1
|
Caza M, Hayman J, Jassem A, Wilmer A. Evaluation of the QIAstat-Dx Respiratory SARS-CoV-2 Panel for detection of pathogens in nasopharyngeal and lower respiratory tract specimens. Diagn Microbiol Infect Dis 2024; 110:116368. [PMID: 38906032 DOI: 10.1016/j.diagmicrobio.2024.116368] [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: 01/08/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/23/2024]
Abstract
This study evaluates the performance of the QIAstat-Dx Respiratory SARS-CoV-2 Panel (RS2P) for the detection of respiratory pathogens. RS2P testing was performed on 440 specimens, including 82 negatives and 358 specimens positive for 1 or more targets (520 targets initially detected). Initial testing was performed on multiple platforms during routine laboratory workflow. Specimens with discordant results on RS2P were re-tested on a different platform to obtain a consensus result based on agreement of 2/3 assays. Percent positive, negative and overall agreement (PPA, PNA, POA), as well as concordance by number of targets and CT value range were calculated. RS2P produced valid results in 439 specimens, with a POA of 91.5 % based on consensus results, with 16/31 (51.6 %) discordant specimens with >1 positive target. When individual targets were examined, PPA, PNA and POA were 93.7 %, 99.9 % and 99.6 % compared to consensus results. Overall, RS2P performed well in detection of respiratory pathogens.
Collapse
Affiliation(s)
- Mélissa Caza
- Kelowna General Hospital, Kelowna, BC, Canada; University of British Columbia, Vancouver, BC, Canada; University of British Columbia Okanagan, Kelowna, BC, Canada.
| | - Jen Hayman
- University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Agatha Jassem
- University of British Columbia, Vancouver, BC, Canada; BCCDC Public Health Microbiology & Reference Laboratory, Vancouver, BC, Canada
| | - Amanda Wilmer
- Kelowna General Hospital, Kelowna, BC, Canada; University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
2
|
Adami ME, Giamarellos-Bourboulis EJ, Polyzogopoulou E. Towards improved point-of-care (POC) testing for patients with suspected sepsis: POC tests for host biomarkers and possible microbial pathogens. Expert Rev Mol Diagn 2024:1-11. [PMID: 39135402 DOI: 10.1080/14737159.2024.2392283] [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: 06/12/2024] [Accepted: 08/11/2024] [Indexed: 08/15/2024]
Abstract
INTRODUCTION Sepsis is a heterogeneous syndrome often misdiagnosed. Point-of-care (POC) diagnostic tests are commonly used to guide decision and include host biomarkers and molecular diagnostics. AREAS COVERED The diagnostic and prognostic accuracy of established and emerging biomarkers for sepsis, including procalcitonin (PCT) soluble urokinase plasminogen activator receptor (suPAR), presepsin, TRAIL/IP-10/CRP, MxA, and MxA-CRP, are analyzed in this review. The clinical utility of the two prevalent molecular techniques for pathogens identification using polymerase chain reaction (PCR) assays is also presented: FILMARRAY and QIAstat-Dx RP. EXPERT OPINION The rising benefits of the combined use of POC biomarkers with molecular diagnostics in daily clinical routine appear to outperform conventional practices in terms of reduced turnaround time, timely diagnosis, and prompt administration of the appropriate treatment. Yet, this must be further demonstrated in future investigations. However, the cost-effectiveness of POC tests and the high rate of false positive and negative results, indicate the need for a comprehensive clinical evaluation.
Collapse
Affiliation(s)
- Maria-Evangelia Adami
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | | | - Effie Polyzogopoulou
- Department of Emergency Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| |
Collapse
|
3
|
Hayden MK, Hanson KE, Englund JA, Lee MJ, Loeb M, Lee F, Morgan DJ, Patel R, El Mikati IK, Iqneibi S, Alabed F, Amarin JZ, Mansour R, Patel P, Falck-Ytter Y, Morgan RL, Murad MH, Sultan S, Bhimraj A, Mustafa RA. The Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19: Molecular Diagnostic Testing (December 2023). Clin Infect Dis 2024; 78:e385-e415. [PMID: 38112284 DOI: 10.1093/cid/ciad646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Indexed: 12/21/2023] Open
Abstract
Accurate molecular diagnostic tests are necessary for confirming a diagnosis of coronavirus disease 2019 (COVID-19) and for identifying asymptomatic carriage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The number of available SARS-CoV-2 nucleic acid detection tests continues to increase as does the COVID-19 diagnostic literature. Thus, the Infectious Diseases Society of America (IDSA) developed an evidence-based diagnostic guideline to assist clinicians, clinical laboratorians, patients, and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. In addition, we provide a conceptual framework for understanding molecular diagnostic test performance, discuss nuances of test result interpretation in a variety of practice settings, and highlight important unmet research needs related to COVID-19 diagnostic testing. IDSA convened a multidisciplinary panel of infectious diseases clinicians, clinical microbiologists, and experts in systematic literature review to identify and prioritize clinical questions and outcomes related to the use of SARS-CoV-2 molecular diagnostics. Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to assess the certainty of evidence and make testing recommendations. The panel agreed on 12 diagnostic recommendations. Access to accurate SARS-CoV-2 nucleic acid testing is critical for patient care, hospital infection prevention, and the public health response to COVID-19 infection. Information on the clinical performance of available tests continues to grow, but the quality of evidence of the current literature to support this updated molecular diagnostic guideline remains moderate to very low. Recognizing these limitations, the IDSA panel weighed available diagnostic evidence and recommends nucleic acid testing for all symptomatic individuals suspected of having COVID-19. In addition, testing is suggested for asymptomatic individuals with known or suspected contact with a COVID-19 case when the results will impact isolation/quarantine/personal protective equipment (PPE) usage decisions. Evidence in support of rapid testing and testing of upper respiratory specimens other than nasopharyngeal swabs, which offer logistical advantages, is sufficient to warrant conditional recommendations in favor of these approaches.
Collapse
Affiliation(s)
- Mary K Hayden
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, Illinois, USA
- Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Kimberly E Hanson
- Divisions of Infectious Diseases and Clinical Microbiology, University of Utah, Salt Lake City, Utah, USA
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Mark J Lee
- Department of Pathology and Clinical Microbiology Laboratory, Duke University School of Medicine, Durham, North Carolina, USA
| | - Mark Loeb
- Division of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Francesca Lee
- Departments of Pathology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Daniel J Morgan
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Robin Patel
- Division of Clinical Microbiology and Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ibrahim K El Mikati
- Outcomes and Implementation Research Unit, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Shahad Iqneibi
- Faculty of Medicine, University of Jordan, Amman, Jordan
| | - Farouk Alabed
- School of Medicine, The University of Kansas, Kansas City, Kansas, USA
| | - Justin Z Amarin
- Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Razan Mansour
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Payal Patel
- Department of Pulmonary, Allergy, Critical Care, and Sleep Medicine and Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Yngve Falck-Ytter
- Department of Medicine, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA
| | - Rebecca L Morgan
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - M Hassan Murad
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Shahnaz Sultan
- Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis VA Healthcare System, Minneapolis, Minnesota, USA
| | - Adarsh Bhimraj
- Houston Methodist Hospital, Center of Excellence for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Reem A Mustafa
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| |
Collapse
|
4
|
Brouwer CWE, Russcher A, Rezek Y, Nijhuis RHT. Evaluation of the fully automated, sample-to-result Seegene STARlet-AIOS platform for detection of SARS-CoV-2, influenza virus A, influenza virus B, and RSV. Eur J Clin Microbiol Infect Dis 2024; 43:87-93. [PMID: 37966626 DOI: 10.1007/s10096-023-04703-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/06/2023] [Indexed: 11/16/2023]
Abstract
Early, accurate, and bulk detection of respiratory pathogens is essential for patient management and infection control. STARlet-All-in-One System (AIOS) (Seegene) is a new, fully automated, sample-to-result, molecular diagnostic platform. This study describes the first evaluation of STARlet-AIOS, by testing the Allplex™ SARS-CoV-2 (AS) and Allplex™ SARS-CoV-2/FluA/FluB/RSV combination (AC) assays in comparison to the SARS-CoV-2 assays used at our institute. Over a 3-week period, all naso-/oropharyngeal specimens tested for SARS-CoV-2 using either GeneXpert, Panther, or in-house developed test (LDT) were tested on the AIOS using the AS or AC assays. In addition, retrospective cohorts of specimens containing SARS-CoV-2, influenza virus A, influenza virus B, and RSV were tested. Discrepant results were re-tested with another assay used in this study. Hands-on time (HOT) and turn-around time (TAT) of the different systems were monitored and compared. A total of 738 specimens were tested on the AIOS using the AS assay. In addition, 210 specimens were tested using the AC assay. Overall agreement for SARS-CoV-2 detection was established as 98.5% and 95.2% for the AS and AC assay, respectively. Retrospective testing revealed high agreements for all targets, except for influenza virus A (agreement of 87.5%). HOT of the system was comparable to the HOT of GeneXpert and Panther and TAT comparable to Panther and LDT. The AIOS proved to be a robust sample-to-result system with low HOT and moderate TAT. This study showed reliable detection of SARS-CoV-2, influenza virus B, and RSV, whereas detection of influenza virus A using the AC assay appeared to be suboptimal.
Collapse
Affiliation(s)
- C W E Brouwer
- Laboratory for Medical Microbiology and Medical Immunology, Meander Medical Center, Maatweg 3, 3813 TZ, Amersfoort, The Netherlands
| | - A Russcher
- Laboratory for Medical Microbiology and Medical Immunology, Meander Medical Center, Maatweg 3, 3813 TZ, Amersfoort, The Netherlands
| | - Y Rezek
- Laboratory for Medical Microbiology and Medical Immunology, Meander Medical Center, Maatweg 3, 3813 TZ, Amersfoort, The Netherlands
| | - R H T Nijhuis
- Laboratory for Medical Microbiology and Medical Immunology, Meander Medical Center, Maatweg 3, 3813 TZ, Amersfoort, The Netherlands.
| |
Collapse
|
5
|
Leblanc J, Dusserre-Telmon L, Chauvin A, Simon T, Sabbatini CE, Hemming K, Colizza V, Bérard L, Convert J, Lazazga S, Jegou C, Taibi N, Dautheville S, Zaghia D, Gerlier C, Domergue M, Larrouturou F, Bonnet F, Fontanet A, Salhi S, LeGoff J, Crémieux AC. Intensified screening for SARS-CoV-2 in 18 emergency departments in the Paris metropolitan area, France (DEPIST-COVID): A cluster-randomized, two-period, crossover trial. PLoS Med 2023; 20:e1004317. [PMID: 38060611 PMCID: PMC10735176 DOI: 10.1371/journal.pmed.1004317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 12/21/2023] [Accepted: 11/02/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Asymptomatic and paucisymptomatic infections account for a substantial portion of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) transmissions. The value of intensified screening strategies, especially in emergency departments (EDs), in reaching asymptomatic and paucisymptomatic patients and helping to improve detection and reduce transmission has not been documented. The objective of this study was to evaluate in EDs whether an intensified SARS-CoV-2 screening strategy combining nurse-driven screening for asymptomatic/paucisymptomatic patients with routine practice (intervention) could contribute to higher detection of SARS-CoV-2 infections compared to routine practice alone, including screening for symptomatic or hospitalized patients (control). METHODS AND FINDINGS We conducted a cluster-randomized, two-period, crossover trial from February 2021 to May 2021 in 18 EDs in the Paris metropolitan area, France. All adults visiting the EDs were eligible. At the start of the first period, 18 EDs were randomized to the intervention or control strategy by balanced block randomization with stratification, with the alternative condition being applied in the second period. During the control period, routine screening for SARS-CoV-2 included screening for symptomatic or hospitalized patients. During the intervention period, in addition to routine screening practice, a questionnaire about risk exposure and symptoms and a SARS-CoV-2 screening test were offered by nurses to all remaining asymptomatic/paucisymptomatic patients. The primary outcome was the proportion of newly diagnosed SARS-CoV-2-positive patients among all adults visiting the 18 EDs. Primary analysis was by intention-to-treat. The primary outcome was analyzed using a generalized linear mixed model (Poisson distribution) with the center and center by period as random effects and the strategy (intervention versus control) and period (modeled as a weekly categorical variable) as fixed effects with additional adjustment for community incidence. During the intervention and control periods, 69,248 patients and 69,104 patients, respectively, were included for a total of 138,352 patients. Patients had a median age of 45.0 years [31.0, 63.0], and women represented 45.7% of the patients. During the intervention period, 6,332 asymptomatic/paucisymptomatic patients completed the questionnaire; 4,283 were screened for SARS-CoV-2 by nurses, leading to 224 new SARS-CoV-2 diagnoses. A total of 1,859 patients versus 2,084 patients were newly diagnosed during the intervention and control periods, respectively (adjusted analysis: 26.7/1,000 versus 26.2/1,000, adjusted relative risk: 1.02 (95% confidence interval (CI) [0.94, 1.11]; p = 0.634)). The main limitation of this study is that it was conducted in a rapidly evolving epidemiological context. CONCLUSIONS The results of this study showed that intensified screening for SARS-CoV-2 in EDs was unlikely to identify a higher proportion of newly diagnosed patients. TRIAL REGISTRATION Trial registration number: ClinicalTrials.gov NCT04756609.
