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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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Domnich A, Massaro E, Icardi G, Orsi A. Multiplex molecular assays for the laboratory-based and point-of-care diagnosis of infections caused by seasonal influenza, COVID-19, and RSV. Expert Rev Mol Diagn 2024:1-12. [PMID: 39364620 DOI: 10.1080/14737159.2024.2408745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 09/22/2024] [Indexed: 10/05/2024]
Abstract
INTRODUCTION SARS-CoV-2, seasonal influenza, and respiratory syncytial virus (RSV) are major causes of acute respiratory infections in all age groups and responsible for an enormous socio-economic burden. The recently coined term 'tripledemic' describes co-circulation of these three viruses, a novel epidemiological paradigm that poses profound public health implications. AREAS COVERED Real-time reverse transcription polymerase chain reaction (RT-PCR) is now considered the reference method for the diagnosis of SARS-CoV-2, influenza, and RSV infections. Syndromic-based multiplex RT-PCR panels that simultaneously detect several respiratory viruses have become increasingly common. This review explores available molecular diagnostics (MDx) platforms for the diagnosis of SARS-CoV-2, influenza, and RSV in the same biological sample. Within some limitations of the published validation and diagnostic accuracy studies, both laboratory-based and point-of-care multiplex panels proved highly performant in identifying SARS-CoV-2, influenza A, influenza B, and RSV. Improved operational efficiency and faster turnaround times make these assays potentially cost-effective or even cost-saving. EXPERT OPINION The adoption of multiplex MDx assays for the contemporary detection of SARS-CoV-2, influenza, RSV, and other respiratory pathogens will likely increase in the next few years. To maximize the clinical usefulness and cost-effectiveness of these assays, locally issued guidelines and protocols on their implementation should be adopted.
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Affiliation(s)
- Alexander Domnich
- Hygiene Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Elvira Massaro
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Giancarlo Icardi
- Hygiene Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences, Genoa, Italy
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
- Interuniversity Research Center on Influenza and Other Transmissible Infections (CIRI-IT), Genoa, Italy
| | - Andrea Orsi
- Hygiene Unit, San Martino Policlinico Hospital - IRCCS for Oncology and Neurosciences, Genoa, Italy
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
- Interuniversity Research Center on Influenza and Other Transmissible Infections (CIRI-IT), Genoa, Italy
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Tan C, Chan CK, Ofner M, O'Brien J, Thomas NR, Callahan J, Pascual B, Palmer SJ, Serapion V, Fabro H, Kozak RA, Candon H, Chan AK, Powis JE, Leis JA. Implementation of point-of-care molecular testing for respiratory viruses in congregate living settings. Infect Control Hosp Epidemiol 2024:1-5. [PMID: 38659123 DOI: 10.1017/ice.2024.72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
OBJECTIVE To implement and evaluate a point-of-care (POC) molecular testing platform for respiratory viruses in congregate living settings (CLS). DESIGN Prospective quality improvement study. SETTING Seven CLS, including three nursing homes and four independent-living facilities. PARTICIPANTS Residents of CLS. METHODS A POC platform for COVID-19, influenza A and B, and respiratory syncytial virus was implemented at participating CLS from December 1, 2022 to April 15, 2023. Residents with respiratory symptoms underwent paired testing, with respiratory specimens tested first with the POC platform and then delivered to an off-site laboratory for multiplex respiratory virus panel (MRVP) polymerase chain reaction (PCR) as per standard protocol. Turn-around time and diagnostic accuracy of the POC platform were compared against MRVP PCR. In an exploratory analysis, time to outbreak declaration among participating CLS was compared against a convenience sample of 19 CLS that did not use the POC platform. RESULTS A total of 290 specimens that underwent paired testing were included. Turn-around time to result was significantly shorter with the POC platform compared to MRVP PCR, with median difference of 36.2 hours (interquartile range 21.8-46.4 hours). The POC platform had excellent diagnostic accuracy compared to MRVP PCR, with area under the curve statistic of .96. Time to outbreak declaration was shorter in CLS that used the POC platform compared to CLS that did not. CONCLUSION Rapid POC testing platforms for respiratory viruses can be implemented in CLS, with high diagnostic accuracy, expedited turn-around times, and shorter time to outbreak declaration.
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Affiliation(s)
- Charlie Tan
- Infection Prevention and Control, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Christina K Chan
- Infection Prevention and Control, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Marianna Ofner
- Infection Prevention and Control, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Jaclyn O'Brien
- Infection Prevention and Control, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Neethu R Thomas
- Infection Prevention and Control, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - James Callahan
- Infection Prevention and Control, Toronto East Health Network, Toronto, ON, Canada
| | - Brigitte Pascual
- Infection Prevention and Control, Toronto East Health Network, Toronto, ON, Canada
| | - Shawn J Palmer
- Infection Prevention and Control, Toronto East Health Network, Toronto, ON, Canada
| | - Victoria Serapion
- Infection Prevention and Control, Toronto East Health Network, Toronto, ON, Canada
| | - Hannah Fabro
- Infection Prevention and Control, Toronto East Health Network, Toronto, ON, Canada
| | - Robert A Kozak
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Heather Candon
- Infection Prevention and Control, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Public Health Sciences, Queen's University, Kingston, ON, Canada
| | - Adrienne K Chan
- Infection Prevention and Control, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Jeff E Powis
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Infection Prevention and Control, Toronto East Health Network, Toronto, ON, Canada
| | - Jerome A Leis
- Infection Prevention and Control, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
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Hardt M, Kaiser F, Voss T, Oelmüller U, Zatloukal K. Pre-analytical properties of different respiratory viruses for PCR-based detection: Comparative analysis of sampling devices and sample stabilization solutions. N Biotechnol 2024; 79:60-70. [PMID: 38145650 DOI: 10.1016/j.nbt.2023.12.005] [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: 08/04/2023] [Accepted: 12/22/2023] [Indexed: 12/27/2023]
Abstract
After the decline of the COVID-19 pandemic, health systems were challenged by the simultaneous prevalence of different respiratory viruses causing a wide overlap in symptoms. This increased the demand for multi-virus diagnostic tests which require suitable pre-analytical workflow solutions in order to receive valid diagnostic results. In this context, the effects of specimen storage duration and temperature on the RNA/DNA copy number stability of influenza A/B, RSV A/B, SARS-CoV-2 and adenovirus were examined for four commercially available transport swab systems and saliva collection devices. The respiratory viruses were more stable in the saliva collection devices than in the transport swab systems when stored at RT or 37 °C for up to 96 h. Moreover, no differences between viral nucleic acid stability of enveloped and non-enveloped viruses were observed. The infectivity of all enveloped viruses could be inactivated by the saliva collection device from PreAnalytiX. The Norgen saliva device completely inactivated influenza A/B, while RSV A/B were partially inactivated. The non-enveloped adenovirus was inactivated by a reduction factor of 10E+ 4 in both saliva collection devices. All respiratory viruses remained infectious in the transport swab systems. Two possible transport medium additives were tested which inactivated or strongly reduced viral replication of tested enveloped viruses but had no effect on the non-enveloped adenovirus. Finally the implementation of multi-target detection procedures involving a direct amplification approach was successfully tested by spike-in of all enveloped viruses simultaneously into transport swab systems. This fast and reproducible setup presents a valuable solution for future implementations in multi-virus testing strategies.
