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Abbasi H, Nikoo HR, Fotouhi F, Khosravi A. Development of a robust TaqMan probe-based one-step multiplex RT-qPCR for simultaneous detection of SARS-CoV-2 and Influenza A/B viruses. BMC Microbiol 2023; 23:335. [PMID: 37951883 PMCID: PMC10640757 DOI: 10.1186/s12866-023-03048-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 10/06/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND During the coronavirus disease 2019 (COVID-19) pandemic, the simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Influenza A, and Influenza B viruses is essential for rapid differential diagnosis in patients with similar symptoms, especially during "flu season" in the post-pandemic era. So far, several multiplex methods have been approved for the simultaneous detection of SARS-CoV-2, Influenza A, and Influenza B. However, due to the rapid mutation rate of the SARS-CoV-2 genome and the emergence of new variants, existing methods must be improved and updated. METHODS To identify a highly conserved region in the SARS-CoV-2 N-gene, a genomic survey was performed to increase the sensitivity and specificity of primer and probe sets targeting the SARS-CoV-2 genome. The 95% LLOD (95% lower limits of detection) were calculated by probit analysis. A total of 70 predetermined clinical samples using singleplex RT-qPCR assays, were included. The clinical performance of the multiplex RT-qPCR assay was determined and compared with a commercial multiplex kit. The Cohen's kappa coefficient, P-value (McNemar's test), Passing-Bablok regression, and Bland Altman agreement analysis were determined to monitor the agreement of the assays. RESULTS The novel SARS-CoV-2 primer and probe set designed in this assay was able to detect all variants of concern (VOCs) and variants of interest (VOIs) with high analytical and clinical performance. The 95% LLOD for the multiplex RT-qPCR was 20 copies per reaction for the N gene of SARS-CoV-2, 2 copies per reaction for M1 gene of Influenza A and NS1 gene of Influenza B. The diagnostic sensitivity of the multiplex RT-qPCR was 94.4%, 93.7%, and 100% for the detection of SARS-CoV-2, Influenza A, and Influenza B genomes, respectively. Moreover, the specificity was identical (100%) in both assays. According to the agreement analysis results, there was no statistical difference between our multiplex assay and the commercial kit. CONCLUSIONS In this study, we developed a novel in-house made multiplex RT-qPCR assay, with high sensitivity, specificity, and reliability for the diagnosis of SARS-CoV-2 infection in clinical samples. This is valuable during Influenza seasons when influenza co-circulates with SARS-CoV-2, as it saves costs, time, and thus specific and timely treatment of patients.
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Affiliation(s)
- Hamidreza Abbasi
- Department of Medical Biotechnology, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
| | - Hadi Razavi Nikoo
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran.
- Infectious Disease Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
| | - Fatemeh Fotouhi
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Ayyoob Khosravi
- Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
- Department of Molecular Medicine, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran.
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Khemiri H, Gdoura M, Ben Halima S, Krichen H, Cammà C, Lorusso A, Ancora M, Di Pasquale A, Cherni A, Touzi H, Sadraoui A, Meddeb Z, Hogga N, Ammi R, Triki H, Haddad-Boubaker S. SARS-CoV-2 excretion kinetics in nasopharyngeal and stool samples from the pediatric population. Front Med (Lausanne) 2023; 10:1226207. [PMID: 38020093 PMCID: PMC10643538 DOI: 10.3389/fmed.2023.1226207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for serious respiratory infections in humans. Even in the absence of respiratory symptoms, gastrointestinal (GI) signs were commonly reported in adults and children. Thus, oral-fecal transmission was suspected as a possible route of infection. The objective of this study was to describe RNA shedding in nasopharyngeal and stool samples obtained from asymptomatic and symptomatic children and to investigate virus viability. Methods This study included 179 stool and 191 nasopharyngeal samples obtained from 71 children, which included symptomatic (n = 64) and asymptomatic (n = 7) ones. They were collected every 7 days from the onset of the infection until negativation. Viral RNA was detected by real-time RT-PCR, targeting the N and ORF1 genes. Whole-genome sequencing was performed for positive cases. Viral isolation was assessed on Vero cells, followed by molecular detection confirmation. Results All cases included in this study (n = 71) were positive in their nasopharyngeal samples. SARS-CoV-2 RNA was detected in 36 stool samples obtained from 15 out of 71 (21.1%) children; 13 were symptomatic and two were asymptomatic. Excretion periods varied from 7 to 21 days and 7 to 14 days in nasopharyngeal and fecal samples, respectively. Four variants were detected: Alpha (n = 3), B.1.160 (n = 3), Delta (n = 7), and Omicron (n = 1). Inoculation of stool samples on cell culture showed no specific cytopathic effect. All cell culture supernatants were negative for RT-qPCR. Conclusion Our study demonstrated nasopharyngeal and fecal shedding of SARS-CoV-2 RNA by children up to 21 and 14 days, respectively. Fecal shedding was recorded in symptomatic and asymptomatic children. Nevertheless, SARS-CoV-2 was not isolated from positive stool samples.
