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Ahmadi F, Zanganeh FZ, Amani Tehrani I, Shoaee S, Choobin H, Bozorg A, Taghipoor M. Evaluating an extraction-free sample preparation method for multiplex detection of SARS-Cov-2, influenza A/B, and RSV with implementation on a microfluidic chip. Diagn Microbiol Infect Dis 2024; 109:116325. [PMID: 38688146 DOI: 10.1016/j.diagmicrobio.2024.116325] [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: 01/20/2024] [Revised: 03/13/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Following the relaxation of COVID-19 restrictions, other respiratory viruses such as influenza and respiratory syncytial virus (RSV), whose transmission were decreased due to COVID-19 precautions, are rising again. Because of similar clinical features and reported co-infections, multiplex detection of SARS-CoV-2, influenza A/B, and RSV is required to use specific treatments. This study assessed an extraction-free sample preparation (heat treatment at 95°C for 3 minutes) for multiplex detection using rRT-PCR. Despite an observed Ct-delay (∆Ct) averageing 1.26 compared to the standard method, an acceptable total sensitivity of 92 % and a negative predictive value (NPV) of 96 % were obtained. Moreover, Implementation on a microfluidic chip demonstrated efficiency, maintaining an excellent correlation (R2=0.983) with the standard method. Combining this extraction-free procedure with rRT-PCR on a microfluidic chip seems promising, because it simplifies the design and reduces the cost and complexity of the integrated assay for multiplex detection of SARS-CoV-2, influenza A/B, and RSV.
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Affiliation(s)
- Fatemeh Ahmadi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, I.R., Iran
| | - Fatemeh Zahra Zanganeh
- Department of Biotechnology, College of Science, University of Tehran, Tehran, I.R., Iran
| | - Iman Amani Tehrani
- Micro Nano System Laboratory (MNSL), Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran
| | - Saeed Shoaee
- Micro Nano System Laboratory (MNSL), Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran
| | - Hamzeh Choobin
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Bozorg
- Department of Biotechnology, College of Science, University of Tehran, Tehran, I.R., Iran
| | - Mojtaba Taghipoor
- Micro Nano System Laboratory (MNSL), Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran.
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Allan-Blitz LT, Sanders G, Shah P, Adams G, Jarolimova J, Ard K, Branda JA, Klausner JD, Sabeti PC, Lemieux JE. Clinical Performance of Cas13a-based Point-of-Care Lateral Flow Assay for Detecting Neisseria gonorrhoeae. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.01.24303603. [PMID: 38496586 PMCID: PMC10942539 DOI: 10.1101/2024.03.01.24303603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Background Diagnosis of Neisseria (N.) gonorrhoeae is dependent on nucleic acid amplification testing (NAAT), which is not available in resource-limited settings where the prevalence of infection is highest. Recent advances in molecular diagnostics leveraging the high specificity of CRISPR enzymes can permit field-deployable, point-of-care lateral flow assays. We previously reported on the development and in vitro performance of a lateral flow assay for detecting N. gonorrhoeae. Here we aimed to pair that assay with point-of-care DNA extraction techniques and assess the performance on clinical urine specimens. Methods We collected an additional urine specimen among individuals enrolling in an ongoing clinical trial at the Massachusetts General Hospital Sexual Health Clinic who presented with symptoms of urethritis or cervicitis (urethral or vaginal discharge, dysuria, or dyspareunia). We then assessed thermal, detergent, and combination DNA extraction conditions, varying the duration of heat at 95°C and concentration of Triton X. We assessed the efficacy of the various DNA extraction methods by quantitative polymerase chain reaction (qPCR). Once an extraction method was selected, we incubated samples for 90 minutes to permit isothermal recombinase polymerase amplification. We then assessed the performance of lateral flow Cas13a-based detection using our previously designed porA probe and primer system for N. gonorrhoeae detection, comparing lateral flow results with NAAT results from clinical care. Results We assessed DNA extraction conditions on 3 clinical urine specimens. There was no consistent significant difference in copies per microliter of DNA obtained using more or less heat. On average, we noted that 0.02% triton combined with 5 minutes of heating to 95°C resulted in the highest DNA yield, however, 0.02% triton alone resulted in a quantity of DNA that was above the previously determined analytic sensitivity of the assay. Given that detergent-based extraction is more easily deployable, we selected that as our method for extraction. We treated 23 clinical specimens with 0.02% triton, which we added to the Cas13a detection system. We ran all lateral flow detections in duplicate. The Cas13a-based assay detected 8 of 8 (100%) positive specimens, and 0 of 15 negative specimens. Conclusion Using point-of-care DNA extraction, isothermal amplification, and Cas13a-based detection, our point-of-care lateral flow N. gonorrhoeae assay correctly identified 23 clinical urine specimens as either positive or negative. Further evaluation of this assay among larger samples and more diverse sample types is warranted.