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Affiliation(s)
- Melina Hardt
- Diagnostic, and Research Center for Molecular Biomedicine, Diagnostic, and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | | | | | | | - Kurt Zatloukal
- Diagnostic, and Research Center for Molecular Biomedicine, Diagnostic, and Research Institute of Pathology, Medical University of Graz, Graz, Austria.
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Gao P, Fan Y, Kong X, Zhang R, Chen L, Jiang Y, Liu Y, Zhao M, Deng G, Cao Y, Ma L. A novel assay based on DNA melting temperature for multiplexed identification of SARS-CoV-2 and influenza A/B viruses. Front Microbiol 2023; 14:1249085. [PMID: 38173675 PMCID: PMC10762780 DOI: 10.3389/fmicb.2023.1249085] [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: 06/28/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and influenza viruses can cause respiratory illnesses with similar clinical symptoms, making their differential diagnoses challenging. Additionally, in critically ill SARS-CoV-2-infected patients, co-infections with other respiratory pathogens can lead to severe cytokine storm and serious complications. Therefore, a method for simultaneous detection of SARS-CoV-2 and influenza A and B viruses will be clinically beneficial. Methods We designed an assay to detect five gene targets simultaneously via asymmetric PCR-mediated melting curve analysis in a single tube. We used specific probes that hybridize to corresponding single-stranded amplicons at low temperature and dissociate at high temperature, creating different detection peaks representing the targets. The entire reaction was conducted in a closed tube, which minimizes the risk of contamination. The limit of detection, specificity, precision, and accuracy were determined. Results The assay exhibited a limit of detection of <20 copies/μL for SARS-CoV-2 and influenza A and <30 copies/μL for influenza B, with high reliability as demonstrated by a coefficient of variation for melting temperature of <1.16% across three virus concentrations. The performance of our developed assay and the pre-determined assay showed excellent agreement for clinical samples, with kappa coefficients ranging from 0.98 (for influenza A) to 1.00 (for SARS-CoV-2 and influenza B). No false-positive, and no cross-reactivity was observed with six common non-influenza respiratory viruses. Conclusion The newly developed assay offers a straightforward, cost-effective and nucleic acid contamination-free approach for simultaneous detection of the SARS-CoV-2, influenza A, and influenza B viruses. The method offers high analytical sensitivity, reliability, specificity, and accuracy. Its use will streamline testing for co-infections, increase testing throughput, and improve laboratory efficacy.
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Affiliation(s)
- Peng Gao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yanyan Fan
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xiaomu Kong
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Lida Chen
- Department of Blood Transfusion, China-Japan Friendship Hospital, Beijing, China
| | - Yongwei Jiang
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yi Liu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Meimei Zhao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Guoxiong Deng
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yongtong Cao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Liang Ma
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
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Asadi M, Hamilton D, Shomachuk C, Oloye FF, De Lange C, Pu X, Osunla CA, Cantin J, El-Baroudy S, Mejia EM, Gregorchuk B, Becker MG, Mangat C, Brinkmann M, Jones PD, Giesy JP, McPhedran KN. Assessment of rapid wastewater surveillance for determination of communicable disease spread in municipalities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166541. [PMID: 37625717 DOI: 10.1016/j.scitotenv.2023.166541] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/02/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
Wastewater surveillance (WS) helps to improve the understanding of the spread of communicable diseases in communities. WS can assist public health decision-makers in the design and implementation of timely mitigation measures. There is an increased need to use reliable, cost-effective, simple, and rapid WS systems, given traditional analytical (or 'gold-standard') programs are instrument/time-intensive, and dependent on highly skilled personnel. This study investigated the application of the portable GeneXpert platform for WS of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A virus (IAV), influenza B virus (IBV), and respiratory syncytial virus (RSV). The GeneXpert system with the Xpert Xpress-SARS-CoV-2/Flu/RSV test kit uses reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to analyze wastewater samples. From September 2022 through January 2023, wastewater samples were collected from the influents of municipal wastewater treatment plants (MWTPs) of Saskatoon, Prince Albert, and North Battleford in the province of Saskatchewan, Canada. Both raw and concentrated wastewater samples were subjected to the GeneXpert analysis. Results showed that the Saskatoon wastewater viral loads were significantly correlated to Saskatchewan's influenza and COVID-19 clinical cases, with a lead time of 10 days for IAV and a lag time of 4 days for SARS-CoV-2. Additionally, the GeneXpert analysis of the three cities' wastewater samples showed that the raw WS could capture the dynamics of SARS-CoV-2 and IAV due to their correlation with concentrated WS. Interestingly, IBV loads were not detected in any wastewater samples, while the Saskatoon and Prince Albert wastewater samples collected following the 2023 holiday season (end of December and beginning of January) were positive for RSV. This study indicates that the GeneXpert has excellent potential for use in the development of an early warning system for transmissible disease in municipalities and limited-resource communities while simultaneously providing stakeholders with an efficient WS methodology.
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Affiliation(s)
- Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada; Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Daniel Hamilton
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Corwyn Shomachuk
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Femi F Oloye
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Chantel De Lange
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Xia Pu
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Charles A Osunla
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Seba El-Baroudy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Edgard M Mejia
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Branden Gregorchuk
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michael G Becker
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chand Mangat
- Wastewater Surveillance Unit, On-Health Division, National Microbiology Laboratory - Winnipeg, Public Health Agency of Canada, Canada
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paul D Jones
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA; Department of Integrative Biology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA
| | - Kerry N McPhedran
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada.
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Alotaibi BS, Tantry BA, Bandy A, Ahmad R, Khursheed SQ, Ahmad A, Hakami MA, Shah NN. Simultaneous Detection of Influenza A/B, Respiratory Syncytial Virus, and SARS-CoV-2 in Nasopharyngeal Swabs by One-Tube Multiplex Reverse Transcription Polymerase Chain Reaction. Trop Med Infect Dis 2023; 8:326. [PMID: 37368744 DOI: 10.3390/tropicalmed8060326] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
The treatment and outcome of respiratory virus infections differ. SARS-CoV-2, as well as other respiratory viruses such as influenza virus (A and B) and respiratory syncytial virus (RSV), require simultaneous, cost-effective, and rapid differential detection. We used a gold standard five-target single-step RT-PCR to detect influenza viruses, RSV, and SARS-CoV-2, and this method can be extended to detect influenza virus subtypes. As a result, this five-target single-step RT-PCR method is ideal for differentiating respiratory viruses. The 5' nuclease activity of Taq DNA polymerase is used in the real-time reverse transcription PCR assay. The Taq man fast viral 1-step enzyme is a 4× Master mix and five-target primer probe mix that detects influenza A, influenza B, SARS-CoV-2 ORF1ab, respiratory syncytial viruses A/B and actin. When compared with TaqMan TM and Invitrogen superscript TM III Platinum and the Meril Kit for SARS-CoV-2, the assay demonstrated 100% sensitivity, specificity, and amplification efficiency of 90.1% for target genes. In conclusion, our one-tube multiplex RT-PCR assay offers a rapid and reliable method for the simultaneous detection of influenza A/B, RSV, and SARS-CoV-2 from nasopharyngeal swabs. This assay has the potential to enhance diagnostic capabilities and improve public health responses during respiratory outbreaks, enabling timely interventions and informed decision making.
