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Lee SS, Kim AL, Park JH, Lee DH, Bae YK. Optimization of duplex digital PCR for the measurement of SARS-CoV-2 RNA. J Virol Methods 2024; 326:114911. [PMID: 38447644 DOI: 10.1016/j.jviromet.2024.114911] [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] [Received: 11/28/2023] [Revised: 01/19/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
Quantitative PCR (qPCR) is the gold standard for detecting nucleic acid sequences specific to the target pathogen. For COVID-19 diagnosis, several molecular assays have been developed. In this study, we present an optimization strategy for the measurement of SARS-CoV-2 RNA via multiplex qPCR and digital PCR (dPCR). Compared to qPCR, both droplet and chip-based dPCR, which are known to be more sensitive and accurate, showed a better resilience to suboptimal assay compositions and cycling conditions following the proposed optimizations. In particular, the formation of heterodimers among assays greatly interfered with qPCR results, but only minimally with dPCR results. In dPCR, existing heterodimers lowered the PCR efficiency, producing a dampened fluorescent signal in positive partitions. This can be corrected by adjusting the PCR cycling conditions, after which dPCR shows the capability of measuring the expected copy number. In addition, we present a process to improve the existing RdRp assay by correcting the primer sequences and matching the melting temperature, ultimately producing highly sensitive and robust assays. The results of this study can reduce the cost and time of SARS-CoV-2 diagnosis while increasing accuracy. Furthermore, our results suggest that dPCR is a reliable method for the accurate measurement of nucleic acid targets.
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Affiliation(s)
- Sang-Soo Lee
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Ah Leum Kim
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| | - Jae-Hyung Park
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Da-Hye Lee
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea.
| | - Young-Kyung Bae
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea.
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2
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Hastie E, Amogan H, Looney D, Mehta SR. Nasopharyngeal SARS-CoV-2 viral load kinetics using digital PCR. Heliyon 2023; 9:e20739. [PMID: 37876488 PMCID: PMC10590800 DOI: 10.1016/j.heliyon.2023.e20739] [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: 04/20/2023] [Revised: 10/01/2023] [Accepted: 10/05/2023] [Indexed: 10/26/2023] Open
Abstract
Background The relationship between the viral kinetics of SARS-CoV-2 and clinical outcomes remains unclear. Methods A convenience sample of 955 remnant nasopharyngeal swabs collected during routine care between 11/18/20 and 9/26/21 were analyzed using digital PCR and associated clinical data extracted from the medical record. 18 individuals had >1 sample within 30 days of onset of symptoms. Results Paired samples were an average of 6 [range: 0-13] days apart. Four individuals sampled twice on the same day had a median 0.52 log10 viral load difference between samples. Of the remaining, 12 individuals had a decrease in viral load over time, with an average decay of -0.23 log10/day. Conclusions Our study found a similar rate of viral decay to others, but did not find associations between viral kinetics and clinical outcomes. Larger studies would be useful to support the use of this measurement as a surrogate endpoint for therapeutic studies.
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Affiliation(s)
- Elizabeth Hastie
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, 9500 Gilman Drive, CA, 92093, USA
| | - Harold Amogan
- Veterans Medical Research Foundation, 3350 La Jolla Village Drive, San Diego, CA, 92163, USA
| | - David Looney
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, 9500 Gilman Drive, CA, 92093, USA
- San Diego Veterans Affairs Medical Center, San Diego, CA, 92163, USA
| | - Sanjay R. Mehta
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, 9500 Gilman Drive, CA, 92093, USA
- San Diego Veterans Affairs Medical Center, San Diego, CA, 92163, USA
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3