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Affiliation(s)
- Lao-Tzu Allan-Blitz
- Division of Global Health Equity: Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, MA
- Division of Infectious Diseases: Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Gabriela Sanders
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, MA
- Division of Infectious Diseases: Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Palak Shah
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, MA
- Division of Infectious Diseases: Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Gordon Adams
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, MA
- Division of Infectious Diseases: Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Jana Jarolimova
- Division of Infectious Diseases: Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Kevin Ard
- Division of Infectious Diseases: Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - John A. Branda
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Jeffrey D. Klausner
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Pardis C. Sabeti
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, MA
| | - Jacob E. Lemieux
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, MA
- Division of Infectious Diseases: Department of Medicine, Massachusetts General Hospital, Boston, MA
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Kang M, Jeong E, Kim JY, Yun SA, Jang MA, Jang JH, Kim TY, Huh HJ, Lee NY. Optimization of extraction-free protocols for SARS-CoV-2 detection using a commercial rRT-PCR assay. Sci Rep 2023; 13:20364. [PMID: 37990045 PMCID: PMC10663557 DOI: 10.1038/s41598-023-47645-0] [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: 08/16/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023] Open
Abstract
In the ongoing global fight against coronavirus disease 2019 (COVID-19), the sample preparation process for real-time reverse transcription polymerase chain reaction (rRT-PCR) faces challenges due to time-consuming steps, labor-intensive procedures, contamination risks, resource demands, and environmental implications. However, optimized strategies for sample preparation have been poorly investigated, and the combination of RNase inhibitors and Proteinase K has been rarely considered. Hence, we investigated combinations of several extraction-free protocols incorporating heat treatment, sample dilution, and Proteinase K and RNase inhibitors, and validated the effectiveness using 120 SARS-CoV-2 positive and 62 negative clinical samples. Combining sample dilution and heat treatment with Proteinase K and RNase inhibitors addition exhibited the highest sensitivity (84.26%) with a mean increase in cycle threshold (Ct) value of + 3.8. Meanwhile, combined sample dilution and heat treatment exhibited a sensitivity of 79.63%, accounting for a 38% increase compared to heat treatment alone. Our findings highlight that the incorporation of Proteinase K and RNase inhibitors with sample dilution and heat treatment contributed only marginally to the improvement without yielding statistically significant differences. Sample dilution significantly impacts SARS-CoV-2 detection, and sample conditions play a crucial role in the efficiency of extraction-free methods. Our findings may provide insights for streamlining diagnostic testing, enhancing its accessibility, cost-effectiveness, and sustainability.
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Affiliation(s)
- Minhee Kang
- Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, Seoul, South Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea
| | - Eunjung Jeong
- Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, Seoul, South Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea
| | - Ji-Yeon Kim
- Samsung Biomedical Research Institute, Center for Clinical Medicine, Samsung Medical Center, Seoul, South Korea
| | - Sun Ae Yun
- Samsung Biomedical Research Institute, Center for Clinical Medicine, Samsung Medical Center, Seoul, South Korea
| | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Hee Jae Huh
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea.
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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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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Armenta-Leyva B, Munguía-Ramírez B, Giménez-Lirola LG, Lin X, Ye F, Zimmerman J. Critical evaluation of strategies to achieve direct real-time PCR detection of swine pathogens in oral fluids. J Vet Diagn Invest 2023; 35:521-527. [PMID: 37337714 PMCID: PMC10467463 DOI: 10.1177/10406387231182102] [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] [Indexed: 06/21/2023] Open
Abstract
Based on publications reporting improvements in real-time PCR (rtPCR) performance, we compared protocols based on heat treatment or dilution followed by direct rtPCR to standard extraction and amplification methods for the detection of porcine reproductive and respiratory syndrome virus (PRRSV), influenza A virus (IAV), porcine epidemic diarrhea virus (PEDV), or Mycoplasma hyopneumoniae (MHP) in swine oral fluids (OFs). In part A, we subjected aliquots of positive OF samples to 1 of 4 protocols: protocol 1: heat (95°C × 30 min) followed by direct rtPCR; protocol 2: heat and cool (25°C × 20 min) followed by direct rtPCR; protocol 3: heat, cool, extraction, and rtPCR; protocol 4 (control): extraction and then rtPCR. In part B, positive OF samples were split into 3, diluted (D1 = 1:2 with Tris-borate-EDTA (TBE); D2 = 1:2 with negative OF; D3 = not diluted), and then tested by rtPCR using the best-performing protocol from part A (protocol 4). In part A, with occasional exceptions, heat treatment resulted in marked reduction in the detection of target and internal sample control (ISC) nucleic acids. In part B, sample dilution with TBE or OF produced no improvement in the detection of targets and ISCs. Thus, standard extraction and amplification methods provided superior detection of PRRSV, IAV, PEDV, and MHP nucleic acids in OFs.
