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Xu Z, Zhang X, Pal C, Rozners E, Callahan BP. Enzyme fragment complementation driven by nucleic acid hybridization sans self-labeling protein. Bioorg Chem 2025; 154:108039. [PMID: 39705932 DOI: 10.1016/j.bioorg.2024.108039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 11/26/2024] [Accepted: 12/03/2024] [Indexed: 12/23/2024]
Abstract
A modified enzyme fragment complementation assay has been designed and validated as a turn-on biosensor for nucleic acid detection in dilute aqueous solution. The assay is target sequence-agonistic and uses fragments of NanoBiT, the split luciferase reporter enzyme, that are esterified enzymatically at their C-termini to steramers, sterol-linked oligonucleotides. The Drosophila hedgehog autoprocessing domain, DHhC, serves as the self-cleaving enzyme for the NanoBiT-steramer bioconjugations. Unlike current approaches, the final bioconjugate generated by DHhC and used for nucleic acid detection is free of self-labeling passenger protein. In the presence of single stranded (ss) DNA or RNA template with adjacent segments complementary to the Nano-BiT steramer oligonucleotides, the two NanoBiT fragments associate productively, reconstituting NanoBiT's luciferase activity. In samples containing ssDNA or RNA template at low nM concentrations, NanoBiT luminescence exceeded background signal by 30- to 60-fold. The steramer probe sequences used to prepare these sensors are unconstrained in length and composition. In the absence of sequence constraints of the probe element and without the added bulk of a self-labeling protein, these NanoBiT-steramer bioconjugates open new applications in the programmable detection of small fragments of coding and noncoding DNA and RNA.
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Affiliation(s)
- Zihan Xu
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York 13902, USA
| | - Xiaoyu Zhang
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York 13902, USA
| | - Chandan Pal
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York 13902, USA
| | - Brian P Callahan
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York 13902, USA.
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Jimenez-Campos AG, Maestas LI, Velappan N, Beck B, Ye C, Wernsing K, Mata-Solis Y, Bruno WJ, Bussmann SC, Bradfute S, Baca JT, Rininsland FH. A cell-based Papain-like Protease (PLpro) activity assay for rapid detection of active SARS-CoV-2 infections and antivirals. PLoS One 2024; 19:e0309305. [PMID: 39724215 DOI: 10.1371/journal.pone.0309305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/09/2024] [Indexed: 12/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants are a continuous threat to human life. An urgent need remains for simple and fast tests that reliably detect active infections with SARS-CoV-2 and its variants in the early stage of infection. Here we introduce a simple and rapid activity-based diagnostic (ABDx) test that identifies SARS-CoV-2 infections by measuring the activity of a viral enzyme, Papain-Like protease (PLpro). The test system consists of a peptide that fluoresces when cleaved by SARS PLpro that is active in crude, unprocessed lysates from human tongue scrapes and saliva. Test results are obtained in 30 minutes or less using widely available fluorescence plate readers, or a battery-operated portable instrument for on-site testing. Proof-of-concept was obtained in a study on clinical specimens collected from patients with COVID-19 like symptoms who tested positive (n = 10) or negative (n = 10) with LIAT RT-PCR using nasal mid turbinate swabs. When saliva from these patients was tested with in-house endpoint RT-PCR, 17 were positive and only 5 specimens were negative, of which 2 became positive when tested 5 days later. PLpro activity correlated in 17 of these cases (3 out of 3 negatives and 14 out of 16 positives, with one invalid specimen). Despite the small number of samples, the agreement was significant (p value = 0.01). Two false negatives were detected, one from a sample with a late Ct value of 35 in diagnostic RT-PCR, indicating that an active infection was no longer present. The PLpro assay is easily scalable and expected to detect all viable SARS-CoV-2 variants, making it attractive as a screening and surveillance tool. Additionally, we show feasibility of the platform as a new homogeneous phenotypic assay for rapid screening of SARS-CoV-2 antiviral drugs and neutralizing antibodies.