Collapse
Affiliation(s)
- Judith Leblanc
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health; Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital St Antoine, Clinical Research Platform Paris-East, Paris, France
| | | | - Anthony Chauvin
- AP-HP, Hôpital Lariboisière, Emergency department; Université Paris Cité, INSERM U942 MASCOT, Paris, France
| | - Tabassome Simon
- AP-HP, Hôpital St Antoine, Clinical Research Platform Paris-East; Sorbonne Université, Department of Clinical Pharmacology, Paris, France
| | - Chiara E. Sabbatini
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Karla Hemming
- University of Birmingham, Institute of Applied Health Research, Birmingham, United Kingdom
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Laurence Bérard
- AP-HP, Hôpital St Antoine, Clinical Research Platform Paris-East, Paris, France
| | - Jérome Convert
- AP-HP, Hôpital Lariboisière, Emergency department, Paris, France
| | - Sonia Lazazga
- Centre Hospitalier de Gonesse, Emergency department, Gonesse, France
| | - Carole Jegou
- AP-HP, Hôpital Avicenne, Emergency department, Bobigny, France
| | - Nabila Taibi
- AP-HP, Hôpital Pitié-Salpêtrière, Emergency department, Paris, France
| | | | - Damien Zaghia
- AP-HP, Hôpital Beaujon, Emergency department, Clichy, France
| | - Camille Gerlier
- Hôpital Paris St Joseph, Emergency department, Paris, France
| | - Muriel Domergue
- AP-HP, Hôpital Européen Georges Pompidou, Emergency department, Paris, France
| | | | - Florence Bonnet
- AP-HP, Hôpital St Antoine, Emergency department, Paris, France
| | - Arnaud Fontanet
- Institut Pasteur, Emerging Diseases Epidemiology Unit; PACRI unit, Conservatoire National des Arts et Métiers, Paris, France
| | - Sarah Salhi
- AP-HP, Hôpital St Antoine, Clinical Research Platform Paris-East, Paris, France
| | - Jérome LeGoff
- Université Paris Cité, INSERM U976, INSIGHT Team; AP-HP, Hôpital St Louis, Virology Department, Paris, France
| | - Anne-Claude Crémieux
- AP-HP, Hôpital St Louis, Infectious Diseases Department; Université Paris Cité, FHU PROTHEE, Paris, France
| | | | | |
Collapse
|
6
|
Batty M, Papadakis G, Zhang C, Tran T, Druce J, Lim CK, Williamson DA, Jackson K. Laboratory assessment of a multi-target assay for the rapid detection of viruses causing vesicular diseases. J Clin Virol 2023; 165:105525. [PMID: 37364498 PMCID: PMC10287189 DOI: 10.1016/j.jcv.2023.105525] [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: 05/10/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND The recent mpox outbreak has highlighted the need to rapidly diagnose the causative agents of viral vesicular disease to inform treatment and control measures. Common causes of vesicular disease include Monkeypox virus (MPXV), clades I and II, Herpes simplex viruses Type 1 and Type 2 (HSV-1, HSV-2), human herpes virus 6 (HHV-6), Varicella-zoster virus (VZV) and Enteroviruses (EVs). Here, we assessed a syndromic viral vesicular panel for rapid and simultaneous detection of these 7 targets in a single cartridge. OBJECTIVE The aim of this study was to evaluate the QIAStat-Dx ® viral vesicular (VV) panel and compare with laboratory developed tests (LDTs). Limit of detection, inter-run variability, cross-reactivity and specificity were assessed. Positive and negative percent agreement, and correlation between assays was determined using 124 clinical samples from multiple anatomical sites. RESULTS The overall concordance between the QIAstat and LDTs was 96%. Positive percent agreement was 82% for HHV-6, 89% for HSV-1 and 100% for MPXV, HSV-2, EV and VZV. Negative percent agreement was 100% for all targets assessed. There was no cross-reactivity with Vaccinia, Orf, Molluscum contagiosum viruses, and a pooled respiratory panel. CONCLUSION The QIAstat VV multi-target syndromic panel combine ease of use, rapid turnaround, good sensitivity and specificity for enhanced diagnosis, clinical care and public health responses.
Collapse
Affiliation(s)
- Mitchell Batty
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Georgina Papadakis
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Changxu Zhang
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Thomas Tran
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Chuan Kok Lim
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Deborah A Williamson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Kathy Jackson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia.
| |
Collapse
|
7
|
Lin SC, Wang HC, Lin WC, Kuo YT, Hsu YH, Tsai YT, Lu SC, Wang YH, Chen SY. Viral Pneumonia during the COVID-19 Pandemic, 2019-2021 Evoking Needs for SARS-CoV-2 and Additional Vaccinations. Vaccines (Basel) 2023; 11:vaccines11050905. [PMID: 37243009 DOI: 10.3390/vaccines11050905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/24/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Coronaviruses can cause pneumonia, with clinical symptoms that may be similar to the symptoms of other viral pneumonias. To our knowledge, there have been no reports regarding cases of pneumonia caused by coronaviruses and other viruses among hospitalized patients in the past 3 years before and during coronavirus disease 2019 (COVID-19). Here, we analysed the causes of viral pneumonia among hospitalized patients during the coronavirus disease 2019 (COVID-19) pandemic (2019-2021). Between September 2019 and April 2021, patients hospitalized at Shuang Ho Hospital in north Taiwan with a diagnosis of pneumonia were enrolled in this study. Age, sex, onset date, and season of occurrence were recorded. Respiratory tract pathogens were identified with molecular detection using the FilmArray® platform from nasopharyngeal swabs. In total, 1147 patients (128 patients aged <18 years and 1019 patients aged ≥18 years) with pneumonia and identified respiratory tract pathogens were assessed. Among the 128 children with pneumonia, the dominant viral respiratory pathogen was rhinovirus (24.2%), followed by respiratory syncytial virus (RSV; 22.7%), parainfluenza virus (1 + 2 + 3 + 4) (17.2%), adenovirus (12.5%), metapneumovirus (9.4%), coronavirus (1.6%), and influenza virus (A + B) (1.6%). Among the 1019 adults with pneumonia, the dominant viral respiratory pathogen was rhinovirus (5.0%), followed by RSV (2.0%), coronavirus (2.0%), metapneumovirus (1.5%), parainfluenza virus (1 + 2 + 3 + 4) (1.1%), adenovirus (0.7%), and influenza virus (A + B) (0%). From 2019-2021, older patients (aged >65 years) with pneumonia tested positive for coronavirus most commonly in autumn. Coronavirus was not detected during summer in children or adults. Among children aged 0-6 years, RSV was the most common viral pathogen, and RSV infection occurred most often in autumn. Metapneumovirus infection occurred most often in spring in both children and adults. In contrast, influenza virus was not detected in patients with pneumonia in any season among children or adults from January 2020 to April 2021. Among all patients with pneumonia, the most common viral pathogens were rhinovirus in spring, adenovirus and rhinovirus in summer, RSV and rhinovirus in autumn, and parainfluenza virus in winter. Among children aged 0-6 years, RSV, rhinovirus, and adenovirus were detected in all seasons during the study period. In conclusion, the proportion of pneumonia cases caused by a viral pathogen was higher in children than the proportion in adults. The COVID-19 pandemic period evoked a need for SARS-CoV-2 (severe acute respiratory disease coronavirus 2) vaccination to prevent the severe complications of COVID-19. However, other viruses were also found. Vaccines for influenza were clinically applied. Active vaccines for other viral pathogens such as RSV, rhinovirus, metapneuomoccus, parainfluenza, and adenovirus may need to be developed for special groups in the future.
Collapse
Affiliation(s)
- Sheng-Chieh Lin
- Division of Allergy, Asthma, and Immunology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei 23561, Taiwan
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Hsiao-Chin Wang
- Division of Neonatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei 23561, Taiwan
| | - Wen-Chuan Lin
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei 23561, Taiwan
| | - Yung-Ting Kuo
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Division of Pediatric Neurology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei 23561, Taiwan
| | - Yi-Hsiang Hsu
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yin-Tai Tsai
- Department of Medicine Laboratory, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Shou-Cheng Lu
- Department of Medicine Laboratory, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Yuan-Hung Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Department of Medical Research, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Shih-Yen Chen
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Division of Pediatric Gastroenterology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, Taipei 23561, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei 11031, Taiwan
| |
Collapse
|
8
|
Time to result advantage of point-of-care SARS-CoV-2 PCR testing to confirm COVID-19 in emergency department: a retrospective multicenter study. Eur J Emerg Med 2023; 30:132-134. [PMID: 36815473 DOI: 10.1097/mej.0000000000000984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
|
9
|
Li W, Wang X, Cui W, Yuan L, Hu X. Clinical Evaluation of a Multiplex PCR Assay for Simultaneous Detection of 18 Respiratory Pathogens in Patients with Acute Respiratory Infections. Pathogens 2022; 12:pathogens12010021. [PMID: 36678368 PMCID: PMC9862116 DOI: 10.3390/pathogens12010021] [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: 11/13/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
Reliable diagnostics are necessary to identify influenza infections, and coronavirus disease 2019 (COVID-19) highlights the need to develop highly specific and sensitive viral detection methods to distinguish severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory pathogens to prevent their further spread. In this prospective study, 1070 clinical respiratory samples were collected from patients with acute respiratory infections from January 2019 to February 2021 to evaluate the diagnostic performance of a multiplex probe amplification (MPA) assay, designed to screen 18 pathogens, mainly those causing acute respiratory infections. Ninety-six positive samples and twenty negative samples for the 18 respiratory pathogens defined by the MPA assay and reverse transcription polymerase chain reaction (RT-PCR) were further confirmed by reference next-generation sequencing (NGS). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the MPA assay were 95.00%, 93.75%, 98.96% and 75.00%, respectively. Additionally, the co-infection rate for these positive samples were 25% (24/95). The MPA assay demonstrated a highly concordant diagnostic performance with NGS in the diagnosis of 18 respiratory pathogens and might play an important role in clinical respiratory pathogen diagnosis.
Collapse
Affiliation(s)
- Wenmin Li
- Division of Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Xiaoxiao Wang
- Division of Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Wenhao Cui
- Division of Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Leyong Yuan
- Department of Clinical Laboratory, Southern University of Science and Technology Hospital, Shenzhen 518055, China
- Correspondence: (L.Y.); (X.H.)
| | - Xuejiao Hu
- Division of Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Correspondence: (L.Y.); (X.H.)
| |
Collapse
|
10
|
Butler KS, Carson BD, Podlevsky JD, Mayes CM, Rowland JM, Campbell D, Ricken JB, Wudiri G, Timlin JA. Singleplex, multiplex and pooled sample real-time RT-PCR assays for detection of SARS-CoV-2 in an occupational medicine setting. Sci Rep 2022; 12:17733. [PMID: 36273023 PMCID: PMC9587995 DOI: 10.1038/s41598-022-22106-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 10/10/2022] [Indexed: 01/18/2023] Open
Abstract
For workplaces which cannot operate as telework or remotely, there is a critical need for routine occupational SARS-CoV-2 diagnostic testing. Although diagnostic tests including the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel (CDC Diagnostic Panel) (EUA200001) were made available early in the pandemic, resource scarcity and high demand for reagents and equipment necessitated priority of symptomatic patients. There is a clearly defined need for flexible testing methodologies and strategies with rapid turnaround of results for (1) symptomatic, (2) asymptomatic with high-risk exposures and (3) asymptomatic populations without preexisting conditions for routine screening to address the needs of an on-site work force. We developed a distinct SARS-CoV-2 diagnostic assay based on the original CDC Diagnostic Panel (EUA200001), yet, with minimum overlap for currently employed reagents to eliminate direct competition for limited resources. As the pandemic progressed with testing loads increasing, we modified the assay to include 5-sample pooling and amplicon target multiplexing. Analytical sensitivity of the pooled and multiplexed assays was rigorously tested with contrived positive samples in realistic patient backgrounds. Assay performance was determined with clinical samples previously assessed with an FDA authorized assay. Throughout the pandemic we successfully tested symptomatic, known contact and travelers within our occupational population with a ~ 24-48-h turnaround time to limit the spread of COVID-19 in the workplace. Our singleplex assay had a detection limit of 31.25 copies per reaction. The three-color multiplexed assay maintained similar sensitivity to the singleplex assay, while tripling the throughput. The pooling assay further increased the throughput to five-fold the singleplex assay, albeit with a subtle loss of sensitivity. We subsequently developed a hybrid 'multiplex-pooled' strategy to testing to address the need for both rapid analysis of samples from personnel at high risk of COVID infection and routine screening. Herein, our SARS-CoV-2 assays specifically address the needs of occupational healthcare for both rapid analysis of personnel at high-risk of infection and routine screening that is essential for controlling COVID-19 disease transmission. In addition to SARS-CoV-2 and COVID-19, this work demonstrates successful flexible assays developments and deployments with implications for emerging highly transmissible diseases and future pandemics.
Collapse
Affiliation(s)
- Kimberly S. Butler
- grid.474520.00000000121519272Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - Bryan D. Carson
- grid.474520.00000000121519272Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - Joshua D. Podlevsky
- grid.474520.00000000121519272Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - Cathryn M. Mayes
- grid.474520.00000000121519272WMD Threats and Aerosol Science, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - Jessica M. Rowland
- grid.474520.00000000121519272Global Chemical and Biological Security, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - DeAnna Campbell
- grid.474520.00000000121519272Biological and Chemical Sensors Department, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - J. Bryce Ricken
- grid.474520.00000000121519272Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | - George Wudiri
- grid.474520.00000000121519272Cooperative Nuclear Counterproliferation, Sandia National Laboratories, Albuquerque, NM 87123 USA
| | | | - Jerilyn A. Timlin
- grid.474520.00000000121519272Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM 87123 USA ,grid.474520.00000000121519272Computational Biology and Biophysics Department, Sandia National Laboratories, Albuquerque, NM 87123 USA
| |
Collapse
|
11
|
Gamage SST, Pahattuge TN, Wijerathne H, Childers K, Vaidyanathan S, Athapattu US, Zhang L, Zhao Z, Hupert ML, Muller RM, Muller-Cohn J, Dickerson J, Dufek D, Geisbrecht BV, Pathak H, Pessetto Z, Gan GN, Choi J, Park S, Godwin AK, Witek MA, Soper SA. Microfluidic affinity selection of active SARS-CoV-2 virus particles. SCIENCE ADVANCES 2022; 8:eabn9665. [PMID: 36170362 PMCID: PMC9519043 DOI: 10.1126/sciadv.abn9665] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 08/10/2022] [Indexed: 06/07/2023]
Abstract
We report a microfluidic assay to select active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral particles (VPs), which were defined as intact particles with an accessible angiotensin-converting enzyme 2 receptor binding domain (RBD) on the spike (S) protein, from clinical samples. Affinity selection of SARS-CoV-2 particles was carried out using injection molded microfluidic chips, which allow for high-scale production to accommodate large-scale screening. The microfluidic contained a surface-bound aptamer directed against the virus's S protein RBD to affinity select SARS-CoV-2 VPs. Following selection (~94% recovery), the VPs were released from the chip's surface using a blue light light-emitting diode (89% efficiency). Selected SARS-CoV-2 VP enumeration was carried out using reverse transcription quantitative polymerase chain reaction. The VP selection assay successfully identified healthy donors (clinical specificity = 100%) and 19 of 20 patients with coronavirus disease 2019 (COVID-19) (95% sensitivity). In 15 patients with COVID-19, the presence of active SARS-CoV-2 VPs was found. The chip can be reprogrammed for any VP or exosomes by simply changing the affinity agent.