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Affiliation(s)
- Bader S Alotaibi
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Shaqra University, Alquwayiyah 19257, Saudi Arabia
| | - Bilal Ahmad Tantry
- Department of Microbiology, Government Medical College, Srinagar 190010, India
| | - Altaf Bandy
- Department of Community Medicine, College of Medicine, Shaqra University, Shaqra 15273, Saudi Arabia
| | - Reyaz Ahmad
- Department of Microbiology, Government Medical College, Srinagar 190010, India
| | | | - Arshid Ahmad
- Department of Pulmonary Medicine, Government Medical College, Srinagar 190001, India
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Shaqra University, Alquwayiyah 19257, Saudi Arabia
| | - Naveed Nazir Shah
- Department of Pulmonary Medicine, Government Medical College, Srinagar 190001, India
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Boukli N, Flamand C, Chea KL, Heng L, Keo S, Sour K, In S, Chhim P, Chhor B, Kruy L, Feenstra JDM, Gandhi M, Okafor O, Ulekleiv C, Auerswald H, Horm VS, Karlsson EA. One assay to test them all: Multiplex assays for expansion of respiratory virus surveillance. Front Med (Lausanne) 2023; 10:1161268. [PMID: 37168265 PMCID: PMC10165998 DOI: 10.3389/fmed.2023.1161268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Molecular multiplex assays (MPAs) for simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza and respiratory syncytial virus (RSV) in a single RT-PCR reaction reduce time and increase efficiency to identify multiple pathogens with overlapping clinical presentation but different treatments or public health implications. Clinical performance of XpertXpress® SARS-CoV-2/Flu/RSV (Cepheid, GX), TaqPath™ COVID-19, FluA/B, RSV Combo kit (Thermo Fisher Scientific, TP), and PowerChek™ SARS-CoV-2/Influenza A&B/RSV Multiplex RT-PCR kit II (KogeneBiotech, PC) was compared to individual Standards of Care (SoC). Thirteen isolates of SARS-CoV-2, human seasonal influenza, and avian influenza served to assess limit of detection (LoD). Then, positive and negative residual nasopharyngeal specimens, collected under public health surveillance and pandemic response served for evaluation. Subsequently, comparison of effectiveness was assessed. The three MPAs confidently detect all lineages of SARS-CoV-2 and influenza viruses. MPA-LoDs vary from 1 to 2 Log10 differences from SoC depending on assay and strain. Clinical evaluation resulted in overall agreement between 97 and 100%, demonstrating a high accuracy to detect all targets. Existing differences in costs, testing burden and implementation constraints influence the choice in primary or community settings. TP, PC and GX, reliably detect SARS-CoV-2, influenza and RSV simultaneously, with reduced time-to-results and simplified workflows. MPAs have the potential to enhance diagnostics, surveillance system, and epidemic response to drive policy on prevention and control of viral respiratory infections.
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Affiliation(s)
- Narjis Boukli
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Claude Flamand
- Epidemiology and Public Health Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, CNRS, Paris, France
| | - Kim Lay Chea
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Leangyi Heng
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Seangmai Keo
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Kimhoung Sour
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sophea In
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Panha Chhim
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Bunthea Chhor
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Lomor Kruy
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | | | - Manoj Gandhi
- Thermo Fisher Scientific, South San Francisco CA, United States
| | - Obiageli Okafor
- Thermo Fisher Scientific, South San Francisco CA, United States
| | | | - Heidi Auerswald
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Viseth Srey Horm
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Erik A. Karlsson
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
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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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10
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Nasrullah A, Gangu K, Garg I, Javed A, Shuja H, Chourasia P, Shekhar R, Sheikh AB. Trends in Hospitalization and Mortality for Influenza and Other Respiratory Viruses during the COVID-19 Pandemic in the United States. Vaccines (Basel) 2023; 11:412. [PMID: 36851289 PMCID: PMC9966237 DOI: 10.3390/vaccines11020412] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Seasonal epidemics of respiratory viruses, respiratory syncytial virus (RSV), influenza viruses, parainfluenza viruses (PIVs), and human metapneumovirus (MPV) are associated with a significant healthcare burden secondary to hundreds of thousands of hospitalizations every year in the United States (US) alone. Preventive measures implemented to reduce the spread of SARS-CoV-2 (COVID-19 infection), including facemasks, hand hygiene, stay-at-home orders, and closure of schools and local/national borders may have impacted the transmission of these respiratory viruses. In this study, we looked at the hospitalization and mortality trends for various respiratory viral infections from January 2017 to December 2020. We found a strong reduction in all viral respiratory infections, with the lowest admission rates and mortality in the last season (2020) compared to the corresponding months from the past three years (2017-2019). This study highlights the importance of public health interventions implemented during the COVID-19 pandemic, which had far-reaching public health benefits. Appropriate and timely use of these measures may help to reduce the severity of future seasonal respiratory viral outbreaks as well as their burden on already strained healthcare systems.
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Affiliation(s)
- Adeel Nasrullah
- Division of Pulmonology and Critical Care, Allegheny Health Network, Pittsburg, PA 15212, USA
| | - Karthik Gangu
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ishan Garg
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
| | - Anam Javed
- Department of Internal Medicine, Allegheny Health Network, Pittsburgh, PA 15512, USA
| | - Hina Shuja
- Department of Medicine, Karachi Medical and Dental College, Karachi 74700, Pakistan
| | - Prabal Chourasia
- Department of Hospital Medicine, Mary Washington Hospital, Fredericksburg, VA 22401, USA
| | - Rahul Shekhar
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
| | - Abu Baker Sheikh
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
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11
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Chuang YC, Lin KP, Wang LA, Yeh TK, Liu PY. The Impact of the COVID-19 Pandemic on Respiratory Syncytial Virus Infection: A Narrative Review. Infect Drug Resist 2023; 16:661-675. [PMID: 36743336 PMCID: PMC9897071 DOI: 10.2147/idr.s396434] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/12/2023] [Indexed: 02/01/2023] Open
Abstract
Respiratory syncytial virus (RSV) is one of the most common respiratory viruses. It not only affects young children but also the elderly and immunocompromised patients. After the emergence of SARS-CoV-2 and the corona virus disease 2019 (COVID-19) era, a dramatic reduction in RSV activity was found, which coincided with the implementation of public health and social measures (PHSMs). However, the correlation is more complicated than we initially thought. After PHSMs were gradually lifted, a seasonality shift and a delayed RSV outbreak with greater number of infected patients were found in numerous countries, such as Israel, Australia, South Africa, New Zealand, France, United States, and Japan. Several hypotheses and possible reasons explaining the interaction between SARS-CoV-2 and RSV were mentioned. Since RSV vaccinations are still under investigation, administration of palivizumab should be considered in high-risk patients. In the post-COVID-19 era, greater attention should be paid to a further resurgence of RSV. In this narrative review, we conducted a thorough review of the current knowledge on the epidemiology of RSV during the COVID-19 era, the out-of-season outbreak of RSV, and the data on co-infection with RSV and SARS-CoV-2.