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Al-Shaibari KSA, Mousa HAL, Alqumber MAA, Alqfail KA, Mohammed A, Bzeizi K. The Diagnostic Performance of Various Clinical Specimens for the Detection of COVID-19: A Meta-Analysis of RT-PCR Studies. Diagnostics (Basel) 2023; 13:3057. [PMID: 37835801 PMCID: PMC10572802 DOI: 10.3390/diagnostics13193057] [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: 06/10/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND The diagnostic performance of numerous clinical specimens to diagnose COVID-19 through RT-PCR techniques is very important, and the test result outcome is still unclear. This review aimed to analyze the diagnostic performance of clinical samples for COVID-19 detection by RT-PCR through a systematic literature review process. METHODOLOGY A compressive literature search was performed in PubMed/Medline, Scopus, Embase, and Cochrane Library from inception to November 2022. A snowball search on Google, Google Scholar, Research Gate, and MedRxiv, as well as bibliographic research, was performed to identify any other relevant articles. Observational studies that assessed the clinical usefulness of the RT-PCR technique in different human samples for the detection or screening of COVID-19 among patients or patient samples were considered for this review. The primary outcomes considered were sensitivity and specificity, while parameters such as positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient were considered secondary outcomes. RESULTS A total of 85 studies out of 10,213 non-duplicate records were included for the systematic review, of which 69 articles were considered for the meta-analysis. The meta-analysis indicated better pooled sensitivity with the nasopharyngeal swab (NPS) than saliva (91.06% vs. 76.70%) and was comparable with the combined NPS/oropharyngeal swab (OPS; 92%). Nevertheless, specificity was observed to be better with saliva (98.27%) than the combined NPS/OPS (98.08%) and NPS (95.57%). The other parameters were comparable among different samples. The respiratory samples and throat samples showed a promising result relative to other specimens. The sensitivity and specificity of samples such as nasopharyngeal swabs, saliva, combined nasopharyngeal/oropharyngeal, respiratory, sputum, broncho aspirate, throat swab, gargle, serum, and the mixed sample were found to be 91.06%, 76.70%, 92.00%, 99.44%, 86%, 96%, 94.4%, 95.3%, 73.63%, and above 98; and 95.57%, 98.27%, 98.08%, 100%, 37%, 100%, 100%, 97.6%, and above 97, respectively. CONCLUSIONS NPS was observed to have relatively better sensitivity, but not specificity when compared with other clinical specimens. Head-to-head comparisons between the different samples and the time of sample collection are warranted to strengthen this evidence.
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Affiliation(s)
| | | | | | | | | | - Khalid Bzeizi
- Department of Liver Transplantation, King Faisal Specialist Hospital and Research Center, Riyadh 13541, Saudi Arabia
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4
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Hastie E, Amogan H, Looney D, Mehta SR. Association between SARS-CoV-2 Viral Load and Patient Symptoms and Clinical Outcomes Using Droplet Digital PCR. Viruses 2023; 15:446. [PMID: 36851660 PMCID: PMC9961727 DOI: 10.3390/v15020446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
The association between nasopharyngeal (NP) SARS-CoV-2 viral loads and clinical outcomes remains debated. Here, we examined the factors that might predict the NP viral load and the role of the viral load as a predictor of clinical outcomes. A convenience sample of 955 positive remnant NP swab eluent samples collected during routine care between 18 November 2020 and 26 September 2021 was cataloged and a chart review was performed. For non-duplicate samples with available demographic and clinical data (i.e., non-employees), an aliquot of eluent was sent for a droplet digital PCR quantification of the SARS-CoV-2 viral load. Univariate and multivariate analyses were performed to identify the clinical predictors of NP viral loads and the predictors of COVID-19-related clinical outcomes. Samples and data from 698 individuals were included in the final analysis. The sample cohort had a mean age of 50 years (range: 19-91); 86.6% were male and 76.3% were unvaccinated. The NP viral load was higher in people with respiratory symptoms (p = 0.0004) and fevers (p = 0.0006). In the predictive models for the clinical outcomes, the NP viral load approached a significance as a predictor for in-hospital mortality. In conclusion, the NP viral load did not appear to be a strong predictor of moderate-to-severe disease in the pre-Delta and Delta phases of the pandemic, but was predictive of symptomatic diseases and approached a significance for in-hospital mortality, providing support to the thesis that early viral control prevents the progression of disease.
