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Sechi I, Muresu N, Puci MV, Saderi L, Del Rio A, Cossu A, Muroni MR, Castriciano S, Martinelli M, Cocuzza CE, Sotgiu G, Piana A. Preliminary Results of Feasibility and Acceptability of Self-Collection for Cervical Screening in Italian Women. Pathogens 2023; 12:1169. [PMID: 37764977 PMCID: PMC10535381 DOI: 10.3390/pathogens12091169] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Given the diagnostic accuracy of HPV-DNA tests in terms of self-collected samples, in order to implement self-sampling in cervical screening programs, the standardization of the pre-analytical phase, including decisions concerning the choice of medium, the volume of elution, and storage conditions, are necessary, in addition to understanding the potential factors involved in acceptability by women. On this basis, we carried out a cross-sectional study to assess (i) the stability of dry vaginal self-collected samples stored at room temperature for up to 4 weeks after elution in 2 mL of eNat® (Copan) medium, and (ii) the acceptability of self-collection in enrolled women. METHODS 185 women were enrolled in the LILT (Italian League Against Tumors) regional project. A self-sampling kit, including a dry FLOQSwab® (Copan), instructions for use, and a satisfaction questionnaire, were supplied for each woman and sent by mail to the laboratory. The HPV-DNA test was carried out using the Anyplex™ II HPV HR (Seegene) kit. To evaluate the specimen's stability, 185 dry vaginal swabs were eluted in eNat®, a lyses-based molecular medium and tested for HPV detection at two different time points (<6 days and 1 month after elution). The Cohen's Kappa coefficients and McNemar test were used to assess the agreement of HPV-DNA at different times. RESULTS We found high agreement in terms of HPV-DNA results among the samples tested at two different time points (Cohen K = 0.98; p < 0.0001). Moreover, most of the women found it easy to use self-collection devices and the pictorial instructions clear to understand. Approximately half of the enrolled women declared preferring self-sampling to clinician-collected methods. CONCLUSION Our results display the high reliability and accuracy of HPV-DNA tests using dry vaginal self-collection FLOQSwabs® devices eluted in 2 mL of molecular medium. The analysis of the questionnaire showed a high acceptability of self-collection among women, although a high percentage preferred standard collection devices. Overall, our preliminary results support the adoption of self-collection in screening programs, even though further analyses should be performed to optimize and standardize protocols for HPV tests on self-samples, and educational campaigns are needed to adequately inform and increase responsiveness in a target population.
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Affiliation(s)
- Illari Sechi
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Padre Manzella 4 Street, 07100 Sassari, Italy; (I.S.); (A.C.); (M.R.M.); (A.P.)
| | - Narcisa Muresu
- Department of Humanities and Social Sciences, University of Sassari, Padre Manzella 4 Street, 07100 Sassari, Italy
| | - Mariangela V. Puci
- Clinical Epidemiology and Medical Statistics Unit, Department of Medical, Surgical and Pharmacological Sciences, University of Sassari-Padre Manzella 4 Street, 07100 Sassari, Italy; (M.V.P.); (L.S.); (G.S.)
| | - Laura Saderi
- Clinical Epidemiology and Medical Statistics Unit, Department of Medical, Surgical and Pharmacological Sciences, University of Sassari-Padre Manzella 4 Street, 07100 Sassari, Italy; (M.V.P.); (L.S.); (G.S.)
| | - Arcadia Del Rio
- Biomedical Science PhD School, Biomedical Science Department, University of Sassari, Padre Manzella 4 Street, 07100 Sassari, Italy;
| | - Andrea Cossu
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Padre Manzella 4 Street, 07100 Sassari, Italy; (I.S.); (A.C.); (M.R.M.); (A.P.)
| | - Maria R. Muroni
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Padre Manzella 4 Street, 07100 Sassari, Italy; (I.S.); (A.C.); (M.R.M.); (A.P.)
| | | | - Marianna Martinelli
- Department of Medicine and Surgery, University of Milano-Bicocca, Cadore 48 street, 20900 Monza, Italy; (M.M.); (C.E.C.)