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Affiliation(s)
- Anahi G Jimenez-Campos
- University of New Mexico Health Sciences Center, Department of Emergency Medicine, Albuquerque, New Mexico, United States of America
| | - Lucas I Maestas
- University of New Mexico Health Sciences Center, Department of Emergency Medicine, Albuquerque, New Mexico, United States of America
| | - Nileena Velappan
- Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Brian Beck
- MicroBiologics, St. Cloud, MN, United States of America
| | - Chunyan Ye
- Health Science Center, Center for Global Health and Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, United States of America
| | | | | | | | - Silas C Bussmann
- University of New Mexico Health Sciences Center, Department of Emergency Medicine, Albuquerque, New Mexico, United States of America
| | - Steven Bradfute
- Health Science Center, Center for Global Health and Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Justin T Baca
- University of New Mexico Health Sciences Center, Department of Emergency Medicine, Albuquerque, New Mexico, United States of America
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Arevalo-Rodriguez I, Mateos-Haro M, Dinnes J, Ciapponi A, Davenport C, Buitrago-Garcia D, Bennouna-Dalero T, Roqué-Figuls M, Van den Bruel A, von Eije KJ, Emperador D, Hooft L, Spijker R, Leeflang MM, Takwoingi Y, Deeks JJ. Laboratory-based molecular test alternatives to RT-PCR for the diagnosis of SARS-CoV-2 infection. Cochrane Database Syst Rev 2024; 10:CD015618. [PMID: 39400904 PMCID: PMC11472845 DOI: 10.1002/14651858.cd015618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
BACKGROUND Diagnosing people with a SARS-CoV-2 infection played a critical role in managing the COVID-19 pandemic and remains a priority for the transition to long-term management of COVID-19. Initial shortages of extraction and reverse transcription polymerase chain reaction (RT-PCR) reagents impaired the desired upscaling of testing in many countries, which led to the search for alternatives to RNA extraction/purification and RT-PCR testing. Reference standard methods for diagnosing the presence of SARS-CoV-2 infection rely primarily on real-time reverse transcription-polymerase chain reaction (RT-PCR). Alternatives to RT-PCR could, if sufficiently accurate, have a positive impact by expanding the range of diagnostic tools available for the timely identification of people infected by SARS-CoV-2, access to testing and the use of resources. OBJECTIVES To assess the diagnostic accuracy of alternative (to RT-PCR assays) laboratory-based molecular tests for diagnosing SARS-CoV-2 infection. SEARCH METHODS We searched the COVID-19 Open Access Project living evidence database from the University of Bern until 30 September 2020 and the WHO COVID-19 Research Database until 31 October 2022. We did not apply language restrictions. SELECTION CRITERIA We included studies of people with suspected or known SARS-CoV-2 infection, or where tests were used to screen for infection, and studies evaluating commercially developed laboratory-based molecular tests for the diagnosis of SARS-CoV-2 infection considered as alternatives to RT-PCR testing. We also included all reference standards to define the presence or absence of SARS-CoV-2, including RT-PCR tests and established clinical diagnostic criteria. DATA COLLECTION AND ANALYSIS Two authors independently screened studies and resolved disagreements by discussing them with a third author. Two authors independently extracted data and assessed the risk of bias and applicability of the studies using the QUADAS-2 tool. We presented sensitivity and specificity, with 95% confidence intervals (CIs), for each test using paired forest plots and summarised results using average sensitivity and specificity using a bivariate random-effects meta-analysis. We illustrated the findings per index test category and assay brand compared to the WHO's acceptable sensitivity and specificity threshold for diagnosing SARS-CoV-2 infection using nucleic acid tests. MAIN RESULTS We included data from 64 studies reporting 94 cohorts of participants and 105 index test evaluations, with 74,753 samples and 7517 confirmed SARS-CoV-2 cases. We did not identify any published or preprint reports of accuracy for a considerable number of commercially produced NAAT assays. Most cohorts were judged at unclear or high risk of bias in more than three QUADAS-2 domains. Around half of the cohorts were considered at high risk of selection bias because of recruitment based on COVID status. Three quarters of 94 cohorts were at high risk of bias in the reference standard domain because of reliance on a single RT-PCR result to determine the absence of SARS-CoV-2 infection or were at unclear risk of bias due to a lack of clarity about the time interval between the index test assessment and the reference standard, the number of missing results, or the absence of a participant flow diagram. For index tests categories with four or more evaluations and when summary estimations were possible, we found that: a) For RT-PCR assays designed to omit/adapt RNA extraction/purification, the average sensitivity was 95.1% (95% CI 91.1% to 97.3%), and the average specificity was 99.7% (95% CI 98.5% to 99.9%; based on 27 evaluations, 2834 samples and 1178 SARS-CoV-2 cases); b) For RT-LAMP assays, the average sensitivity was 88.4% (95% CI 83.1% to 92.2%), and the average