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Owusu M, Adu E, Kalu LE, Martey E, Acheampong G, Enimil A, Appiah JA, Badu-Peprah A, Sylverken J, Sylverken AA, Nguah SB, Westeel E, Pouzol S, Drosten C, Adu-Sarkodie Y. Aetiological agents of pneumonia among HIV and non-HIV infected children in Ghana: A case-control study. PLoS One 2024; 19:e0299222. [PMID: 38517865 PMCID: PMC10959341 DOI: 10.1371/journal.pone.0299222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 02/05/2024] [Indexed: 03/24/2024] Open
Abstract
Pneumonia is the leading cause of death in children, however, the microbial aetiology of pneumonia is not well elucidated in low- and middle-income countries. Our study was aimed at determining the microbial aetiologies of childhood pneumonia and associated risk factors in HIV and non-HIV infected children. We conducted a case-control study that enrolled children with pneumonia as cases and non-pneumonia as controls from July 2017 to May 2020. Induced sputum and blood samples were investigated for microbial organisms using standard microbiological techniques. DNA/RNA was extracted from sputum samples and tested for viral and bacterial agents. Four hundred and four (404) subjects consisting of 231 (57.2%) cases and 173 (42.8%) controls were enrolled. We identified a significant (p = 0.011) proportion of viruses in cases (125; 54.1%, 95%CI: 47.4-60.7) than controls (71; 33.6%, 95%CI: 33.6-48.8) and these were mostly contributed to by Respiratory Syncytial Virus. Staphylococcus aureus (16; 4.0%), Klebsiella spp. (15, 3.7%) and Streptococcus pneumoniae (8, 2.0%) were the main bacterial agents identified in sputum or induced sputum samples. HIV infected children with viral-bacterial co-detection were found to have very severe pneumonia compared to those with only viral or bacterial infection. Indoor cooking (OR = 2.36; 95%CI:1.41-3.96) was found to be associated with pneumonia risk in patients. This study demonstrates the importance of various microbial pathogens, particularly RSV, in contributing to pneumonia in HIV and non-HIV paediatric populations. There is a need to accelerate clinical trials of RSV vaccines in African populations to support improvement of patient care.
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Affiliation(s)
- Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Eric Adu
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Lotenna Elsie Kalu
- Department of Child Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Eugene Martey
- Department of Child Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Anthony Enimil
- Department of Child Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - John Adabie Appiah
- Department of Child Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Justice Sylverken
- Department of Child Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samuel Blay Nguah
- Department of Child Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | | | - Yaw Adu-Sarkodie
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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2
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Ding J, Xu X, Deng Y, Zheng X, Zhang T. Comparison of RT-ddPCR and RT-qPCR platforms for SARS-CoV-2 detection: Implications for future outbreaks of infectious diseases. ENVIRONMENT INTERNATIONAL 2024; 183:108438. [PMID: 38232505 DOI: 10.1016/j.envint.2024.108438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
The increased frequency of human infectious disease outbreaks caused by RNA viruses worldwide in recent years calls for enhanced public health surveillance for better future preparedness. Wastewater-based epidemiology (WBE) is emerging as a valuable epidemiological tool for providing timely population-wide surveillance for disease prevention and response complementary to the current clinical surveillance system. Here, we compared the analytical performance and practical applications between predominant molecular detection methods of RT-qPCR and RT-ddPCR on SARS-CoV-2 detection in wastewater surveillance. When pure viral RNA was tested, RT-ddPCR exhibited superior quantification accuracy at higher concentration levels and achieved more sensitive detection with reduced variation at low concentration levels. Furthermore, RT-ddPCR consistently demonstrated more robust and accurate measurement either in the background of the wastewater matrix or with the presence of mismatches in the target regions of the consensus assay. Additionally, by detecting mock variant RNA samples, we found that RT-ddPCR outperformed RT-qPCR in virus genotyping by targeting specific loci with signature mutations in allele-specific (AS) assays, especially at low levels of allele frequencies and concentrations, which increased the possibility for sensitive low-prevalence variant detection in the population. Our study provides insights for detection method selection in the WBE applications for future infectious disease outbreaks.
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Affiliation(s)
- Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region.
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3
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Ju DU, Park D, Kim IH, Kim S, Yoo HM. Development of Human Rhinovirus RNA Reference Material Using Digital PCR. Genes (Basel) 2023; 14:2210. [PMID: 38137032 PMCID: PMC10742479 DOI: 10.3390/genes14122210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The human rhinovirus (RV) is a positive-stranded RNA virus that causes respiratory tract diseases affecting both the upper and lower halves of the respiratory system. RV enhances its replication by concentrating RNA synthesis within a modified host membrane in an intracellular compartment. RV infections often occur alongside infections caused by other respiratory viruses, and the RV virus may remain asymptomatic for extended periods. Alongside qualitative detection, it is essential to accurately quantify RV RNA from clinical samples to explore the relationships between RV viral load, infections caused by the virus, and the resulting symptoms observed in patients. A reference material (RM) is required for quality evaluation, the performance evaluation of molecular diagnostic products, and evaluation of antiviral agents in the laboratory. The preparation process for the RM involves creating an RV RNA mixture by combining RV viral RNA with RNA storage solution and matrix. The resulting RV RNA mixture is scaled up to a volume of 25 mL, then dispensed at 100 µL per vial and stored at -80 °C. The process of measuring the stability and homogeneity of RV RMs was conducted by employing reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Digital PCR is useful for the analysis of standards and can help to improve measurement compatibility: it represents the equivalence of a series of outcomes for reference materials and samples being analyzed when a few measurement procedures are employed, enabling objective comparisons between quantitative findings obtained through various experiments. The number of copies value represents a measured result of approximately 1.6 × 105 copies/μL. The RM has about an 11% bottle-to-bottle homogeneity and shows stable results for 1 week at temperatures of 4 °C and -20 °C and for 12 months at a temperature of -80 °C. The developed RM can enhance the dependability of RV molecular tests by providing a precise reference value for the absolute copy number of a viral target gene. Additionally, it can serve as a reference for diverse studies.
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Affiliation(s)
- Dong U Ju
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Dongju Park
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Il-Hwan Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Seil Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Hee Min Yoo
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
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4
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Nemes K, Persson S, Simonsson M. Hepatitis A Virus and Hepatitis E Virus as Food- and Waterborne Pathogens-Transmission Routes and Methods for Detection in Food. Viruses 2023; 15:1725. [PMID: 37632066 PMCID: PMC10457876 DOI: 10.3390/v15081725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Foodborne viruses are an important threat to food safety and public health. Globally, there are approximately 5 million cases of acute viral hepatitis due to hepatitis A virus (HAV) and hepatitis E virus (HEV) every year. HAV is responsible for numerous food-related viral outbreaks worldwide, while HEV is an emerging pathogen with a global health burden. The reported HEV cases in Europe have increased tenfold in the last 20 years due to its zoonotic transmission through the consumption of infected meat or meat products. HEV is considered the most common cause of acute viral hepatitis worldwide currently. This review focuses on the latest findings on the foodborne transmission routes of HAV and HEV and the methods for their detection in different food matrices.
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Affiliation(s)
- Katalin Nemes
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Dag Hammarskjölds väg 56 A, 75237 Uppsala, Sweden; (S.P.); (M.S.)
