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Khan S, Rathod P, Gupta VK, Khedekar PB, Chikhale RV. Evolution and Impact of Nucleic Acid Amplification Test (NAAT) for Diagnosis of Coronavirus Disease. Anal Chem 2024; 96:8124-8146. [PMID: 38687959 PMCID: PMC11112543 DOI: 10.1021/acs.analchem.3c05225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Affiliation(s)
- Sumbul
Fatma Khan
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Priyanka Rathod
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Vivek K. Gupta
- Department
of Biochemistry, National JALMA Institute
for Leprosy & Other Mycobacterial Diseases (ICMR), Agra -282004, India
| | - Pramod B. Khedekar
- Department
of Pharmaceutical Sciences, Rashtrasant
Tukadoji Maharaj Nagpur University, Nagpur 440033, MS India
| | - Rupesh V. Chikhale
- UCL
School of Pharmacy, Department of Pharmaceutical and Biological Chemistry, University College London, London WC1N 1AX, United Kingdom
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2
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Matic N, Lawson T, Ritchie G, Lowe CF, Romney MG. Testing the limits of multiplex respiratory virus assays for SARS-CoV-2 at high cycle threshold values: Comparative performance of cobas 6800/8800 SARS-CoV-2 & Influenza A/B, Xpert Xpress SARS-CoV-2/Flu/RSV, and cobas Liat SARS-CoV-2 & Influenza A/B. JOURNAL OF THE ASSOCIATION OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASE CANADA = JOURNAL OFFICIEL DE L'ASSOCIATION POUR LA MICROBIOLOGIE MEDICALE ET L'INFECTIOLOGIE CANADA 2024; 8:328-335. [PMID: 38250621 PMCID: PMC10797767 DOI: 10.3138/jammi-2022-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 01/23/2024]
Abstract
Background Multiplex real-time RT-PCR assays for respiratory pathogens are valuable tools to optimize laboratory workflow and turnaround time. At a time when resurgence of influenza and respiratory syncytial virus (RSV) cases have been widely observed along with continued transmission of SARS-CoV-2, timely identification of all circulating respiratory viruses is crucial. This study evaluates the detection of low viral loads of SARS-CoV-2 by four multiplex molecular assays: Roche cobas 6800/8800 SARS-CoV-2 & Influenza A/B Test, Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV, cobas Liat SARS-CoV-2 & Influenza A/B, and a laboratory-developed test (LDT). Methods Retrospective upper respiratory tract specimens positive for various respiratory viruses at a range of cycle threshold (Ct) values (18-40) were tested by four multiplex assays. Positive and negative percent agreement (PPA and NPA) with validated RT-PCR assays were calculated. Results A total of 82 samples were assessed, with discordant results observed in a portion of the samples (10/82, 12.2%) where Ct values were >33. The majority of the discordant results (6/10, 60%) were false negatives. Overall, PPA was 100% (58/58) for cobas 6800, 97.4% (38/39) for GeneXpert, 100% (17/17) for Liat, and 90.5% (57/63) for the LDT. PPA for the LDT increased to 92.1% after manual review of amplification curves. Conclusions Commercial multiplex respiratory virus assays have good performance for samples with medium to high viral loads (Ct values <33). Laboratories should consider appropriate test result review and confirmation protocols to optimize sensitivity, and may consider reporting samples with additional interpretive comments when low viral loads are detected.