Collapse
Affiliation(s)
- Sachindra S. T. Gamage
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Thilanga N. Pahattuge
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Harshani Wijerathne
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Katie Childers
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Swarnagowri Vaidyanathan
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Uditha S. Athapattu
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Lulu Zhang
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Zheng Zhao
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | | | | | | | | | | | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Harsh Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | | | - Gregory N. Gan
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Department of Industrial and Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Department of Industrial and Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Andrew K. Godwin
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Malgorzata A. Witek
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
| |
Collapse
|
12
|
Juanola-Falgarona M, Peñarrubia L, Jiménez-Guzmán S, Porco R, Congost-Teixidor C, Varo-Velázquez M, Rao SN, Pueyo G, Manissero D, Pareja J. Ct values as a diagnostic tool for monitoring SARS-CoV-2 viral load using the QIAstat-Dx® Respiratory SARS-CoV-2 Panel. Int J Infect Dis 2022; 122:930-935. [PMID: 35840097 PMCID: PMC9273520 DOI: 10.1016/j.ijid.2022.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/17/2022] [Accepted: 07/07/2022] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVES Qualitative real-time polymerase chain reaction tests are not designed to provide quantitative or semiquantitative results because cycle threshold (Ct) values are not normalized to standardized controls of known concentration. The aim of this study was to characterize SARS-CoV-2 viral loads based on Ct values, using the QIAstat-Dx® Respiratory SARS-CoV-2 Panel. METHODS Different lineages of SARS-CoV-2 clinical samples and the World Health Organization international standard were used to assess the linearity of the QIAstat-Dx Respiratory SARS-CoV-2 Panel. Limit of detection for the different lineages was characterized. RESULTS Comparable efficiencies and linearity for all samples resulted in R2 ≥0.99, covering a dynamic range of 1,000,000-100 copies/mL for the SARS-CoV-2 assay, showing linear correlation between Ct values and viral load down to 300 copies/mL. CONCLUSION The SARS-CoV-2 Ct values provided by the QIAstat-Dx® Respiratory SARS-CoV-2 Panel could be used as a surrogate for viral load given the linear correlation between Ct values and viral concentration down to limit of detection. This panel allows to obtain reproducible Ct values for SARS-CoV-2 ribonucleic acid downstream of the sample collection, reducing the sample-to-Ct workflow variability. Ct values can help provide a reliable assessment and comparison of viral loads in patients when tested with the QIAstat-Dx Respiratory SARS-CoV-2 Panel.
Collapse
Affiliation(s)
- Martí Juanola-Falgarona
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain,Corresponding author
| | - Luis Peñarrubia
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain
| | - Sara Jiménez-Guzmán
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain
| | - Roberto Porco
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain
| | | | - Marta Varo-Velázquez
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain
| | - Sonia N Rao
- QIAGEN Inc., 19300 Germantown Road, Germantown, MD, 20874, USA
| | - Gemma Pueyo
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain
| | - Davide Manissero
- QIAGEN Manchester Ltd, Citylabs 2.0. Hathersage Road, Manchester, M13 0BH, UK
| | - Josep Pareja
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain
| |
Collapse
|
13
|
Ogunbayo AE, Mogotsi MT, Sondlane H, Nkwadipo KR, Sabiu S, Nyaga MM. Pathogen Profile of Children Hospitalised with Severe Acute Respiratory Infections during COVID-19 Pandemic in the Free State Province, South Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph191610418. [PMID: 36012053 PMCID: PMC9408356 DOI: 10.3390/ijerph191610418] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/10/2022] [Accepted: 08/17/2022] [Indexed: 05/30/2023]
Abstract
Severe acute respiratory infections (SARI) contribute to mortality in children ≤5 years. Their microbiological aetiologies are often unknown and may be exacerbated in light of coronavirus disease 19 (COVID-19). This study reports on respiratory pathogens in children ≤5 years (n = 84) admitted with SARI during and between the second and third waves of COVID-19 infection in South Africa. Nasopharyngeal/oropharyngeal swabs collected were subjected to viral detection using QIAstat-Dx® Respiratory SARS-CoV-2 Panel. The results revealed viral positivity and negativity detection rates of 88% (74/84) and 12% (10/84), respectively. Of the 21 targeted pathogens, human rhinovirus/enterovirus (30%), respiratory syncytial virus (RSV; 26%), and severe acute respiratory syndrome coronavirus 2 (24%) were mostly detected, with other viruses being 20% and a co-infection rate of 64.2% (54/84). Generally, RSV-positive samples had lower Ct values, and fewer viruses were detected during the third wave. Changes in the circulation patterns of respiratory viruses with total absence of influenza virus could be attributed to measures against COVID-19 transmission, which may result in waned immunity, thereby increasing susceptibility to severe infections in the following season. High viral co-infection rate, as detected, may complicate diagnosis. Nonetheless, accurate identification of the pathogens may guide treatment decisions and infection control.
Collapse
Affiliation(s)
- Ayodeji E. Ogunbayo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Milton T. Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Hlengiwe Sondlane
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Kelebogile R. Nkwadipo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| |
Collapse
|
14
|
Mansbridge CT, Tanner AR, Beard KR, Borca F, Phan HT, Brendish NJ, Poole S, Hill C, Kiuber M, Crouch R, Waddington D, Clark TW. FebriDx host response point-of-care testing improves patient triage for coronavirus disease 2019 (COVID-19) in the emergency department. Infect Control Hosp Epidemiol 2022; 43:979-986. [PMID: 35094739 PMCID: PMC8828393 DOI: 10.1017/ice.2021.531] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Patients presenting to hospital with suspected coronavirus disease 2019 (COVID-19), based on clinical symptoms, are routinely placed in a cohort together until polymerase chain reaction (PCR) test results are available. This procedure leads to delays in transfers to definitive areas and high nosocomial transmission rates. FebriDx is a finger-prick point-of-care test (PoCT) that detects an antiviral host response and has a high negative predictive value for COVID-19. We sought to determine the clinical impact of using FebriDx for COVID-19 triage in the emergency department (ED). DESIGN We undertook a retrospective observational study evaluating the real-world clinical impact of FebriDx as part of an ED COVID-19 triage algorithm. SETTING Emergency department of a university teaching hospital. PATIENTS Patients presenting with symptoms suggestive of COVID-19, placed in a cohort in a 'high-risk' area, were tested using FebriDx. Patients without a detectable antiviral host response were then moved to a lower-risk area. RESULTS Between September 22, 2020, and January 7, 2021, 1,321 patients were tested using FebriDx, and 1,104 (84%) did not have a detectable antiviral host response. Among 1,104 patients, 865 (78%) were moved to a lower-risk area within the ED. The median times spent in a high-risk area were 52 minutes (interquartile range [IQR], 34-92) for FebriDx-negative patients and 203 minutes (IQR, 142-255) for FebriDx-positive patients (difference of -134 minutes; 95% CI, -144 to -122; P < .0001). The negative predictive value of FebriDx for the identification of COVID-19 was 96% (661 of 690; 95% CI, 94%-97%). CONCLUSIONS FebriDx improved the triage of patients with suspected COVID-19 and reduced the time that severe acute respiratory coronavirus virus 2 (SARS-CoV-2) PCR-negative patients spent in a high-risk area alongside SARS-CoV-2-positive patients.
Collapse
Affiliation(s)
- Christopher T. Mansbridge
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Alex R. Tanner
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Kate R. Beard
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Florina Borca
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Clinical Informatics Research Unit, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Hang T.T. Phan
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Clinical Informatics Research Unit, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Nathan J. Brendish
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Stephen Poole
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- NIHR Post Doctoral Fellowship Programme, University Hospital Southampton NHS Foundation Trust, Hampshire, United Kingdom
| | - Christopher Hill
- Department of Emergency Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Michael Kiuber
- Department of Emergency Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Robert Crouch
- Department of Emergency Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Health Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Daniel Waddington
- Department of Emergency Medicine, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Tristan W. Clark
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- NIHR Post Doctoral Fellowship Programme, University Hospital Southampton NHS Foundation Trust, Hampshire, United Kingdom
| |
Collapse
|
15
|
Ravina, Kumar A, Manjeet, Twinkle, Subodh, Narang J, Mohan H. Analytical performances of different diagnostic methods for SARS-CoV-2 virus - A review. SENSORS INTERNATIONAL 2022; 3:100197. [PMID: 35935464 PMCID: PMC9338831 DOI: 10.1016/j.sintl.2022.100197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/01/2022] Open
|
16
|
Filchakova O, Dossym D, Ilyas A, Kuanysheva T, Abdizhamil A, Bukasov R. Review of COVID-19 testing and diagnostic methods. Talanta 2022; 244:123409. [PMID: 35390680 PMCID: PMC8970625 DOI: 10.1016/j.talanta.2022.123409] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 01/09/2023]
Abstract
More than six billion tests for COVID-19 has been already performed in the world. The testing for SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) virus and corresponding human antibodies is essential not only for diagnostics and treatment of the infection by medical institutions, but also as a pre-requisite for major semi-normal economic and social activities such as international flights, off line work and study in offices, access to malls, sport and social events. Accuracy, sensitivity, specificity, time to results and cost per test are essential parameters of those tests and even minimal improvement in any of them may have noticeable impact on life in the many countries of the world. We described, analyzed and compared methods of COVID-19 detection, while representing their parameters in 22 tables. Also, we compared test performance of some FDA approved test kits with clinical performance of some non-FDA approved methods just described in scientific literature. RT-PCR still remains a golden standard in detection of the virus, but a pressing need for alternative less expensive, more rapid, point of care methods is evident. Those methods that may eventually get developed to satisfy this need are explained, discussed, quantitatively compared. The review has a bioanalytical chemistry prospective, but it may be interesting for a broader circle of readers who are interested in understanding and improvement of COVID-19 testing, helping eventually to leave COVID-19 pandemic in the past.
Collapse
Affiliation(s)
- Olena Filchakova
- Biology Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Dina Dossym
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Aisha Ilyas
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Tamila Kuanysheva
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Altynay Abdizhamil
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Rostislav Bukasov
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan,Corresponding author
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Combined RT-PCR and Host Response Point-of-Care Testing in Patients Hospitalised with Suspected COVID-19: A Prospective Diagnostic Accuracy Study. Infect Dis Ther 2022; 11:1267-1280. [PMID: 35534764 PMCID: PMC9083481 DOI: 10.1007/s40121-022-00646-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/20/2022] [Indexed: 11/27/2022] Open
Abstract
Introduction RT-PCR has suboptimal sensitivity for the diagnosis of COVID-19. A composite reference standard comprising RT-PCR plus radiological and clinical features has been recommended for diagnostic accuracy studies. The FebriDx finger prick point-of-care test detects an antiviral host response protein (MxA) in 10 min. We evaluated the diagnostic accuracy of FebriDx and RT-PCR compared to a composite reference standard. Methods Adults presenting to hospital with suspected COVID-19 were tested by FebriDx and RT-PCR. A composite reference standard was used to classify patients as having COVID-19 based on RT-PCR positivity, or RT-PCR negativity with COVID-19 radiological findings or other clinical criteria. Measures of accuracy were calculated for MxA alone, RT-PCR alone, and both combined. This study is registered with the ISRCTN (ISRCTN14966673) and has completed. Results A total of 478 patients were tested, with valid results in 475. Of these 475 patients, 222 (46.7%) were classified as having COVID-19; 192 (40.4%) were RT-PCR positive, and 30 (6.3%) were RT-PCR negative and diagnosed on radiological/clinical criteria. Sensitivity of FebriDx MxA vs the composite reference standard was 186/222 (83.8%, 95% CI 78.3–88.4) and was similar to the sensitivity of RT-PCR (192/222 (86.5%, 95% CI 81.3–90.7), (difference of 2.7%, 95% CI − 3.9 to 9.3, p = 0.42). The sensitivity of combined FebriDx and RT-PCR was 208/222 (93.7%) which was superior to both RT-PCR alone (difference of 9.9, 95% CI 4.1–15.9; p = 0.001) and FebriDx MxA alone (difference of 7.2, 95% CI 1.6–12.9; p = 0.011). Conclusion Sensitivity of combined FebriDx and RT-PCR testing was superior to each alone for the detection of COVID-19 in hospital and may improve infection control and treatment decisions. Supplementary Information The online version contains supplementary material available at 10.1007/s40121-022-00646-4.