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5
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Zhao H, Yan C, Feng Y, Du B, Feng J, Cui X, Cui J, Gan L, Fan Z, Xu Z, Fu T, Yu Z, Yuan J, Xue G. Absolute quantification of Mycoplasma pneumoniae in infected patients by droplet digital PCR to track disease severity and treatment efficacy. Front Microbiol 2023; 14:1177273. [PMID: 37426001 PMCID: PMC10324665 DOI: 10.3389/fmicb.2023.1177273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
Mycoplasma pneumoniae is a common causative pathogen of community-acquired pneumonia. An accurate and sensitive detection method is important for evaluating disease severity and treatment efficacy. Digital droplet PCR (ddPCR) is a competent method enabling the absolute quantification of DNA copy number with high precision and sensitivity. We established ddPCR for M. pneumoniae detection, using clinical specimens for validation, and this showed excellent specificity for M. pneumoniae. The limit of detection of ddPCR was 2.9 copies/reaction, while that for real-time PCR was 10.8 copies/reaction. In total, 178 clinical samples were used to evaluate the ddPCR assay, which correctly identified and differentiated 80 positive samples, whereas the real-time PCR tested 79 samples as positive. One sample that tested negative in real-time PCR was positive in ddPCR, with a bacterial load of three copies/test. For samples that tested positive in both methods, the cycle threshold of real-time PCR was highly correlated with the copy number of ddPCR. Bacterial loads in patients with severe M. pneumoniae pneumonia were significantly higher than those in patients with general M. pneumoniae pneumonia. The ddPCR showed that bacterial loads were significantly decreased after macrolide treatment, which could have reflected the treatment efficacy. The proposed ddPCR assay was sensitive and specific for the detection of M. pneumoniae. Quantitative monitoring of bacterial load in clinical samples could help clinicians to evaluate treatment efficacy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Jing Yuan
- *Correspondence: Jing Yuan, ; Guanhua Xue,
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6
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Xu H, Lin M, Zheng Y, Fang X, Huang X, Huang Q, Xu J, Duan W, Wei J, Jia L. In situ imaging miRNAs using multifunctional linear DNA nanostructure. Talanta 2023; 253:123997. [PMID: 36228560 DOI: 10.1016/j.talanta.2022.123997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022]
Abstract
The microRNAs (miRNAs) play a critical role in many biological processes and are essential biomarkers for diagnosing disease. However, the sensitive and specific quantification of microRNAs (miRNAs) expression in living cells still faces a huge challenge. Our study designed a multifunctional linear DNA nanostructure (MLN) as a carrier of molecular beacons (MB-21) for detecting and intracellular imaging miRNA-21. The MLN-MB consists of three parts: aptamer, MLN, and MB-21. The aptamer (AS1411) could media MLN-MB enter live cells without additional transfection reagents. Once inside the cells, the intracellular miRNA-21 could hybridize the MB-21s, resulting in significantly enhanced fluorescence signals. The whole process was enzyme-free, autonomous, and continuous, which avoided the necessity of adding external fuel strands or enzymes. We demonstrated that the MLN-MB could be used to screen the miRNA-21 with a detection limit of 320 pM in a short time (10 min) and show high specificity toward miRNA-21 against other miRNAs. Moreover, the proposed MLN-MB could detect the miRNA-21 in complex matrixes stably. With its outstanding stability, dual recognition, and biocompatibility, MLN-MB is capable of delivering into living cells to identify specific cancer cells. Therefore, our sensing approach, with high sensitivity, specificity, and simplicity advantages, holds great potential for early cancer diagnosis.
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Affiliation(s)
- Huo Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian, 350108, China
| | - Min Lin
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian, 350108, China
| | - Yanhui Zheng
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian, 350108, China
| | - Xiaojun Fang
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian, 350108, China; Cancer Metastasis Alert and Prevention Center, and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Xinmei Huang
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian, 350108, China
| | - Qi Huang
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian, 350108, China
| | - Jiawei Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian, 350108, China
| | - Wei Duan
- School of Medicine and Centre for Molecular and Medical Research Deakin University Geelong, Victoria, 3216, Australia
| | - Juan Wei
- School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, China.
| | - Lee Jia
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian, 350108, China.
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7
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Tan LL, Loganathan N, Agarwalla S, Yang C, Yuan W, Zeng J, Wu R, Wang W, Duraiswamy S. Current commercial dPCR platforms: technology and market review. Crit Rev Biotechnol 2022; 43:433-464. [PMID: 35291902 DOI: 10.1080/07388551.2022.2037503] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.
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Affiliation(s)
- Li Ling Tan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore.,Materials Science and Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Nitin Loganathan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Sushama Agarwalla
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Chun Yang
- Mechanical and Aerospace Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Weiyong Yuan
- Faculty of Materials & Energy, Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing, China.,Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, Chongqing, China
| | - Jasmine Zeng
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Ruige Wu
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Wei Wang
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Suhanya Duraiswamy
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
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8
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Burstein R, Althouse BM, Adler A, Akullian A, Brandstetter E, Cho S, Emanuels A, Fay K, Gamboa L, Han P, Huden K, Ilcisin M, Izzo M, Jackson ML, Kim AE, Kimball L, Lacombe K, Lee J, Logue JK, Rogers J, Chung E, Sibley TR, Van Raay K, Wenger E, Wolf CR, Boeckh M, Chu H, Duchin J, Rieder M, Shendure J, Starita LM, Viboud C, Bedford T, Englund JA, Famulare M. Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.02.04.22270474. [PMID: 35169816 PMCID: PMC8845514 DOI: 10.1101/2022.02.04.22270474] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because sampling from symptomatic individuals can create biased estimates. Methods We conducted an observational, cross-sectional study using samples collected by the Seattle Flu Study between 11 November 2018 and 20 August 2021. Samples that tested positive via RT-qPCR for at least one of 17 potential respiratory pathogens were included in this study. Semi-quantitative cycle threshold (Ct) values were used to measure pathogen load. Differences in pathogen load between monoinfected and coinfected samples were assessed using linear regression adjusting for age, season, and recruitment channel. Results 21,686 samples were positive for at least one potential pathogen. Most prevalent were rhinovirus (33·5%), Streptococcus pneumoniae (SPn, 29·0%), SARS-CoV-2 (13.8%) and influenza A/H1N1 (9·6%). 140 potential pathogen pairs were included for analysis, and 56 (40%) pairs yielded significant Ct differences (p < 0.01) between monoinfected and co-infected samples. We observed no virus-virus pairs showing evidence of significant facilitating interactions, and found significant viral load decrease among 37 of 108 (34%) assessed pairs. Samples positive with SPn and a virus were consistently associated with increased SPn load. Conclusions Viral load data can be used to overcome sampling bias in studies of pathogen-pathogen interactions. When applied to respiratory pathogens, we found evidence of viral-SPn facilitation and several examples of viral-viral interference. Multipathogen surveillance is a cost-efficient data collection approach, with added clinical and epidemiological informational value over single-pathogen testing, but requires careful analysis to mitigate selection bias.
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Affiliation(s)
- Roy Burstein
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | - Benjamin M. Althouse
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
- Department of Biology, New Mexico State University, Las Cruces, NM
| | - Amanda Adler
- Seattle Children’s Research Institute, Seattle WA USA
| | - Adam Akullian
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | | | - Shari Cho
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Anne Emanuels
- Department of Medicine, University of Washington, Seattle WA USA
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Luis Gamboa
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Peter Han
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Kristen Huden
- Department of Medicine, University of Washington, Seattle WA USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Mandy Izzo
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | | | - Ashley E. Kim
- Department of Medicine, University of Washington, Seattle WA USA
| | - Louise Kimball
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Julia Rogers
- Department of Medicine, University of Washington, Seattle WA USA
| | - Erin Chung
- Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle
| | - Thomas R. Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Edward Wenger
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | - Caitlin R. Wolf
- Department of Medicine, University of Washington, Seattle WA USA
| | - Michael Boeckh
- Department of Medicine, University of Washington, Seattle WA USA
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Helen Chu
- Department of Medicine, University of Washington, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Jeff Duchin
- Department of Medicine, University of Washington, Seattle WA USA
- Public Health Seattle & King County, Seattle WA USA
| | - Mark Rieder
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Department of Genome Sciences, University of Washington, Seattle WA USA
- Howard Hughes Medical Institute, Seattle WA USA
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Department of Genome Sciences, University of Washington, Seattle WA USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
- Howard Hughes Medical Institute, Seattle WA USA
| | - Janet A. Englund
- Seattle Children’s Research Institute, Seattle WA USA
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Michael Famulare
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
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9
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Valença IN, Santos RBD, Peronni KC, Sauvage V, Vandenbogaert M, Caro V, Silva Junior WAD, Covas DT, Silva-Pinto AC, Laperche S, Kashima S, Slavov SN. Deep sequencing applied to the analysis of viromes in patients with beta-thalassemia. Rev Inst Med Trop Sao Paulo 2021; 63:e40. [PMID: 34037156 PMCID: PMC8149102 DOI: 10.1590/s1678-9946202163040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/18/2021] [Indexed: 11/22/2022] Open
Abstract
To date, blood banks apply routine diagnosis to a specific spectrum of
transfusion-transmitted viruses. Even though this measure is considered highly
efficient to control their transmission, the threat imposed by emerging viruses
is increasing globally, which can impact transfusion safety, especially in the
light of the accelerated viral discovery by novel sequencing technologies. One
of the most important groups of patients, who may indicate the presence of
emerging viruses in the field of blood transfusion, is the group of individuals
who receive multiple transfusions due to hereditary hemoglobinopathies. It is
possible that they harbor unknown or unsuspected parenterally-transmitted
viruses. In order to elucidate this, nucleic acids from 30 patients with
beta-thalassemia were analyzed by Illumina next-generation sequencing and
bioinformatics analysis. Three major viral families:
Anelloviridae, Flaviviridae and
Hepadnaviridae were identified. Among
them, anelloviruses were the most representative, being detected with high
number of reads in all tested samples. Human Pegivirus 1 (HPgV-1, or GBV-C),
Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) were also identified. HBV
and HCV detection was expected due to the high seroprevalence in patients with
beta thalassemia. Our results do not confirm the presence of emerging or
unsuspected viruses threatening the transfusion safety at present, but can be
used to actively search for viruses that threaten blood transfusion safety. We
believe that the application of viral metagenomics in multiple-transfused
patients is highly useful to monitor possible viral transfusion threats and for
the annotation of their virome composition.