specificity was 99.7% (95% CI 98.7% to 99.9%; 24 evaluations, 29,496 samples and 2255 SARS-CoV-2 cases); c) for TMA assays, the average sensitivity was 97.6% (95% CI 95.2% to 98.8%), and the average specificity was 99.4% (95% CI 94.9% to 99.9%; 14 evaluations, 2196 samples and 942 SARS-CoV-2 cases); d) for digital PCR assays, the average sensitivity was 98.5% (95% CI 95.2% to 99.5%), and the average specificity was 91.4% (95% CI 60.4% to 98.7%; five evaluations, 703 samples and 354 SARS-CoV-2 cases); e) for RT-LAMP assays omitting/adapting RNA extraction, the average sensitivity was 73.1% (95% CI 58.4% to 84%), and the average specificity was 100% (95% CI 98% to 100%; 24 evaluations, 14,342 samples and 1502 SARS-CoV-2 cases). Only two index test categories fulfil the WHO-acceptable sensitivity and specificity requirements for SARS-CoV-2 nucleic acid tests: RT-PCR assays designed to omit/adapt RNA extraction/purification and TMA assays. In addition, WHO-acceptable performance criteria were met for two assays out of 35 when tests were used according to manufacturer instructions. At 5% prevalence using a cohort of 1000 people suspected of SARS-CoV-2 infection, the positive predictive value of RT-PCR assays omitting/adapting RNA extraction/purification will be 94%, with three in 51 positive results being false positives, and around two missed cases. For TMA assays, the positive predictive value of RT-PCR assays will be 89%, with 6 in 55 positive results being false positives, and around one missed case. AUTHORS' CONCLUSIONS Alternative laboratory-based molecular tests aim to enhance testing capacity in different ways, such as reducing the time, steps and resources needed to obtain valid results. Several index test technologies with these potential advantages have not been evaluated or have been assessed by only a few studies of limited methodological quality, so the performance of these kits was undetermined. Only two index test categories with enough evaluations for meta-analysis fulfil the WHO set of acceptable accuracy standards for SARS-CoV-2 nucleic acid tests: RT-PCR assays designed to omit/adapt RNA extraction/purification and TMA assays. These assays might prove to be suitable alternatives to RT-PCR for identifying people infected by SARS-CoV-2, especially when the alternative would be not having access to testing. However, these findings need to be interpreted and used with caution because of several limitations in the evidence, including reliance on retrospective samples without information about the symptom status of participants and the timing of assessment. No extrapolation of found accuracy data for these two alternatives to any test brands using the same techniques can be made as, for both groups, one test brand with high accuracy was overrepresented with 21/26 and 12/14 included studies, respectively. Although we used a comprehensive search and had broad eligibility criteria to include a wide range of tests that could be alternatives to RT-PCR methods, further research is needed to assess the performance of alternative COVID-19 tests and their role in pandemic management.
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Affiliation(s)
- Ingrid Arevalo-Rodriguez
- Clinical Biostatistics Unit, Hospital Universitario Ramón y Cajal (IRYCIS). CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Evidence Production & Methods Directorate, Cochrane, London, UK
| | - Miriam Mateos-Haro
- Clinical Biostatistics Unit, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- Doctoral programme in Clinical Medicine and Public Health, Universidad de Granada, Granada, Spain
| | - Jacqueline Dinnes
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Agustín Ciapponi
- Argentine Cochrane Centre, Institute for Clinical Effectiveness and Health Policy (IECS-CONICET), Buenos Aires, Argentina
| | - Clare Davenport
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Diana Buitrago-Garcia
- Institute for Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Hospital Universitario Mayor - Méderi. Universidad del Rosario, Bogotá, Colombia
| | - Tayeb Bennouna-Dalero
- Preventive Medicine and Public Health Department, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Marta Roqué-Figuls
- Iberoamerican Cochrane Centre, Institut de Recerca Sant Pau (IR SANT PAU), CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | | | - Karin J von Eije
- Department of Viroscience, ErasmusMC, University Medical Center, Rotterdam, Netherlands
| | | | - Lotty Hooft
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - René Spijker
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Mariska Mg Leeflang
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Yemisi Takwoingi
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Jonathan J Deeks
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
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Segura-Ulate I, Apú N, Cortés B, Querol-Audi J, Zaldívar Y, Ortega CA, Flores-Mora F, Gatica-Arias A, Madrigal-Redondo G. Cross comparison of alternative diagnostic protocols including substitution to the clinical sample, RNA extraction method and nucleic acid amplification technology for COVID-19 diagnosis. Front Mol Biosci 2024; 11:1445142. [PMID: 39247206 PMCID: PMC11377848 DOI: 10.3389/fmolb.2024.1445142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 07/31/2024] [Indexed: 09/10/2024] Open
Abstract