Collapse
|
19
|
Cassidy H, van Genne M, Lizarazo-Forero E, Niesters HGM, Gard L. Evaluation of the QIAstat-Dx RP2.0 and the BioFire FilmArray RP2.1 for the Rapid Detection of Respiratory Pathogens Including SARS-CoV-2. Front Microbiol 2022; 13:854209. [PMID: 35401449 PMCID: PMC8989387 DOI: 10.3389/fmicb.2022.854209] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/28/2022] [Indexed: 02/04/2023] Open
Abstract
Point-of-care syndromic panels allow for simultaneous and rapid detection of respiratory pathogens from nasopharyngeal swabs. The clinical performance of the QIAstat-Dx Respiratory SARS-CoV-2 panel RP2.0 (QIAstat-Dx RP2.0) and the BioFire FilmArray Respiratory panel RP2.1 (BioFire RP2.1) was evaluated for the detection of SARS-CoV-2 and other common respiratory pathogens. A total of 137 patient samples were retrospectively selected based on emergency department admission, along with 33 SARS-CoV-2 positive samples tested using a WHO laboratory developed test. The limit of detection for SARS-CoV-2 was initially evaluated for both platforms. The QIAstat-Dx RP2.0 detected SARS-CoV-2 at 500 copies/mL and had a positive percent agreement (PPA) of 85%. The BioFire RP2.1 detected SARS-CoV-2 at 50 copies/mL and had a PPA of 97%. Both platforms showed a negative percent agreement of 100% for SARS-CoV-2. Evaluation of analytical specificity from a range of common respiratory targets showed a similar performance between each platform. The QIAstat-Dx RP2.0 had an overall PPA of 82% (67–100%) in clinical samples, with differences in sensitivity depending on the respiratory target. Both platforms can be used to detect acute cases of SARS-CoV-2. While the QIAstat-Dx RP2.0 is suitable for detecting respiratory viruses within a clinical range, it has less analytical and clinical sensitivity for SARS-CoV-2 compared to the BioFire RP2.1.
Collapse
|
20
|
Liv L, Kayabay H. An Electrochemical Biosensing Platform for the SARS-CoV-2 Spike Antibody Detection Based on the Functionalised SARS-CoV-2 Spike Antigen Modified Electrode. ChemistrySelect 2022; 7:e202200256. [PMID: 35601978 PMCID: PMC9111083 DOI: 10.1002/slct.202200256] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/01/2022] [Indexed: 12/15/2022]
Abstract
We developed an electrochemical biosensing platform using gold-clusters, cysteamine, the spike protein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) antigen and bovine serum albumin on a glassy carbon electrode able to determine the SARS-CoV-2 spike antibody. The developed biosensor could detect 9.3 ag/mL of the SARS-CoV-2 spike antibody in synthetic media in 20 min in a linear range from 0.1 fg/mL to 10.0 pg/mL. The developed method demonstrated good selectivity in the presence of spike antigens from other viruses. Clinical samples consisting of gargle and mouthwash liquids were analyzed with both RT-PCR and the developed biosensor system to reveal the sensitivity and specificity of the proposed method. Moreover, the developed method was compared with the lateral flow immunoassay method in terms of sensitivity.
Collapse
Affiliation(s)
- Lokman Liv
- Electrochemistry LaboratoryChemistry GroupThe Scientific and Technological Research Council of TurkeyNational Metrology InstituteTUBITAK UME)41470GebzeKocaeliTurkey
| | - Hilal Kayabay
- Electrochemistry LaboratoryChemistry GroupThe Scientific and Technological Research Council of TurkeyNational Metrology InstituteTUBITAK UME)41470GebzeKocaeliTurkey
| |
Collapse
|
21
|
Single-tube collection and nucleic acid analysis of clinical samples for SARS-CoV-2 saliva testing. Sci Rep 2022; 12:3951. [PMID: 35273232 PMCID: PMC8913774 DOI: 10.1038/s41598-022-07871-4] [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: 08/02/2021] [Accepted: 02/25/2022] [Indexed: 11/09/2022] Open
Abstract
The SARS-CoV-2 pandemic has brought to light the need for expedient diagnostic testing. Cost and availability of large-scale testing capacity has led to a lag in turnaround time and hindered contact tracing efforts, resulting in a further spread of SARS-CoV-2. To increase the speed and frequency of testing, we developed a cost-effective single-tube approach for collection, denaturation, and analysis of clinical samples. The approach utilizes 1 µL microbiological inoculation loops to collect saliva, sodium dodecyl sulfate (SDS) to inactivate and release viral genomic RNA, and a diagnostic reaction mix containing polysorbate 80 (Tween 80). In the same tube, the SDS-denatured clinical samples are introduced to the mixtures containing all components for nucleic acids detection and Tween 80 micelles to absorb the SDS and allow enzymatic reactions to proceed, obviating the need for further handling of the samples. The samples can be collected by the tested individuals, further decreasing the need for trained personnel to administer the test. We validated this single-tube sample-to-assay method with reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) and discovered little-to-no difference between Tween- and SDS-containing reaction mixtures, compared to control reactions. This approach reduces the logistical burden of traditional large-scale testing and provides a method of deployable point-of-care diagnostics to increase testing frequency.
Collapse
|
22
|
Davies E, Farooq HZ, Brown B, Tilston P, McEwan A, Birtles A, O'Hara RW, Ahmad S, Machin N, Hesketh L, Guiver M. An Overview of SARS-CoV-2 Molecular Diagnostics in Europe. Clin Lab Med 2022; 42:161-191. [PMID: 35636820 PMCID: PMC8901364 DOI: 10.1016/j.cll.2022.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emma Davies
- Department of Virology, UK Health Security Agency, Manchester Foundation Trust, Oxford Road, Manchester M13 9WL, UK.
| | - Hamzah Z Farooq
- Department of Virology, UK Health Security Agency, Manchester Foundation Trust, Oxford Road, Manchester M13 9WL, UK; Department of Infectious Diseases and Tropical Medicine, North Manchester General Hospital, Manchester Foundation Trust, Manchester, UK
| | - Benjamin Brown
- Department of Virology, UK Health Security Agency, Manchester Foundation Trust, Oxford Road, Manchester M13 9WL, UK
| | - Peter Tilston
- Department of Virology, UK Health Security Agency, Manchester Foundation Trust, Oxford Road, Manchester M13 9WL, UK
| | - Ashley McEwan
- Department of Virology, UK Health Security Agency, Manchester Foundation Trust, Oxford Road, Manchester M13 9WL, UK
| | - Andrew Birtles
- Department of Virology, UK Health Security Agency, Manchester Foundation Trust, Oxford Road, Manchester M13 9WL, UK
| | - Robert William O'Hara
- Department of Virology, UK Health Security Agency, Manchester Foundation Trust, Oxford Road, Manchester M13 9WL, UK
| | - Shazaad Ahmad
- Department of Virology, UK Health Security Agency, Manchester Foundation Trust, Oxford Road, Manchester M13 9WL, UK
| | - Nicholas Machin
- Department of Virology, UK Health Security Agency, Manchester Foundation Trust, Oxford Road, Manchester M13 9WL, UK
| | - Louise Hesketh
- Department of Virology, UK Health Security Agency, Manchester Foundation Trust, Oxford Road, Manchester M13 9WL, UK
| | - Malcolm Guiver
- Department of Virology, UK Health Security Agency, Manchester Foundation Trust, Oxford Road, Manchester M13 9WL, UK
| |
Collapse
|
23
|
Ishikane M, Unoki-Kubota H, Moriya A, Kutsuna S, Ando H, Kaburagi Y, Suzuki T, Iwamoto N, Kimura M, Ohmagari N. Evaluation of the QIAstat-Dx Respiratory SARS-CoV-2 pPanel, a rRapid mMultiplex PCR mMethod for the dDiagnosis of COVID-19. J Infect Chemother 2022; 28:729-734. [PMID: 35184977 PMCID: PMC8825349 DOI: 10.1016/j.jiac.2022.02.004] [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: 11/08/2021] [Revised: 12/10/2021] [Accepted: 02/04/2022] [Indexed: 11/24/2022]
Abstract
Introduction Rapid, simple, and accurate methods are required to diagnose coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to evaluate the performance of the QIAstat-Dx Respiratory SARS-CoV-2 Panel (QIAstat-SARS-CoV-2), a rapid multiplex PCR assay for SARS-CoV-2 detection. Methods Nasopharyngeal swabs (NPS) that were obtained from patients with COVID-19 who were diagnosed at the National Center for Global Health and Medicine were used in this study. When the NPS samples were found to be negative for SARS-CoV-2 after treatment, they were used as negative samples. We evaluated the performance of the QIAstat-SARS-CoV-2 comparing SARS-CoV-2 detection with the National Institute of Infectious Diseases in Japan-recommended real-time polymerase chain reaction (RT-PCR) method (NIID-RT-PCR). Results In total, 45 NPS samples were analyzed. The proportion of overall agreement between QIAstat-SARS-CoV-2 and NIID-RT-PCR on 45 samples was 91.0% with a sensitivity of 84.0% (21/25), specificity at 100% (20/20), negative predictive value at 83.3% (20/24), and positive predictive value at 100% (21/21). There were no patients with co-infections with pathogens other than SARS-CoV-2. Conclusions QIAstat-SARS-CoV-2 showed a high agreement in comparison with the NIID-RT-PCR for the detection of SARS-CoV-2. The QIAstat-SARS-CoV-2 also provided a rapid and accurate diagnosis for COVID-19, even when the concurrent detection of other respiratory pathogens was desired, and therefore, has the potential to direct appropriate therapy and infection control precautions.
Collapse
|
24
|
Ding X, Li Z, Liu C. Monolithic, 3D-printed lab-on-disc platform for multiplexed molecular detection of SARS-CoV-2. SENSORS AND ACTUATORS. B, CHEMICAL 2022; 351:130998. [PMID: 34725537 PMCID: PMC8550893 DOI: 10.1016/j.snb.2021.130998] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/06/2021] [Accepted: 10/23/2021] [Indexed: 05/09/2023]
Abstract
Multiplexed detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rather than detection targeting a single gene is crucial to ensure more accurate coronavirus disease 2019 (COVID-19) diagnostics. Here, we develop a monolithic, 3D-printed, lab-on-disc platform for multiplexed molecular detection of SARS-CoV-2. The centrifugal lab-on-disc is fabricated in one step using simple 3D printing technology, circumventing the need for aligning and binding multiple layers. By combining isothermal amplification technology, this lab-on-disc platform is capable of simultaneously detecting the nucleoprotein and envelope genes of SARS-CoV-2 as well as an internal control of the human POP7 gene. Within a 50-minute incubation period, 100 copies SARS-CoV-2 RNA can be detected through visual observation according to color and fluorescence changes in the disc. Further, we clinically validated the lab-on-disc platform by testing 20 nasopharyngeal swab samples and demonstrated a sensitivity of 100% and an accuracy of 95%. Therefore, the monolithic, 3D-printed, lab-on-disc platform provides simple, rapid, disposable, sensitive, reliable, and multiplexed molecular detection of SARS-CoV-2, holding promise for COVID-19 diagnostics at the point of care.
Collapse
Affiliation(s)
- Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030, United States
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030, United States
- Department of Biomedical Engineering, University of Connecticut, 260 Glenbrook Road, Storrs, CT 06029, United States
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030, United States
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Liv L, Yener M, Çoban G, Can ŞA. Electrochemical biosensing platform based on hydrogen bonding for detection of the SARS-CoV-2 spike antibody. Anal Bioanal Chem 2022; 414:1313-1322. [PMID: 34741650 PMCID: PMC8571674 DOI: 10.1007/s00216-021-03752-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022]
Abstract
Among the deadliest pandemics in history, coronavirus disease 2019 (COVID-19) has wreaked havoc on human lives, economies and public health systems worldwide. To temper its effects, diagnostic methods that are simple, rapid, inexpensive, accurate, selective and sensitive continue to be necessary. In our study, we developed an electrochemical biosensing platform based on gold clusters, mercaptoethanol, the spike protein of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) antigen and bovine serum albumin-modified glassy carbon electrode able to detect the SARS-CoV-2 spike antibody. Moreover, during the detection of the SARS-CoV-2 spike antibody in spiked-real samples, the anodic signal of the produced biosensor at 0.85 V decreased as the amount of the SARS-CoV-2 spike antibody increased. Meanwhile, the recovery and relative standard deviation values for saliva and oropharyngeal swab samples were 97.73% and 3.35% and 102.43% and 4.63%, respectively. In 35 min, the biosensing platform could detect 0.03 fg/mL of the SARS-CoV-2 spike antibody in synthetic media and spiked-saliva or -oropharyngeal swab samples. The method thus issues a linear response to the SARS-CoV-2 spike antibody from 0.1 fg/mL to 10 pg/mL. The cross-reactivity studies with spike antigens of Middle East respiratory syndrome-coronavirus and influenza A and the antigen of pneumonia confirmed the excellent selectivity of the proposed method. The developed method was compared with the lateral flow immunoassay method in terms of sensitivity and it was found to be approximately 109 times more sensitive. Biosensing mechanism of the platform to the SARS-CoV-2 spike antibody.