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Affiliation(s)
- Ian Nunes Valença
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Programa de Mestrado em Oncologia Clínica, Células-Tronco e Terapia Celular, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Rafael Bezerra Dos Santos
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Programa de Mestrado em Oncologia Clínica, Células-Tronco e Terapia Celular, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Kamila Chagas Peronni
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Virginie Sauvage
- Centre National de Référence Risques Infectieux Transfusionnels, Institut National de la Transfusion Département d'études des Agents Transmissibles par le Sang, Paris, France
| | - Mathias Vandenbogaert
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, Paris, France
| | - Valérie Caro
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, Paris, France
| | - Wilson Araújo da Silva Junior
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, São Paulo, Brazil
| | - Dimas Tadeu Covas
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Clínica Médica, Ribeirão Preto, São Paulo, Brazil
| | - Ana Cristina Silva-Pinto
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Syria Laperche
- Centre National de Référence Risques Infectieux Transfusionnels, Institut National de la Transfusion Département d'études des Agents Transmissibles par le Sang, Paris, France
| | - Simone Kashima
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Clínica Médica, Ribeirão Preto, São Paulo, Brazil
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10
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Falak S, Macdonald R, Busby EJ, O'Sullivan DM, Milavec M, Plauth A, Kammel M, Zeichhardt H, Grunert HP, Kummrow A, Huggett JF. An assessment of the reproducibility of reverse transcription digital PCR quantification of HIV-1. Methods 2021; 201:34-40. [PMID: 33722693 DOI: 10.1016/j.ymeth.2021.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/28/2021] [Accepted: 03/08/2021] [Indexed: 11/30/2022] Open
Abstract
Viral load monitoring in human immunodeficiency virus type 1 (HIV-1) infection is often performed using reverse transcription quantitative PCR (RT-qPCR) to observe response to treatment and identify the development of resistance. Traceability is achieved using a calibration hierarchy traceable to the International Unit (IU). IU values are determined using consensus agreement derived from estimations by different laboratories. Such a consensus approach is necessary due to the fact that there are currently no reference measurement procedures available that can independently assign a reference value to viral reference materials for molecular in vitro diagnostic tests. Digital PCR (dPCR) is a technique that has the potential to be used for this purpose. In this paper, we investigate the ability of reverse transcriptase dPCR (RT-dPCR) to quantify HIV-1 genomic RNA without calibration. Criteria investigated included the performance of HIV-1 RNA extraction steps, choice of reverse transcription approach and selection of target gene with assays performed in both single and duplex format. We developed a protocol which was subsequently applied by two independent laboratories as part of an external quality assurance (EQA) scheme for HIV-1 genome detection. Our findings suggest that RT-dPCR could be used as reference measurement procedure to aid the value assignment of HIV-1 reference materials to support routine calibration of HIV-1 viral load testing by RT-qPCR.
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Affiliation(s)
- Samreen Falak
- Physikalisch Technische Bundesanstalt, Abbestr. 2-12, 10587 Berlin, Germany.
| | - Rainer Macdonald
- Physikalisch Technische Bundesanstalt, Abbestr. 2-12, 10587 Berlin, Germany
| | - Eloise J Busby
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Denise M O'Sullivan
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Annabell Plauth
- Physikalisch Technische Bundesanstalt, Abbestr. 2-12, 10587 Berlin, Germany
| | - Martin Kammel
- INSTAND, Gesellschaft zur Foerderung der Qualitaetssicherung in medizinischen Laboratorien e.V., Ubierstr.20, D-40223 Düsseldorf, Germany; IQVD GmbH, Institut fuer Qualitaetssicherung in der Virusdiagnostik, Potsdamer Chaussee 80, 14129 Berlin, Germany
| | - Heinz Zeichhardt
- INSTAND, Gesellschaft zur Foerderung der Qualitaetssicherung in medizinischen Laboratorien e.V., Ubierstr.20, D-40223 Düsseldorf, Germany; IQVD GmbH, Institut fuer Qualitaetssicherung in der Virusdiagnostik, Potsdamer Chaussee 80, 14129 Berlin, Germany
| | - Hans-Peter Grunert
- GBD Gesellschaft fuer Biotechnologische Diagnostik mbH, Berlin, Potsdamer Chaussee 80, 14129 Berlin, Germany
| | - Andreas Kummrow
- Physikalisch Technische Bundesanstalt, Abbestr. 2-12, 10587 Berlin, Germany
| | - Jim F Huggett
- National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, United Kingdom; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford GU2 7XH, United Kingdom.
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11
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Limothai U, Chuaypen N, Poovorawan K, Chotiyaputta W, Tanwandee T, Poovorawan Y, Tangkijvanich P. Reverse transcriptase droplet digital PCR vs reverse transcriptase quantitative real-time PCR for serum HBV RNA quantification. J Med Virol 2020; 92:3365-3372. [PMID: 32219874 DOI: 10.1002/jmv.25792] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/27/2020] [Accepted: 03/23/2020] [Indexed: 01/02/2023]
Abstract
Serum hepatitis B virus (HBV) RNA is a novel marker reflecting the activity of covalently closed circular DNA. However, the methodology for detecting HBV RNA has been a technical challenge. In this study, the performance of reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) for quantifying HBV RNA was compared with that of reverse transcription quantitative real-time PCR (RT-qPCR) in serum samples collected from treatment-naïve patients with different phases of chronic hepatitis B (CHB). A total of 417 serum samples, including 136 HBeAg-positive CHB and 281 HBeAg-negative CHB were examined. HBV RNA levels measured by RT-ddPCR and RT-qPCR showed a high degree of linearity and quantitative correlation. The limit of detections of RT-ddPCR and RT-qPCR assays were 102 and 103 copies/mL, respectively. Our results also demonstrated that RT-ddPCR was superior to RT-qPCR in terms of its consistency for quantifying HBV RNA across all concentrations. In the HBeAg-positive group, serum HBV RNA levels based on RT-ddPCR were moderately correlated with HBV DNA (r = 0.591, P < .001) and HBsAg (r = 0.502, P < .001). Among patients with HBeAg-negative CHB, serum HBV RNA levels were moderately correlated with HBV DNA (r = 0.603, P < .001) but had weak correlation with HBsAg (r = 0.203, P = .001). In summary, RT-ddPCR could enhance the sensitivity of serum HBV RNA detection, particularly among the HBeAg-negative group with low viral loads. Thus, RT-ddPCR could serve as an optimal method for HBV RNA quantification in clinical practice.