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Affiliation(s)
- Betsy Armenta-Leyva
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Berenice Munguía-Ramírez
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Luis G. Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Xue Lin
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Fangshu Ye
- Department of Statistics, College of Liberal Arts and Sciences, Iowa State University, Ames, IA, USA
| | - Jeffrey Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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Rivas-Macho A, Sorarrain A, Marimón JM, Goñi-de-Cerio F, Olabarria G. Extraction-Free Colorimetric RT-LAMP Detection of SARS-CoV-2 in Saliva. Diagnostics (Basel) 2023; 13:2344. [PMID: 37510088 PMCID: PMC10377860 DOI: 10.3390/diagnostics13142344] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The pandemic situation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need of fast, simple, and cost-effective tests for the diagnosis of emerging pathogens. RT-qPCR has been established as the reference technique for the diagnosis of SARS-CoV-2 infections. This method requires a time-consuming protocol for the extraction of the nucleic acids present in the sample. A colorimetric reverse transcription loop-mediated isothermal amplification using the calcein molecule combined with a simple extraction-free method for saliva samples (calcein RT-LAMP) has been developed. Samples are heated 95 °C for 10 min before amplification at 63 °C for 40 min. The results can be observed by fluorescence or by the naked eye with a color change from orange to green. The method was compared with commercialized available colorimetric and fluorescent RT-LAMP kits. The developed method shows better sensitivity and specificity than the colorimetric commercial RT-LAMP and the same as the fluorescent RT-LAMP, without the need of a fluorescent reader. Moreover, the calcein RT-LAMP has, compared to RT-qPCR, a sensitivity of 90% and a specificity of 100% for saliva samples with a Ct ≤ 34, without the need for expensive RT-qPCR instruments, demonstrating the potential of this method for population screening.
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Affiliation(s)
- Ane Rivas-Macho
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, Parque Tecnológico, Ed. 202, 48170 Zamudio, Spain
- Molecular Biology and Biomedicine PhD Program, University of the Basque Country UPV/EHU, 48940 Leioa, Spain
| | - Ane Sorarrain
- Biodonostia Health Research Institute, Infectious Diseases Area, Microbiology Department, Osakidetza Basque Health Service, Donostialdea Integrated Health Organization, 20014 San Sebastián, Spain
| | - José M Marimón
- Biodonostia Health Research Institute, Infectious Diseases Area, Microbiology Department, Osakidetza Basque Health Service, Donostialdea Integrated Health Organization, 20014 San Sebastián, Spain
| | - Felipe Goñi-de-Cerio
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, Parque Tecnológico, Ed. 202, 48170 Zamudio, Spain
| | - Garbiñe Olabarria
- Gaiker, GAIKER Technology Centre, Basque Research and Technology Alliance, Parque Tecnológico, Ed. 202, 48170 Zamudio, Spain
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Qiu S, Xu D, Dai J, Zhang L, Tian X, Li X, Chen D, Zhou R, Liu W. Improving the efficiency and biosafety of respiratory syncytial virus identification using a nucleic acid extraction-free reagent. J Med Virol 2023; 95:e28287. [PMID: 36345579 DOI: 10.1002/jmv.28287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/27/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
Respiratory syncytial virus (RSV) is the most important virus that causes lower respiratory tract disease in children; efficient viral identification is an important component of disease prevention and treatment. Here, we developed and evaluated a ready-to-use (RTU) nucleic acid extraction-free direct reagent for identification of RSV (RTU-Direct test) in clinical samples. The limit of detection (LOD) of the RSV RTU-Direct test was consistent with the LOD of the standard test using extracted nucleic acids. The virus inactivation ability of RTU-Direct reagent was confirmed by viral infectivity assays involving RTU-Direct-treated samples containing RSV and human coronavirus OC43. RSV RNA stability was significantly better in RTU-Direct reagent than in conventional virus transport medium (VTM) at room temperature and 4°C (p < 0.05). The clinical performance of the RTU-Direct test was evaluated using 155 respiratory specimens from patients with suspected RSV infection. Positive agreement between the RTU-Direct test and the VTM standard test was 100% (42/42); negative agreement was 99.1% (112/113), and the kappa statistic was 0.968 (p < 0.001). The distributions of Ct values did not significantly differ between the RTU-Direct test and the standard test (p > 0.05). Overall, the RTU-Direct reagent can improve the efficiency and biosafety of RSV detection, while reducing the cost of detection.