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Affiliation(s)
- Yu-Chuan Chuang
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Kuan-Pei Lin
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Li-An Wang
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ting-Kuang Yeh
- Division of Infectious Disease, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Po-Yu Liu
- Division of Infectious Disease, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan,Ph.D. in Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan,Correspondence: Po-Yu Liu, Division of Infectious Disease, Department of Internal Medicine, Taichung Veterans General Hospital, No. 1650, Sec. 4, Taiwan Blvd., Xitun Dist, Taichung City, 407219, Taiwan, Tel +886 4 2359 2525, Email
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12
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BOUKLI N, FLAMAND C, CHEA KL, HENG L, KEO S, SOUR K, IN S, CHHIM P, CHHOR B, KRUY L, FEENSTRA JDM, GANDHI M, OKAFOR O, ULEKLIEV C, AUERSWALD H, HORM VS, KARLSSON EA. ONE ASSAY TO TEST THEM ALL: COMPARING MULTIPLEX ASSAYS FOR EXPANSION OF RESPIRATORY VIRUS SURVEILLANCE. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.19.23284806. [PMID: 36711477 PMCID: PMC9882628 DOI: 10.1101/2023.01.19.23284806] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Background Molecular multiplex assays (MPAs) for simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza and respiratory syncytial virus (RSV) in a single RT-PCR reaction reduce time and increase efficiency to identify multiple pathogens with overlapping clinical presentation but different treatments or public health implications. Methods Clinical performance of XpertXpress ® SARS-CoV-2/Flu/RSV (Cepheid, GX), TaqPath™ COVID-19, FluA/B, RSV Combo kit (Thermo Fisher Scientific, TP), and PowerChek™ SARS-CoV-2/Influenza A&B/RSV Multiplex RT-PCR kit II (KogeneBiotech, PC) was compared to individual Standards of Care (SoC). Thirteen isolates of SARS-CoV-2, human seasonal influenza, and avian influenza served to assess limit of detection (LoD). Then, positive and negative residual nasopharyngeal specimens, collected under public health surveillance and pandemic response served for evaluation. Subsequently, comparison of effectiveness was assessed. Results The three MPAs confidently detect all lineages of SARS-CoV-2 and influenza viruses. MPA-LoDs vary from 1-2 Log10 differences from SoC depending on assay and strain. Clinical evaluation resulted in overall agreement between 97% and 100%, demonstrating a high accuracy to detect all targets. Existing differences in costs, testing burden and implementation constraints influence the choice in primary or community settings. Conclusion TP, PC and GX, reliably detect SARS-CoV-2, influenza and RSV simultaneously, with reduced time-to-results and simplified workflows. MPAs have the potential to enhancediagnostics, surveillance system, and epidemic response to drive policy on prevention and control of viral respiratory infections. IMPORTANCE Viral respiratory infections represent a major burden globally, weighed down by the COVID-19 pandemic, and threatened by spillover of novel zoonotic influenza viruses. Since respiratory infections share clinical presentations, identification of the causing agent for patient care and public health measures requires laboratory testing for several pathogens, including potential zoonotic spillovers. Simultaneous detection of SARS-CoV-2, influenza, and RSV in a single RT-PCR accelerates time from sampling to diagnosis, preserve consumables, and streamline human resources to respond to other endemic or emerging pathogens. Multiplex assays have the potential to sustain and even expand surveillance systems, can utilize capacity/capability developed during the COVID-19 pandemic worldwide, thereby strengthening epidemic/pandemic preparedness, prevention, and response.
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Affiliation(s)
- Narjis BOUKLI
- Virology Unit, National Influenza Center, WHO H5 Regional reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Claude FLAMAND
- Epidemiology Unit, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Kim Lay CHEA
- Virology Unit, National Influenza Center, WHO H5 Regional reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Leangyi HENG
- Virology Unit, National Influenza Center, WHO H5 Regional reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Seangmai KEO
- Virology Unit, National Influenza Center, WHO H5 Regional reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Kimhoung SOUR
- Virology Unit, National Influenza Center, WHO H5 Regional reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sophea IN
- Virology Unit, National Influenza Center, WHO H5 Regional reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Panha CHHIM
- Virology Unit, National Influenza Center, WHO H5 Regional reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Bunthea CHHOR
- Virology Unit, National Influenza Center, WHO H5 Regional reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Lomor KRUY
- Virology Unit, National Influenza Center, WHO H5 Regional reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | | | - Manoj GANDHI
- Thermo Fisher Scientific, South San Francisco CA, United States
| | - Obiageli OKAFOR
- Thermo Fisher Scientific, South San Francisco CA, United States
| | | | - Heidi AUERSWALD
- Virology Unit, National Influenza Center, WHO H5 Regional reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Viseth Srey HORM
- Virology Unit, National Influenza Center, WHO H5 Regional reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Erik A KARLSSON
- Virology Unit, National Influenza Center, WHO H5 Regional reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
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13
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Pourmomen M, Younesian O, Hosseinzadeh S, Hosseini Alarzi SS, Pourmomen M, Joshaghani H. Frequency of Influenza Infection in Symptomatic Patients Suspected of Having COVID-19. IRANIAN JOURNAL OF MEDICAL MICROBIOLOGY 2023. [DOI: 10.30699/ijmm.17.1.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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14
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Hu T, Ke X, Li W, Lin Y, Liang A, Ou Y, Chen C. CRISPR/Cas12a-Enabled Multiplex Biosensing Strategy Via an Affordable and Visual Nylon Membrane Readout. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204689. [PMID: 36442853 PMCID: PMC9839848 DOI: 10.1002/advs.202204689] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Most multiplex nucleic acids detection methods require numerous reagents and high-priced instruments. The emerging clustered regularly interspaced short palindromic repeats (CRISPR)/Cas has been regarded as a promising point-of-care (POC) strategy for nucleic acids detection. However, how to achieve CRISPR/Cas multiplex biosensing remains a challenge. Here, an affordable means termed CRISPR-RDB (CRISPR-based reverse dot blot) for multiplex target detection in parallel, which possesses the advantages of high sensitivity and specificity, cost-effectiveness, instrument-free, ease to use, and visualization is reported. CRISPR-RDB integrates the trans-cleavage activity of CRISPR-Cas12a with a commercial RDB technique. It utilizes different Cas12a-crRNA complexes to separately identify multiple targets in one sample and converts targeted information into colorimetric signals on a piece of accessible nylon membrane that attaches corresponding specific-oligonucleotide probes. It has demonstrated that the versatility of CRISPR-RDB by constructing a four-channel system to simultaneously detect influenza A, influenza B, respiratory syncytial virus, and SARS-CoV-2. With a simple modification of crRNAs, the CRISPR-RDB can be modified to detect human papillomavirus, saving two-thirds of the time compared to a commercial PCR-RDB kit. Further, a user-friendly microchip system for convenient use, as well as a smartphone app for signal interpretation, is engineered. CRISPR-RDB represents a desirable option for multiplexed biosensing and on-site diagnosis.