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Affiliation(s)
- Umaporn Limothai
- Center of Excellence in Hepatitis and Liver Cancer, Chulalongkorn University, Bangkok, Thailand
| | - Natthaya Chuaypen
- Center of Excellence in Hepatitis and Liver Cancer, Chulalongkorn University, Bangkok, Thailand
| | - Kittiyod Poovorawan
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Watcharasak Chotiyaputta
- Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tawesak Tanwandee
- Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pisit Tangkijvanich
- Center of Excellence in Hepatitis and Liver Cancer, Chulalongkorn University, Bangkok, Thailand
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12
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Persson S, Alm E, Karlsson M, Enkirch T, Norder H, Eriksson R, Simonsson M, Ellström P. A new assay for quantitative detection of hepatitis A virus. J Virol Methods 2020; 288:114010. [PMID: 33152410 DOI: 10.1016/j.jviromet.2020.114010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/19/2020] [Accepted: 10/30/2020] [Indexed: 01/18/2023]
Abstract
Hepatitis A virus (HAV) is mainly transmitted via contaminated food or water or through person-to-person contact. Here, we describe development and evaluation of a reverse transcription droplet digital PCR (RT-ddPCR) and reverse transcription real-time PCR (RT-qPCR) assay for detection of HAV in food and clinical specimens. The assay was evaluated by assessing limit of detection, precision, matrix effects, sensitivity and quantitative agreement. The 95 % limit of detection (LOD95 %) was 10 % higher for RT-ddPCR than for RT-qPCR. A Bayesian model was used to estimate precision on different target concentrations. From this, we found that RT-ddPCR had somewhat greater precision than RT-qPCR within runs and markedly greater precision between runs. By analysing serum from naturally infected persons and a naturally contaminated food sample, we found that the two methods agreed well in quantification and had comparable sensitivities. Tests with artificially contaminated food samples revealed that neither RT-ddPCR nor RT-qPCR was severely inhibited by presence of oysters, raspberries, blueberries or leafy-green vegetables. For this assay, we conclude that RT-qPCR should be considered if rapid, qualitative detection is the main interest and that RT-ddPCR should be considered if precise quantification is the main interest. The high precision of RT-ddPCR allows for detection of small changes in viral concentration over time, which has direct implications for both food control and clinical studies.
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Affiliation(s)
- Sofia Persson
- European Union Reference Laboratory (EURL) for Foodborne Viruses, Swedish Food Agency, Box 622, SE-751 26, Uppsala, Sweden; Department of Medical Sciences, Zoonosis Science Centre, Uppsala University, Husargatan 3, SE-751 23, Uppsala, Sweden.
| | - Erik Alm
- Unit for Laboratory Development, Department of Microbiology, The Public Health Agency of Sweden, Nobels väg 18, SE-171 65, Solna, Sweden
| | - Måns Karlsson
- Department of Mathematics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Theresa Enkirch
- Unit for Laboratory Surveillance of Viral Pathogens and Vaccine Preventable Diseases, Department of Microbiology, The Public Health Agency of Sweden, Nobels väg 18, SE-171 65, Solna, Sweden
| | - Heléne Norder
- Department of Infectious Diseases, Institute of Biomedicine at Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Microbiology, SE-413 45 Gothenburg, Sweden
| | - Ronnie Eriksson
- European Union Reference Laboratory (EURL) for Foodborne Viruses, Swedish Food Agency, Box 622, SE-751 26, Uppsala, Sweden
| | - Magnus Simonsson
- European Union Reference Laboratory (EURL) for Foodborne Viruses, Swedish Food Agency, Box 622, SE-751 26, Uppsala, Sweden
| | - Patrik Ellström
- Department of Medical Sciences, Zoonosis Science Centre, Uppsala University, Husargatan 3, SE-751 23, Uppsala, Sweden
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13
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Hattori Y, Ishii H, Tahara S, Morita A, Ozawa H. Accurate assessment of estrogen receptor profiles in non-functioning pituitary adenomas using RT-digital PCR and immunohistochemistry. Life Sci 2020; 260:118416. [PMID: 32926922 DOI: 10.1016/j.lfs.2020.118416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Non-functioning pituitary adenomas (NFPAs) are common pituitary tumors, and surgery is generally the only treatment option. Few attempts have been made to explore target molecules for the development of NFPA pharmacological treatments. METHOD We quantitatively assessed the expression profiles of estrogen receptor (ER) transcripts and proteins in NFPA samples, using reverse transcription-digital polymerase chain reaction (RT-dPCR) and immunohistochemistry, and further investigated the correlations between the expression levels of ER and those of downstream responsive genes. All patients had undergone surgery at the same high-volume hospital. A total of 20 patients with NFPAs were included. All patients were new-onset, and none were diagnosed with intratumoral hemorrhages or cysts. RESULTS NFPA samples exhibited a bimodal ESR1 expression pattern and were categorized into significantly different high- and low-ESR1 expression level groups (P < 0.05). In contrast, expression levels of ESR1 variants and ESR2 could barely be detected. Similar results were obtained through the immunohistochemical staining of NFPAs, using well-validated antibodies against ERs. The expression levels of ESR1 positively correlated with those of GREB1, an estrogen-responsive gene [correlation coefficient (r) = 0.623, P = 0.003]. CONCLUSIONS ESR1 expression levels in NFPAs exhibited a bimodal pattern and were positively correlated with GREB1 expression levels. The accurate assessment of ER expression levels may further advance future NFPA-related research.
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Affiliation(s)
- Yujiro Hattori
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan; Department of Neurological Surgery, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan.
| | - Hirotaka Ishii
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Shigeyuki Tahara
- Department of Neurological Surgery, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Akio Morita
- Department of Neurological Surgery, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Hitoshi Ozawa
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
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14
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Veyer D, Kernéis S, Poulet G, Wack M, Robillard N, Taly V, L'Honneur AS, Rozenberg F, Laurent-Puig P, Bélec L, Hadjadj J, Terrier B, Péré H. Highly sensitive quantification of plasma SARS-CoV-2 RNA shelds light on its potential clinical value. Clin Infect Dis 2020; 73:e2890-e2897. [PMID: 32803231 PMCID: PMC7454373 DOI: 10.1093/cid/ciaa1196] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 01/08/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) is a global public health problem that has already caused more than 662,000 deaths worldwide. Although the clinical manifestations of COVID-19 are dominated by respiratory symptoms, some patients present other severe damage such as cardiovascular, renal and liver injury or/and multiple organ failure, suggesting a spread of the SARS-CoV-2 in blood. Recent ultrasensitive polymerase chain reaction (PCR) technology now allows absolute quantification of nucleic acids in plasma. We herein intended to use the droplet-based digital PCR technology to obtain sensitive detection and precise quantification of plasma SARS-CoV-2 viral load (SARS-CoV-2 RNAaemia) in hospitalized COVID-19 patients. Methods Fifty-eight consecutive COVID-19 patients with pneumonia 8 to 12 days after onset of symptoms and 12 healthy controls were analyzed. Disease severity was categorized as mild-to-moderate in 17 patients, severe in 16 patients and critical in 26 patients. Plasma SARS-CoV-2 RNAaemia was quantified by droplet digital Crystal Digital PCR™ next-generation technology (Stilla Technologies, Villejuif, France). Results Overall, SARS-CoV-2 RNAaemia was detected in 43 (74.1%) patients. Prevalence of positive SARS-CoV-2 RNAaemia correlated with disease severity, ranging from 53% in mild-to-moderate patients to 88% in critically ill patients (p=0.036). Levels of SARS-CoV-2 RNAaemia were associated with severity (p=0.035). Among nine patients who experienced clinical deterioration during follow-up, eight had positive SARS-CoV-2 RNAaemia at baseline while only one critical patient with undetectable SARS-CoV-2 RNAaemia at the time of analysis died at day 27. Conclusion SARS-CoV-2 RNAaemia measured by droplet-based digital PCR constitutes a promising prognosis biomarker in COVID-19 patients
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Affiliation(s)
- David Veyer
- Assistance Publique Hôpitaux de Paris-Centre (AP-HP.Centre), Service de Microbiologie (Unité de virologie), Hôpital Européen Georges Pompidou, Paris, France.,Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Solen Kernéis
- Equipe Mobile d'Infectiologie, AP-HP, APHP.CUP, Hôpital Cochin, F-75014 Paris, France.,Université de Paris, INSERM, IAME, F-75006 Paris, France.,Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), F-75015 Paris, France
| | - Geoffroy Poulet
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Personalized Medicine Pharmacogenomics, therapeutic optimization, eDIAG plateform, laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Maxime Wack
- Eurofins-Biomnis, Lyon.,Département d'Informatique Médicale, Biostatistiques et Santé Publique, Hôpital Européen Georges Pompidou, AP-HP CUP, Paris, France
| | - Nicolas Robillard