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Affiliation(s)
- Elizabeth Hastie
- Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA 92039, USA
| | - Harold Amogan
- Veterans Medical Research Foundation, San Diego, CA 92161, USA
| | - David Looney
- Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA 92039, USA
- San Diego Veterans Affairs Medical Center, Department of Medicine, San Diego, CA 92161, USA
| | - Sanjay R. Mehta
- Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA 92039, USA
- San Diego Veterans Affairs Medical Center, Department of Medicine, San Diego, CA 92161, USA
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5
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Xie L, Li J, Ai Y, He H, Chen X, Yin M, Li W, Huang W, Luo MY, He J. Current strategies for SARS-CoV-2 molecular detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4625-4642. [PMID: 36349688 DOI: 10.1039/d2ay01313d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The molecular detection of SARS-CoV-2 is extremely important for the discovery and prevention of pandemic dissemination. Because SARS-CoV-2 is not always present in the samples that can be collected, the sample chosen for testing has inevitably become the key to the SARS-CoV-2 positive cases screening. The nucleotide amplification strategy mainly includes Q-PCR assays and isothermal amplification assays. The Q-PCR assay is the most used SARS-CoV-2 detection assay. Due to heavy expenditures and other drawbacks, isothermal amplification cannot replace the dominant position of the Q-PCR assay. The antibody-based detection combined with Q-PCR can help to find more positive cases than only using nucleotide amplification-based assays. Pooled testing based on Q-PCR significantly increases efficiency and reduces the cost of massive-scale screening. The endless stream of variants emerging across the world poses a great challenge to SARS-CoV-2 molecular detection. The multi-target assays and several other strategies have proved to be efficient in the detection of mutated SARS-CoV-2 variants. Further research work should concentrate on: (1) identifying more ideal sample plucking strategies, (2) ameliorating the Q-PCR primer and probes targeted toward mutated SARS-CoV-2 variants, (3) exploring more economical and precise isothermal amplification assays, and (4) developing more advanced strategies for antibody/antigen or engineered antibodies to ameliorate the antibody/antigen-based strategy.
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Affiliation(s)
- Lei Xie
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Junlin Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Ying Ai
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510080, China
| | - Haolan He
- Guangzhou Eighth People's Hospital, Guangzhou 510080, China
| | - Xiuyun Chen
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Mingyu Yin
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Wanxi Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Wenguan Huang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Min-Yi Luo
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Jinyang He
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
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6
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Development and validation of methods that enable high-quality droplet digital PCR and hematological profiling data from microvolume blood samples. Bioanalysis 2022; 14:1197-1211. [PMID: 36331037 DOI: 10.4155/bio-2022-0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aim: Mouse models have been crucial to preclinical studies in the increasingly relevant fields of cell and gene therapy. However, only small quantities of mouse blood can be collected without producing adverse physiological effects that compromise data integrity. Results: To address this limitation, two combined methods were developed to create detailed droplet digital PCR (ddPCR) and hematological profiles using only ∼20 μl of mouse blood. The validation of these methods, which can serve as a foundation for a standardized regulatory pipeline for ddPCR, is discussed. Even when using small amounts of input, this ddPCR protocol is accurate, precise, selective, specific, stable and robust. Conclusion: These techniques enable more frequent sample collection for higher-resolution pharmacokinetic data that meets or exceeds quality standards.
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Truyols Vives J, Muncunill J, Toledo Pons N, Baldoví HG, Sala Llinàs E, Mercader Barceló J. SARS-CoV-2 detection in bioaerosols using a liquid impinger collector and ddPCR. INDOOR AIR 2022; 32:e13002. [PMID: 35225399 PMCID: PMC9111801 DOI: 10.1111/ina.13002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
The airborne route is the dominant form of COVID-19 transmission, and therefore, the development of methodologies to quantify SARS-CoV-2 in bioaerosols is needed. We aimed to identify SARS-CoV-2 in bioaerosols by using a highly efficient sampler for the collection of 1-3 µm particles, followed by a highly sensitive detection method. 65 bioaerosol samples were collected in hospital rooms in the presence of a COVID-19 patient using a liquid impinger sampler. The SARS-CoV-2 genome was detected by ddPCR using different primer/probe sets. 44.6% of the samples resulted positive for SARS-CoV-2 following this protocol. By increasing the sampled air volume from 339 to 650 L, the percentage of positive samples went from 41% to 50%. We detected five times less positives with a commercial one-step RT-PCR assay. However, the selection of primer/probe sets might be one of the most determining factor for bioaerosol SARS-CoV-2 detection since with the ORF1ab set more than 40% of the samples were positive, compared to <10% with other sets. In conclusion, the use of a liquid impinger collector and ddPCR is an adequate strategy to detect SARS-CoV-2 in bioaerosols. However, there are still some methodological aspects that must be adjusted to optimize and standardize a definitive protocol.
