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Gao N, Huo Y, Yu D, Cheng F, Wang T, Zhang X, Zhang L, Hu W, Li J, Yuan P, Liu J, Wang Y, Yan J. Evaluation of reverse transcription yield of RNA standards and forensic samples based on droplet digital PCR. Biochem Biophys Res Commun 2024; 711:149909. [PMID: 38615573 DOI: 10.1016/j.bbrc.2024.149909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
RNA analysis has shown great value in forensic science, such as body fluids and tissue identification, postmortem interval estimation, biological age prediction, etc. Currently, most RNA follow-up experiments involve reverse transcription (RT) procedures. It has been shown that the RT step is variable and has a greater impact on subsequent data analysis, especially for forensic trace samples. However, the pattern of variation between different RNA template inputs and complementary DNA (cDNA) yield is unclear. In this study, a series of 2-fold gradient dilutions of RNA standards (1 μg/μL - 0.24 ng/μL) and forensic samples (including blood samples, saliva samples, bloodstains, and saliva stains) were reverse-transcribed using EasyQuick RT MasterMix. The obtained cDNA was quantified by droplet digital PCR (ddPCR) to assess the RT yield of the ACTB gene. The results showed that the 125 ng RNA template had the highest RT yield in a 10 μL RT reaction system with the selected kit. For all stain samples, the RT yield improved as the amount of RNA template input increased since RNA quantities were below 125 ng. As many commercialized reverse transcription kits using different kinds of enzymes are available for forensic RNA research, we recommend that systematic experiments should be performed in advance to determine the amount of RNA input at the optimum RT yield when using any kit for reverse transcription experiments.
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Affiliation(s)
- Niu Gao
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Yumei Huo
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Tian Wang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Liwei Zhang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Wenjing Hu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Piao Yuan
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China.
| | - Yan Wang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China; Clinical Biobank Center, Medical Innovation Research Division of Chinese, PLA General Hospital, Beijing, China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China.
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Liu M, Tian C, Chen Y, Zhu J, Zheng Y, Chen J, Li Z, Xu F, Wu L, Wang X, Xie L, Tan X, Cai Y. Effectiveness of a standardized quality control management procedure for COVID-19 RT-PCR testing: a large-scale diagnostic accuracy study in China. Diagn Microbiol Infect Dis 2024; 109:116287. [PMID: 38574444 DOI: 10.1016/j.diagmicrobio.2024.116287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 03/14/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND The study aimed to construct a standardized quality control management procedure (QCMP) and access its accuracy in the quality control of COVID-19 reverse transcriptase-polymerase chain reaction (RT-PCR). METHODS Considering the initial RT-PCR results without applying QCMP as the gold standard, a large-scale diagnostic accuracy study including 4,385,925 participants at three COVID-19 RT-PCR testing sites in China, Foshan (as a pilot test), Guangzhou and Shenyang (as validation sites), was conducted from May 21, 2021, to December 15, 2022. RESULTS In the pilot test, the RT-PCR with QCMP had a high accuracy of 99.18% with 100% specificity, 100% positive predictive value (PPV), and 99.17% negative predictive value (NPV). The rate of retesting was reduced from 1.98% to 1.16%. Its accuracy was then consistently validated in Guangzhou and Shenyang. CONCLUSIONS The RT-PCR with QCMP showed excellent accuracy in identifying true negative COVID-19 and relieved the labor and time spent on retesting.
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Affiliation(s)
- Mengyu Liu
- Clinical Research Center, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, PR China; Joint Laboratory of Shantou University Medical College and Guangdong Hybribio Biotech Ltd., Shantou University Medical College, Shantou, Guangdong 515041, PR China
| | - Cuihong Tian
- Clinical Research Center, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, PR China; Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, PR China; Center for Precision Health, Edith Cowan University, Perth, WA 6027, Australia
| | - Yequn Chen
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, PR China
| | - Jinxiu Zhu
- Institute of Clinical Electrocardiography, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, PR China; Longgang Maternity and Child Institute of Shantou University Medical College, Shenzhen, Guangdong 518172, PR China
| | - Yan Zheng
- Department of Research and Development, Guangdong Research Institute of Genetic Diagnostic and Engineering Technologies for Thalassemia, Chaozhou, Guangdong 521011, PR China
| | - Jianhua Chen
- Human Papillomavirus Molecular Diagnostic Engineering Technology Research Center, Chaozhou, Guangdong 521000, PR China
| | - Zhen Li
- Hybribio Medical Laboratory Group Ltd., Chaozhou, Guangdong 521000, PR China
| | - Feng Xu
- Hybribio Medical Laboratory Group Ltd., Chaozhou, Guangdong 521000, PR China
| | - Liang Wu
- Clinical Research Center, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, PR China; Shenzhen Key Laboratory of Single-Cell Omics, Shenzhen, Guangdong 518083, PR China; BGI-Shenzhen, Shenzhen, Guangdong 518083, PR China
| | - Xingyu Wang
- Clinical Research Center, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, PR China; Beijing Hypertension League Institute, Beijing 100043, PR China
| | - Longxu Xie
- Joint Laboratory of Shantou University Medical College and Guangdong Hybribio Biotech Ltd., Shantou University Medical College, Shantou, Guangdong 515041, PR China; Human Papillomavirus Molecular Diagnostic Engineering Technology Research Center, Chaozhou, Guangdong 521000, PR China.
| | - Xuerui Tan
- Clinical Research Center, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, PR China; Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, PR China; Phenomics Research Center, Shantou University Medical College, Shantou, Guangdong 515041, PR China.
| | - Yingmu Cai
- Joint Laboratory of Shantou University Medical College and Guangdong Hybribio Biotech Ltd., Shantou University Medical College, Shantou, Guangdong 515041, PR China; Hybribio Medical Laboratory Group Ltd., Chaozhou, Guangdong 521000, PR China.
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Abstract
OBJECTIVES To investigate the proportion of lateral flow tests (LFTs) that produce negative results in those with a high risk of infectiousness from SARS-CoV-2, to investigate the impact of the stage and severity of disease, and to compare predictions made by influential mathematical models with findings of empirical studies. DESIGN Linked data analysis combining empirical evidence of the accuracy of the Innova LFT, the probability of positive viral culture or transmission to secondary cases, and the distribution of viral loads of SARS-CoV-2 in individuals in different settings. SETTING Testing of individuals with symptoms attending NHS Test-and-Trace centres across the UK, residents without symptoms attending municipal mass testing centres in Liverpool, and students without symptoms screened at the University of Birmingham. PARTICIPANTS Evidence for the sensitivity of the Innova LFT, based on 70 individuals with SARS-CoV-2 and LFT results. Infectiousness was based on viral culture rates on 246 samples (176 people with SARS-CoV-2) and secondary cases among 2 474 066 contacts; distributions of cycle threshold (Ct) values from 231 497 index individuals attending NHS Test-and-Trace centres; 70 people with SARS-CoV-2 detected in Liverpool and 62 people with SARS-CoV-2 in Birmingham (54 imputed). MAIN OUTCOME MEASURES The predicted proportions who were missed by LFT and viral culture positive and missed by LFT and sources of secondary cases, in each of the three settings. Predictions were compared with those made by mathematical models. RESULTS The analysis predicted that of those with a viral culture positive result, Innova would miss 20% attending an NHS Test-and-Trace centre, 29% without symptoms attending municipal mass testing, and 81% attending university screen testing without symptoms, along with 38%, 47%, and 90% of sources of secondary cases. In comparison, two mathematical models underestimated the numbers of missed infectious individuals (8%, 10%, and 32% in the three settings for one model, whereas the assumptions from the second model made it impossible to miss an infectious individual). Owing to the paucity of usable data, the inputs to the analyses are from limited sources. CONCLUSIONS The proportion of infectious people with SARS-CoV-2 missed by LFTs is substantial enough to be of clinical importance. The proportion missed varied between settings because of different viral load distributions and is likely to be highest in those without symptoms. Key models have substantially overestimated the sensitivity of LFTs compared with empirical data. An urgent need exists for additional robust well designed and reported empirical studies from intended use settings to inform evidence based policy.
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Affiliation(s)
- Jonathan J Deeks
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham B15 2TT, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, UK and University of Birmingham, UK
| | - Anika Singanayagam
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, UK
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Hamish Houston
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, UK
| | - Alice J Sitch
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham B15 2TT, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, UK and University of Birmingham, UK
| | - Seran Hakki
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, UK
| | - Jake Dunning
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | - Ajit Lalvani
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, UK
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Kaur H, Mukhopadhyay L, Gupta N, Aggarwal N, Sangal L, Potdar V, Inbanathan FY, Narayan J, Gupta S, Rana S, Vijay N, Singh H, Kaur J, Kumar V, Kaundal N, Abraham P, Ravi V. External quality assessment of COVID-19 real time reverse transcription PCR laboratories in India. PLoS One 2022; 17:e0263736. [PMID: 35134089 PMCID: PMC8824319 DOI: 10.1371/journal.pone.0263736] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/25/2022] [Indexed: 11/18/2022] Open
Abstract
Sudden emergence and rapid spread of COVID-19 created an inevitable need for expansion of the COVID-19 laboratory testing network across the world. The strategy to test-track-treat was advocated for quick detection and containment of the disease. Being the second most populous country in the world, India was challenged to make COVID-19 testing available and accessible in all parts of the country. The molecular laboratory testing network was augmented expeditiously, and number of laboratories was increased from one in January 2020 to 2951 till mid-September, 2021. This rapid expansion warranted the need to have inbuilt systems of quality control/ quality assurance. In addition to the ongoing inter-laboratory quality control (ILQC), India implemented an External Quality Assurance Program (EQAP) with assistance from World Health Organization (WHO) and Royal College of Pathologists, Australasia. Out of the 953 open system rRTPCR laboratories in both public and private sector who participated in the first round of EQAP, 891(93.4%) laboratories obtained a passing score of > = 80%. The satisfactory performance of Indian COVID-19 testing laboratories has boosted the confidence of the public and policy makers in the quality of testing. ILQC and EQAP need to continue to ensure adherence of the testing laboratories to the desired quality standards.
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Affiliation(s)
- Harmanmeet Kaur
- Virology Unit, Indian Council of Medical Research, DHR, MoHFW, New Delhi, Delhi, India
| | - Labanya Mukhopadhyay
- Virology Unit, Indian Council of Medical Research, DHR, MoHFW, New Delhi, Delhi, India
| | - Nivedita Gupta
- Virology Unit, Indian Council of Medical Research, DHR, MoHFW, New Delhi, Delhi, India
- * E-mail:
| | - Neeraj Aggarwal
- Virology Unit, Indian Council of Medical Research, DHR, MoHFW, New Delhi, Delhi, India
| | - Lucky Sangal
- WHO South-East Asia Regional Office, New Delhi, Delhi, India
| | - Varsha Potdar
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | | | - Jitendra Narayan
- Virology Unit, Indian Council of Medical Research, DHR, MoHFW, New Delhi, Delhi, India
| | - Swati Gupta
- Virology Unit, Indian Council of Medical Research, DHR, MoHFW, New Delhi, Delhi, India
| | - Salaj Rana
- Virology Unit, Indian Council of Medical Research, DHR, MoHFW, New Delhi, Delhi, India
| | - Neetu Vijay
- Virology Unit, Indian Council of Medical Research, DHR, MoHFW, New Delhi, Delhi, India
| | - Harpreet Singh
- Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, Delhi, India
| | - Jasmine Kaur
- Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, Delhi, India
| | - Vinit Kumar
- Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, Delhi, India
| | | | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India
| | - Vasanthapuram Ravi
- National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
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Su RR, Huang ZY, Qin CW, Zheng XL, Lu W, Wang XY. Evaluation of Reference Genes in Glenea cantor (Fabricius) by Using qRT-PCR. Genes (Basel) 2021; 12:1984. [PMID: 34946935 PMCID: PMC8701190 DOI: 10.3390/genes12121984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/07/2021] [Accepted: 12/11/2021] [Indexed: 12/04/2022] Open
Abstract
Kapok is the main host of Glenea cantor (Fabricius), which causes serious damage and is difficult to control. In severe cases, it often causes the kapok trees to die continuously, which seriously affects the results of urban landscaping. To provide reference for the functional research on related genes in G. cantor, we screened the stable expression of candidate reference genes at different developmental stages (i.e., eggs, larvae, pupae, and adults), in various adult tissues (i.e., head, thorax, abdomen, feet, antennae, and wings), and sexes (i.e., male pupae, female pupae, male adults, and female adults). In this study, 12 candidate reference genes (i.e., ACTINLIKE, ACTININ, TUB, RPL36, RPL32, RPS20, TBP, GAPDH, 18S rRNA, EF1A1, EF1A2, and UBQ) were evaluated using different adult tissues, developmental stages, and sexes. RefFinder, geNorm, NormFinder, and BestKeeper were used to evaluate and comprehensively analyze the stability of the expression of the candidate reference genes. The results show that RPL32 and EF1A1 were the most suitable reference genes in the different adult tissues, and RPL36 and EF1A1 were best at the different developmental stages. RPL36 and EF1A2 were the best fit for the qRT-PCR reference genes in the different sexes, while RPL36 and EF1A1 were the most appropriate qRT-PCR reference genes in all samples. Results from geNorm showed that the optimal number of reference genes was two. We also surveyed the expression of cellulase at the different developmental stages and in the different adult tissues. Results further verified the reliability of the reference genes, and confirmed the best reference genes under the different experimental conditions. This study provides a useful tool for molecular biological studies on G. cantor.
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Affiliation(s)
| | | | | | | | | | - Xiao-Yun Wang
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China; (R.-R.S.); (Z.-Y.H.); (C.-W.Q.); (X.-L.Z.); (W.L.)
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Polese-Bonatto M, Sartor ITS, Varela FH, Giannini GLT, Azevedo TR, Kern LB, Fernandes IR, Zavaglia GO, de David CN, Santos AP, de Almeida WAF, Porto VBG, Scotta MC, Stein RT. Children Have Similar Reverse Transcription Polymerase Chain Reaction Cycle Threshold for Severe Acute Respiratory Syndrome Coronavirus 2 in Comparison With Adults. Pediatr Infect Dis J 2021; 40:e413-e417. [PMID: 34596626 PMCID: PMC8505158 DOI: 10.1097/inf.0000000000003300] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/29/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND The viral dynamics and the role of children in the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not completely understood. Our aim was to evaluate reverse transcription polymerase chain reaction (RT-PCR) cycle threshold (Ct) values among children with confirmed SARS-CoV-2 compared with that of adult subjects. METHODS Patients (from 2 months to ≤18 years of age and adults) with signs and symptoms of acute SARS-CoV-2 infection for less than 7 days were prospectively enrolled in the study from May to November 2020. All participants performed RT-PCR assay for SARS-CoV-2 detection; Ct values of ORF1ab, N and S gene targets and the average of all the 3 probes were used as surrogates of viral load. RESULTS There were 21 infants (2 months to <2 years), 40 children (≥2 to <12 years), 22 adolescents (≥12 to <18 years) and 293 adults of 376 participants with confirmed SARS-CoV-2 infections. RT-PCR Ct values from all participants less than 18 years of age, as well as from all childhood subgroups, were not significantly different from adults, comparing ORF1ab, N, S and all the gene targets together (P = 0.453). CONCLUSIONS Ct values for children were comparable with that of adults. Although viral load is not the only determinant of SARS-CoV-2 transmission, children may play a role in the spread of coronavirus disease 2019 in the community.
