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Luštrek M, Cesar Z, Suljič A, Kogoj R, Knap N, Virant MJ, Uršič T, Petrovec M, Avšič-Županc T, Korva M. Influenza A, Influenza B, human respiratory syncytial virus and SARSCoV-2 molecular diagnostics and epidemiology in the post COVID-19 era. Respir Res 2024; 25:234. [PMID: 38840154 PMCID: PMC11151539 DOI: 10.1186/s12931-024-02862-7] [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: 12/21/2023] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND The concurrent circulation of SARS-CoV-2 with other respiratory viruses is unstoppable and represents a new diagnostic reality for clinicians and clinical microbiology laboratories. Multiplexed molecular testing on automated platforms that focus on the simultaneous detection of multiple respiratory viruses in a single tube is a useful approach for current and future diagnosis of respiratory infections in the clinical setting. METHODS Two time periods were included in the study: from February to April 2022, an early 2022 period, during the gradual lifting of COVID-19 prevention measures in the country, and from October 2022 to April 2023, the 2022/23 respiratory infections season. We analysed a total of 1,918 samples in the first period and 18,131 respiratory samples in the second period using a multiplex molecular assay for the simultaneous detection of Influenza A (Flu-A), Influenza B (Flu-B), Human Respiratory Syncytial Virus (HRSV) and SARS-CoV-2. RESULTS The results from early 2022 showed a strong dominance of SARS-CoV-2 infections with 1,267/1,918 (66.1%) cases. Flu-A was detected in 30/1,918 (1.6%) samples, HRSV in 14/1,918 (0.7%) samples, and Flu-B in 2/1,918 (0.1%) samples. Flu-A/SARS-CoV-2 co-detections were observed in 11/1,267 (0.9%) samples, and HRSV/SARS-CoV-2 co-detection in 5/1,267 (0.4%) samples. During the 2022/23 winter respiratory season, SARS-CoV-2 was detected in 1,738/18,131 (9.6%), Flu-A in 628/18,131 (3.5%), Flu-B in 106/18,131 (0.6%), and HRSV in 505/18,131 (2.8%) samples. Interestingly, co-detections were present to a similar extent as in early 2022. CONCLUSION The results show that the multiplex molecular approach is a valuable tool for the simultaneous laboratory diagnosis of SARS-CoV-2, Flu-A/B, and HRSV in hospitalized and outpatients. Infections with Flu-A/B, and HRSV occurred shortly after the COVID-19 control measures were lifted, so a strong reoccurrence of various respiratory infections and co-detections in the post COVID-19 period was to be expected.
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Affiliation(s)
- Manca Luštrek
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Zala Cesar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Alen Suljič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Rok Kogoj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Nataša Knap
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Monika Jevšnik Virant
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Tina Uršič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Miša Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia.
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2
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Karuppaiah G, Vashist A, Nair M, Veerapandian M, Manickam P. Emerging trends in point-of-care biosensing strategies for molecular architectures and antibodies of SARS-CoV-2. BIOSENSORS & BIOELECTRONICS: X 2023; 13:100324. [PMID: 36844889 PMCID: PMC9941073 DOI: 10.1016/j.biosx.2023.100324] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/01/2023] [Accepted: 02/18/2023] [Indexed: 02/23/2023]
Abstract
COVID-19, a highly contagious viral infection caused by the occurrence of severe acute respiratory syndrome coronavirus (SARS-CoV-2), has turned out to be a viral pandemic then ravaged many countries worldwide. In the recent years, point-of-care (POC) biosensors combined with state-of-the-art bioreceptors, and transducing systems enabled the development of novel diagnostic tools for rapid and reliable detection of biomarkers associated with SARS-CoV-2. The present review thoroughly summarises and discusses various biosensing strategies developed for probing SARS-CoV-2 molecular architectures (viral genome, S Protein, M protein, E protein, N protein and non-structural proteins) and antibodies as a potential diagnostic tool for COVID-19. This review discusses the various structural components of SARS-CoV-2, their binding regions and the bioreceptors used for recognizing the structural components. The various types of clinical specimens investigated for rapid and POC detection of SARS-CoV-2 is also highlighted. The importance of nanotechnology and artificial intelligence (AI) approaches in improving the biosensor performance for real-time and reagent-free monitoring the biomarkers of SARS-CoV-2 is also summarized. This review also encompasses existing practical challenges and prospects for developing new POC biosensors for clinical monitoring of COVID-19.