| | - Clementina E. Cocuzza
- Department of Medicine and Surgery, University of Milano-Bicocca, Cadore 48 street, 20900 Monza, Italy; (M.M.); (C.E.C.)
| | - Giovanni Sotgiu
- Clinical Epidemiology and Medical Statistics Unit, Department of Medical, Surgical and Pharmacological Sciences, University of Sassari-Padre Manzella 4 Street, 07100 Sassari, Italy; (M.V.P.); (L.S.); (G.S.)
| | - Andrea Piana
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Padre Manzella 4 Street, 07100 Sassari, Italy; (I.S.); (A.C.); (M.R.M.); (A.P.)
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Yang X, Guo C, Zhang Q, Chen Y, Liu Y, Zhang X. A portable thermostatic molecular diagnosis device based on high-efficiency photothermal conversion material for rapid field detection of SARS-CoV-2. Talanta 2023; 258:124422. [PMID: 36907162 PMCID: PMC9988313 DOI: 10.1016/j.talanta.2023.124422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023]
Abstract
The outbreak of the novel coronavirus (SARS-CoV-2) has seriously harmed human health and economic development worldwide. Studies have shown that timely diagnosis and isolation are the most effective ways to prevent the spread of the epidemic. However, the current polymerase chain reaction (PCR) based molecular diagnostic platform has the problems of expensive equipment, high operation difficulty, and the need for stable power resources support, so it is difficult to popularize in low-resource areas. This study established a portable (<300 g), low-cost (<$10), and reusable molecular diagnostic device based on solar energy photothermal conversion strategy, which creatively introduces a sunflower-like light tracking system to improve light utilization, making the device suitable for both high and low-light areas. The experimental results show that the device can detect SARS-CoV-2 nucleic acid samples as low as 1 aM within 30 min.
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Affiliation(s)
- Xinyao Yang
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, PR China
| | - Chuanghao Guo
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, PR China
| | - Qianling Zhang
- Graphene Composite Research Center, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, PR China
| | - Yong Chen
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, PR China; Graphene Composite Research Center, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, PR China.
| | - Yizhen Liu
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, PR China.
| | - Xueji Zhang
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, PR China
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Giubbi C, Martinelli M, Vallini I, Paganoni S, Dafa'alla T, Perdoni F, Musumeci R, Wu W, Castriciano S, Romano P, Cocuzza CE. Human papillomavirus (HPV) detection in vaginal self-samples: evaluation of eNat® as an alternative suspension medium to ThinPrep®PreservCyt® for vaginal swabs. OPEN RESEARCH EUROPE 2022; 2:35. [PMID: 37645291 PMCID: PMC10446064 DOI: 10.12688/openreseurope.14344.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/14/2022] [Indexed: 08/31/2023]
Abstract
Human Papillomavirus (HPV) testing on self-collected samples allows for improved coverage rates of cervical cancer (CC) screening programs. ThinPrep®PreservCyt® (HOLOGIC®, USA) medium is widely used for the suspension of cervical and vaginal self-samples. However, this medium is costly, toxic, and flammable, involving special handling procedures which make its use difficult in screening programs, particularly in low- and middle-income countries. This pilot study aimed to evaluate the analytical performance of eNat ® (Copan SpA), an alternative non-alcohol-based suspension medium, compared to ThinPrep®PreservCyt® (HOLOGIC®) for high-risk HPV (hrHPV) detection in vaginal self-collected swabs using three different real-time polymerase chain reaction (RT-PCR) HPV assays: Anyplex™II HPV28 (Seegene, Korea), Papilloplex® High Risk HPV (GeneFirst, UK), and HPV OncoPredict (Hiantis, Italy). 30 women, referred to colposcopy, were enrolled in this observational, prospective pilot study and asked to collect two vaginal self-taken samples, which were suspended in 5 mL of ThinPrep®PreservCyt® or eNat®. Nucleic acids were extracted from 200 μL using Microlab Nimbus platform (Seegene, Korea) and tested with the three different RT-PCR full-genotyping high-risk HPV assays. The HPV results of vaginal samples resuspended in the two different media were compared to those obtained from the reference clinician-collected cervical sample from the same woman. hrHPV detection in vaginal self-samples suspended in both media demonstrated a substantial agreement with cervical samples with the three assays under-investigation (0.667