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Affiliation(s)
- Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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3
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Aravind Kumar N, Aradhana S, Harleen, Vishnuraj MR. SARS-CoV-2 in digital era: Diagnostic techniques and importance of nucleic acid quantification with digital PCRs. Rev Med Virol 2023; 33:e2471. [PMID: 37529971 DOI: 10.1002/rmv.2471] [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: 04/19/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023]
Abstract
Studies related to clinical diagnosis and research of SARS-CoV-2 are important in the current pandemic era. Although molecular biology has emphasised the importance of qualitative analysis, quantitative analysis with nucleic acids in relation to SARS-CoV-2 needs to be clearly emphasised, which can provide perspective for viral dynamic studies of SARS-CoV-2. In this regard, the requirement and utilization of digital PCR in COVID-19 research has substantially increased during the pandemic, necessitating the aggregation of its cardinal applications and future scopes. Hence, this meta-review comprehensively addresses and emphasises the importance of nucleic acid quantification of SARS-CoV-2 RNA with digital PCR (dPCR). Various quantitative techniques of clinical significance like immunological, proteomic and nucleic acid-based diagnosis and quantification, have been comparatively discussed. Furthermore, the core part of the article focusses on the working principle and advantages of digital PCR, along with its applications in COVID-19 research. Several important applications like viral load quantitation, environmental surveillance and assay validation have been extensively investigated and discussed. Certain key future scopes of clinical importance, like mortality prediction, viral/variant-symbiosis, and antiviral studies were also identified, suggesting several possible digital PCR applications in COVID-19 research.
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Affiliation(s)
- N Aravind Kumar
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
| | - S Aradhana
- Department of Biotechnology, School of Bio Sciences & Technology (SBST), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Harleen
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - M R Vishnuraj
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
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4
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Pomari E, Mori A, Accordini S, Donini A, Cordioli M, Tacconelli E, Castilletti C. Evaluation of a ddPCR Commercial Assay for the Absolute Quantification of the Monkeypox Virus West Africa in Clinical Samples. Diagnostics (Basel) 2023; 13:diagnostics13071349. [PMID: 37046567 PMCID: PMC10093040 DOI: 10.3390/diagnostics13071349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 03/23/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND Monkeypox virus (MPXV) is a double-stranded DNA virus belonging to the orthopoxvirus genus in the family Poxviridae. Distinct clades are identified: the clade I belonging to the Central African (or Congo Basin) clade and the subclades IIa and IIb belonging to the West African clade. Here, a commercial droplet digital PCR (ddPCR) assay was evaluated for the quantification of the MPXV West Africa clade in clinical samples. METHODS The ddPCR reaction was assessed as a duplex assay using RPP30 as an internal amplification control. A total of 60 clinical specimens were tested, 40 positives (skin lesions, n=10; rectal swabs, n = 10; pharyngeal swabs, n = 10; and whole blood, n = 10), and 20 negatives (n = 5 for each biological matrix) were found at the routine molecular diagnostics (orthopoxvirus qPCR followed by confirmation with Sanger sequencing). To evaluate the analytical sensitivity, the ddPCR reaction was first analyzed on serial dilutions of synthetic DNA spiked in water and in negative biological matrices, achieving a limit of detection of 3.5 copy/µL. RESULTS Regarding the clinical samples, compared to routine molecular diagnostics, the ddPCR duplex assay showed 100% of specificity for all biological matrices and 100% sensitivity (10/10) for lesions, 100% (10/10) for rectal swabs, 90% (9/10) for pharyngeal swabs, and 60% (6/10) for whole blood. CONCLUSION Overall, our data showed that the commercial ddPCR assay allowed the DNA detection of MPXV in 87.5% (35/40) of our cohort, highlighting useful technical indications for the different specimens with a potential greatest performance for skin lesions and rectal swabs.
