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Mdunyelwa A, Seema C, Mabaso A, Mlambo K, Mtsweni M, Maphanga M, Rammutla E, Tempelman HA, Umunnakwe CN. Evaluation of the Seegene Allplex TM RV Master Assay for One-Step Simultaneous Detection of Eight Respiratory Viruses in Nasopharyngeal Specimens. J Virol Methods 2024:115042. [PMID: 39384158 DOI: 10.1016/j.jviromet.2024.115042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 09/27/2024] [Accepted: 10/06/2024] [Indexed: 10/11/2024]
Abstract
BACKGROUND The Seegene AllplexTM RV Master (RVM) assay is a one-step multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) system for detecting eight viral respiratory pathogens from nasopharyngeal swab, aspirate, and bronchoalveolar lavage specimens. The eight RVM targets are: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Influenza A (Flu A), Influenza B (Flu B), Human respiratory syncytial virus (RSV), adenovirus (AdV), rhinovirus (HRV), parainfluenza virus (PIV), and metapneumovirus (MPV). The assay is based on Seegene's multiple detection temperature (MuDT) technology and provides cycle threshold (Ct) values for each of its viral targets upon PCR completion. OBJECTIVE We aimed to evaluate the diagnostic performance of the RVM assay by calculating sensitivity, specificity, accuracy, Positive Predictive Value (PPV), Negative Predictive Value (NPV), Positive Percent Agreement (PPA), Negative Percent Agreement (NPA), and Overall Percent Agreement (OPA) compared to definite diagnosis and analogous reference assays. STUDY DESIGN Diagnostic sensitivity, specificity, accuracy, PPV, and NPV were calculated by comparing the results of the RVM assay to that of definite diagnosis assays; while PPA, NPA, and OPA were calculated by comparing results of the RVM assay to that of analogous reference products. Definite diagnosis and reference methods comprised whole genome sequencing and PCR genotyping, the AllplexTM SARS-CoV-2/FluA/FluB/RSV and Respiratory Panels 1, 2, and 3 assays (Seegene), and the Xpert® Xpress SARS-CoV-2/FluA/FluB/RSV Plus assay (Cepheid). Reproducibility of the RVM assay using fully-automated and semi-automated nucleic acid (NA) extraction workflows and as performed by independent operators was also assessed. In total, 249 positive respiratory specimens and at least 50 negative specimens for each target tested were used for this evaluation study. RESULTS Sensitivity, specificity, accuracy, PPV, NPV, PPA, NPA, and OPA ranged from 95.7% to 100% for detecting all eight targets tested on the RVM assay. Reproducibility PPA, NPA, and OPA between automated and semi-automated NA extraction workflows were all >97.9%, while the reproducibility PPA, NPA and OPA between independent operators were all 100%. CONCLUSION These results demon6strate a high level of sensitivity, specificity, accuracy and diagnostic predictive value of the RVM assay and high agreement with comparable reference assays in identifying all eight of its targets. Taken together, our study underscores the diagnostic utility of the RVM assay in detecting eight viral respiratory pathogens.
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Affiliation(s)
- Anele Mdunyelwa
- Ndlovu Research Centre, Ndlovu Laboratories, Elandsdoorn, Dennilton, Limpopo, South Africa
| | - Colette Seema
- Ndlovu Research Centre, Ndlovu Laboratories, Elandsdoorn, Dennilton, Limpopo, South Africa
| | - Anna Mabaso
- Ndlovu Research Centre, Ndlovu Laboratories, Elandsdoorn, Dennilton, Limpopo, South Africa
| | - Khamusi Mlambo
- Ndlovu Research Centre, Ndlovu Laboratories, Elandsdoorn, Dennilton, Limpopo, South Africa
| | - Mandisa Mtsweni
- Ndlovu Research Centre, Ndlovu Laboratories, Elandsdoorn, Dennilton, Limpopo, South Africa
| | - Mathapelo Maphanga
- Ndlovu Research Centre, Ndlovu Laboratories, Elandsdoorn, Dennilton, Limpopo, South Africa
| | - Elizabeth Rammutla
- Ndlovu Research Centre, Ndlovu Laboratories, Elandsdoorn, Dennilton, Limpopo, South Africa
| | - Hugo A Tempelman
- Ndlovu Research Centre, Ndlovu Laboratories, Elandsdoorn, Dennilton, Limpopo, South Africa; Wits Reproductive Health and HIV Institute, University of the Witwatersrand, Johannesburg, South Africa; Utrecht University, Netherlands
| | - Chijioke N Umunnakwe
- Ndlovu Research Centre, Ndlovu Laboratories, Elandsdoorn, Dennilton, Limpopo, South Africa.