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Affiliation(s)
- Chiara Giubbi
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Marianna Martinelli
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | | | | | | | - Federica Perdoni
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Rosario Musumeci
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Winnie Wu
- GeneFirst Ltd., Abingdon, OX14 3DB, UK
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Considerations regarding Interpretation of Positive SARS-CoV-2 Molecular Results with Late Cycle Threshold Values. J Clin Microbiol 2022; 60:e0050122. [PMID: 35658526 PMCID: PMC9491168 DOI: 10.1128/jcm.00501-22] [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] [Indexed: 11/22/2022] Open
Abstract
COVID-19 disease lies on a spectrum, ranging from completely asymptomatic to mild disease to severe and critical disease. Studies have shown that prolonged shedding or sporadic detection of SARS-CoV-2 RNA can occur long after symptom resolution. Adding to these clinical complexities is the demand for testing for SARS-CoV-2 at all stages of diseases, frequently driven by screening of asymptomatic persons, something that traditionally has not been performed for other viral respiratory diseases. This can lead to positive results from nucleic acid amplification tests (NAATs), such as RT-PCR, with late cycle threshold (CT) values near the test’s limit of detection. In this commentary, we review unique attributes of COVID-19 and causes of NAAT late CT values. We provide interpretation considerations as well as strategies to aid in test interpretation.
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Domnich A, Orsi A, Trombetta CS, Costa E, Guarona G, Lucente M, Ricucci V, Bruzzone B, Icardi G. Comparative Diagnostic Accuracy of the STANDARD M10 Assay for the Molecular Diagnosis of SARS-CoV-2 in the Point-of-Care and Critical Care Settings. J Clin Med 2022; 11:2465. [PMID: 35566591 PMCID: PMC9105343 DOI: 10.3390/jcm11092465] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 02/06/2023] Open
Abstract
Accurate and rapid molecular diagnosis of COVID-19 is a crucial step to tackle the ongoing pandemic. The primary objective of this study was to estimate the real-world performance of the novel RT-PCR STANDARD M10 SARS-CoV-2 assay in a large number of nasopharyngeal (NP) specimens eluted in universal transport medium. The secondary objective was to evaluate the compatibility of this kit in testing NP samples eluted in an inactivated transport medium (essential for point-of-care testing) and lower respiratory tract (LRT) specimens, which are commonly collected in critical care. A total of 591 samples were analyzed. Compared with the standard extraction-based RT-PCR Allplex 2019-nCoV (time-to-result of 270 min), the sensitivities of the STANDARD M10 were 100% (95% CI: 98.1-100%), 95.5% (95% CI: 91.7-97.6%), and 99.5% (95% CI: 97.2-99.9%) for ≥1 gene, the ORF1ab gene, and the E gene, respectively, while the specificity was 100% (95% CI: 98.7-100%). The diagnostic accuracy was 100% in testing both NP samples eluted in an inactivated transport medium and LRT specimens. STANDARD M10 reliably detects SARS-CoV-2 in 60 min, may be used as a POC tool, and is suitable for testing LRT specimens in the critical care setting.
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Affiliation(s)
- Alexander Domnich
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
| | - Andrea Orsi
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (C.-S.T.); (E.C.)
| | - Carlo-Simone Trombetta
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (C.-S.T.); (E.C.)
| | - Elisabetta Costa
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (C.-S.T.); (E.C.)
| | - Giulia Guarona
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
| | - Miriana Lucente
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
| | - Valentina Ricucci
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
| | - Bianca Bruzzone
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
| | - Giancarlo Icardi
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (A.O.); (G.G.); (M.L.); (V.R.); (B.B.); (G.I.)
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (C.-S.T.); (E.C.)