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Affiliation(s)
- Tao Hu
- The Children's HospitalZhejiang University School of MedicineNational Clinical Research Center for Child HealthHangzhouZhejiang310052China
| | - Xinxin Ke
- The Children's HospitalZhejiang University School of MedicineNational Clinical Research Center for Child HealthHangzhouZhejiang310052China
| | - Wei Li
- The Children's HospitalZhejiang University School of MedicineNational Clinical Research Center for Child HealthHangzhouZhejiang310052China
| | - Yu Lin
- International Peace Maternity & Child Health HospitalShanghai Municipal Key Clinical SpecialtyInstitute of Embryo‐Fetal Original Adult DiseaseSchool of MedicineShanghai Jiao Tong UniversityShanghai200030China
| | - Ajuan Liang
- Center of Reproductive MedicineShanghai First Maternity and Infant HospitalTongji University School of MedicineShanghai201204China
| | - Yangjing Ou
- International Peace Maternity & Child Health HospitalShanghai Municipal Key Clinical SpecialtyInstitute of Embryo‐Fetal Original Adult DiseaseSchool of MedicineShanghai Jiao Tong UniversityShanghai200030China
| | - Chuanxia Chen
- School of Materials Science and EngineeringUniversity of JinanJinanShandong250022China
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15
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Noble LD, Scott LE, Munir R, Du Plessis M, Steegen K, Hans L, Marokane P, Da Silva P, Stevens WS. Rapid Evaluation of the Xpert ® Xpress CoV-2 plus and Xpert ® Xpress CoV-2/Flu/RSV plus Tests. Diagnostics (Basel) 2022; 13:34. [PMID: 36611325 PMCID: PMC9818900 DOI: 10.3390/diagnostics13010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/25/2022] Open
Abstract
The Xpert® Xpress SARS-CoV-2 and Xpert® Xpress SARS-CoV-2/Flu/RSV tests were rapidly developed and widely used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. In response to emerging genetic variability, a new SARS-CoV-2 target (RNA-dependent RNA-polymerase) has been added to both tests: Xpert® Xpress CoV-2 plus and Xpert® Xpress CoV-2/Flu/RSV plus test. A rapid evaluation of both tests was performed in South Africa, using residual respiratory specimens. Residual respiratory specimens (n = 125) were used to evaluate the Xpert® Xpress CoV-2 plus test and included 50 genotyped specimens. The Xpert® Xpress CoV-2/Flu/RSV plus test was assessed using 45 genotyped SARS-CoV-2 specimens, 10 influenza A, 10 influenza B and 20 respiratory syncytial virus specimens. Results were compared to in-country standard-of-care tests. Genotyped specimens tested the performance of the test under pressure from circulating SARS-CoV-2 variants of concern. Reference material was included to assess the test limits and linearity. The Xpert® Xpress CoV-2 plus test performance compared to reference results across residual respiratory specimens was good (positive percentage agreement (PPA) = 95.2%, negative percentage agreement (NPA) = 95.0%) The Xpert® Xpress CoV-2/Flu/RSV plus test showed good performance across all residual respiratory specimens (PPA = 100%, NPA = 98.3%). All genotyped variants of concern were detected by both tests. The Xpert® Xpress CoV-2 plus and Xpert® Xpress CoV-2/Flu/RSV plus tests can be used to diagnose SARS-CoV-2, and to diagnose and differentiate SARS-CoV-2, influenza A, influenza B and respiratory syncytial virus, respectively. The NPA was lower than the recommended 99%, but was influenced by the low number of negative specimens tested. The variants of concern assessed did not affect test performance. It is recommended that sites perform their own assessments compared to in-country standard-of-care tests.
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Affiliation(s)
- Lara Dominique Noble
- WITS Diagnostic Innovation Hub, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Lesley Erica Scott
- WITS Diagnostic Innovation Hub, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Riffat Munir
- WITS Diagnostic Innovation Hub, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Mignon Du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg 2192, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Kim Steegen
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
- National Priority Programmes, National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Lucia Hans
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
- National Priority Programmes, National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Puleng Marokane
- National Priority Programmes, National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Pedro Da Silva
- National Priority Programmes, National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Wendy Susan Stevens
- WITS Diagnostic Innovation Hub, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
- National Priority Programmes, National Health Laboratory Service, Johannesburg 2000, South Africa
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COVID-19 and Influenza Coinfection Outcomes among Hospitalized Patients in the United States: A Propensity Matched Analysis of National Inpatient Sample. Vaccines (Basel) 2022; 10:vaccines10122159. [PMID: 36560569 PMCID: PMC9783554 DOI: 10.3390/vaccines10122159] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
This study aims to provide comparative data on clinical features and in-hospital outcomes among U.S. adults admitted to the hospital with COVID-19 and influenza infection using a nationwide inpatient sample (N.I.S.) data 2020. Data were collected on patient characteristics and in-hospital outcomes, including patient's age, race, sex, insurance status, median income, length of stay, mortality, hospitalization cost, comorbidities, mechanical ventilation, and vasopressor support. Additional analysis was performed using propensity matching. In propensity-matched cohort analysis, influenza-positive (and COVID-positive) patients had higher mean hospitalization cost (USD 129,742 vs. USD 68,878, p = 0.04) and total length of stay (9.9 days vs. 8.2 days, p = 0.01), higher odds of needing mechanical ventilation (OR 2.01, 95% CI 1.19-3.39), and higher in-hospital mortality (OR 2.09, 95% CI 1.03-4.24) relative to the COVID-positive and influenza-negative cohort. In conclusion, COVID-positive and influenza-negative patients had lower hospital charges, shorter hospital stays, and overall lower mortality, thereby supporting the use of the influenza vaccine in COVID-positive patients.
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Ellis JE, Guest P, Lawson V, Loecherbach J, Lindner N, McCulloch A. Performance Evaluation of the Microfluidic Antigen LumiraDx SARS-CoV-2 and Flu A/B Test in Diagnosing COVID-19 and Influenza in Patients with Respiratory Symptoms. Infect Dis Ther 2022; 11:2099-2109. [PMID: 36152227 PMCID: PMC9510530 DOI: 10.1007/s40121-022-00696-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/07/2022] [Indexed: 11/28/2022] Open
Abstract
Introduction Coronavirus disease 2019 (COVID-19) and influenza share similar symptoms, which hampers diagnosis. Given that they require different containment and treatment strategies, fast and accurate distinction between the two infections is needed. This study evaluates the sensitivity and specificity of the microfluidic antigen LumiraDx SARS-CoV-2 and Flu A/B Test for simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A/B from a single nasal swab. Methods Nasal samples were collected from patients as part of the ASPIRE (NCT04557046) and INSPIRE (NCT04288921) studies at point-of-care testing sites in the USA. ASPIRE study participants were included after developing COVID-19 symptoms in the last 14 days or following a positive SARS-CoV-2 test in the last 48 h. INSPIRE study participants were included after developing influenza symptoms in the last 4 days. Samples were extracted into proprietary buffer and analysed using the LumiraDx SARS-CoV-2 and Flu A/B Test. A reference sample was taken from each subject, placed into universal transport medium and tested using reference SARS-CoV-2 and influenza reverse transcription polymerase chain reaction (RT-PCR) tests. The test and reference samples were compared using the positive percent agreement (PPA) and negative percent agreement (NPA), together with their 95% confidence intervals (CIs). Results Analysis of the data from the ASPIRE (N = 124) and INSPIRE (N = 159) studies revealed high levels of agreement between the LumiraDx SARS-CoV-2 and Flu A/B Test and the reference tests in detecting SARS-CoV-2 (PPA = 95.5% [95% CI 84.9%, 98.7%]; NPA = 96.0% [95% CI 90.9%, 98.3%]), influenza A (PPA = 83.3% [95% CI 66.4%, 92.7%]; NPA = 97.7% [95% CI 93.4%, 99.2%]) and influenza B (PPA = 80.0% [95% CI 62.7%, 90.5%]; NPA = 95.3% [95% CI 90.2%, 97.9%]). Conclusions The LumiraDx SARS-CoV-2 and Flu A/B Test shows a high agreement with the reference RT-PCR tests while simultaneously detecting and differentiating between SARS-CoV-2 and influenza A/B. Trial Registration ClinicalTrials.gov identifiers NCT04557046 and NCT04288921. Supplementary Information The online version contains supplementary material available at 10.1007/s40121-022-00696-8.