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Affiliation(s)
- Elena Pomari
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Antonio Mori
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Silvia Accordini
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Annalisa Donini
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Maddalena Cordioli
- Division of Infectious Diseases, Department of Diagnostic and Public Health, University of Verona, 37100 Verona, Italy
- Division of Infectious Diseases, Department of Medicine, Verona University Hospital, 37100 Verona, Italy
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Medicine, Verona University Hospital, 37100 Verona, Italy
| | - Concetta Castilletti
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
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Wagner K, Fox P, Gordon E, Hahn W, Olsen K, Markham A, Buglewicz D, Selemenakis P, Lessard A, Goldstein D, Threatt A, Davis L, Miller-Dawson J, Stockett H, Sanders H, Rugh K, Turner H, Remias M, Williams M, Chavez J, Galindo G, Cialek C, Koch A, Fout A, Fosdick B, Broeckling B, Zabel MD. A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva. Sci Rep 2023; 13:3075. [PMID: 36813822 PMCID: PMC9944410 DOI: 10.1038/s41598-023-29858-5] [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] [Accepted: 02/11/2023] [Indexed: 02/24/2023] Open
Abstract
In response to the SARS-CoV-2 pandemic, we developed a multiplexed, paired-pool droplet digital PCR (MP4) screening assay. Key features of our assay are the use of minimally processed saliva, 8-sample paired pools, and reverse-transcription droplet digital PCR (RT-ddPCR) targeting the SARS-CoV-2 nucleocapsid gene. The limit of detection was determined to be 2 and 12 copies per µl for individual and pooled samples, respectively. Using the MP4 assay, we routinely processed over 1,000 samples a day with a 24-h turnaround time and over the course of 17 months, screened over 250,000 saliva samples. Modeling studies showed that the efficiency of 8-sample pools was reduced with increased viral prevalence and that this could be mitigated by using 4-sample pools. We also present a strategy for, and modeling data supporting, the creation of a third paired pool as an additional strategy to employ under high viral prevalence.
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Affiliation(s)
- Kaitlyn Wagner
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Phil Fox
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Elizabeth Gordon
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Westen Hahn
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Kenzie Olsen
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Alex Markham
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Dylan Buglewicz
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Platon Selemenakis
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Avery Lessard
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Daniella Goldstein
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Alissa Threatt
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Luke Davis
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Jake Miller-Dawson
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Halie Stockett
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | | | - Kristin Rugh
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Houston Turner
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Michelle Remias
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Maggie Williams
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Jorge Chavez
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Gabriel Galindo
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Charlotte Cialek
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Amanda Koch
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Alex Fout
- Department of Statistics, Colorado State University, Fort Collins, CO, 80523, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Bailey Fosdick
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Bettina Broeckling
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA
- Colorado State University, Fort Collins, CO, 80523, USA
| | - Mark D Zabel
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, USA.
- Colorado State University, Fort Collins, CO, 80523, USA.
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Development and Evaluation of a Novel One-Step RT-qPCR Targeting the Vero Gene for the Identification of False-Positive Results Caused by Inactivated Virus Vaccine Contamination. Vaccines (Basel) 2023; 11:vaccines11020372. [PMID: 36851250 PMCID: PMC9959469 DOI: 10.3390/vaccines11020372] [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: 12/14/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
To identify false-positive SARS-CoV-2 test results caused by novel coronavirus inactivated vaccine contamination, a novel RT-qPCR targeting the ORF1ab and N genes of SARS-CoV-2 and Vero gene was developed. The amplification efficiency, precision, and lower limit of detection (LLOD) of the RT-qPCR assay were determined. A total of 346 clinical samples and 132 environmental samples were assessed, and the diagnostic performance was evaluated. The results showed that the amplification efficiency of the ORF1ab, N, and Vero genes was 95%, 97%, and 93%, respectively. The coefficients of variation of Ct values at a concentration of 3 × 104 copies/mL were lower than 5%. The LLOD for the ORF1ab, N, and Vero genes reached 8.0, 3.3, and 8.2 copies/reaction, respectively. For the 346 clinical samples, our RT-qPCR assay identified SARS-CoV-2-positive and SARS-CoV-2-negative samples with a sensitivity of 100.00% and a specificity of 99.30% and novel coronavirus inactivated vaccine-contaminated samples with a sensitivity of 100% and a specificity of 100%. For the environmental samples, our RT-qPCR assay identified novel coronavirus inactivated vaccine-contaminated samples with a sensitivity of 88.06% and a specificity of 95.38%. In conclusion, the RT-qPCR assay we established can be used to diagnose COVID-19 and, to a certain extent, false-positive results due to vaccine contamination.