- Assistance Publique Hôpitaux de Paris-Centre (AP-HP.Centre), Service de Microbiologie (Unité de virologie), Hôpital Européen Georges Pompidou, Paris, France
| | - Valérie Taly
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), F-75015 Paris, France
| | - Anne-Sophie L'Honneur
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Information sciences to support medicine Paris, France
| | - Flore Rozenberg
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Information sciences to support medicine Paris, France
| | - Pierre Laurent-Puig
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), F-75015 Paris, France.,Assistance Publique Hôpitaux de Paris-Centre (AP-HP.Centre), Service de Virologie, Hôpital Cochin, Paris, France
| | - Laurent Bélec
- Assistance Publique Hôpitaux de Paris-Centre (AP-HP.Centre), Service de Microbiologie (Unité de virologie), Hôpital Européen Georges Pompidou, Paris, France.,Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, AP-HP CUP, Paris, France
| | - Jérôme Hadjadj
- Assistance Publique Hôpitaux de Paris-Centre (AP-HP.Centre), Service de Biochimie, Hôpital Européen Georges Pompidou, Paris, France.,Imagine Institute, laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163
| | - Benjamin Terrier
- Imagine Institute, laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163.,Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, AP-HP CUP, Paris, France
| | - Hélène Péré
- Assistance Publique Hôpitaux de Paris-Centre (AP-HP.Centre), Service de Microbiologie (Unité de virologie), Hôpital Européen Georges Pompidou, Paris, France.,PARCC, Université de Paris, INSERM U970, Paris, France
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15
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Influence of Different Inactivation Methods on Severe Acute Respiratory Syndrome Coronavirus 2 RNA Copy Number. J Clin Microbiol 2020; 58:JCM.00958-20. [PMID: 32467359 PMCID: PMC7383554 DOI: 10.1128/jcm.00958-20] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/27/2020] [Indexed: 01/08/2023] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) has spread across the world and was characterized as a pandemic. To protect medical laboratory personnel from infection, most laboratories inactivate the virus causing COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in clinical samples before testing. However, the effect of inactivation on the detection results remains unknown. Here, we used a digital PCR assay to determine the absolute SARS-CoV-2 RNA copy number in 63 nasopharyngeal swab samples and assess the effect of inactivation methods on viral RNA copy number. Viral inactivation was performed by three different methods: (i) incubation with the TRIzol LS reagent for 10 min at room temperature, (ii) heating in a water bath at 56°C for 30 min, and (iii) high-temperature treatment, including autoclaving at 121°C for 20 min, boiling at 100°C for 20 min, and heating at 80°C for 20 min. Compared to the amount of RNA in the original sample, TRIzol treatment destroyed 47.54% of the nucleocapsid protein (N) gene and 39.85% of open reading frame (ORF) 1ab. For samples treated at 56°C for 30 min, the copy number of the N gene and ORF 1ab was reduced by 48.55% and 56.40%, respectively. The viral RNA copy number dropped by 50 to 66% after heating at 80°C for 20 min. Nearly no viral RNA was detected after autoclaving at 121°C or boiling at 100°C for 20 min. These results indicate that inactivation reduced the quantity of detectable viral RNA and may cause false-negative results, especially in weakly positive cases. Thus, use of the TRIzol reagent rather than heat inactivation is recommended for sample inactivation, as the TRIzol reagent had the least effect on the RNA copy number among the tested methods.
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16
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Rocchigiani AM, Tilocca MG, Portanti O, Vodret B, Bechere R, Di Domenico M, Savini G, Lorusso A, Puggioni G. Development of a Digital RT-PCR Method for Absolute Quantification of Bluetongue Virus in Field Samples. Front Vet Sci 2020; 7:170. [PMID: 32373633 PMCID: PMC7186476 DOI: 10.3389/fvets.2020.00170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/11/2020] [Indexed: 11/24/2022] Open
Abstract
Bluetongue (BT) is a major Office International des Epizooties (OIE)-listed disease of wild and domestic ruminants caused by several serotypes of Bluetongue virus (BTV), a virus with a segmented dsRNA genome belonging to the family Reoviridae, genus Orbivirus. BTV is transmitted through the bites of Culicoides midges. The aim of this study was to develop a new method for quantification of BTV Seg-10 by droplet digital RT-PCR (RTdd-PCR), using nucleic acids purified from complex matrices such as blood, tissues, and midges, that notoriously contain strong PCR inhibitors. First, RTdd-PCR was optimized by using RNAs purified from serially 10-fold dilutions of a BTV-1 isolate (105.43TCID50/ml up to 10−0.57 TCID50/ml) and from the same dilutions spiked into fresh ovine EDTA-blood and spleen homogenate. The method showed a good degree of linearity (R2 ≥ 0.995). The limit of detection (LoD) and the limit of quantification (LoQ) established were 10−0.67TCID50/ml (0.72 copies/μl) and 100.03TCID50/ml (3.05 copies/μl) of BTV-1, respectively. Second, the newly developed test was compared, using the same set of biological samples, to the quantitative RT-PCR (RT-qPCR) detecting Seg-10 assay widely used for the molecular diagnosis of BTV from field samples. Results showed a difference mean of 0.30 log between the two assays with these samples (p < 0.05). Anyway, the analysis of correlation demonstrated that both assays provided similar measurements with a very close agreement between the systems.
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Affiliation(s)
- Angela M Rocchigiani
- Department of Sanità Animale, Istituto Zooprofilattico Sperimentale Della Sardegna, Sassari, Italy
| | - Maria G Tilocca
- Department of Sanità Animale, Istituto Zooprofilattico Sperimentale Della Sardegna, Sassari, Italy
| | - Ottavio Portanti
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale Abruzzo e Molise, Teramo, Italy
| | - Bruna Vodret
- Department of Sanità Animale, Istituto Zooprofilattico Sperimentale Della Sardegna, Sassari, Italy
| | - Roberto Bechere
- Department of Sanità Animale, Istituto Zooprofilattico Sperimentale Della Sardegna, Sassari, Italy
| | - Marco Di Domenico
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale Abruzzo e Molise, Teramo, Italy
| | - Giovanni Savini
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale Abruzzo e Molise, Teramo, Italy
| | - Alessio Lorusso
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale Abruzzo e Molise, Teramo, Italy
| | - Giantonella Puggioni
- Department of Sanità Animale, Istituto Zooprofilattico Sperimentale Della Sardegna, Sassari, Italy
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17
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Cao Y, Yu M, Dong G, Chen B, Zhang B. Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation. Molecules 2020; 25:E706. [PMID: 32041334 PMCID: PMC7037809 DOI: 10.3390/molecules25030706] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 11/16/2022] Open
Abstract
Biodegradation of contaminants is extremely complicated due to unpredictable microbial behaviors. Monitoring of microbial biodegradation drives us to determine (1) the amounts of specific degrading microbes, (2) the abundance, and (3) expression level of relevant functional genes. To this endeavor, the cultivation independent polymerase chain reaction (PCR)-based monitoring technique develops from endpoint PCR, real-time quantitative PCR, and then into novel digital PCR. In this review, we introduce these three categories of PCR techniques and summarize the timely applications of digital PCR and its superiorities than qPCR for biodegradation monitoring. Digital PCR technique, emerging as the most accurately absolute quantification method, can serve as the most promising and robust tool for monitoring of microbial biodegradation.
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Affiliation(s)
| | | | | | - Bing Chen
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John’s, NL A1B 3X5, Canada; (Y.C.); (M.Y.); (G.D.)
| | - Baiyu Zhang
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John’s, NL A1B 3X5, Canada; (Y.C.); (M.Y.); (G.D.)
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18
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Salipante SJ, Jerome KR. Digital PCR—An Emerging Technology with Broad Applications in Microbiology. Clin Chem 2019; 66:117-123. [DOI: 10.1373/clinchem.2019.304048] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/18/2019] [Indexed: 01/10/2023]
Abstract
Abstract
BACKGROUND
The PCR and its variant, quantitative PCR (qPCR), have revolutionized the practice of clinical microbiology. Continued advancements in PCR have led to a new derivative, digital PCR (dPCR), which promises to address certain limitations inherent to qPCR.
CONTENT
Here we highlight the important technical differences between qPCR and dPCR, and the potential advantages and disadvantages of each. We then review specific situations in which dPCR has been implemented in clinical microbiology and the results of such applications. Finally, we attempt to place dPCR in the context of other emerging technologies relevant to the clinical laboratory, including next-generation sequencing.
SUMMARY
dPCR offers certain clear advantages over traditional qPCR, but these are to some degree offset by limitations of the technology, at least as currently practiced. Laboratories considering implementation of dPCR should carefully weigh the potential advantages and disadvantages of this powerful technique for each specific application planned.
