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Katsuno T, Kimura M, Terada-Hirashima J, Kazuyama Y, Ikeda M, Moriya A, Kurokawa M, Motohashi A, Isaka E, Morishita M, Kawajiri K, Hakkaku K, Saito S, Terayama Y, Sugiura Y, Yamaguchi Y, Takumida H, Watanabe H, Morita C, Tsukada A, Kusaba Y, Tsujimoto Y, Ishida A, Sakamoto K, Hashimoto M, Suzuki M, Takasaki J, Izumi S, Hojo M, Sugiyama H, Sugiura W. Diagnostic accuracy of direct reverse transcription-polymerase chain reaction using guanidine-based and guanidine-free inactivators for SARS-CoV-2 detection in saliva samples. J Virol Methods 2024; 326:114909. [PMID: 38452822 DOI: 10.1016/j.jviromet.2024.114909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 12/30/2023] [Accepted: 03/02/2024] [Indexed: 03/09/2024]
Abstract
This study aimed to evaluate diagnostic accuracy of SARS-CoV-2 RNA detection in saliva samples treated with a guanidine-based or guanidine-free inactivator, using nasopharyngeal swab samples (NPS) as referents. Based on the NPS reverse transcription-polymerase chain reaction (RT-PCR) results, participants were classified as with or without COVID-19. Fifty sets of samples comprising NPS, self-collected raw saliva, and saliva with a guanidine-based, and guanidine-free inactivator were collected from each group. In patients with COVID-19, the sensitivity of direct RT-PCR using raw saliva and saliva treated with a guanidine-based and guanidine-free inactivator was 100.0%, 65.9%, and 82.9%, respectively, with corresponding concordance rates of 94.3% (κ=88.5), 82.8% (κ=64.8), and 92.0% (κ=83.7). Among patients with a PCR Ct value of <30 in the NPS sample, the positive predictive value for the three samples was 100.0%, 80.0%, and 96.0%, respectively. The sensitivity of SARS-CoV-2 RNA detection was lower in inactivated saliva than in raw saliva and lower in samples treated with a guanidine-based than with a guanidine-free inactivator. However, in individuals contributing to infection spread, inactivated saliva showed adequate accuracy regardless of the inactivator used. Inactivators can be added to saliva samples collected for RT-PCR to reduce viral transmission risk while maintaining adequate diagnostic accuracy.
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Affiliation(s)
- Takashi Katsuno
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan.
| | - Moto Kimura
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Junko Terada-Hirashima
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Masato Ikeda
- SB Coronavirus Inspection Center Corp., Tokyo, Japan
| | - Ataru Moriya
- Clinical Laboratory Department, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masami Kurokawa
- Clinical Laboratory Department, National Center for Global Health and Medicine, Tokyo, Japan
| | - Ayano Motohashi
- Clinical Laboratory Department, National Center for Global Health and Medicine, Tokyo, Japan
| | - Erina Isaka
- Clinical Laboratory Department, National Center for Global Health and Medicine, Tokyo, Japan
| | - Momoko Morishita
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuki Kawajiri
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuo Hakkaku
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Susumu Saito
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuriko Terayama
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuriko Sugiura
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoh Yamaguchi
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hiroshi Takumida
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hiromu Watanabe
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Chie Morita
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Akinari Tsukada
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yusaku Kusaba
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshie Tsujimoto
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Akane Ishida
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Keita Sakamoto
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masao Hashimoto
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Manabu Suzuki
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Jin Takasaki
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinyu Izumi
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masayuki Hojo
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Haruhito Sugiyama
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Wataru Sugiura
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
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Costa JND, Siqueira JAM, Teixeira DM, Lobo PDS, Guerra SDFDS, Souza IM, Cardoso BTM, Farias LSS, Resque HR, Gabbay YB, Silva LDD. Epidemiological and molecular surveillance of norovirus in the Brazilian Amazon: description of recombinant genotypes and improvement of evolutionary analysis. Rev Inst Med Trop Sao Paulo 2024; 66:e22. [PMID: 38656038 DOI: 10.1590/s1678-9946202466022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/12/2024] [Indexed: 04/26/2024] Open
Abstract
Noroviruses are highly infectious, genetically diverse viruses. Global outbreaks occur frequently, making molecular surveillance important for infection monitoring. This cross-sectional descriptive study aimed to monitor cases of norovirus gastroenteritis in the Brazilian Amazon. Fecal samples were tested by immunoenzymatic assay, RT-PCR and genetic sequencing for the ORF1/ORF2 and protease regions. Bayesian inference with a molecular clock was employed to construct the phylogeny. The norovirus prevalence was 25.8%, with a higher positivity rate among children aged 0-24 months. Genogroup GII accounted for 98.1% of the sequenced samples, while GI accounted for 1.9% of them. The GII.P16/GII.4 genotype was the most prevalent, with an evolution rate of 2.87x10-3 and TMRCA estimated in 2012. This study demonstrates that norovirus is a primary causative agent of gastroenteritis and provides data on viral genetic diversity that may facilitate infection surveillance and vaccine development.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hugo Reis Resque
- Instituto Evandro Chagas, Seção de Virologia, Ananindeua, Pará, Brazil
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Teixeira EB, Khayat AS, Assumpção PP, Casseb SM, Moreira-Nunes CA, Moreira FC. EndoGeneAnalyzer: A tool for selection and validation of reference genes. PLoS One 2024; 19:e0299993. [PMID: 38568963 PMCID: PMC10990236 DOI: 10.1371/journal.pone.0299993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/20/2024] [Indexed: 04/05/2024] Open
Abstract
The selection of proper reference genes is critical for accurate gene expression analysis in all fields of biological and medical research, mainly because there are many distinctions between different tissues and specimens. Given this variability, even in known classic reference genes, demands of a comprehensive analysis platform is needed to identify the most suitable genes for each study. For this purpose, we present an analysis tool for assisting in decision-making in the analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) data. EndoGeneAnalyzer, an open-source web tool for reference gene analysis in RT-qPCR studies, was used to compare the groups/conditions under investigation. This interactive application offers an easy-to-use interface that allows efficient exploration of datasets. Through statistical and stability analyses, EndoGeneAnalyzer assists in the select of the most appropriate reference gene or set of genes for each condition. It also allows researchers to identify and remove unwanted outliers. Moreover, EndoGeneAnalyzer provides a graphical interface to compare the evaluated groups, providing a visually informative differential analysis.
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Affiliation(s)
| | - André Salim Khayat
- Oncology Research Center, Federal University of Pará, Belém, Pará, Brazil
| | | | | | - Caroline Aquino Moreira-Nunes
- Oncology Research Center, Federal University of Pará, Belém, Pará, Brazil
- Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Department of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Clementino Fraga Group, Central Unity, Molecular Biology Laboratory, Fortaleza, CE, Brazil
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4
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Sampieri L, Rodríguez-Lombardi G, Bernardi ME. In-house RT-PCR detection of hepatitis A virus in human plasma pools used for the manufacture of medicinal products. Transfus Apher Sci 2024; 63:103869. [PMID: 38278704 DOI: 10.1016/j.transci.2024.103869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/04/2023] [Accepted: 01/06/2024] [Indexed: 01/28/2024]
Abstract
Hepatitis A virus (HAV) is the most frequent cause of viral hepatitis worldwide and is transmitted through the fecal-oral route. However, HAV can also be transmitted by blood-derived products. This is due to the fact that viremia occurs during the asymptomatic phase of HAV infection, enabling infected blood or plasma donations to occur. Viral inactivation/removal steps are included during manufacturing of plasmaderived products. However, HAV is a small non-enveloped virus very difficult to remove with traditional viral inactivation procedures. To accomplish European guidelines for pooled human plasma (treated for virus inactivation), plasma manufacturers have been implementing HAV nucleic acid test (NAT) screening on plasma pools. In this study, we validate an in-house multiplex reverse-transcription real-time PCR (RT-PCR) assay targeting HAV RNA and an internal control with hydrolysis probes for amplicon detection. The HAV RNA test was validated by assessing limit of detection, robustness, sensitivity and specificity according to European Pharmacopoeia (Ph. Eur.) guidelines. Our assay is able to detect 100 IU/mL of all human HAV genotypes that have been described so far. The multiplex assay shows remarkable sensitivity with a 95% lower limit of detection of 5.2 IU/mL. Also, our HAV test shows good robustness, precision, and specificity. We conclude that our assay broadly meets the requirements for its purpose. The implementation of this test in the production process of plasma-derived products will increase their safety.
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Affiliation(s)
- Luciana Sampieri
- Área de Desarrollo de Productos y Procesos, Laboratorio de Hemoderivados, Universidad Nacional de Córdoba, Córdoba, Argentina.
| | - Gonzalo Rodríguez-Lombardi
- Área de Desarrollo de Productos y Procesos, Laboratorio de Hemoderivados, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María Eugenia Bernardi
- Área de Desarrollo de Productos y Procesos, Laboratorio de Hemoderivados, Universidad Nacional de Córdoba, Córdoba, Argentina
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Shaikh A, Sriraman K, Vaswani S, Shah I, Poojari V, Oswal V, Mane S, Rajagara S, Mistry N. SMaRT-PCR: sampling using masks and RT-PCR, a non-invasive diagnostic tool for paediatric pulmonary TB. Int J Tuberc Lung Dis 2024; 28:189-194. [PMID: 38563336 DOI: 10.5588/ijtld.23.0291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Key challenges in paediatric TB diagnosis are invasive sampling and poor sensitivity of standard methods. This study demonstrates the diagnostic potential of non-invasive sampling of bioaerosols from children using SMaRT-PCR, comprising mask sampling combined with reverse transcriptase-polymerase chain reaction (RT-PCR) for TB.METHODS Exhaled bioaerosols were captured on modified N-95 masks in a 10-min talk-cough-breathe process from 51 children (30 with TB confirmed using standard sampling methods and 21 without TB) aged 2-15 years. All mask samples were tested using in-house RT-PCR for 16s and rpoB RNA transcripts. Additional mask samples from children with TB were tested using Xpert® MTB/RIF (n = 3) and Xpert® MTB/RIF Ultra (n = 27).RESULTS SMaRT-PCR sensitivity for detecting TB among treatment-naïve children was 96% if 16s or rpoB was present, and 75% if both genes were present, comparable to standard methods (71%) in the same cohort. Specificity was better for both genes, at 95%, than 85% for a single gene detection. Mask sampling with Xpert MTB/RIF or Ultra had a sensitivity of only 13%.CONCLUSION This is the first study to provide evidence for testing bioaerosols as a promising alternative for detecting paediatric TB. Sampling is non-invasive and simple, with the potential for point-of-care applications. This pilot study also suggests that RNA transcript-based detection may improve TB diagnostic sensitivity in children; however, further investigation is required to establish its adaptability in clinical settings..
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Affiliation(s)
- A Shaikh
- The Foundation for Medical Research, Mumbai
| | - K Sriraman
- The Foundation for Medical Research, Mumbai
| | - S Vaswani
- The Foundation for Medical Research, Mumbai
| | - I Shah
- Paediatric TB Clinic, State Centre of Excellence for Paediatric DR-TB, Department of Paediatric Infectious Diseases, B.J. Wadia Hospital for Children, Mumbai
| | - V Poojari
- Paediatric TB Clinic, State Centre of Excellence for Paediatric DR-TB, Department of Paediatric Infectious Diseases, B.J. Wadia Hospital for Children, Mumbai
| | | | - S Mane
- State Centre of Excellence for Tuberculosis, Grant Medical College, Sir JJ Group of Hospitals, Mumbai, India
| | - S Rajagara
- State Centre of Excellence for Tuberculosis, Grant Medical College, Sir JJ Group of Hospitals, Mumbai, India
| | - N Mistry
- The Foundation for Medical Research, Mumbai
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6
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Artuvan Z, Cetin H. The effect of video informing adolescents having Polymerase Chain Reaction (rRT-PCR) test on anxiety during the Coronavirüs (COVID-19) pandemic: A randomized controlled study. J Pediatr Nurs 2024; 75:125-132. [PMID: 38154419 DOI: 10.1016/j.pedn.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023]
Abstract
AIM This study aimed to determine if video information on Polymerase Chain Reaction (rRT-PCR) testing reduces anxiety in adolescents. DESIGN AND METHODS A randomized controlled experimental study with a parallel-group design was conducted. The sample size was determined by G*Power analysis, and 136 adolescents were included in each group accordingly. The data were collected using the Child/Parent Information Form, State and Trait Anxiety Inventory, and Coronavirus Anxiety Scale. Chi-square, Independent Sample t-test, and Paired Sample t-test were used to analyze the data. RESULTS It was determined that adolescents experienced moderate anxiety before the procedure. It was found that the majority of adolescents did not have a COVID-19 positive patient in their relatives (83.1%) or in the same house (82.7%). It was determined that they had COVID-19 positive friends at school (56.2%) but not in class (61.4%) and had no contact with positive friends (69.1%). While the post-operative state anxiety level of the adolescents informed by video was 38.76 ± 10.77, the anxiety level of the adolescents in the control group was 41.68 ± 11.92. Informing with video significantly decreased the anxiety level of adolescents (p = 0.035). CONCLUSION Video information reduces state anxiety after the procedure. PRACTICE IMPLICATIONS It is recommended that video information before rRT-PCR test should be implemented in all hospitals, tablets, televisions, or phones should be used to provide information against the risk of contamination, and other studies should be conducted to show the effectiveness of video information.
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Affiliation(s)
| | - Hacer Cetin
- Department of Pediatric Nursing, Faculty of Nursing, Mersin University, 33343 Mersin, Turkey.
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Faleye TOC, Driver EM, Wright JM, Halden RU, Varsani A, Scotch M. Direct detection of canine picornavirus complete coding sequence in wastewater using long-range reverse-transcriptase polymerase chain reaction and long-read sequencing. Infect Genet Evol 2024; 118:105550. [PMID: 38199505 PMCID: PMC10923025 DOI: 10.1016/j.meegid.2024.105550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/03/2024] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
We describe four complete coding sequence (cCDS) of canine picornavirus from wastewater in Arizona, USA detected by coupling cCDS single-contig (∼7.5 kb) reverse-transcriptase polymerase chain reaction (RT-PCR) and low-cost long-read high-throughput sequencing. For viruses of medical/veterinary importance, this workflow expands possibilities of wastewater based genomic epidemiology for exploring virus evolutionary dynamics especially in low-resource settings.
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Affiliation(s)
- Temitope O C Faleye
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Erin M Driver
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jillian M Wright
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Rolf U Halden
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
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8
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Mak GCK, Hung DLL. Non-specific signals in real-time RT-PCR for detecting respiratory viruses. Diagn Microbiol Infect Dis 2024; 108:116163. [PMID: 38157637 DOI: 10.1016/j.diagmicrobio.2023.116163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
We describe our experiences in investigating the origin of non-specific signals during the development phase of a multiplex PCR assay for respiratory viruses. After ruling out various sources of error, eventually we discovered the non-specific signal was related to the particular lot of the PCR kit.