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Tian Y, Fei J, Luo J, Chen L, Ye J, Du W, Yu C. Development of a reverse-transcription droplet digital PCR method for quantitative detection of Cucumber green mottle mosaic virus. Heliyon 2022; 9:e12643. [PMID: 36865460 PMCID: PMC9970901 DOI: 10.1016/j.heliyon.2022.e12643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/27/2022] Open
Abstract
Cucumber green mottle mosaic virus (CGMMV) is a re-emerging threat to the production of greenhouse cucumber and other Cucurbitaceae crops worldwide. This seed-borne virus can easily spread from a contaminated seed to seedlings and adjacent plants by mechanical contact between the foliage of diseased and healthy plants, causing extensive yield losses. An accurate method for detecting and quantifying this virus is urgently needed to ensure the safety of the global seed trade. Here, we report the development of a reverse-transcription droplet digital polymerase chain reaction (RT-ddPCR)-based method for specific and high-sensitive detection of CGMMV. By testing three primer-probe sets and optimizing reaction conditions, we showed that the newly developed RT-ddPCR method is highly specific and sensitive, with a detection limit of 1 fg/μL (0.39 copy/μL). The sensitivity of the RT-ddPCR method was compared with that of real-time fluorescence quantitative RT-PCR (RT-qPCR) using a series of plasmid dilutions and total RNAs extracted from infected cucumber seeds, and the detection limit of RT-ddPCR was 10 times higher than RT-qPCR with plasmid dilutions and 100 times higher than RT-qPCR for detecting CGMMV from infected cucumber seeds. The RT-ddPCR method was further assessed for detecting CGMMV from a total of 323 samples of Cucurbitaceae seeds, seedlings, and fruits as compared with the RT-qPCR method. We found that the infection rate of CGMMV on symptomatic fruits was as high as 100%, whereas infection rates were lower for seeds and lowest for seedlings. Notably, the results of two methods in detecting CGMMV from different cucurbit tissues showed the high consistency with Kappa value from 0.84 to 1.0, demonstrating that the newly developed RT-ddPCR method is highly reliable and practically useful for large-scale CGMMV detection and quantification.
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Affiliation(s)
- Yimin Tian
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs District, Shanghai 200135, China
| | - Jing Fei
- Technical Center for Industrial Product and Raw Material Inspection and Testing, Shanghai Customs District, Shanghai 200135, China
| | - Jinyan Luo
- Shanghai Agricultural Technology Extension Center, Shanghai 201103, China
| | - Lei Chen
- Shanghai Agricultural Technology Extension Center, Shanghai 201103, China
| | - Jun Ye
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs District, Shanghai 200135, China
| | - Wei Du
- Agricultural Technology Extension Station of Ningxia, Yinchuan 750001, China
| | - Cui Yu
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs District, Shanghai 200135, China,Corresponding author.
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8
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Donia A, Furqan Shahid M, Hassan SU, Shahid R, Ahmad A, Javed A, Nawaz M, Yaqub T, Bokhari H. Integration of RT-LAMP and Microfluidic Technology for Detection of SARS-CoV-2 in Wastewater as an Advanced Point-of-Care Platform. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:364-373. [PMID: 35508752 PMCID: PMC9067896 DOI: 10.1007/s12560-022-09522-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/04/2022] [Indexed: 05/21/2023]
Abstract
Development of lab-on-a-chip (LOC) system based on integration of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and microfluidic technology is expected to speed up SARS-CoV-2 diagnostics allowing early intervention. In the current work, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and RT-LAMP assays were performed on extracted RNA of seven wastewater samples from COVID-19 hotspots. RT‑LAMP assay was also performed on wastewater samples without RNA extraction. Current detection of SARS-CoV-2 is mainly by RT-qPCR of ORF (ORF1ab) and N genes so we targeted both to find the best target gene for SARS-CoV-2 detection. We also performed RT-LAMP with/without RNA extraction inside microfluidic device to target both genes. Positivity rates of RT-qPCR and RT-LAMP performed on extracted RNA were 100.0% (7/7) and 85.7% (6/7), respectively. RT-qPCR results revealed that all 7 wastewater samples were positive for N gene (Ct range 37-39), and negative for ORF1ab, suggesting that N gene could be the best target gene for SARS-CoV-2 detection. RT-LAMP of N and ORF (ORF1a) genes performed on wastewater samples without RNA extraction indicated that all 7 samples remains pink (negative). The color remains pink in all microchannels except microchannels which subjected to RT-LAMP for targeting N region after RNA extraction (yellow color) in 6 out of 7 samples. This study shows that SARS-CoV-2 was successfully detected from wastewater samples using RT-LAMP in microfluidic chips. This study brings the novelty involving the use of wastewater samples for detection of SARS-CoV-2 without previous virus concentration and with/without RNA extraction.