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Affiliation(s)
- Joan Truyols Vives
- Molecular Biology and One Health research group (MolONE)Universitat de les Illes Balears (UIB)PalmaSpain
| | - Josep Muncunill
- Health Research Institute of the Balearic Islands (IdISBa)Balearic IslandsSpain
| | - Núria Toledo Pons
- Health Research Institute of the Balearic Islands (IdISBa)Balearic IslandsSpain
- Department of Pulmonary MedicineHospital Universitari Son Espases (HUSE)Balearic IslandsSpain
| | - Herme G. Baldoví
- Department of ChemistryUniversitat Politècnica de València (UPV)ValenciaSpain
| | - Ernest Sala Llinàs
- Molecular Biology and One Health research group (MolONE)Universitat de les Illes Balears (UIB)PalmaSpain
- Health Research Institute of the Balearic Islands (IdISBa)Balearic IslandsSpain
- Department of Pulmonary MedicineHospital Universitari Son Espases (HUSE)Balearic IslandsSpain
- Biomedical Research Networking Center on Respiratory Diseases (CIBERES)MadridSpain
| | - Josep Mercader Barceló
- Molecular Biology and One Health research group (MolONE)Universitat de les Illes Balears (UIB)PalmaSpain
- Health Research Institute of the Balearic Islands (IdISBa)Balearic IslandsSpain
- Foners Medicina Veterinària i Innovació SLPPalmaSpain
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8
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Mio C, Dal Secco C, Marzinotto S, Pipan C, Sozio E, Tascini C, Damante G, Curcio F. Monitoring the SPREAD of the SARS-CoV-2 lineage B.1.621 in Udine, Italy. J Clin Pathol 2021; 75:jclinpath-2021-207810. [PMID: 34911747 PMCID: PMC9510432 DOI: 10.1136/jclinpath-2021-207810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/21/2021] [Indexed: 12/24/2022]
Affiliation(s)
- Catia Mio
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Chiara Dal Secco
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Stefania Marzinotto
- Department of Laboratory Medicine, Udine University Health Integrated Agency, Udine, Italy
| | - Corrado Pipan
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Laboratory Medicine, Udine University Health Integrated Agency, Udine, Italy
| | - Emanuela Sozio
- Clinic of Infectious Diseases, Udine University Health Integrated Agency, Udine, Italy
| | - Carlo Tascini
- Clinic of Infectious Diseases, Udine University Health Integrated Agency, Udine, Italy
| | - Giuseppe Damante
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Laboratory Medicine, Udine University Health Integrated Agency, Udine, Italy
| | - Francesco Curcio
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Laboratory Medicine, Udine University Health Integrated Agency, Udine, Italy
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9
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Mio C, Dal Secco C, Marzinotto S, Bruno C, Pimpo S, Betto E, Bertoni M, Pipan C, Sozio E, Tascini C, Damante G, Curcio F. Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. PLoS One 2021; 16:e0261229. [PMID: 34905574 PMCID: PMC8670677 DOI: 10.1371/journal.pone.0261229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/24/2021] [Indexed: 11/27/2022] Open
Abstract
In-depth study of the entire SARS-CoV-2 genome has uncovered many mutations, which have replaced the lineage that characterized the first wave of infections all around the world. In December 2020, the outbreak of variant of concern (VOC) 202012/01 (lineage B.1.1.7) in the United Kingdom defined a turning point during the pandemic, immediately posing a worldwide threat on the Covid-19 vaccination campaign. Here, we reported the evolution of B.1.1.7 lineage-related infections, analyzing samples collected from January 1st 2021, until April 15th 2021, in Friuli Venezia Giulia, a northeastern region of Italy. A cohort of 1508 nasopharyngeal swabs was analyzed by High Resolution Melting (HRM) and 479 randomly selected samples underwent Next Generation Sequencing analysis (NGS), uncovering a steady and continuous accumulation of B.1.1.7 lineage-related specimens, joined by sporadic cases of other known lineages (i.e. harboring the Spike glycoprotein p.E484K mutation). All the SARS-CoV-2 genome has been analyzed in order to highlight all the rare mutations that may eventually result in a new variant of interest. This work suggests that a thorough monitoring of the SARS-CoV-2 genome by NGS is essential to contain any new variant that could jeopardize all the efforts that have been made so far to resolve the emergence of the pandemic.