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Affiliation(s)
- Gannon C K Mak
- All from Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, People's Republic of China.
| | - Derek L L Hung
- All from Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, People's Republic of China
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9
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Kawakami GDS, Pereira MA, Kubrusly MS, Carrasco AGM, Ramos MFKP, Ribeiro Júnior U. TUMOR MARKERS EXPRESSION LEVELS IN GASTRIC CANCER PATIENT'S PERIPHERAL BLOOD BY RT-PCR ASSESSMENT. Arq Bras Cir Dig 2024; 36:e1789. [PMID: 38324850 PMCID: PMC10841496 DOI: 10.1590/0102-672020230071e1789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 02/09/2024]
Abstract
BACKGROUND Hematological recurrence is the second most frequent cause of failure in the treatment of gastric cancer. The detection of circulating tumor markers in peripheral blood by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) method may be a useful tool to predict recurrence and determine the patient's prognosis. However, no consensus has been reached regarding the association between the tumor markers level in peripheral blood and its impact on patient survival. AIMS To evaluate the expression of the circulating tumor markers CK20 and MUC1 in peripheral blood samples from patients with gastric cancer by qRT-PCR, and to verify the association of their expression levels with clinicopathological characteristics and survival. METHODS A total of 31 patients with gastric adenocarcinoma were prospectively included in this study. CK20 and MUC1 expression levels were analyzed from peripheral blood by the qRT-PCR technique. RESULTS There was no statistically significant (p>0.05) association between CK20 expression levels and clinical, pathological, and surgical features. Higher MUC1 expression levels were associated with female patients (p=0.01). There was a correlation between both gene levels (R=0.81, p<0.001), and CK20 level and tumor size (R=0.39, p=0.034). CONCLUSIONS CK20 and MUC1 expression levels could be assessed by qRT-PCR from total peripheral blood samples of patients with gastric cancer. CK20 levels were correlated to MUC1 levels as well as to tumor size. There was no difference in disease-free survival and overall survival regarding both genetic markers expression in this series.
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Affiliation(s)
- Gabriel da Silva Kawakami
- Universidade de São Paulo, Instituto do Câncer, Hospital das Clínicas, Faculty of Medicine, Department of Gastroenterology, São Paulo (SP), Brazil
| | - Marina Alessandra Pereira
- Universidade de São Paulo, Instituto do Câncer, Hospital das Clínicas, Faculty of Medicine, Department of Gastroenterology, São Paulo (SP), Brazil
| | - Márcia Saldanha Kubrusly
- Universidade de São Paulo, Instituto do Câncer, Hospital das Clínicas, Faculty of Medicine, Department of Gastroenterology, São Paulo (SP), Brazil
| | - Alexis Germán Murillo Carrasco
- Universidade de São Paulo, Instituto do Câncer, Hospital das Clínicas, Faculty of Medicine, Department of Gastroenterology, São Paulo (SP), Brazil
| | | | - Ulysses Ribeiro Júnior
- Universidade de São Paulo, Instituto do Câncer, Hospital das Clínicas, Faculty of Medicine, Department of Gastroenterology, São Paulo (SP), Brazil
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Bray N, Sopwith W, Edmunds M, Vansteenhouse H, Feenstra JDM, Jacobs P, Rajput K, O'Connell AM, Smith ML, Blomquist P, Hatziioanou D, Elson R, Vivancos R, Gallagher E, Wigglesworth MJ, Dominiczak A, Hopkins S, Lake IR. RT-PCR genotyping assays to identify SARS-CoV-2 variants in England in 2021: a design and retrospective evaluation study. Lancet Microbe 2024; 5:e173-e180. [PMID: 38244555 DOI: 10.1016/s2666-5247(23)00320-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 01/22/2024]
Abstract
BACKGROUND Whole-genome sequencing (WGS) is the gold standard diagnostic tool to identify and genetically characterise emerging pathogen mutations (variants), but cost, capacity, and timeliness limit its use when large populations need rapidly assessing. We assessed the potential of genotyping assays to provide accurate and timely variant information at scale by retrospectively examining surveillance for SARS-CoV-2 variants in England between March and September, 2021, when genotyping assays were used widely for variant detection. METHODS We chose a panel of four RT-PCR genotyping assays to detect circulating variants of SARS-COV-2 in England and developed a decision algorithm to assign a probable SARS-CoV-2 variant to samples using the assay results. We extracted surveillance data from the UK Health Security Agency databases for 115 934 SARS-CoV-2-positive samples (March 1-Sept 6, 2021) when variant information was available from both genotyping and WGS. By comparing the genotyping and WGS variant result, we calculated accuracy metrics (ie, sensitivity, specificity, and positive predictive value [PPV]) and the time difference between the sample collection date and the availability of variant information. We assessed the number of samples with a variant assigned from genotyping or WGS, or both, over time. FINDINGS Genotyping and an initial decision algorithm (April 10-May 11, 2021 data) were accurate for key variant assignment: sensitivities and PPVs were 0·99 (95% CI 0·99-0·99) for the alpha, 1·00 (1·00-1·00) for the beta, and 0·91 (0·80-1·00) for the gamma variants; specificities were 0·97 (0·96-0·98), 1·00 (1·00-1·00), and 1·00 (1·00-1·00), respectively. A subsequent decision algorithm over a longer time period (May 27-Sept 6, 2021 data) remained accurate for key variant assignment: sensitivities were 0·91 (95% CI 0·74-1·00) for the beta, 0·98 (0·98-0·99) for the delta, and 0·93 (0·81-1·00) for the gamma variants; specificities were 1·00 (1·00-1·00), 0·96 (0·96-0·97), and 1·00 (1·00-1·00), respectively; and PPVs were 0·83 (0·62-1·00), 1·00 (1·00-1·00), and 0·78 (0·59-0·97), respectively. Genotyping produced variant information a median of 3 days (IQR 2-4) after the sample collection date, which was faster than with WGS (9 days [8-11]). The flexibility of genotyping enabled a nine-times increase in the quantity of samples tested for variants by this method (from 5000 to 45 000). INTERPRETATION RT-PCR genotyping assays are suitable for high-throughput variant surveillance and could complement WGS, enabling larger scale testing for known variants and timelier results, with important implications for effective public health responses and disease control globally, especially in settings with low WGS capacity. However, the choice of panels of RT-PCR assays is highly dependent on database information on circulating variants generated by WGS, which could limit the use of genotyping assays when new variants are emerging and spreading rapidly. FUNDING UK Health Security Agency and National Institute for Health Research Health Protection Research Unit in Emergency Preparedness and Response.
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Affiliation(s)
- Neil Bray
- UK Health Security Agency, London, UK
| | | | | | - Harper Vansteenhouse
- UK Health Security Agency, London, UK; BioClavis, Glasgow, UK; NHS Test and Trace, Department of Health & Social Care, London, UK; Alderley Lighthouse Labs, Macclesfield, UK
| | | | - Peter Jacobs
- Thermo Fisher Scientific, South San Francisco, CA, USA
| | - Kamal Rajput
- NHS Test and Trace, Department of Health & Social Care, London, UK
| | | | | | | | | | - Richard Elson
- UK Health Security Agency, London, UK; School of Environmental Sciences, University of East Anglia, Norwich, UK; NIHR Health Protection Research Unit in Emergency Preparedness and Response, London, UK
| | - Roberto Vivancos
- UK Health Security Agency, London, UK; NIHR Health Protection Research Unit in Gastrointestinal Infections and NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | | | | | - Anna Dominiczak
- UK Health Security Agency, London, UK; NHS Test and Trace, Department of Health & Social Care, London, UK; School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Susan Hopkins
- UK Health Security Agency, London, UK; NIHR Health Protection Research Unit in in Health Care Acquired Infections and Antimicrobial Resistance, London, UK
| | - Iain R Lake
- UK Health Security Agency, London, UK; School of Environmental Sciences, University of East Anglia, Norwich, UK; NIHR Health Protection Research Unit in Emergency Preparedness and Response, London, UK.
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11
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Pérez-Rodríguez FJ, Cherpillod P, Thomasson V, Vetter P, Schibler M. Identification of a measles variant displaying mutations impacting molecular diagnostics, Geneva, Switzerland, 2023. Euro Surveill 2024; 29. [PMID: 38304951 PMCID: PMC10835752 DOI: 10.2807/1560-7917.es.2024.29.5.2400034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
Real-time PCR is one of the most widely used techniques to diagnose measles cases. Here we report measles virus variants with three genetic mutations in the reverse primer annealing site of a widely used PCR. The mutations result in a slight loss of the PCR sensitivity. Variants bearing the three mutations presently circulate in different countries since at least the end of 2021. Our findings highlight the usefulness of molecular surveillance in monitoring if oligonucleotides in diagnostic tests remain adequate.
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Affiliation(s)
- Francisco-Javier Pérez-Rodríguez
- Geneva Center for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- National Measles and Rubella Reference Laboratory (CNRRR), Geneva University Hospitals, Geneva, Switzerland
- Laboratory of virology, Laboratory Medicine Division, Geneva University Hospitals, Geneva, Switzerland
| | - Pascal Cherpillod
- Geneva Center for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- National Measles and Rubella Reference Laboratory (CNRRR), Geneva University Hospitals, Geneva, Switzerland
- Laboratory of virology, Laboratory Medicine Division, Geneva University Hospitals, Geneva, Switzerland
| | - Valentine Thomasson
- Laboratory of virology, Laboratory Medicine Division, Geneva University Hospitals, Geneva, Switzerland
| | - Pauline Vetter
- Geneva Center for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of virology, Laboratory Medicine Division, Geneva University Hospitals, Geneva, Switzerland
| | - Manuel Schibler
- Geneva Center for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- National Measles and Rubella Reference Laboratory (CNRRR), Geneva University Hospitals, Geneva, Switzerland
- Laboratory of virology, Laboratory Medicine Division, Geneva University Hospitals, Geneva, Switzerland
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12
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Harish G, Shetty U, Varamballi P, Mukhopadhyay C, Jagadesh A. Optimization of an allelic discrimination real-time RT-PCR assay for detection of H275Y oseltamivir resistance gene mutation among influenza A(H1N1)pdm09 patients from 2020 to 2022. J Med Virol 2024; 96:e29427. [PMID: 38288882 DOI: 10.1002/jmv.29427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/06/2024] [Accepted: 01/14/2024] [Indexed: 02/01/2024]
Abstract
Influenza virus is known to cause mild to severe respiratory infections and is also prone to genetic mutations. Of all the mutations, neuraminidase (NA) gene mutations are a matter of concern, as most approved antivirals target this protein. During the 2020 influenza season, an emergence of mutation in the NA gene, affecting the binding of the World Health Organization (WHO)-recommended probes to the specific site of the NA gene, was reported by our group. As a result of this mutation, the WHO-recommended allelic discrimination real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was unable to detect wild-type (H275) or mutant oseltamivir-resistant (Y275) strains of influenza A(H1N1)pmd09 viruses. In the current study, the WHO-recommended probes were redesigned according to the mutation in the probe binding site. Fifty undetermined samples (2020-2021) from the previous study were retested with the newly designed probes and found to be positive for H275 and/or Y275. The results obtained were similar to the Sanger sequencing results from the previous study, suggesting that the redesigned probes were efficient in discriminating between wild-type and mutant-type viruses. Furthermore, 133 samples from 2022, making a total of 183 samples (2020-2022), were tested using improved allelic discrimination real-time RT-PCR, and the overall prevalence rate of oseltamivir resistance in 2020-2022 was found to be 0.54%.
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Affiliation(s)
- Gandhapu Harish
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - Ujwal Shetty
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - Prasad Varamballi
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | | | - Anitha Jagadesh
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
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13
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Fazzina M, Bergonzoni M, Massenzio F, Monti B, Frabetti F, Casadei R. Selection of suitable reference genes for gene expression studies in HMC3 cell line by quantitative real-time RT-PCR. Sci Rep 2024; 14:2431. [PMID: 38287074 PMCID: PMC10825209 DOI: 10.1038/s41598-024-52415-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 01/18/2024] [Indexed: 01/31/2024] Open
Abstract
Microglia represent the primary immune defense system within the central nervous system and play a role in the inflammatory processes occurring in numerous disorders, such as Parkinson's disease (PD). PD onset and progression are associated with factors considered possible causes of neuroinflammation, i.e. genetic mutations. In vitro models of microglial cells were established to identify specific molecular targets in PD through the analysis of gene expression data. Recently, the Human Microglial Clone 3 cell line (HMC3) has been characterized and a new human microglia model has emerged. Here we perform RT-qPCR analyses to evaluate the expression of ten reference genes in HMC3, untreated or stimulated to a pro-inflammatory status. The comparative ∆CT method, BestKeeper, Normfinder, geNorm and RefFinder algorithms were used to assess the stability of the candidate genes. The results showed that the most suitable internal controls are HPRT1, RPS18 and B2M genes. In addition, the most stable and unstable reference genes were used to normalize the expression of a gene of interest in HMC3, resulting in a difference in the statistical significance in cells treated with Rotenone. This is the first reference gene validation study in HMC3 cell line in pro-inflammatory status and can contribute to more reliable gene expression analysis in the field of neurodegenerative and neuroinflammatory research.
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Affiliation(s)
- Martina Fazzina
- Department for Life Quality Studies - QUVI, University of Bologna, Rimini, Italy
| | - Matteo Bergonzoni
- Department of Pharmacy and Biotechnology - FABIT, University of Bologna, Bologna, Italy
| | - Francesca Massenzio
- Department of Pharmacy and Biotechnology - FABIT, University of Bologna, Bologna, Italy
| | - Barbara Monti
- Department of Pharmacy and Biotechnology - FABIT, University of Bologna, Bologna, Italy
| | - Flavia Frabetti
- Department of Medical and Surgical Sciences - DIMEC, University of Bologna, Bologna, Italy
| | - Raffaella Casadei
- Department for Life Quality Studies - QUVI, University of Bologna, Rimini, Italy.