Background the gold-standard diagnostic protocol (GSDP) for COVID-19 consists of a nasopharyngeal swab (NPS) sample processed through traditional RNA extraction (TRE) and amplified with retrotranscription quantitative polymerase chain reaction (RT-qPCR). Multiple alternatives were developed to decrease time/cost of GSDP, including alternative clinical samples, RNA extraction methods and nucleic acid amplification. Thus, we carried out a cross comparison of various alternatives methods against GSDP and each other. Methods we tested alternative diagnostic methods using saliva, heat-induced RNA release (HIRR) and a colorimetric retrotranscription loop-mediated isothermal amplification (RT-LAMP) as substitutions to the GSDP. Results RT-LAMP using NPS processed by TRE showed high sensitivity (96%) and specificity (97%), closely matching GSDP. When saliva was processed by TRE and amplified with both RT-LAMP and RT-qPCR, RT-LAMP yielded high diagnostic parameters (88%-96% sensitivity and 95%-100% specificity) compared to RT-qPCR. Nonetheless, when saliva processed by TRE and detected by RT-LAMP was compared against the GSDP, the resulting diagnostic values for sensitivity (78%) and specificity (87%) were somewhat high but still short of those of the GSDP. Finally, saliva processed with HIRR and detected via RT-LAMP was the simplest and fastest method, but its sensitivity against GSDP was too low (56%) for any clinical application. Also, in this last method, the acidity of a large percentage of saliva samples (9%-22%) affected the pH-sensitive colorimetric indicator used in the test, requiring the exclusion of these acidic samples or an extra step for pH correction. Discussion our comparison shows that RT-LAMP technology has diagnostic performance on par with RT-qPCR; likewise, saliva offers the same diagnostic functionality as NPS when subjected to a TRE method. Nonetheless, use of direct saliva after a HIRR and detected with RT-LAMP does not produce an acceptable diagnostic performance.
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Affiliation(s)
- Ismael Segura-Ulate
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica
| | - Navilla Apú
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica
| | - Bernal Cortés
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | - Jordi Querol-Audi
- Laboratorio de Microbiología Experimental y Aplicada (LAMEXA), Universidad de Panamá, Ciudad de Panamá, Panama
- Sistema Nacional de Investigación (SNI), SENACYT, Ciudad de Panamá, Panama
| | - Yamitzel Zaldívar
- Instituto Conmemorativo Gorgas de Estudio de la Salud, Ciudad de Panamá, Panama
| | - Carlos Alexander Ortega
- Sección de Virología, Facultad de Medicina, Universidad de El Salvador, San Salvador, El Salvador
| | - Fernando Flores-Mora
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica
| | - Andrés Gatica-Arias
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | - Germán Madrigal-Redondo
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica
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Turbawaty DK, Sudjadi A, Lismayanti L, Rostini T, Logito V. The Performance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Virus Using the Colorimetric Reverse-Transcription Loop Mediated Isothermal Amplification (RT-LAMP) Method in Saliva Specimens of Suspected COVID-19 Patients. Int J Gen Med 2024; 17:3329-3335. [PMID: 39081671 PMCID: PMC11288315 DOI: 10.2147/ijgm.s461613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 07/09/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction Corona Virus Disease-19 (COVID-19) is a disease caused by Severe-Acute-Respiratory-Syndrome-Coronavirus-2 (SARS-CoV-2). The most reliable and widely accepted method for diagnosing this infection, despite facing various challenges, is the Reverse Transcription Polymerase Chain Reaction (RT-PCR) method, which utilizes nasopharyngeal swab sample. Reverse-transcription loop mediated isothermal amplification (RT-LAMP) is a simpler nucleic acid amplification method compared to the RT-PCR method. This method has several advantages, including: of amplification at constant temperature, faster results, and potentially greater examination capacity. Purpose This study aimed to compare the validity of the RT-LAMP method using saliva specimens with that of the RT-PCR method using nasopharyngeal smears. Methods This was an analytical observational study with a cross-sectional design. The participants were inpatients in the COVID-19 special isolation building of Hasan Sadikin General Hospital, Indonesia with a probable (clinical symptoms of covid, but not confirm NAAT examination) or confirmed diagnosis of COVID-19 from September 2021 to February 2022. The inclusion criteria are COVID-19 patients with symptoms, adult subjects, and composite mentions. Patients who were unable to secrete saliva were also excluded. Results In total, 118 specimens were collected. The validity test results of the saliva specimens using the RT-LAMP method showed sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV), of 65.5%, 100%, 100%, and 75%, respectively. The results increased in subjects treated between 3 and 7 days after symptom onset ie 73.2%, 100%, 100%, and 82.3%, respectively. Conclusion The very strong specificity accompanied by good sensitivity and NPV in the group of subjects treated 3-7 days after the onset of symptoms indicates that the RT-LAMP method using saliva specimens can be an efficient and reliable alternative tool in detecting the SARS-CoV-2 virus.