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Affiliation(s)
- Gopi Karuppaiah
- Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi, 630 003, Tamil Nadu, India
| | - Arti Vashist
- Center for Personalized Nanomedicine, Institute of NeuroImmune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, 33199, USA
| | - Madhavan Nair
- Center for Personalized Nanomedicine, Institute of NeuroImmune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, 33199, USA
| | - Murugan Veerapandian
- Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi, 630 003, Tamil Nadu, India
- Academy of Scientific and Innovative Research, Ghaziabad, 201 002, Uttar Pradesh, India
| | - Pandiaraj Manickam
- Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi, 630 003, Tamil Nadu, India
- Academy of Scientific and Innovative Research, Ghaziabad, 201 002, Uttar Pradesh, India
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3
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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] [MESH Headings] [Grants] [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.
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Affiliation(s)
- Kimberly S Butler
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Bryan D Carson
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Joshua D Podlevsky
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Cathryn M Mayes
- WMD Threats and Aerosol Science, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Jessica M Rowland
- Global Chemical and Biological Security, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - DeAnna Campbell
- Biological and Chemical Sensors Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - J Bryce Ricken
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - George Wudiri
- Cooperative Nuclear Counterproliferation, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Jerilyn A Timlin
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA.
- Computational Biology and Biophysics Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA.
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4
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Performing under Pressure: Insights into the Diagnostic Testing Burden at a UK National Health Service Clinical Virology Laboratory during the SARS-CoV-2 Pandemic. Viruses 2022; 14:v14102233. [PMID: 36298788 PMCID: PMC9609557 DOI: 10.3390/v14102233] [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: 09/12/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/23/2022] Open
Abstract
UK National Health Service (NHS) Clinical Virology Departments provide a repertoire of tests on clinical samples to detect the presence of viral genomic material or host immune responses to viral infection. In December 2019, a novel coronavirus (SARS-CoV-2) emerged which quickly developed into a global pandemic; NHS laboratories responded rapidly to upscale their testing capabilities. To date, there is little information on the impact of increased SARS-CoV-2 screening on non-SARS-CoV-2 testing within NHS laboratories. This report details the virology test requests received by the Leicester-based NHS Virology laboratory from January 2018 to May 2022. Data show that in spite of a dramatic increase in screening, along with multiple logistic and staffing issues, the Leicester Virology Department was mostly able to maintain the same level of service for non-respiratory virus testing while meeting the new increase in SARS-CoV-2 testing.
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5
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Evaluation of Two Broadly Used Commercial Methods for Detection of Respiratory Viruses with a Recently Added New Target for Detection of SARS-CoV-2. Viruses 2022; 14:v14071530. [PMID: 35891511 PMCID: PMC9324506 DOI: 10.3390/v14071530] [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: 05/23/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/20/2022] Open
Abstract
The clinical symptoms caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are nonspecific and can be associated with most other respiratory viruses that cause acute respiratory tract infections (ARI). Because the clinical differentiation of COVID-19 patients from those with other respiratory viruses is difficult, the evaluation of automated methods to detect important respiratory viruses together with SARS-CoV-2 seems necessary. Therefore, this study compares two molecular assays for the detection of respiratory viruses, including SARS-CoV-2: the Respiratory Viruses 16-Well Assay (AusDiagnostics, Pty Ltd., Mascot, Australia) and the Allplex™ RV Essential Assay coupled with the Allplex™-nCoV Assay (Seegene Inc., Seoul, Korea). The two methods (AusDiagnostics and AlplexTM-nCoV Assay SARS-CoV-2) had 98.6% agreement with the reference method, cobas 6800, for the detection of SARS-CoV-2. Agreement between the AusDiagnostics assay and the AlplexTM RV Essential Assay for the detection of seven respiratory viruses was 99%. In our experience, the Respiratory Viruses 16-Well Assay proved to be the most valuable and useful medium-throughput method for simultaneous detection of important respiratory viruses and SARS-CoV-2. The main advantages of the method are high specificity for all targets included and their simultaneous detection and medium throughput with the option of having multiple instruments provide a constant run.