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14
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Markewitz R, Dargvainiene J, Junker R, Wandinger KP. Cycle threshold of SARS-CoV-2 RT-PCR as a driver of retesting. Sci Rep 2024; 14:2423. [PMID: 38287120 PMCID: PMC10825127 DOI: 10.1038/s41598-024-52984-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/25/2024] [Indexed: 01/31/2024] Open
Abstract
SARS-CoV-2 RT-PCR is a critical and, at times, limited resource. Frequent Retesting of patients may strain testing infrastructure unduly. Recommendations that include cycle threshold (Ct) cutoffs may incentivize early retesting when the Ct value is reported. We aimed to investigate patterns of retesting in association with initial Ct-values. We performed a retrospective analysis of RT-PCR results (including Ct-values) for patients from whom ≥ 2 samples were collected within 14 days, the first of which had to be positive. We calculated absolute and baseline-corrected kinetics of Ct-values over time, as well as the median initial Ct-values in dependence of the timing of the first retesting and the time until RT-PCR negativity for SARS-CoV-2. Retesting after an initial positive SARS-CoV-2 RT-PCR was most commonly performed on day 7, with patients being retested as early as day 1. The majority of patients retested within 14 days remained SARS-CoV-2 positive in the RT-PCR. Baseline-corrected Ct-values showed a quasi-linear increase over 14 days since the initial positive result. Both the timing until the first retesting and until RT-PCR negativity were inversely correlated with the initial Ct-value. The timing of retesting after a positive SARS-CoV-2 RT-PCR appears to be significantly influenced by the initial Ct-value. Although it can be assumed that Ct-values will increase steadily over time, strategies that rely on rigid Ct-cutoffs should be discussed critically, not only because of methodological caveats but also because of the strain on testing infrastructure caused by the incentive for early retesting that Ct-values apparently represent.
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Affiliation(s)
- Robert Markewitz
- Institute of Clinical Chemistry, University Hospital of Schleswig-Holstein, Arnold-Heller-Straße 3, 24105, Kiel, Germany.
| | - Justina Dargvainiene
- Institute of Clinical Chemistry, University Hospital of Schleswig-Holstein, Arnold-Heller-Straße 3, 24105, Kiel, Germany
| | - Ralf Junker
- Institute of Clinical Chemistry, University Hospital of Schleswig-Holstein, Arnold-Heller-Straße 3, 24105, Kiel, Germany
| | - Klaus-Peter Wandinger
- Institute of Clinical Chemistry, University Hospital of Schleswig-Holstein, Arnold-Heller-Straße 3, 24105, Kiel, Germany
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15
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Pessoa FMCDP, Viana VBDJ, de Oliveira MB, Nogueira BMD, Ribeiro RM, Oliveira DDS, Lopes GS, Vieira RPG, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira FC, Moreira-Nunes CA. Validation of Endogenous Control Genes by Real-Time Quantitative Reverse Transcriptase Polymerase Chain Reaction for Acute Leukemia Gene Expression Studies. Genes (Basel) 2024; 15:151. [PMID: 38397141 PMCID: PMC10887733 DOI: 10.3390/genes15020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Reference genes are used as internal reaction controls for gene expression analysis, and for this reason, they are considered reliable and must meet several important criteria. In view of the absence of studies regarding the best reference gene for the analysis of acute leukemia patients, a panel of genes commonly used as endogenous controls was selected from the literature for stability analysis: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Abelson murine leukemia viral oncogene human homolog 1 (ABL), Hypoxanthine phosphoribosyl-transferase 1 (HPRT1), Ribosomal protein lateral stalk subunit P0 (RPLP0), β-actin (ACTB) and TATA box binding protein (TBP). The stability of candidate reference genes was analyzed according to three statistical methods of assessment, namely, NormFinder, GeNorm and R software (version 4.0.3). From this study's analysis, it was possible to identify that the endogenous set composed of ACTB, ABL, TBP and RPLP0 demonstrated good performances and stable expressions between the analyzed groups. In addition to that, the GAPDH and HPRT genes could not be classified as good reference genes, considering that they presented a high standard deviation and great variability between groups, indicating low stability. Given these findings, this study suggests the main endogenous gene set for use as a control/reference for the gene expression in peripheral blood and bone marrow samples from patients with acute leukemias is composed of the ACTB, ABL, TBP and RPLP0 genes. Researchers may choose two to three of these housekeeping genes to perform data normalization.
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Affiliation(s)
- Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Vitória Beatriz de Jesus Viana
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Marcelo Braga de Oliveira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Beatriz Maria Dias Nogueira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | | | - Deivide de Sousa Oliveira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Hematology, Fortaleza General Hospital (HGF), Fortaleza 60150-160, CE, Brazil
| | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil;
| | | | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Fabiano Cordeiro Moreira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
- Central Unity, Molecular Biology Laboratory, Clementino Fraga Group, Fortaleza 60115-170, CE, Brazil
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16
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Rai A, Ammi Z, Anes-Boulahbal DL, Assadi AA, Amrane A, Baaloudj O, Mouni L. Molecular Amplification and Cell Culturing Efficiency for Enteroviruses' Detection in Cerebrospinal Fluids of Algerian Patients Suffering from Meningitis. Viruses 2024; 16:170. [PMID: 38399946 PMCID: PMC10891896 DOI: 10.3390/v16020170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/25/2024] Open
Abstract
Enteroviruses (EVs) represent a major cause of viral meningitis, being responsible for nearly 1 billion infections each year worldwide. Several techniques were developed to obtain better diagnostic results of EV infections. Herein, we evaluated the efficiency of EV detection through isolation on both Rhabdomyosarcoma (RD) and Vero cell line cultures, conventional reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR. Thus, 50 cerebrospinal fluid (CSF) samples belonging to patients suspected to have viral meningitis in northern Algeria were collected, anonymously numbered from 1 to 50 and subjected to the above-mentioned techniques for EV detection. Using real-time RT-PCR, 34 CSF samples were revealed to be positive for viral origin of meningitis (68%). Thirteen of them were positive when the conventional RT-PCR was used (26%), and only three samples gave positive results when the cell culture technique was used (6%). Surprisingly, two cell culture-positive CSF samples, namely, 31 and 39, were negative using RT-PCR directly on the original samples. However, they turned to be positive when amplification was carried out on their corresponding cell culture supernatant. The cell-cultured viral isolates were then identified by sequencing their viral genome's VP1 regions. All of them were revealed to belong to the echovirus 27 strain. This investigation demonstrates that RT-PCR techniques are often more sensitive, accurate and much faster, providing reliable results within a clinically acceptable timeframe. However, viral isolation on cell cultures remains crucial to obtain enough viral load for serological tests or even to avoid the rare, but existing, false negative PCR.
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Affiliation(s)
- Abdelwahab Rai
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité, Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
| | - Zohra Ammi
- Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
| | - Dahbia Leila Anes-Boulahbal
- Laboratoire des Entérovirus, Département de Virologie, Institut Pasteur d’Alger, Annexe de Sidi-Fredj, Alger 16000, Algeria;
| | - Aymen Amin Assadi
- College of Engineering, Imam Mohammad Ibn Saud Islamic University, IMSIU, Riyadh 11432, Saudi Arabia;
- Ecole Nationale Supérieure de Chimie de Rennes, University Rennes, CNRS, ISCR-UMR 6226, 35000 Rennes, France;
| | - Abdeltif Amrane
- Ecole Nationale Supérieure de Chimie de Rennes, University Rennes, CNRS, ISCR-UMR 6226, 35000 Rennes, France;
| | - Oussama Baaloudj
- Laboratory of Reaction Engineering, Faculty of Mechanical Engineering and Process Engineering, Université des Sciences et de la Technologie Houari Boumediene, BP 32, Algiers 16111, Algeria;
| | - Lotfi Mouni
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité, Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
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17
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Kosińska-Selbi B, Kowalczyk J, Pierscińska J, Wełeszczuk J, Peñarrubia L, Turner B, Pareja J, Porco R, Diaz-Hernandez R, Juanola-Falgarona M, Rey M, Manissero D, Blacha A. Monitoring SARS-CoV-2 genetic variability: A post-market surveillance workflow for combined bioinformatic and laboratory evaluation of commercial RT-PCR assay performance. PLoS One 2024; 19:e0294271. [PMID: 38215170 PMCID: PMC10786374 DOI: 10.1371/journal.pone.0294271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/27/2023] [Indexed: 01/14/2024] Open
Abstract
OBJECTIVE The speed at which Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is mutating has made it necessary to frequently assess how these genomic changes impact the performance of diagnostic real-time polymerase chain reaction (RT-PCR) assays. Herein, we describe a generic three-step workflow to assess the effect of genomic mutations on inclusivity and sensitivity of RT-PCR assays. METHODS Sequences collected from the Global Initiative on Sharing All Influenza Data (GISAID) were mapped to a SARS-CoV-2 reference genome to evaluate the position and prevalence of mismatches in the oligonucleotide-binding sites of the QIAstat-Dx, an RT-PCR panel designed to detect SARS-CoV-2. The frequency of mutations and their impact on melting temperature were assessed, and sequences flagged by risk-based criteria were examined in vitro. RESULTS Out of 8,900,393 SARS-CoV-2 genome sequences analyzed, only 173 (0.0019%) genomes contained potentially critical mutations for the QIAstat-Dx; follow-up in-vitro testing confirmed no impact on the assays' performance. CONCLUSIONS The current study demonstrates that SARS-CoV-2 genetic variants do not affect the performance of the QIAstat-Dx device. It is recommended that manufacturers incorporate this workflow into obligatory post-marketing surveillance activities, as this approach could potentially enhance genetic monitoring of their product.
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Affiliation(s)
| | | | | | | | | | | | - Josep Pareja
- QIAGEN (Previously STAT-Dx Life S.L.), Barcelona, Spain
| | - Roberto Porco
- QIAGEN (Previously STAT-Dx Life S.L.), Barcelona, Spain
| | | | | | - Melisa Rey
- QIAGEN (Previously STAT-Dx Life S.L.), Barcelona, Spain
| | | | - Anna Blacha
- QIAGEN Manchester Ltd, CityLabs, Manchester, United Kingdom
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18
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Shihab SR, Iqbal BN, Arunasalam S, Noordeen F. Quality of the sample-based RNA determines the real-time RT-PCR results in the laboratory diagnosis of COVID-19. Diagn Microbiol Infect Dis 2024; 108:116076. [PMID: 37980858 DOI: 10.1016/j.diagmicrobio.2023.116076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/27/2023] [Accepted: 08/30/2023] [Indexed: 11/21/2023]
Abstract
Effect of the quality of sample-based RNA on COVID-19 real-time RT-PCR results was investigated. The purity of the extracts was dependent on the extraction method (P<0.0001) and affected the test interpretations (P = 0.002). Gross RNA concentration negatively correlated with Ct values (P < 0.0001). The presence of impurities contributed to inconclusive test results.
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Affiliation(s)
- Sibra Rm Shihab
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka; Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Bushran N Iqbal
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Shiyamalee Arunasalam
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Faseeha Noordeen
- Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka.
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19
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Khyati, Manchanda V, Pumma P, Chawla R, Garg S, Saxena S. Diagnostic performance of saliva RT-PCR test as a diagnostic tool and its utility in the detection of SARS-CoV-2 shedding with different patient characteristics: Prospective observational study. Indian J Med Microbiol 2024; 47:100490. [PMID: 37890412 DOI: 10.1016/j.ijmmb.2023.100490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Salivary shedding of SARS-CoV-2 is a known entity and its role has been established in transmission of the disease. The present study was performed to evaluate the duration of viral shedding in saliva in COVID-19 patients and its variation among symptomatic and asymptomatic patients with or without co-morbidities. METHODS The present prospective observational study was conducted at the COVID-19 care hospital associated with primary to tertiary care in New Delhi, India. A total of 124 COVID-19 confirmed cases enrolled in two phases (January-March 2021; April-June 2021) who consented for 48hrly saliva and nasopharyngeal swab (NPS) specimens till discharge from the hospital for SARS-CoV-2 detection were included. The specimens obtained were tested for SARS-CoV-2 by Real-Time PCR. RESULTS The sensitivity and the specificity of RT-PCR on saliva were 81.7 % and 85.0 %, respectively. The sensitivity of saliva-based PCR was comparable in symptomatic and asymptomatic patients (81.6 % vs 82.1 %). The sensitivity of saliva-based PCR markedly increased in the second phase of enrollment as compared to the first phase (92.6 % vs 78.5 %) indicating higher level of salivary shedding by the delta variant of SARS-CoV-2. The sensitivity of PCR on saliva was the highest up to day seven of illness. The median duration of RNA shedding in saliva was comparable among the symptomatic and asymptomatic patients. The severity of the disease was not associated with the duration of SARS-CoV-2 shedding in saliva. CONCLUSIONS SARS-CoV-2 shedding in saliva continued till seven days in large number of patients including asymptomatic patients. Saliva is non-inferior to NPS specimen in the diagnosis of SARS-CoV-2. Saliva specimen is recommended as a good alternate to NPS for SARS-CoV-2 testing.
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Affiliation(s)
- Khyati
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India
| | - V Manchanda
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India.
| | - P Pumma
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India
| | - R Chawla
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India
| | - S Garg
- Department of Medicine, Maulana Azad Medical College, 110002, New Delhi, India
| | - S Saxena
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India
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20
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Hazan G, Goldstein Y, Greenberg D, Khalde F, Mahajna R, Keren-Naos A, Hershkovitz E, Faingelernt Y, Givon-Lavi N, Danino D. Comparing single versus multiple virus detection in pediatric acute gastroenteritis postimplementation of routine multiplex RT-PCR diagnostic testing. J Med Virol 2024; 96:e29344. [PMID: 38149453 DOI: 10.1002/jmv.29344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
Utilizing multiplex real time polymerase chain reaction (RT-PCR) for rapid diagnosis of gastroenteritis, enables simultaneous detection of multiple pathogens. A comparative analysis of disease characteristics was conducted between cases with single and multiple viruses. Rotavirus vaccine was introduced in 2010, reaching a 70% coverage in 2 years. All rectal swabs collected from diarrheic children (<5 years) between December 2017 and March 2022 were included. Detection of the same viruses within 2 months was considered a single episode. Episodes with positive stool bacterial PCR were excluded. A total of 5879 samples were collected, revealing 86.9% (1509) with single virus detection and 13.1% (227) with multiple viruses. The most frequent combination was rotavirus and norovirus (27.8%), these infections followed a winter-spring seasonality akin to rotavirus. Children with multivirus infections exhibited higher immunodeficiency (OR 2.06) rates, but lower food allergy (OR 0.45) and prematurity rates (OR 0.55) compared to single infections. Greater disease severity, evaluated by the Vesikari score, was observed in multivirus episodes (p < 0.001, OR 1.12). Multivirus infections accounted for 13.1% of symptomatic cases in hospitalized young children. Despite vaccination efforts, rotavirus remained prominent, frequently in co-infections with norovirus. Overall, multivirus infections were linked to more severe diseases than single virus cases.