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Affiliation(s)
- Dewi Kartika Turbawaty
- Department of Clinical Pathology, Faculty of Medicine Padjadjaran University/ Dr. Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
| | - Andy Sudjadi
- Department of Clinical Pathology, Faculty of Medicine Padjadjaran University/ Dr. Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
| | - Leni Lismayanti
- Department of Clinical Pathology, Faculty of Medicine Padjadjaran University/ Dr. Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
| | - Tiene Rostini
- Department of Clinical Pathology, Faculty of Medicine Padjadjaran University/ Dr. Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
| | - Verina Logito
- Department of Clinical Pathology, Faculty of Medicine Padjadjaran University/ Dr. Hasan Sadikin General Hospital, Bandung, West Java, Indonesia
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Abugattas-Núñez del Prado J, Quintana Reyes A, Leon J, Blume La Torre J, Gutiérrez Loli R, Pinzón Olejua A, Chamorro Chirinos ER, Loza Mauricio FA, Maguiña JL, Rodriguez-Aliaga P, Málaga-Trillo E. Clinical validation of RCSMS: A rapid and sensitive CRISPR-Cas12a test for the molecular detection of SARS-CoV-2 from saliva. PLoS One 2024; 19:e0290466. [PMID: 38527001 PMCID: PMC10962837 DOI: 10.1371/journal.pone.0290466] [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: 03/14/2023] [Accepted: 08/08/2023] [Indexed: 03/27/2024] Open
Abstract
Peru's holds the highest COVID death rate per capita worldwide. Key to this outcome is the lack of robust, rapid, and accurate molecular tests to circumvent the elevated costs and logistics of SARS-CoV-2 detection via RT-qPCR. To facilitate massive and timely COVID-19 testing in rural and socioeconomically deprived contexts, we implemented and validated RCSMS, a rapid and sensitive CRISPR-Cas12a test for the molecular detection of SARS-CoV-2 from saliva. RCSMS uses the power of CRISPR-Cas technology and lateral flow strips to easily visualize the presence of SARS-CoV-2 even in laboratories with limited equipment. We show that a low-cost thermochemical treatment with TCEP/EDTA is sufficient to inactivate viral particles and cellular nucleases in saliva, eliminating the need to extract viral RNA with commercial kits, as well as the cumbersome nasopharyngeal swab procedure and the requirement of biosafety level 2 laboratories for molecular analyses. Notably, RCSMS performed outstandingly in a clinical validation done with 352 patients from two hospitals in Lima, detecting as low as 50 viral copies per 10 μl reaction in 40 min, with sensitivity and specificity of 96.5% and 99.0%, respectively, relative to RT-qPCR. The negative and positive predicted values obtained from this field validation indicate that RCSMS can be confidently deployed in both high and low prevalence settings. Like other CRISPR-Cas-based biosensors, RCSMS can be easily reprogrammed for the detection of new SARS-CoV-2 variants. We conclude that RCSMS is a fast, efficient and inexpensive alternative to RT-qPCR for expanding COVID-19 testing capacity in Peru and other low- and middle-income countries with precarious healthcare systems.
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Affiliation(s)
| | | | - Julio Leon
- IMS RIKEN Center for Integrative Medical Sciences, Japan
- University of California San Francisco, San Francisco, California, United States of America
| | - Juan Blume La Torre
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Renzo Gutiérrez Loli
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | | | | | - Jorge L. Maguiña
- Instituto de Evaluación de Tecnologías en Salud e Investigación (IETSI), EsSalud, Lima, Perú
| | - Piere Rodriguez-Aliaga
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Edward Málaga-Trillo
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
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Li Z, Sinha A, Zhang Y, Tanner N, Cheng HT, Premsrirut P, Carlow CKS. Extraction-free LAMP assays for generic detection of Old World Orthopoxviruses and specific detection of Mpox virus. Sci Rep 2023; 13:21093. [PMID: 38036581 PMCID: PMC10689478 DOI: 10.1038/s41598-023-48391-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/26/2023] [Indexed: 12/02/2023] Open
Abstract
Mpox is a neglected zoonotic disease endemic in West and Central Africa. The Mpox outbreak with more than 90,000 cases worldwide since 2022 generated great concern about future outbreaks and highlighted the need for a simple and rapid diagnostic test. The Mpox virus, MPV, is a member of the Orthopoxvirus (OPV) genus that also contains other pathogenic viruses including variola virus, vaccinia virus, camelpox virus, and cowpox virus. Phylogenomic analysis of 200 OPV genomes identified 10 distinct phylogroups with the New World OPVs placed on a very long branch distant from the Old World OPVs. Isolates derived from infected humans were found to be distributed across multiple phylogroups interspersed with isolates from animal sources, indicating the zoonotic potential of these viruses. In this study, we developed a simple and sensitive colorimetric LAMP assay for generic detection of Old World OPVs. We also developed an MPV-specific probe that differentiates MPV from other OPVs in the N1R LAMP assay. In addition, we described an extraction-free protocol for use directly with swab eluates in LAMP assays, thereby eliminating the time and resources needed to extract DNA from the sample. Our direct LAMP assays are well-suited for low-resource settings and provide a valuable tool for rapid and scalable diagnosis and surveillance of OPVs and MPV.