Collapse
Affiliation(s)
- Lokman Liv
- Electrochemistry Laboratory, Chemistry Group, The Scientific and Technological Research Council of Turkey, National Metrology Institute, (TUBITAK UME), 41470, Gebze, Kocaeli, Turkey.
| | - Melisa Yener
- Electrochemistry Laboratory, Chemistry Group, The Scientific and Technological Research Council of Turkey, National Metrology Institute, (TUBITAK UME), 41470, Gebze, Kocaeli, Turkey
| | - Gizem Çoban
- Electrochemistry Laboratory, Chemistry Group, The Scientific and Technological Research Council of Turkey, National Metrology Institute, (TUBITAK UME), 41470, Gebze, Kocaeli, Turkey
| | - Şevval Arzu Can
- Electrochemistry Laboratory, Chemistry Group, The Scientific and Technological Research Council of Turkey, National Metrology Institute, (TUBITAK UME), 41470, Gebze, Kocaeli, Turkey
| |
Collapse
|
27
|
Current clinical testing approach of COVID. SENSING TOOLS AND TECHNIQUES FOR COVID-19 2022. [PMCID: PMC9334984 DOI: 10.1016/b978-0-323-90280-9.00003-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
28
|
Szunerits S, Pagneux Q, Swaidan A, Mishyn V, Roussel A, Cambillau C, Devos D, Engelmann I, Alidjinou EK, Happy H, Boukherroub R. The role of the surface ligand on the performance of electrochemical SARS-CoV-2 antigen biosensors. Anal Bioanal Chem 2022; 414:103-113. [PMID: 33616686 PMCID: PMC7897554 DOI: 10.1007/s00216-020-03137-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/10/2020] [Accepted: 12/17/2020] [Indexed: 01/07/2023]
Abstract
Point-of-care (POC) technologies and testing programs hold great potential to significantly improve diagnosis and disease surveillance. POC tests have the intrinsic advantage of being able to be performed near the patient or treatment facility, owing to their portable character. With rapid results often in minutes, these diagnostic platforms have a high positive impact on disease management. POC tests are, in addition, advantageous in situations of a shortage of skilled personnel and restricted availability of laboratory-based analytics. While POC testing programs are widely considered in addressing health care challenges in low-income health systems, the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections could largely benefit from fast, efficient, accurate, and cost-effective point-of-care testing (POCT) devices for limiting COVID-19 spreading. The unrestrained availability of SARS-CoV-2 POC tests is indeed one of the adequate means of better managing the COVID-19 outbreak. A large number of novel and innovative solutions to address this medical need have emerged over the last months. Here, we critically elaborate the role of the surface ligands in the design of biosensors to cope with the current viral outbreak situation. Their notable effect on electrical and electrochemical sensors' design will be discussed in some given examples. Graphical abstract.
Collapse
Affiliation(s)
- Sabine Szunerits
- Univ. Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, UMR 8520 - IEMN, F-59000, Lille, France.
| | - Quentin Pagneux
- Univ. Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, UMR 8520 - IEMN, F-59000, Lille, France
| | - Abir Swaidan
- Univ. Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, UMR 8520 - IEMN, F-59000, Lille, France
| | - Vladyslav Mishyn
- Univ. Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, UMR 8520 - IEMN, F-59000, Lille, France
| | - Alain Roussel
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, CEDEX 20, 13020, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, CEDEX 20, 13020, Marseille, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, CEDEX 20, 13020, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, CEDEX 20, 13020, Marseille, France
| | - David Devos
- Univ. Lille, CHU-Lille, Inserm, U1172, Lille Neuroscience & Cognition, LICEND, 59000, Lille, France
| | - Ilka Engelmann
- Univ. Lille, CHU Lille, Laboratoire de Virologie ULR3610, 59000, Lille, France
| | | | - Henri Happy
- Univ. Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, UMR 8520 - IEMN, F-59000, Lille, France
| | - Rabah Boukherroub
- Univ. Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, UMR 8520 - IEMN, F-59000, Lille, France
| |
Collapse
|
29
|
Dried blood spot specimens for SARS-CoV-2 antibody testing: A multi-site, multi-assay comparison. PLoS One 2021; 16:e0261003. [PMID: 34874948 PMCID: PMC8651133 DOI: 10.1371/journal.pone.0261003] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
The true severity of infection due to COVID-19 is under-represented because it is based on only those who are tested. Although nucleic acid amplifications tests (NAAT) are the gold standard for COVID-19 diagnostic testing, serological assays provide better population-level SARS-CoV-2 prevalence estimates. Implementing large sero-surveys present several logistical challenges within Canada due its unique geography including rural and remote communities. Dried blood spot (DBS) sampling is a practical solution but comparative performance data on SARS-CoV-2 serological tests using DBS is currently lacking. Here we present test performance data from a well-characterized SARS-CoV-2 DBS panel sent to laboratories across Canada representing 10 commercial and 2 in-house developed tests for SARS-CoV-2 antibodies. Three commercial assays identified all positive and negative DBS correctly corresponding to a sensitivity, specificity, positive predictive value, and negative predictive value of 100% (95% CI = 72.2, 100). Two in-house assays also performed equally well. In contrast, several commercial assays could not achieve a sensitivity greater than 40% or a negative predictive value greater than 60%. Our findings represent the foundation for future validation studies on DBS specimens that will play a central role in strengthening Canada's public health policy in response to COVID-19.
Collapse
|
30
|
Bui LM, Thi Thu Phung H, Ho Thi TT, Singh V, Maurya R, Khambhati K, Wu CC, Uddin MJ, Trung DM, Chu DT. Recent findings and applications of biomedical engineering for COVID-19 diagnosis: a critical review. Bioengineered 2021; 12:8594-8613. [PMID: 34607509 PMCID: PMC8806999 DOI: 10.1080/21655979.2021.1987821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/28/2021] [Indexed: 12/23/2022] Open
Abstract
COVID-19 is one of the most severe global health crises that humanity has ever faced. Researchers have restlessly focused on developing solutions for monitoring and tracing the viral culprit, SARS-CoV-2, as vital steps to break the chain of infection. Even though biomedical engineering (BME) is considered a rising field of medical sciences, it has demonstrated its pivotal role in nurturing the maturation of COVID-19 diagnostic technologies. Within a very short period of time, BME research applied to COVID-19 diagnosis has advanced with ever-increasing knowledge and inventions, especially in adapting available virus detection technologies into clinical practice and exploiting the power of interdisciplinary research to design novel diagnostic tools or improve the detection efficiency. To assist the development of BME in COVID-19 diagnosis, this review highlights the most recent diagnostic approaches and evaluates the potential of each research direction in the context of the pandemic.
Collapse
Affiliation(s)
- Le Minh Bui
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Thuy-Tien Ho Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Mehsana, Gujarat, India
| | - Rupesh Maurya
- Department of Biosciences, School of Science, Indrashil University, Mehsana, Gujarat, India
| | - Khushal Khambhati
- Department of Biosciences, School of Science, Indrashil University, Mehsana, Gujarat, India
| | - Chia-Ching Wu
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Md Jamal Uddin
- ABEx Bio-Research Center, East Azampur, Dhaka, Bangladesh
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Republic of Korea
| | - Do Minh Trung
- Institute of Biomedicine and Pharmacy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Dinh Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| |
Collapse
|
31
|
Navarro A, Gómez L, Sanseverino I, Niegowska M, Roka E, Pedraccini R, Vargha M, Lettieri T. SARS-CoV-2 detection in wastewater using multiplex quantitative PCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:148890. [PMID: 34298359 PMCID: PMC8278834 DOI: 10.1016/j.scitotenv.2021.148890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 05/03/2023]
Abstract
A multiplex reverse transcription quantitative PCR (RT-qPCR)-based method was designed for the simultaneous detection of different SARS-CoV-2 genes. In this study, we used three target genes encoding for the nucleocapsid 1 and 3 (N1, N3), and the spike (S) proteins, all commonly used in the detection of SARS-CoV-2 in human and environmental samples. The performance of the multiplex assay, compared to the single assay was assessed for the standard calibration curve, required for absolute quantification, and then, for the real environmental samples to detect SARS-CoV-2. For this latter, four environmental samples were collected at a local wastewater treatment plant (WWTP). The results showed that the cycle threshold (Ct) values of the multiplex were comparable to the values obtained by the singleplex PCR. The amplification of the three target genes indicated the presence of SARS-CoV-2 in the four water samples with an increasing trend in February and these results were confirmed in the multiplex approach, showing the robustness of this method and its applicability for the relative abundance analysis among the samples. Overall, both the laboratory and field work results demonstrated that the multiplex PCR assay developed in this study could provide a method for SARS-CoV-2 detection as robust as the single qPCR, but faster and cost-effective, reducing by three times the number of reactions, and consequently the handling time and reagents.
Collapse
Affiliation(s)
- Anna Navarro
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Livia Gómez
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Isabella Sanseverino
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Magdalena Niegowska
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Eszter Roka
- Department of Public Health Laboratory, National Public Health Centre, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | | | - Marta Vargha
- Department of Public Health Laboratory, National Public Health Centre, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | - Teresa Lettieri
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy.
| |
Collapse
|
32
|
Schuele L, Cassidy H, Peker N, Rossen JWA, Couto N. Future potential of metagenomics in clinical laboratories. Expert Rev Mol Diagn 2021; 21:1273-1285. [PMID: 34755585 DOI: 10.1080/14737159.2021.2001329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Rapid and sensitive diagnostic strategies are necessary for patient care and public health. Most of the current conventional microbiological assays detect only a restricted panel of pathogens at a time or require a microbe to be successfully cultured from a sample. Clinical metagenomics next-generation sequencing (mNGS) has the potential to unbiasedly detect all pathogens in a sample, increasing the sensitivity for detection and enabling the discovery of unknown infectious agents. AREAS COVERED High expectations have been built around mNGS; however, this technique is far from widely available. This review highlights the advances and currently available options in terms of costs, turnaround time, sensitivity, specificity, validation, and reproducibility of mNGS as a diagnostic tool in clinical microbiology laboratories. EXPERT OPINION The need for a novel diagnostic tool to increase the sensitivity of microbial diagnostics is clear. mNGS has the potential to revolutionise clinical microbiology. However, its role as a diagnostic tool has yet to be widely established, which is crucial for successfully implementing the technique. A clear definition of diagnostic algorithms that include mNGS is vital to show clinical utility. Similarly to real-time PCR, mNGS will one day become a vital tool in any testing algorithm.
Collapse
Affiliation(s)
- Leonard Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Hayley Cassidy
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Nilay Peker
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| |
Collapse
|
33
|
Tanner AR, Phan H, Brendish NJ, Borca F, Beard KR, Poole S, W Clark T. SARS-CoV-2 viral load at presentation to hospital is independently associated with the risk of death. J Infect 2021; 83:458-466. [PMID: 34363885 PMCID: PMC8339449 DOI: 10.1016/j.jinf.2021.08.003] [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: 03/24/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 01/09/2023]
Abstract
Objectives Previous studies have suggested that SARS-CoV-2 viral load, measured on upper respiratory tract samples at presentation to hospital using PCR Cycle threshold (Ct) value, has prognostic utility. However, these studies have not comprehensively adjusted for factors known to be intimately related to viral load. We aimed to evaluate the association between Ct value at admission and patient outcome whilst adjusting carefully for covariates. Methods We evaluated the association between Ct value at presentation and the outcomes of ICU admission and death, in patients hospitalised during the first wave of the pandemic in Southampton, UK. We adjusted for covariates including age, duration of illness and antibody sero-status, measured by neutralisation assay. Results 185 patients were analysed, with a median [IQR] Ct value of 27.9 [22.6-32.1]. On univariate analysis the Ct value at presentation was associated with the risk of both ICU admission and death. In addition, Ct value significantly differed according to age, the duration of illness at presentation and antibody sero-status. On multivariate analysis, Ct value was independently associated with risk of death (aOR 0.84, 95% CI 0.72-0.96; p = 0.011) but not ICU admission (aOR 1.04, 95% CI 0.93-1.16; p = 0.507). Neutralising antibody status at presentation was not associated with mortality or ICU admission (aOR 10.62, 95% CI 0.47-889; p = 0.199 and aOR 0.46, 95% CI 0.10-2.00; p = 0.302, respectively). Conclusions SARS-CoV-2 Ct value on admission to hospital was independently associated with mortality, when comprehensively adjusting for other factors and could be used for risk stratification.
Collapse
Affiliation(s)
- Alex R Tanner
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Hang Phan
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom,Clinical Informatics Research Unit, University of Southampton, Southampton, United Kingdom
| | - Nathan J Brendish
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom,NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom,School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Florina Borca
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom,Clinical Informatics Research Unit, University of Southampton, Southampton, United Kingdom
| | - Kate R Beard
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom,NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom,School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Stephen Poole
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom,NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom,School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Tristan W Clark
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom,NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom,School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom,NIHR Post Doctoral Research Fellowship Programme, LF101, South Academic block, Southampton General Hospital, Southampton SO16 6YD, United Kingdom,Corresponding author at: LF101, South Academic block, Southampton General Hospital, Southampton SO16 6YD, United Kingdom
| |
Collapse
|
34
|
Akter N, Hasan MM, Pala N. A Review of THz Technologies for Rapid Sensing and Detection of Viruses including SARS-CoV-2. BIOSENSORS 2021; 11:349. [PMID: 34677305 PMCID: PMC8534088 DOI: 10.3390/bios11100349] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/12/2021] [Accepted: 09/18/2021] [Indexed: 12/15/2022]
Abstract
Virus epidemics such as Ebola virus, Zika virus, MERS-coronavirus, and others have wreaked havoc on humanity in the last decade. In addition, a coronavirus (SARS-CoV-2) pandemic and its continuously evolving mutants have become so deadly that they have forced the entire technical advancement of healthcare into peril. Traditional ways of detecting these viruses have been successful to some extent, but they are costly, time-consuming, and require specialized human resources. Terahertz-based biosensors have the potential to lead the way for low-cost, non-invasive, and rapid virus detection. This review explores the latest progresses in terahertz technology-based biosensors for the virus, viral particle, and antigen detection, as well as upcoming research directions in the field.