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Affiliation(s)
| | | | - Fernanda Hammes Varela
- From the Social Responsibility – PROADI-SUS, Hospital Moinhos de Vento
- School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul
| | | | | | | | | | | | | | - Amanda Paz Santos
- From the Social Responsibility – PROADI-SUS, Hospital Moinhos de Vento
| | | | | | - Marcelo Comerlato Scotta
- From the Social Responsibility – PROADI-SUS, Hospital Moinhos de Vento
- School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul
| | - Renato T. Stein
- From the Social Responsibility – PROADI-SUS, Hospital Moinhos de Vento
- School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul
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7
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Abstract
The rapid spread and evolution of various strains of SARS-CoV-2, the virus responsible for COVID-19, continues to challenge the disease controlling measures globally. Alarming concern is, the number of second wave infections surpassed the first wave and the onset of severe symptoms manifesting rapidly. In this scenario, testing of maximum population in less time and minimum cost with existing diagnostic amenities is the only possible way to control the spread of the virus. The previously described RNA extraction-free methods using dry swab have been shown to be advantageous in these critical times by different studies. In this work, we show the temporal stability and performance of the dry swab viral detection method at two different temperatures. Contrived dry swabs holding serially diluted SARS-CoV-2 strains A2a and A3i at 25°C (room temperature; RT) and 4°C were subjected to direct RT-PCR and compared with standard VTM-RNA based method. The results clearly indicate that dry swab method of RNA detection is as efficient as VTM-RNA-based method in both strains, when checked for up to 72 h. The lesser CT values of dry swab samples in comparison to that of the VTM-RNA samples suggest better sensitivity of the method within 48 h of time. The results collectively suggest that dry swab samples are stable at RT for 24 h and the detection of SARS-CoV-2 RNA by RT-PCR do not show variance from VTM-RNA. This extraction free, direct RT-PCR method holds phenomenal standing in the present life-threatening circumstances due to SARS-CoV-2.
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Affiliation(s)
- C G Gokulan
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Uday Kiran
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002 India
| | - Santosh Kumar Kuncha
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Rakesh K Mishra
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002 India
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Berruien NNA, Murray JF, Smith CL. Pregnancy influences the selection of appropriate reference genes in mouse tissue: Determination of appropriate reference genes for quantitative reverse transcription PCR studies in tissues from the female mouse reproductive axis. Gene 2021; 801:145855. [PMID: 34293448 DOI: 10.1016/j.gene.2021.145855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022]
Abstract
Selecting stably expressed reference genes which are not affected by physiological or pathophysiological conditions is crucial for reliable quantification in gene expression studies. This study examined the expression stability of a panel of twelve reference genes in tissues from the female mouse reproductive axis and the uterus. Gene expression studies were carried out using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). cDNA was synthesised from RNA extracted from hypothalami, pituitaries, ovaries and uteri of female mice at ages representing weaning, puberty and adulthood as well as pregnancy (13 ± 1 days post-coitus) (n = a minimum of 3 at each age and at pregnancy). The reference genes examined included 18 s, Actb, Atp5b, B2m, Canx, Cyc1, Eif4a2, Gapdh, Rpl13a, Sdha, Ubc and Ywhaz. The RT-qPCR raw data were imported into the qBASE+ software to analyse the expression stability using GeNorm. These data were also subsequently analysed using other software packages (Delta CT, Normfinder, BestKeeper). A comprehensive ranking was conducted considering all stability rankings generated from the different software analyses. B2m and Eif4a2 deviated from the acceptable range for amplification efficiency and therefore were excluded from the further analyses. The stability of the reference genes is influenced by the software used for the analysis with BestKeeper providing markedly different results than the other analyses. GeNorm analysis of tissues taken at different ages but not including pregnant animals, indicated that the expression of the reference genes is tissue specific with the most stable genes being: in the hypothalamus, Canx and Actb; in the pituitary, Sdha and Cyc1; in the ovary, 18s, Sdha and Ubc; and in the uterus, Ywhaz, Cyc1, Atp5b, 18s and Rpl13a. The optimal number of reference genes to be used was determined to be 2 in the first three tissues while in the uterus, the V-score generated by the GeNorm analysis was higher than 0.15 suggesting that 3 or more genes should be used for normalisation. Inclusion of tissues from pregnant mice changed the reference genes identified as being the most stable: Ubc and Sdha were the most stable genes in the hypothalamus, pituitary and the ovary. The addition of pregnant tissue had no effect on the stability of the genes in uterus (Ywhaz, Cyc1, Atp5b, 18s and Rpl13a). Identification of these stable reference genes will be of use to those interested in studying female fertility and researchers should be alert to the effects of pregnancy on reference gene stability. This study also signifies the importance of re-examining reference gene stability if the experimental conditions are changed, as shown with the introduction of pregnancy as a new factor in this research.
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Affiliation(s)
- Nasrin N A Berruien
- University of Westminster, School of Life Sciences, 115 New Cavendish Street, London W1W 6UW, United Kingdom
| | - Joanne F Murray
- University of Edinburgh, Centre for Discovery Brain Science, Hugh Robson Building, 15 George Square, Edinburgh EH8 9XD, United Kingdom
| | - Caroline L Smith
- University of Westminster, School of Life Sciences, 115 New Cavendish Street, London W1W 6UW, United Kingdom.
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Dai Y, Kou H, Guo X, Gong Z, Liu H, Liu Y, Wang H, Guo Y. Identification and validation of reference genes for RT-qPCR analysis in fetal rat pancreas. Reprod Toxicol 2021; 105:211-220. [PMID: 34537367 DOI: 10.1016/j.reprotox.2021.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/20/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022]
Abstract
The choice of reference gene is crucial for quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) assay. To screen and determine the suitable reference genes in fetal rat pancreas, we selected eight candidate reference genes (Gapdh, Actb, Rn18 s, B2m, Rpl13a, Tbp, Ywhaz and Ubc), and evaluated the constancy of gene expression from fetal rat pancreases in non-pathological situation and prenatal dexamethasone exposure (PDE) model, using four algorithms: GeNorm, NormFinder, Bestkeeper and Comparative ΔCt method. In addition, the alteration of mRNA levels of pancreatic insulin was compared between control and PDE groups to validate the reliability of selected reference genes for data normalization of RT-qPCR. The comprehensive ranking of reference genes under physiological condition was as follow: Gapdh > Actb > Ywhaz > Ubc > Rn18s > Rpl13a > B2m > Tbp (female); Actb > Ywhaz > Gapdh > Ubc > B2m > Rpl13a > Rn18 s | Tbp (male). The top ranking reference genes were also stably expressed in PDE fetal pancreas. The best reference gene combinations are: Ywhaz+Actb for female and Ywhaz+Gapdh for male fetal rat pancreas, respectively. Compared with low ranking or single reference gene, the change trend of insulin mRNA normalized by the best reference gene combination between control and PDE groups was more significant and consistent with that of serum insulin level. In conclusion, our results provided the optimal combination of stable reference genes for RT-qPCR assay in pancreatic developmental toxicity study.
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Affiliation(s)
- Yongguo Dai
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Hao Kou
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China; Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Xiaoling Guo
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Zheng Gong
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Heze Liu
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Yi Liu
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Hui Wang
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China.
| | - Yu Guo
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China.
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10
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Wu Y, Zhang C, Yang H, Lyu L, Li W, Wu W. Selection and Validation of Candidate Reference Genes for Gene Expression Analysis by RT-qPCR in Rubus. Int J Mol Sci 2021; 22:ijms221910533. [PMID: 34638877 PMCID: PMC8508773 DOI: 10.3390/ijms221910533] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/19/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022] Open
Abstract
Due to the lack of effective and stable reference genes, studies on functional genes in Rubus, a genus of economically important small berry crops, have been greatly limited. To select the best internal reference genes of different types, we selected four representative cultivars of blackberry and raspberry (red raspberry, yellow raspberry, and black raspberry) as the research material and used RT-qPCR technology combined with three internal stability analysis software programs (geNorm, NormFinder, and BestKeeper) to analyze 12 candidate reference genes for the stability of their expression. The number of most suitable internal reference genes for different cultivars, tissues, and fruit developmental stages of Rubus was calculated by geNorm software to be two. Based on the results obtained with the three software programs, the most stable genes in the different cultivars were RuEEF1A and Ru18S. Finally, to validate the reliability of selected reference genes, the expression pattern of the RuCYP73A gene was analyzed, and the results highlighted the importance of appropriate reference gene selection. RuEEF1A and Ru18S were screened as reference genes for their relatively stable expression, providing a reference for the further study of key functional genes in blackberry and raspberry and an effective tool for the analysis of differential gene expression.
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Affiliation(s)
- Yaqiong Wu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (H.Y.); (L.L.)
| | - Chunhong Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (H.Y.); (L.L.)
| | - Haiyan Yang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (H.Y.); (L.L.)
| | - Lianfei Lyu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (H.Y.); (L.L.)
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
- Correspondence: (W.L.); (W.W.); Tel.: +86-25-8542-8531 (W.L.); +86-25-8434-7063 (W.W.)
| | - Wenlong Wu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (H.Y.); (L.L.)
- Correspondence: (W.L.); (W.W.); Tel.: +86-25-8542-8531 (W.L.); +86-25-8434-7063 (W.W.)
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11
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Kerr C, Dunne J, Hughes G, Cox F, Healy M, Holmes P, O'Rourke F, O'Brien C, Coyne D, Crowley V, Crowley B, Conlon N, Bergin C. A Comparison of the Performance of SARS-CoV-2 Antibody Assays in Healthcare Workers with COVID-19. Ir Med J 2021; 114:414. [PMID: 34520649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Aims Since its emergence, significant interest surrounds the use of SARS-CoV-2 serological tests as an alternative or as an adjunct to molecular testing. However, given the speed of this pandemic, paralleled with the pressure to develop and provide serological tests in an expediated manner, not every assay has undergone the rigorous evaluation that is usually associated with medical diagnostic assays. We aimed to examine the performance of several commercially available SARS-CoV-2 IgG antibody assays among participants with confirmed COVID-19 disease and negative controls. Methods Serum taken between day 17 and day 40 post onset of symptoms from 41 healthcare workers with RT-PCR confirmed COVID-19 disease, and pre-pandemic serum from 20 negative controls, were tested for the presence of SARS-CoV-2 IgG using 7 different assays including point-of-care (POC) and laboratory-based assays. Results Assay performance varied. The lab-based Abbott diagnostics SARS-CoV-2 IgG assay proved to be the assay with the best positive and negative predictive value, and overall accuracy. The POC Nal von Minden GmbH and Biozek assays also performed well. Conclusion Our research demonstrates the variations in performance of several commercially available SARS-CoV-2 antibody assays. These findings identify the limitations of some serological tests for SARS-CoV-2. This information will help inform test selection and may have particular relevance to providers operating beyond accredited laboratories.
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Affiliation(s)
- C Kerr
- Genitourinary Medicine and Infectious Diseases Department (GUIDe), St. James's Hospital, Dublin
- Department of Medicine, School of Medicine, Trinity College Dublin, Dublin
| | - J Dunne
- Department of Immunology, St. James's Hospital, Dublin
| | - G Hughes
- Genitourinary Medicine and Infectious Diseases Department (GUIDe), St. James's Hospital, Dublin
- Department of Medicine, School of Medicine, Trinity College Dublin, Dublin
| | - F Cox
- Department of Immunology, St. James's Hospital, Dublin
| | - M Healy
- Department of Biochemistry, St. James's Hospital, Dublin
| | - P Holmes
- Department of Biochemistry, St. James's Hospital, Dublin
| | - F O'Rourke
- Department of Microbiology, St. James's Hospital, Dublin
| | - C O'Brien
- Department of Immunology, St. James's Hospital, Dublin
| | - D Coyne
- Department of Virology, National Blood Centre, St James's Hospital, Dublin
| | - V Crowley
- Department of Biochemistry, St. James's Hospital, Dublin
| | - B Crowley
- Department of Microbiology, St. James's Hospital, Dublin
| | - N Conlon
- Department of Immunology, St. James's Hospital, Dublin
| | - C Bergin
- Genitourinary Medicine and Infectious Diseases Department (GUIDe), St. James's Hospital, Dublin
- Department of Medicine, School of Medicine, Trinity College Dublin, Dublin
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Diaz-Lara A, Stevens KA, Klaassen V, Hwang MS, Al Rwahnih M. Sequencing a Strawberry Germplasm Collection Reveals New Viral Genetic Diversity and the Basis for New RT-qPCR Assays. Viruses 2021; 13:v13081442. [PMID: 34452308 PMCID: PMC8402890 DOI: 10.3390/v13081442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/13/2021] [Accepted: 07/21/2021] [Indexed: 11/21/2022] Open
Abstract
Viruses are considered of major importance in strawberry (Fragaria × ananassa Duchesne) production given their negative impact on plant vigor and growth. Strawberry accessions from the National Clonal Germplasm Repository were screened for viruses using high throughput sequencing (HTS). Analyses of sequence information from 45 plants identified multiple variants of 14 known viruses, comprising strawberry mottle virus (SMoV), beet pseudo yellows virus (BPYV), strawberry pallidosis-associated virus (SPaV), tomato ringspot virus (ToRSV), strawberry mild yellow edge virus (SMYEV), strawberry vein banding virus (SVBV), strawberry crinkle virus (SCV), strawberry polerovirus 1 (SPV-1), apple mosaic virus (ApMV), strawberry chlorotic fleck virus (SCFaV), strawberry crinivirus 4 (SCrV-4), strawberry crinivirus 3 (SCrV-3), Fragaria chiloensis latent virus (FClLV) and Fragaria chiloensis cryptic virus (FCCV). Genetic diversity of sequenced virus isolates was investigated via sequence homology analysis, and partial-genome sequences were deposited into GenBank. To confirm the HTS results and expand the detection of strawberry viruses, new reverse transcription quantitative PCR (RT-qPCR) assays were designed for the above-listed viruses. Further in silico and in vitro validation of the new diagnostic assays indicated high efficiency and reliability. Thus, the occurrence of different viruses, including divergent variants, among the strawberries was verified. This is the first viral metagenomic survey in strawberry, additionally, this study describes the design and validation of multiple RT-qPCR assays for strawberry viruses, which represent important detection tools for clean plant programs.
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Affiliation(s)
- Alfredo Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA;
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Kristian A. Stevens
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA; (K.A.S.); (V.K.); (M.S.H.)
- Department of Computer Science, University of California-Davis, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - Vicki Klaassen
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA; (K.A.S.); (V.K.); (M.S.H.)
| | - Min Sook Hwang
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA; (K.A.S.); (V.K.); (M.S.H.)
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA;
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA; (K.A.S.); (V.K.); (M.S.H.)