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Affiliation(s)
- Zhiru Li
- Molecular Genetics and Genomics Division, New England Biolabs, Ipswich, MA, 01938, USA.
| | - Amit Sinha
- Molecular Genetics and Genomics Division, New England Biolabs, Ipswich, MA, 01938, USA
| | - Yinhua Zhang
- Molecular Genetics and Genomics Division, New England Biolabs, Ipswich, MA, 01938, USA
| | - Nathan Tanner
- Molecular Genetics and Genomics Division, New England Biolabs, Ipswich, MA, 01938, USA
| | | | | | - Clotilde K S Carlow
- Molecular Genetics and Genomics Division, New England Biolabs, Ipswich, MA, 01938, USA
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Sritong N, Ngo WW, Ejendal KFK, Linnes JC. Development of an Integrated Sample Amplification Control for Salivary Point-of-Care Pathogen Testing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.03.23296477. [PMID: 37873363 PMCID: PMC10593008 DOI: 10.1101/2023.10.03.23296477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background The COVID-19 pandemic has led to a rise in point-of-care (POC) and home-based tests, but concerns over usability, accuracy, and effectiveness have arisen. The incorporation of internal amplification controls (IACs), essential control for translational POC diagnostics, could mitigate false-negative and false-positive results due to sample matrix interference or inhibition. Although emerging POC nucleic acid amplification tests (NAATs) for detecting SARS-CoV-2 show impressive analytical sensitivity in the lab, the assessment of clinical accuracy with IACs is often overlooked. In some cases, the IACs were run spatially, complicating assay workflow. Therefore, the multiplex assay for pathogen and IAC is needed. Results We developed a one-pot duplex reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for saliva samples, a non-invasive and simple collected specimen for POC NAATs. The ORF1ab gene of SARS-CoV-2 was used as a target and a human 18S ribosomal RNA in human saliva was employed as an IAC to ensure clinical reliability of the RT-LAMP assay. The optimized assay could detect SARS-CoV-2 viral particles down to 100 copies/μL of saliva within 30 minutes without RNA extraction. The duplex RT-LAMP for SARS-CoV-2 and IAC is successfully amplified in the same reaction without cross-reactivity. The valid results were easily visualized in triple-line lateral flow immunoassay, in which two lines (flow control and IAC lines) represent valid negative results and three lines (flow control, IAC, and test line) represent valid positive results. This duplex assay demonstrated a clinical sensitivity of 95%, specificity of 100%, and accuracy of 96% in 30 clinical saliva samples. Significance IACs play a crucial role in ensuring user confidence with respect to the accuracy and reliability of at-home and POC molecular diagnostics. We demonstrated the multiplex capability of SARS-COV-2 and human18S ribosomal RNA RT-LAMP without complicating assay design. This generic platform can be extended in a similar manner to include human18S ribosomal RNA IACs into different clinical sample matrices.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Winston Wei Ngo
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Karin F. K. Ejendal
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Jacqueline C. Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Department of Public Health, Purdue University, West Lafayette, IN, USA
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9
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Liu Y, Kumblathan T, Tao J, Xu J, Feng W, Xiao H, Hu J, Huang CV, Wu Y, Zhang H, Li XF, Le XC. Recent advances in RNA sample preparation techniques for the detection of SARS-CoV-2 in saliva and gargle. Trends Analyt Chem 2023; 165:117107. [PMID: 37317683 PMCID: PMC10204347 DOI: 10.1016/j.trac.2023.117107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Molecular detection of SARS-CoV-2 in gargle and saliva complements the standard analysis of nasopharyngeal swabs (NPS) specimens. Although gargle and saliva specimens can be readily obtained non-invasively, appropriate collection and processing of gargle and saliva specimens are critical to the accuracy and sensitivity of the overall analytical method. This review highlights challenges and recent advances in the treatment of gargle and saliva samples for subsequent analysis using reverse transcription polymerase chain reaction (RT-PCR) and isothermal amplification techniques. Important considerations include appropriate collection of gargle and saliva samples, on-site inactivation of viruses in the sample, preservation of viral RNA, extraction and concentration of viral RNA, removal of substances that inhibit nucleic acid amplification reactions, and the compatibility of sample treatment protocols with the subsequent nucleic acid amplification and detection techniques. The principles and approaches discussed in this review are applicable to molecular detection of other microbial pathogens.
