all time points and conditions; and iii) their overall accuracy. Four vials of SARS-CoV-2 cultured virus (2 high and 2 low concentration samples) and 1 negative control sample were prepared for each media type (SUTM, RVTM, PBS and normal saline) and stored at the following temperatures, -80°C, 4°C, 25°C and 37°C for 7 days. Viral RNA extractions and qRT-PCR were performed at 1, 2, 3, 4 and 7 days after inoculation with the cultured virus to assess virus stability and viral recovery. Ct values fell over time at 25°C and 37°C, but normal saline, PBS, RVTM and SUTM all showed comparable performance in maintaining virus integrity and stability allowing for the detection of SARS-CoV-2 RNA. Overall, this study demonstrated that normal saline, PBS and the locally manufactured VTM can be used for COVID-19 sample collection and testing, thus expanding the range of SARS-CoV-2 viral collection media.
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Affiliation(s)
- Caroline Ngetsa
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Victor Osoti
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Dorcas Okanda
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Faith Marura
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Krupali Shah
- Revital Healthcare (EPZ) Limited, Mombasa, Kenya
| | - Henry Karanja
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Daisy Mugo
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research Coast, Kilifi, Kenya
| | - John Gitonga
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Martin Mutunga
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Clement Lewa
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Benedict Orindi
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research Coast, Kilifi, Kenya
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research Coast, Kilifi, Kenya
- Nuffield Department of Medicine, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
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Clinical Evaluation of Nasopharyngeal, Oropharyngeal, Nasal Swabs, and Saliva for the Detection of SARS-CoV-2 by Direct RT-PCR. Diagnostics (Basel) 2022; 12:diagnostics12051091. [PMID: 35626247 PMCID: PMC9140003 DOI: 10.3390/diagnostics12051091] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Nasopharyngeal swab (NPS) and oropharyngeal swab (OPS) are the most widely used upper respiratory tract specimens for diagnosis of SARS-CoV-2 using RT-qPCR. In contrast, nasal swab (NS) and saliva (SS), recently recommended by the WHO, are rarely used, and their test accuracy is limited. The method for direct RT-PCR detection of SARS-CoV-2 does not require an RNA extraction and is faster and easier than standard RT-PCR tests with RNA extraction. This study aimed to compare the diagnostic performance of upper respiratory tract samples for SARS-CoV-2 detection using the direct RT-PCR without preliminary heat inactivation. Here we report the application and validation of direct RT-PCR SARS-CoV-2 RNA on 165 clinical specimens of NPS/OP, and 36 samples of NS/NPS and 37 saliva samples (for the latter with prior deproteinization). The overall sensitivity estimates were 95.9%, 94.2%, 88.9%, and 94.6% for NPS/OPS/NS/SS samples, respectively, and the specificity was 100% against standard RT-PCR with RNA extraction. Overall, NS and SS testing by direct RT-PCR had sufficient sensitivity to detect SARS-CoV-2. They can be acceptable alternative to NPS/OPS for rapid detection of SARS-CoV-2 infections in future.
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