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Graziani A, Bozza S, Borghi M, Mencacci A, Camilloni B. Circulation and Seasonality of Respiratory Viruses in Hospitalized Patients during Five Consecutive Years (2019-2023) in Perugia, Italy. Viruses 2024; 16:1394. [PMID: 39339870 PMCID: PMC11437418 DOI: 10.3390/v16091394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/26/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024] Open
Abstract
The emergence of SARS-CoV-2 and the non-pharmacological interventions adopted to counter its spread appear to have led to changes in the normal circulation and seasonality of respiratory viruses. Our study aims to investigate changes related to the circulation of respiratory viruses, not SARS-CoV-2, among hospitalized patients in Perugia, Central Italy, between 2019 and 2023. The samples were collected from individuals who went to the emergency room (ER) or were hospitalized and analyzed using a molecular multiplex test. The results underline that non-pharmaceutical interventions altered the typical seasonal circulation patterns of different respiratory viruses. Those mostly affected were enveloped viruses like influenza viruses that disappeared in 2021; the least impact was recorded for Rhinovirus, which was detected during the pandemic period, maintaining the same seasonality observed in the pre-pandemic period although with a reduction in the number of positive samples. Our data underline the importance of the continuous monitoring of these viruses, especially to understand the timing with which prevention measures, not only non-pharmacological interventions but also the equipment of vaccine doses and monoclonal antibodies, should be adopted to reduce their circulation, particularly in the population at risk of developing severe forms of lower respiratory tract infection.
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Affiliation(s)
- Alessandro Graziani
- Microbiology and Clinical Microbiology Section, Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (A.G.); (S.B.); (A.M.)
| | - Silvia Bozza
- Microbiology and Clinical Microbiology Section, Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (A.G.); (S.B.); (A.M.)
- Microbiology Unit, Santa Maria della Misericordia Hospital, 06132 Perugia, Italy
| | - Monica Borghi
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche, 06126 Perugia, Italy;
| | - Antonella Mencacci
- Microbiology and Clinical Microbiology Section, Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (A.G.); (S.B.); (A.M.)
- Microbiology Unit, Santa Maria della Misericordia Hospital, 06132 Perugia, Italy
| | - Barbara Camilloni
- Microbiology and Clinical Microbiology Section, Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (A.G.); (S.B.); (A.M.)
- Microbiology Unit, Santa Maria della Misericordia Hospital, 06132 Perugia, Italy
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3
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Panatto D, Domnich A, Lai PL, Ogliastro M, Bruzzone B, Galli C, Stefanelli F, Pariani E, Orsi A, Icardi G. Epidemiology and molecular characteristics of respiratory syncytial virus (RSV) among italian community-dwelling adults, 2021/22 season. BMC Infect Dis 2023; 23:134. [PMID: 36882698 PMCID: PMC9990006 DOI: 10.1186/s12879-023-08100-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infections worldwide. While historically RSV research has been focused on children, data on RSV infection in adults are limited. The goal of this study was to establish the prevalence of RSV in community-dwelling Italian adults and analyze its genetic variability during the 2021/22 winter season. METHODS In this cross-sectional study, a random sample of naso-/oropharyngeal specimens from symptomatic adults seeking for SARS-CoV-2 molecular testing between December 2021 and March 2022 were tested for RSV and other respiratory pathogens by means of reverse-transcription polymerase chain reaction. RSV-positive samples were further molecularly characterized by sequence analysis. RESULTS Of 1,213 samples tested, 1.6% (95% CI: 0.9-2.4%) were positive for RSV and subgroups A (44.4%) and B (55.6%) were identified in similar proportions. The epidemic peak occurred in December 2021, when the RSV prevalence was as high as 4.6% (95% CI: 2.2-8.3%). The prevalence of RSV detection was similar (p = 0.64) to that of influenza virus (1.9%). All RSV A and B strains belonged to the ON1 and BA genotypes, respectively. Most (72.2%) RSV-positive samples were also positive for other pathogens being SARS-CoV-2, Streptococcus pneumoniae and rhinovirus the most frequent. RSV load was significantly higher among mono-detections than co-detections. CONCLUSION During the 2021/22 winter season, characterized by the predominant circulation of SARS-CoV-2 and some non-pharmaceutical containment measures still in place, a substantial proportion of Italian adults tested positive for genetically diversified strains of both RSV subtypes. In view of the upcoming registration of vaccines, establishment of the National RSV surveillance system is urgently needed.