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Affiliation(s)
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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19
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Qing Z, Hu J, Xu J, Zou Z, Lei Y, Qing T, Yang R. An intramolecular catalytic hairpin assembly on a DNA tetrahedron for mRNA imaging in living cells: improving reaction kinetics and signal stability. Chem Sci 2019; 11:1985-1990. [PMID: 34123293 PMCID: PMC8148388 DOI: 10.1039/c9sc04916a] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Enzyme-free amplification techniques based on dynamic DNA self-assembly (DDSA) have recently been developed for the in situ detection of mRNA in living cells. However, signal generation in traditional DDSA amplifiers is mainly dependent on the random diffusion of dissociative probes in a bulk solution, which is generally accompanied by poor kinetics and interference from complex biological systems. In this work, a new amplifier based on the design of an intramolecular catalytic hairpin assembly (intra-CHA) is proposed for the FRET imaging of mRNA in living cells. Compared with that in the free catalytic hairpin assembly (free-CHA), probes H1 and H2 in intra-CHA were simultaneously fixed on a DNA tetrahedron. The distance between them was closer, the local concentration of H1 and H2 in intra-CHA was theoretically approximately 808-times higher than that in free-CHA, and the initial reaction rate was enhanced 15.6 fold. Due to the spatial confinement effect, the reaction kinetics for target-catalyzed signal generation were significantly improved. By virtue of the three-dimensional nanostructure, H1 and H2 in the intra-CHA amplifier entered cells without any transfection or nanocarrier, and the probes and their products were free from biological interference, providing much higher signal stability for the reliable imaging of mRNA in living cells. An intramolecular catalytic hairpin assembly is implemented on a DNA tetrahedron for mRNA imaging in living cells. The spatial confinement effect enables the acceleration of target-triggered signal generation, with excellent cell permeability and FRET signal stability.![]()
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Affiliation(s)
- Zhihe Qing
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, Hunan Provincial Engineering Research Center for Food Processing of Aquatic Biotic Resources, School of Chemistry and Food Engineering, Changsha University of Science and Technology Changsha 410114 P. R. China
| | - Jinlei Hu
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, Hunan Provincial Engineering Research Center for Food Processing of Aquatic Biotic Resources, School of Chemistry and Food Engineering, Changsha University of Science and Technology Changsha 410114 P. R. China
| | - Jingyuan Xu
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, Hunan Provincial Engineering Research Center for Food Processing of Aquatic Biotic Resources, School of Chemistry and Food Engineering, Changsha University of Science and Technology Changsha 410114 P. R. China
| | - Zhen Zou
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, Hunan Provincial Engineering Research Center for Food Processing of Aquatic Biotic Resources, School of Chemistry and Food Engineering, Changsha University of Science and Technology Changsha 410114 P. R. China
| | - Yanli Lei
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, Hunan Provincial Engineering Research Center for Food Processing of Aquatic Biotic Resources, School of Chemistry and Food Engineering, Changsha University of Science and Technology Changsha 410114 P. R. China
| | - Taiping Qing
- College of Environment and Resources, Xiangtan University Xiangtan 411105 P. R. China
| | - Ronghua Yang
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, Hunan Provincial Engineering Research Center for Food Processing of Aquatic Biotic Resources, School of Chemistry and Food Engineering, Changsha University of Science and Technology Changsha 410114 P. R. China
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20
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Hopken MW, Piaggio AJ, Pabilonia KL, Pierce J, Anderson T, Abdo Z. Predicting whole genome sequencing success for archived avian influenza virus (Orthomyxoviridae) samples using real-time and droplet PCRs. J Virol Methods 2019; 276:113777. [PMID: 31730870 DOI: 10.1016/j.jviromet.2019.113777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/05/2019] [Accepted: 11/10/2019] [Indexed: 01/01/2023]
Abstract
Long-term viral archives are valuable sources of research data. Each archive can store hundreds of thousands of diverse sample types. In the current era of whole genome sequencing, archived samples become a rich source of evolutionary and epidemiological data that can span years, and even decades. However, the ability to obtain high quality viral whole genome sequences from samples of various types, age, and quality is inconsistent. A minimum quality threshold that helps predict the best success of obtaining high quality genomic sequences for both recent and archived samples is highly valuable. Real-time reverse transcription PCR (rrt-PCR) and droplet digital PCR (ddPCR) are useful tools to evaluate nucleic acid integrity. We hypothesized that diagnostic rrt-PCR and ddPCR data for avian influenza virus (AIV) can predict viral whole genome sequencing success. To test this hypothesis we used RNA extracted from cloacal and oropharyngeal swabs stored in the USDA-APHIS National Wildlife Disease Program Wildlife Tissue Archive. We determined that a specific rrt-PCR Cq value or ddPCR copies/μL resulted in recovery of complete sequences of all eight AIV gene segments. We used logistic regression to estimate probabilities of whole genome recovery at 0.95 (Cq = 15, copies/μL = 49,350), 0.75 (Cq = 24, copies/μL = 16,800), 0.50 (Cq = 29, copies/μL = <1), and 0.25 (Cq = 235, copies/μL = <1). We also identified values at which we predictably recovered HA and NA segments for diagnosing subtypes (Cq = 27.29; copies/μL = 757.50). This approach will allow researchers to assess the potential success of AIV whole genome recovery from diagnostic samples collected in routine AIV surveillance.
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Affiliation(s)
- Matthew W Hopken
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA; United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, 80521, USA
| | - Antoinette J Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, 80521, USA
| | - Kristy L Pabilonia
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA; Veterinary Diagnostics Laboratory, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80526, USA
| | - James Pierce
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Theodore Anderson
- Veterinary Diagnostics Laboratory, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80526, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
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21
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Starr K, Greninger AL, Makhsous N, Jerome KR, Cook L. Comparison of Three Adenovirus Quantitative PCR Assays with ATCC Reference Strains and Clinical Samples. J Clin Microbiol 2019; 57:e00735-19. [PMID: 31434723 PMCID: PMC6813019 DOI: 10.1128/jcm.00735-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 08/12/2019] [Indexed: 01/09/2023] Open
Abstract
Adenoviruses (AdV) have been associated with a variety of human diseases and are recognized as causing significant morbidity and mortality in immunocompromised or transplant patients. Quantification of AdV DNA in plasma is notoriously difficult due to the genetic diversity of the 71 different serotypes identified to date. There is no World Health Organization standard available to harmonize quantitative data, so results between labs vary widely. In this study, we compared a laboratory-developed multiplex PCR assay with primers and probes specific for each group (A to G) and subgroup E4 (Octaplex) to one with a single primer and probe set (modified from N. Jothikumar et al., Appl Environ Microbiol 71:3131-3136, 2005) and one utilizing bisulfite pretreatment of DNA to reduce variation prior to amplification (Genetic Signatures). Our Octaplex assay detected all low-copy-number clinical samples, while the other two assays had subsets of samples that did not amplify. The modified Jothikumar assay failed to efficiently amplify three of the high-copy-number cultured strains, while the Genetic Signatures 3base assay had a positive bias, resulting in higher copies/ml (>0.5 log10) for all culture fluids tested. All three assays resulted in endpoint detection of the available 51 AdV types. Using two different materials to generate a standard curve revealed that the Octaplex TaqMan assay and the modified Jothikumar assay both consistently gave adenovirus levels lower than the commercial platform for AdV culture fluids but not patient samples. This study highlights the differences in detection of AdV between laboratories that can be attributed to both the PCR method, as well as the reference material used for quantitation.
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Affiliation(s)
- Kimberly Starr
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Negar Makhsous
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Linda Cook
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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22
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Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR. PLoS One 2019; 14:e0220908. [PMID: 31479459 PMCID: PMC6720028 DOI: 10.1371/journal.pone.0220908] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/25/2019] [Indexed: 02/07/2023] Open
Abstract
Acute respiratory tract infections are a major cause of respiratory morbidity and mortality in pediatric patients worldwide. However, accurate viral and immunologic markers to predict clinical outcomes of this patient population are still lacking. Droplet digital PCR assays for influenza and respiratory syncytial virus (RSV) were designed and performed in 64 respiratory samples from 23 patients with influenza virus infection and 73 samples from 19 patients with RSV infection. Samples of patients with hematologic malignancies, solid tumors, or sickle cell disease were included. Clinical information from institutional medical records was reviewed to assess disease severity. Samples from patients with fever or respiratory symptoms had a significantly higher viral loads than those from asymptomatic patients. Samples from patients with influenza virus and RSV infection collected at presentation had significantly higher viral loads than those collected from patients after completing a course of oseltamivir or ribavirin, respectively. RSV loads correlated positively with clinical symptoms in patients ≤5 years of age, whereas influenza viral loads were associated with clinical symptoms, irrespective of age. Patients receiving antivirals for influenza and RSV had a significant reduction in viral loads after completing therapy. Digital PCR offers an effective method to monitor the efficacy of antiviral treatment for respiratory tract infections in immunocompromised hosts.