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Affiliation(s)
- Ahmed Donia
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Furqan Shahid
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Sammer-ul Hassan
- Department of Mechanical Engineering, University of Hong Kong, Pok Fu Lam, Hong Kong, Hong Kong
| | - Ramla Shahid
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Aneela Javed
- Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Nawaz
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Tahir Yaqub
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Habib Bokhari
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
- Kohsar University Murree, Murree, Pakistan
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9
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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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Nyaruaba R, Mwaliko C, Dobnik D, Neužil P, Amoth P, Mwau M, Yu J, Yang H, Wei H. Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks. Clin Microbiol Rev 2022; 35:e0016821. [PMID: 35258315 PMCID: PMC9491181 DOI: 10.1128/cmr.00168-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.
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Affiliation(s)
- Raphael Nyaruaba
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- International College, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Caroline Mwaliko
- International College, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Pavel Neužil
- Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Matilu Mwau
- Center for Infectious and Parasitic Diseases Control Research, Kenya Medical Research Institute, Busia, Kenya
| | - Junping Yu
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hang Yang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hongping Wei
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
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Matic N, Lowe CF, Ritchie G, Young M, Lawson T, Romney MG. Omicron (B.1.1.529) SARS-CoV-2 viral load among nasopharyngeal and oral samples compared to other Variants of Concern and impact on diagnostic testing strategy. Clin Microbiol Infect 2022; 28:1302-1303. [PMID: 35568306 PMCID: PMC9093080 DOI: 10.1016/j.cmi.2022.04.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 11/18/2022]
Affiliation(s)
- Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Matthew Young
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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Gentilini F, Turba ME, Taddei F, Gritti T, Fantini M, Dirani G, Sambri V. Modelling RT-qPCR cycle-threshold using digital PCR data for implementing SARS-CoV-2 viral load studies. PLoS One 2021; 16:e0260884. [PMID: 34928966 PMCID: PMC8687578 DOI: 10.1371/journal.pone.0260884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 11/18/2021] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES To exploit the features of digital PCR for implementing SARS-CoV-2 observational studies by reliably including the viral load factor expressed as copies/μL. METHODS A small cohort of 51 Covid-19 positive samples was assessed by both RT-qPCR and digital PCR assays. A linear regression model was built using a training subset, and its accuracy was assessed in the remaining evaluation subset. The model was then used to convert the stored cycle threshold values of a large dataset of 6208 diagnostic samples into copies/μL of SARS-CoV-2. The calculated viral load was used for a single cohort retrospective study. Finally, the cohort was randomly divided into a training set (n = 3095) and an evaluation set (n = 3113) to establish a logistic regression model for predicting case-fatality and to assess its accuracy. RESULTS The model for converting the Ct values into copies/μL was suitably accurate. The calculated viral load over time in the cohort of Covid-19 positive samples showed very low viral loads during the summer inter-epidemic waves in Italy. The calculated viral load along with gender and age allowed building a predictive model of case-fatality probability which showed high specificity (99.0%) and low sensitivity (21.7%) at the optimal threshold which varied by modifying the threshold (i.e. 75% sensitivity and 83.7% specificity). Alternative models including categorised cVL or raw cycle thresholds obtained by the same diagnostic method also gave the same performance. CONCLUSION The modelling of the cycle threshold values using digital PCR had the potential of fostering studies addressing issues regarding Sars-CoV-2; furthermore, it may allow setting up predictive tools capable of early identifying those patients at high risk of case-fatality already at diagnosis, irrespective of the diagnostic RT-qPCR platform in use. Depending upon the epidemiological situation, public health authority policies/aims, the resources available and the thresholds used, adequate sensitivity could be achieved with acceptable low specificity.