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Affiliation(s)
- Donatella Panatto
- Department of Health Sciences, University of Genoa, Via A. Pastore, 1, 16132, Genoa, Italy. .,Interuniversity Research Center on Influenza and Other Transmissible Infections (CIRI-IT), Genoa, Italy.
| | - Alexander Domnich
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Piero Luigi Lai
- Department of Health Sciences, University of Genoa, Via A. Pastore, 1, 16132, Genoa, Italy
| | - Matilde Ogliastro
- Department of Health Sciences, University of Genoa, Via A. Pastore, 1, 16132, Genoa, Italy
| | - Bianca Bruzzone
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Federica Stefanelli
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Andrea Orsi
- Department of Health Sciences, University of Genoa, Via A. Pastore, 1, 16132, Genoa, Italy.,Interuniversity Research Center on Influenza and Other Transmissible Infections (CIRI-IT), Genoa, Italy.,Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Giancarlo Icardi
- Department of Health Sciences, University of Genoa, Via A. Pastore, 1, 16132, Genoa, Italy.,Interuniversity Research Center on Influenza and Other Transmissible Infections (CIRI-IT), Genoa, Italy.,Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, Genoa, Italy
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Domnich A, Bruzzone B, Trombetta CS, De Pace V, Ricucci V, Varesano S, Garzillo G, Ogliastro M, Orsi A, Icardi G. Rapid differential diagnosis of SARS-CoV-2, influenza A/B and respiratory syncytial viruses: Validation of a novel RT-PCR assay. J Clin Virol 2023; 161:105402. [PMID: 36805601 DOI: 10.1016/j.jcv.2023.105402] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/06/2023] [Accepted: 02/12/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Influenza and respiratory syncytial (RSV) viruses are expected to co-circulate with SARS-CoV-2 in the upcoming seasons and clinical differential diagnosis between them is difficult. Laboratory-based RT-PCR is a gold standard diagnostic method for influenza, RSV and SARS-CoV-2. The objective of this study was to estimate the diagnostic performance of a novel point-of-care RT-PCR assay STANDARD M10 Flu/RSV/SARS-CoV-2 (SD Biosensor) in a large number of clinical specimens with diversified (co)-infection patterns and viral loads. METHODS This was a retrospective study, in which all samples were tested in both STANDARD M10 Flu/RSV/SARS-CoV-2 index and Allplex SARS-CoV-2/Respiratory Panel 1 (Seegene) reference kits. Samples with discordant results were further processed in a third resolver test (Resp-4-Plex, Abbott). RESULTS A total of 1,019 naso-/oropharyngeal samples (50.3% positive for at least one virus) were processed in both STANDARD M10 Flu/RSV/SARS-CoV-2 and Allplex assays and the overall between-assay agreement was as high as 94.6%. Positive percent agreement of the STANDARD M10 Flu/RSV/SARS-CoV-2 was 100%, 96.6%, 97.3% and 99.4% for influenza A, B, RSV and SARS-CoV-2, respectively. The corresponding negative percent agreement was 99.7%. 100%, 100% and 98.4%, respectively. The expected positive and negative predictive values for all viruses were constantly above 96% in a reasonable range of disease prevalence. CONCLUSIONS STANDARD M10 Flu/RSV/SARS-CoV-2 is a reliable RT-PCR assay able to detect influenza A, influenza B, RSV and SARS-CoV-2 in one hour or less, fostering a rapid differential diagnosis of common respiratory viruses.
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Affiliation(s)
- Alexander Domnich
- Hygiene Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences, Genoa, Italy.