- Correspondence:
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13
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Šimenc L, Knific T, Toplak I. The Comparison of Honeybee Viral Loads for Six Honeybee Viruses (ABPV, BQCV, CBPV, DWV, LSV3 and SBV) in Healthy and Clinically Affected Honeybees with TaqMan Quantitative Real-Time RT-PCR Assays. Viruses 2021; 13:v13071340. [PMID: 34372546 PMCID: PMC8310196 DOI: 10.3390/v13071340] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 01/17/2023] Open
Abstract
The viral loads of acute bee paralysis virus (ABPV), black queen cell virus (BQCV), chronic bee paralysis virus (CBPV), deformed wing virus (DWV), Lake Sinai virus 3 (LSV3), and sacbrood bee virus (SBV) were determined in samples with the use of quantitative TaqMan real-time reverse transcription and polymerase chain reaction (RT-qPCR). A total of 108 samples of healthy adult honeybees from four differently located apiaries and samples of honeybees showing different clinical signs of viral infections from 89 apiaries were collected throughout Slovenia. The aim of this study was to discover correlations between viral loads and clinical signs in adult honeybees and confirm previously set threshold viral load levels between healthy and clinically affected honeybees. Within this study, two new RT-qPCR assays for quantification of LSV3 and SBV were developed. Statistically significant differences in viral loads of positive samples were identified between healthy and clinically affected honeybees for ABPV, CBPV, DWV, and SBV, while for BQCV and LSV3, no statistical differences were observed between both groups. Despite high detected LSV3 prevalence and viral loads around 6.00 log10 viral copies/bee, this lineage probably has a limited impact on the health status of honeybee colonies. The determined viral loads between 3.94 log10 and 13.17 log10 in positive samples for six viruses, collected over 10 consecutive months, including winter, present additional information of high viral load variations in healthy honeybee colonies.
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Affiliation(s)
- Laura Šimenc
- Virology Unit, Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1115 Ljubljana, Slovenia;
- Correspondence:
| | - Tanja Knific
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1115 Ljubljana, Slovenia;
| | - Ivan Toplak
- Virology Unit, Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1115 Ljubljana, Slovenia;
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Wu J, Fan H, Hu Y, Guo H, Lin H, Jiao Y, Lu Z, Du S, Liu X, Shahid MQ. Identification of stable pollen development related reference genes for accurate qRT-PCR analysis and morphological variations in autotetraploid and diploid rice. PLoS One 2021; 16:e0253244. [PMID: 34185803 PMCID: PMC8241056 DOI: 10.1371/journal.pone.0253244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/01/2021] [Indexed: 11/26/2022] Open
Abstract
Autotetraploid rice exhibited hybrid vigor and greater genetic variation compared to diploid rice, but low pollen fertility is a major hindrance for its utilization. Our previous analysis revealed that large number of pollen fertility genes were exhibited down-regulation in autotetraploid rice. Hence, it is of utmost importance to reveal the expression patterns of pollen fertility genes with high accuracy. To find stable reference genes for autotetraploid rice, we compared the pollen development stages between diploid and autotetraploid rice, and 14 candidate genes were selected based on transcriptome analysis to evaluate their expression levels. Autotetraploid rice (i.e. Taichung65-4x) displayed lower seed set (40.40%) and higher percentage of abnormalities during the pollen development process than its diploid counterpart. To detect the candidate reference genes for pollen development of autotetraploid and diploid rice, we used five different algorithms, including NormFinder, BestKeeper, ΔCt method, geNorm and Re-Finder to evaluate their expression patterns stability. Consequently, we identified two genes, Cytochrome b5 and CPI, as the best candidate reference genes for qRT-PCR normalization in autotetraploid and diploid rice during pre-meiosis, meiosis, single microspore and bicellular pollen development stages. However, Cytochrome b5 was found to be the most stably expressed gene during different pollen development stages in autotetraploid rice. The results of our study provide a platform for subsequent gene expression analyses in autotetraploid rice, which could also be used in other polyploid plants.
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Affiliation(s)
- Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Hao Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yifan Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Haibin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Hong Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yinzhi Jiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Zijun Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Susu Du
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
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Ghanbari S, Salimi A, Rahmani S, Nafissi N, Sharifi-Zarchi A, Mowla SJ. miR-361-5p as a promising qRT-PCR internal control for tumor and normal breast tissues. PLoS One 2021; 16:e0253009. [PMID: 34101749 PMCID: PMC8186776 DOI: 10.1371/journal.pone.0253009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/27/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND One of the most widely used evaluation methods in miRNA experiments is qRT-PCR. However, selecting suitable internal controls (IC) is crucial for qRT-PCR experiments. Currently, there is no consensus on the ICs for miRNA qRT-PCR experiments in breast cancer. To this end, we tried to identify the most stable (the least expression alteration) and promising miRNAs in normal and tumor breast tissues by employing TCGA miRNA-Seq data and then experimentally validated them on fresh clinical samples. METHODS A multi-component scoring system was used which takes into account multiple expression stability criteria as well as correlation with clinical characteristics. Furthermore, we extended the scoring system for more than two biological sub-groups. TCGA BRCA samples were analyzed based on two grouping criteria: Tumor & Normal samples and Tumor subtypes. The top 10 most stable miRNAs were further investigated by differential expression and survival analysis. Then, we examined the expression level of the top scored miRNA (hsa-miR-361-5p) along with two commonly used ICs hsa-miR-16-5p and U48 on 34 pairs of Primary breast tumor and their adjacent normal tissues using qRT-PCR. RESULTS According to our multi-component scoring system, hsa-miR-361-5p had the highest stability score in both grouping criteria and hsa-miR-16-5p showed significantly lower scores. Based on our qRT-PCR assay, while U48 was the most abundant IC, hsa-miR-361-5p had lower standard deviation and also was the only IC capable of detecting a significant up-regulation of hsa-miR-21-5p in breast tumor tissue. CONCLUSIONS miRNA-Seq data is a great source to discover stable ICs. Our results demonstrated that hsa-miR-361-5p is a highly stable miRNA in tumor and non-tumor breast tissue and we recommend it as a suitable reference gene for miRNA expression studies in breast cancer. Additionally, although hsa-miR-16-5p is a commonly used IC, it's not a suitable one for breast cancer studies.
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Affiliation(s)
- Sogol Ghanbari
- Molecular Genetics Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
| | - Adel Salimi
- Computer Engineering Department, Sharif University of Technology, Tehran, Iran
| | - Saeid Rahmani
- Computer Engineering Department, Sharif University of Technology, Tehran, Iran
| | - Nahid Nafissi
- Surgical Department, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Sharifi-Zarchi
- Computer Engineering Department, Sharif University of Technology, Tehran, Iran
| | - Seyed Javad Mowla
- Molecular Genetics Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
- * E-mail:
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Peltan ID, Beesley SJ, Webb BJ, Lopansri BK, Sinclair W, Jacobs JR, Brown SM. Evaluation of potential COVID-19 recurrence in patients with late repeat positive SARS-CoV-2 testing. PLoS One 2021; 16:e0251214. [PMID: 33945583 PMCID: PMC8096096 DOI: 10.1371/journal.pone.0251214] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/22/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND SARS-CoV-2 reinfection and reactivation has mostly been described in case reports. We therefore investigated the epidemiology of recurrent COVID-19 SARS-CoV-2. METHODS Among patients testing positive for SARS-CoV-2 between March 11 and July 31, 2020 within an integrated healthcare system, we identified patients with a recurrent positive SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) assay ≥60 days after an initial positive test. To assign an overall likelihood of COVID-19 recurrence, we combined quantitative data from initial and recurrent positive RT-PCR cycle thresholds-a value inversely correlated with viral RNA burden- with a clinical recurrence likelihood assigned based on independent, standardized case review by two physicians. "Probable" or "possible" recurrence by clinical assessment was confirmed as the final recurrence likelihood only if a cycle threshold value obtained ≥60 days after initial testing was lower than its preceding cycle threshold or if the patient had an interval negative RT-PCR. RESULTS Among 23,176 patients testing positive for SARS-CoV-2, 1,301 (5.6%) had at least one additional SARS-CoV-2 RT-PCRs assay ≥60 days later. Of 122 testing positive, 114 had sufficient data for evaluation. The median interval to the recurrent positive RT-PCR was 85.5 (IQR 74-107) days. After combining clinical and RT-PCR cycle threshold data, four patients (3.5%) met criteria for probable COVID-19 recurrence. All four exhibited symptoms at recurrence and three required a higher level of medical care compared to their initial diagnosis. After including six additional patients (5.3%) with possible recurrence, recurrence incidence was 4.3 (95% CI 2.1-7.9) cases per 10,000 COVID-19 patients. CONCLUSIONS Only 0.04% of all COVID-19 patients in our health system experienced probable or possible recurrence; 90% of repeat positive SARS-CoV-2 RT-PCRs were not consistent with true recurrence. Our pragmatic approach combining clinical and quantitative RT-PCR data could aid assessment of COVID-19 reinfection or reactivation by clinicians and public health personnel.
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Affiliation(s)
- Ithan D. Peltan
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Intermountain Healthcare, Salt Lake City, UT, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, United States of America
- * E-mail:
| | - Sarah J. Beesley
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Intermountain Healthcare, Salt Lake City, UT, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, United States of America
| | - Brandon J. Webb
- Division of Infectious Disease and Clinical Epidemiology, Intermountain Healthcare, Salt Lake City, UT, United States of America
| | - Bert K. Lopansri
- Intermountain Laboratory Services, Department of Pathology, Intermountain Healthcare, Salt Lake City, UT, United States of America
| | - Will Sinclair
- Intermountain Laboratory Services, Department of Pathology, Intermountain Healthcare, Salt Lake City, UT, United States of America
| | - Jason R. Jacobs
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Intermountain Healthcare, Salt Lake City, UT, United States of America
| | - Samuel M. Brown
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Intermountain Healthcare, Salt Lake City, UT, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, United States of America
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Mekonnen D, Mengist HM, Derbie A, Nibret E, Munshea A, He H, Li B, Jin T. Diagnostic accuracy of serological tests and kinetics of severe acute respiratory syndrome coronavirus 2 antibody: A systematic review and meta-analysis. Rev Med Virol 2021; 31:e2181. [PMID: 33152146 DOI: 10.1002/rmv.2181] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/22/2022]
Abstract
This study aimed to assess the diagnostic test accuracy (DTA) of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) serological test methods and the kinetics of antibody positivity. Systematic review and meta-analysis were conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guideline. We included articles evaluating the diagnostic accuracy of serological tests and the kinetics of antibody positivity. MEDLINE through PubMed, Scopus, medRxiv and bioRxiv were sources of articles. Methodological qualities of included articles were appraised using QUADAS-2 while Metandi performs bivariate meta-analysis of DTA using a generalized linear mixed-model approach. Stata 14 and Review Manager 5.3 were used for data analysis. The summary sensitivity/specificity of chemiluminescence immunoassay (CLIA), enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay (LFIA) were 92% (95% CI: 86%-95%)/99% (CI: 97%-99%), 86% (CI: 82%-89%)/99% (CI: 98%-100%) and 78% (CI: 71%-83%)/98% (95% CI: 96%-99%), respectively. Moreover, CLIA-based assays produced nearly 100% sensitivity within 11-15 days post-symptom onset (DPSO). Based on antibody type, the sensitivity of ELISA-total antibody, CLIA-IgM/G and CLIA-IgG gauged at 94%, 92% and 92%, respectively. The sensitivity of CLIA-RBD assay reached 96%, while LFIA-S demonstrated the lowest sensitivity, 71% (95% CI: 58%-80%). CLIA assays targeting antibodies against RBD considered the best DTA. The antibody positivity rate increased corresponding with DPSO, but there was some decrement when moving from acute phase to convalescent phase of infection. As immunoglobulin isotope-related DTA was heterogeneous, our data have insufficient evidence to recommend CLIA/ELISA for clinical decision-making, but likely to have comparative advantage over RT-qPCR in certain circumstances and geographic regions.
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Affiliation(s)
- Daniel Mekonnen
- Department of Obstetrics and Gynecology, Division of Molecular Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Diseases, University of Science and Technology of China, Hefei, Anhui, China
- School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science & Technology of China, Hefei, Anhui, China
- Department of Medical Microbiology, Immunology and Parasitology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Hylemariam Mihiretie Mengist
- Department of Obstetrics and Gynecology, Division of Molecular Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Diseases, University of Science and Technology of China, Hefei, Anhui, China
- School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science & Technology of China, Hefei, Anhui, China
| | - Awoke Derbie
- Department of Medical Microbiology, Immunology and Parasitology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- The Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDTAfrica), Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Abaineh Munshea
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Hongliang He
- Department of Obstetrics and Gynecology, Division of Molecular Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Diseases, University of Science and Technology of China, Hefei, Anhui, China
- School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science & Technology of China, Hefei, Anhui, China
| | - Bofeng Li
- School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science & Technology of China, Hefei, Anhui, China
- Department of Medical Oncology, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, Division of Molecular Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Diseases, University of Science and Technology of China, Hefei, Anhui, China
- School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science & Technology of China, Hefei, Anhui, China
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Francis R, Le Bideau M, Jardot P, Grimaldier C, Raoult D, Bou Khalil JY, La Scola B. High-speed large-scale automated isolation of SARS-CoV-2 from clinical samples using miniaturized co-culture coupled to high-content screening. Clin Microbiol Infect 2021; 27:128.e1-128.e7. [PMID: 32979576 PMCID: PMC7510445 DOI: 10.1016/j.cmi.2020.09.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/01/2020] [Accepted: 09/11/2020] [Indexed: 01/12/2023]
Abstract
OBJECTIVES A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is responsible for the current coronavirus disease 2019 global pandemic. Only a few laboratories routinely isolate the virus, which is because the current co-culture strategy is highly time-consuming and requires a biosafety level 3 laboratory. This work aimed to develop a new high-throughput isolation strategy using novel technologies for rapid and automated isolation of SARS-CoV-2. METHODS We used an automated microscope based on high-content screening (HCS), and we applied specific image analysis algorithms targeting cytopathic effects of SARS-CoV-2 on Vero E6 cells. A randomized panel of 104 samples, including 72 that tested positive by RT-PCR and 32 that tested negative, were processed with our HCS strategy and were compared with the classical isolation procedure. RESULTS The isolation rate was 43% (31/72) with both strategies on RT-PCR-positive samples and was correlated with the initial RNA viral load in the samples, in which we obtained a positivity threshold of 27 Ct. Co-culture delays were shorter with the HCS strategy, where 80% (25/31) of the positive samples were recovered by the third day of co-culture, compared with only 26% (8/30) with the classic strategy. Moreover, only the HCS strategy allowed us to recover all the positive samples (31 with HCS versus 27 with classic strategy) after 1 week of co-culture. CONCLUSIONS This system allows the rapid and automated screening of clinical samples with minimal operator workload, which reduces the risk of contamination and paves the way for future applications in clinical microbiology, such as large-scale drug susceptibility testing.
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Affiliation(s)
- Rania Francis
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), AP-HM, Marseille, France
| | - Marion Le Bideau
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), AP-HM, Marseille, France
| | - Priscilla Jardot
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), AP-HM, Marseille, France
| | - Clio Grimaldier
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), AP-HM, Marseille, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), AP-HM, Marseille, France
| | | | - Bernard La Scola
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), AP-HM, Marseille, France.
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Eckel F, Küsters F, Drossel B, Konert M, Mattes H, Schopf S. Variplex™ test system fails to reliably detect SARS-CoV-2 directly from respiratory samples without RNA extraction. Eur J Clin Microbiol Infect Dis 2020; 39:2373-2377. [PMID: 32681309 PMCID: PMC7367510 DOI: 10.1007/s10096-020-03983-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/03/2020] [Indexed: 12/22/2022]
Abstract
Diagnosis of COVID is performed by PCR methods, but their capacity is limited by the requirement of high-level facilities and instruments. The loop-mediated isothermal amplification (LAMP) method has been utilized for the detection of isolated virus-specific RNA. Preliminary data suggest the possibility of isothermal amplification directly from respiratory samples without RNA extraction. All patients admitted to our hospital were screened for SARS-CoV-2 by routine. Respiratory samples were tested by variplex system based on LAMP method directly without RNA extraction and by PCR. Primary endpoint was the false-negative rate of variplex test compared with PCR as gold standard. In 109 patients variplex test and PCR assay were performed simultaneously. Median age was 80 years and male/female ratio was 40/60%. The prevalence of PCR-confirmed COVID diagnosis was 43.1%. Variplex test was positive in 13.8%. False-negative rate of variplex test compared with PCR was 83.0%. The potential of LAMP technology using isolated RNA has been demonstrated impressively by others, and excellent sensitivity and specificity of detecting SARS-CoV-2 has been reported. However, without RNA extraction, the variplex test system failed to reliably detect SARS-CoV-2 directly in respiratory samples.