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6
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Feathers L, Hinde T, Bale T, Hyde J, Bird PW, Holmes CW, Tang JW. Outbreak of SARS-CoV-2 at a hospice: terminated after the implementation of enhanced aerosol infection control measures. Interface Focus 2022; 12:20210066. [PMID: 35261730 PMCID: PMC8831080 DOI: 10.1098/rsfs.2021.0066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/08/2021] [Indexed: 12/17/2022] Open
Abstract
Outbreaks of COVID-19 in hospices for palliative care patients pose a unique and difficult situation. Staff, relatives and patients may be possible sources and recipients of infection. We present an outbreak of COVID-19 in a hospice setting, during the UK's first pandemic wave. During the outbreak period, 26 patients and 30 staff tested SARS-CoV-2 positive by laboratory-based RT-PCR testing. Most infected staff exhibited some mild, non-specific symptoms so affected staff members may not have voluntarily self-isolated or had themselves tested on this basis. Similarly, for infected patients, most became symptomatic and were then isolated. Additional, enhanced aerosol infection control measures were implemented, including opening of all windows where available; universal masking for all staff, including in non-clinical areas and taking breaks separately; screening for asymptomatic infection among staff and patients, with appropriate isolation (at home for staff) if infected; performing a ventilation survey of the hospice facility. After these measures were instigated, the numbers of COVID-19 cases decreased to zero over the following three weeks. This outbreak study demonstrated that an accurate understanding of the routes of infection for a new pathogen, as well as the nature of symptomatic versus asymptomatic infection and transmission, is crucial for controlling its spread.
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Affiliation(s)
| | | | | | - Jo Hyde
- LOROS Hospice Care, Leicester, UK
| | - Paul W. Bird
- Clinical Microbiology, University of Leicester Hospitals, 5/F Sandringham Building, Leicester Royal Infirmary, Infirmary Square, Leicester LE1 5WW, UK
| | - Christopher W. Holmes
- Clinical Microbiology, University of Leicester Hospitals, 5/F Sandringham Building, Leicester Royal Infirmary, Infirmary Square, Leicester LE1 5WW, UK
| | - Julian W. Tang
- Clinical Microbiology, University of Leicester Hospitals, 5/F Sandringham Building, Leicester Royal Infirmary, Infirmary Square, Leicester LE1 5WW, UK
- Respiratory Sciences, University of Leicester, Leicester, UK
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7
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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.
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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.
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8
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Van Walle I, Leitmeyer K, Broberg EK. Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid and antibody tests up to 22 August 2020. ACTA ACUST UNITED AC 2021; 26. [PMID: 34763752 PMCID: PMC8646979 DOI: 10.2807/1560-7917.es.2021.26.45.2001675] [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] [Indexed: 12/23/2022]
Abstract
BackgroundReliable testing for SARS-CoV-2 is key for the management of the COVID-19 pandemic.AimWe estimate diagnostic accuracy for nucleic acid and antibody tests 5 months into the COVID-19 pandemic, and compare with manufacturer-reported accuracy.MethodsWe reviewed the clinical performance of SARS-CoV-2 nucleic acid and antibody tests based on 93,757 test results from 151 published studies and 20,205 new test results from 12 countries in the European Union and European Economic Area (EU/EEA).ResultsPooling the results and considering only results with 95% confidence interval width ≤ 5%, we found four nucleic acid tests, including one point-of-care test and three antibody tests, with a clinical sensitivity ≥ 95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Nine nucleic acid tests and 25 antibody tests, 12 of them point-of-care tests, had a clinical specificity of ≥ 98%. Three antibody tests achieved both thresholds. Evidence for nucleic acid point-of-care tests remains scarce at present, and sensitivity varied substantially. Study heterogeneity was low for eight of 14 sensitivity and 68 of 84 specificity results with confidence interval width ≤ 5%, and lower for nucleic acid tests than antibody tests. Manufacturer-reported clinical performance was significantly higher than independently assessed in 11 of 32 and four of 34 cases, respectively, for sensitivity and specificity, indicating a need for improvement in this area.ConclusionContinuous monitoring of clinical performance within more clearly defined target populations is needed.