| | - Bianca Bruzzone
- Hygiene Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences, Genoa, Italy
| | | | - Vanessa De Pace
- Hygiene Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Valentina Ricucci
- Hygiene Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Serena Varesano
- Hygiene Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Giada Garzillo
- Department of Health Sciences, University of Genoa, Genoa, Italy
| | | | - Andrea Orsi
- Hygiene Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences, Genoa, Italy; Department of Health Sciences, University of Genoa, Genoa, Italy; Interuniversity Research Center on Influenza and Other Transmissible Infections (CIRI-IT), Genoa, Italy
| | - Giancarlo Icardi
- Hygiene Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences, Genoa, Italy; Department of Health Sciences, University of Genoa, Genoa, Italy; Interuniversity Research Center on Influenza and Other Transmissible Infections (CIRI-IT), Genoa, Italy
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Mboumba Bouassa RS, Tonen-Wolyec S, Veyer D, Péré H, Bélec L. Analytical performances of the AMPLIQUICK® Respiratory Triplex assay for simultaneous detection and differentiation of SARS-CoV-2, influenza A/B and respiratory syncytial viruses in respiratory specimens. PLoS One 2022; 17:e0262258. [PMID: 34986156 PMCID: PMC8730414 DOI: 10.1371/journal.pone.0262258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 12/21/2021] [Indexed: 12/28/2022] Open
Abstract
Although patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, influenza B and respiratory syncytial virus (RSV) show comparable or very similar manifestations, the therapeutic approaches of these respiratory viral infections are different, which requires an accurate diagnosis. Recently, the novel multiplex real-time reverse transcription-polymerase chain reaction assay AMPLIQUICK® Respiratory Triplex (BioSynex SA, Illkirch-Graffenstaden, France) allows simultaneous detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory tract samples. We herein evaluated the performance of the AMPLIQUICK® Respiratory Triplex for the detection of the four viruses in respiratory specimens, using Allplex™ Respiratory Panel 1 and 2019-nCoV assays (Seegene, Seoul, Korea) as reference comparator assays. A total of 359 archived predetermined respiratory samples, including 83, 145, 19 and 95 positive specimens for SARS-CoV-2, influenza A, influenza B and RSV respectively, were included. The AMPLIQUICK® Respiratory Triplex showed high concordance with the reference assays, with an overall agreement for SARS-CoV-2, influenza A, influenza B, and RSV at 97.6%, 98.8%, 98.3% and 100.0%, respectively, and high κ values ranging from 0.93 to 1.00, indicating an almost perfect agreement between assays. Furthermore, high correlations of cycle threshold (Ct) values were observed for positive samples of the four viruses between the AMPLIQUICK® Respiratory Triplex and comparator assays, with an overall high agreement between Ct values assessed by Bland-Altman analyses. In conclusion, these observations demonstrate that the multiplex AMPLIQUICK® Respiratory Triplex is a reliable assay for the qualitative detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory specimens, which may prove useful for streamlining diagnostics during the winter influenza-seasons.
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Affiliation(s)
- Ralph-Sydney Mboumba Bouassa
- Ecole Doctorale d’Infectiologie Tropicale, Franceville, Gabon
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Serge Tonen-Wolyec
- Ecole Doctorale d’Infectiologie Tropicale, Franceville, Gabon
- Faculty of Medicine and Pharmacy, University of Kisangani, Kisangani, The Democratic Republic of the Congo
| | - David Veyer
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Hélène Péré
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Laurent Bélec
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
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Comparative Evaluation of Allplex Respiratory Panels 1, 2, 3, and BioFire FilmArray Respiratory Panel for the Detection of Respiratory Infections. Diagnostics (Basel) 2021; 12:diagnostics12010009. [PMID: 35054176 PMCID: PMC8775103 DOI: 10.3390/diagnostics12010009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/17/2021] [Indexed: 12/02/2022] Open
Abstract
Multiplex nucleic acid amplification assays that simultaneously detect multiple respiratory pathogens in a single nasopharyngeal swab (NPS) specimen are widely used for rapid clinical diagnostics. We evaluated Allplex Respiratory Panel (RP) 1, 2, 3, and the BioFire FilmArray RP assay for detecting respiratory pathogens from NPS specimens. In all, 181 NPS specimens obtained from patients suspected of having respiratory infections during the non-influenza season (August–December 2019) were included. The Allplex RP 1, 2, and 3 detected 154 samples positive for respiratory viruses, whereas the BioFire FilmArray detected viruses in 98 samples. Co-infection with two or more viruses was detected in 41 and 17 NPS specimens by Allplex RP and the BioFire FilmArray RP, respectively. For adenoviruses, Allplex RP 1 detected 31 specimens, compared to 34 by the BioFire FilmArray. In all, 64 NPS specimens were positive for human enterovirus (HEV) and human rhinovirus (HRV) on the Allplex RP, in contrast to 39 HEV/HRV on the BioFire FilmArray. The parainfluenza virus (PIV-1–4) detection rate differed between the two systems. Most discrepant results were observed for NPS specimens with high cycle threshold values obtained by Allplex RP. This study showed concordant performance of the Allplex RP 1, 2, 3, and the BioFire FilmArray RP for the simultaneous detection of multiple respiratory viruses.