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Affiliation(s)
- Florian Eckel
- Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
- Medical Department, RoMed Klink Bad Aibling, Harthauser Str. 16, 83043, Bad Aibling, Germany.
| | - Franziska Küsters
- Medical Department, RoMed Klink Bad Aibling, Harthauser Str. 16, 83043, Bad Aibling, Germany
| | - Bernhard Drossel
- Hospital Laboratory, RoMed Klink Bad Aibling, Harthauser Str. 16, 83043, Bad Aibling, Germany
| | - Markus Konert
- Department of Anesthesia, RoMed Klink Bad Aibling, Harthauser Str. 16, 83043, Bad Aibling, Germany
| | - Hans Mattes
- Hospital Hygiene, RoMed Klinikum Rosenheim, Pettenkoferstr. 10, 83022, Rosenheim, Germany
| | - Stefan Schopf
- Surgical Department, RoMed Klink Bad Aibling, Harthauser Str. 16, 83043, Bad Aibling, Germany
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Buetti N, Trimboli P, Mazzuchelli T, Lo Priore E, Balmelli C, Trkola A, Conti M, Martinetti G, Elzi L, Ceschi A, Consonni V, Ogna A, Forni-Ogna V, Bernasconi E. Diabetes mellitus is a risk factor for prolonged SARS-CoV-2 viral shedding in lower respiratory tract samples of critically ill patients. Endocrine 2020; 70:454-460. [PMID: 32870469 PMCID: PMC7459254 DOI: 10.1007/s12020-020-02465-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/19/2020] [Indexed: 12/28/2022]
Abstract
PURPOSE The length of time a critically ill coronavirus disease 2019 (COVID-19) patient remains infectious and should therefore be isolated remains unknown. This prospective study was undertaken in critically ill patients to evaluate the reliability of single negative real-time polymerase chain reaction (RT-PCR) in lower tracheal aspirates (LTA) in predicting a second negative test and to analyze clinical factors potentially influencing the viral shedding. METHODS From April 9, 2020 onwards, intubated COVID-19 patients treated in the intensive care unit were systematically evaluated for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by RT-PCR of nasopharyngeal swabs and LTA. The time to negativity was defined as the time between the onset of symptoms and the viral clearance in LTA. In order to identify risk factors for prolonged viral shedding, we used univariate and multivariate Cox proportional hazards models. RESULTS Forty-eight intubated SARS-CoV-2 patients were enrolled. Overall, we observed that the association of the first negative RT-PCR with a second negative result was 96.7%. Median viral shedding was 25 (IQR: 21.5-28) days since symptoms' onset. In the univariate Cox model analysis, type 2 diabetes mellitus was associated with a prolonged viral RNA shedding (hazard ratio [HR]: 0.41, 95% CI: 0.06-3.11, p = 0.04). In the multivariate Cox model analysis, type 2 diabetes was associated with a prolonged viral RNA shedding (HR: 0.31, 95% CI: 0.11-0.89, p = 0.029). CONCLUSION Intubated patients with type 2 diabetes mellitus may have prolonged SARS-CoV-2 shedding. In critically ill COVID-19 patients, one negative LTA should be sufficient to assess and exclude infectivity.
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Affiliation(s)
- Niccolò Buetti
- Ente Ospedaliero Cantonale, Regional Hospital Locarno, Locarno, Switzerland
- University of Paris, INSERM IAME, U1137, Team DeSCID, Paris, France
- Infection Control Program and World Health Organization Collaborating Centre on Patient Safety, University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pierpaolo Trimboli
- Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Lugano, Switzerland.
- Clinic for Nuclear Medicine and Competence Center for Thyroid Diseases, Imaging Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland.
| | | | - Elia Lo Priore
- Ente Ospedaliero Cantonale, Infection Control Program, Ticino, Switzerland
- Ente Ospedaliero Cantonale, Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Carlo Balmelli
- Ente Ospedaliero Cantonale, Infection Control Program, Ticino, Switzerland
- Ente Ospedaliero Cantonale, Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marco Conti
- Ente Ospedaliero Cantonale, Regional Hospital Locarno, Locarno, Switzerland
| | | | - Luigia Elzi
- Ente Ospedaliero Cantonale, Regional Hospital Locarno, Locarno, Switzerland
- Division Infectious Diseases, Regional Hospital Bellinzona, Bellinzona, Switzerland
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Vera Consonni
- Ente Ospedaliero Cantonale, Regional Hospital Locarno, Locarno, Switzerland
| | - Adam Ogna
- Ente Ospedaliero Cantonale, Regional Hospital Locarno, Locarno, Switzerland
| | - Valentina Forni-Ogna
- Ente Ospedaliero Cantonale, Regional Hospital Locarno, Locarno, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Lugano, Switzerland
| | - Enos Bernasconi
- Ente Ospedaliero Cantonale, Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
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21
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Wang Y, Liu Y, Wang M, Yu L, Ma C, Li X, Guo T, Bao H, Kou K, Chen Y, Gong H, Zhou X. Establishment of a cell-based quantitative reverse transcription-polymerase chain reaction (RT-qPCR) assay for detection of multivalent rotavirus vaccine. J Med Virol 2020; 92:3157-3164. [PMID: 32492198 DOI: 10.1002/jmv.26128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 11/10/2022]
Abstract
Because of deficiencies of traditional potency tests in rotavirus detection, a one-step TaqMan probe-based quantitative reverse transcription-polymerase chain reaction (RT-qPCR) assay combined with cell-based method was established to determine the infectious potency of the target virus in multivalent live rotavirus vaccines in vitro. Series dilutions of rotavirus samples were inoculated into Vero cells and cultured for 24 hours. The cells were lysed and the potency was detected by RT-qPCR. The reference standards with a known titer (lgCCID50 /mL) were assayed in parallel, and the potencies of each sample were determined using parallel line method. The specificity, precision and accuracy of the assay were evaluated, respectively. The results showed that messenger RNA produced during rotavirus replication was the primary template of RT-qPCR and the primers and probes were specific to each strain. The coefficient of variation of different wells and different working days did not exceed 6% and the results of the assay were proved to be concordant with those of cell culture infective dose 50% with a relative deviation less than 5%. This assay is a more rapid, cost-effective and high-throughput way for detecting multivalent rotavirus vaccine, and will be a valuable tool in the quality control and stability monitoring of live multivalent rotavirus vaccine.
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Affiliation(s)
- Yunjin Wang
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Yueyue Liu
- Division of Enteric Virus Vaccine, National Institutes for Food and Drug Control, Beijing, China
| | - Mingqiang Wang
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Li Yu
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Chao Ma
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Xiongxiong Li
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Tai Guo
- Division of Enteric Virus Vaccine, National Institutes for Food and Drug Control, Beijing, China
| | - Hong Bao
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Kuiying Kou
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Yueru Chen
- The Second Department, Lanzhou Institute of Biological Products Co, Ltd, Lanzhou, China
| | - Hanbo Gong
- Faculty of Science, University of Alberta, Alberta, Canada
| | - Xu Zhou
- General Manager's Office, Shanghai Institute of Biological Products Co, Ltd, Shanghai, China
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Stegeman I, Ochodo EA, Guleid F, Holtman GA, Yang B, Davenport C, Deeks JJ, Dinnes J, Dittrich S, Emperador D, Hooft L, Spijker R, Takwoingi Y, Van den Bruel A, Wang J, Langendam M, Verbakel JY, Leeflang MM. Routine laboratory testing to determine if a patient has COVID-19. Cochrane Database Syst Rev 2020; 11:CD013787. [PMID: 33211319 PMCID: PMC8078159 DOI: 10.1002/14651858.cd013787] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Specific diagnostic tests to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and resulting COVID-19 disease are not always available and take time to obtain results. Routine laboratory markers such as white blood cell count, measures of anticoagulation, C-reactive protein (CRP) and procalcitonin, are used to assess the clinical status of a patient. These laboratory tests may be useful for the triage of people with potential COVID-19 to prioritize them for different levels of treatment, especially in situations where time and resources are limited. OBJECTIVES To assess the diagnostic accuracy of routine laboratory testing as a triage test to determine if a person has COVID-19. SEARCH METHODS On 4 May 2020 we undertook electronic searches in the Cochrane COVID-19 Study Register and the COVID-19 Living Evidence Database from the University of Bern, which is updated daily with published articles from PubMed and Embase and with preprints from medRxiv and bioRxiv. In addition, we checked repositories of COVID-19 publications. We did not apply any language restrictions. SELECTION CRITERIA We included both case-control designs and consecutive series of patients that assessed the diagnostic accuracy of routine laboratory testing as a triage test to determine if a person has COVID-19. The reference standard could be reverse transcriptase polymerase chain reaction (RT-PCR) alone; RT-PCR plus clinical expertise or and imaging; repeated RT-PCR several days apart or from different samples; WHO and other case definitions; and any other reference standard used by the study authors. DATA COLLECTION AND ANALYSIS Two review authors independently extracted data from each included study. They also assessed the methodological quality of the studies, using QUADAS-2. We used the 'NLMIXED' procedure in SAS 9.4 for the hierarchical summary receiver operating characteristic (HSROC) meta-analyses of tests for which we included four or more studies. To facilitate interpretation of results, for each meta-analysis we estimated summary sensitivity at the points on the SROC curve that corresponded to the median and interquartile range boundaries of specificities in the included studies. MAIN RESULTS We included 21 studies in this review, including 14,126 COVID-19 patients and 56,585 non-COVID-19 patients in total. Studies evaluated a total of 67 different laboratory tests. Although we were interested in the diagnotic accuracy of routine tests for COVID-19, the included studies used detection of SARS-CoV-2 infection through RT-PCR as reference standard. There was considerable heterogeneity between tests, threshold values and the settings in which they were applied. For some tests a positive result was defined as a decrease compared to normal vaues, for other tests a positive result was defined as an increase, and for some tests both increase and decrease may have indicated test positivity. None of the studies had either low risk of bias on all domains or low concerns for applicability for all domains. Only three of the tests evaluated had a summary sensitivity and specificity over 50%. These were: increase in interleukin-6, increase in C-reactive protein and lymphocyte count decrease. Blood count Eleven studies evaluated a decrease in white blood cell count, with a median specificity of 93% and a summary sensitivity of 25% (95% CI 8.0% to 27%; very low-certainty evidence). The 15 studies that evaluated an increase in white blood cell count had a lower median specificity and a lower corresponding sensitivity. Four studies evaluated a decrease in neutrophil count. Their median specificity was 93%, corresponding to a summary sensitivity of 10% (95% CI 1.0% to 56%; low-certainty evidence). The 11 studies that evaluated an increase in neutrophil count had a lower median specificity and a lower corresponding sensitivity. The summary sensitivity of an increase in neutrophil percentage (4 studies) was 59% (95% CI 1.0% to 100%) at median specificity (38%; very low-certainty evidence). The summary sensitivity of an increase in monocyte count (4 studies) was 13% (95% CI 6.0% to 26%) at median specificity (73%; very low-certainty evidence). The summary sensitivity of a decrease in lymphocyte count (13 studies) was 64% (95% CI 28% to 89%) at median specificity (53%; low-certainty evidence). Four studies that evaluated a decrease in lymphocyte percentage showed a lower median specificity and lower corresponding sensitivity. The summary sensitivity of a decrease in platelets (4 studies) was 19% (95% CI 10% to 32%) at median specificity (88%; low-certainty evidence). Liver function tests The summary sensitivity of an increase in alanine aminotransferase (9 studies) was 12% (95% CI 3% to 34%) at median specificity (92%; low-certainty evidence). The summary sensitivity of an increase in aspartate aminotransferase (7 studies) was 29% (95% CI 17% to 45%) at median specificity (81%) (low-certainty evidence). The summary sensitivity of a decrease in albumin (4 studies) was 21% (95% CI 3% to 67%) at median specificity (66%; low-certainty evidence). The summary sensitivity of an increase in total bilirubin (4 studies) was 12% (95% CI 3.0% to 34%) at median specificity (92%; very low-certainty evidence). Markers of inflammation The summary sensitivity of an increase in CRP (14 studies) was 66% (95% CI 55% to 75%) at median specificity (44%; very low-certainty evidence). The summary sensitivity of an increase in procalcitonin (6 studies) was 3% (95% CI 1% to 19%) at median specificity (86%; very low-certainty evidence). The summary sensitivity of an increase in IL-6 (four studies) was 73% (95% CI 36% to 93%) at median specificity (58%) (very low-certainty evidence). Other biomarkers The summary sensitivity of an increase in creatine kinase (5 studies) was 11% (95% CI 6% to 19%) at median specificity (94%) (low-certainty evidence). The summary sensitivity of an increase in serum creatinine (four studies) was 7% (95% CI 1% to 37%) at median specificity (91%; low-certainty evidence). The summary sensitivity of an increase in lactate dehydrogenase (4 studies) was 25% (95% CI 15% to 38%) at median specificity (72%; very low-certainty evidence). AUTHORS' CONCLUSIONS Although these tests give an indication about the general health status of patients and some tests may be specific indicators for inflammatory processes, none of the tests we investigated are useful for accurately ruling in or ruling out COVID-19 on their own. Studies were done in specific hospitalized populations, and future studies should consider non-hospital settings to evaluate how these tests would perform in people with milder symptoms.
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Affiliation(s)
- Inge Stegeman
- Department of Otorhinolaryngology & Head and Neck Surgery, University Medical Center Utrecht, Utrecht, Netherlands
- Epidemiology and Data Science, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands
| | - Eleanor A Ochodo
- Centre for Evidence-based Health Care, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Fatuma Guleid
- KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
| | - Gea A Holtman
- Department of General Practice, University of Groningen, University Medical Centre Groningen, Groningen, Netherlands
| | - Bada Yang
- Epidemiology and Data Science, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Clare Davenport
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Jonathan J Deeks
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Jacqueline Dinnes
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | | | | | - Lotty Hooft
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - René Spijker
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Medical Library, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health, Amsterdam, Netherlands
| | - Yemisi Takwoingi
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Ann Van den Bruel
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Junfeng Wang
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | - Miranda Langendam
- Epidemiology and Data Science, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Jan Y Verbakel
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Mariska Mg Leeflang
- Epidemiology and Data Science, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
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Zhou Y, Qiu Q, Luo K, Liao Q, Li Y, Cui P, Liang L, Cheng Y, Wang L, Wang K, Van Tan L, Rogier van Doorn H, Yu H. Molecular strategy for the direct detection and identification of human enteroviruses in clinical specimens associated with hand, foot and mouth disease. PLoS One 2020; 15:e0241614. [PMID: 33166321 PMCID: PMC7652283 DOI: 10.1371/journal.pone.0241614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 10/19/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Diseases caused by human enteroviruses (EVs) are a major global public health problem. Thus, the effective diagnosis of all human EVs infections and the monitoring of epidemiological and ecological dynamic changes are urgently needed. METHODS Based on two comprehensive virological surveillance systems of hand, foot and mouth disease (HFMD), real-time PCR and nested RT-PCR (RT-snPCR) methods based on the enteroviral VP1, VP4-VP2 and VP4 regions were designed to directly detect all human EVs serotypes in clinical specimens. RESULTS The results showed that the proposed serotyping strategy exhibit very high diagnostic efficiency (Study 1: 99.9%; Study 2: 89.5%), and the variance between the study was due to inclusion of the specific Coxsackie virus A6 (CVA6) real-time RT-PCR and VP4 RT-snPCR in Study 1 but not Study 2. Furthermore, only throat swabs were collected and analyzed in Study 2, whereas in Study 1, if a specific EV serotype was not identified in the primary stool sample, other sample types (rectal swab and throat swab) were further tested where available. During the study period from 2013 to 2018, CVA6 became one of the main HFMD causative agents, whereas the level of enterovirus A71 (EV-A71) declined in 2017. CONCLUSION The findings of this study demonstrate the appropriate application of PCR methods and the combination of biological sample types that are useful for etiological studies and propose a molecular strategy for the direct detection of human EVs in clinical specimens associated with HFMD.