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Affiliation(s)
- Jayne E Ellis
- LumiraDx Ltd, Stirling, UK. .,LumiraDx Ltd, 3 More London Riverside, London, SE1 2AQ, UK.
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18
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Miniaturized Real-Time PCR systems for SARS-CoV-2 detection at the Point-of-Care. Clin Chim Acta 2022; 536:104-111. [PMID: 36126763 PMCID: PMC9482443 DOI: 10.1016/j.cca.2022.09.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 12/12/2022]
Abstract
Over the past two years, SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) infection has spread globally causing multi-organ disease and severely impacting the healthcare systems of all countries. Accordingly, the development of easy-to-access diagnostic devices has become essential to limit the effect of the virus worldwide. Real-Time PCR is considered the gold standard to identify SARS-CoV-2 infection due to high sensitivity, affordability, and capacity to detect low viral loads at early disease stage. Advances in lab on a chip technology has led to the development of some Point-of-Care (POC) devices using Real-Time PCR and approved by the United States Food and Drug Administration. We provide an overview on recently developed POC tests for the rapid diagnosis of COVID-19 infection. Practical applications of miniaturized devices based on viral genome amplification as well as favorable features such as reduced sample processing time, ease of use by non-specialized personnel, and the potential of PCR-based POC technologies will be highlighted and reviewed.
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Impact of COVID-19 on the Changing Patterns of Respiratory Syncytial Virus Infections. Infect Dis Rep 2022; 14:558-568. [PMID: 35893478 PMCID: PMC9394296 DOI: 10.3390/idr14040059] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
Seasonal epidemics of respiratory syncytial virus (RSV) is one of the leading causes of hospitalization and mortality among children. Preventive measures implemented to reduce the spread of SARS-CoV-2, including facemasks, stay-at-home orders, closure of schools and local-national borders, and hand hygiene, may have also prevented the transmission of RSV and influenza. However, with the easing of COVID-19 imposed restrictions, many regions are noticing a delayed RSV outbreak. Some of these regions have also noted an increase in severity of these delayed RSV outbreaks partly due to a lack of protective immunity in the community following a lack of exposure from the previous season. Lessons learned from the COVID-19 pandemic can be implemented for controlling RSV outbreaks, including: (1) measures to reduce the spread, (2) effective vaccine development, and (3) genomic surveillance tools and computational modeling to predict the timing and severity of RSV outbreaks. These measures can help reduce the severity and prepare the health care system to deal with future RSV outbreaks by appropriate and timely allocation of health care resources.
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Kim TY, Kim JY, Shim HJ, Yun SA, Jang JH, Huh HJ, Kim JW, Lee NY. Performance Evaluation of the PowerChek SARS-CoV-2, Influenza A & B Multiplex Real-Time PCR Kit in Comparison with the BioFire Respiratory Panel. Ann Lab Med 2022; 42:473-477. [PMID: 35177568 PMCID: PMC8859561 DOI: 10.3343/alm.2022.42.4.473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/27/2021] [Accepted: 11/26/2021] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and influenza viruses may pose enormous challenges to our healthcare system. We evaluated the performance of the PowerChek SARS-CoV-2, Influenza A & B Multiplex Real-time PCR Kit (PowerChek; Kogene Biotech, Seoul, Korea) in comparison with the BioFire Respiratory Panels 2 and 2.1 (RP2 and RP2.1; bioMérieux, Marcy l’Étoile, France), using 147 nasopharyngeal swabs. The limit of detection (LOD) of the PowerChek assay was determined using SARS-CoV-2, influenza A, and B RNA standards. The LOD values of the PowerChek assay for SARS-CoV-2 and influenza A and B were 1.12, 1.24, and 0.61 copies/μL, respectively. The positive and negative percent agreements of the PowerChek assay compared with RP2 and RP2.1 were 97.5% (39/40) and 100% (107/107) for SARS-CoV-2; 100% (39/39) and 100% (108/108) for influenza A; and 100% (35/35) and 100% (112/112) for influenza B, respectively. The performance of the PowerChek assay was comparable to that of RP2 and RP2.1 for detecting SARS-CoV-2 and influenza A and B, suggesting its use in diagnosing SARS-CoV-2 and influenza infections.
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Affiliation(s)
- Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ji-Youn Kim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Hyang Jin Shim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Sun Ae Yun
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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21
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Quinton M, Geahr M, Gluck L, Jarrett J, Mostafa HH. Evaluation of the respiratory NeuMoDx™ Flu A-B/RSV/SARS-CoV-2 Vantage and Alinity m Resp-4-Plex assays. J Clin Virol 2022; 150-151:105164. [PMID: 35468544 PMCID: PMC9014635 DOI: 10.1016/j.jcv.2022.105164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/14/2022] [Accepted: 04/17/2022] [Indexed: 11/02/2022]
Abstract
Background Methods Results Conclusion
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22
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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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Clinical performance of the Xpert® Xpress Flu/RSV assay for the detection of Influenza A, B, and respiratory syncytial virus on ESwab™ medium. JOURNAL OF CLINICAL VIROLOGY PLUS 2022. [DOI: 10.1016/j.jcvp.2022.100066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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24
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Yun J, Park JH, Kim N, Roh EY, Shin S, Yoon JH, Kim TS, Park H. Evaluation of Three Multiplex Real-time Reverse Transcription PCR Assays for Simultaneous Detection of SARS-CoV-2, Influenza A/B, and Respiratory Syncytial Virus in Nasopharyngeal Swabs. J Korean Med Sci 2021; 36:e328. [PMID: 34904407 PMCID: PMC8668494 DOI: 10.3346/jkms.2021.36.e328] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/10/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND In the coronavirus disease 2019 (COVID-19) pandemic era, the simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus (Flu), and respiratory syncytial virus (RSV) is important in the rapid differential diagnosis in patients with respiratory symptoms. Three multiplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assays have been recently developed commercially in Korea: PowerChek™ SARS-CoV-2, Influenza A&B Multiplex Real-time PCR Kit (PowerChek; KogeneBiotech); STANDARD™ M Flu/SARS-CoV-2 Real-time Detection Kit (STANDARD M; SD BioSensor); and Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay (Allplex; Seegene). We evaluated the analytical and clinical performances of these kits. METHODS A limit of detection tests were performed and cross-reactivity analysis was executed using clinical respiratory samples. Ninety-seven SARS-CoV-2-positive, 201 SARS-CoV-2-negative, 71 influenza A-positive, 50 influenza B-positive, 78 RSV-positive, and 207 other respiratory virus-positive nasopharyngeal swabs were tested using the three assays. The AdvanSure™ respiratory viruses rRT-PCR assay (AdvanSure; LG Life Sciences) was used as a comparator assay for RSV. RESULTS Except in influenza B, in SARS-CoV-2 and influenza A, there were no significant differences in detecting specific genes of the viruses among the three assays. All three kits did not cross-react with common respiratory viruses. All three kits had greater than 92% positive percent agreement and negative percent agreement and ≥ 0.95 kappa value in the detection of SARS-CoV-2 and flu A/B. Allplex detected RSV more sensitively than AdvanSure. CONCLUSION The overall performance of three multiplex rRT-PCR assays for the concurrent detection of SARS-CoV-2, influenza A/B, and RSV was comparable. These kits will promote prompt differential diagnosis of COVID-19, influenza, and RSV infection in the COVID-19 pandemic era.