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Mboumba Bouassa RS, Tonen-Wolyec S, Rodary J, Bélec L. Comparative practicability and analytical performances of Credo VitaPCR™ Flu A&B and Cepheid Xpert® Xpress Flu/RSV platforms. Diagn Microbiol Infect Dis 2021; 100:115381. [PMID: 33852989 DOI: 10.1016/j.diagmicrobio.2021.115381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 10/21/2022]
Abstract
To compare the practicability (usability and satisfaction) and analytical performances of VitaPCR™ Flu A&B Assay (Credo Diagnostics Biomedical Pte. Ltd., Singapore, Republic of Singapore) and Xpert® Xpress Flu/RSV kit (Cepheid, Sunnyvale, USA), two rapid point-of-care (POC) nucleic acid amplification tests (NAATs) by reference to multiplex RT-PCR for respiratory viruses. Nasopharyngeal swabs (n=117) were collected from patients with influenza-like illness in Paris, France. Thawed specimens were further analyzed with both NAATs. The usability was comparable for both NAATs. Satisfaction questionnaire was better for the VitaPCR™ platform for the short time of test result in 20 minutes. Both NAATs showed comparable sensitivities (VitaPCRTM: 95.0%; Xpert® Xpress: 97.5%) and specificities (100%) for influenza A/B RNA detection, with excellent reliability and accuracy between both NAATs. Both VitaPCR™ and Xpert® Xpress NAATs can be implemented in hospital setting as POC NAATs to rapidly detect influenza A/B RNA in symptomatic patients.
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Affiliation(s)
- Ralph-Sydney Mboumba Bouassa
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France; Ecole Doctorale Régionale D'Afrique Centrale en Infectiologie Tropicale, Franceville, Gabon
| | - Serge Tonen-Wolyec
- Ecole Doctorale Régionale D'Afrique Centrale en Infectiologie Tropicale, Franceville, Gabon; Faculté de Médecine et Pharmacie, Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Julien Rodary
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laurent Bélec
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France; Faculté de Médecine Paris Descartes, Centre Université de Paris, Université de Paris, Sorbonne Paris Cité, and INSERM, Paris, France.
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Alosaimi B, Naeem A, Alghoribi MF, Okdah L, Hamed ME, AlYami AS, Alotaibi A, Enani M. Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. Viruses 2021; 13:136. [PMID: 33477951 PMCID: PMC7835825 DOI: 10.3390/v13010136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/24/2020] [Accepted: 01/05/2021] [Indexed: 12/15/2022] Open
Abstract
In December 2019, the emergence of SARS-CoV-2 virus in China led to a pandemic. Since both Influenza Like Illness (ILI) and COVID-19 case definitions overlap, we re-investigated the ILI cases using PCR for the presence of SARS-CoV-2 in 739 nasopharyngeal swabs collected from November 2019 to March 2020. SARS-CoV-2 RNA was found in 37 samples (5%) collected mostly during February 2020. It was followed by confirmation of evolutionary and spatial relationships using next generation sequencing (NGS). We observed that the overall incidence of ILI cases during 2019-2020 influenza season was considerably higher than previous years and was gradually replaced with SARS-CoV-2, which indicated a silent transmission among ambulatory patients. Sequencing of representative isolates confirmed independent introductions and silent transmission earlier than previously thought. Evolutionary and spatial analyses revealed clustering in the GH clade, characterized by three amino acid substitutions in spike gene (D614G), RdRp (P323L) and NS3 (Q57H). P323L causes conformational change near nsp8 binding site that might affect virus replication and transcription. In conclusion, assessment of the community transmission among patients with mild COVID-19 illness, particularly those without epidemiological link for acquiring the virus, is of utmost importance to guide policy makers to optimize public health interventions. The detection of SARS-CoV-2 in ILI cases shows the importance of ILI surveillance systems and warrants its further strengthening to mitigate the ongoing transmission of SARS-CoV-2. The effect of NS3 substitutions on oligomerization or membrane channel function (intra- and extracellular) needs functional validation.