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Affiliation(s)
- Yonghong Zhou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Qi Qiu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Kaiwei Luo
- Hunan Provincial Center for Disease Control and Prevention, Changsha, Hunan Province, China
| | - Qiaohong Liao
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Yu Li
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Peng Cui
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Lu Liang
- West China School of Public Health, Sichuan University, Chengdu, China
| | - Yibing Cheng
- Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou, China
| | - Lili Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Kai Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
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Mallett S, Allen AJ, Graziadio S, Taylor SA, Sakai NS, Green K, Suklan J, Hyde C, Shinkins B, Zhelev Z, Peters J, Turner PJ, Roberts NW, di Ruffano LF, Wolff R, Whiting P, Winter A, Bhatnagar G, Nicholson BD, Halligan S. At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR-based tests? A systematic review of individual participant data. BMC Med 2020; 18:346. [PMID: 33143712 PMCID: PMC7609379 DOI: 10.1186/s12916-020-01810-8] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/08/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA) using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity. METHODS We conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. We searched PubMed, LitCOVID, medRxiv, and COVID-19 Living Evidence databases. We assessed risk of bias using a QUADAS-2 adaptation. Outcomes were the percentage of positive test results by time and the duration of detectable virus, by anatomical sampling sites. RESULTS Of 5078 studies screened, we included 32 studies with 1023 SARS-CoV-2 infected participants and 1619 test results, from - 6 to 66 days post-symptom onset and hospitalisation. The highest percentage virus detection was from nasopharyngeal sampling between 0 and 4 days post-symptom onset at 89% (95% confidence interval (CI) 83 to 93) dropping to 54% (95% CI 47 to 61) after 10 to 14 days. On average, duration of detectable virus was longer with lower respiratory tract (LRT) sampling than upper respiratory tract (URT). Duration of faecal and respiratory tract virus detection varied greatly within individual participants. In some participants, virus was still detectable at 46 days post-symptom onset. CONCLUSIONS RT-PCR misses detection of people with SARS-CoV-2 infection; early sampling minimises false negative diagnoses. Beyond 10 days post-symptom onset, lower RT or faecal testing may be preferred sampling sites. The included studies are open to substantial risk of bias, so the positivity rates are probably overestimated.
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Affiliation(s)
- Sue Mallett
- Centre for Medical Imaging, University College London, 2nd Floor, Charles Bell House, 43-45 Foley Street, London, W1W 7TS, UK.
| | - A Joy Allen
- NIHR In Vitro Diagnostics Co-operative, Newcastle University, Newcastle upon Tyne, NE2 7RU, UK
| | - Sara Graziadio
- NIHR In Vitro Diagnostics Co-operative, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
| | - Stuart A Taylor
- Centre for Medical Imaging, University College London, 2nd Floor, Charles Bell House, 43-45 Foley Street, London, W1W 7TS, UK
| | - Naomi S Sakai
- Centre for Medical Imaging, University College London, 2nd Floor, Charles Bell House, 43-45 Foley Street, London, W1W 7TS, UK
| | - Kile Green
- NIHR In Vitro Diagnostics Co-operative, Newcastle University, Newcastle upon Tyne, NE2 7RU, UK
| | - Jana Suklan
- NIHR In Vitro Diagnostics Co-operative, Newcastle University, Newcastle upon Tyne, NE2 7RU, UK
| | - Chris Hyde
- Exeter Test Group, Institute of Health Research, University of Exeter Medical School, University of Exeter, College House, St Luke's Campus, Exeter, EX1 2LU, UK
| | - Bethany Shinkins
- Test Evaluation Group, Academic Unit of Health Economics, Leeds Institute of Health Sciences, University of Leeds, Worsley Building , Clarendon Way, Leeds, LS2 9LJ, UK
| | - Zhivko Zhelev
- Exeter Test Group, Institute of Health Research, University of Exeter Medical School, University of Exeter, College House, St Luke's Campus, Exeter, EX1 2LU, UK
| | - Jaime Peters
- Exeter Test Group, Institute of Health Research, University of Exeter Medical School, University of Exeter, College House, St Luke's Campus, Exeter, EX1 2LU, UK
| | - Philip J Turner
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Nia W Roberts
- Cancer Services, Gastroenterology, Population Health & Primary Care, Bodleian Health Care Libraries, University of Oxford, Oxford, OX2 6HT, UK
| | - Lavinia Ferrante di Ruffano
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Penny Whiting
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Amanda Winter
- NIHR In Vitro Diagnostics Co-operative, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
| | | | - Brian D Nicholson
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Steve Halligan
- Centre for Medical Imaging, University College London, 2nd Floor, Charles Bell House, 43-45 Foley Street, London, W1W 7TS, UK
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25
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Dramé M, Tabue Teguo M, Proye E, Hequet F, Hentzien M, Kanagaratnam L, Godaert L. Should RT-PCR be considered a gold standard in the diagnosis of COVID-19? J Med Virol 2020; 92:2312-2313. [PMID: 32383182 PMCID: PMC7267274 DOI: 10.1002/jmv.25996] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Moustapha Dramé
- Department of Clinical Research and InnovationUniversity Hospital of MartiniqueFort‐de‐FranceMartiniqueFrance
| | - Maturin Tabue Teguo
- Department of GeriatricsUniversity Hospital of GuadeloupePointe‐à‐PitreGuadeloupe
| | - Emeline Proye
- Department of GeriatricsGeneral Hospital of ValenciennesValenciennesFrance
| | - Fanny Hequet
- Department of GeriatricsGeneral Hospital of ValenciennesValenciennesFrance
| | - Maxime Hentzien
- Department of Infectious DiseasesUniversity Hospital of ReimsReimsFrance
| | - Lukshe Kanagaratnam
- Department of Clinical Research and Public HealthUniversity Hospital of ReimsReimsFrance
| | - Lidvine Godaert
- Department of GeriatricsGeneral Hospital of ValenciennesValenciennesFrance
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26
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Assandri R, Canetta C, Viganò G, Buscarini E, Scartabellati A, Montanelli A. Laboratory markers included in the Corona Score can identify false negative results on COVID-19 RT-PCR in the emergency room. Biochem Med (Zagreb) 2020; 30:030402. [PMID: 32774118 PMCID: PMC7394256 DOI: 10.11613/bm.2020.030402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/25/2020] [Indexed: 12/20/2022] Open
Abstract
After December 2019 outbreak in China, the novel Coronavirus infection (COVID-19) has very quickly overflowed worldwide. Infection causes a clinical syndrome encompassing a wide range of clinical features, from asymptomatic or oligosymptomatic course to acute respiratory distress and death. In a very recent work we preliminarily observed that several laboratory tests have been shown as characteristically altered in COVID-19. We aimed to use the Corona score, a validated point-based algorithm to predict the likelihood of COVID-19 infection in patients presenting at the Emergency rooms. This approach combines chest images-relative score and several laboratory parameters to classify emergency room patients. Corona score accuracy was satisfactory, increasing the detection of positive patients' rate.
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Affiliation(s)
- Roberto Assandri
- Clinical Investigation Laboratory, ASST-Crema, Maggiore Hospital, Crema, Italy
| | - Ciro Canetta
- Internal Medicine Unit, ASST-Crema, Maggiore Hospital, Crema, Italy
| | - Giovanni Viganò
- Emergency Medicine Unit,ASST-Crema, Maggiore Hospital, Crema, Italy
| | | | | | - Alessandro Montanelli
- Clinical Investigation Laboratory, ASST-Bergamo Est, Bolognini Hospital Seriate, Bergamo, Italy
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27
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Abstract
BACKGROUND Reverse transcription-polymerase chain reaction (RT-PCR) is an extremely common clinical method for detecting pathogens, particularly for emerging infectious diseases such as the new coronavirus disease (COVID-19). Currently, detection of the RNA from the novel coronavirus SARS-CoV-2 is the gold standard for establishing a COVID-19 diagnosis. This study evaluates the characteristic performance of the analytical system in a clinical laboratory. METHODS A commercial SARS-CoV-2 RNA RT-PCR Kit used in a clinical laboratory is assessed based on ISO 15189 verification requirements. A multiple real-time RT-PCR assay for the RdRP, N, and E genes in SARS-CoV-2 is verified. RESULTS The analytical system exhibits good analytical sensitivity (1000 copies/mL) and specificity (100%); however, the values of 86.7% and 100% for analytical accuracy deserved attention, compared with two other types of methods. Overall, the kit is potentially useful for SARS-CoV-2 diagnostic testing and meets the verification requirements. CONCLUSION Compliance with international standards, such as ISO 15189, is valuable for clinical laboratories and for improving laboratory medicine quality and safety. Normalization is essential for obtaining reliable results from the SARS-CoV-2 RNA RT-PCR assay. This study aims to develop an improved SARS-CoV-2 verification framework compared with traditional molecular diagnostic methods, given the urgency of implementing new assays in clinical laboratories.
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Affiliation(s)
- Yingping Wu
- Department of Clinical LaboratoryFourth Affiliated Hospital of Zhejiang University School of MedicineJinhuaChina
| | - Wei Xu
- Department of Clinical LaboratoryFourth Affiliated Hospital of Zhejiang University School of MedicineJinhuaChina
| | - Zhiqiang Zhu
- Department of Clinical LaboratoryFourth Affiliated Hospital of Zhejiang University School of MedicineJinhuaChina
| | - Xiaoping Xia
- Department of Clinical LaboratoryFourth Affiliated Hospital of Zhejiang University School of MedicineJinhuaChina
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28
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Sung H, Han MG, Yoo CK, Lee SW, Chung YS, Park JS, Kim MN, Lee H, Hong KH, Seong MW, Lee K, Chun S, Lee WG, Kwon GC, Min WK. Nationwide External Quality Assessment of SARS-CoV-2 Molecular Testing, South Korea. Emerg Infect Dis 2020; 26:2353-2360. [PMID: 32723432 PMCID: PMC7510727 DOI: 10.3201/eid2610.202551] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
External quality assessment (EQA) is essential for ensuring reliable test results, especially when laboratories are using assays authorized for emergency use for newly emerging pathogens. We developed an EQA panel to assess the quality of real-time reverse transcription PCR assays being used in South Korea to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the participation of 23 public health organization laboratories and 95 nongovernmental laboratories involved in SARS-CoV-2 testing, we conducted qualitative and semiquantitative performance assessments by using pooled respiratory samples containing different viral loads of SARS-CoV-2 or human coronavirus OC43. A total of 110 (93.2%) laboratories reported correct results for all qualitative tests; 29 (24.6%) laboratories had >1 outliers according to cycle threshold values. Our EQA panel identified the potential weaknesses of currently available commercial reagent kits. The methodology we used can provide practical experience for those planning to conduct evaluations for testing of SARS-CoV-2 and other emerging pathogens in the future.
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Affiliation(s)
| | - Myung-Guk Han
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Cheon-Kwon Yoo
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Sang-Won Lee
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Yoon-Seok Chung
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Jae-Sun Park
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Mi-Na Kim
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Hyukmin Lee
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Ki Ho Hong
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Moon-Woo Seong
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Kyunghoon Lee
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Sail Chun
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Wee Gyo Lee
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
| | - Gye-Cheol Kwon
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea (H. Sung, M.-N. Kim, S. Chun, W.K. Min)
- Korea Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea (M.-G. Han, C.-K. Yoo, S.-W. Lee, Y.-S. Chung, J.-S. Park)
- Yonsei University College of Medicine, Seoul (H. Lee)
- Seoul Medical Center, Seoul (K.-H. Hong)
- Seoul National University College of Medicine, Seoul (M.-W. Seong, K. Lee)
- Ajou University School of Medicine, Suwon, South Korea (W.G. Lee)
- Chungnam National University School of Medicine, Daejeon, South Korea (G.-C. Kwon)
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29
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Kudo E, Israelow B, Vogels CBF, Lu P, Wyllie AL, Tokuyama M, Venkataraman A, Brackney DE, Ott IM, Petrone ME, Earnest R, Lapidus S, Muenker MC, Moore AJ, Casanovas-Massana A, Omer SB, Dela Cruz CS, Farhadian SF, Ko AI, Grubaugh ND, Iwasaki A. Detection of SARS-CoV-2 RNA by multiplex RT-qPCR. PLoS Biol 2020; 18:e3000867. [PMID: 33027248 PMCID: PMC7571696 DOI: 10.1371/journal.pbio.3000867] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/19/2020] [Accepted: 09/24/2020] [Indexed: 11/18/2022] Open
Abstract
The current quantitative reverse transcription PCR (RT-qPCR) assay recommended for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing in the United States requires analysis of 3 genomic targets per sample: 2 viral and 1 host. To simplify testing and reduce the volume of required reagents, we devised a multiplex RT-qPCR assay to detect SARS-CoV-2 in a single reaction. We used existing N1, N2, and RP primer and probe sets by the Centers for Disease Control and Prevention, but substituted fluorophores to allow multiplexing of the assay. The cycle threshold (Ct) values of our multiplex RT-qPCR were comparable to those obtained by the single assay adapted for research purposes. Low copy numbers (≥500 copies/reaction) of SARS-CoV-2 RNA were consistently detected by the multiplex RT-qPCR. Our novel multiplex RT-qPCR improves upon current single diagnostics by saving reagents, costs, time, and labor.