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Affiliation(s)
- Shuyan Qiu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Duo Xu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Jing Dai
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Li Zhang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Xingui Tian
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Xiao Li
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Dehui Chen
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
| | - Rong Zhou
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China.,Guangzhou Laboratory, Guangzhou, China
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou Medical University, Guangzhou, China
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Ma C, Tian Z, Yang L, Cao J. Validation of qPCR from a crude extract for the rapid detection of white spot syndrome virus. AQUACULTURE INTERNATIONAL : JOURNAL OF THE EUROPEAN AQUACULTURE SOCIETY 2022; 30:2679-2690. [PMID: 35910332 PMCID: PMC9309450 DOI: 10.1007/s10499-022-00920-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED White spot disease (WSD) has posed a serious threat to the China and the global shrimp aquaculture. In order to diagnose white spot syndrome virus (WSSV) early and prevent the spread and outbreak of WSD, it is necessary to establish a highly sensitive WSSV diagnosis method suitable for shrimp farming sites. In this study, a pre-amplification qPCR assay from the crude extract of samples heated lysis was established, which was further compared with the universal qPCR assay to verify the shrimp samples. The limit of detection (LOD) of pre-amplification qPCR assay and universal qPCR assay was 2.80 copies and 20.57 copies per reaction at 95% CI, respectively. It had good WSSV specificity and did not show cross-detection of infectious hypodermal and hematopoietic necrosis virus (IHHNV), hepatopancreatic parvovirus (HPV), Enterocytozoon hepatopenaei (EHP), acute hepatopancreas necrosis disease (AHPND), necrotizing hepatopancreatitis bacteria (NHPB), and decapod iridescent virus 1 (DIV1). A total of 36 shrimp samples were detected as WSSV DNA positive by pre-amplification qPCR with crude extract from samples heated lysis and universal qPCR with DNA extraction. The diagnostic sensitivity and specificity were 97.22% (85.5 ~ 99.9%, 95% CI) and 100% (81.5 ~ 100%, 95% CI), respectively. The agreement Kappa value was 0.959 (0.879 ~ 1, 95% CI), and the analysis results were basically consistent. Eliminating the tedious steps of extracting DNA and using pre-amplified qPCR to detect WSSV in shrimp, it is a good choice for aquaculture farms. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10499-022-00920-9.
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Affiliation(s)
- Chao Ma
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, China
| | - Zhuo Tian
- Dalian Customs Technology Center, Dalian, China
| | - Lili Yang
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, China
| | - Jijuan Cao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, China
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Comparative Evaluation of Six SARS-CoV-2 Real-Time RT-PCR Diagnostic Approaches Shows Substantial Genomic Variant–Dependent Intra- and Inter-Test Variability, Poor Interchangeability of Cycle Threshold and Complementary Turn-Around Times. Pathogens 2022; 11:pathogens11040462. [PMID: 35456137 PMCID: PMC9029830 DOI: 10.3390/pathogens11040462] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/30/2022] [Accepted: 04/10/2022] [Indexed: 12/23/2022] Open
Abstract
Several professional societies advise against using real-time Reverse-Transcription PCR (rtRT-PCR) cycle threshold (Ct) values to guide clinical decisions. We comparatively assessed the variability of Ct values generated by six diagnostic approaches by testing serial dilutions of well-characterized isolates of 10 clinically most relevant SARS-CoV-2 genomic variants: Alpha, Beta, Gamma, Delta, Eta, Iota, Omicron, A.27, B.1.258.17, and B.1 with D614G mutation. Comparison of three fully automated rtRT-PCR analyzers and a reference manual rtRT-PCR assay using RNA isolated with three different nucleic acid isolation instruments showed substantial inter-variant intra-test and intra-variant inter-test variability. Ct value differences were dependent on both the rtRT-PCR platform and SARS-CoV-2 genomic variant. Differences ranging from 2.0 to 8.4 Ct values were observed when testing equal concentrations of different SARS-CoV-2 variants. Results confirm that Ct values are an unreliable surrogate for viral load and should not be used as a proxy of infectivity and transmissibility, especially when different rtRT-PCR assays are used in parallel and multiple SARS-CoV-2 variants are circulating. A detailed turn-around time (TAT) comparative assessment showed substantially different TATs, but parallel use of different diagnostic approaches was beneficial and complementary, allowing release of results for more than 81% of non-priority samples within 8 h after admission.