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Affiliation(s)
- Bandar Alosaimi
- Department of Research labs, Research Center, King Fahad Medical City, Riyadh 11525, Saudi Arabia;
- College of Medicine, King Fahad Medical City, Riyadh 11525, Saudi Arabia
| | - Asif Naeem
- Department of Research labs, Research Center, King Fahad Medical City, Riyadh 11525, Saudi Arabia;
| | - Majed F. Alghoribi
- King Abdullah International Medical Research Center, Riyadh 11211, Saudi Arabia; (M.F.A.); (L.O.)
| | - Lilian Okdah
- King Abdullah International Medical Research Center, Riyadh 11211, Saudi Arabia; (M.F.A.); (L.O.)
| | - Maaweya E. Hamed
- College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Ahmad S. AlYami
- Pathology and Clinical Laboratory Medicine Administration, King Fahad Medical City, Riyadh 11525, Saudi Arabia;
| | - Athari Alotaibi
- General Administration for Research and Studies, Ministry of Health, Riyadh 11176, Saudi Arabia;
| | - Mushira Enani
- Medical Specialties Department, King Fahad Medical City, Riyadh 11525, Saudi Arabia;
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9
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Wabe N, Lindeman R, Post JJ, Rawlinson W, Miao M, Westbrook JI, Georgiou A. Cepheid Xpert ® Flu/RSV and Seegene Allplex ™ RP1 show high diagnostic agreement for the detection of influenza A/B and respiratory syncytial viruses in clinical practice. Influenza Other Respir Viruses 2020; 15:245-253. [PMID: 32815622 PMCID: PMC7461471 DOI: 10.1111/irv.12799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 12/15/2022] Open
Abstract
Background Molecular assays based on reverse transcription‐polymerase chain reaction (RT‐PCR) provide reliable results for the detection of respiratory pathogens, although diagnostic agreement varies. This study determined the agreement between the RT‐PCR assays (Xpert® Flu/RSV vs Allplex™ RP1) in detecting influenza A, influenza B, and respiratory syncytial viruses (RSVs) in clinical practice. Methods We retrospectively identified 914 patient encounters where testing with both Xpert® Flu/RSV and Allplex™ RP1 was undertaken between October 2015 and September 2019 in seven hospitals across New South Wales, Australia. The diagnostic agreement of the two assays was evaluated using positive percent agreement, negative percent agreement, and prevalence and bias‐adjusted kappa. Results The positive percent agreement was 95.1% for influenza A, 87.5% for influenza B, and 77.8% for RSV. The negative percent agreement was 99.4% for influenza A, 99.9% for influenza B, and 100% for RSV. The prevalence and bias‐adjusted kappa was 0.98 for influenza A, 0.99 for influenza B, and 0.97 for RSV. In a sensitivity analysis, the positive percent agreement values were significantly higher during the non‐influenza season than the influenza season for influenza B and RSV. Conclusions The Xpert® Flu/RSV and Allplex™ RP1 demonstrated a high diagnostic agreement for all three viruses assessed. The seasonal variation in the positive percent agreement of the two assays for influenza B and RSV may have been due to lower numbers assessed, variability in the virology of infections outside the peak season, or changes in the physiology of the infected host in different seasons.
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Affiliation(s)
- Nasir Wabe
- Centre for Health Systems and Safety Research, Australian Institute of Health Innovation, Macquarie University, North Ryde, NSW, Australia
| | | | - Jeffrey J Post
- Department of Infectious Diseases, Prince of Wales Hospital and Community Health Services, Randwick, NSW, Australia.,Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - William Rawlinson
- NSW Health Pathology Randwick, Prince of Wales Hospital and Community Health Services, Randwick, NSW, Australia.,School of Medical Sciences, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Melissa Miao
- Centre for Health Systems and Safety Research, Australian Institute of Health Innovation, Macquarie University, North Ryde, NSW, Australia
| | - Johanna I Westbrook
- Centre for Health Systems and Safety Research, Australian Institute of Health Innovation, Macquarie University, North Ryde, NSW, Australia
| | - Andrew Georgiou
- Centre for Health Systems and Safety Research, Australian Institute of Health Innovation, Macquarie University, North Ryde, NSW, Australia
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10
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Folgueira L, Moral N, Pascual C, Delgado R. Comparison of the Panther Fusion and Allplex assays for the detection of respiratory viruses in clinical samples. PLoS One 2019; 14:e0226403. [PMID: 31881030 PMCID: PMC6934309 DOI: 10.1371/journal.pone.0226403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/26/2019] [Indexed: 12/27/2022] Open
Abstract