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Affiliation(s)
- Ivo Van Walle
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, The Netherlands.,European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Katrin Leitmeyer
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Eeva K Broberg
- European Centre for Disease Prevention and Control, Stockholm, Sweden
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- The members of the European COVID-19 microbiological laboratories group are listed under Investigators
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9
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Neeland MR, Bannister S, Clifford V, Nguyen J, Dohle K, Overmars I, Toh ZQ, Anderson J, Donato CM, Sarkar S, Do LAH, McCafferty C, Licciardi PV, Ignjatovic V, Monagle P, Bines JE, Mulholland K, Curtis N, McNab S, Steer AC, Burgner DP, Saffery R, Tosif S, Crawford NW. Children and Adults in a Household Cohort Study Have Robust Longitudinal Immune Responses Following SARS-CoV-2 Infection or Exposure. Front Immunol 2021; 12:741639. [PMID: 34721408 PMCID: PMC8548628 DOI: 10.3389/fimmu.2021.741639] [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: 07/15/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Children have reduced severity of COVID-19 compared to adults and typically have mild or asymptomatic disease. The immunological mechanisms underlying these age-related differences in clinical outcomes remain unexplained. Here, we quantify 23 immune cell populations in 141 samples from children and adults with mild COVID-19 and their PCR-negative close household contacts at acute and convalescent time points. Children with COVID-19 displayed marked reductions in myeloid cells during infection, most prominent in children under the age of five. Recovery from infection in both children and adults was characterised by the generation of CD8 TCM and CD4 TCM up to 9 weeks post infection. SARS-CoV-2-exposed close contacts also had immunological changes over time despite no evidence of confirmed SARS-CoV-2 infection on PCR testing. This included an increase in low-density neutrophils during convalescence in both exposed children and adults, as well as increases in CD8 TCM and CD4 TCM in exposed adults. In comparison to children with other common respiratory viral infections, those with COVID-19 had a greater change in innate and T cell-mediated immune responses over time. These findings provide new mechanistic insights into the immune response during and after recovery from COVID-19 in both children and adults.
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Affiliation(s)
- Melanie R Neeland
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Samantha Bannister
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Infectious Diseases Unit, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Vanessa Clifford
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Infectious Diseases Unit, The Royal Children's Hospital, Parkville, VIC, Australia.,Laboratory Services, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Jill Nguyen
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Kate Dohle
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Isabella Overmars
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Zheng Quan Toh
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Jeremy Anderson
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Celeste M Donato
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Sohinee Sarkar
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Lien Anh Ha Do
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Conor McCafferty
- Clinical Sciences Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Paul V Licciardi
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Vera Ignjatovic
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Clinical Sciences Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Paul Monagle
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Clinical Sciences Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Clinical Haematology, The Royal Children's Hospital, Parkville, VIC, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Julie E Bines
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Department of Gastroenterology and Clinical Nutrition, Royal Children's Hospital, Parkville, VIC, Australia
| | - Kim Mulholland
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Infectious Diseases Epidemiology Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Nigel Curtis
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Infectious Diseases Unit, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Sarah McNab
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Department of Gastroenterology and Clinical Nutrition, Royal Children's Hospital, Parkville, VIC, Australia
| | - Andrew C Steer
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Infectious Diseases Unit, The Royal Children's Hospital, Parkville, VIC, Australia
| | - David P Burgner
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Infectious Diseases Unit, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Richard Saffery
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Shidan Tosif
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Department of General Medicine, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Nigel W Crawford
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Department of General Medicine, The Royal Children's Hospital, Parkville, VIC, Australia
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10
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Graham M, Muhi S, Hoang T, Ballard SA, McAuley J, Kwong JC, Williamson DA, Howden BP. Multi-site point of care assessment of Abbott ID NOW rapid molecular test for SARS-CoV-2 in a low-prevalence setting. Pathology 2021; 53:912-914. [PMID: 34561096 PMCID: PMC8416649 DOI: 10.1016/j.pathol.2021.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/24/2021] [Accepted: 07/29/2021] [Indexed: 11/03/2022]
Affiliation(s)
- Maryza Graham
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Microbiology and Infectious Diseases, Monash Health, Clayton, Vic, Australia.