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Affiliation(s)
- Guy Hazan
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
- Pediatric Pulmonary Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Yoav Goldstein
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - David Greenberg
- Pediatric Infectious Diseases Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Firas Khalde
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Rofaida Mahajna
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Ayelet Keren-Naos
- Clinical Virology Laboratory, Soroka University Medical Center, Beer Sheva, Israel
| | - Eli Hershkovitz
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Yaniv Faingelernt
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
- Pediatric Gastroenterology Hepatology and Nutrition Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Noga Givon-Lavi
- Pediatric Infectious Diseases Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
| | - Dana Danino
- Pediatric Department D., Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
- Pediatric Infectious Diseases Unit, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University, Beer Sheva, Israel
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21
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Becker AS, Lopes TRR, Pedroso NH, Silva Júnior JVJ, Weiblen R, Flores EF. Novel high-coverage primers for detection of canine morbillivirus by end-point and real-time RT-PCR assays. J Virol Methods 2024; 323:114853. [PMID: 37979697 DOI: 10.1016/j.jviromet.2023.114853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023]
Abstract
Canine distemper virus (CDV) is a major threat to domestic dogs and wildlife worldwide. Molecular assays are the most sensitive and specific tests to diagnose the disease, however, the high CDV genetic variability may compromise laboratory diagnosis. Herein, we designed a high-coverage primer set for end-point (RT-PCR) and real-time (RT-qPCR) for CDV detection. Initially, we collected 194 complete/near-complete CDV genomes (GenBank) and analyzed them for highly conserved regions for primer design. We then assessed the in silico coverage, analytical sensitivity, specificity and diagnostic performance of RT-PCR/RT-qPCR reactions based on our primers. Furthermore, the coverage of our primers, as well as their analytical sensitivity and diagnostic performance, were compared to a commonly used primer set for CDV detection (named PP-I). Our forward (F) and reverse (R) primers fully matched 100 % (194/194) and 99 % (192/194) of the analyzed sequences, whereas the PP-I F and R primers fully matched 15 % (29/194) and 9 % (18/194) sequences, respectively. The detection limit of our RT-PCR and RT-qPCR was equivalent to that of PP-I primers (0.001 TCID50/mL). Out of 70 clinical samples tested, 38 were positive by our RT-PCR/RT-qPCR assays, whereas reactions with primers PP-I failed to detect 9/28 (32 %) positive samples selected for comparison purposes. In addition, our assays did not amplify other canine viruses associated with respiratory and neurological diseases: canine adenovirus 2, canine parainfluenza virus 2, canine herpesvirus 1 and rabies virus. Overall, we describe a high-coverage primer set for CDV detection, which represents an attractive tool for laboratory diagnosis of canine distemper.
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Affiliation(s)
- Alice Silveira Becker
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil; Programa de Pós-graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Thaísa Regina Rocha Lopes
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil; Programa de Pós-graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Natália Hettwer Pedroso
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil; Programa de Pós-graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - José Valter Joaquim Silva Júnior
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil; Setor de Virologia, Laboratório de Imunopatologia Keizo Asami, Universidade Federal de Pernambuco, Pernambuco, Brazil.
| | - Rudi Weiblen
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Eduardo Furtado Flores
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil.
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22
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Osborne CM, Langelier C, Kamm J, Williamson K, Ambroggio L, Reeder RW, Locandro C, Kirk Harris J, Wagner BD, Maddux AB, Caldera S, Lyden A, Soesanto V, Simões EAF, Leroue MK, Carpenter TC, Hall MW, Zuppa AF, Carcillo JA, Meert KL, Pollack MM, McQuillen PS, Notterman DA, DeRisi J, Mourani PM. Viral Detection by Reverse Transcriptase Polymerase Chain Reaction in Upper Respiratory Tract and Metagenomic RNA Sequencing in Lower Respiratory Tract in Critically Ill Children With Suspected Lower Respiratory Tract Infection. Pediatr Crit Care Med 2024; 25:e1-e11. [PMID: 37732845 PMCID: PMC10756702 DOI: 10.1097/pcc.0000000000003336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
OBJECTIVES Viral lower respiratory tract infection (vLRTI) contributes to substantial morbidity and mortality in children. Diagnosis is typically confirmed by reverse transcriptase polymerase chain reaction (RT-PCR) of nasopharyngeal specimens in hospitalized patients; however, it is unknown whether nasopharyngeal detection accurately reflects presence of virus in the lower respiratory tract (LRT). This study evaluates agreement between viral detection from nasopharyngeal specimens by RT-PCR compared with metagenomic next-generation RNA sequencing (RNA-Seq) from tracheal aspirates (TAs). DESIGN This is an analysis of of a seven-center prospective cohort study. SETTING Seven PICUs within academic children's hospitals in the United States. PATIENTS Critically ill children (from 1 mo to 18 yr) who required mechanical ventilation via endotracheal tube for greater than or equal to 72 hours. INTERVENTIONS We evaluated agreement in viral detection between paired upper and LRT samples. Results of clinical nasopharyngeal RT-PCR were compared with TA RNA-Seq. Positive and negative predictive agreement and Cohen's Kappa were used to assess agreement. MEASUREMENTS AND MAIN RESULTS Of 295 subjects with paired testing available, 200 (68%) and 210 (71%) had positive viral testing by RT-PCR from nasopharyngeal and RNA-Seq from TA samples, respectively; 184 (62%) were positive by both nasopharyngeal RT-PCR and TA RNA-Seq for a virus, and 69 (23%) were negative by both methods. Nasopharyngeal RT-PCR detected the most abundant virus identified by RNA-Seq in 92.4% of subjects. Among the most frequent viruses detected, respiratory syncytial virus demonstrated the highest degree of concordance (κ = 0.89; 95% CI, 0.83-0.94), whereas rhinovirus/enterovirus demonstrated lower concordance (κ = 0.55; 95% CI, 0.44-0.66). Nasopharyngeal PCR was more likely to detect multiple viruses than TA RNA-Seq (54 [18.3%] vs 24 [8.1%], p ≤ 0.001). CONCLUSIONS Viral nucleic acid detection in the upper versus LRT reveals good overall agreement, but concordance depends on the virus. Further studies are indicated to determine the utility of LRT sampling or the use of RNA-Seq to determine LRTI etiology.
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Affiliation(s)
- Christina M Osborne
- Department of Pediatrics, Section of Critical Care Medicine, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO
- Department of Pediatrics, Section of Infectious Diseases, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO
| | - Charles Langelier
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
| | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, CA
| | - Kayla Williamson
- Department of Biostatistics and Informatics, University of Colorado, Colorado School of Public Health, Aurora, CO
| | - Lilliam Ambroggio
- Department of Epidemiology, University of Colorado School of Medicine, Aurora, CO
- Department of Pediatrics, Section of Emergency Medicine, University of Colorado School of Medicine, Aurora, CO
| | - Ron W Reeder
- Department of Pediatrics, University of Utah, Salt Lake City, UT
| | | | - J Kirk Harris
- Department of Pediatrics, Section of Pulmonary Medicine, University of Colorado School of Medicine, Aurora, CO
| | - Brandie D Wagner
- Department of Biostatistics and Informatics, University of Colorado, Colorado School of Public Health, Aurora, CO
| | - Aline B Maddux
- Department of Pediatrics, Section of Critical Care Medicine, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO
| | | | - Amy Lyden
- Chan Zuckerberg Biohub, San Francisco, CA
| | - Victoria Soesanto
- Department of Biostatistics and Informatics, University of Colorado, Colorado School of Public Health, Aurora, CO
| | - Eric A F Simões
- Department of Pediatrics, Section of Infectious Diseases, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO
| | - Matthew K Leroue
- Department of Pediatrics, Section of Critical Care Medicine, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO
| | - Todd C Carpenter
- Department of Pediatrics, Section of Critical Care Medicine, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO
| | - Mark W Hall
- Division of Critical Care Medicine, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH
| | - Athena F Zuppa
- Anesthesiology and Critical Care, Hospital of the University of Pennsylvania and the Children's Hospital of Philadelphia, Philadelphia, PA
| | - Joseph A Carcillo
- Department of Anesthesia and Critical Care Medicine, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh, Pittsburgh, PA
| | - Kathleen L Meert
- Department of Pediatrics, Critical Care Medicine, Children's Hospital of Michigan, Central Michigan University, Detroit, MI
| | - Murray M Pollack
- Department of Pediatrics, Critical Care Medicine, Children's National Hospital, Washington, DC
| | - Patrick S McQuillen
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA
| | | | | | - Peter M Mourani
- Department of Pediatrics, Critical Care, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, AR
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23
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Carrera JP, Araúz D, Rojas A, Cardozo F, Stittleburg V, Morales Claro I, Galue J, Lezcano-Coba C, Romero Rebello Moreira F, -Rivera LF, Chen-Germán M, Moreno B, Capitan-Barrios Z, López-Vergès S, Pascale JM, Sabino EC, Valderrama A, Hanley KA, Donnelly CA, Vasilakis N, Faria NR, Waggoner JJ. Real-time RT-PCR for Venezuelan equine encephalitis complex, Madariaga, and Eastern equine encephalitis viruses: application in human and mosquito public health surveillance in Panama. J Clin Microbiol 2023; 61:e0015223. [PMID: 37982611 PMCID: PMC10729654 DOI: 10.1128/jcm.00152-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/08/2023] [Indexed: 11/21/2023] Open
Abstract
Eastern equine encephalitis virus (EEEV), Madariaga virus (MADV), and Venezuelan equine encephalitis virus complex (VEEV) are New World alphaviruses transmitted by mosquitoes. They cause febrile and sometimes severe neurological diseases in human and equine hosts. Detecting them during the acute phase is hindered by non-specific symptoms and limited diagnostic tools. We designed and clinically assessed real-time reverse transcription polymerase chain reaction assays (rRT-PCRs) for VEEV complex, MADV, and EEEV using whole-genome sequences. Validation involved 15 retrospective serum samples from 2015 to 2017 outbreaks, 150 mosquito pools from 2015, and 118 prospective samples from 2021 to 2022 surveillance in Panama. The rRT-PCRs detected VEEV complex RNA in 10 samples (66.7%) from outbreaks, with one having both VEEV complex and MADV RNAs. VEEV complex RNA was found in five suspected dengue cases from disease surveillance. The rRT-PCR assays identified VEEV complex RNA in three Culex (Melanoconion) vomerifer pools, leading to VEEV isolates in two. Phylogenetic analysis revealed the VEEV ID subtype in positive samples. Notably, 11.9% of dengue-like disease patients showed VEEV infections. Together, our rRT-PCR validation in human and mosquito samples suggests that this method can be incorporated into mosquito and human encephalitic alphavirus surveillance programs in endemic regions.
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Affiliation(s)
- Jean-Paul Carrera
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Dimelza Araúz
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Alejandra Rojas
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Fátima Cardozo
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Victoria Stittleburg
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Ingra Morales Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis (MRC-GIDA), Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Josefrancisco Galue
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Carlos Lezcano-Coba
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Filipe Romero Rebello Moreira
- MRC Centre for Global Infectious Disease Analysis (MRC-GIDA), Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luis Felipe -Rivera
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Maria Chen-Germán
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Brechla Moreno
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Zeuz Capitan-Barrios
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Ciudad de Panamá, Panama
| | - Sandra López-Vergès
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Juan Miguel Pascale
- Clinical of Tropical Diseases and Research Unit, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Anayansi Valderrama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Department of Medical Entomology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Kathryn A. Hanley
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
| | - Christl A. Donnelly
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- MRC Centre for Global Infectious Disease Analysis (MRC-GIDA), Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, Texas, USA
- Department of Preventive Medicine and Population Health, The University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, Texas, USA
- Center for Vector-Borne and Zoonotic Diseases, The University of Texas Medical Branch, Galveston, Texas, USA
- Center for Tropical Diseases, The University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infection and Immunity, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Nuno R. Faria
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis (MRC-GIDA), Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Jesse J. Waggoner
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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24
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Banada PP, Green R, Streck D, Kurvathi R, Reiss R, Banik S, Daivaa N, Montalvan I, Jones R, Marras SAE, Chakravorty S, Alland D. An expanded RT-PCR melting temperature coding assay to rapidly identify all known SARS-CoV-2 variants and sub-variants of concern. Sci Rep 2023; 13:21927. [PMID: 38081834 PMCID: PMC10713575 DOI: 10.1038/s41598-023-48647-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
The continued emergence of vaccine-resistant SARS-CoV-2 variants of concern (VOC) requires specific identification of each VOC as it arises. Here, we report an expanded version of our previously described sloppy molecular beacon (SMB) melting temperature (Tm) signature-based assay for VOCs, now modified to include detection of Delta (B.1.617.2) and Omicron (B.1.1.529) sub-variants. The SMB-VOC assay targets the signature codons 501, 484 and 452 in the SARS-CoV-2 spike protein which we show can specifically detect and differentiate all known VOCs including the Omicron subvariants (BA.1, BA.2, BA.2.12.1, BA.4/BA.5). The limit of detection (LOD) of the assay was 20, 22 and 36 genomic equivalents (GE) per reaction with the Delta, Omicron BA.1 and BA.2 respectively. Clinical validation of the 3-codon assay in the LC480 instrument showed the assay detected 94% (81/86) of the specimens as WT or VOCs and 6% (5/86) of the tests producing indeterminate results compared to sequencing. Sanger sequencing also failed for four samples. None of the specimens were incorrectly identified as WT or as a different VOC by our assay. Thus, excluding specimens with indeterminant results, the assay was 100% sensitive and 100% specific compared to Sanger sequencing for variant identification. This new assay concept can be easily expanded to add newer variants and can serve as a robust diagnostic tool for selecting appropriate monoclonal antibody therapy and rapid VOC surveillance.
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Affiliation(s)
- Padmapriya P Banada
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA.
| | - Raquel Green
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA
| | - Deanna Streck
- Institute of Genomic Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Rohini Kurvathi
- Institute of Genomic Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Robert Reiss
- Division of Infectious Diseases, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Sukalyani Banik
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA
| | - Naranjargal Daivaa
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA
| | | | | | - Salvatore A E Marras
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA
| | - Soumitesh Chakravorty
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA
- Cepheid, Sunnyvale, CA, USA
| | - David Alland
- Rutgers New Jersey Medical School, Public Health Research Institute, Newark, NJ, USA.
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25
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Sugimoto S, Kawase M, Suwa R, Kakizaki M, Kume Y, Chishiki M, Ono T, Okabe H, Norito S, Hosoya M, Hashimoto K, Shirato K. Development of a duplex real-time RT-PCR assay for the detection and identification of two subgroups of human metapneumovirus in a single tube. J Virol Methods 2023; 322:114812. [PMID: 37741464 DOI: 10.1016/j.jviromet.2023.114812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/25/2023]
Abstract
Human metapneumovirus (hMPV) is a common cause of respiratory infections in children. Many genetic diagnostic assays have been developed, but most detect hMPV regardless of the subgroup. In this study, we developed a real-time RT-PCR assay that can detect and identify the two major subgroups of hMPV (A and B) in one tube. Primers and probes were designed based on the sequences of recent clinical isolates in Japan. The assay showed comparable analytical sensitivity to a previously reported real-time RT-PCR assay and specific reactions to hMPV subgroups. The assay also showed no cross-reactivity to clinical isolates of 19 species of other respiratory viruses. In a validation assay using post-diagnosed clinical specimens, 98% (167/170) positivity was confirmed for the duplex assay, and the three specimens not detected were of low copy number. The duplex assay also successfully distinguished the two major subgroups for all 12 clinical specimens, for which the subgroup had already been determined by genomic sequencing analysis. The duplex assay described here will contribute to the rapid and accurate identification and surveillance of hMPV infections.