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Affiliation(s)
- Haifa Khemiri
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mariem Gdoura
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Samar Ben Halima
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Krichen
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Massimo Ancora
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Adriano Di Pasquale
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Asma Cherni
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Amel Sadraoui
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Zina Meddeb
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nahed Hogga
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Radhia Ammi
- Service of External Consultants, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sondes Haddad-Boubaker
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
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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] [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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Dávila SL, Leguizamón JE, León AF, Holguín K, Barros EC, Gomez SY. Development of a national proficiency test for SARS-CoV-2 detection by PCR in Colombia. J Glob Health 2023; 13:06029. [PMID: 37824175 PMCID: PMC10569378 DOI: 10.7189/jogh.13.06029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Background Proficiency testing (PT) is a tool for ensuring the validity of results of testing laboratories and is essential when laboratories are working with assays authorised for emergency use or implementing novel techniques for detecting emerging pathogens. Methods In collaboration with the National Health Institute of Colombia and with international support, we developed a qualitative PT for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse transcription polymerase chain reaction (RT-PCR). A proficiency test item (PTI) based on reference material (research grade) produced by the National Institute of Standards and Technologies (NIST) was prepared and characterised using three positive samples with varying concentrations of SARS-CoV-2 ribonucleic acid (RNA) and two negative (control) samples. Tests were distributed to 121 laboratories across the national network of public health laboratories in Colombia. Results Positive samples had varying concentrations of SARS-CoV-2 RNA and were quantified by digital PCR (RT-ddPCR) assays for the E gene of SARS-CoV-2. We tested the ability of laboratories to detect low and high levels of viral RNA using samples with SARS-CoV-2 RNA concentrations of 1417 ± 216, 146 ± 28, and 14 ± 10 copies /uL (expanded uncertainty, k = 2, 95% confidence level) We also performed a semiquantitative analysis of instrumental responses (Ct values) reported by participating laboratories and homogeneity, stability, and characterisation studies of the produced materials to determine the adequacy of these materials and methods for use in the qualitative PT scheme. The PT evaluated reports for individual target genes from each laboratory; 98.3% of laboratories had satisfactory performance and the remaining 1.7% of laboratories had unsatisfactory performance for the detection of at least one of the reported genes. Conclusions This PT scheme identified the potential metrological weaknesses of laboratories in the detection of SARS-CoV-2 by RT-PCR and may facilitate improvements in the quality of measurements from the perspective of public health surveillance.