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Affiliation(s)
- Catia Mio
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Chiara Dal Secco
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Stefania Marzinotto
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Claudio Bruno
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Santa Pimpo
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Elena Betto
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Martina Bertoni
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Corrado Pipan
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Emanuela Sozio
- Infectious Diseases Clinic, University Hospital of Udine, Udine, Italy
| | - Carlo Tascini
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Infectious Diseases Clinic, University Hospital of Udine, Udine, Italy
| | - Giuseppe Damante
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Francesco Curcio
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
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10
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Ishak A, AlRawashdeh MM, Esagian SM, Nikas IP. Diagnostic, Prognostic, and Therapeutic Value of Droplet Digital PCR (ddPCR) in COVID-19 Patients: A Systematic Review. J Clin Med 2021; 10:5712. [PMID: 34884414 PMCID: PMC8658157 DOI: 10.3390/jcm10235712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 02/07/2023] Open
Abstract
Accurate detection of SARS-CoV-2, the pathogen causing the global pandemic of COVID-19, is essential for disease surveillance and control. Quantitative reverse transcription PCR (RT-qPCR) is considered the reference standard test for the diagnosis of SARS-CoV-2 by the World Health Organization and Centers for Disease Control and Prevention. However, its limitations are a prompt for a more accurate assay to detect SARS-CoV-2, quantify its levels, and assess the prognosis. This article aimed to systematically review the literature and assess the diagnostic performance of droplet digital PCR (ddPCR), also to evaluate its potential role in prognosis and management of COVID-19 patients. PubMed and Scopus databases were searched to identify relevant articles published until 13 July 2021. An additional PubMed search was performed on 21 October 2021. Data from the 39 eligible studies were extracted and an overall 3651 samples from 2825 patients and 145 controls were used for our qualitative analysis. Most studies reported ddPCR was more accurate than RT-qPCR in detecting and quantifying SARS-CoV-2 levels, especially in patients with low viral loads. ddPCR was also found highly effective in quantifying SARS-CoV-2 RNAemia levels in hospitalized patients, monitoring their disease course, and predicting their response to therapy. These findings suggest ddPCR could serve as a complement or alternative SARS-CoV-2 tool with emerging diagnostic, prognostic, and therapeutic value, especially in hospital settings. Additional research is still needed to standardize its laboratory protocols, also to accurately assess its role in monitoring COVID-19 therapy response and in identifying SARS-CoV-2 emerging variants.
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Affiliation(s)
- Angela Ishak
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (A.I.); (M.M.A.)
| | - Mousa M. AlRawashdeh
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (A.I.); (M.M.A.)
| | - Stepan M. Esagian
- Jacobi Medical Center, Department of Medicine, Albert Einstein College of Medicine, The Bronx, New York, NY 10461, USA;
| | - Ilias P. Nikas
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (A.I.); (M.M.A.)
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11
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Zhang W, Zheng K, Ye Y, Ji J, Cheng X, He S. Pipette-Tip-Enabled Digital Nucleic Acid Analyzer for COVID-19 Testing with Isothermal Amplification. Anal Chem 2021; 93:15288-15294. [PMID: 34735121 DOI: 10.1021/acs.analchem.1c02414] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Herein, a pipette-tip-enabled digital nucleic acid analyzer for high-performance COVID-19 testing is demonstrated. This is achieved by digital loop-mediated isothermal amplification (digital LAMP or dLAMP) using common laboratory equipment and materials. It is shown that simply fixing a glass capillary inside conventional pipette tips enables the generation of monodisperse, water-in-oil microdroplets with benchtop centrifugation. It is shown that using LAMP, the ORF1a/b gene, a standard test region for COVID-19 screening, can be amplified without a thermal cycler. The amplification allows counting of fluorescent microdroplets so that Poisson analysis can be performed to allow quantification with a limit of detection that is 1 order of magnitude better than those of nondigital techniques and comparable to those of commercial dLAMP platforms. It is envisioned that this work will inspire studies on ultrasensitive digital nucleic acid analyzers demanding both sensitivity and accessibility, which is pivotal to their large-scale applications.