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Affiliation(s)
- Jiwon Yun
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Namhee Kim
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Hyun Yoon
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea.
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SARS-CoV-2 and Variant Diagnostic Testing Approaches in the United States. Viruses 2021; 13:v13122492. [PMID: 34960762 PMCID: PMC8703625 DOI: 10.3390/v13122492] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 12/23/2022] Open
Abstract
Purpose of Review Given the rapid development of diagnostic approaches to test for and diagnose infection with SARS-CoV-2 and its associated variants including Omicron (B.1.1.529), many options are available to diagnose infection. Multiple established diagnostic companies are now providing testing platforms whereas initially, testing was being performed with simple PCR-based tests using standard laboratory reagents. Recent Findings Additional testing platforms continue to be developed, including those to detect specific variants, but challenges with testing, including obtaining testing reagents and other related supplies, are frequently encountered. With time, the testing supply chain has improved, and more established companies are providing materials to support these testing efforts. In the United States (U.S.), the need for rapid assay development and subsequent approval through the attainment of emergency use authorization (EUA) has superseded the traditional arduous diagnostic testing approval workflow mandated by the FDA. Through these efforts, the U.S. has been able to continue to significantly increase its testing capabilities to address this pandemic; however, challenges still remain due to the diversity of the performance characteristics of tests being utilized and newly discovered viral variants. Summary This review provides an overview of the current diagnostic testing landscape, with pertinent information related to SARS-CoV-2 virology, variants and antibody responses that are available to diagnose infection in the U.S.
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26
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Chung HY, Jian MJ, Chang CK, Lin JC, Yeh KM, Yang YS, Chen CW, Hsieh SS, Tang SH, Perng CL, Chang FY, Hung KS, Chen ES, Yang MH, Shang HS. Multicenter study evaluating one multiplex RT-PCR assay to detect SARS-CoV-2, influenza A/B, and respiratory syncytia virus using the LabTurbo AIO open platform: epidemiological features, automated sample-to-result, and high-throughput testing. Aging (Albany NY) 2021; 13:24931-24942. [PMID: 34897035 PMCID: PMC8714143 DOI: 10.18632/aging.203761] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 11/23/2021] [Indexed: 04/20/2023]
Abstract
Since the Coronavirus 19 (COVID-19) pandemic, several SARS-CoV-2 variants of concern (SARS-CoV-2 VOC) have been reported. The B.1.1.7 variant has been associated with increased mortality and transmission risk. Furthermore, cluster and possible co-infection cases could occur in the next influenza season or COVID-19 pandemic wave, warranting efficient diagnosis and treatment decision making. Here, we aimed to detect SARS-CoV-2 and other common respiratory viruses using multiplex RT-PCR developed on the LabTurbo AIO 48 open system. We performed a multicenter study to evaluate the performance and analytical sensitivity of the LabTurbo AIO 48 system for SARS-CoV-2, influenza A/B, and respiratory syncytial virus (RSV) using 652 nasopharyngeal swab clinical samples from patients. The LabTurbo AIO 48 system demonstrated a sensitivity of 9.4 copies/per PCR for N2 of SARS-CoV-2; 24 copies/per PCR for M of influenza A and B; and 24 copies/per PCR for N of RSV. The assay presented consistent performance in the multicenter study. The multiplex RT-PCR applied on the LabTurbo AIO 48 open platform provided highly sensitive, robust, and accurate results and enabled high-throughput detection of B.1.1.7, influenza A/B, and RSV with short turnaround times. Therefore, this automated molecular diagnostic assay could enable streamlined testing if COVID-19 becomes a seasonal disease.
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Affiliation(s)
- Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Ming-Jr Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Kuo-Ming Yeh
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Ya-Sung Yang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chien-Wen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Shan-Shan Hsieh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Sheng-Hui Tang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Kuo-Sheng Hung
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - En-Sung Chen
- Department of Clinical Pathology, Cathay General Hospital, Taipei, Taiwan, ROC
| | - Mei-Hsiu Yang
- Department of Clinical Pathology, Cathay General Hospital, Taipei, Taiwan, ROC
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
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Isles N, Badman SG, Ballard S, Zhang B, Howden BP, Guy R, Williamson DA. Analytical sensitivity and specificity of the Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV assay. Pathology 2021; 54:120-122. [PMID: 34776245 PMCID: PMC8531023 DOI: 10.1016/j.pathol.2021.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 10/31/2022]
Affiliation(s)
- Nicole Isles
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Steven G Badman
- Kirby Institute, University of New South Wales, Sydney, NSW, Australia.
| | - Susan Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Bowen Zhang
- Department of Microbiology, Royal Melbourne Hospital, Melbourne, Vic, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Rebecca Guy
- Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Microbiology, Royal Melbourne Hospital, Melbourne, Vic, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
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Comparison of the PowerChek SARS-CoV-2, Influenza A&B, RSV Multiplex Real-time PCR Kit and BioFire Respiratory Panel 2.1 for simultaneous detection of SARS-CoV-2, influenza A and B, and respiratory syncytial virus. J Virol Methods 2021; 298:114304. [PMID: 34592335 PMCID: PMC8482523 DOI: 10.1016/j.jviromet.2021.114304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/23/2021] [Accepted: 09/26/2021] [Indexed: 11/20/2022]
Abstract
The potential co-circulation of SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) could pose an unprecedented challenge to healthcare systems worldwide. Here, we compared the performance of the PowerChek SARS-CoV-2, Influenza A&B, RSV Multiplex Real-time PCR Kit (PowerChek) for simultaneous detection of SARS-CoV-2, influenza A and B, and respiratory syncytial virus with that of BioFire Respiratory Panel 2.1 (RP2.1) using 175 nasopharyngeal swab (NPS) specimens. Positive percent agreement and negative percent agreement of the PowerChek assay compared to RP2.1 were as follows: 100 % (40/40) and 100 % (135/135) for SARS-CoV-2; 100 % (39/39) and 100 % (136/136) for influenza A; 100 % (35/35) and 100 % (140/140) for influenza B; and 93.1 % (27/29) and 100 % (146/146) for RSV, respectively. The limit of detection (LOD) was accessed using RNA standards for each virus, and the LOD values of the PowerChek assay for SARS-CoV-2, influenza A and B, and RSV were 0.36, 1.24, 0.09, and 0.63 copies/μL, respectively. Our results demonstrate that the PowerChek assay is sensitive and accurate for detection of SARS-CoV-2, influenza A and B, and RSV, suggesting that this assay can be a valuable diagnostic tool when SARS-CoV-2, influenza, and RSV are co-circulating.