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Affiliation(s)
- Sergio L Dávila
- Universidad Nacional de Colombia, Department of Chemistry, Faculty of Science, Bogotá, Colombia
| | - John E Leguizamón
- Instituto Nacional de Metrología, Bioanalysis Working Group, Bogotá, Colombia
| | - Andrés F León
- Instituto Nacional de Metrología, Bioanalysis Working Group, Bogotá, Colombia
| | - Katherin Holguín
- Instituto Nacional de Metrología, Bioanalysis Working Group, Bogotá, Colombia
| | - Esther C Barros
- Instituto Nacional de Salud, Virology department, Bogotá, Colombia
| | - Sergio Y Gomez
- Instituto Nacional de Salud, Virology department, Bogotá, Colombia
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5
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Ho KL, Ding J, Fan JS, Tsui WNT, Bai J, Fan SK. Digital Microfluidic Multiplex RT-qPCR for SARS-CoV-2 Detection and Variants Discrimination. MICROMACHINES 2023; 14:1627. [PMID: 37630161 PMCID: PMC10456927 DOI: 10.3390/mi14081627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/05/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023]
Abstract
Continuous mutations have occurred in the genome of the SARS-CoV-2 virus since the onset of the COVID-19 pandemic. The increased transmissibility of the mutated viruses has not only imposed medical burdens but also prolonged the duration of the pandemic. A point-of-care (POC) platform that provides multitarget detection will help to track and reduce disease transmissions. Here we detected and discriminated three genotypes of SARS-CoV-2, including the wildtype and two variants of concern (VOCs), the Delta variant and Omicron variant, through reverse transcription quantitative polymerase chain reaction (RT-qPCR) on a digital microfluidics (DMF)-based cartridge. Upon evaluating with the RNA samples of Omicron variant, the DMF RT-qPCR presented a sensitivity of 10 copies/μL and an amplification efficiency of 96.1%, capable for clinical diagnosis. When spiking with SARS-CoV-2 RNA (wildtype, Delta variant, or Omicron variant) and 18S rDNA, the clinical analog samples demonstrated accurate detection and discrimination of different SARS-CoV-2 strains in 49 min.
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Affiliation(s)
- Kuan-Lun Ho
- Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506, USA; (K.-L.H.); (J.D.)
| | - Jing Ding
- Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506, USA; (K.-L.H.); (J.D.)
| | - Jia-Shao Fan
- Department of Electrical and Computer Engineering, Kansas State University, Manhattan, KS 66506, USA;
| | - Wai Ning Tiffany Tsui
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA; (W.N.T.T.); (J.B.)
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA; (W.N.T.T.); (J.B.)
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Shih-Kang Fan
- Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506, USA; (K.-L.H.); (J.D.)
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Jiang M, Chen W, Chen Y, Chen J, Zhang Y, Yin H, Li Y, Liu W. Analytical performance of rapid nucleic acid detection assays and routine RT-qPCR assays for detection of SARS-CoV-2 in Shanghai, China in 2022. Diagn Microbiol Infect Dis 2023; 105:115860. [PMID: 36459887 PMCID: PMC9708047 DOI: 10.1016/j.diagmicrobio.2022.115860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/28/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Diagnostic accuracy of COVID-19 varies among different assays. In this study, the analytical performance of 1 rapid nucleic acid detection assay (Coyote assay) and 2 routine RT-qPCR assays (BioGerm assay and DaAn assay) was evaluated, using 1196 clinical samples. Disagreement in the results of 2 paired targets occurred in all 3 assays. The Coyote assay failed to detect 15 samples, and the DaAn assay failed to detect 5 samples. The Cohen's kappa coefficient was 0.970 between the BioGerm and DaAn assays, 0.907 between the Coyote and BioGerm assays, and 0.936 between the Coyote and DaAn assays. The positive percent agreement, and negative percent agreement of the Coyote assay were 84.04%, and 100%, respectively. Our study revealed that the results of the Coyote, BioGerm, and DaAn assays were highly consistent, which provided reference for the application of these assays for diagnosis of COVID-19.
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Affiliation(s)
- Min Jiang
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Department of Laboratory Medicine and Central Laboratory, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Weiqin Chen
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yong Chen
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jia Chen
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yue Zhang
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongmei Yin
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Li
- Department of Nephropathy, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Weiwei Liu
- Department of Laboratory Medicine, LongHua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
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Marchini A, Petrillo M, Parrish A, Buttinger G, Tavazzi S, Querci M, Betsou F, Elsinga G, Medema G, Abdelrahman T, Gawlik B, Corbisier P. New RT-PCR Assay for the Detection of Current and Future SARS-CoV-2 Variants. Viruses 2023; 15:206. [PMID: 36680246 PMCID: PMC9863853 DOI: 10.3390/v15010206] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/05/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023] Open
Abstract
Multiple lineages of SARS-CoV-2 have been identified featuring distinct sets of genetic changes that confer to the virus higher transmissibility and ability to evade existing immunity. The continuous evolution of SARS-CoV-2 may pose challenges for current treatment options and diagnostic tools. In this study, we have first evaluated the performance of the 14 WHO-recommended real-time reverse transcription (RT)-PCR assays currently in use for the detection of SARS-CoV-2 and found that only one assay has reduced performance against Omicron. We then developed a new duplex real-time RT-PCR assay based on the amplification of two ultra-conserved elements present within the SARS-CoV-2 genome. The new duplex assay successfully detects all of the tested SARS-CoV-2 variants of concern (including Omicron sub-lineages BA.4 and BA.5) from both clinical and wastewater samples with high sensitivity and specificity. The assay also functions as a one-step droplet digital RT-PCR assay. This new assay, in addition to clinical testing, could be adopted in surveillance programs for the routine monitoring of SARS-CoV-2's presence in a population in wastewater samples. Positive results with our assay in conjunction with negative results from an Omicron-specific assay may provide timely indication of the emergence of a novel SARS-CoV-2 variant in a certain community and thereby aid public health interventions.