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Affiliation(s)
- Satoko Sugimoto
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan; Management Department of Biosafety, Laboratory Animals, and Pathogen Bank, National Institute of Infectious Disease, Musashimurayama, Tokyo, Japan
| | - Miyuki Kawase
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Reiko Suwa
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Masatoshi Kakizaki
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Yohei Kume
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Mina Chishiki
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Takashi Ono
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hisao Okabe
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Sakurako Norito
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Mitsuaki Hosoya
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Koichi Hashimoto
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Kazuya Shirato
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan.
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26
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Nguyen UD, Le Do Q, Vu QAN, Trieu NT, Dao TT, Van Le N, Nguyen ST, Hoang TT, Nguyen CT, Nguyen TH, Van Nguyen D, Ho TH. Selective detection of HBV pre-genomic RNA in chronic hepatitis B patients using a novel RT-PCR assay. Clin Exp Med 2023; 23:5281-5289. [PMID: 37572154 DOI: 10.1007/s10238-023-01162-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/31/2023] [Indexed: 08/14/2023]
Abstract
In chronic hepatitis B (CHB) patients, quantification of HBV pgRNA in plasma has the potential to provide information on disease prognosis and liver injury or histopathology. However, current methods for detecting HBV pgRNA present technical difficulties due to the co-existence of HBV DNA in plasma samples. We have successfully established a novel one-step RT-PCR assay that allows selective quantification of HBV pgRNA. Two cohorts of participants were recruited for assay validation, including treatment-naïve patients with CHB and HBeAg-positive CHB patients who were treated with Tenofovir and monitored for 6 months to assess the predictive value of baseline HBV RNA for HBeAg seroclearance. Statistical analysis was performed using MedCalc version 20.019 software. The novel selective one-step RT-PCR assay for detecting HBV pgRNA was validated with a limit of detection of 100 copies/mL. The assay was able to selectively measure HBV pgRNA even in the presence of excess HBV rcDNA. In treatment-naïve CHB patients, HBV pgRNA levels were significantly lower than HBV DNA concentration. Serum HBV DNA levels and HBeAg status were positively associated with HBV pgRNA. Baseline serum HBV pgRNA levels were found to be strong predictors of HBeAg seroclearance after 6 months of Tenofovir treatment. The study presents a novel RT-PCR assay that allows accurate measurement of plasma HBV pgRNA in chronic hepatitis B patients, even in the presence of excess HBV DNA. The assay is highly selective and represents a significant advancement with potential for further breakthroughs in understanding the clinical significance of HBV pgRNA.
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Affiliation(s)
- Ung Dinh Nguyen
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, Hanoi, Vietnam
| | - Quyen Le Do
- Department of Infectious Disease, 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Quynh Anh Nguyen Vu
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, Hanoi, Vietnam
| | - Nguyet Thi Trieu
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, Hanoi, Vietnam
| | - Trang Thuy Dao
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, Hanoi, Vietnam
| | - Nam Van Le
- Department of Infectious Disease, 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Son Thai Nguyen
- Department of Microbiology, 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
- Medical Testing Center, Medlatec Group, Hanoi, Vietnam
| | - Tuyen Tien Hoang
- Department of Infectious Disease, 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Chinh Trong Nguyen
- Department of Infectious Disease, 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Thang Hong Nguyen
- Outpatient Department, 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Dien Van Nguyen
- Department of Infectious Disease, 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Tho Huu Ho
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, Hanoi, Vietnam.
- Department of Microbiology, 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam.
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Van der Moeren N, Zwart VF, Louise van Leest M, Thijssen M, Groenewegen R, Heer MKD, Murk JL, Tjhie JT, Diederen BMW, Stohr JJJM. A SARS-CoV-2 and influenza rapid antigen test-based hospital isolation policy awaiting RT-PCR, a prospective observational study. Clin Microbiol Infect 2023; 29:1595-1599. [PMID: 37739262 DOI: 10.1016/j.cmi.2023.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/30/2023] [Accepted: 09/14/2023] [Indexed: 09/24/2023]
Abstract
OBJECTIVES This study aimed to evaluate the clinical performance of a combined SARS-CoV-2/influenza rapid antigen test (SIRAT) and to evaluate a SIRAT-based hospital isolation policy awaiting RT-PCR results for patients presenting at the emergency department (ED). METHODS We performed a prospective observational study including all adult patients presenting with influenza-like symptoms at the ED of two hospitals from 31 October 2022 to 31 March 2023. A SIRAT and SARS-CoV-2 and influenza RT-PCR were performed on upper respiratory samples. SIRAT results were compared with RT-PCR. Droplet and contact isolation measures (DCIM) were imposed based on SIRAT results awaiting RT-PCR. We monitored symptomatic nosocomial SARS-CoV-2 and influenza infections potentially caused by delayed isolation of patients with false negative SIRAT and the hours of unnecessary DCIM saved. RESULTS We included 1740 patients of whom 1296 were hospitalized. SARS-CoV-2 and influenza A/B prevalence were 12.7% (221/1740) and 9.9% (171/1740). Sensitivity and specificity of the SIRAT were 67.7% (95% CI 61.1-73.9%) (149/220) and 99.4% (95% CI 99.0-99.8%) (1510/1518) for SARS-CoV-2 and 52.7% (95% CI 44.9-60.4%) (89/169) and 99.1% (95% CI 98.5-99.5%) (1530/1544) for influenza A/B. We found a 0% nosocomial transmission risk for SARS-CoV-2 (95% CI 0-8.8%) and influenza (95% CI 0-10%). In all, 8712 hours in total or a median up to 6 hours 59 minutes (IQR (interquartile range) 11h03) per patient of unnecessary DCIM were saved. DISCUSSION A SIRAT-guided hospital isolation policy awaiting RT-PCR results for patients who present at the ED can save unnecessary isolation hours without having to lead to significant symptomatic nosocomial transmission of SARS-CoV-2 or influenza viruses.
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Affiliation(s)
- Nathalie Van der Moeren
- Department of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands; Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands.
| | - Vivian F Zwart
- Department of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands; Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Marie Louise van Leest
- Emergency Department, Bravis Hospital, Roosendaal, The Netherlands; Emergency Department, Bravis Hospital, Bergen op Zoom, The Netherlands
| | - Marcel Thijssen
- Emergency Department, Bravis Hospital, Roosendaal, The Netherlands
| | | | | | - Jean-Luc Murk
- Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Jeroen T Tjhie
- Department of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Bram M W Diederen
- Microvida, Laboratory of Medical Microbiology, Bravis Hospital, Roosendaal, The Netherlands
| | - Joep J J M Stohr
- Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
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Fortin A, Laconi A, Monne I, Zohari S, Andersson K, Grund C, Cecchinato M, Crimaudo M, Valastro V, D'Amico V, Bortolami A, Gastaldelli M, Varotto M, Terregino C, Panzarin V. A novel array of real-time RT-PCR assays for the rapid pathotyping of type I avian paramyxovirus (APMV-1). J Virol Methods 2023; 322:114813. [PMID: 37722509 DOI: 10.1016/j.jviromet.2023.114813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023]
Abstract
Newcastle disease (ND) caused by virulent avian paramyxovirus type I (APMV-1) is a WOAH and EU listed disease affecting poultry worldwide. ND exhibits different clinical manifestations that may either be neurological, respiratory and/or gastrointestinal, accompanied by high mortality. In contrast, mild or subclinical forms are generally caused by lentogenic APMV-1 and are not subject to notification. The rapid discrimination of virulent and avirulent viruses is paramount to limit the spread of virulent APMV-1. The appropriateness of molecular methods for APMV-1 pathotyping is often hampered by the high genetic variability of these viruses that affects sensitivity and inclusivity. This work presents a new array of real-time RT-PCR (RT-qPCR) assays that enable the identification of virulent and avirulent viruses in dual mode, i.e., through pathotype-specific probes and subsequent Sanger sequencing of the amplification product. Validation was performed according to the WOAH recommendations. Performance indicators on sensitivity, specificity, repeatability and reproducibility yielded favourable results. Reproducibility highlighted the need for assays optimization whenever major changes are made to the procedure. Overall, the new RT-qPCRs showed its ability to detect and pathotype all tested APMV-1 genotypes and its suitability for routine use in clinical samples.
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Affiliation(s)
- Andrea Fortin
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy; Department of Animal Medicine, Production and Health, University of Padua (Unipd), 35020 Legnaro, Italy
| | - Andrea Laconi
- Department of Comparative Biomedicine and Food Science, University of Padua (Unipd), 35020 Legnaro, Italy
| | - Isabella Monne
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Siamak Zohari
- Department of Microbiology, Swedish National Veterinary Institute (SVA), SE751 89 Uppsala, Sweden
| | - Kristofer Andersson
- Department of Microbiology, Swedish National Veterinary Institute (SVA), SE751 89 Uppsala, Sweden
| | - Christian Grund
- Institute of Diagnostic Virology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut (FLI), 17493 Greifswald-Insel Riems, Germany
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health, University of Padua (Unipd), 35020 Legnaro, Italy
| | - Marika Crimaudo
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Viviana Valastro
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Valeria D'Amico
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Alessio Bortolami
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Michele Gastaldelli
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Maria Varotto
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Calogero Terregino
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy
| | - Valentina Panzarin
- EU/WOAH/National Reference Laboratory for Avian Influenza and Newcastle Disease, FAO Reference Centre for Animal Influenza and Newcastle Disease, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 35020 Legnaro, Italy.
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Lee DH, Han E, Ryu S, Choi HJ, Kim J, Kim J, Bae MH. Clinical performance of the STANDARD M10 SARS-CoV-2 rapid RT-PCR assay in patients visiting an emergency department. J Med Virol 2023; 95:e29330. [PMID: 38117224 DOI: 10.1002/jmv.29330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
In emergency departments, rapid screening of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was important for arranging limited isolation resources and patient care during the coronavirus disease 2019 (COVID-19) pandemic. STANDARD M10 SARS-CoV-2 (SD Biosensor) is a recently developed cartridge-based RT-PCR that provides a turnaround time of 1 h, which is shorter than that for conventional RT-PCR. This study evaluated the clinical performance of STANDARD M10 in patients visiting an emergency department. From March to June 2022, two specimens were collected from patients visiting an emergency department. Each specimen comprised one nasopharyngeal and one oropharyngeal swab. Respective specimens underwent rapid RT-PCR using STANDARD M10 and conventional RT-PCR using Allplex SARS-CoV-2 (Seegene). When discordant results occurred, specimens undergoing the STANDARD M10 were retested with the Allplex to exclude specimen variations. Retest results replaced initial results of the Allplex. Clinical performance of STANDARD M10 was compared with Allplex. The study enrolled 1971 patients. COVID-19 prevalence was 6.2% based on the Allplex. Compared with the Allplex, overall agreement, positive percent agreement, and negative percent agreement of STANDARD M10 were 99.5% (95% CI: 99.1%-99.8%), 95.9% (95% CI: 90.8%-98.3%), and 99.8% (95% CI: 99.4%-99.9%), respectively. Nine discordant results were all positive on droplet digital PCR, except for one specimen that was positive with STANDARD M10. The STANDARD M10 showed reliable diagnostic performance for detecting SARS-CoV-2 from patients visiting in emergency departments and is a useful tool in emergency healthcare systems because of its easy-to-use cartridge-based assay and short resulting time for detecting SARS-CoV-2.
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Affiliation(s)
- Dong-Hyun Lee
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Jinju, South Korea
| | - Eunhee Han
- Department of Laboratory Medicine, Daejeon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Soorack Ryu
- Biostatistical Consulting and Research Laboratory, Medical Research Collaborating Center, Hanyang University, Seoul, South Korea
| | - Hyuk Joong Choi
- Department of Emergency Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Jieun Kim
- Department of Internal Medicine, Division of Infectious Disease, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Jinyeong Kim
- Department of Internal Medicine, Division of Infectious Disease, Hanyang University Guri Hospital, Guri, South Korea
| | - Mi Hyun Bae
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
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30
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Ruan M, Zhang LL, Li YM, Li DY, Yuan ZY, Zheng ZZ, Zeng QS. [Detection of BCR-ABL Fusion Gene in Chronic Myeloid Leukemia by Novel Digital PCR]. Zhongguo Shi Yan Xue Ye Xue Za Zhi 2023; 31:1647-1656. [PMID: 38071041 DOI: 10.19746/j.cnki.issn.1009-2137.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
OBJECTIVE To establish a new digital polymerase chain reaction (dPCR) system for the detection of BCR-ABL fusion gene in patients with chronic myeloid leukemia (CML), and explore its analytical performance and clinical applicability in the detection of BCR-ABLp190/210/230. METHODS A new dPCR system for detecting BCR-ABLp190/210/230 was successfully developed, and its sensitivity difference with qPCR and improvement of drug side effects in patients with CML during drug reduction or withdrawal were compared. RESULTS Among 176 samples, qPCR and dPCR showed high consistency in the sensitivity of detecting BCR-ABL (82.39%), and the positive rate of dPCR was about 5 times higher that of qPCR (20.45% vs 3.98%). During follow-up, blood routine (25% vs 10%), kidney/liver/stomach (25% vs 20%) and cardiac function (10% vs 0) were significantly improved after drug reduction or withdrawal in patients with initial dPCR negative compared with before drug reduction or withdrawal. CONCLUSIONS This new dPCR detection system can be applied to the detection of BCR-ABLp190/210/230. It has better consistency and higher positive detection rate than qPCR. Drug withdrawal or dose reduction guided by dPCR has a certain effect on improving drug side effects.
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Affiliation(s)
- Min Ruan
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui Province, China
| | - Li-Li Zhang
- Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai 201318, China
| | - Ye-Mo Li
- Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai 201318, China
| | - Dai-Yang Li
- Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai 201318, China
| | - Zhi-Yang Yuan
- Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai 201318, China
| | | | - Qing-Shu Zeng
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui Province, China.E-mail:
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31
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Sawada H, Mase K, Koyama R, Suenaga A. Inhibitory Effect on RT-PCR and Restriction Enzyme Activity by Ommochrome and Its Mechanism. Zoolog Sci 2023; 40:431-436. [PMID: 38064369 DOI: 10.2108/zs230068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/20/2023] [Indexed: 12/18/2023]
Abstract
To explore the physiological role and/or pharmacological effects of ommochrome, which is a natural organic pigment widely distributed in Protostomia, we attempted to investigate the influence of ommochrome on RT-PCR and activities of restriction enzymes. It was found that ommin, an ommochrome purified from the diapause eggs of Bombyx mori, inhibited the RT-PCR and restriction enzyme activities. The mechanism of these inhibitory reactions is assumed to be the direct binding of ommochrome to DNA rather than acting against the enzymes because, similarly to actinomycin D, there is a phenoxazine ring in the structure of ommin that is known to be intercalated to DNA. To reveal the ommin/DNA interaction, it was investigated by computational approaches such as molecular docking, molecular dynamics simulation, and free energy calculation. From the computational analyses, it was expected that ommin would bind to DNA with almost the same strength as actinomycin D and intercalate into DNA. This is the first report on the pharmacological effect of ommochrome and its inhibitory mechanism obtained from biochemical and computational analyses.