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Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
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Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
- *Correspondence: Carina Almeida,
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Influence of preanalytical parameters on influenza and respiratory syncytial virus molecular detection. J Clin Virol 2022; 147:105063. [PMID: 35032794 DOI: 10.1016/j.jcv.2021.105063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 12/24/2021] [Accepted: 12/31/2021] [Indexed: 11/24/2022]
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Banada P, Elson D, Daivaa N, Park C, Desind S, Montalvan I, Kwiatkowski R, Chakravorty S, Alland D, Xie YL. Sample collection and transport strategies to enhance yield, accessibility, and biosafety of COVID-19 RT-PCR testing. J Med Microbiol 2021; 70. [PMID: 34486972 PMCID: PMC8697510 DOI: 10.1099/jmm.0.001380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Introduction Non-invasive sample collection and viral sterilizing buffers have independently enabled workflows for more widespread COVID-19 testing by reverse-transcriptase polymerase chain reaction (RT-PCR). Gap Statement The combined use of sterilizing buffers across non-invasive sample types to optimize sensitive, accessible, and biosafe sampling methods has not been directly and systematically compared. Aim We aimed to evaluate diagnostic yield across different non-invasive samples with standard viral transport media (VTM) versus a sterilizing buffer eNAT- (Copan diagnostics Murrieta, CA) in a point-of-care diagnostic assay system. Methodos We prospectively collected 84 sets of nasal swabs, oral swabs, and saliva, from 52 COVID-19 RT-PCR-confirmed patients, and nasopharyngeal (NP) swabs from 37 patients. Nasal swabs, oral swabs, and saliva were placed in either VTM or eNAT, prior to testing with the Xpert Xpress SARS-CoV-2 (Xpert). The sensitivity of each sampling strategy was compared using a composite positive standard. Results Swab specimens collected in eNAT showed an overall superior sensitivity compared to swabs in VTM (70 % vs 57 %, P=0.0022). Direct saliva 90.5 %, (95 % CI: 82 %, 95 %), followed by NP swabs in VTM and saliva in eNAT, was significantly more sensitive than nasal swabs in VTM (50 %, P<0.001) or eNAT (67.8 %, P=0.0012) and oral swabs in VTM (50 %, P<0.0001) or eNAT (58 %, P<0.0001). Saliva and use of eNAT buffer each increased detection of SARS-CoV-2 with the Xpert; however, no single sample matrix identified all positive cases. Conclusion Saliva and eNAT sterilizing buffer can enhance safe and sensitive detection of COVID-19 using point-of-care GeneXpert instruments.
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Affiliation(s)
- Padmapriya Banada
- The Public Health Research Institute and Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - David Elson
- The Public Health Research Institute and Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Naranjargal Daivaa
- The Public Health Research Institute and Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Claire Park
- The Public Health Research Institute and Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Samuel Desind
- The Public Health Research Institute and Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | | | | | - Soumitesh Chakravorty
- The Public Health Research Institute and Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.,Cepheid, Sunnyvale, CA, USA
| | - David Alland
- The Public Health Research Institute and Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Yingda L Xie
- The Public Health Research Institute and Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
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Banik S, Saibire K, Suryavanshi S, Johns G, Chakravorty S, Kwiatkowski R, Alland D, Banada PP. Inactivation of SARS-CoV-2 virus in saliva using a guanidium based transport medium suitable for RT-PCR diagnostic assays. PLoS One 2021; 16:e0252687. [PMID: 34115762 PMCID: PMC8195355 DOI: 10.1371/journal.pone.0252687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/20/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Upper respiratory samples used to test for SARS-CoV-2 virus may be infectious and present a hazard during transport and testing. A buffer with the ability to inactivate SARS-CoV-2 at the time of sample collection could simplify and expand testing for COVID-19 to non-conventional settings. METHODS We evaluated a guanidium thiocyanate-based buffer, eNAT™ (Copan) as a possible transport and inactivation medium for downstream Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) testing to detect SARS-CoV-2. Inactivation of SARS-CoV-2 USA-WA1/2020 in eNAT and in diluted saliva was studied at different incubation times. The stability of viral RNA in eNAT was also evaluated for up to 7 days at room temperature (28°C), refrigerated conditions (4°C) and at 35°C. RESULTS SARS-COV-2 virus spiked directly in eNAT could be inactivated at >5.6 log10 PFU/ml within a minute of incubation. When saliva was diluted 1:1 in eNAT, no cytopathic effect (CPE) on VeroE6 cells was observed, although SARS-CoV-2 RNA could be detected even after 30 min incubation and after two cell culture passages. A 1:2 (saliva:eNAT) dilution abrogated both CPE and detectable viral RNA after as little as 5 min incubation in eNAT. SARS-CoV-2 RNA from virus spiked at 5X the limit of detection remained positive up to 7 days of incubation in all tested conditions. CONCLUSION eNAT and similar guanidinium thiocyanate-based media may be of value for transport, stabilization, and processing of clinical samples for RT-PCR based SARS-CoV-2 detection.