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23
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Persson S, Karlsson M, Borsch-Reniers H, Ellström P, Eriksson R, Simonsson M. Missing the Match Might Not Cost You the Game: Primer-Template Mismatches Studied in Different Hepatitis A Virus Variants. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:297-308. [PMID: 31004336 PMCID: PMC6689102 DOI: 10.1007/s12560-019-09387-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/10/2019] [Indexed: 05/11/2023]
Abstract
Mismatches between template sequences and reverse transcription (RT) or polymerase chain reaction (PCR) primers can lead to underestimation or false negative results during detection and quantification of sequence-diverse viruses. We performed an in silico inclusivity analysis of a widely used RT-PCR assay for detection of hepatitis A virus (HAV) in food, described in ISO 15216-1. One of the most common mismatches found was a single G (primer) to U (template) mismatch located at the terminal 3'-end of the reverse primer region. This mismatch was present in all genotype III sequences available in GenBank. Partial HAV genomes with common or potentially severe mismatches were produced by in vitro transcription and analysed using RT-ddPCR and RT-qPCR. When using standard conditions for RT-qPCR, the mismatch identified resulted in underestimation of the template concentration by a factor of 1.7-1.8 and an increase in 95% limit of detection from 8.6 to 19 copies/reaction. The effect of this mismatch was verified using full-length viral genomes. Here, the same mismatch resulted in underestimation of the template concentration by a factor of 2.8. For the partial genomes, the presence of additional mismatches resulted in underestimation of the template concentration by up to a factor of 232. Quantification by RT-ddPCR and RT-qPCR was equally affected during analysis of RNA templates with mismatches within the reverse primer region. However, on analysing DNA templates with the same mismatches, we found that ddPCR quantification was less affected by mismatches than qPCR due to the end-point detection technique.
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Affiliation(s)
- Sofia Persson
- European Union Reference Laboratory (EURL) for Foodborne Viruses, National Food Agency, Hamnesplanaden 5, 453 23, Uppsala, Sweden
- Department of Medical Sciences, Zoonosis Science Centre, Uppsala University, Uppsala, Sweden
| | - Måns Karlsson
- Department of Mathematics, Stockholm University, Stockholm, Sweden
| | | | - Patrik Ellström
- Department of Medical Sciences, Zoonosis Science Centre, Uppsala University, Uppsala, Sweden
| | - Ronnie Eriksson
- European Union Reference Laboratory (EURL) for Foodborne Viruses, National Food Agency, Hamnesplanaden 5, 453 23, Uppsala, Sweden
| | - Magnus Simonsson
- European Union Reference Laboratory (EURL) for Foodborne Viruses, National Food Agency, Hamnesplanaden 5, 453 23, Uppsala, Sweden.
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24
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Myerski A, Siegel A, Engstrom J, McGowan I, Brand RM. The Use of Droplet Digital PCR to Quantify HIV-1 Replication in the Colorectal Explant Model. AIDS Res Hum Retroviruses 2019; 35:326-334. [PMID: 30618283 DOI: 10.1089/aid.2018.0227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ex vivo explant models are used to characterize in vitro efficacy of preexposure prophylaxis (PrEP) agents. Tissue is challenged with virus in culture and HIV-1 p24 levels are quantified with enzyme-linked immunosorbent assay (ELISA) on supernatants collected throughout a 14-21-day incubation. Due to the narrow dynamic range of HIV-1 p24 kits, we evaluated whether droplet digital PCR (ddPCR) provides an alternative method to quantify HIV-1 replication in supernatant samples. We used samples from the MWRI-01 study, which evaluated the pharmacokinetic/pharmacodynamic profile of long-acting rilpivirine using the explant model (McGowan et al. Lancet HIV 2016). HIV-1 pol RNA was measured with ddPCR, either directly with a one-step method or reverse transcribed to cDNA before ddPCR (two-step method) on supernatants from the MWRI-01 study. Previously analyzed HIV-1 p24 antigen levels (Alliance; Perkin-Elmer) were available for comparison purposes. Both ddPCR methods strongly correlated with HIV-1 p24 and displayed similar patterns of HIV-1 suppression before and after rilpivirine. Compared to the p24 ELISA, two-step and one-step ddPCR reduced the amount of hands-on time by approximately one-half and two-thirds, respectively. ddPCR also required less sample and based on p24 versus ddPCR correlation, could potentially reduce the explant culture time from 14 to 10 days (r2 = 0.78, p < .001) due to the increased sensitivity of ddPCR. We demonstrate that ddPCR is a suitable alternative to HIV-1 p24 ELISA to quantify HIV-1 infection in the explant model and has the potential to decrease explant culture time.
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Affiliation(s)
- Ashley Myerski
- Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania
| | - Aaron Siegel
- Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania
| | - Jarret Engstrom
- Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania
| | - Ian McGowan
- Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania
- Department of Medicine University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Rhonda M. Brand
- Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania
- Department of Medicine University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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25
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Waghmare A, Xie H, Kuypers J, Sorror ML, Jerome KR, Englund JA, Boeckh M, Leisenring WM. Human Rhinovirus Infections in Hematopoietic Cell Transplant Recipients: Risk Score for Progression to Lower Respiratory Tract Infection. Biol Blood Marrow Transplant 2018; 25:1011-1021. [PMID: 30537551 PMCID: PMC6511300 DOI: 10.1016/j.bbmt.2018.12.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/04/2018] [Indexed: 12/22/2022]
Abstract
Risk factors for rhinovirus lower respiratory tract infection are not well characterized. Several risk factors in hematopoietic cell transplant recipients were identified. A risk score for progression to lower respiratory tract infection was developed.
Human rhinovirus lower respiratory tract infection (LRTI) is associated with mortality after hematopoietic cell transplantation (HCT); however, risk factors for LRTI are not well characterized. We sought to develop a risk score for progression to LRTI from upper respiratory tract infection (URTI) in HCT recipients. Risk factors for LRTI within 90 days were analyzed using Cox regression among HCT recipients with rhinovirus URTI between January 2009 and March 2016. The final multivariable model included factors with a meaningful effect on the bootstrapped optimism corrected concordance statistic. Weighted score contributions based on hazard ratios were determined. Cumulative incidence curves estimated the probability of LRTI at various score cut-offs. Of 588 rhinovirus URTI events, 100 (17%) progressed to LRTI. In a final multivariable model allogeneic grafts, prior rhinovirus URTI, low lymphocyte count, low albumin, positive cytomegalovirus serostatus, recipient statin use, and steroid use ≥2 mg/kg/day were associated with progression to LRTI. A weighted risk score cut-off with the highest sensitivity and specificity was determined. Risk scores above this cut-off were associated with progression to LRTI (cumulative incidence 28% versus 11% below cut-off; P < .001). The weighted risk score for progression to rhinovirus LRTI can help identify and stratify patients for clinical management and for future clinical trials of therapeutics in HCT recipients.