| | - Stephen Muhi
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Vic, Australia
| | - Tuyet Hoang
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Julie McAuley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Jason C Kwong
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, Austin Hospital, Heidelberg, Vic, Australia
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Microbiology, Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, Austin Hospital, Heidelberg, Vic, Australia
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11
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Clinical utility of a rapid 'on-demand' laboratory-based SARS-CoV-2 diagnostic testing service in an acute hospital setting admitting COVID-19 patients. CLINICAL INFECTION IN PRACTICE 2021; 12:100086. [PMID: 34337384 PMCID: PMC8316982 DOI: 10.1016/j.clinpr.2021.100086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/02/2021] [Accepted: 07/17/2021] [Indexed: 12/17/2022] Open
Abstract
Background With the onset of the COVID-19 pandemic in 2020, hospital clinical teams have realised that there is a need for a rapid, accurate testing facility that will allow them to move patients quickly into isolation rooms or specific COVID-19 cohort wards as soon as possible after admission. Methods Starting from July 2020, PCR-based test platforms, which could test 4–8 samples in parallel with turnaround (sample-to-result) times of 50–80 min, were placed in a satellite laboratory. This laboratory was on the same floor and within walking distance to the acute respiratory admissions ward. It was staffed by a team of three mid-Band 4 staff that split a 0700–2200 h-work day, 7 days a week, with 2 senior supervisors. Urgent sample testing was decided upon by the clinical teams and requested by phone. The test results were entered manually in real-time as they became available, and sent electronically to the requesting ward teams. Results The daily/monthly PCR positive test numbers approximately followed the local and national UK trend in COVID-19 case numbers, with the daily case numbers being reflective of the November and December 2020 surges. Test results were used to rapidly segregate positive patients into dedicated COVID-19 ward areas to minimise risk of potential nosocomial transmission in crowded waiting areas. Testing capacity was sufficient to include cases with uncertain diagnosis likely to require hospital admission. Following completion of other admission processes, based on these rapid test results, patients were allocated to dedicated COVID-19 positive or negative cohort wards. Conclusions This rapid testing facility reduced unnecessary ‘length-of-stay’ in a busy acute respiratory ward. In the current absence of a treatment for mild-to-moderate COVID-19, on which patients could be discharged home to complete, the rapid test facility has become a successful aid to patient flow and reduced exposure and nosocomial transmission.
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12
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Hafez A, Futami R, Arastehfar A, Daneshnia F, Miguel A, Roig FJ, Soriano B, Perez-Sánchez J, Boekhout T, Gabaldón T, Llorens C. SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files. Bioinformatics 2021; 37:1610-1612. [PMID: 33079985 DOI: 10.1093/bioinformatics/btaa903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/07/2020] [Accepted: 10/07/2020] [Indexed: 12/27/2022] Open
Abstract
MOTIVATION Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user's expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences' analysis. RESULT SeqEditor is a cross-platform desktop application for the analysis of nucleotide and protein sequences. It is managed through a Graphical User Interface and can work either as a graphical sequence browser or as a fasta task manager for multi-fasta files. SeqEditor has been optimized for the management of large sequences, such as contigs, scaffolds or even chromosomes, and includes a GTF/GFF viewer to visualize and manage annotation files. In turn, this allows for content mining from reference genomes and transcriptomes with similar efficiency to that of command line tools. SeqEditor also incorporates a set of tools for singleplex and multiplex PCR primer design and pooling that uses a newly optimized and validated search strategy for target and species-specific primers. All these features make SeqEditor a flexible application that can be used to analyses complex sequences, design primers in PCR assays oriented for diagnosis, and/or manage, edit and personalize reference sequence datasets. AVAILABILITYAND IMPLEMENTATION SeqEditor was developed in Java using Eclipse Rich Client Platform and is publicly available at https://gpro.biotechvana.com/download/SeqEditor as binaries for Windows, Linux and Mac OS. The user manual and tutorials are available online at https://gpro.biotechvana.com/tool/seqeditor/manual. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ahmed Hafez
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Faculty of Computers and Information, Minia University, Minia, Egypt
| | - Ricardo Futami
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain
| | - Amir Arastehfar
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA.,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Farnaz Daneshnia
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Ana Miguel
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain
| | - Francisco J Roig
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain.,Facultad de Ciencias de la Salud, Universidad San Jorge, Zaragoza, Spain
| | - Beatriz Soriano
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain
| | | | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Toni Gabaldón
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.,Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain.,Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carlos Llorens
- Biotechvana, Parc Científic Universitat de València, Valencia, Spain
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13
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Muhi S, Tayler N, Hoang T, Ballard SA, Graham M, Rojek A, Kwong JC, Trubiano JA, Smibert O, Drewett G, James F, Gardiner E, Chea S, Isles N, Sait M, Pasricha S, Taiaroa G, McAuley J, Williams E, Gibney KB, Stinear TP, Bond K, Lewin SR, Putland M, Howden BP, Williamson DA. Multi-site assessment of rapid, point-of-care antigen testing for the diagnosis of SARS-CoV-2 infection in a low-prevalence setting: A validation and implementation study. LANCET REGIONAL HEALTH-WESTERN PACIFIC 2021; 9:100115. [PMID: 33937887 PMCID: PMC8076656 DOI: 10.1016/j.lanwpc.2021.100115] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/22/2021] [Accepted: 02/08/2021] [Indexed: 12/18/2022]
Abstract
Background In Australia, COVID-19 diagnosis relies on RT-PCR testing which is relatively costly and time-consuming. To date, few studies have assessed the performance and implementation of rapid antigen-based SARS-CoV-2 testing in a setting with a low prevalence of COVID-19 infections, such as Australia. Methods This study recruited participants presenting for COVID-19 testing at three Melbourne metropolitan hospitals during a period of low COVID-19 prevalence. The Abbott PanBioTM COVID-19 Ag point-of-care test was performed alongside RT-PCR. In addition, participants with COVID-19 notified to the Victorian Government were invited to provide additional swabs to aid validation. Implementation challenges were also documented. Findings The specificity of the Abbott PanBioTM COVID-19 Ag test was 99.96% (95% CI 99.73 - 100%). Sensitivity amongst participants with RT-PCR-confirmed infection was dependent upon the duration of symptoms reported, ranging from 77.3% (duration 1 to 33 days) to 100% in those within seven days of symptom onset. A range of implementation challenges were identified which may inform future COVID-19 testing strategies in a low prevalence setting. Interpretation Given the high specificity, antigen-based tests may be most useful in rapidly triaging public health and hospital resources while expediting confirmatory RT-PCR testing. Considering the limitations in test sensitivity and the potential for rapid transmission in susceptible populations, particularly in hospital settings, careful consideration is required for implementation of antigen testing in a low prevalence setting. Funding This work was funded by the Victorian Department of Health and Human Services. The funder was not involved in data analysis or manuscript preparation.