Respiratory viral infections are the most frequent clinical syndrome affecting both children and adults, and early detection is fundamental to avoid infection-related risks and reduce the healthcare costs incurred by unnecessary antibiotic treatments. In this study, performance characteristics of two commercial methods, the Panther Fusion® assay (Hologic Inc., San Diego, CA, USA) were compared to Allplex™ respiratory panels (Seegene, Seoul, South Korea) for the detection of influenza A (Flu A), influenza B (Flu B), respiratory syncytial virus (RSV), parainfluenza virus (PIV), human metapneumovirus (hMPV), rhinovirus (RV) and adenovirus (AdV) targets. A total of 865 specimens collected prospectively and retrospectively were included, and discordant results were further examined using another commercial product, R-GENE™ respiratory kits (bioMérieux, Marcy l'Etoile, France). There was high agreement between both methods, with 98.6% concordance and a kappa (k) value of 0.9 (95% CI: 0.89-0.92). A specific analysis of both methods for each viral agent demonstrated comparable sensitivity and specificity, both ranging from 0.83 to 1 with good predictive values for the prospective part of the study. Good agreement between both methods was also found for the κ values obtained (ranging from 97.55% to 98.9%), with the lowest for hMPV (k = 0.83, 95% CI: 0.75-0.91) and RV (k = 0.73, 95% CI: 0.65-0.81). Amplification efficiency, measured according to the value of the cycle threshold (Ct) obtained in each of the amplifications in both tests, was significantly better with Panther Fusion for Flu A, Flu B, hMPV and RV. Regarding discordant results, R-GENE showed higher agreement with Panther Fusion-positive specimens (negative for Allplex; n = 28/71, 34.9%) than with Allplex-positive samples (negative for Panther Fusion; n = 7/49, 14.3%). In summary, Panther Fusion proved to be a more efficient fully-automated methodology, requiring shorter hands-on and turnaround times than Allplex.
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Affiliation(s)
- Lola Folgueira
- Microbiology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
- Biomedical Research Institute imas12, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Noelia Moral
- Microbiology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Consuelo Pascual
- Microbiology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Rafael Delgado
- Microbiology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
- Biomedical Research Institute imas12, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense, Madrid, Spain
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11
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Vandendriessche S, Padalko E, Wollants E, Verfaillie C, Verhasselt B, Coorevits L. Evaluation of the Seegene Allplex™ Respiratory Panel for diagnosis of acute respiratory tract infections. Acta Clin Belg 2019; 74:379-385. [PMID: 30307378 DOI: 10.1080/17843286.2018.1531605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Objectives: The Seegene AllplexTM Respiratory panel was retrospectively challenged using a collection of quality control samples (QCMD) and clinical samples previously analysed with validated routine methods. Methods: A collection of 111 samples [43 QCMD samples, 13 bronchoalveolar lavage fluids and 55 nasopharyngeal aspirates/swabs] was tested with Seegene AllplexTM. The clinical samples were tested previously using either FTD® Respiratory Pathogens 21 qPCR assay (Fast Track Diagnostics), an in-house multiplex PCR for Bordetella, or BioGX Sample-ReadyTM Atypical pneumo panel (Becton Dickinson). Samples were stored at -80°C prior to analysis with Seegene Allplex™, nucleic acids were automatically extracted with NucliSENS Easymag (bioMérieux). Samples returning discordant results were subjected to repeat testing and/or additional testing by reference laboratories. Results: Seegene correctly identified 41/43 QCMD samples (95.4%); two samples positive for respiratory syncytial virus (RSV) and human metapneumovirus, respectively, were only correctly identified following repeat testing. In the 56 clinical samples, overall, 97 pathogens were identified: 65 pathogens (67.0%) were detected both by routine methods and Seegene, 24 pathogens (24.7%) only by routine methods, and 8 pathogens (8.2%) only by Seegene. The majority of discordant results was detected in samples with low pathogen load (22/32, 68.8%) and in samples containing multiple pathogens (25/32, 78.1%). Full agreement between methods was observed for influenza, RSV, adenovirus, Bordetella (para)pertussis and Chlamydia pneumoniae. Discordance was observed for human metapneumovirus, coronavirus OC43, bocavirus and parainfluenza virus, mainly type 4. Conclusion: Overall, the Seegene AllplexTM assay performed well for routine detection of important respiratory targets. Acceptable agreement was observed between Seegene and other routine assays.