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Arbaciauskaite S, Babakhani P, Sandetskaya N, Vitkus D, Jancoriene L, Karosiene D, Karciauskaite D, Zablockiene B, Kuhlmeier D. Self-Sampled Gargle Water Direct RT-LAMP as a Screening Method for the Detection of SARS-CoV-2 Infections. Diagnostics (Basel) 2022; 12:diagnostics12040775. [PMID: 35453823 PMCID: PMC9030430 DOI: 10.3390/diagnostics12040775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 11/16/2022] Open
Abstract
We assessed the viability of self-sampled gargle water direct RT-LAMP (LAMP) for detecting SARS-CoV-2 infections by estimating its sensitivity with respect to the gold standard indirect RT-PCR of paired oro-nasopharyngeal swab samples. We also assessed the impact of symptom onset to test time (STT)—i.e., symptom days at sampling, on LAMP. In addition, we appraised the viability of gargle water self-sampling versus oro-nasopharyngeal swab sampling, by comparing paired indirect RT-PCR results. 202 oro-nasopharyngeal swab and paired self-sampled gargle water samples were collected from hospital patients with COVID-19 associated symptoms. LAMP, indirect and direct RT-PCR were performed on all gargle water samples, and indirect RT-PCR was performed on all oro-nasopharyngeal samples. LAMP presented a sensitivity of 80.8% (95% CI: 70.8–90.8%) for sample pairs with sub-25 Ct oro-nasopharyngeal indirect RT-PCR results, and 77.6% (66.2–89.1%) sensitivity for sub-30 Ct samples with STT ≤ 7 days. STT, independently of Ct value, correlated negatively with LAMP performance. 80.7% agreement was observed between gargle water and oro-nasopharyngeal indirect RT-PCR results. In conclusion, LAMP presents an acceptable sensitivity for low Ct and low STT samples. Gargle water may be considered as a viable sampling method, and LAMP as a screening method, especially for symptomatic persons with low STT values.
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Affiliation(s)
- Skaiste Arbaciauskaite
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, Perlickstraße 1, 04103 Leipzig, Germany; (N.S.); (D.K.)
- Institute of Cell Biology and Neurobiology, Charité—Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Correspondence:
| | - Pouya Babakhani
- Department of Computer Science, University of Bath, Claverton Down, Bath BA2 7AY, UK;
| | - Natalia Sandetskaya
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, Perlickstraße 1, 04103 Leipzig, Germany; (N.S.); (D.K.)
| | - Dalius Vitkus
- Institute of Biomedical Sciences, Vilnius University Faculty of Medicine, M.K. Ciurlionio 21, LT-03101 Vilnius, Lithuania; (D.V.); (D.K.)
- Centre of Laboratory Medicine, Vilnius University Hospital Santaros Klinikos, Santariskiu 14, LT-08406 Vilnius, Lithuania;
| | - Ligita Jancoriene
- Clinic of Infectious Diseases and Dermatovenerology, Institute of Clinical Medicine, Vilnius University Faculty of Medicine, M.K. Ciurlionio 21, LT-03101 Vilnius, Lithuania; (L.J.); (B.Z.)
- Center of Infectious Diseases, Vilnius University Hospital Santaros Klinikos, Santariskiu 14, LT-08406 Vilnius, Lithuania
| | - Dovile Karosiene
- Centre of Laboratory Medicine, Vilnius University Hospital Santaros Klinikos, Santariskiu 14, LT-08406 Vilnius, Lithuania;
| | - Dovile Karciauskaite
- Institute of Biomedical Sciences, Vilnius University Faculty of Medicine, M.K. Ciurlionio 21, LT-03101 Vilnius, Lithuania; (D.V.); (D.K.)