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Affiliation(s)
- Eriko Kudo
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Benjamin Israelow
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Peiwen Lu
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Anne L. Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Maria Tokuyama
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Arvind Venkataraman
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Doug E. Brackney
- The Connecticut Agricultural Experiment Station, Department of Environmental Sciences, New Haven, Connecticut, United States of America
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Sarah Lapidus
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - M. Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Adam J. Moore
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | | | - Saad B. Omer
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale Institute of Global Health, New Haven, Connecticut, United States of America
- Yale School of Nursing, New Haven, Connecticut, United States of America
| | - Charles S. Dela Cruz
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Shelli F. Farhadian
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Albert I. Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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Plebani M, Padoan A, Negrini D, Carpinteri B, Sciacovelli L. Diagnostic performances and thresholds: The key to harmonization in serological SARS-CoV-2 assays? Clin Chim Acta 2020; 509:1-7. [PMID: 32485157 PMCID: PMC7261100 DOI: 10.1016/j.cca.2020.05.050] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND The evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) specific antibody (Ab) assay performances is of the utmost importance in establishing and monitoring virus spread in the community. In this study focusing on IgG antibodies, we compare reliability of three chemiluminescent (CLIA) and two enzyme linked immunosorbent (ELISA) assays. METHODS Sera from a total of 271 subjects, including 64 reverse transcription-polymerase chain reaction (RT-PCR) confirmed SARS-CoV-2 patients were tested for specific Ab using Maglumi (Snibe), Liaison (Diasorin), iFlash (Yhlo), Euroimmun (Medizinische Labordiagnostika AG) and Wantai (Wantai Biological Pharmacy) assays. Diagnostic sensitivity and specificity, positive and negative likelihood ratios were evaluated using manufacturers' and optimized thresholds. RESULTS Optimized thresholds (Maglumi 2 kAU/L, Liaison 6.2 kAU/L and iFlash 15.0 kAU/L) allowed us to achieve a negative likelihood ratio and an accuracy of: 0.06 and 93.5% for Maglumi; 0.03 and 93.1% for Liaison; 0.03 and 91% for iFlash. Diagnostic sensitivities and specificities were above 93.8% and 85.9%, respectively for all CLIA assays. Overall agreement was 90.3% (Cohen's kappa = 0.805 and SE = 0.041) for CLIA, and 98.4% (Cohen's kappa = 0.962 and SE = 0.126) for ELISA. CONCLUSIONS The results obtained indicate that, for CLIA assays, it might be possible to define thresholds that improve the negative likelihood ratio. Thus, a negative test result enables the identification of subjects at risk of being infected, who should then be closely monitored over time with a view to preventing further viral spread. Redefined thresholds, in addition, improved the overall inter-assay agreement, paving the way to a better harmonization of serologic tests.
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Affiliation(s)
- Mario Plebani
- Department of Laboratory Medicine, University Hospital of Padova, Italy; Department of Medicine-DIMED, University of Padova, Italy.
| | - Andrea Padoan
- Department of Laboratory Medicine, University Hospital of Padova, Italy; Department of Medicine-DIMED, University of Padova, Italy
| | - Davide Negrini
- Department of Medicine-DIMED, University of Padova, Italy
| | | | - Laura Sciacovelli
- Department of Laboratory Medicine, University Hospital of Padova, Italy
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31
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Bruce EA, Huang ML, Perchetti GA, Tighe S, Laaguiby P, Hoffman JJ, Gerrard DL, Nalla AK, Wei Y, Greninger AL, Diehl SA, Shirley DJ, Leonard DGB, Huston CD, Kirkpatrick BD, Dragon JA, Crothers JW, Jerome KR, Botten JW. Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step. PLoS Biol 2020; 18:e3000896. [PMID: 33006983 PMCID: PMC7556528 DOI: 10.1371/journal.pbio.3000896] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/14/2020] [Accepted: 09/10/2020] [Indexed: 11/24/2022] Open
Abstract
The ongoing COVID-19 pandemic has created an unprecedented need for rapid diagnostic testing. The World Health Organization (WHO) recommends a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. The goal of this study was to determine whether SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether. The direct RT-qPCR approach correctly identified 92% of a reference set of blinded NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Importantly, the direct method had sufficient sensitivity to reliably detect those patients with viral loads that correlate with the presence of infectious virus. Thus, this strategy has the potential to ease supply choke points to substantially expand COVID-19 testing and screening capacity and should be applicable throughout the world.
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Affiliation(s)
- Emily A. Bruce
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Meei-Li Huang
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Garrett A. Perchetti
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Scott Tighe
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Pheobe Laaguiby
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Jessica J. Hoffman
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Diana L. Gerrard
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, Vermont, United States of America
| | - Arun K. Nalla
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Yulun Wei
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Alexander L. Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Sean A. Diehl
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Vaccine Testing Center, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - David J. Shirley
- Data Science Division, IXIS, Burlington, Vermont, United States of America
| | - Debra G. B. Leonard
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- University of Vermont Health Network, Burlington, Vermont, United States of America
| | - Christopher D. Huston
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Division of Infectious Disease, Department of Medicine, University of Vermont Medical Center, Burlington, Vermont, United States of America
| | - Beth D. Kirkpatrick
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Vaccine Testing Center, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Division of Infectious Disease, Department of Medicine, University of Vermont Medical Center, Burlington, Vermont, United States of America
| | - Julie A. Dragon
- Vermont Integrative Genomics Resource, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Jessica W. Crothers
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- University of Vermont Health Network, Burlington, Vermont, United States of America
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jason W. Botten
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Vaccine Testing Center, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
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Smyrlaki I, Ekman M, Lentini A, Rufino de Sousa N, Papanicolaou N, Vondracek M, Aarum J, Safari H, Muradrasoli S, Rothfuchs AG, Albert J, Högberg B, Reinius B. Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR. Nat Commun 2020; 11:4812. [PMID: 32968075 PMCID: PMC7511968 DOI: 10.1038/s41467-020-18611-5] [Citation(s) in RCA: 294] [Impact Index Per Article: 73.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/02/2020] [Indexed: 11/24/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is commonly diagnosed by reverse transcription polymerase chain reaction (RT-PCR) to detect viral RNA in patient samples, but RNA extraction constitutes a major bottleneck in current testing. Methodological simplification could increase diagnostic availability and efficiency, benefitting patient care and infection control. Here, we describe methods circumventing RNA extraction in COVID-19 testing by performing RT-PCR directly on heat-inactivated or lysed samples. Our data, including benchmarking using 597 clinical patient samples and a standardised diagnostic system, demonstrate that direct RT-PCR is viable option to extraction-based tests. Using controlled amounts of active SARS-CoV-2, we confirm effectiveness of heat inactivation by plaque assay and evaluate various generic buffers as transport medium for direct RT-PCR. Significant savings in time and cost are achieved through RNA-extraction-free protocols that are directly compatible with established PCR-based testing pipelines. This could aid expansion of COVID-19 testing.
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Affiliation(s)
- Ioanna Smyrlaki
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Martin Ekman
- Department of Clinical Microbiology, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Nuno Rufino de Sousa
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Natali Papanicolaou
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Martin Vondracek
- Department of Clinical Microbiology, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Johan Aarum
- Department of Clinical Microbiology, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Hamzah Safari
- Department of Clinical Microbiology, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | | | | | - Jan Albert
- Department of Clinical Microbiology, Karolinska University Hospital, 171 76, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden.
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Ganguli A, Mostafa A, Berger J, Aydin MY, Sun F, Ramirez SASD, Valera E, Cunningham BT, King WP, Bashir R. Rapid isothermal amplification and portable detection system for SARS-CoV-2. Proc Natl Acad Sci U S A 2020; 117:22727-22735. [PMID: 32868442 PMCID: PMC7502724 DOI: 10.1073/pnas.2014739117] [Citation(s) in RCA: 246] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay protocols and primer sequences become widely known, many laboratories perform diagnostic tests using methods such as RT-PCR or reverse transcription loop mediated isothermal amplification (RT-LAMP). Here, we report an RT-LAMP isothermal assay for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and demonstrate the assay on clinical samples using a simple and accessible point-of-care (POC) instrument. We characterized the assay by dipping swabs into synthetic nasal fluid spiked with the virus, moving the swab to viral transport medium (VTM), and sampling a volume of the VTM to perform the RT-LAMP assay without an RNA extraction kit. The assay has a limit of detection (LOD) of 50 RNA copies per μL in the VTM solution within 30 min. We further demonstrate our assay by detecting SARS-CoV-2 viruses from 20 clinical samples. Finally, we demonstrate a portable and real-time POC device to detect SARS-CoV-2 from VTM samples using an additively manufactured three-dimensional cartridge and a smartphone-based reader. The POC system was tested using 10 clinical samples, and was able to detect SARS-CoV-2 from these clinical samples by distinguishing positive samples from negative samples after 30 min. The POC tests are in complete agreement with RT-PCR controls. This work demonstrates an alternative pathway for SARS-CoV-2 diagnostics that does not require conventional laboratory infrastructure, in settings where diagnosis is required at the point of sample collection.
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Affiliation(s)
- Anurup Ganguli
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Ariana Mostafa
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Jacob Berger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Mehmet Y Aydin
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Fu Sun
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Sarah A Stewart de Ramirez
- Emergency Medicine, University of Illinois College of Medicine at Peoria & OSF Healthcare, Peoria, IL 61637
| | - Enrique Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Brian T Cunningham
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - William P King
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801
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Abstract
Clinical laboratory testing routinely provides actionable results, which help direct patient care in the inpatient and outpatient settings. Since December 2019, a novel coronavirus (SARS-CoV-2) has been causing disease (COVID-19 [coronavirus disease 2019]) in patients, beginning in China and now extending worldwide. In this context of a novel viral pandemic, clinical laboratories have developed multiple novel assays for SARS-CoV-2 diagnosis and for managing patients afflicted with this illness. These include molecular and serologic-based tests, some with point-of-care testing capabilities. Herein, we present an overview of the types of testing available for managing patients with COVID-19, as well as for screening of potential plasma donors who have recovered from COVID-19.
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Affiliation(s)
- Marie C Smithgall
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, NY
| | - Mitra Dowlatshahi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, NY
| | - Steven L Spitalnik
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, NY
| | - Eldad A Hod
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, NY
| | - Alex J Rai
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, NY
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35
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Guedez-López GV, Alguacil-Guillén M, González-Donapetry P, Bloise I, Tornero-Marin C, González-García J, Mingorance J, García-Rodríguez J. Evaluation of three immunochromatographic tests for rapid detection of antibodies against SARS-CoV-2. Eur J Clin Microbiol Infect Dis 2020; 39:2289-2297. [PMID: 32808111 PMCID: PMC7431115 DOI: 10.1007/s10096-020-04010-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/11/2020] [Indexed: 12/28/2022]
Abstract
Lateral flow immunoassays (LFIA) for rapid detection of specific antibodies (IgM and IgG) against SARS-CoV-2 in different human specimens have been developed in response to the pandemic. The aim of this study is to evaluate three immunocromathographic assays (Sienna®, Wondfo® and Prometheus®) for detection of antibodies against SARS-CoV-2 in serum samples, considering RT-qPCR as a reference. A total of 145 serum samples from 145 patients with clinical suspicion of COVID-19 were collected: all of the samples were tested with Sienna®, 117 with Wondfo® and 89 with Prometheus®. The overall results of sensitivity, specificity, positive predictive value and negative predictive value obtained were as follows: 64.4%, 75%, 85.5% and 47.8% with Sienna®; 45.2%, 81.8%, 80.5% and 47.4% with Wondfo® and 75.5%, 12.5%, 51.4% and 29.4% with Prometheus®. The accuracy of the test for Sienna®, Wondfo® and Prometheus® was 67.6%, 59% and 47.2%, with a prevalence of COVID-19 of 69.7%, 62.4% and 55.1% respectively. Sensitivity of the three tests (Sienna®, Wondfo® and Prometheus® respectively) along the three different stages was 36.6%, 18.8% and 68.6% in the early stage (first week); 81.3%, 74.1% and 90.9% in the intermediate stage (second week) and 100%, 83.3% and 100% in the late stage (third week). The results demonstrate that even though Prometheus® presented a high sensitivity, the specificity was notably lower than the other two tests. Sienna® showed the greatest contrast between sensitivity and specificity, achieving the best accuracy, followed by Wondfo®. The sensitivity of the three ICT assays was higher in late stages of the disease.
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Affiliation(s)
- Gladys Virginia Guedez-López
- Clinical Microbiology Department, Hospital Universitario La Paz, Paseo de La Castellana 261, 28046, Madrid, Spain
| | - Marina Alguacil-Guillén
- Clinical Microbiology Department, Hospital Universitario La Paz, Paseo de La Castellana 261, 28046, Madrid, Spain.
| | - Patricia González-Donapetry
- Clinical Microbiology Department, Hospital Universitario La Paz, Paseo de La Castellana 261, 28046, Madrid, Spain
| | - Ivan Bloise
- Clinical Microbiology Department, Hospital Universitario La Paz, Paseo de La Castellana 261, 28046, Madrid, Spain
| | | | | | - Jesus Mingorance
- Clinical Microbiology Department, Hospital Universitario La Paz, Paseo de La Castellana 261, 28046, Madrid, Spain
| | - Julio García-Rodríguez
- Clinical Microbiology Department, Hospital Universitario La Paz, Paseo de La Castellana 261, 28046, Madrid, Spain
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Albendín-Iglesias H, Mira-Bleda E, Roura-Piloto AE, Hernández-Torres A, Moral-Escudero E, Fuente-Mora C, Iborra-Bendicho A, Moreno-Docón A, Galera-Peñaranda C, García-Vázquez E. Usefulness of the epidemiological survey and RT-PCR test in pre-surgical patients for assessing the risk of COVID-19. J Hosp Infect 2020; 105:773-775. [PMID: 32540464 PMCID: PMC7837131 DOI: 10.1016/j.jhin.2020.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 11/29/2022]
Affiliation(s)
- H Albendín-Iglesias
- HIV Unit, Internal Medicine Department, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain; Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain.