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Affiliation(s)
- Stien Vandendriessche
- Department of Laboratory Medicine, Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Elizaveta Padalko
- Department of Laboratory Medicine, Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Elke Wollants
- Rega Institute, Laboratory of Clinical & Epidemiological Virology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Charlotte Verfaillie
- Department of Laboratory Medicine, Medical Microbiology, AZ Sint-Lucas Ghent, Ghent, Belgium
| | - Bruno Verhasselt
- Department of Laboratory Medicine, Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Liselotte Coorevits
- Department of Laboratory Medicine, Medical Microbiology, Ghent University Hospital, Ghent, Belgium
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12
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Esposito S, Mencacci A, Cenci E, Camilloni B, Silvestri E, Principi N. Multiplex Platforms for the Identification of Respiratory Pathogens: Are They Useful in Pediatric Clinical Practice? Front Cell Infect Microbiol 2019; 9:196. [PMID: 31275863 PMCID: PMC6593267 DOI: 10.3389/fcimb.2019.00196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/21/2019] [Indexed: 01/31/2023] Open
Abstract
Respiratory tract infections (RTIs) are extremely common especially in the first year of life. Knowledge of the etiology of a RTI is essential to facilitate the appropriate management and the implementation of the most effective control measures. This perspective explains why laboratory methods that can identify pathogens in respiratory secretions have been developed over the course of many years. High-complexity multiplex panel assays that can simultaneously detect up to 20 viruses and up to four bacteria within a few hours have been marketed. However, are these platforms actually useful in pediatric clinical practice? In this manuscript, we showed that these platforms appear to be particularly important for epidemiological studies and clinical research. On the contrary, their routine use in pediatric clinical practice remains debatable. They can be used only in the hospital as they require specific equipment and laboratory technicians with considerable knowledge, training, and experience. Moreover, despite more sensitive and specific than other tests routinely used for respiratory pathogen identification, they do not offer significantly advantage for detection of the true etiology of a respiratory disease. Furthermore, knowledge of which virus is the cause of a respiratory disease is not useful from a therapeutic point of view unless influenza virus or respiratory syncytial virus are the infecting agents as effective drugs are available only for these pathogens. On the other hand, multiplex platforms can be justified in the presence of severe clinical manifestations, and in immunocompromised patients for whom specific treatment option can be available, particularly when they can be used simultaneously with platforms that allow identification of antimicrobial resistance to commonly used drugs. It is highly likely that these platforms, particularly those with high sensitivity and specificity and with low turnaround time, will become essential when new drugs effective and safe against most of the respiratory viruses will be available. Further studies on how to differentiate carriers from patients with true disease, as well as studies on the implications of coinfections and identification of antimicrobial resistance, are warranted.
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Affiliation(s)
- Susanna Esposito
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Antonella Mencacci
- Microbiology Unit, Department of Medicine, Università degli Studi di Perugia, Perugia, Italy
| | - Elio Cenci
- Microbiology Unit, Department of Medicine, Università degli Studi di Perugia, Perugia, Italy
| | - Barbara Camilloni
- Microbiology Unit, Department of Medicine, Università degli Studi di Perugia, Perugia, Italy
| | - Ettore Silvestri
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
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Kim J, Nam J, Jang W, Lim CS. Clinical Performance of the AllplexTM Respiratory Panel 1 Test Compared to SimplexaTM Flu A/B and RSV for Detection of Influenza Virus and Respiratory Syncytial Virus Infection Including Their Subtyping. Med Princ Pract 2019; 28:380-386. [PMID: 30831570 PMCID: PMC6639576 DOI: 10.1159/000499313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 03/03/2019] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE TheAllplexTM Respiratory Panel 1 (ARP) is a new assay based on a real-time polymerase chain reaction (RT-PCR) for the detection of influenza A (Flu A), influenza B virus (Flu B), and respiratory syncytial virus (RSV), including subtyping by multiple detection temperature (MuDT) technology. We evaluated the performance of the Allplex Respiratory Panel compared to the SimplexaTM Flu A/B & RSV assay (SP) and other diagnostic tools. MATERIALS AND METHODS A total of 372 samples were collected from patients at the Korea University Guro Hospital in Seoul, Korea. All samples were tested for influenza virus and RSV by ARP, SP, and an in-house RT-PCR. RESULTS The sensitivity of ARP was 95.56, 100, and 95.24% for Flu A, Flu B, and RSV, respectively. The specificity of ARP was 100, 100, and 100% for Flu A, Flu B, and RSV, respectively. SP had sensitivities and specificities of 98.89 and 100% for Flu A, 100 and 100% for Flu B, and 100 and 100% for RSV. CONCLUSION The Allplex panelshowed high sensitivity, specificity, positive predictive, and negative predictive values for the detection of Flu A, Flu B, and RSV. This assay is fast and easy to perform because it takes only about 150 min and there is no need for post-PCR electrophoresis. The ARP can be used as a reliable and convenient assay in clinical laboratories.
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Affiliation(s)
- Jeeyong Kim
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jeonghun Nam
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Woongsik Jang
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea,
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