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Affiliation(s)
- Hiroshi Sawada
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Setagaya-ku, Tokyo 156-8550, Japan,
| | - Keisuke Mase
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Setagaya-ku, Tokyo 156-8550, Japan
| | - Rimi Koyama
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Setagaya-ku, Tokyo 156-8550, Japan
| | - Atsushi Suenaga
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Setagaya-ku, Tokyo 156-8550, Japan
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32
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Ferguson JD, Tayyar R, Contreras G, Kiener M, Zimmet AN, Contag CA, Rodriguez Nava G, Tompkins LS, Shepard J, Rosenthal A, Subramanian AK, Pinsky BA, Salinas JL. Use of a severe acute respiratory coronavirus virus 2 (SARS-CoV-2) strand-specific assay to evaluate for prolonged viral replication >20 days from illness onset. Infect Control Hosp Epidemiol 2023; 44:2078-2080. [PMID: 37381726 DOI: 10.1017/ice.2023.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) real-time reverse-transcription polymerase chain reaction (rRT-PCR) strand-specific assay can be used to identify active SARS-CoV-2 viral replication. We describe the characteristics of 337 hospitalized patients with at least 1 minus-strand SARS-CoV-2 assay performed >20 days after illness onset. This test is a novel tool to identify high-risk hospitalized patients with prolonged SARS-CoV-2 replication.
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Affiliation(s)
- Jessica D Ferguson
- Stanford University School of Medicine and Stanford Hospital & Clinics, Stanford, California
| | - Ralph Tayyar
- Stanford University School of Medicine and Stanford Hospital & Clinics, Stanford, California
| | - Gustavo Contreras
- Stanford University School of Medicine and Stanford Hospital & Clinics, Stanford, California
| | - Melanie Kiener
- Stanford University School of Medicine and Stanford Hospital & Clinics, Stanford, California
| | - Alex N Zimmet
- Stanford University School of Medicine and Stanford Hospital & Clinics, Stanford, California
| | - Caitlin A Contag
- Stanford University School of Medicine and Stanford Hospital & Clinics, Stanford, California
| | | | - Lucy S Tompkins
- Stanford University School of Medicine and Stanford Hospital & Clinics, Stanford, California
| | - John Shepard
- Stanford University School of Medicine and Stanford Hospital & Clinics, Stanford, California
| | - Ayelet Rosenthal
- Stanford University School of Medicine and Stanford Hospital & Clinics, Stanford, California
| | - Aruna K Subramanian
- Stanford University School of Medicine and Stanford Hospital & Clinics, Stanford, California
| | - Benjamin A Pinsky
- Stanford University School of Medicine and Stanford Hospital & Clinics, Stanford, California
| | - Jorge L Salinas
- Stanford University School of Medicine and Stanford Hospital & Clinics, Stanford, California
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Punia M, Maan S, Batra K, Chaudhary D, Devi B, Kumar A, Gahlawat SK, Maan NS. Development of real-time RT-PCR systems for detection and quantitation of bovine enteric viral pathogens. Anim Biotechnol 2023; 34:4658-4666. [PMID: 38347693 DOI: 10.1080/10495398.2023.2182314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The enteric viruses in animals are responsible for severe and devastating losses to the livestock owners with a profound negative impact on animal, health, welfare, and productivity. These viruses are usually transmitted via the feco-oral route and primarily infect the digestive tract of the humans, bovines and different mammals as well as birds. Some of the important enteric viruses in ruminants are: Rotavirus A (RVA), Peste des petits virus (PPRV), Norovirus (NV), Bovine corona virus (BoCV) and Bluetongue virus (BTV). In the present study, sensitive, specific and reliable TaqMan probe-based RT-qPCRs were developed and standardized for the rapid detection and quantification of enteric viruses from fecal samples. The assays result in efficient amplification of the RVA, BTV and BoCV RNA with a limit of detection (LoD) of 5, 5 and 4 copies, respectively, which is 1000 times more sensitive than the traditional gel-based RT-PCR. The reproducibility of each assay was satisfactory, thus allowing for a sensitive and accurate measurement of the viral RNA load in clinical samples. In conclusion, real time PCR developed for these viruses are highly specific and sensitive technique for the detection of diarrheic viral pathogens of cattle and buffalo.
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Affiliation(s)
- Monika Punia
- Department of Biotechnology, Ch. Devi Lal University, Sirsa, India
| | - Sushila Maan
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | - Kanisht Batra
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | - Deepika Chaudhary
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | - Bhanita Devi
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | - Aman Kumar
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | | | - Narender Singh Maan
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
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Srivastava P, Prasad D. Human Norovirus Detection: How Much Are We Prepared? Foodborne Pathog Dis 2023; 20:531-544. [PMID: 37792418 DOI: 10.1089/fpd.2023.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
Norovirus (NoV) is known to be the second nonbacterial enteric pathogen after rotavirus that causes acute gastroenteritis. They can be spread from person to person through fecal-oral routes. Infection can lead to severe diarrhea, causing stomach pain, vomiting, and nausea. Rapid detection of NoV can control huge economic and productive losses. Genotyping various emerging NoV strains is important to compare the severity among different strains. Conventional immunological and molecular methods have evolved and contributed to developing detection techniques. Immunological (enzyme-linked immunosorbent assay) and molecular detection (reverse transcriptase polymerase chain reaction [RT-PCR], RT-quantitative PCR, loop-mediated isothermal amplification, nucleic acid sequence-based alignment, recombinase polymerase amplification) methods have been mainly used. The development of biosensors using aptasensor, affinity peptides, nanoparticles, microfluidics, and so on, are currently the most researched topics. The availability of next-generation sequencing technologies has greatly influenced the diagnosis of NoV. The complementation of advanced technologies is helpful in identification of new variants. In this study, techniques that are useful in detecting NoV are discussed. This review has investigated the availability of recent methods used in the detection, present status, and futuristic plan of action in case of outbreak and pandemic.
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Affiliation(s)
- Pulkit Srivastava
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
| | - Dinesh Prasad
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
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35
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Onwuchekwa C, Atwell J, Moreo LM, Menon S, Machado B, Siapka M, Agarwal N, Rubbrecht M, Aponte-Torres Z, Rozenbaum M, Curcio D, Nair H, Kalina WV, Vroling H, Gessner B, Begier E. Pediatric Respiratory Syncytial Virus Diagnostic Testing Performance: A Systematic Review and Meta-analysis. J Infect Dis 2023; 228:1516-1527. [PMID: 37285396 PMCID: PMC10681870 DOI: 10.1093/infdis/jiad185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/11/2023] [Accepted: 06/06/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Adding additional specimen types (eg, serology or sputum) to nasopharyngeal swab (NPS) reverse transcription polymerase chain reaction (RT-PCR) increases respiratory syncytial virus (RSV) detection among adults. We assessed if a similar increase occurs in children and quantified underascertainment associated with diagnostic testing. METHODS We searched databases for studies involving RSV detection in persons <18 years using ≥2 specimen types or tests. We assessed study quality using a validated checklist. We pooled detection rates by specimen and diagnostic tests and quantified performance. RESULTS We included 157 studies. Added testing of additional specimens to NP aspirate (NPA), NPS, and/or nasal swab (NS) RT-PCR resulted in statistically nonsignificant increases in RSV detection. Adding paired serology testing increased RSV detection by 10%, NS by 8%, oropharyngeal swabs by 5%, and NPS by 1%. Compared to RT-PCR, direct fluorescence antibody tests, viral culture, and rapid antigen tests were 87%, 76%, and 74% sensitive, respectively (pooled specificities all ≥98%). Pooled sensitivity of multiplex versus singleplex RT-PCR was 96%. CONCLUSIONS RT-PCR was the most sensitive pediatric RSV diagnostic test. Adding multiple specimens did not substantially increase RSV detection, but even small proportional increases could result in meaningful changes in burden estimates. The synergistic effect of adding multiple specimens should be evaluated.
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Affiliation(s)
| | | | | | - Sonia Menon
- P95 Epidemiology and Pharmacovigilance, Leuven, Belgium
| | - Belen Machado
- P95 Epidemiology and Pharmacovigilance, Leuven, Belgium
| | - Mariana Siapka
- P95 Epidemiology and Pharmacovigilance, Leuven, Belgium
- Impact Epilysis, Thessaloniki, Greece
| | - Neha Agarwal
- P95 Epidemiology and Pharmacovigilance, Leuven, Belgium
| | | | | | | | | | - Harish Nair
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Hilde Vroling
- P95 Epidemiology and Pharmacovigilance, Leuven, Belgium
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36
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Baggio F, Hetzel U, Prähauser B, Dervas E, Michalopoulou E, Thiele T, Kipar A, Hepojoki J. A Multiplex RT-PCR Method for the Detection of Reptarenavirus Infection. Viruses 2023; 15:2313. [PMID: 38140554 PMCID: PMC10747477 DOI: 10.3390/v15122313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Reptarenaviruses cause Boid Inclusion Body Disease (BIBD), a fatal disease of boid snakes with an economic and ecological impact, as it affects both captive and wild constrictor snakes. The clinical picture of BIBD is highly variable but often only limited. Intracytoplasmic inclusion bodies (IB), which develop in most cell types including blood cells, are the pathognomonic hallmark of BIBD; their detection represents the diagnostic gold standard of the disease. However, IBs are not consistently present in clinically healthy reptarenavirus carriers, which can, if undetected, lead to and maintain the spread of the disease within and between snake populations. Sensitive viral detection tools are required for screening and control purposes; however, the genetic diversity of reptarenaviruses hampers the reverse transcription (RT) PCR-based diagnostics. Here, we describe a multiplex RT-PCR approach for the molecular diagnosis of reptarenavirus infection in blood samples. The method allows the detection of a wide range of reptarenaviruses with the detection limit reaching 40 copies per microliter of blood. Using 245 blood samples with a reference RT-PCR result, we show that the technique performs as well as the segment-specific RT-PCRs in our earlier studies. It can identify virus carriers and serve to limit reptarenavirus spreading in captive snake collections.
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Affiliation(s)
- Francesca Baggio
- The BIBD Group and Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; (U.H.); (B.P.); (E.D.); (E.M.); (T.T.); (A.K.); (J.H.)
- Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Udo Hetzel
- The BIBD Group and Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; (U.H.); (B.P.); (E.D.); (E.M.); (T.T.); (A.K.); (J.H.)
| | - Barbara Prähauser
- The BIBD Group and Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; (U.H.); (B.P.); (E.D.); (E.M.); (T.T.); (A.K.); (J.H.)
- Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Eva Dervas
- The BIBD Group and Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; (U.H.); (B.P.); (E.D.); (E.M.); (T.T.); (A.K.); (J.H.)
| | - Eleni Michalopoulou
- The BIBD Group and Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; (U.H.); (B.P.); (E.D.); (E.M.); (T.T.); (A.K.); (J.H.)
| | - Tanja Thiele
- The BIBD Group and Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; (U.H.); (B.P.); (E.D.); (E.M.); (T.T.); (A.K.); (J.H.)
| | - Anja Kipar
- The BIBD Group and Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; (U.H.); (B.P.); (E.D.); (E.M.); (T.T.); (A.K.); (J.H.)
| | - Jussi Hepojoki
- The BIBD Group and Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; (U.H.); (B.P.); (E.D.); (E.M.); (T.T.); (A.K.); (J.H.)
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
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Kang M, Jeong E, Kim JY, Yun SA, Jang MA, Jang JH, Kim TY, Huh HJ, Lee NY. Optimization of extraction-free protocols for SARS-CoV-2 detection using a commercial rRT-PCR assay. Sci Rep 2023; 13:20364. [PMID: 37990045 PMCID: PMC10663557 DOI: 10.1038/s41598-023-47645-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023] Open
Abstract
In the ongoing global fight against coronavirus disease 2019 (COVID-19), the sample preparation process for real-time reverse transcription polymerase chain reaction (rRT-PCR) faces challenges due to time-consuming steps, labor-intensive procedures, contamination risks, resource demands, and environmental implications. However, optimized strategies for sample preparation have been poorly investigated, and the combination of RNase inhibitors and Proteinase K has been rarely considered. Hence, we investigated combinations of several extraction-free protocols incorporating heat treatment, sample dilution, and Proteinase K and RNase inhibitors, and validated the effectiveness using 120 SARS-CoV-2 positive and 62 negative clinical samples. Combining sample dilution and heat treatment with Proteinase K and RNase inhibitors addition exhibited the highest sensitivity (84.26%) with a mean increase in cycle threshold (Ct) value of + 3.8. Meanwhile, combined sample dilution and heat treatment exhibited a sensitivity of 79.63%, accounting for a 38% increase compared to heat treatment alone. Our findings highlight that the incorporation of Proteinase K and RNase inhibitors with sample dilution and heat treatment contributed only marginally to the improvement without yielding statistically significant differences. Sample dilution significantly impacts SARS-CoV-2 detection, and sample conditions play a crucial role in the efficiency of extraction-free methods. Our findings may provide insights for streamlining diagnostic testing, enhancing its accessibility, cost-effectiveness, and sustainability.
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Affiliation(s)
- Minhee Kang
- Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, Seoul, South Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea
| | - Eunjung Jeong
- Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, Seoul, South Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea
| | - Ji-Yeon Kim
- Samsung Biomedical Research Institute, Center for Clinical Medicine, Samsung Medical Center, Seoul, South Korea
| | - Sun Ae Yun
- Samsung Biomedical Research Institute, Center for Clinical Medicine, Samsung Medical Center, Seoul, South Korea
| | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Hee Jae Huh
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea.
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Delamare-Deboutteville J, Meemetta W, Pimsannil K, Sangpo P, Gan HM, Mohan CV, Dong HT, Senapin S. A multiplexed RT-PCR assay for nanopore whole genome sequencing of Tilapia lake virus (TiLV). Sci Rep 2023; 13:20276. [PMID: 37985860 PMCID: PMC10661697 DOI: 10.1038/s41598-023-47425-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023] Open
Abstract
Tilapia lake virus (TiLV) is a highly contagious viral pathogen that affects tilapia, a globally significant and affordable source of fish protein. To prevent the introduction and spread of TiLV and its impact, there is an urgent need for increased surveillance, improved biosecurity measures, and continuous development of effective diagnostic and rapid sequencing methods. In this study, we have developed a multiplexed RT-PCR assay that can amplify all ten complete genomic segments of TiLV from various sources of isolation. The amplicons generated using this approach were immediately subjected to real-time sequencing on the Nanopore system. By using this approach, we have recovered and assembled 10 TiLV genomes from total RNA extracted from naturally TiLV-infected tilapia fish, concentrated tilapia rearing water, and cell culture. Our phylogenetic analysis, consisting of more than 36 TiLV genomes from both newly sequenced and publicly available TiLV genomes, provides new insights into the high genetic diversity of TiLV. This work is an essential steppingstone towards integrating rapid and real-time Nanopore-based amplicon sequencing into routine genomic surveillance of TiLV, as well as future vaccine development.