Collapse
Affiliation(s)
| | | | - Nezih Pala
- Department of Electrical and Computer Engineering, Florida International University, Miami, FL 33174, USA; (N.A.); (M.M.H.)
| |
Collapse
|
35
|
Taher J, Randell EW, Arnoldo S, Bailey D, De Guire V, Kaur S, Knauer M, Petryayeva E, Poutanen SM, Shaw JLV, Uddayasankar U, White-Al Habeeb N, Konforte D. Canadian Society of Clinical Chemists (CSCC) consensus guidance for testing, selection and quality management of SARS-CoV-2 point-of-care tests. Clin Biochem 2021; 95:1-12. [PMID: 34048776 PMCID: PMC8144094 DOI: 10.1016/j.clinbiochem.2021.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/02/2021] [Accepted: 05/22/2021] [Indexed: 01/12/2023]
Abstract
OBJECTIVES A consensus guidance is provided for testing, utility and verification of SARS-CoV-2 point-of-care test (POCT) performance and implementation of a quality management program, focusing on nucleic acid and antigen targeted technologies. DESIGN AND METHODS The recommendations are based on current literature and expert opinion from the members of Canadian Society of Clinical Chemists (CSCC), and are intended for use inside or outside of healthcare settings that have varied levels of expertise and experience with POCT. RESULTS AND CONCLUSIONS Here we discuss sampling requirements, biosafety, SARS-CoV-2 point-of-care testing methodologies (with focus on Health Canada approved tests), test performance and limitations, test selection, testing utility, development and implementation of quality management systems, quality improvement, and medical and scientific oversight.
Collapse
Affiliation(s)
- Jennifer Taher
- Pathology and Laboratory Medicine, Sinai Health System, Toronto, Canada; University of Toronto, Laboratory Medicine and Pathobiology, Toronto, Canada
| | - Edward W Randell
- Department of Laboratory Medicine, Faculty of Medicine, Memorial University of Newfoundland, Newfoundland, Canada
| | - Saranya Arnoldo
- University of Toronto, Laboratory Medicine and Pathobiology, Toronto, Canada; William Osler Health System, Brampton, Canada
| | | | - Vincent De Guire
- Clinical Biochemistry, Maisonneuve-Rosemont Hospital, Optilab-CHUM Laboratory Network, Montreal, Canada; Biochemistry, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Canada
| | - Sukhbir Kaur
- Fraser Health Authority, Vancouver, Canada; Pathology and Laboratory Medicine, University of British Columbia, Canada
| | - Michael Knauer
- Pathology and Laboratory Medicine, London Health Sciences Center, London, Canada; Pathology and Laboratory Medicine, University of Western Ontario, London, Canada
| | - Eleonora Petryayeva
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
| | - Susan M Poutanen
- University of Toronto, Laboratory Medicine and Pathobiology, Toronto, Canada; University of Toronto, Medicine, Toronto, Canada; University Health Network/Sinai Health Department of Microbiology, Toronto, Canada
| | - Julie L V Shaw
- Eastern Ontario Regional Laboratory Association, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Canada
| | | | | | | |
Collapse
|
36
|
Chen Z, Xu W, Ma W, Shi X, Li S, Hao M, Fang Y, Zhang L. Clinical laboratory evaluation of COVID-19. Clin Chim Acta 2021; 519:172-182. [PMID: 33939954 PMCID: PMC8086377 DOI: 10.1016/j.cca.2021.04.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 01/08/2023]
Abstract
COVID-19, caused by SARS-CoV-2, is a highly infectious disease, and clinical laboratory detection has played important roles in its diagnosis and in evaluating progression of the disease. Nucleic acid amplification testing or gene sequencing can serve as pathogenic evidence of COVID-19 diagnosing for clinically suspected cases, and dynamic monitoring of specific antibodies (IgM, IgA, and IgG) is an effective complement for false-negative detection of SARS-CoV-2 nucleic acid. Antigen tests to identify SARS-CoV-2 are recommended in the first week of infection, which is associated with high viral loads. Additionally, many clinical laboratory indicators are abnormal as the disease evolves. For example, from moderate to severe and critical cases, leukocytes, neutrophils, and the neutrophil-lymphocyte ratio increase; conversely, lymphocytes decrease progressively but are over activated. LDH, AST, ALT, CK, high-sensitivity troponin I, and urea also increase progressively, and increased D-dimer is an indicator of severe disease and an independent risk factor for death. Severe infection leads to aggravation of inflammation. Inflammatory biomarkers and cytokines, such as CRP, SAA, ferritin, IL-6, and TNF-α, increase gradually. High-risk COVID-19 patients with severe disease, such as the elderly and those with underlying diseases (cardiovascular disease, diabetes, chronic respiratory disease, hypertension, obesity, and cancer), should be monitored dynamically, which will be helpful as an early warning of serious diseases.
Collapse
Affiliation(s)
- Zhufeng Chen
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, PR China
| | - Wanju Xu
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, PR China
| | - Wanshan Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, PR China
| | - Xiaohong Shi
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, PR China
| | - Shuomin Li
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, PR China
| | - Mingju Hao
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, PR China
| | - Yuanxun Fang
- Rural Vitalization Research Institute of Qilu, Shandong Agriculture and Engineering University, Jinan, PR China
| | - Li Zhang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, PR China,Corresponding author at: Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, 16766 Jingshi Road, Jinan, Shandong Province, PR China
| |
Collapse
|
37
|
A View on Polymerase Chain Reaction as an Outstanding Molecular Diagnostic Technique in Periodontology. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9979948. [PMID: 34337068 PMCID: PMC8315861 DOI: 10.1155/2021/9979948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/11/2021] [Accepted: 07/13/2021] [Indexed: 12/12/2022]
Abstract
Objectives This study presents a discussion on the fundamentals of polymerase chain reaction (PCR) and its use as a diagnostic tool in periodontology. Materials and Methods A computer-aided as well as hand-made search in PubMed and Scopus indexed journals (relevant to the topic) was done by keywords of molecular technique in periodontology, PCR, applications of PCR, and PCR in periodontics. Only the papers in the English language and outlining PCR and its association with periodontology were collected and utilized to provide a succinct review. There was no limitation for publication time. Results The results of our search showed that PCR has turned into a standard in diagnosis in the field of periodontology. A variety of researches has demonstrated that its sensitive, and specific characteristics make it a quick and effective technique of recognition, identification, and quantification of microorganisms. Identification of various immunoinflammatory markers at the mRNA expression level as well as ascertaining gene-related polymorphisms can also be performed. Conclusions The mechanisms of periodontal disease can further become clarified using PCR. Clinical Relevance. PCR as a diagnostic method can play a main part in the validation of the clinical diagnosis of periodontal disease indicating the reason, pathogenesis, clinical steps, progress, and prognosis of the disease.
Collapse
|
38
|
Al-Hail H, Mirza F, Al Hashemi A, Ahmad MN, Iqbal M, Tang P, Hasan MR. Evaluation of automated molecular tests for the detection of SARS-CoV-2 in pooled nasopharyngeal and saliva specimens. J Clin Lab Anal 2021; 35:e23876. [PMID: 34132419 PMCID: PMC8373324 DOI: 10.1002/jcla.23876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 12/31/2022] Open
Abstract
Background Pooling of samples for SARS‐CoV‐2 testing in low‐prevalence settings has been used as an effective strategy to expand testing capacity and mitigate challenges with the shortage of supplies. We evaluated two automated molecular test systems for the detection of SARS‐CoV‐2 RNA in pooled specimens. Methods Pooled nasopharyngeal and saliva specimens were tested by Qiagen QIAstat‐Dx Respiratory SARS‐CoV‐2 Panel (QIAstat) or Cepheid Xpert Xpress SARS‐CoV‐2 (Xpert), and the results were compared to that of standard RT‐qPCR tests without pooling. Results In nasopharyngeal specimens, the sensitivity/specificity of the pool testing approach, with 5 and 10 specimens per pool, were 77%/100% (n = 105) and 74.1%/100% (n = 260) by QIAstat, and 97.1%/100% (n = 250) and 100%/99.5% (n = 200) by Xpert, respectively. Pool testing of saliva (10 specimens per pool; n = 150) by Xpert resulted in 87.5% sensitivity and 99.3% specificity compared to individual tests. Pool size of 5 or 10 specimens did not significantly affect the difference of RT‐qPCR cycle threshold (CT) from standard testing. RT‐qPCR CT values obtained with pool testing by both QIAstat and Xpert were positively correlated with that of individual testing (Pearson's correlation coefficient r = 0.85 to 0.99, p < 0.05). However, the CT values from Xpert were significantly stronger (p < 0.01, paired t test) than that of QIAstat in a subset of SARS‐CoV‐2 positive specimens, with mean differences of −4.3 ± 2.43 and −4.6 ± 2 for individual and pooled tests, respectively. Conclusion Our results suggest that Xpert SARS‐CoV‐2 can be utilized for pooled sample testing for COVID‐19 screening in low‐prevalence settings providing significant cost savings and improving throughput without affecting test quality.
Collapse
Affiliation(s)
| | | | | | | | | | - Patrick Tang
- Sidra Medicine, Doha, Qatar.,Weill Cornell Medical College in Qatar, Doha, Qatar
| | | |
Collapse
|
39
|
Liv L. Electrochemical immunosensor platform based on gold-clusters, cysteamine and glutaraldehyde modified electrode for diagnosing COVID-19. Microchem J 2021; 168:106445. [PMID: 34054147 PMCID: PMC8141695 DOI: 10.1016/j.microc.2021.106445] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/30/2022]
Abstract
Amid the global threat caused by the coronavirus disease 2019 (COVID-19) pandemic, developing sufficiently rapid, accurate, sensitive and selective methods of diagnosing both symptomatic and asymptomatic cases is essential to alleviating and controlling the pandemic’s effects. This article describes an electrochemical immunoassay platform developed to determine the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) spike antibody by using gold-clusters capped with cysteamine, glutaraldehyde, the spike protein of the SARS-CoV-2 antigen and bovine serum albumin on a glassy carbon electrode. The electrochemical oxidation signal of the antigen-based immunosensor at 0.9 V was used to detect the SARS-CoV-2 spike antibody. When saliva and oropharyngeal swab samples were analysed, the recovery and relative standard deviation values were 96.97%–101.99% and 4.99%–5.74%, respectively. The method’s limit of detection relative to the SARS-CoV-2 spike antibody in synthetic media and in saliva or oropharyngeal swab samples was 0.01 ag/mL, while the immunosensor’s linear response to the SARS-CoV-2 spike antibody varied from 0.1 to 1000 ag/mL. The cross-reactivity of the Middle East respiratory syndrome-coronavirus spike antigen was evaluated after being immobilised onto the functionalised gold-cluster based sensor, indicated that the good specifity of the produced immunosensor.
Collapse
Affiliation(s)
- Lokman Liv
- Electrochemistry Laboratory, Chemistry Group, The Scientific and Technological Research Council of Turkey, National Metrology Institute, (TUBITAK UME), Gebze, Kocaeli 41470 Turkey
| |
Collapse
|
40
|
Song Q, Sun X, Dai Z, Gao Y, Gong X, Zhou B, Wu J, Wen W. Point-of-care testing detection methods for COVID-19. LAB ON A CHIP 2021; 21:1634-1660. [PMID: 33705507 DOI: 10.1039/d0lc01156h] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
COVID-19 is an acute respiratory disease caused by SARS-CoV-2, which has high transmissibility. People infected with SARS-CoV-2 can develop symptoms including cough, fever, pneumonia and other complications, which in severe cases could lead to death. In addition, a proportion of people infected with SARS-CoV-2 may be asymptomatic. At present, the primary diagnostic method for COVID-19 is reverse transcription-polymerase chain reaction (RT-PCR), which tests patient samples including nasopharyngeal swabs, sputum and other lower respiratory tract secretions. Other detection methods, e.g., isothermal nucleic acid amplification, CRISPR, immunochromatography, enzyme-linked immunosorbent assay (ELISA) and electrochemical sensors are also in use. As the current testing methods are mostly performed at central hospitals and third-party testing centres, the testing systems used mostly employ large, high-throughput, automated equipment. Given the current situation of the epidemic, point-of-care testing (POCT) is advantageous in terms of its ease of use, greater approachability on the user's end, more timely detection, and comparable accuracy and sensitivity, which could reduce the testing load on central hospitals. POCT is thus conducive to daily epidemic control and achieving early detection and treatment. This paper summarises the latest research advances in POCT-based SARS-CoV-2 detection methods, compares three categories of commercially available products, i.e., nucleic acid tests, immunoassays and novel sensors, and proposes the expectations for the development of POCT-based SARS-CoV-2 detection including greater accessibility, higher sensitivity and lower costs.
Collapse
Affiliation(s)
- Qi Song
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. and Guangzhou HKUST Fok Ying Tung Research Institute, Guangzhou, Guangdong, China
| | - Xindi Sun
- Materials Genome Institute, Shanghai University, Shanghai, China.
| | - Ziyi Dai
- Joint Key Laboratory of the Ministry of Education, Institute of Applied Physics and Materials Engineering, University of Macau, Macau, China.
| | - Yibo Gao
- Shenzhen Shineway Technology Corporation, Shenzhen, Guangdong, China
| | - Xiuqing Gong
- Materials Genome Institute, Shanghai University, Shanghai, China.
| | - Bingpu Zhou
- Joint Key Laboratory of the Ministry of Education, Institute of Applied Physics and Materials Engineering, University of Macau, Macau, China.
| | - Jinbo Wu
- Materials Genome Institute, Shanghai University, Shanghai, China.
| | - Weijia Wen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
| |
Collapse
|
41
|
Lebourgeois S, Storto A, Gout B, Le Hingrat Q, Ardila Tjader G, Cerdan MDC, English A, Pareja J, Love J, Houhou-Fidouh N, Manissero D, Descamps D, Visseaux B. Performance evaluation of the QIAstat-Dx® Respiratory SARS-CoV-2 Panel. Int J Infect Dis 2021; 107:179-181. [PMID: 33901651 PMCID: PMC8064816 DOI: 10.1016/j.ijid.2021.04.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 12/05/2022] Open
Abstract
Objective The aim of this study was to evaluate the QIAstat-Dx® Respiratory SARS-CoV-2 Panel (QIAstat-SARS-CoV-2), which is a closed, fully automated, multiplex polymerase chain reaction (PCR) assay that detects severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and 21 other pathogens that cause respiratory disease. Methods Nasopharyngeal swabs from patients with or suspected of having coronavirus disease 2019 were collected and tested at Bichat–Claude Bernard Hospital, Paris, France. Using the World Health Organisation-approved real-time-PCR assay developed by the Charité Institute of Virology as the reference, positive percent agreement (PPA) and negative percent agreement (NPA) were calculated. Results In total, 189 negative and 88 positive samples were analyzed. QIAstat-SARS-CoV-2 had an NPA of 90.48% (95% confidence interval (CI), 85.37%, 94.26%) and a PPA of 94.32% (95% CI, 87.24%, 98.13%). Co-infections were detected by QIAstat-SARS-CoV-2 in 4/277 specimens. The methods exhibited comparable failure rates (23/307 [7.5%] vs. 6/298 [2.0%] for QIAstat-SARS-CoV-2 and reference methods, respectively). The turnaround time was shorter for QIAstat-SARS-CoV-2 compared with the reference method (difference in mean –14:30 h [standard error, 0:03:23; 95% CI, –14:37, –14:24]; P < 0.001). Conclusions QIAstat-SARS-CoV-2 shows good agreement with the reference assay, providing faster and accurate results for detecting SARS-CoV-2.