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Affiliation(s)
- Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jingyang Xu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Huyan Xiao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Camille V Huang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yiping Wu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
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10
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Sritong N, Sala de Medeiros M, Basing LA, Linnes JC. Promise and perils of paper-based point-of-care nucleic acid detection for endemic and pandemic pathogens. LAB ON A CHIP 2023; 23:888-912. [PMID: 36688463 PMCID: PMC10028599 DOI: 10.1039/d2lc00554a] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
From HIV and influenza to emerging pathogens like COVID-19, each new infectious disease outbreak has highlighted the need for massively-scalable testing that can be performed outside centralized laboratory settings at the point-of-care (POC) in order to prevent, track, and monitor endemic and pandemic threats. Nucleic acid amplification tests (NAATs) are highly sensitive and can be developed and scaled within weeks while protein-based rapid tests require months for production. Combining NAATs with paper-based detection platforms are promising due to the manufacturability, scalability, and simplicity of each of these components. Typically, paper-based NAATs consist of three sequential steps: sample collection and preparation, amplification of DNA or RNA from pathogens of interest, and detection. However, these exist within a larger ecosystem of sample collection and interpretation workflow, usability, and manufacturability which can be vastly perturbed during a pandemic emergence. This review aims to explore the challenges of paper-based NAATs covering sample-to-answer procedures along with three main types of clinical samples; blood, urine, and saliva, as well as broader operational, scale up, and regulatory aspects of device development and implementation. To fill the technological gaps in paper-based NAATs, a sample-in-result-out system that incorporates the integrated sample collection, sample preparation, and integrated internal amplification control while also balancing needs of users and manufacturability upfront in the early design process is required.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | | | - Laud Anthony Basing
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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11
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Tan SH, Allicock OM, Katamba A, Carrington CVF, Wyllie AL, Armstrong-Hough M. Saliva-based methods for SARS-CoV-2 testing in low- and middle-income countries. Bull World Health Organ 2022; 100:808-814. [PMID: 36466209 PMCID: PMC9706358 DOI: 10.2471/blt.22.288526] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/04/2022] [Accepted: 08/26/2022] [Indexed: 12/05/2022] Open
Abstract
As the coronavirus disease 2019 (COVID-19) continues to disproportionately affect low- and middle-income countries, the need for simple, accessible and frequent diagnostic testing grows. In lower-resource settings, case detection is often limited by a lack of available testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To address global inequities in testing, alternative sample types could be used to increase access to testing by reducing the associated costs. Saliva is a sensitive, minimally invasive and inexpensive diagnostic sample for SARS-CoV-2 detection that is appropriate for asymptomatic surveillance, symptomatic testing and at-home collection. Saliva testing can lessen two major challenges faced by lower- and middle-income countries: constrained resources and overburdened health workers. Saliva sampling enables convenient self-collection and requires fewer resources than swab-based methods. However, saliva testing for SARS-CoV-2 diagnostics has not been implemented on a large scale in low- and middle-income countries. While numerous studies based in these settings have demonstrated the usefulness of saliva sampling, there has been insufficient attention on optimizing its implementation in practice. We argue that implementation science research is needed to bridge this gap between evidence and practice. Low- and middle-income countries face many barriers as they continue their efforts to provide mass COVID-19 testing in the face of substantial inequities in global access to vaccines. Laboratories should look to replicate successful approaches for sensitive detection of SARS-CoV-2 in saliva, while governments should act to facilitate mass testing by lifting restrictions that limit implementation of saliva-based methods.