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Affiliation(s)
- Sukalyani Banik
- Department of Medicine, Center for Emerging Pathogens, Rutgers-New Jersey Medical School, Newark, New Jersey, United States of America
| | - Kaheerman Saibire
- Department of Medicine, Center for Emerging Pathogens, Rutgers-New Jersey Medical School, Newark, New Jersey, United States of America
| | - Shraddha Suryavanshi
- Department of Medicine, Center for Emerging Pathogens, Rutgers-New Jersey Medical School, Newark, New Jersey, United States of America
| | - Glenn Johns
- Cepheid, Sunnyvale, California, United States of America
| | | | | | - David Alland
- Department of Medicine, Center for Emerging Pathogens, Rutgers-New Jersey Medical School, Newark, New Jersey, United States of America
| | - Padmapriya P. Banada
- Department of Medicine, Center for Emerging Pathogens, Rutgers-New Jersey Medical School, Newark, New Jersey, United States of America
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Richard-Greenblatt M, Ziegler MJ, Bromberg V, Huang E, Abdallah H, Tolomeo P, Lautenbach E, Glaser L, Kelly BJ. Quantifying the Impact of Nasopharyngeal Specimen Quality on Severe Acute Respiratory Syndrome Coronavirus 2 Test Performance. Open Forum Infect Dis 2021; 8:ofab235. [PMID: 34095340 PMCID: PMC8136075 DOI: 10.1093/ofid/ofab235] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/05/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse-transcription polymerase chain reaction (RT-PCR) cycle threshold (Ct) has been used to estimate quantitative viral load, with the goal of targeting isolation precautions for individuals with coronavirus disease 2019 (COVID-19) and guiding public health interventions. However, variability in specimen quality can alter the Ct values obtained from SARS-CoV-2 clinical assays. We sought to define how variable nasopharyngeal (NP) swab quality impacts clinical SARS-CoV-2 test sensitivity. METHODS We performed amplification of a human gene target (β-actin) in parallel with a clinical RT-PCR targeting the SARS-CoV-2 ORF1ab gene for 1282 NP specimens collected from patients with clinical concern for COVID-19. We evaluated the relationship between NP specimen quality, characterized by late Ct values for the human gene target β-actin Ct, and the probability of SARS-CoV-2 detection via logistic regression, as well as the linear relationship between SARS-CoV-2 and β-actin Ct. RESULTS Low-quality NP swabs are less likely to detect SARS-CoV-2 (odds ratio, 0.607 [95% credible interval {CrI}, .487-.753]). We observed a positive linear relationship between SARS-CoV-2 and β-actin Ct values (slope, 0.181 [95% CrI, .097-.264]), consistent with a reduction in detection of 0.181 cycles for each additional cycle of the β-actin target. COVID-19 disease severity was not associated with β-actin Ct values. CONCLUSIONS Variability in NP specimen quality significantly impacts the performance of clinical SARS-CoV-2 assays, and caution should be taken when interpreting quantitative SARS-CoV-2 Ct results. If unrecognized, low-quality NP specimens, which are characterized by a low level of amplifiable human DNA target, may limit the successful application of SARS-CoV-2 Ct values to direct infection control and public health interventions.
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Affiliation(s)
- Melissa Richard-Greenblatt
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew J Ziegler
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Valerie Bromberg
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth Huang
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hatem Abdallah
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pam Tolomeo
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ebbing Lautenbach
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Laurel Glaser
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J Kelly
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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