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Affiliation(s)
- Antonio Marchini
- European Commission, Joint Research Centre (JRC), 2440 Geel, Belgium
| | | | - Amy Parrish
- Department of Microbiology, Laboratoire National de Santé, 3583 Dudelange, Luxembourg
| | - Gerhard Buttinger
- European Commission, Joint Research Centre (JRC), 2440 Geel, Belgium
| | - Simona Tavazzi
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy
| | - Maddalena Querci
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy
| | - Fay Betsou
- Department of Microbiology, Laboratoire National de Santé, 3583 Dudelange, Luxembourg
- Biological Resource Center of Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Goffe Elsinga
- KWR Water Research Institute, 3433 PE Nieuwegein, The Netherlands
| | - Gertjan Medema
- KWR Water Research Institute, 3433 PE Nieuwegein, The Netherlands
| | - Tamir Abdelrahman
- Department of Microbiology, Laboratoire National de Santé, 3583 Dudelange, Luxembourg
| | - Bernd Gawlik
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy
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SARS-CoV-2 Serology: Utility and Limits of Different Antigen-Based Tests through the Evaluation and the Comparison of Four Commercial Tests. Biomedicines 2022; 10:biomedicines10123106. [PMID: 36551862 PMCID: PMC9775032 DOI: 10.3390/biomedicines10123106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/07/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
Introduction: SARS-CoV-2 serology have several indications. Currently, as there are various types available, it is important to master their performance in order to choose the best test for the indication. We evaluated and compared four different commercial serology tests, three of them had the Food and Drug Administration Emergency Use Authorization (FDA-EUA). Our goal was to provide new data to help guide the interpretation and the choice of the serological tests. Methods: Four commercial tests were studied: Elecsys® Roche® on Cobas® (total anti-nucleocapsid (N) antibodies), VIDAS® Biomerieux® (IgM and IgG anti- receptor binding domain (RBD) antibodies), Mindray® (IgM and IgG anti-N and anti-RBD antibodies) and Access® Beckman Coulter® (IgG anti-RBD antibodies). Two panels were tested: a positive panel (n = 72 sera) obtained from COVID-19-confirmed patients with no vaccination history and a negative panel (n = 119) of pre-pandemic sera. The analytical performances were evaluated and the ROC curve was drawn to assess the manufacturer’s cut-off for each test. Results: A large range of variability between the tests was found. The Mindray®IgG and Cobas® tests showed the best overall sensitivity, which was equal to 79.2% CI 95% (67.9−87.8). The Cobas® test showed the best sensitivity after 14 days of COVID-19 molecular confirmation; which was equal to 85.4% CI 95% (72.2−93.9). The Access® test had a lower sensitivity, even after day 14 (55.5% CI 95% (43.4−67.3)). The best specificity was noted for the Cobas®, VIDAS®IgG and Access® IgG tests (100% CI 95% (96.9−100)). The IgM tests, VIDAS®IgM and Mindray®IgM, showed the lowest specificity and sensitivity rates. Overall, only 43 out of 72 sera (59.7%) showed concordant results by all tests. Retained cut-offs for a significantly better sensitivity and accuracy, without significant change in the specificity, were: 0.87 for Vidas®IgM (p = 0.01) and 0.14 for Access® (p < 10−4). The combination of Cobas® with Vidas® IgM and IgG offered the best accuracy in comparison with all other tests combinations. Conclusion: Although using an FDA-EUA approved serology test, each laboratory should carry out its own evaluation. Tests variability may raise some concerns that seroprevalence studies may vary significantly based on the used serology test.