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Affiliation(s)
- Fabio Gentilini
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell’Emilia, Bologna, Italy
| | | | - Francesca Taddei
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Italy
| | - Tommaso Gritti
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Italy
| | - Michela Fantini
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Italy
| | - Giorgio Dirani
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Italy
| | - Vittorio Sambri
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Italy
- Department of Experimental, Diagnostic and Specialty Medicine - DIMES, University of Bologna, Bologna, Italy
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Van Poelvoorde LAE, Gand M, Fraiture MA, De Keersmaecker SCJ, Verhaegen B, Van Hoorde K, Cay AB, Balmelle N, Herman P, Roosens N. Strategy to Develop and Evaluate a Multiplex RT-ddPCR in Response to SARS-CoV-2 Genomic Evolution. Curr Issues Mol Biol 2021; 43:1937-1949. [PMID: 34889894 PMCID: PMC8928932 DOI: 10.3390/cimb43030134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022] Open
Abstract
The worldwide emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since 2019 has highlighted the importance of rapid and reliable diagnostic testing to prevent and control the viral transmission. However, inaccurate results may occur due to false negatives (FN) caused by polymorphisms or point mutations related to the virus evolution and compromise the accuracy of the diagnostic tests. Therefore, PCR-based SARS-CoV-2 diagnostics should be evaluated and evolve together with the rapidly increasing number of new variants appearing around the world. However, even by using a large collection of samples, laboratories are not able to test a representative collection of samples that deals with the same level of diversity that is continuously evolving worldwide. In the present study, we proposed a methodology based on an in silico and in vitro analysis. First, we used all information offered by available whole-genome sequencing data for SARS-CoV-2 for the selection of the two PCR assays targeting two different regions in the genome, and to monitor the possible impact of virus evolution on the specificity of the primers and probes of the PCR assays during and after the development of the assays. Besides this first essential in silico evaluation, a minimal set of testing was proposed to generate experimental evidence on the method performance, such as specificity, sensitivity and applicability. Therefore, a duplex reverse-transcription droplet digital PCR (RT-ddPCR) method was evaluated in silico by using 154 489 whole-genome sequences of SARS-CoV-2 strains that were representative for the circulating strains around the world. The RT-ddPCR platform was selected as it presented several advantages to detect and quantify SARS-CoV-2 RNA in clinical samples and wastewater. Next, the assays were successfully experimentally evaluated for their sensitivity and specificity. A preliminary evaluation of the applicability of the developed method was performed using both clinical and wastewater samples.
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Affiliation(s)
- Laura A. E. Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Mathieu Gand
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Marie-Alice Fraiture
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Sigrid C. J. De Keersmaecker
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
| | - Bavo Verhaegen
- Food Pathogens, Sciensano, 1050 Brussels, Belgium; (B.V.); (K.V.H.)
| | | | - Ann Brigitte Cay
- Enzootic, Vector-Borne and Bee Diseases, Sciensano, 1180 Brussels, Belgium; (A.B.C.); (N.B.)
| | - Nadège Balmelle
- Enzootic, Vector-Borne and Bee Diseases, Sciensano, 1180 Brussels, Belgium; (A.B.C.); (N.B.)
| | - Philippe Herman
- Expertise and Service Provision, Sciensano, 1050 Brussels, Belgium;
| | - Nancy Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (L.A.E.V.P.); (M.G.); (M.-A.F.); (S.C.J.D.K.)
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