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Affiliation(s)
- Stephen Muhi
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia
| | - Nick Tayler
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia.,Department of Emergency Medicine, Royal Melbourne Hospital, Melbourne, Australia
| | - Tuyet Hoang
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia
| | - Maryza Graham
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia.,Department of Microbiology, Monash Health, Melbourne, Australia
| | - Amanda Rojek
- Department of Emergency Medicine, Royal Melbourne Hospital, Melbourne, Australia
| | - Jason C Kwong
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia.,Department of Infectious Diseases, Austin Hospital, Melbourne, Australia
| | - Jason A Trubiano
- Department of Infectious Diseases, Austin Hospital, Melbourne, Australia
| | - Olivia Smibert
- Department of Infectious Diseases, Austin Hospital, Melbourne, Australia
| | - George Drewett
- Department of Infectious Diseases, Austin Hospital, Melbourne, Australia
| | - Fiona James
- Department of Infectious Diseases, Austin Hospital, Melbourne, Australia
| | - Emma Gardiner
- Department of Emergency Medicine, Royal Melbourne Hospital, Melbourne, Australia
| | - Socheata Chea
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia
| | - Nicole Isles
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia
| | - Michelle Sait
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia
| | - Shivani Pasricha
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia
| | - George Taiaroa
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia
| | - Julie McAuley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia
| | - Eloise Williams
- Department of Microbiology, Royal Melbourne Hospital, Melbourne, Australia
| | - Katherine B Gibney
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, Australia.,Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infectious Diseases and Immunity, Melbourne, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia
| | - Katherine Bond
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia.,Department of Microbiology, Royal Melbourne Hospital, Melbourne, Australia
| | - Sharon R Lewin
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, Australia.,Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infectious Diseases and Immunity, Melbourne, Australia.,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Mark Putland
- Department of Emergency Medicine, Royal Melbourne Hospital, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia.,Department of Infectious Diseases, Austin Hospital, Melbourne, Australia
| | - Deborah A Williamson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia.,Department of Microbiology, Royal Melbourne Hospital, Melbourne, Australia
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14
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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.
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Affiliation(s)
- Bijal A. Parikh
- Corresponding author. 660 South Euclid Ave., Campus Box 8118, St. Louis, MO, 63110, United States
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15
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Neeland MR, Bannister S, Clifford V, Dohle K, Mulholland K, Sutton P, Curtis N, Steer AC, Burgner DP, Crawford NW, Tosif S, Saffery R. Innate cell profiles during the acute and convalescent phase of SARS-CoV-2 infection in children. Nat Commun 2021; 12:1084. [PMID: 33597531 PMCID: PMC7889848 DOI: 10.1038/s41467-021-21414-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/27/2021] [Indexed: 12/15/2022] Open
Abstract
Children have mild severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) confirmed disease (COVID-19) compared to adults and the immunological mechanisms underlying this difference remain unclear. Here, we report acute and convalescent innate immune responses in 48 children and 70 adults infected with, or exposed to, SARS-CoV-2. We find clinically mild SARS-CoV-2 infection in children is characterised by reduced circulating subsets of monocytes (classical, intermediate, non-classical), dendritic cells and natural killer cells during the acute phase. In contrast, SARS-CoV-2-infected adults show reduced proportions of non-classical monocytes only. We also observe increased proportions of CD63+ activated neutrophils during the acute phase to SARS-CoV-2 in infected children. Children and adults exposed to SARS-CoV-2 but negative on PCR testing display increased proportions of low-density neutrophils that we observe up to 7 weeks post exposure. This study characterises the innate immune response during SARS-CoV-2 infection and household exposure in children. Childhood infection with SARS CoV2 is associated with a milder course of infection but the immunopathogenesis of this remains unclear. Here the authors explore immunological differences in the innate immune system during acute and convalescent SARS CoV2 infection in the young.
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Affiliation(s)
- Melanie R Neeland
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia. .,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.
| | - Samantha Bannister
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Infectious Diseases Unit, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Vanessa Clifford
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Laboratory Services, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Kate Dohle
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Kim Mulholland
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Philip Sutton
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Nigel Curtis
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Infectious Diseases Unit, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Andrew C Steer
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Infectious Diseases Unit, The Royal Children's Hospital, Parkville, VIC, Australia
| | - David P Burgner
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Infectious Diseases Unit, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Nigel W Crawford
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Department of General Medicine, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Shidan Tosif
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Department of General Medicine, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Richard Saffery
- Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
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16
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Rahimi A, Mirzazadeh A, Tavakolpour S. Genetics and genomics of SARS-CoV-2: A review of the literature with the special focus on genetic diversity and SARS-CoV-2 genome detection. Genomics 2021; 113:1221-1232. [PMID: 33007398 PMCID: PMC7525243 DOI: 10.1016/j.ygeno.2020.09.059] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
The outbreak of 2019-novel coronavirus disease (COVID-19), caused by SARS-CoV-2, started in late 2019; in a short time, it has spread rapidly all over the world. Although some possible antiviral and anti-inflammatory medications are available, thousands of people are dying daily. Well-understanding of the SARS-CoV-2 genome is not only essential for the development of new treatments/vaccines, but it also can be used for improving the sensitivity and specificity of current approaches for virus detection. Accordingly, we reviewed the most critical findings related to the genetics of the SARS-CoV-2, with a specific focus on genetic diversity and reported mutations, molecular-based diagnosis assays, using interfering RNA technology for the treatment of patients, and genetic-related vaccination strategies. Additionally, considering the unanswered questions or uncertainties in these regards, different topics were discussed.