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Tang Y, Li Y, Zhang S, Li J, Hu Y, Yang W, Chen Y, Qin C, Jiang T, Kang X. Preparation of the luciferase-labeled antibody for improving the detection sensitivity of viral antigen. Virol J 2022; 19:126. [PMID: 35902865 PMCID: PMC9332066 DOI: 10.1186/s12985-022-01855-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/17/2022] [Indexed: 11/12/2022] Open
Abstract
Background Viral antigen detection test is the most common method used to detect viruses in the field rapidly. However, due to the low sensitivity, it can only be used as an auxiliary diagnosis method for virus infection. Improving sensitivity is crucial for developing more accurate viral antigen tests. Nano luciferase (Nluc) is a sensitive reporter that has not been used in virus detection. Results In this study, we produced an intracellularly Nluc labeled detection antibody (Nluc-ch2C5) and evaluated its ability to improve the detection sensitivity of respiratory syndrome coronavirus 2 (SARS-CoV-2) antigens. Compared with the traditional horse-radish peroxidase (HRP) labeled antibody (HRP-ch2C5), Nluc-ch2C5 was 41 times more sensitive for inactivated SARS-CoV-2 virus by sandwich chemiluminescence ELISA. Then we applied Nluc-ch2C5 to establish an automatic magnet chemiluminescence immune assay (AMCA) for the SARS-CoV-2 viral spike protein, the limit of detection was 68 pfu/reaction. The clinical sensitivity and specificity reached 75% (24/32) and 100% (48/48) using 32 PCR-positive and 48 PCR-negative swab samples for clinical evaluation, which is more sensitive than the commercial ELSA kit and colloid gold strip kit. Conclusions Here, monoclonal antibody ch2C5 served as a model antibody and the SARS-CoV-2 served as a model pathogen. The Nluc labeled detecting antibody (Nluc-ch2C5) significantly improved the detection sensitivity of SARS-CoV-2 antigen. This labeling principle applies to other viral infections, so this labeling and test format could be expected to play an important role in detecting other virus antigens. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01855-6.
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Affiliation(s)
- Ying Tang
- State Key Laboratory of Pathogen and Biosecurity, The Academy of Military Medical Science. Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Yuchang Li
- State Key Laboratory of Pathogen and Biosecurity, The Academy of Military Medical Science. Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Sen Zhang
- State Key Laboratory of Pathogen and Biosecurity, The Academy of Military Medical Science. Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Jing Li
- State Key Laboratory of Pathogen and Biosecurity, The Academy of Military Medical Science. Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Yi Hu
- State Key Laboratory of Pathogen and Biosecurity, The Academy of Military Medical Science. Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Wenguang Yang
- State Key Laboratory of Pathogen and Biosecurity, The Academy of Military Medical Science. Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Yuehong Chen
- State Key Laboratory of Pathogen and Biosecurity, The Academy of Military Medical Science. Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Chengfeng Qin
- State Key Laboratory of Pathogen and Biosecurity, The Academy of Military Medical Science. Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Tao Jiang
- State Key Laboratory of Pathogen and Biosecurity, The Academy of Military Medical Science. Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Xiaoping Kang
- State Key Laboratory of Pathogen and Biosecurity, The Academy of Military Medical Science. Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing, 100071, China.
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Technique Evolutions for Microorganism Detection in Complex Samples: A Review. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12125892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rapid detection of microorganisms is a major challenge in the medical and industrial sectors. In a pharmaceutical laboratory, contamination of medical products may lead to severe health risks for patients, such as sepsis. In the specific case of advanced therapy medicinal products, contamination must be detected as early as possible to avoid late production stop and unnecessary costs. Unfortunately, the conventional methods used to detect microorganisms are based on time-consuming and labor-intensive approaches. Therefore, it is important to find new tools to detect microorganisms in a shorter time frame. This review sums up the current methods and represents the evolution in techniques for microorganism detection. First, there is a focus on promising ligands, such as aptamers and antimicrobial peptides, cheaper to produce and with a broader spectrum of detection. Then, we describe methods achieving low limits of detection, thanks to Raman spectroscopy or precise handling of samples through microfluids devices. The last part is dedicated to techniques in real-time, such as surface plasmon resonance, preventing the risk of contamination. Detection of pathogens in complex biological fluids remains a scientific challenge, and this review points toward important areas for future research.
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