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Affiliation(s)
- Alpana Waghmare
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Pediatrics, University of Washington, Seattle, WA; Department of Pediatrics, Seattle Children's Hospital, Seattle, WA.
| | - Hu Xie
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jane Kuypers
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Mohamed L Sorror
- Department of Medicine, University of Washington, Seattle, WA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Keith R Jerome
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle, WA; Department of Pediatrics, Seattle Children's Hospital, Seattle, WA
| | - Michael Boeckh
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Medicine, University of Washington, Seattle, WA
| | - Wendy M Leisenring
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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26
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Hung HM, Yang SL, Chen CJ, Chiu CH, Kuo CY, Huang KYA, Lin TY, Hsieh YC, Gong YN, Tsao KC, Huang YC. Molecular epidemiology and clinical features of rhinovirus infections among hospitalized patients in a medical center in Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2018; 52:233-241. [PMID: 30201131 DOI: 10.1016/j.jmii.2018.08.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Human rhinovirus (HRV) can cause severe illnesses in hospitalized patients. However, there are no studies regarding the prevalence of HRV infection, particularly the recently identified HRV-C, in hospitalized patients reported from Taiwan. METHODS Respiratory specimens collected from 487 hospitalized patients in designated wards between 2013 and 2014 in a medical center in northern Taiwan were retrospectively detected for HRV. Positive specimens were further determined for genotyping. Medical charts of the HRV-positive patients were reviewed retrospectively. RESULTS Totally, 76 patients (15.6%) were HRV positive, of which 60 were pediatric patients. HRV-A was identified in 41 (54%) patients, HRV-B in 6 patients (7.9%) and HRV-C in 29 patients (38%). A total of 47 different genotypes were identified. HRV infections were predominant during fall and winter seasons. 21.1% were affected by HRV alone and 78.9% were found to be co-infected with other microorganisms. The detection rate of HRV in children (18.6%) was significantly higher than in adults (9.6%). Compared with pediatric patients, adult patients were significantly associated with underlying disease, Pneumocystis jirovesii pneumonia co-infection, a diagnosis of pneumonia, fatal outcome, hospital acquisition of HRV, antibiotics administration and requiring intensive care, while pediatric patients were significantly associated with viral co-infection. CONCLUSIONS HRV was a common cause of respiratory tract infection in Taiwan, particularly in pediatric patients. Eighty percent of HRV-infected inpatients had other microorganisms co-infection. Adult patients were more likely to be associated with a severe respiratory disease entity.
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Affiliation(s)
- Huei-Min Hung
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Shu-Li Yang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Jung Chen
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Chen-Yen Kuo
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Kuan-Ying A Huang
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Tzou-Yien Lin
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Yu-Chia Hsieh
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Yu-Nong Gong
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Chien Tsao
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Yhu-Chering Huang
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan.
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27
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Ogimi C, Xie H, Leisenring WM, Kuypers JM, Jerome KR, Campbell AP, Englund JA, Boeckh M, Waghmare A. Initial High Viral Load Is Associated with Prolonged Shedding of Human Rhinovirus in Allogeneic Hematopoietic Cell Transplant Recipients. Biol Blood Marrow Transplant 2018; 24:2160-2163. [PMID: 30009982 PMCID: PMC6239940 DOI: 10.1016/j.bbmt.2018.07.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/05/2018] [Indexed: 02/05/2023]
Abstract
We examined prolonged shedding of rhinovirus after stem cell transplantation. The median shedding duration of rhinovirus was similar between species. Initial high viral load was a risk factor for prolonged shedding of rhinovirus.
Recent data suggest human rhinovirus (HRV) is associated with lower respiratory tract infection and mortality in hematopoietic cell transplant (HCT) recipients. Examining risk factors for prolonged viral shedding may provide critical insight for the development of novel therapeutics and help inform infection prevention practices. Our objective was to identify risk factors for prolonged shedding of HRV post-HCT. We prospectively collected weekly nasal samples from allogeneic HCT recipients from day 0 to day 100 post-transplant, and performed real-time reverse transcriptase PCR (December 2005 to February 2010). Subjects with symptomatic HRV infection and a negative test within 2 weeks of the last positive were included. Duration of shedding was defined as time between the first positive and first negative samples. Cycle threshold (Ct) values were used as a proxy for viral load. HRV species were identified by sequencing the 5′ noncoding region. Logistic regression analyses were performed to evaluate factors associated with prolonged shedding (≥21 days). We identified 38 HCT recipients with HRV infection fulfilling study criteria (32 adults, 6 children). Median duration of shedding was 9.5 days (range, 2 to 89 days); 18 patients had prolonged shedding. Among 26 samples sequenced, 69% were species A, and species B and C accounted for 15% each; the median shedding duration of HRV did not differ among species (P = .17). Bivariable logistic regression analyses suggest that initial high viral load (low Ct value) is associated with prolonged shedding. HCT recipients with initial high viral loads are at risk for prolonged HRV viral shedding.
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Affiliation(s)
- Chikara Ogimi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Pediatrics, University of Washington, Seattle, Washington; Pediatric Infectious Diseases Division, Seattle Children's Hospital, Seattle, Washington
| | - Hu Xie
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Wendy M Leisenring
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jane M Kuypers
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Angela P Campbell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Pediatrics, University of Washington, Seattle, Washington; Pediatric Infectious Diseases Division, Seattle Children's Hospital, Seattle, Washington
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle, Washington; Pediatric Infectious Diseases Division, Seattle Children's Hospital, Seattle, Washington
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Medicine, University of Washington, Seattle, Washington
| | - Alpana Waghmare
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Pediatrics, University of Washington, Seattle, Washington; Pediatric Infectious Diseases Division, Seattle Children's Hospital, Seattle, Washington
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28
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González-Parra G, Dobrovolny HM. Modeling of fusion inhibitor treatment of RSV in African green monkeys. J Theor Biol 2018; 456:62-73. [PMID: 30048719 DOI: 10.1016/j.jtbi.2018.07.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 04/18/2018] [Accepted: 07/22/2018] [Indexed: 10/28/2022]
Abstract
Respiratory syncytial virus (RSV) is a respiratory infection that can cause serious illness, particularly in infants. In this study, we test four different model implementations for the effect of a fusion inhibitor, including one model that combines different drug effects, by fitting the models to data from a study of TMC353121 in African green monkeys. We use mathematical modeling to estimate the drug efficacy parameters, εmax, the maximum efficacy of the drug, and EC50, the drug concentration needed to achieve half the maximum effect. We find that if TMC353121 is having multiple effects on viral kinetics, more detailed data, using different treatment delays, is needed to detect this effect.
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Affiliation(s)
- Gilberto González-Parra
- Department of Physics & Astronomy, Texas Christian University, 2800 S University Dr. Fort Worth, TX 76129, USA; Department of Mathematics, New Mexico Tech, Socorro, NM, USA
| | - Hana M Dobrovolny
- Department of Physics & Astronomy, Texas Christian University, 2800 S University Dr. Fort Worth, TX 76129, USA.
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29
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30
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Powell EA, Babady NE. Digital PCR in the Clinical Microbiology Laboratory: Another Tool on the Molecular Horizon. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.clinmicnews.2018.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Monteiro S, Santos R. Nanofluidic digital PCR for the quantification of Norovirus for water quality assessment. PLoS One 2017; 12:e0179985. [PMID: 28749991 PMCID: PMC5531372 DOI: 10.1371/journal.pone.0179985] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/07/2017] [Indexed: 12/24/2022] Open
Abstract
Sensitive detection of water- and foodborne enteric viruses is extremely relevant, especially due to the low concentrations in which they are found. Accurate and sensitive detection of Norovirus, the primary responsible for water- and foodborne outbreaks, is of particular importance. Quantification of Norovirus is commonly performed by quantitative RT-PCR (RT-qPCR). In recent years a new platform was developed, digital PCR, that quantifies without the need for a standard curve thus decreasing the errors associated with its utilization. The platform developed by LifeTechnologies, QuantStudio 3D Digital PCR is amongst the least studied digital platform and although it allows the direct detection of DNA targets it requires a two-step RT-PCR for the detection of RNA targets. In this work we developed a new protocol able to detect Norovirus using a one-step digital PCR reaction (RT-dPCR). The performance of the newly developed one-step digital PCR was compared to RT-qPCR for the detection of Norovirus genogroup I and genogroup II. The sensitivity of RT-dPCR was identical to that of RT-qPCR, and the quantitative data determined by both methods were not significantly different for most samples. This one-step absolute quantification approach is a useful tool to minimize the time spent currently using this particular platform to amplify viral RNA and to standardize quantification of enteric viruses in food and environmental samples. This study proved the usefulness of the newly developed RT-dPCR protocol for a sensitive and accurate detection of low-copy targets.
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Affiliation(s)
- Silvia Monteiro
- Instituto Superior Técnico, Laboratório Analises, Universidade Lisboa, Lisbon, Portugal
- * E-mail:
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- Instituto Superior Técnico, Laboratório Analises, Universidade Lisboa, Lisbon, Portugal
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Abstract
Digital PCR (dPCR) is an important new tool for use in the clinical microbiology laboratory. Its advantages over quantitative PCR (qPCR), including absolute quantification without a standard curve, improved precision, improved accuracy in the presence of inhibitors, and more accurate quantitation when amplification efficiency is low, make dPCR the assay of choice for several specimen testing applications. This minireview will discuss the advantages and disadvantages of dPCR compared to qPCR, its applications in clinical microbiology, and considerations for implementation of the method in a clinical laboratory.
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