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Affiliation(s)
- Wenyao Zhang
- National Engineering Research Center for Optical Instruments, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310052, China
| | - Kaixin Zheng
- National Engineering Research Center for Optical Instruments, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310052, China
| | - Yang Ye
- National Engineering Research Center for Optical Instruments, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310052, China.,Ningbo Research Institute, Ningbo 310050, China.,ZJU-TU/e Joint Research Institute of Design, Optoelectronic and Sensing, Hangzhou 310052, China
| | - Jiali Ji
- National Engineering Research Center for Optical Instruments, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310052, China
| | - Xiaoyu Cheng
- National Engineering Research Center for Optical Instruments, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310052, China.,Ningbo Research Institute, Ningbo 310050, China.,ZJU-TU/e Joint Research Institute of Design, Optoelectronic and Sensing, Hangzhou 310052, China
| | - Sailing He
- National Engineering Research Center for Optical Instruments, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310052, China.,Ningbo Research Institute, Ningbo 310050, China.,ZJU-TU/e Joint Research Institute of Design, Optoelectronic and Sensing, Hangzhou 310052, China
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12
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Current diagnostic approaches to detect two important betacoronaviruses: Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pathol Res Pract 2021; 225:153565. [PMID: 34333398 PMCID: PMC8305226 DOI: 10.1016/j.prp.2021.153565] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are two common betacoronaviruses, which are still causing transmission among the human population worldwide. The major difference between the two coronaviruses is that MERS-CoV is now causing sporadic transmission worldwide, whereas SARS-CoV-2 is causing a pandemic outbreak globally. Currently, different guidelines and reports have highlighted several diagnostic methods and approaches which could be used to screen and confirm MERS-CoV and SARS-CoV-2 infections. These methods include clinical evaluation, laboratory diagnosis (nucleic acid-based test, protein-based test, or viral culture), and radiological diagnosis. With the presence of these different diagnostic approaches, it could cause a dilemma to the clinicians and diagnostic laboratories in selecting the best diagnostic strategies to confirm MERS-CoV and SARS-CoV-2 infections. Therefore, this review aims to provide an up-to-date comparison of the advantages and limitations of different diagnostic approaches in detecting MERS-CoV and SARS-CoV-2 infections. This review could provide insights for clinicians and scientists in detecting MERS-CoV and SARS-CoV-2 infections to help combat the transmission of these coronaviruses.
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Pathogenic Characterization of a Porcine Circovirus Type 3 Isolate from Heilongjiang, China. DISEASE MARKERS 2021; 2021:9434944. [PMID: 34257749 PMCID: PMC8253634 DOI: 10.1155/2021/9434944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/30/2021] [Indexed: 12/23/2022]
Abstract
The clinical outcome of porcine circovirus 3 (PCV3) infection is still controversial. Herein, a novel PCV3 isolate (PCV3-China/DB-1/2017) with the molecular characterization of 24A and 27K in the Cap protein was used to inoculate three-week-old cesarean-derived, colostrum-deprived piglets. The nine PCV3 DB-1 inoculated piglets exhibited no obvious clinical symptoms or macroscopic lesions. PCV3 displayed a broad histotropism, including the heart, liver, spleen, lung, kidney, brain, lymph nodes, and tonsil, and the lungs and lymph nodes contained a higher quantity of viral genomes compared to that of the other organs. From 7 days after PCV3 DB-1 inoculation, the piglets showed obvious IgG antibody responses against PCV3 rCap-VLPs. The cumulative results demonstrated that PCV3 trend to low pathogenicity.
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Application of One-Step Reverse Transcription Droplet Digital PCR for Dengue Virus Detection and Quantification in Clinical Specimens. Diagnostics (Basel) 2021; 11:diagnostics11040639. [PMID: 33916081 PMCID: PMC8066273 DOI: 10.3390/diagnostics11040639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Detection and quantification of viruses in laboratory and clinical samples are standard assays in dengue virus (DENV) studies. The quantitative reverse transcription polymerase chain reaction (qRT-PCR) is considered to be the standard for DENV detection and quantification due to its high sensitivity. However, qRT-PCR offers only quantification relative to a standard curve and consists of several "in-house" components resulting in interlaboratory variations. We developed and optimized a protocol for applying one-step RT-droplet digital PCR (RT-ddPCR) for DENV detection and quantification. The lower limit of detection (LLOD95) and the lower limit of quantification (LLOQ) for RT-ddPCR were estimated to be 1.851 log10-copies/reaction and 2.337 log10-copies/reaction, respectively. The sensitivity of RT-ddPCR was found to be superior to qRT-PCR (94.87% vs. 90.38%, p = 0.039) while no false positives were detected. Quantification of DENV in clinical samples was independently performed in three laboratories showing interlaboratory variations with biases <0.5 log10-copies/mL. The RT-ddPCR protocol presented here could help harmonize DENV quantification results and improve findings in the field such as identifying a DENV titer threshold correlating with disease severity.
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