| | - E Mira-Bleda
- HIV Unit, Internal Medicine Department, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - A E Roura-Piloto
- Infectious Diseases Unit, Internal Medicine Department, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - A Hernández-Torres
- Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain; Infectious Diseases Unit, Internal Medicine Department, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain; Internal Medicine Department, Faculty of Medicine, Universidad de Murcia, Spain
| | - E Moral-Escudero
- Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain; Infectious Diseases Unit, Internal Medicine Department, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain; Internal Medicine Department, Faculty of Medicine, Universidad de Murcia, Spain
| | - C Fuente-Mora
- Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | - A Iborra-Bendicho
- Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain; Microbiology Department, Universitario Virgen de la Arrixaca, Murcia, Spain
| | - A Moreno-Docón
- Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain; Microbiology Department, Universitario Virgen de la Arrixaca, Murcia, Spain
| | - C Galera-Peñaranda
- HIV Unit, Internal Medicine Department, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain; Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | - E García-Vázquez
- Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain; Infectious Diseases Unit, Internal Medicine Department, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain; Internal Medicine Department, Faculty of Medicine, Universidad de Murcia, Spain
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37
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Deeks JJ, Dinnes J, Takwoingi Y, Davenport C, Spijker R, Taylor-Phillips S, Adriano A, Beese S, Dretzke J, Ferrante di Ruffano L, Harris IM, Price MJ, Dittrich S, Emperador D, Hooft L, Leeflang MM, Van den Bruel A. Antibody tests for identification of current and past infection with SARS-CoV-2. Cochrane Database Syst Rev 2020; 6:CD013652. [PMID: 32584464 PMCID: PMC7387103 DOI: 10.1002/14651858.cd013652] [Citation(s) in RCA: 432] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and resulting COVID-19 pandemic present important diagnostic challenges. Several diagnostic strategies are available to identify current infection, rule out infection, identify people in need of care escalation, or to test for past infection and immune response. Serology tests to detect the presence of antibodies to SARS-CoV-2 aim to identify previous SARS-CoV-2 infection, and may help to confirm the presence of current infection. OBJECTIVES To assess the diagnostic accuracy of antibody tests to determine if a person presenting in the community or in primary or secondary care has SARS-CoV-2 infection, or has previously had SARS-CoV-2 infection, and the accuracy of antibody tests for use in seroprevalence surveys. SEARCH METHODS We undertook electronic searches in the Cochrane COVID-19 Study Register and the COVID-19 Living Evidence Database from the University of Bern, which is updated daily with published articles from PubMed and Embase and with preprints from medRxiv and bioRxiv. In addition, we checked repositories of COVID-19 publications. We did not apply any language restrictions. We conducted searches for this review iteration up to 27 April 2020. SELECTION CRITERIA We included test accuracy studies of any design that evaluated antibody tests (including enzyme-linked immunosorbent assays, chemiluminescence immunoassays, and lateral flow assays) in people suspected of current or previous SARS-CoV-2 infection, or where tests were used to screen for infection. We also included studies of people either known to have, or not to have SARS-CoV-2 infection. We included all reference standards to define the presence or absence of SARS-CoV-2 (including reverse transcription polymerase chain reaction tests (RT-PCR) and clinical diagnostic criteria). DATA COLLECTION AND ANALYSIS We assessed possible bias and applicability of the studies using the QUADAS-2 tool. We extracted 2x2 contingency table data and present sensitivity and specificity for each antibody (or combination of antibodies) using paired forest plots. We pooled data using random-effects logistic regression where appropriate, stratifying by time since post-symptom onset. We tabulated available data by test manufacturer. We have presented uncertainty in estimates of sensitivity and specificity using 95% confidence intervals (CIs). MAIN RESULTS We included 57 publications reporting on a total of 54 study cohorts with 15,976 samples, of which 8526 were from cases of SARS-CoV-2 infection. Studies were conducted in Asia (n = 38), Europe (n = 15), and the USA and China (n = 1). We identified data from 25 commercial tests and numerous in-house assays, a small fraction of the 279 antibody assays listed by the Foundation for Innovative Diagnostics. More than half (n = 28) of the studies included were only available as preprints. We had concerns about risk of bias and applicability. Common issues were use of multi-group designs (n = 29), inclusion of only COVID-19 cases (n = 19), lack of blinding of the index test (n = 49) and reference standard (n = 29), differential verification (n = 22), and the lack of clarity about participant numbers, characteristics and study exclusions (n = 47). Most studies (n = 44) only included people hospitalised due to suspected or confirmed COVID-19 infection. There were no studies exclusively in asymptomatic participants. Two-thirds of the studies (n = 33) defined COVID-19 cases based on RT-PCR results alone, ignoring the potential for false-negative RT-PCR results. We observed evidence of selective publication of study findings through omission of the identity of tests (n = 5). We observed substantial heterogeneity in sensitivities of IgA, IgM and IgG antibodies, or combinations thereof, for results aggregated across different time periods post-symptom onset (range 0% to 100% for all target antibodies). We thus based the main results of the review on the 38 studies that stratified results by time since symptom onset. The numbers of individuals contributing data within each study each week are small and are usually not based on tracking the same groups of patients over time. Pooled results for IgG, IgM, IgA, total antibodies and IgG/IgM all showed low sensitivity during the first week since onset of symptoms (all less than 30.1%), rising in the second week and reaching their highest values in the third week. The combination of IgG/IgM had a sensitivity of 30.1% (95% CI 21.4 to 40.7) for 1 to 7 days, 72.2% (95% CI 63.5 to 79.5) for 8 to 14 days, 91.4% (95% CI 87.0 to 94.4) for 15 to 21 days. Estimates of accuracy beyond three weeks are based on smaller sample sizes and fewer studies. For 21 to 35 days, pooled sensitivities for IgG/IgM were 96.0% (95% CI 90.6 to 98.3). There are insufficient studies to estimate sensitivity of tests beyond 35 days post-symptom onset. Summary specificities (provided in 35 studies) exceeded 98% for all target antibodies with confidence intervals no more than 2 percentage points wide. False-positive results were more common where COVID-19 had been suspected and ruled out, but numbers were small and the difference was within the range expected by chance. Assuming a prevalence of 50%, a value considered possible in healthcare workers who have suffered respiratory symptoms, we would anticipate that 43 (28 to 65) would be missed and 7 (3 to 14) would be falsely positive in 1000 people undergoing IgG/IgM testing at days 15 to 21 post-symptom onset. At a prevalence of 20%, a likely value in surveys in high-risk settings, 17 (11 to 26) would be missed per 1000 people tested and 10 (5 to 22) would be falsely positive. At a lower prevalence of 5%, a likely value in national surveys, 4 (3 to 7) would be missed per 1000 tested, and 12 (6 to 27) would be falsely positive. Analyses showed small differences in sensitivity between assay type, but methodological concerns and sparse data prevent comparisons between test brands. AUTHORS' CONCLUSIONS The sensitivity of antibody tests is too low in the first week since symptom onset to have a primary role for the diagnosis of COVID-19, but they may still have a role complementing other testing in individuals presenting later, when RT-PCR tests are negative, or are not done. Antibody tests are likely to have a useful role for detecting previous SARS-CoV-2 infection if used 15 or more days after the onset of symptoms. However, the duration of antibody rises is currently unknown, and we found very little data beyond 35 days post-symptom onset. We are therefore uncertain about the utility of these tests for seroprevalence surveys for public health management purposes. Concerns about high risk of bias and applicability make it likely that the accuracy of tests when used in clinical care will be lower than reported in the included studies. Sensitivity has mainly been evaluated in hospitalised patients, so it is unclear whether the tests are able to detect lower antibody levels likely seen with milder and asymptomatic COVID-19 disease. The design, execution and reporting of studies of the accuracy of COVID-19 tests requires considerable improvement. Studies must report data on sensitivity disaggregated by time since onset of symptoms. COVID-19-positive cases who are RT-PCR-negative should be included as well as those confirmed RT-PCR, in accordance with the World Health Organization (WHO) and China National Health Commission of the People's Republic of China (CDC) case definitions. We were only able to obtain data from a small proportion of available tests, and action is needed to ensure that all results of test evaluations are available in the public domain to prevent selective reporting. This is a fast-moving field and we plan ongoing updates of this living systematic review.
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Affiliation(s)
- Jonathan J Deeks
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Jacqueline Dinnes
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Yemisi Takwoingi
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Clare Davenport
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - René Spijker
- Medical Library, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health, Amsterdam, Netherlands
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Sian Taylor-Phillips
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Ada Adriano
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Sophie Beese
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Janine Dretzke
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Lavinia Ferrante di Ruffano
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Isobel M Harris
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Malcolm J Price
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | | | | | - Lotty Hooft
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Mariska Mg Leeflang
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
- Biomarker and Test Evaluation Programme (BiTE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ann Van den Bruel
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
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Krsak M, Johnson SC, Poeschla EM. COVID-19 Serosurveillance May Facilitate Return-to-Work Decisions. Am J Trop Med Hyg 2020; 102:1189-1190. [PMID: 32329432 PMCID: PMC7253118 DOI: 10.4269/ajtmh.20-0302] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/22/2022] Open
Abstract
Public health measures are needed to resolve the novel coronavirus disease (COVID-19) pandemic, although a looming economic fallout merits close attention. Early safe reintroduction of immune individuals into the workforce may be essential to protecting the economic welfare of communities. Reverse transcriptase-polymerase chain reaction testing, our primary diagnostic tool to date, has sensitivity and timing concerns, owing to sampling/handling errors, as well as a complex virus-host interaction. Reverse transcriptase-polymerase chain reaction assays do not establish immune status once the virus has been cleared. Targeted serosurveillance for the determination of individuals' potential for transmissibility, particularly if paired with direct pathogen testing, may aid in "cleared for business" decision-making.
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Affiliation(s)
- Martin Krsak
- University of Colorado School of Medicine, Aurora, Colorado
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39
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Herath S, Dai H, Erlich J, Au AYM, Taylor K, Succar L, Endre ZH. Selection and validation of reference genes for normalisation of gene expression in ischaemic and toxicological studies in kidney disease. PLoS One 2020; 15:e0233109. [PMID: 32437461 PMCID: PMC7241806 DOI: 10.1371/journal.pone.0233109] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/28/2020] [Indexed: 12/16/2022] Open
Abstract
Normalisation to standard reference gene(s) is essential for quantitative real-time polymerase chain reaction (RT-qPCR) to obtain reproducible and comparable results of a gene of interest (GOI) between subjects and under varying experimental conditions. There is limited evidence to support selection of the commonly used reference genes in rat ischaemic and toxicological kidney models. Employing these models, we determined the most stable reference genes by comparing 4 standard methods (NormFinder, qBase+, BestKeeper and comparative ΔCq) and developed a new 3-way linear mixed-effects model for evaluation of reference gene stability. This new technique utilises the intra-class correlation coefficient as the stability measure for multiple continuous and categorical covariates when determining the optimum normalisation factor. The model also determines confidence intervals for each candidate normalisation gene to facilitate selection and allow sample size calculation for designing experiments to identify reference genes. Of the 10 candidate reference genes tested, the geometric mean of polyadenylate-binding nuclear protein 1 (PABPN1) and beta-actin (ACTB) was the most stable reference combination. In contrast, commonly used ribosomal 18S and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were the most unstable. We compared the use of PABPN1×ACTB and 2 commonly used genes 18S and GAPDH on the expression of 4 genes of interest know to vary after renal injury and expressed by different kidney cell types (KIM-1, HIF1α, TGFβ1 and PECAM1). The less stable reference genes gave varying patterns of GOI expression in contrast to the use of the least unstable reference PABPN1×ACTB combination; this improved detection of differences in gene expression between experimental groups. Reduced within-group variation of the now more accurately normalised GOI may allow for reduced experimental group size particularly for comparison between various models. This objective selection of stable reference genes increased the reliability of comparisons within and between experimental groups.
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Affiliation(s)
- Sanjeeva Herath
- Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia
| | - Hongying Dai
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Jonathan Erlich
- Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia
- * E-mail:
| | - Amy YM Au
- Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia
- Department of Nephrology, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Kylie Taylor
- Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia
| | - Lena Succar
- Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia
| | - Zoltán H. Endre
- Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia
- Department of Nephrology, Prince of Wales Hospital, Randwick, New South Wales, Australia
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40
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Mögling R, Meijer A, Berginc N, Bruisten S, Charrel R, Coutard B, Eckerle I, Enouf V, Hungnes O, Korukluoglu G, Kossyvakis T, Mentis A, Molenkamp R, Muradrasoli S, Papa A, Pigny F, Thirion L, van der Werf S, Reusken C. Delayed Laboratory Response to COVID-19 Caused by Molecular Diagnostic Contamination. Emerg Infect Dis 2020; 26:1944-1946. [PMID: 32433015 PMCID: PMC7392437 DOI: 10.3201/eid2608.201843] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) created an exceptional situation in which numerous laboratories in Europe simultaneously implemented SARS-CoV-2 diagnostics. These laboratories reported in February 2020 that commercial primer and probe batches for SARS-CoV-2 detection were contaminated with synthetic control material, causing delays of regional testing roll-out in various countries.
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41
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Hadweh P, Orfanidou T, Tsiamita M, Timologos G, Papadopoulos T. SARS-CoV2: Diagnostic tests available to the clinician. Hell J Nucl Med 2020; 23 Suppl:8-14. [PMID: 32860390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
On December 2019, a new coronavirus disease (COVID-19) emerged in China and spread worldwide, causing acute severe respiratory syndrome. Due to the increased transmission rate of the virus, it became of great importance the early diagnosis of the disease. The coronavirus pandemic led to the development of numerous tests in order to mass screening population for active viral load and for the identification of antibodies for epidemiological purposes. This review summarizes the different diagnostic tests available to the clinicians for the diagnosis and follow up of the SARS COV-2 infections.
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Affiliation(s)
- Paul Hadweh
- KARYO Ltd, Molecular Diagnostics Laboratory, Ermou 51 str, P.C 54623, Thessaloniki, Greece.
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42
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Shyu D, Dorroh J, Holtmeyer C, Ritter D, Upendran A, Kannan R, Dandachi D, Rojas-Moreno C, Whitt SP, Regunath H. Laboratory Tests for COVID-19: A Review of Peer-Reviewed Publications and Implications for Clinical Use. Mo Med 2020; 117:184-195. [PMID: 32636542 PMCID: PMC7302033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Diagnostic tests for the coronavirus infection 2019 (COVID-19) are critical for prompt diagnosis, treatment and isolation to break the cycle of transmission. A positive real-time reverse-transcriptase polymerase chain reaction (RT-PCR), in conjunction with clinical and epidemiologic data, is the current standard for diagnosis, but several challenges still exist. Serological assays help to understand epidemiology better and to evaluate vaccine responses but they are unreliable for diagnosis in the acute phase of illness or assuming protective immunity. Serology is gaining attention, mainly because of convalescent plasma gaining importance as treatment for clinically worsening COVID-19 patients. We provide a narrative review of peer-reviewed research studies on RT-PCR, serology and antigen immune-assays for COVID-19, briefly describe their lab methods and discuss their limitations for clinical practice.
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Affiliation(s)
- Daniel Shyu
- Department of Medicine, University of Missouri - Columbia, Columbia, Missouri
| | - James Dorroh
- Department of Medicine, University of Missouri - Columbia, Columbia, Missouri
| | - Caleb Holtmeyer
- Department of Medicine, University of Missouri - Columbia, Columbia, Missouri
| | - Detlef Ritter
- Department of Pathology and Anatomical Sciences, University of Missouri - Columbia, Columbia, Missouri
| | - Anandhi Upendran
- Department of Medical Pharmacology and Physiology and at the University of Missouri Institute of Clinical And Translational Science (MU-iCATS), University of Missouri - Columbia, Columbia, Missouri
| | - Raghuraman Kannan
- Departments of Radiology and Bioengineering, University of Missouri - Columbia, Columbia, Missouri
| | - Dima Dandachi
- Department of Medicine - Division of Infectious Diseases, University of Missouri - Columbia, Columbia, Missouri
| | - Christian Rojas-Moreno
- Department of Medicine - Division of Infectious Diseases, University of Missouri - Columbia, Columbia, Missouri
| | - Stevan P Whitt
- MSMA member since 2019 and Missouri Medicine Editorial Board Member for Infectious Disease, Divisions of Infectious Diseases, Pulmonary, Critical Care and Environmental Medicine, University of Missouri - Columbia, Columbia, Missouri
| | - Hariharan Regunath
- MSMA member since 2019 and Missouri Medicine Editorial Board Member for Infectious Disease, Divisions of Infectious Diseases, Pulmonary, Critical Care and Environmental Medicine, University of Missouri - Columbia, Columbia, Missouri
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43
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Pinheiro DH, Siegfried BD. Selection of reference genes for normalization of RT-qPCR data in gene expression studies in Anthonomus eugenii Cano (Coleoptera: Curculionidae). Sci Rep 2020; 10:5070. [PMID: 32193506 PMCID: PMC7081190 DOI: 10.1038/s41598-020-61739-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/25/2020] [Indexed: 01/29/2023] Open
Abstract
The pepper weevil, Anthonomus eugenii Cano (Coleoptera: Curculionidae), is the main insect pest of peppers (Capsicum spp.) throughout the southern U.S. and a potential target for novel control methods that may require gene expression analyses. Careful selection of adequate reference genes to normalize RT-qPCR data is an important prerequisite for gene expression studies since the expression stability of reference genes can be affected by the experimental conditions leading to biased or erroneous results. The lack of studies on validation of reference genes for RT-qPCR analysis in A. eugenii limits the investigation of gene expression, therefore it is needed a systematic selection of suitable reference genes for data normalization. In the present study, three programs (BestKeeper, geNorm and NormFinder) were used to analyze the expression stability of candidate reference genes (β-ACT, ArgK, EF1-α, GAPDH, RPL12, RPS23, α-TUB, 18S and 28S) in A. eugenii under different experimental conditions. Our results revealed that the most stably expressed reference genes in A. eugenii varied according to the experimental condition evaluated: developmental stages (EF1-α, 18S and RPL12), sex (RPS23 and RPL12), low temperature (GAPDH and α-TUB), high temperature (α-TUB and RPS23), all temperatures (α-TUB and GAPDH), starvation (RPL12 and α-TUB), and dsRNA exposure (α-TUB and RPL12). Our study provides for the first time valuable information on appropriate reference genes that can be used in the analysis of gene expression by RT-qPCR in biological experiments involving A. eugenii.