- Centre of Laboratory Medicine, Vilnius University Hospital Santaros Klinikos, Santariskiu 14, LT-08406 Vilnius, Lithuania;
| | - Birute Zablockiene
- Clinic of Infectious Diseases and Dermatovenerology, Institute of Clinical Medicine, Vilnius University Faculty of Medicine, M.K. Ciurlionio 21, LT-03101 Vilnius, Lithuania; (L.J.); (B.Z.)
- Center of Infectious Diseases, Vilnius University Hospital Santaros Klinikos, Santariskiu 14, LT-08406 Vilnius, Lithuania
| | - Dirk Kuhlmeier
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, Perlickstraße 1, 04103 Leipzig, Germany; (N.S.); (D.K.)
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Yoshioka N, Deguchi M, Hagiya H, Kagita M, Tsukamoto H, Takao M, Yoshida H, Hamaguchi S, Maeda I, Hidaka Y, Tomono K. Comparison of Extraction-based and Elution-based Polymerase Chain Reaction Testing, and Automated and Rapid Antigen Testing for the Diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2. J Med Virol 2022; 94:3155-3159. [PMID: 35274327 PMCID: PMC9088563 DOI: 10.1002/jmv.27709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 11/21/2022]
Abstract
We aimed to compare the differences in testing performance of extraction‐based polymerase chain reaction (PCR) assays, elution‐based direct PCR assay, and rapid antigen detection tests for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). We used nasopharyngeal swab samples of patients with coronavirus disease 2019 (COVID‐19). We used the MagNA Pure 24 System (Roche Diagnostics K.K.) or magLEAD 12gC (Precision System Science Co., Ltd.) for RNA extraction, mixed the concentrates with either the LightMix Modular SARS‐CoV PCR mixture (Roche Diagnostics K.K.) or Takara SARS‐CoV‐2 direct PCR detection kit (Takara Bio Inc.), and amplified it using COBAS® z480 (Roche Diagnostics K.K.). For elution‐based PCR, we directly applied clinical samples to the Takara SARS‐CoV‐2 direct PCR detection kit before the same amplification step. Additionally, we performed Espline SARS‐CoV‐2 (Fuji Rebio Co., Ltd.) for rapid diagnostic test (RDT), and used Lumipulse SARS‐CoV‐2 antigen (Fuji Rebio Co., Ltd.) and Elecsys SARS‐CoV‐2 antigen (Roche Diagnostics K.K.) for automated antigen tests (ATs). Extraction‐based and elution‐based PCR tests detected the virus up to 214–216 and 210 times dilution, respectively. ATs remained positive up to 24–26 times dilution, while RDT became negative after 22 dilutions. For 153 positive samples, positivity rates of the extraction‐based PCR assay were 85.6% to 98.0%, while that of the elution‐based PCR assay was 73.2%. Based on the RNA concentration process, extraction‐based PCR assays were superior to elution‐based direct PCR assays for detecting SARS‐CoV‐2.
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Affiliation(s)
- Nori Yoshioka
- Division of Infection Control and Prevention, Osaka University Hospital, Japan.,Laboratory for Clinical Investigation, Osaka University Hospital, Japan
| | - Matsuo Deguchi
- Division of Infection Control and Prevention, Osaka University Hospital, Japan
| | - Hideharu Hagiya
- Division of Infection Control and Prevention, Osaka University Hospital, Japan.,Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Japan
| | - Masanori Kagita
- Division of Infection Control and Prevention, Osaka University Hospital, Japan.,Laboratory for Clinical Investigation, Osaka University Hospital, Japan
| | - Hiroko Tsukamoto
- Division of Infection Control and Prevention, Osaka University Hospital, Japan.,Laboratory for Clinical Investigation, Osaka University Hospital, Japan
| | - Miyuki Takao
- Division of Infection Control and Prevention, Osaka University Hospital, Japan.,Laboratory for Clinical Investigation, Osaka University Hospital, Japan
| | - Hisao Yoshida
- Division of Infection Control and Prevention, Osaka University Hospital, Japan
| | - Shigeto Hamaguchi
- Division of Infection Control and Prevention, Osaka University Hospital, Japan
| | - Ikuhiro Maeda
- Laboratory for Clinical Investigation, Osaka University Hospital, Japan
| | - Yoh Hidaka
- Laboratory for Clinical Investigation, Osaka University Hospital, Japan
| | - Kazunori Tomono
- Division of Infection Control and Prevention, Osaka University Hospital, Japan
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