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Affiliation(s)
- Steph H Tan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St, New Haven, CT06510, United States of America (USA)
| | - Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St, New Haven, CT06510, United States of America (USA)
| | - Achilles Katamba
- Uganda TB Implementation Research Consortium, Makerere University, Kampala, Uganda
| | - Christine V F Carrington
- Department of Preclinical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St, New Haven, CT06510, United States of America (USA)
| | - Mari Armstrong-Hough
- Departments of Social & Behavioral Science and Epidemiology, New York University School of Global Public Health, New York, USA
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12
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The Future of Point-of-Care Nucleic Acid Amplification Diagnostics after COVID-19: Time to Walk the Walk. Int J Mol Sci 2022; 23:ijms232214110. [PMID: 36430586 PMCID: PMC9693045 DOI: 10.3390/ijms232214110] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
Since the onset of the COVID-19 pandemic, over 610 million cases have been diagnosed and it has caused over 6.5 million deaths worldwide. The crisis has forced the scientific community to develop tools for disease control and management at a pace never seen before. The control of the pandemic heavily relies in the use of fast and accurate diagnostics, that allow testing at a large scale. The gold standard diagnosis of viral infections is the RT-qPCR. Although it provides consistent and reliable results, it is hampered by its limited throughput and technical requirements. Here, we discuss the main approaches to rapid and point-of-care diagnostics based on RT-qPCR and isothermal amplification diagnostics. We describe the main COVID-19 molecular diagnostic tests approved for self-testing at home or for point-of-care testing and compare the available options. We define the influence of specimen selection and processing, the clinical validation, result readout improvement strategies, the combination with CRISPR-based detection and the diagnostic challenge posed by SARS-CoV-2 variants for different isothermal amplification techniques, with a particular focus on LAMP and recombinase polymerase amplification (RPA). Finally, we try to shed light on the effect the improvement in molecular diagnostics during the COVID-19 pandemic could have in the future of other infectious diseases.
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13
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Efficient multiplexing and variant discrimination in reverse-transcription loop-mediated isothermal amplification with sequence-specific hybridization probes. Biotechniques 2022; 73:247-255. [DOI: 10.2144/btn-2022-0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) has proven a robust and reliable nucleic acid amplification method that is well suited for simplified and rapid molecular diagnostics. Various approaches have emerged for sequence-specific detection of LAMP products, but with limitations to their widespread utility or applicability for single-nucleotide polymorphism detection and multiplexing. Here we demonstrate the use of simple hybridization probes (as used for qPCR) that enable simple multiplexing and SARS-CoV-2 variant typing in reverse-transcription LAMP. This approach requires no modification to the LAMP primers and is amenable to the detection of single-nucleotide polymorphisms and small sequence changes, which is usually difficult in LAMP. By extending LAMP’s ability to be utilized for multitarget and single-base change detection, we hope to increase its potential to enable more and better molecular diagnostic testing.
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14
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Bei Y, Pinet K, Vrtis KB, Borgaro JG, Sun L, Campbell M, Apone L, Langhorst BW, Nichols NM. Overcoming variant mutation-related impacts on viral sequencing and detection methodologies. Front Med (Lausanne) 2022; 9:989913. [PMID: 36388914 PMCID: PMC9650041 DOI: 10.3389/fmed.2022.989913] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/05/2022] [Indexed: 11/30/2022] Open
Abstract
Prompt and accurate pathogen identification, by diagnostics and sequencing, is an effective tool for tracking and potentially curbing pathogen spread. Targeted detection and amplification of viral genomes depends on annealing complementary oligonucleotides to genomic DNA or cDNA. However, genomic mutations that occur during viral evolution may perturb annealing, which can result in incomplete sequence coverage of the genome and/or false negative diagnostic test results. Herein, we demonstrate how to assess, test, and optimize sequencing and detection methodologies to attenuate the negative impact of mutations on genome targeting efficiency. This evaluation was conducted using in vitro-transcribed (IVT) RNA as well as RNA extracted from clinical SARS-CoV-2 variant samples, including the heavily mutated Omicron variant. Using SARS-CoV-2 as a current example, these results demonstrate how to maintain reliable targeted pathogen sequencing and how to evaluate detection methodologies as new variants emerge.
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15
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Improved visual detection of DNA amplification using pyridylazophenol metal sensing dyes. Commun Biol 2022; 5:999. [PMID: 36130997 PMCID: PMC9491268 DOI: 10.1038/s42003-022-03973-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
Detection of nucleic acid amplification has typically required sophisticated laboratory instrumentation, but as the amplification techniques have moved away from the lab, complementary detection techniques have been implemented to facilitate point-of-care, field, and even at-home applications. Simple visual detection approaches have been widely used for isothermal amplification methods, but have generally displayed weak color changes or been highly sensitive to sample and atmospheric effects. Here we describe the use of pyridylazophenol dyes and binding to manganese ion to produce a strong visible color that changes in response to nucleic acid amplification. This detection approach is easily quantitated with absorbance, rapidly and clearly visible by eye, robust to sample effects, and notably compatible with both isothermal and PCR amplification. Nucleic acid amplification and molecular diagnostic methods are being used in an increasing number of novel applications and settings, and the ability to reliably and sensitively detect them without the need for additional instrumentation will enable even more access to these powerful techniques.
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