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Affiliation(s)
- Daniele H Pinheiro
- University of Florida, Entomology and Nematology Department, Charles Steinmetz Hall, P. O. Box 110620, Gainesville, FL, 32611-0620, United States
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, P. O. Box 02372, Brasília, DF, 70770-917, Brazil
| | - Blair D Siegfried
- University of Florida, Entomology and Nematology Department, Charles Steinmetz Hall, P. O. Box 110620, Gainesville, FL, 32611-0620, United States.
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Abstract
Meiosis is a specialized type of cell division occurring in sexually reproducing organisms to generate haploid cells known as gametes. In flowering plants, male gametes are produced in anthers, being encased in pollen grains. Understanding the genetic regulation of meiosis key events such as chromosome recognition and pairing, synapsis and recombination, is needed to manipulate chromosome associations for breeding purposes, particularly in important cereal crops like wheat. Reverse transcription-quantitative PCR (RT-qPCR) is widely used to analyse gene expression and to validate the results obtained by other transcriptomic analyses, like RNA-seq. Selection and validation of appropriate reference genes for RT-qPCR normalization is essential to obtain reproducible and accurate expression data. In this work, twelve candidate reference genes were evaluated using the mainstream algorithms geNorm, Normfinder, BestKeeper and ΔCt, then ranked from most to least suitable for normalization with RefFinder. Different sets of reference genes were recommended to normalize gene expression data in anther meiosis of bread and durum wheat, their corresponding genotypes in the absence of the Ph1 locus and for comparative studies among wheat genotypes. Comparisons between meiotic (anthers) and somatic (leaves and roots) wheat tissues were also carried out. To the best of our knowledge, our study provides the first comprehensive list of reference genes for robust RT-qPCR normalization to study differentially expressed genes during male meiosis in wheat in a breeding framework.
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Affiliation(s)
- José Garrido
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, Apartado 4084, 14080, Córdoba, Spain
| | - Miguel Aguilar
- Área de Fisiología Vegetal. Universidad de Córdoba. Campus de Rabanales, edif. C4, 3ª planta, Córdoba, Spain
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, Apartado 4084, 14080, Córdoba, Spain.
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45
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Nunes BTD, de Mendonça MHR, Simith DDB, Moraes AF, Cardoso CC, Prazeres ITE, de Aquino AA, Santos ADCM, Queiroz ALN, Rodrigues DSG, Andriolo RB, Travassos da Rosa ES, Martins LC, Vasconcelos PFDC, Medeiros DBDA. Development of RT-qPCR and semi-nested RT-PCR assays for molecular diagnosis of hantavirus pulmonary syndrome. PLoS Negl Trop Dis 2019; 13:e0007884. [PMID: 31877142 PMCID: PMC6932758 DOI: 10.1371/journal.pntd.0007884] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 10/26/2019] [Indexed: 12/02/2022] Open
Abstract
Hantavirus Pulmonary Syndrome is an, often fatal, emerging zoonotic disease in the Americas caused by hantaviruses (family: Hantaviridae). In Brazil, hantavirus routine diagnosis is based on serology (IgM-ELISA) while RT-PCR is often used to confirm acute infection. A Semi-nested RT-PCR and an internally controlled RT-qPCR assays were developed for detection and quantification of four hantaviruses strains circulating in the Brazilian Amazon: Anajatuba (ANAJV) and Castelo dos Sonhos (CASV) strains of Andes virus (ANDV) species; and Rio Mamoré (RIOMV) and Laguna Negra (LNV) strains of LNV species. A consensus region in the N gene of these hantaviruses was used to design the primer sets and a hydrolysis probe. In vitro transcribed RNA was diluted in standards with known concentration. MS2 bacteriophage RNA was detected together with hantavirus RNA as an exogenous control in a duplex reaction. RT-qPCR efficiency was around 100% and the limit of detection was 0.9 copies/μL of RNA for RT-qPCR and 10 copies/μL of RNA for Semi-nested RT-PCR. There was no amplification of either negative samples or samples positive to other pathogens. To assess the protocol for clinical sensitivity, specificity and general accuracy values, both assays were used to test two groups of samples: one comprising patients with disease (n = 50) and other containing samples from healthy individuals (n = 50), according to IgM-ELISA results. A third group of samples (n = 27) infected with other pathogens were tested for specificity analysis. RT-qPCR was more sensitive than semi-nested RT-PCR, being able to detect three samples undetected by conventional RT-PCR. RT-qPCR clinical sensitivity, specificity and general accuracy values were 92.5%, 100% and 97.63%, respectively. Thus, the assays developed in this study were able to detect the four Brazilian Amazon hantaviruses with good specificity and sensitivity, and may become powerful tools in diagnostic, surveillance and research applications of these and possibly other hantaviruses. Hantavirus Pulmonary Syndrome (HPS) is a serious and often fatal disease caused by viruses known as hantaviruses. These viruses are harbored by wild rodents and people can become infected through contact with infected-rodents droppings, urine or saliva. After an incubation time of 1–8 weeks, patients usually present flu-like symptoms such as fever, fatigue and muscle aches, although some patients may also present headaches, dizziness, chills, nausea, vomiting, diarrhea, and abdominal pain. It is only 4–10 days after initial symptoms, however, that the severe stage of disease takes place. Symptoms include coughing, shortness of breath and eventually the lungs fill with fluid which can lead to shock and death. As such, HPS should be diagnosed quickly as any delay may have great impact on patient recovery. However, given the unspecific nature of early symptoms, clinical diagnosis of HPS is difficult and laboratory assays are needed to confirm hantavirus infection as soon as possible, helping physicians to choose the most adequate treatment. In this study, we developed new laboratory assays that can help detect the virus in infected patients in early stages of disease. In addition, we showed these assays have a good performance in discriminating HPS from other similar diseases by testing not only several samples collected from both HPS patients and healthy individuals but also samples infected with other pathogens. Our results show that these assays may become important tools for rapid, sensitive and specific diagnosis of HPS.
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Affiliation(s)
- Bruno Tardelli Diniz Nunes
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
- Post-Graduation Program in Virology, Evandro Chagas Institute, Ananindeua, Brazil
| | | | - Darlene de Brito Simith
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
- Post-Graduation Program in Virology, Evandro Chagas Institute, Ananindeua, Brazil
| | - Adriana Freitas Moraes
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
| | - Carla Conceição Cardoso
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
| | | | - Ana Alice de Aquino
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
| | | | | | | | | | | | - Livia Carício Martins
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
| | - Pedro Fernando da Costa Vasconcelos
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
- Post-Graduation Program in Virology, Evandro Chagas Institute, Ananindeua, Brazil
| | - Daniele Barbosa de Almeida Medeiros
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua, Brazil
- Post-Graduation Program in Virology, Evandro Chagas Institute, Ananindeua, Brazil
- * E-mail:
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Li X, Yang Y, Ahmad S, Sun M, Yuan C, Zheng T, Han Y, Cheng T, Wang J, Zhang Q. Selection of optimal reference genes for qRT-PCR analysis of shoot development and graviresponse in prostrate and erect chrysanthemums. PLoS One 2019; 14:e0225241. [PMID: 31774840 PMCID: PMC6880974 DOI: 10.1371/journal.pone.0225241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 10/31/2019] [Indexed: 11/19/2022] Open
Abstract
The prostrate cultivars of ground-cover chrysanthemum have been used in landscape gardening due to their small stature, large crown width and strong branching ability. qRT-PCR is a rapid and powerful tool for gene expression analysis, while its accuracy highly depends on the stability of reference genes. The paucity of authentic reference genes presents a major hurdle in understanding the genetic regulators of prostrate architecture. Therefore, in order to reveal the regulatory mechanism of prostrate growth of chrysanthemum stems, here, stable reference genes were selected for expression analysis of key genes involved in shoot development and graviresponse. Based on transcriptome data, eleven reference genes with relatively stable expression were identified as the candidate reference genes. After the comprehensive analysis of the stability of these reference genes with four programs (geNorm, NormFinder, BestKeeper and RefFinder), we found that TIP41 was the most stable reference gene in all of the samples. SAND was determined as a superior reference gene in different genotypes and during the process of shoot development. The optimal reference gene for gravitropic response was PP2A-1. In addition, the expression patterns of LA1 and PIN1 further verified the reliability of the screened reference genes. These results can provide more accurate and reliable qRT-PCR normalization for future studies on the expression patterns of genes regulating plant architecture of chrysanthemums.
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Affiliation(s)
- Xiaowei Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Yujie Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Sagheer Ahmad
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Ming Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Cunquan Yuan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangchun Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Yu Han
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Jia Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
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Šubr ZW, Király KD, Fail J, Almási A, Salánki K, Fedor P. Efficient RT-PCR tool for tomato spotted wilt virus detection in its vectors Thrips tabaci and Frankliniella occidentalis. Acta Virol 2019; 63:341-343. [PMID: 31507203 DOI: 10.4149/av_2019_315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Zhang H, Wang Y, Porter E, Lu N, Li Y, Yuan F, Lohman M, Noll L, Zheng W, Stoy C, Lang Y, Huber VC, Ma W, Peddireddi L, Fang Y, Shi J, Anderson G, Liu X, Bai J. Development of a multiplex real-time RT-PCR assay for simultaneous detection and differentiation of influenza A, B, C, and D viruses. Diagn Microbiol Infect Dis 2019; 95:59-66. [PMID: 31130238 PMCID: PMC6697560 DOI: 10.1016/j.diagmicrobio.2019.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/08/2019] [Accepted: 04/23/2019] [Indexed: 01/18/2023]
Abstract
Influenza is a common and contagious respiratory disease caused by influenza A, B, C, and D viruses (IAV, IBV, ICV, and IDV). A multiplex real-time RT-PCR assay was developed for simultaneous detection of IAV, IBV, ICV, and IDV. The assay was designed to target unique sequences in the matrix gene of IBV and ICV, the RNA polymerase subunit PB1 of IDV, and combined with USDA and CDC IAV assays, both target the matrix gene. The host 18S rRNA gene was included as an internal control. In silico analyses indicated high strain coverages: 97.9% for IBV, 99.5% for ICV, and 100% for IDV. Transcribed RNA, viral isolates and clinical samples were used for validation. The assay specifically detected target viruses without cross-reactivity, nor detection of other common pathogens. The limit of detection was approximately 30 copies for each viral RNA template, which was equivalent to a threshold cycle value of ~37.
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Affiliation(s)
- Hewei Zhang
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; College of Food and Drugs, Luoyang Polytechnic, Luo Yang, Henan, China
| | - Yin Wang
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Elizabeth Porter
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Nanyan Lu
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yanhua Li
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Fangfeng Yuan
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Molly Lohman
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Lance Noll
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Wanglong Zheng
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Colin Stoy
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yuekun Lang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Victor C Huber
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, Vermillion, SD, USA
| | - Wenjun Ma
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Lalitha Peddireddi
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Ying Fang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Jishu Shi
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Gary Anderson
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Xuming Liu
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
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Hossain MS, Ahmed R, Haque MS, Alam MM, Islam MS. Identification and validation of reference genes for real-time quantitative RT-PCR analysis in jute. BMC Mol Biol 2019; 20:13. [PMID: 31035927 PMCID: PMC6489354 DOI: 10.1186/s12867-019-0130-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/16/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND With the availability of genome sequences, gene expression analysis of jute has drawn considerable attention for understanding the regulatory mechanisms of fiber development and improving fiber quality. Gene expression profiles of a target gene can provide valuable clues towards the understanding of its biological function. Reverse transcription quantitative real-time PCR (qRT-PCR) is the best method for targeted gene expression analysis due to its sensitivity and reproducibility. However, calculating relative expression requires reference genes, which must be stable across various biological conditions. For this purposes, 11 prospective genes namely, 28S RNA, ACT7, CYP, EF1A, EF2, ETIF3E, GAPDH, PP2Ac, PTB, UBC2 and UBI1 were evaluated for their potential use as reference genes in jute. RESULTS The expression stabilities of eleven prospective genes were analyzed in various jute plant tissues, such as the root, stick, bark, leaf, flower, seed and fiber, as well as under abiotic (waterlogged, drought and salinity) and biotic stress (infestation with Macrophomina phaseolina) conditions with different time points. All 11 genes were variably expressed in different tissues and stress conditions. To find suitable reference genes in different sample sets, a comprehensive approach based on four statistical algorithms such as GeNorm, BestKeeper, NormFinder the ΔCt was used. The PP2Ac and EF2 genes were the most stably expressed across the different tissues. ACT7 and UBC2 were suitable reference genes under drought stress, and CYP and PP2Ac were the most appropriate after inoculation with Macrophomina phaseolina. Under salinity stress, PP2Ac and UBC2 were the best genes, and ACT7 and PP2Ac were the most suitable under waterlogged conditions. CONCLUSION Expression stability of reference genes from jute varied in different tissues and selected experimental conditions. Our results provide a valuable resource for the accurate normalization of gene expression experiments in fiber research for important bast fiber crops.
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Affiliation(s)
- Md. Sabbir Hossain
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Rasel Ahmed
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Md. Samiul Haque
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Md. Monjurul Alam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Md. Shahidul Islam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
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50
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Pombo MA, Ramos RN, Zheng Y, Fei Z, Martin GB, Rosli HG. Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana. Sci Rep 2019; 9:1632. [PMID: 30733563 PMCID: PMC6367355 DOI: 10.1038/s41598-018-38247-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/20/2018] [Indexed: 12/17/2022] Open
Abstract
RT-qPCR is a widely used technique for the analysis of gene expression. Accurate estimation of transcript abundance relies strongly on a normalization that requires the use of reference genes that are stably expressed in the conditions analyzed. Initially, they were adopted from those used in Northern blot experiments, but an increasing number of publications highlight the need to find and validate alternative reference genes for the particular system under study. The development of high-throughput sequencing techniques has facilitated the identification of such stably expressed genes. Nicotiana benthamiana has been extensively used as a model in the plant research field. In spite of this, there is scarce information regarding suitable RT-qPCR reference genes for this species. Employing RNA-seq data previously generated from tomato plants, combined with newly generated data from N. benthamiana leaves infiltrated with Pseudomonas fluorescens, we identified and tested a set of 9 candidate reference genes. Using three different algorithms, we found that NbUbe35, NbNQO and NbErpA exhibit less variable gene expression in our pathosystem than previously used genes. Furthermore, the combined use of the first two is sufficient for robust gene expression analysis. We encourage employing these novel reference genes in future RT-qPCR experiments involving N. benthamiana and Pseudomonas spp.
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Affiliation(s)
- Marina A Pombo
- Instituto de Fisiología Vegetal, INFIVE, Universidad Nacional de La Plata, CONICET, La Plata, Buenos Aires, Argentina
| | - Romina N Ramos
- Instituto de Fisiología Vegetal, INFIVE, Universidad Nacional de La Plata, CONICET, La Plata, Buenos Aires, Argentina
| | - Yi Zheng
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY, 14853, USA
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY, 14853, USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY, 14853, USA
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Hernan G Rosli
- Instituto de Fisiología Vegetal, INFIVE, Universidad Nacional de La Plata, CONICET, La Plata, Buenos Aires, Argentina.
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