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of COVID-19. Testing for SARS-CoV-2 infection is a critical element of the public health response to COVID-19. Point-of-care (POC) tests can drive patient management decisions for infectious diseases, including COVID-19. POC tests are available for the diagnosis of SARS-CoV-2 infections and include those that detect SARS-CoV-2 antigens as well as amplified RNA sequences. We provide a review of SARS-CoV-2 POC tests including their performance, settings for which they might be used, their impact and future directions. Further optimization and validation, new technologies as well as studies to determine clinical and epidemiological impact of SARS-CoV-2 POC tests are needed.
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Brukner I, Resendes A, Eintracht S, Papadakis AI, Oughton M. Sample Adequacy Control (SAC) Lowers False Negatives and Increases the Quality of Screening: Introduction of "Non-Competitive" SAC for qPCR Assays. Diagnostics (Basel) 2021; 11:diagnostics11071133. [PMID: 34206413 PMCID: PMC8305439 DOI: 10.3390/diagnostics11071133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/15/2021] [Accepted: 06/20/2021] [Indexed: 01/15/2023] Open
Abstract
Sample Adequacy Control (SAC) has critical analytical, clinical and epidemiological value that increases confidence in a negative test result. The SAC is an integral qPCR assay control, which ensures that all pre-analytical and analytical steps are adequate for accurate testing and reporting. As such, a negative SAC with a negative result on pathogen screen specifies that the result should be reported as inconclusive instead of negative. Despite this, many regulatory approved tests do not incorporate SAC into their assay design. Herein, we emphasize the universal value of SAC and offer for the first time, a simple technical strategy to introduce non-competitive SAC which does not interfere with the limit of detection for the screened pathogen. Integration of SAC can provide key benefits towards identifying, isolating, quarantining and contact tracing infected individuals and in turn can improve worldwide efforts in infection control.
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Affiliation(s)
- Ivan Brukner
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (A.R.); (A.I.P.)
- Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada;
- Correspondence: (I.B.); (M.O.); Tel.: +1-514-8038782 (I.B.); +1-514-3408222 (ext. 22662) (M.O.)
| | - Alex Resendes
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (A.R.); (A.I.P.)
| | - Shaun Eintracht
- Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada;
| | - Andreas I. Papadakis
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (A.R.); (A.I.P.)
| | - Matthew Oughton
- Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada;
- Correspondence: (I.B.); (M.O.); Tel.: +1-514-8038782 (I.B.); +1-514-3408222 (ext. 22662) (M.O.)
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Assay System for Simultaneous Detection of SARS-CoV-2 and Other Respiratory Viruses. Diagnostics (Basel) 2021; 11:diagnostics11061084. [PMID: 34199257 PMCID: PMC8231941 DOI: 10.3390/diagnostics11061084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 01/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggers disease with nonspecific symptoms that overlap those of infections caused by other seasonal respiratory viruses (RVs), such as the influenza virus (Flu) or respiratory syncytial virus (RSV). A molecular assay for accurate and rapid detection of RV and SARS-CoV-2 is crucial to manage these infections. Here, we compared the analytical performance and clinical reliability of Allplex™ SARS-CoV-2/FluA/FluB/RSV (SC2FabR; Seegene Inc., Seoul, South Korea) kit with those of four commercially available RV detection kits. Upon testing five target viral strains (SARS-CoV-2, FluA, FluB, RSV A, and RSV B), the analytical performance of SC2FabR was similar to that of the other kits, with no significant difference (p ≥ 0.78) in z-scores. The efficiency of SC2FabR (E-value, 81-104%) enabled reliable SARS-CoV-2 and seasonal RV detection in 888 nasopharyngeal swab specimens processed using a fully automated nucleic acid extraction platform. Bland-Altman analyses revealed an agreement value of 95.4% (SD ± 1.96) for the kits, indicating statistically similar results for all five. In conclusion, SC2FabR is a rapid and accurate diagnostic tool for both SARS-CoV-2 and seasonal RV detection, allowing for high-throughput RV analysis with efficiency comparable to that of commercially available kits. This can be used to help manage respiratory infections in patients during and after the coronavirus disease 2019 pandemic.
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Johnson G, Zubrzycki A, Henry M, Ranadheera C, Corbett C, Meyers AF, Sandstrom PA, Becker MG. Clinical evaluation of the GeneXpert® Xpert® Xpress SARS-CoV-2/Flu/RSV combination test. JOURNAL OF CLINICAL VIROLOGY PLUS 2021; 1:100014. [PMID: 35262002 PMCID: PMC8040320 DOI: 10.1016/j.jcvp.2021.100014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
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Zhou H, Tsou JH, Chinthalapally M, Liu H, Jiang F. Detection and Differentiation of SARS-CoV-2, Influenza, and Respiratory Syncytial Viruses by CRISPR. Diagnostics (Basel) 2021; 11:diagnostics11050823. [PMID: 34062939 PMCID: PMC8147329 DOI: 10.3390/diagnostics11050823] [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: 03/24/2021] [Revised: 04/29/2021] [Accepted: 04/29/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2, influenza, and respiratory syncytial viruses (RSVs) cause acute respiratory infections with similar symptoms. Since the treatments and outcomes of these infections are different, the early detection and accurate differentiation of the viruses are clinically important for the prevention and treatment of the diseases. We previously demonstrated that clustered regularly interspaced short palindromic repeats (CRISPR) could rapidly and precisely detect SARS-CoV-2. The objective of this study was to develop CRISPR as a test for simultaneously detecting and accurately distinguishing the viruses. The CRISPR assay with an RNA guide against each virus was performed in the reference standards of SARS-CoV-2, influenza A and B, and RSV. The CRISPR assay had a limit of detection of 1-100 copies/µL for specifically detecting SARS-CoV-2, influenza A and B, and RSV without cross-reaction with other respiratory viruses. The validation of the test in nasopharyngeal specimens showed that it had a 90-100% sensitivity and 100% specificity for the detection of SARS-CoV-2, influenza A and B, and RSV. The CRISPR assay could potentially be used for sensitive detection and specific differentiation of the respiratory viruses.
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Affiliation(s)
- Huifen Zhou
- Department of Pathology, University of Maryland School of Medicine, 10 S. Pine St., Baltimore, MD 21201, USA; (H.Z.); (J.-H.T.)
| | - Jen-Hui Tsou
- Department of Pathology, University of Maryland School of Medicine, 10 S. Pine St., Baltimore, MD 21201, USA; (H.Z.); (J.-H.T.)
| | - Molangur Chinthalapally
- Environmental Science and Technology, College of Agriculture and Natural Resources, University of Maryland, College Park, MD 20742, USA;
| | - Hongjie Liu
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, MD 20742, USA;
| | - Feng Jiang
- Department of Pathology, University of Maryland School of Medicine, 10 S. Pine St., Baltimore, MD 21201, USA; (H.Z.); (J.-H.T.)
- Correspondence:
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