Collapse
Affiliation(s)
- Samuel Lebourgeois
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France; Université de Paris, Assistance Publique - Hôpitaux de Paris, Service de Virologie, Hôpital Bichat, Paris, France
| | - Alexandre Storto
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France; Université de Paris, Assistance Publique - Hôpitaux de Paris, Service de Virologie, Hôpital Bichat, Paris, France
| | - Bernard Gout
- ARC Regulatory Ltd., Moneymore, Magherafelt, Northern Ireland, UK
| | - Quentin Le Hingrat
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France; Université de Paris, Assistance Publique - Hôpitaux de Paris, Service de Virologie, Hôpital Bichat, Paris, France
| | - Gustave Ardila Tjader
- Université de Paris, Assistance Publique - Hôpitaux de Paris, Service de Virologie, Hôpital Bichat, Paris, France
| | | | | | - Josep Pareja
- STAT-Dx Life, S.L. (a QIAGEN Company), Barcelona, Spain
| | - Joanna Love
- STAT-Dx Life, S.L. (a QIAGEN Company), Barcelona, Spain
| | - Nadhira Houhou-Fidouh
- Université de Paris, Assistance Publique - Hôpitaux de Paris, Service de Virologie, Hôpital Bichat, Paris, France
| | | | - Diane Descamps
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France; Université de Paris, Assistance Publique - Hôpitaux de Paris, Service de Virologie, Hôpital Bichat, Paris, France
| | - Benoit Visseaux
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France; Université de Paris, Assistance Publique - Hôpitaux de Paris, Service de Virologie, Hôpital Bichat, Paris, France.
| |
Collapse
|
42
|
Shaffaf T, Ghafar-Zadeh E. COVID-19 Diagnostic Strategies. Part I: Nucleic Acid-Based Technologies. Bioengineering (Basel) 2021; 8:49. [PMID: 33920513 PMCID: PMC8072613 DOI: 10.3390/bioengineering8040049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
The novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused respiratory infection, resulting in more than two million deaths globally and hospitalizing thousands of people by March 2021. A considerable percentage of the SARS-CoV-2 positive patients are asymptomatic or pre-symptomatic carriers, facilitating the viral spread in the community by their social activities. Hence, it is critical to have access to commercialized diagnostic tests to detect the infection in the earliest stages, monitor the disease, and follow up the patients. Various technologies have been proposed to develop more promising assays and move toward the mass production of fast, reliable, cost-effective, and portable PoC diagnostic tests for COVID-19 detection. Not only COVID-19 but also many other pathogens will be able to spread and attach to human bodies in the future. These technologies enable the fast identification of high-risk individuals during future hazards to support the public in such outbreaks. This paper provides a comprehensive review of current technologies, the progress in the development of molecular diagnostic tests, and the potential strategies to facilitate innovative developments in unprecedented pandemics.
Collapse
Affiliation(s)
- Tina Shaffaf
- Biologically Inspired Sensors and Actuators Laboratory (BioSA), York University, Toronto, ON M3J1P3, Canada;
- Faculty of Science, Department of Biology, York University, Toronto, ON M3J1P3, Canada
| | - Ebrahim Ghafar-Zadeh
- Biologically Inspired Sensors and Actuators Laboratory (BioSA), York University, Toronto, ON M3J1P3, Canada;
- Faculty of Science, Department of Biology, York University, Toronto, ON M3J1P3, Canada
- Lassonde School of Engineering, Department of Electrical Engineering and Computer Science, York University, Toronto, ON M3J1P3, Canada
| |
Collapse
|
43
|
Le Hingrat Q, Bouzid D, Choquet C, Laurent O, Lescure FX, Timsit JF, Houhou-Fidouh N, Casalino E, Lucet JC, Descamps D, Visseaux B. Viral epidemiology and SARS-CoV-2 co-infections with other respiratory viruses during the first COVID-19 wave in Paris, France. Influenza Other Respir Viruses 2021; 15:425-428. [PMID: 33817971 PMCID: PMC8189235 DOI: 10.1111/irv.12853] [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: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 12/15/2022] Open
Abstract
Objectives Our work assessed the prevalence of co‐infections in patients with SARS‐CoV‐2. Methods All patients hospitalized in a Parisian hospital during the first wave of COVID‐19 were tested by multiplex PCR if they presented ILI symptoms. Results A total of 806 patients (21%) were positive for SARS‐CoV‐2, 755 (20%) were positive for other respiratory viruses. Among the SARS‐CoV‐2‐positive patients, 49 (6%) had viral co‐infections. They presented similar age, symptoms, except for fever (P = .013) and headaches (P = .048), than single SARS‐CoV‐2 infections. Conclusions SARS‐CoV‐2‐infected patients presenting viral co‐infections had similar clinical characteristics and prognosis than patients solely infected with SARS‐CoV‐2.
Collapse
Affiliation(s)
- Quentin Le Hingrat
- INSERM, IAME, Université de Paris, Paris, France.,AP-HP Nord, Virology Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Donia Bouzid
- INSERM, IAME, Université de Paris, Paris, France.,AP-HP Nord, Emergency Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Christophe Choquet
- AP-HP Nord, Emergency Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Odile Laurent
- AP-HP Nord, Emergency Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - François-Xavier Lescure
- INSERM, IAME, Université de Paris, Paris, France.,AP-HP Nord, Infectious Diseases Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Jean-François Timsit
- INSERM, IAME, Université de Paris, Paris, France.,AP-HP Nord, Medical and Infectious Diseases Intensive Care Unit, Bichat-Claude Bernard University Hospital, Paris, France
| | - Nadhira Houhou-Fidouh
- AP-HP Nord, Virology Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Enrique Casalino
- INSERM, IAME, Université de Paris, Paris, France.,AP-HP Nord, Emergency Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Jean-Christophe Lucet
- INSERM, IAME, Université de Paris, Paris, France.,AP-HP Nord, Infection Control Unit, Bichat-Claude Bernard University Hospital, Paris, France
| | - Diane Descamps
- INSERM, IAME, Université de Paris, Paris, France.,AP-HP Nord, Virology Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Benoit Visseaux
- INSERM, IAME, Université de Paris, Paris, France.,AP-HP Nord, Virology Department, Bichat-Claude Bernard University Hospital, Paris, France
| |
Collapse
|
44
|
Noor FA, Safain KS, Hossain MW, Arafath K, Mannoor K, Kabir M. Development and performance evaluation of the first in-house multiplex rRT-PCR assay in Bangladesh for highly sensitive detection of SARS-CoV-2. J Virol Methods 2021; 293:114147. [PMID: 33812943 PMCID: PMC8015390 DOI: 10.1016/j.jviromet.2021.114147] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 03/27/2021] [Accepted: 03/30/2021] [Indexed: 12/20/2022]
Abstract
Background The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic is posing a great threat to global health and economy. Due to the lack of broad diagnostic setup, consistent reagent supply lines, and access to laboratory instruments and equipment, it is undoubtedly an enormous burden for developing countries to face the crisis. Objectives To develop a cost-effective, reliable and sensitive multiplex assay for SARS-CoV-2 screening which would expand the testing capacities of a developing and low-income country like Bangladesh. Study design Initially a singleplex and then a multiplex real-time reverse-transcriptase PCR assays were developed targeting 2 nucleocapsid genes of SARS-CoV-2, and the human RNase P gene as an internal control using laboratory-made mastermixes. Three sets of primer- probes were designed for each of the target genes and one set was optimized for the final reaction set-up. Limit of detection, cross-reactivity and reproducibility were checked in order to assess the sensitivity and specificity of the assays, and validation was done using clinical specimens. Results Clinical evaluation of the new assays using 240 nasopharyngeal swabs showed 100 % sensitivity, specificity, and accuracy in detecting SARS-CoV-2 infection in human. Equal efficiency and concordant results were observed between the singleplex and multiplex approaches. Notably, the kit was able to detect SARS-CoV-2 RNA at very low concentration upto 5 copies/reaction. Conclusion This is the first locally developed multiplex rRT-PCR kit in Bangladesh providing rapid and low-cost screening of COVID-19 which would be valuable for infection prevention and clinical management in the perspective of Bangladesh.
Collapse
Affiliation(s)
- Farjana Akther Noor
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh; Department of Biochemistry & Molecular Biology, Tejgaon College, Tejgaon, Dhaka, 1215, Bangladesh
| | - Kazi Sarjana Safain
- Molecular Division, OMC Healthcare (Pvt.) Ltd, Rupnagar, Dhaka, 1216, Bangladesh
| | - Md Walid Hossain
- Molecular Division, OMC Healthcare (Pvt.) Ltd, Rupnagar, Dhaka, 1216, Bangladesh
| | - Khalid Arafath
- Molecular Division, OMC Healthcare (Pvt.) Ltd, Rupnagar, Dhaka, 1216, Bangladesh
| | - Kaiissar Mannoor
- Infectious Diseases Laboratory, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mazbahul Kabir
- Molecular Division, OMC Healthcare (Pvt.) Ltd, Rupnagar, Dhaka, 1216, Bangladesh.