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Affiliation(s)
| | - Watcharachai Meemetta
- Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
| | - Khaettareeya Pimsannil
- Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
| | - Pattiya Sangpo
- Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
| | - Han Ming Gan
- Patriot Biotech Sdn Bhd, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | | | - Ha Thanh Dong
- School of Environment, Resources and Development, Asian Institute of Technology, Pathum Thani, 12120, Thailand
| | - Saengchan Senapin
- Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand.
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
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Tscherner AK, McClatchie T, Macaulay AD, Baltz JM. Relationship of quantitative reverse transcription polymerase chain reaction (RT-PCR) to RNA Sequencing (RNAseq) transcriptome identifies mouse preimplantation embryo reference genes†. Biol Reprod 2023; 109:601-617. [PMID: 37669129 PMCID: PMC10651071 DOI: 10.1093/biolre/ioad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/04/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023] Open
Abstract
Numerous reference genes for use with quantitative reverse transcription polymerase chain reaction (RT-qPCR) have been used for oocytes, eggs, and preimplantation embryos. However, none are actually suitable because of their large variations in expression between developmental stages. To address this, we produced a standardized and merged RNA sequencing (RNAseq) data set by combining multiple publicly available RNAseq data sets that spanned mouse GV oocytes, MII eggs, and 1-cell, 2-cell, 4-cell, 8-cell, morula, and blastocyst stage embryos to identify transcripts with essentially constant expression across all stages. Their expression was then measured using RT-qPCR, with which they did not exhibit constant expression but instead revealed a fixed quantitative relationship between measurements by the two techniques. From this, the relative amounts of total messenger RNA at each stage from the GV oocyte through blastocyst stages were calculated. The quantitative relationship between measurements by RNAseq and RT-qPCR was then used to find genes predicted to have constant expression across stages in RT-qPCR. Candidates were assessed by RT-qPCR to confirm constant expression, identifying Hmgb3 and Rb1cc1 or the geometric mean of those plus either Taf1d or Cd320 as suitable reference genes. This work not only identified transcripts with constant expression from mouse GV oocytes to blastocysts, but also determined a general quantitative relationship between expression measured by RNAseq and RT-qPCR across stages that revealed the relative levels of total mRNA at each stage. The standardized and merged RNA data set should also prove useful in determining transcript expression in mouse oocytes, eggs, and embryos.
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Affiliation(s)
- Allison K Tscherner
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Obstetrics and Gynecology, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
| | - Taylor McClatchie
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Obstetrics and Gynecology, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
| | | | - Jay M Baltz
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Obstetrics and Gynecology, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
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40
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Alewaidat H, Bataineh Z, Bani-Ahmad M, Alali M, Almakhadmeh A. Investigation of the diagnostic importance and accuracy of CT in the chest compared to the RT-PCR test for suspected COVID-19 patients in Jordan. F1000Res 2023; 12:741. [PMID: 37822316 PMCID: PMC10562777 DOI: 10.12688/f1000research.130388.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/09/2023] [Indexed: 10/13/2023] Open
Abstract
This article aims to synthesize the existing literature on the implementation of public policies to incentivize the development of treatments for rare diseases, (diseases with very low prevalence and therefore with low commercial interest) otherwise known as orphan drugs. The implementation of these incentives in the United States (US), Japan, and in the European Union (EU) seems to be related to a substantial increase in treatments for these diseases, and has influenced the way the pharmaceutical research & development (R&D) system operates beyond this policy area. Despite the success of the Orphan Drug model, the academic literature also highlights the negative implications that these public policies have on affordability and access to orphan drugs, as well as on the prioritization of certain disease rare areas over others. The synthesis focuses mostly on the United States' Orphan Drug Act (ODA) as a model for subsequent policies in other regions and countries. It starts with a historical overview of the creation of the term "rare diseases", continues with a summary of the evidence available on the US ODA's positive and negative impacts, and provides a summary of the different proposals to reform these incentives in light of the negative outcomes described. Finally, it describes some key aspects of the Japanese and European policies, as well as some of the challenges captured in the literature related to their impact in Low- and Middle-Income Countries (LMICs).
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Affiliation(s)
- Haytham Alewaidat
- Applied Medical Sciences, Jordan University of Science and Technology, irbid, 22110, Jordan
| | - Ziad Bataineh
- Anatomy, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Mohammad Bani-Ahmad
- Medical Laboratory Science, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Manar Alali
- Medical Laboratory Science, Zarqa University, Zarqa, Jordan
| | - Ali Almakhadmeh
- Radiologic Technology, Jordan University of Science and Technology, Irbid, 22110, Jordan
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Rawal G, Krueger KM, Yim-im W, Li G, Gauger PC, Almeida MN, Aljets EK, Zhang J. Development, Evaluation, and Clinical Application of PRRSV-2 Vaccine-like Real-Time RT-PCR Assays. Viruses 2023; 15:2240. [PMID: 38005917 PMCID: PMC10675446 DOI: 10.3390/v15112240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
In this study, we developed and validated (1) singleplex real-time RT-PCR assays for specific detection of five PRRSV-2 MLV vaccine viruses (Ingelvac MLV, Ingelvac ATP, Fostera, Prime Pac, and Prevacent) and (2) a four-plex real-time RT-PCR assay (IngelvacMLV/Fostera/Prevacent/XIPC) including the internal positive control XIPC for detecting and distinguishing the three most commonly used vaccines in the USA (Prevacent, Ingelvac MLV, and Fostera). The singleplex and 4-plex vaccine-like PCRs and the reference PCR (VetMAXTM PRRSV NA&EU, Thermo Fisher Scientific, Waltham, MA, USA) did not cross-react with non-PRRSV swine viral and bacterial pathogens. The limits of detection of vaccine-like PCRs ranged from 25 to 50 genomic copies/reactions. The vaccine-like PCRs all had excellent intra-assay and inter-assay repeatability. Based on the testing of 531 clinical samples and in comparison to the reference PCR, the diagnostic sensitivity, specificity, and agreement were in the respective range of 94.67-100%, 100%, and 97.78-100% for singleplex PCRs and 94.94-100%, 100%, and 97.78-100% for the 4-plex PCR, with a CT cutoff of 37. In addition, 45 PRRSV-2 isolates representing different genetic lineages/sublineages were tested with the vaccine-like PCRs and the results were verified with sequencing. In summary, the vaccine-like PCRs specifically detect the respective vaccine-like viruses with comparable performances to the reference PCR, and the 4-plex PCR allows to simultaneously detect and differentiate the three most commonly used vaccine viruses in the same sample. PRRSV-2 vaccine-like PCRs provide an additional tool for detecting and characterizing PRRSV-2.
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Affiliation(s)
| | | | | | | | | | | | | | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (K.M.K.); (W.Y.-i.); (G.L.); (P.C.G.); (M.N.A.); (E.K.A.)
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42
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Da Silva L, Klopfenstein T, Gendrin V, Clouet J, Toko L, Richier Q, Leriche T, Nicolas R, Queijo A, Sreiri N, Lacombe K, Zayet S. Prolonged SARS-CoV-2 Infection in Patients Receiving Anti-CD20 Monoclonal Antibodies: A Diagnostic Challenged by Negative Nasopharyngeal RT-PCR and Successful Treatment with COVID-19 High-Titer Convalescent Plasma. Viruses 2023; 15:2220. [PMID: 38005897 PMCID: PMC10675708 DOI: 10.3390/v15112220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 10/29/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
We highlighted in this current paper similar prolonged respiratory presentation with COVID-19 pneumonia in four severely immunocompromised patients currently being treated with anti-CD20 monoclonal antibodies (mAbs), such as ocrelizumab and rituximab, for multiple sclerosis or rheumatoid polyarthritis. Real-time reverse transcription-polymerase chain reaction on a nasopharyngeal swab specimen was negative in all patients. SARS-CoV-2 infection was confirmed from bronchoalveolar lavage fluid. A high titer of post-vaccine COVID-19 convalescent plasma was administered with complete recovery in all patients.
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Affiliation(s)
- Léa Da Silva
- Infectious Diseases Department, Nord Franche-Comté Hospital, 90400 Trevenans, France; (L.D.S.); (V.G.); (L.T.); (A.Q.); (N.S.)
| | - Timothée Klopfenstein
- Infectious Diseases Department, Nord Franche-Comté Hospital, 90400 Trevenans, France; (L.D.S.); (V.G.); (L.T.); (A.Q.); (N.S.)
| | - Vincent Gendrin
- Infectious Diseases Department, Nord Franche-Comté Hospital, 90400 Trevenans, France; (L.D.S.); (V.G.); (L.T.); (A.Q.); (N.S.)
| | - Julien Clouet
- Infectious Diseases Department, Nord Franche-Comté Hospital, 90400 Trevenans, France; (L.D.S.); (V.G.); (L.T.); (A.Q.); (N.S.)
| | - Lynda Toko
- Infectious Diseases Department, Nord Franche-Comté Hospital, 90400 Trevenans, France; (L.D.S.); (V.G.); (L.T.); (A.Q.); (N.S.)
| | - Quentin Richier
- Infectious Diseases Department, Assistance Publique Hopitaux de Paris, Saint-Antoine Hospital, 75012 Paris, France; (Q.R.)
| | - Thomas Leriche
- Rheumatology Department, Nord Franche-Comte Hospital, 90400 Trevenans, France;
| | - Raoul Nicolas
- Pneumologie Department, Nord Franche-Comte Hospital, 90400 Trevenans, France;
| | - Alexis Queijo
- Infectious Diseases Department, Nord Franche-Comté Hospital, 90400 Trevenans, France; (L.D.S.); (V.G.); (L.T.); (A.Q.); (N.S.)
| | - Nour Sreiri
- Infectious Diseases Department, Nord Franche-Comté Hospital, 90400 Trevenans, France; (L.D.S.); (V.G.); (L.T.); (A.Q.); (N.S.)
| | - Karine Lacombe
- Infectious Diseases Department, Assistance Publique Hopitaux de Paris, Saint-Antoine Hospital, 75012 Paris, France; (Q.R.)
- INSERM, Pierre Louis Institute of Epidemiology and Public Health (IPLESP), Sorbonne University, 75646 Paris, France
| | - Souheil Zayet
- Infectious Diseases Department, Nord Franche-Comté Hospital, 90400 Trevenans, France; (L.D.S.); (V.G.); (L.T.); (A.Q.); (N.S.)
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Pratt GW, Rao LV. Comparison of SARS-CoV-2 RT-PCR Ct Values across Multiple Assays with Different Targets. J Appl Lab Med 2023; 8:1193-1195. [PMID: 37610414 DOI: 10.1093/jalm/jfad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/28/2023] [Indexed: 08/24/2023]
Affiliation(s)
- George W Pratt
- Quest Diagnostics, North Region, Marlborough, MA, United States
| | - Lokinendi V Rao
- Quest Diagnostics, North Region, Marlborough, MA, United States
- UMass Chan Medical School, Pathology, Worcester, MA, United States
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Kim TK, Waldman J, Ibanez-Carrasco F, Tirloni L, Waltero C, Calixo C, Braz GR, Mulenga A, da Silva Vaz Junior I, Logullo C. Stable internal reference genes for quantitative RT-PCR analyses in Rhipicephalus microplus during embryogenesis. Ticks Tick Borne Dis 2023; 14:102251. [PMID: 37708803 PMCID: PMC10555470 DOI: 10.1016/j.ttbdis.2023.102251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023]
Abstract
Studies on the transcriptional control of gene expression are crucial to understand changes in organism's physiological or cellular conditions. To obtain reliable data on mRNA amounts and the estimation of gene expression levels, it is crucial to normalize the target gene with one or more internal reference gene(s). However, the use of constitutive genes as reference genes is controversial, as their expression patterns are sometimes more complex than previously thought. In various arthropod vectors, including ticks, several constitutive genes have been identified by studying gene expression in different tissues and life stages. The cattle tick Rhipicephalus microplus is a major vector for several pathogens and is widely distributed in tropical and subtropical regions globally. Tick developmental physiology is an essential aspect of research, particularly embryogenesis, where many important developmental events occur, thus the identification of stable reference genes is essential for the interpretation of reliable gene expression data. This study aimed to identify and select R. microplus housekeeping genes and evaluate their stability during embryogenesis. Reference genes used as internal control in molecular assays were selected based on previous studies. These genes were screened by quantitative PCR (qPCR) and tested for gene expression stability during embryogenesis. Results demonstrated that the relative stability of reference genes varied at different time points during the embryogenesis. The GeNorm tool showed that elongation factor 1α (Elf1a) and ribosomal protein L4 (Rpl4) were the most stable genes, while H3 histone family 3A (Hist3A) and ribosomal protein S18 (RpS18) were the least stable. The NormFinder tool showed that Rpl4 was the most stable gene, while the ranking of Elf1a was intermediate in all tested conditions. The BestKeeper tool showed that Rpl4 and cyclophilin A (CycA) were the more and less stable genes, respectively. These data collectively demonstrate that Rpl4, Elf1a, and GAPDH are suitable internal controls for normalizing qPCR during R. microplus embryogenesis. These genes were consistently identified as the most stable in various analysis methods employed in this study. Thus, findings presented in this study offer valuable information for the study of gene expression during embryogenesis in R. microplus.
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Affiliation(s)
- Tae Kwon Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; Laboratório de Bioquímica de Artrópodes Hematófagos, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Jéssica Waldman
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Freddy Ibanez-Carrasco
- Department of Entomology, Minnie Bell Heep Center, Texas A&M University, Suite 412, 2475 TAMU, 370 Olsen Blvd, College Station, TX, USA; Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX 78596, USA
| | - Lucas Tirloni
- Tick-Pathogen Transmission Unit, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Camila Waltero
- Laboratório de Bioquímica de Artrópodes Hematófagos, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Christiano Calixo
- Laboratório de Bioquímica de Artrópodes Hematófagos, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Gloria R Braz
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, RJ, Brazil
| | - Albert Mulenga
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
| | - Itabajara da Silva Vaz Junior
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, RJ, Brazil; Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Carlos Logullo
- Laboratório de Bioquímica de Artrópodes Hematófagos, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, RJ, Brazil,; Instituto Nacional de Ciência e Tecnologia - Entomologia Molecular, Rio de Janeiro, RJ, Brazil
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45
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Wang HB, Du T, Lin JH, Chen XB, Tu CN. Development and evaluation of an external quality control and internal quality control containing real-time RT-PCR assay for the detection of o'nyong-nyong virus. Biologicals 2023; 84:101717. [PMID: 37801802 DOI: 10.1016/j.biologicals.2023.101717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 06/20/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
O'nyong-nyong fever is a mosquito-borne tropical viral disease while few molecular diagnostic tools have been established for its surveillance until now. In the current study, a single-step, dual-color real-time reverse transcription polymerase chain reaction (RT-PCR) assay which contained both external quality control (EQC) and internal quality control (IQC) prepared by armored RNA technique was developed and evaluated for the detection of o'nyong-nyong virus (ONNV). Results showed that the assay was established successfully without cross-reaction with genetically related or symptom-alike diseases, which showed high specificity of the assay. The coefficient of variation of the assay was 0.97%, far less than 5%, indicating good repeatability of the assay. The lower limit of detection of the assay could reach as low as 100 copies of genome equivalent. During evaluation, the assay could correctly detect ONNV from spiked human serum samples and Anopheles species mosquito samples, while no ONNV positive was observed either from serum samples of patients with acute febrile illness or from local Anopheles species mosquitoes, suggesting no ONNV had been transmitted locally. In conclusion, the assay could potentially provide a valuable platform for ONNV molecular detection, which may improve the preparedness for future o'nyong-nyong fever outbreaks.
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Affiliation(s)
- Hai-Bo Wang
- Key Laboratory of Emerging Infectious Disease Detection, Zhuhai International Travel Healthcare Center, Zhuhai, 519020, Guangdong, China.
| | - Tian Du
- Futian District Center for Disease Control and Prevention, Shenzhen, 518040, Guangdong, China
| | - Ji-Hong Lin
- Zhongshan International Travel Healthcare Center, Zhongshan, 528400, Guangdong, China
| | - Xin-Bin Chen
- Key Laboratory of Emerging Infectious Disease Detection, Zhuhai International Travel Healthcare Center, Zhuhai, 519020, Guangdong, China
| | - Cheng-Ning Tu
- Key Laboratory of Emerging Infectious Disease Detection, Zhuhai International Travel Healthcare Center, Zhuhai, 519020, Guangdong, China
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Petersen PE, Dahl MM, Vest NMO, Jansen MD, Fosse JH, Falk K, Christiansen DH. Validation of a TaqMan one-step real-time RT-PCR assay targeting ISAV segment 7 spliced mRNA. J Virol Methods 2023; 321:114791. [PMID: 37562733 DOI: 10.1016/j.jviromet.2023.114791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
Infectious salmon anaemia virus (ISAV) can cause severe systemic infection in Atlantic salmon (Salmo salar L.), and a timely diagnosis is critical. Conventional real-time reverse transcription PCR (RT-qPCR) assays target unspliced RNA from either ISAV segment 7 or 8 and provide data on viral load. Here, we evaluate a TaqMan one-step RT-qPCR assay that detects explicitly a spliced messenger RNA (mRNA) of ISAV segment 7, thus providing evidence of active viral transcription. Assay performance was comparable with existing unspliced segment 7 and segment 8 assays. PCR efficiency as evaluated from dilutions of a synthetic DNA fragment was 98 % (R2 = 1.00). The assay also performed well on clinical heart samples with PCR efficiency of 108 % (R2 = 1.00). Finally, evaluation on kidney samples from experimental infection revealed higher levels of active transcription for high-virulent compared to low-virulent ISAV. At early, peak, and late infection, mean ratios of spliced to unspliced segment 7 RNA were 3.0 % (± 0.7), 1.7 % (± 0.3), and 1.5 % (± 0.1) for the low virulent and 9.4 % (± 2.2), 4.7 % (± 0.8), and 6.2 % (± 0.1) for the high virulent isolate, respectively. By detection and quantification of active ISAV transcription, this assay may provide a more detailed understanding of ISAV infection dynamics.
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Affiliation(s)
- Petra Elisabeth Petersen
- Faroese Food and Veterinary Authority, National Reference Laboratory for Fish Diseases, V.U. Hammershaimbsg. 11, FO-100 Tórshavn, the Faroe Islands.
| | - Maria Marjunardóttir Dahl
- Faroese Food and Veterinary Authority, National Reference Laboratory for Fish Diseases, V.U. Hammershaimbsg. 11, FO-100 Tórshavn, the Faroe Islands
| | - Nicolina Maria Ovadóttir Vest
- Faroese Food and Veterinary Authority, National Reference Laboratory for Fish Diseases, V.U. Hammershaimbsg. 11, FO-100 Tórshavn, the Faroe Islands
| | - Mona Dverdal Jansen
- Norwegian Veterinary Institute, Elizabeth Stephansens vei 1, Pb 64, N-1431 Ås, Norway
| | - Johanna Hol Fosse
- Norwegian Veterinary Institute, Elizabeth Stephansens vei 1, Pb 64, N-1431 Ås, Norway
| | - Knut Falk
- Norwegian Veterinary Institute, Elizabeth Stephansens vei 1, Pb 64, N-1431 Ås, Norway
| | - Debes Hammershaimb Christiansen
- Faroese Food and Veterinary Authority, National Reference Laboratory for Fish Diseases, V.U. Hammershaimbsg. 11, FO-100 Tórshavn, the Faroe Islands
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Lanic MD, Guérin R, Wassef M, Durdilly P, Rainville V, Sater V, Jardin F, Ruminy P, Costes-Martineau V, Laé M. Detection of salivary gland and sinonasal fusions by a next-generation sequencing based, ligation-dependent, multiplex RT-PCR assay. Histopathology 2023; 83:685-699. [PMID: 37350081 DOI: 10.1111/his.14971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023]
Abstract
AIMS The discovery of tumour type-specific gene fusion oncogenes in benign and malignant salivary gland and sinonasal (SGSN) tumours has significantly increased our knowledge about their molecular pathology and classification. METHODS AND RESULTS We developed a new targeted multiplexed next-generation sequencing (NGS)-based method that utilizes ligation dependent reverse-transcriptase polymerase chain reaction (LD-RT-PCR) to detect oncogenic fusion transcripts involving 116 genes, leading to 96 gene fusions known to be recurrently rearranged in these tumours. In all, 180 SGSN tumours (formalin-fixed, paraffin-embedded samples, 141 specimens and 39 core needle biopsies) from the REFCORpath (French network for rare head and neck cancers) with previously identified fusion genes by fluorescent in situ hybridisation (FISH), RT-PCR, or molecular immunohistochemistry were selected to test its specificity and sensitivity and validate its diagnostic use. Tested tumours encompassed 14 major tumours types, including secretory carcinoma, mucoepidermoid carcinoma, adenoid cystic carcinoma, salivary gland intraductal carcinoma, clear cell carcinoma, pleomorphic adenoma, adamantinoma-like Ewing Sarcoma, EWSR1::COLCA2 sinonasal sarcoma, DEK::AFF2 sinonasal carcinoma, and biphenotypic sinonasal sarcoma. In-frame fusion transcripts were detected in 97.8% of cases (176/180). Gene fusion assay results correlated with conventional techniques (immunohistochemistry [IHC], FISH, and RT-PCR) in 176/180 tumours (97.8%). CONCLUSION This targeted multiplexed NGS-based LD-RT-PCR method is a robust, highly sensitive method for the detection of recurrent gene fusions from routine clinical SGSN tumours. It can be easily customized to cover new fusions. These results are promising for implementing an integrated NGS system to rapidly detect genetic aberrations, facilitating accurate, genomics-based diagnoses, and accelerate time to precision therapies in SGSN tumours.
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Affiliation(s)
- Marie-Delphine Lanic
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - René Guérin
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Michel Wassef
- Department of Pathology, Hôpital Lariboisière, Paris, France
| | | | - Vinciane Rainville
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Vincent Sater
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | | | - Marick Laé
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
- Department of Pathology, Centre Henri Becquerel, Rouen, France
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Goto Y, Fukunari K, Tada S, Ichimura S, Chiba Y, Suzuki T. A multiplex real-time RT-PCR system to simultaneously diagnose 16 pathogens associated with swine respiratory disease. J Appl Microbiol 2023; 134:lxad263. [PMID: 37951290 DOI: 10.1093/jambio/lxad263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/13/2023]
Abstract
AIMS Swine respiratory disease (SRD) is a major disease complex in pigs that causes severe economic losses. SRD is associated with several intrinsic and extrinsic factors such as host health status, viruses, bacteria, and environmental factors. Particularly, it is known that many pathogens are associated with SRD to date, but most of the test to detect those pathogens can be normally investigated only one pathogen while taking time and labor. Therefore, it is desirable to develop rapidly and efficiently detectable methods those pathogens to minimize the damage caused by SRD. METHODS AND RESULTS We designed a multiplex real-time RT-PCR (RT-qPCR) system to diagnose simultaneously 16 pathogens, including nine viruses and seven bacteria associated with SRD, on the basis of single qPCR and RT-qPCR assays reported in previous studies. Multiplex RT-qPCR system we designed had the same ability to single RT-qPCR without significant differences in detection sensitivity for all target pathogens at minimum to maximum genomic levels. Moreover, the primers and probes used in this system had highly specificity because the sets had not been detected pathogens other than the target and its taxonomically related pathogens. Furthermore, our data demonstrated that this system would be useful to detect a causative pathogen in the diagnosis using oral fluid from healthy pigs and lung tissue from pigs with respiratory disorders collected in the field. CONCLUSIONS The rapid detection of infected animals from the herd using our system will contribute to infection control and prompt treatment in the field.
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Affiliation(s)
- Yusuke Goto
- Central Iwate Prefectural Livestock Health and Hygiene Center, Takizawa, Iwate 020-0605, Japan
| | - Kazuhiro Fukunari
- Central Iwate Prefectural Livestock Health and Hygiene Center, Takizawa, Iwate 020-0605, Japan
| | - Shigekatsu Tada
- Central Iwate Prefectural Livestock Health and Hygiene Center, Takizawa, Iwate 020-0605, Japan
| | - Satoki Ichimura
- Central Iwate Prefectural Livestock Health and Hygiene Center, Takizawa, Iwate 020-0605, Japan
| | - Yuzumi Chiba
- Central Iwate Prefectural Livestock Health and Hygiene Center, Takizawa, Iwate 020-0605, Japan
| | - Tohru Suzuki
- Division of Zoonosis Research, Sapporo Research Station, National Institute of Animal Health, NARO, Sapporo, Hokkaido 062-0045, Japan
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Oh C, Zhou A, O'Brien K, Schmidt AR, Geltz J, Shisler JL, Schmidt AR, Keefer L, Brown WM, Nguyen TH. Improved performance of nucleic acid-based assays for genetically diverse norovirus surveillance. Appl Environ Microbiol 2023; 89:e0033123. [PMID: 37791775 PMCID: PMC10654041 DOI: 10.1128/aem.00331-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/07/2023] [Indexed: 10/05/2023] Open
Abstract
Nucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of their genetic diversity. Here, we calculated the variability of nucleotides within the genomes of 10 human viral species in silico and found that endemic viruses exhibit a high percentage of variable nucleotides (e.g., 51.4% for norovirus genogroup II). This genetic diversity led to the variable probability of detection of PCR assays (the proportion of viral sequences that contain the assay's target sequences divided by the total number of viral sequences). We then experimentally confirmed that the probability of the target sequence detection is indicative of the number of mismatches between PCR assays and norovirus genomes. Next, we developed a degenerate PCR assay that detects 97% of known norovirus genogroup II genome sequences and recognized norovirus in eight clinical samples. By contrast, previously developed assays with 31% and 16% probability of detection had 1.1 and 2.5 mismatches on average, respectively, which negatively impacted RNA quantification. In addition, the two PCR assays with a lower probability of detection also resulted in false negatives for wastewater-based epidemiology. Our findings suggest that the probability of detection serves as a simple metric for evaluating nucleic acid-based assays for genetically diverse virus surveillance.IMPORTANCENucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are employed widely as a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of the rapid evolution and genetic variation of viruses. The study analyzed clinical and wastewater samples using multiple PCR assays and found significant performance variation among the PCR assays for genetically diverse norovirus surveillance. This finding suggests that some PCR assays may miss detecting certain virus strains, leading to a compromise in detection sensitivity. To address this issue, we propose a metric called the probability of detection, which can be simply calculated in silico using a code developed in this study, to evaluate nucleic acid-based assays for genetically diverse virus surveillance. This new approach can help improve the sensitivity and accuracy of virus detection, which is crucial for effective infectious disease surveillance and control.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USA
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kate O'Brien
- School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Arthur R. Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Joshua Geltz
- Division of Laboratories, Illinois Department of Public Health, Springfield, Illinois, USA
| | - Joanna L. Shisler
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Arthur R. Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Laura Keefer
- Illinois State Water Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - William M. Brown
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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de Mello Malta F, Amgarten D, Marra AR, Petroni RC, da Silva Nali LH, Siqueira RA, Neto MC, Oler SC, Pinho JRR. Nucleocapsid single point-mutation associated with drop-out on RT-PCR assay for SARS-CoV-2 detection. BMC Infect Dis 2023; 23:714. [PMID: 37872472 PMCID: PMC10591358 DOI: 10.1186/s12879-023-08707-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Since its beginning, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been a challenge for clinical and molecular diagnostics, because it has been caused by a novel viral agent. Whole-genome sequencing assisted in the characterization and classification of SARS-CoV-2, and it is an essential tool to genomic surveillance aiming to identify potentials hot spots that could impact on vaccine immune response and on virus diagnosis. We describe two cases of failure at the N2 target of the RT-PCR test Xpert® Xpress SARS-CoV-2. METHODS Total nucleic acid from the Nasopharyngeal (NP) and oropharyngeal (OP) swab samples and cell supernatant isolates were obtained. RNA samples were submitted to random amplification. Raw sequencing data were subjected to sequence quality controls, removal of human contaminants by aligning against the HG19 reference genome, taxonomic identification of other pathogens and genome recovery through assembly and manual curation. RT-PCR test Xpert® Xpress SARS-CoV-2 was used for molecular diagnosis of SARS-CoV-2 infection, samples were tested in duplicates. RESULTS We identified 27 samples positive for SARS-CoV-2 with a nucleocapsid (N) gene drop out on Cepheid Xpert® Xpress SARS-CoV-2 assay. Sequencing of 2 of 27 samples revealed a single common mutation in the N gene C29197T, potentially involved in the failed detection of N target. CONCLUSIONS This study highlights the importance of genomic data to update molecular tests and vaccines.
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Affiliation(s)
- Fernanda de Mello Malta
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Deyvid Amgarten
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Alexandre Rodrigues Marra
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Roberta Cardoso Petroni
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Luiz Henrique da Silva Nali
- Post-Graduation Program in Health Sciences, Santo Amaro University, Rua Prof. Enéas de Siqueira Neto, 340 - Jardim das Imbuias, Sao Paulo, SP, Brazil
| | - Ricardo Andreotti Siqueira
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Miguel Cendoroglo Neto
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Silvia Cassiano Oler
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - João Renato Rebello Pinho
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil.
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