| |
Collapse
|
45
|
Goh KC, Tan SYL, Tan WL, Lim KL, Ko KKK, Oon LLE, Chan KS. Evaluation of the QIAstat-Dx Respiratory SARS-CoV-2 Panel for early diagnosis of COVID-19. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2021; 50:369-370. [PMID: 33990831 DOI: 10.47102/annals-acadmedsg.2020528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Kenneth C Goh
- Department of Microbiology, Singapore General Hospital, Singapore
| | | | | | | | | | | | | |
Collapse
|
46
|
Dinnes J, Deeks JJ, Berhane S, Taylor M, Adriano A, Davenport C, Dittrich S, Emperador D, Takwoingi Y, Cunningham J, Beese S, Domen J, Dretzke J, Ferrante di Ruffano L, Harris IM, Price MJ, Taylor-Phillips S, Hooft L, Leeflang MM, McInnes MD, Spijker R, Van den Bruel A. Rapid, point-of-care antigen and molecular-based tests for diagnosis of SARS-CoV-2 infection. Cochrane Database Syst Rev 2021; 3:CD013705. [PMID: 33760236 PMCID: PMC8078597 DOI: 10.1002/14651858.cd013705.pub2] [Citation(s) in RCA: 298] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Accurate rapid diagnostic tests for SARS-CoV-2 infection could contribute to clinical and public health strategies to manage the COVID-19 pandemic. Point-of-care antigen and molecular tests to detect current infection could increase access to testing and early confirmation of cases, and expediate clinical and public health management decisions that may reduce transmission. OBJECTIVES To assess the diagnostic accuracy of point-of-care antigen and molecular-based tests for diagnosis of SARS-CoV-2 infection. We consider accuracy separately in symptomatic and asymptomatic population groups. SEARCH METHODS Electronic searches of the Cochrane COVID-19 Study Register and the COVID-19 Living Evidence Database from the University of Bern (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) were undertaken on 30 Sept 2020. We checked repositories of COVID-19 publications and included independent evaluations from national reference laboratories, the Foundation for Innovative New Diagnostics and the Diagnostics Global Health website to 16 Nov 2020. We did not apply language restrictions. SELECTION CRITERIA We included studies of people with either suspected SARS-CoV-2 infection, known SARS-CoV-2 infection or known absence of infection, or those who were being screened for infection. We included test accuracy studies of any design that evaluated commercially produced, rapid antigen or molecular tests suitable for a point-of-care setting (minimal equipment, sample preparation, and biosafety requirements, with results within two hours of sample collection). We included all reference standards that define the presence or absence of SARS-CoV-2 (including reverse transcription polymerase chain reaction (RT-PCR) tests and established diagnostic criteria). DATA COLLECTION AND ANALYSIS Studies were screened independently in duplicate with disagreements resolved by discussion with a third author. Study characteristics were extracted by one author and checked by a second; extraction of study results and assessments of risk of bias and applicability (made using the QUADAS-2 tool) were undertaken independently in duplicate. We present sensitivity and specificity with 95% confidence intervals (CIs) for each test and pooled data using the bivariate model separately for antigen and molecular-based tests. We tabulated results by test manufacturer and compliance with manufacturer instructions for use and according to symptom status. MAIN RESULTS Seventy-eight study cohorts were included (described in 64 study reports, including 20 pre-prints), reporting results for 24,087 samples (7,415 with confirmed SARS-CoV-2). Studies were mainly from Europe (n = 39) or North America (n = 20), and evaluated 16 antigen and five molecular assays. We considered risk of bias to be high in 29 (50%) studies because of participant selection; in 66 (85%) because of weaknesses in the reference standard for absence of infection; and in 29 (45%) for participant flow and timing. Studies of antigen tests were of a higher methodological quality compared to studies of molecular tests, particularly regarding the risk of bias for participant selection and the index test. Characteristics of participants in 35 (45%) studies differed from those in whom the test was intended to be used and the delivery of the index test in 39 (50%) studies differed from the way in which the test was intended to be used. Nearly all studies (97%) defined the presence or absence of SARS-CoV-2 based on a single RT-PCR result, and none included participants meeting case definitions for probable COVID-19. Antigen tests Forty-eight studies reported 58 evaluations of antigen tests. Estimates of sensitivity varied considerably between studies. There were differences between symptomatic (72.0%, 95% CI 63.7% to 79.0%; 37 evaluations; 15530 samples, 4410 cases) and asymptomatic participants (58.1%, 95% CI 40.2% to 74.1%; 12 evaluations; 1581 samples, 295 cases). Average sensitivity was higher in the first week after symptom onset (78.3%, 95% CI 71.1% to 84.1%; 26 evaluations; 5769 samples, 2320 cases) than in the second week of symptoms (51.0%, 95% CI 40.8% to 61.0%; 22 evaluations; 935 samples, 692 cases). Sensitivity was high in those with cycle threshold (Ct) values on PCR ≤25 (94.5%, 95% CI 91.0% to 96.7%; 36 evaluations; 2613 cases) compared to those with Ct values >25 (40.7%, 95% CI 31.8% to 50.3%; 36 evaluations; 2632 cases). Sensitivity varied between brands. Using data from instructions for use (IFU) compliant evaluations in symptomatic participants, summary sensitivities ranged from 34.1% (95% CI 29.7% to 38.8%; Coris Bioconcept) to 88.1% (95% CI 84.2% to 91.1%; SD Biosensor STANDARD Q). Average specificities were high in symptomatic and asymptomatic participants, and for most brands (overall summary specificity 99.6%, 95% CI 99.0% to 99.8%). At 5% prevalence using data for the most sensitive assays in symptomatic people (SD Biosensor STANDARD Q and Abbott Panbio), positive predictive values (PPVs) of 84% to 90% mean that between 1 in 10 and 1 in 6 positive results will be a false positive, and between 1 in 4 and 1 in 8 cases will be missed. At 0.5% prevalence applying the same tests in asymptomatic people would result in PPVs of 11% to 28% meaning that between 7 in 10 and 9 in 10 positive results will be false positives, and between 1 in 2 and 1 in 3 cases will be missed. No studies assessed the accuracy of repeated lateral flow testing or self-testing. Rapid molecular assays Thirty studies reported 33 evaluations of five different rapid molecular tests. Sensitivities varied according to test brand. Most of the data relate to the ID NOW and Xpert Xpress assays. Using data from evaluations following the manufacturer's instructions for use, the average sensitivity of ID NOW was 73.0% (95% CI 66.8% to 78.4%) and average specificity 99.7% (95% CI 98.7% to 99.9%; 4 evaluations; 812 samples, 222 cases). For Xpert Xpress, the average sensitivity was 100% (95% CI 88.1% to 100%) and average specificity 97.2% (95% CI 89.4% to 99.3%; 2 evaluations; 100 samples, 29 cases). Insufficient data were available to investigate the effect of symptom status or time after symptom onset. AUTHORS' CONCLUSIONS Antigen tests vary in sensitivity. In people with signs and symptoms of COVID-19, sensitivities are highest in the first week of illness when viral loads are higher. The assays shown to meet appropriate criteria, such as WHO's priority target product profiles for COVID-19 diagnostics ('acceptable' sensitivity ≥ 80% and specificity ≥ 97%), can be considered as a replacement for laboratory-based RT-PCR when immediate decisions about patient care must be made, or where RT-PCR cannot be delivered in a timely manner. Positive predictive values suggest that confirmatory testing of those with positive results may be considered in low prevalence settings. Due to the variable sensitivity of antigen tests, people who test negative may still be infected. Evidence for testing in asymptomatic cohorts was limited. Test accuracy studies cannot adequately assess the ability of antigen tests to differentiate those who are infectious and require isolation from those who pose no risk, as there is no reference standard for infectiousness. A small number of molecular tests showed high accuracy and may be suitable alternatives to RT-PCR. However, further evaluations of the tests in settings as they are intended to be used are required to fully establish performance in practice. Several important studies in asymptomatic individuals have been reported since the close of our search and will be incorporated at the next update of this review. Comparative studies of antigen tests in their intended use settings and according to test operator (including self-testing) are required.
Collapse
Affiliation(s)
- Jacqueline Dinnes
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham , UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Jonathan J Deeks
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Sarah Berhane
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Melissa Taylor
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ada Adriano
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Clare Davenport
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | | | | | - Yemisi Takwoingi
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva , Switzerland
| | - Sophie Beese
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Julie Domen
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Janine Dretzke
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Lavinia Ferrante di Ruffano
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Isobel M Harris
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Malcolm J Price
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Sian Taylor-Phillips
- Division of Health Sciences, Warwick Medical School, University of Warwick , Coventry, UK
| | - Lotty Hooft
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht , Netherlands
| | - Mariska Mg Leeflang
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | | | - René Spijker
- Medical Library, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health, Amsterdam, Netherlands
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Ann Van den Bruel
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| |
Collapse
|
47
|
Harris C, Harris RJ, Downey L, Gwiggner M. Management of Crohn's disease in an immunosuppressed COVID-19-positive patient: safety-driven prioritisation of nutritional therapy as a bridge to restarting immunosuppression. BMJ Case Rep 2021; 14:e239404. [PMID: 33753379 PMCID: PMC7986758 DOI: 10.1136/bcr-2020-239404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2021] [Indexed: 01/08/2023] Open
Abstract
Active inflammatory bowel disease (IBD), combined immunosuppression and corticosteroid therapy have all been identified as risk factors for a poor outcome in COVID-19 infection. The management of patients with both COVID-19 infection and active IBD is therefore complex. We present the case of a 31-year-old patient with Crohn's disease, on dual immunosuppression with infliximab and mercaptopurine presenting with inflammatory small bowel obstruction and COVID-19 infection. The case highlights the use of nutritional therapy, which remains underused in the management of adults with IBD, to manage his flare acutely. Following negative SARS-CoV-2 PCR testing and SARS-CoV-2 IgG testing confirming an antibody response, ustekinumab (anti-interleukin 12/23) was prescribed for long-term maintenance.
Collapse
Affiliation(s)
- Clare Harris
- Department of Gastroenterology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Richard James Harris
- Department of Gastroenterology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Louise Downey
- Department of Gastroenterology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Markus Gwiggner
- Department of Gastroenterology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| |
Collapse
|
48
|
Oishee MJ, Ali T, Jahan N, Khandker SS, Haq MA, Khondoker MU, Sil BK, Lugova H, Krishnapillai A, Abubakar AR, Kumar S, Haque M, Jamiruddin MR, Adnan N. COVID-19 Pandemic: Review of Contemporary and Forthcoming Detection Tools. Infect Drug Resist 2021; 14:1049-1082. [PMID: 33762831 PMCID: PMC7982560 DOI: 10.2147/idr.s289629] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/30/2021] [Indexed: 01/10/2023] Open
Abstract
Recent severe acute respiratory syndrome 2 (SARS-CoV-2) known as COVID-19, presents a deadly challenge to the global healthcare system of developing and developed countries, exposing the limitations of health facilities preparedness for emerging infectious disease pandemic. Opportune detection, confinement, and early treatment of infected cases present the first step in combating COVID-19. In this review, we elaborate on various COVID-19 diagnostic tools that are available or under investigation. Consequently, cell culture, followed by an indirect fluorescent antibody, is one of the most accurate methods for detecting SARS-CoV-2 infection. However, restrictions imposed by the regulatory authorities prevented its general use and implementation. Diagnosis via radiologic imaging and reverse transcriptase PCR assay is frequently employed, considered as standard procedures, whereas isothermal amplification methods are currently on the verge of clinical introduction. Notably, techniques such as CRISPR-Cas and microfluidics have added new dimensions to the SARS-CoV-2 diagnosis. Furthermore, commonly used immunoassays such as enzyme-linked immunosorbent assay (ELISA), lateral flow immunoassay (LFIA), neutralization assay, and the chemiluminescent assay can also be used for early detection and surveillance of SARS-CoV-2 infection. Finally, advancement in the next generation sequencing (NGS) and metagenomic analysis are smoothing the viral detection further in this global challenge.
Collapse
Affiliation(s)
| | - Tamanna Ali
- Gonoshasthaya-RNA Molecular Diagnostic and Research Center, Dhaka, Bangladesh
| | - Nowshin Jahan
- Gonoshasthaya-RNA Molecular Diagnostic and Research Center, Dhaka, Bangladesh
| | | | - Md Ahsanul Haq
- Gonoshasthaya-RNA Molecular Diagnostic and Research Center, Dhaka, Bangladesh
| | | | | | - Halyna Lugova
- Faculty of Medicine and Defence Health, National Defence University of Malaysia, Kuala Lumpur, Malaysia
| | - Ambigga Krishnapillai
- Faculty of Medicine and Defence Health, National Defence University of Malaysia, Kuala Lumpur, Malaysia
| | - Abdullahi Rabiu Abubakar
- Department of Pharmacology and Therapeutics, Faculty of Pharmaceutical Sciences, Bayero University, Kano, 700233, Kano, Nigeria
| | - Santosh Kumar
- Department of Periodontology and Implantology, Karnavati University, Gandhinagar, 382422, India
| | - Mainul Haque
- The Unit of Pharmacology, Faculty of Medicine and Defence Health Universiti Pertahanan, Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur, Malaysia
| | | | - Nihad Adnan
- Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh
| |
Collapse
|
49
|
Abd-Alrazaq A, Schneider J, Mifsud B, Alam T, Househ M, Hamdi M, Shah Z. A Comprehensive Overview of the COVID-19 Literature: Machine Learning-Based Bibliometric Analysis. J Med Internet Res 2021; 23:e23703. [PMID: 33600346 PMCID: PMC7942394 DOI: 10.2196/23703] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/14/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Shortly after the emergence of COVID-19, researchers rapidly mobilized to study numerous aspects of the disease such as its evolution, clinical manifestations, effects, treatments, and vaccinations. This led to a rapid increase in the number of COVID-19-related publications. Identifying trends and areas of interest using traditional review methods (eg, scoping and systematic reviews) for such a large domain area is challenging. OBJECTIVE We aimed to conduct an extensive bibliometric analysis to provide a comprehensive overview of the COVID-19 literature. METHODS We used the COVID-19 Open Research Dataset (CORD-19) that consists of a large number of research articles related to all coronaviruses. We used a machine learning-based method to analyze the most relevant COVID-19-related articles and extracted the most prominent topics. Specifically, we used a clustering algorithm to group published articles based on the similarity of their abstracts to identify research hotspots and current research directions. We have made our software accessible to the community via GitHub. RESULTS Of the 196,630 publications retrieved from the database, we included 28,904 in our analysis. The mean number of weekly publications was 990 (SD 789.3). The country that published the highest number of COVID-19-related articles was China (2950/17,270, 17.08%). The highest number of articles were published in bioRxiv. Lei Liu affiliated with the Southern University of Science and Technology in China published the highest number of articles (n=46). Based on titles and abstracts alone, we were able to identify 1515 surveys, 733 systematic reviews, 512 cohort studies, 480 meta-analyses, and 362 randomized control trials. We identified 19 different topics covered among the publications reviewed. The most dominant topic was public health response, followed by clinical care practices during the COVID-19 pandemic, clinical characteristics and risk factors, and epidemic models for its spread. CONCLUSIONS We provide an overview of the COVID-19 literature and have identified current hotspots and research directions. Our findings can be useful for the research community to help prioritize research needs and recognize leading COVID-19 researchers, institutes, countries, and publishers. Our study shows that an AI-based bibliometric analysis has the potential to rapidly explore a large corpus of academic publications during a public health crisis. We believe that this work can be used to analyze other eHealth-related literature to help clinicians, administrators, and policy makers to obtain a holistic view of the literature and be able to categorize different topics of the existing research for further analyses. It can be further scaled (for instance, in time) to clinical summary documentation. Publishers should avoid noise in the data by developing a way to trace the evolution of individual publications and unique authors.
Collapse
Affiliation(s)
- Alaa Abd-Alrazaq
- Division of Information and Computing Technology, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Jens Schneider
- Division of Information and Computing Technology, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Borbala Mifsud
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Tanvir Alam
- Division of Information and Computing Technology, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Mowafa Househ
- Division of Information and Computing Technology, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Mounir Hamdi
- Division of Information and Computing Technology, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Zubair Shah
- Division of Information and Computing Technology, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| |
Collapse
|
50
|
Abstract
Laboratory evaluation of SARS-CoV-2 involves the detection of viral nucleic acid, viral protein antigens, and the antibody response. Molecular detection of SARS-CoV-2 is the only diagnostic test currently available in acutely or recently infected individuals. In contrast, serological testing is typically performed once viral RNA has been cleared and symptoms have resolved. This leads to some confusion among clinicians as to which test to order and when each is appropriate. While SARS-CoV-2 assays can suffer from poor sensitivity, all FDA authorized assays to date are intended to be qualitative. Serological tests have multiple assay formats, detect various classes of immunoglobulins, and have a distinct role in seroprevalence studies; however, the association with long-term protection remains unclear. Both molecular and serological testing for SARS-CoV-2 have complementary roles in patient management, and we highlight the challenges faced by clinicians and laboratorians alike in the evaluation and interpretation of the currently available laboratory assays.
Collapse
Affiliation(s)
- Bijal A. Parikh
- Corresponding author. 660 South Euclid Ave., Campus Box 8118, St. Louis, MO, 63110, United States
| | | |
Collapse
|