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Affiliation(s)
- Azadeh Rahimi
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Azin Mirzazadeh
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran; Joint Bioinformatics Graduate Program, University of Arkansas Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Soheil Tavakolpour
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, United States.
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17
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Sheikhzadeh E, Eissa S, Ismail A, Zourob M. Diagnostic techniques for COVID-19 and new developments. Talanta 2020; 220:121392. [PMID: 32928412 PMCID: PMC7358765 DOI: 10.1016/j.talanta.2020.121392] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/23/2022]
Abstract
COVID-19 pandemic is a serious global health issue today due to the rapid human to human transmission of SARS-CoV-2, a new type of coronavirus that causes fatal pneumonia. SARS -CoV-2 has a faster rate of transmission than other coronaviruses such as SARS and MERS and until now there are no approved specific drugs or vaccines for treatment. Thus, early diagnosis is crucial to prevent the extensive spread of the disease. The reverse transcription-polymerase chain reaction (RT-PCR) is the most routinely used method until now to detect SARS-CoV-2 infections. However, several other faster and accurate assays are being developed for the diagnosis of COVID-19 aiming to control the spread of infection through the identification of patients and immediate isolation. In this review, we will discuss the various detection methods of the SARS-CoV-2 virus including the recent developments in immunological assays, amplification techniques as well as biosensors.
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Affiliation(s)
- Elham Sheikhzadeh
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia16150 Kubang Kerian, Kelantan, Malaysia
| | - Shimaa Eissa
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Road, Riyadh, 11533, Saudi Arabia
| | - Aziah Ismail
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia16150 Kubang Kerian, Kelantan, Malaysia
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Road, Riyadh, 11533, Saudi Arabia; King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh, 12713, Saudi Arabia.
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18
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Kumaran N, Sekhawat V, Mahadeva U, Green A, Douthwaite S, Wong R. Absence of severe acute respiratory syndrome coronavirus 2 in ocular postmortem studies. Can J Ophthalmol 2020; 56:142-143. [PMID: 33157002 PMCID: PMC7574852 DOI: 10.1016/j.jcjo.2020.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/18/2020] [Accepted: 10/16/2020] [Indexed: 11/17/2022]
Affiliation(s)
- Neruban Kumaran
- St Thomas' Hospital, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom; Frimley Park Hospital, Frimley Health NHS Foundation Trust, Frimley, United Kingdom
| | - Vivek Sekhawat
- St Thomas' Hospital, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Ula Mahadeva
- St Thomas' Hospital, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom; King's College Medical School, London, United Kingdom
| | - Anna Green
- St Thomas' Hospital, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Sam Douthwaite
- St Thomas' Hospital, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Roger Wong
- St Thomas' Hospital, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom; Frimley Park Hospital, Frimley Health NHS Foundation Trust, Frimley, United Kingdom; King's College Medical School, London, United Kingdom.
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19
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Gulholm T, Basile K, Kok J, Chen SCA, Rawlinson W. Laboratory diagnosis of severe acute respiratory syndrome coronavirus 2. Pathology 2020; 52:745-753. [PMID: 33131799 PMCID: PMC7543760 DOI: 10.1016/j.pathol.2020.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 12/20/2022]
Abstract
The first laboratory confirmed case of Coronavirus disease 2019 (COVID-19) in Australia was in Victoria on 25 January 2020 in a man returning from Wuhan city, Hubei province, the People's Republic of China. This was followed by three cases in New South Wales the following day. The Australian Government activated the Australian Health Sector Emergency Response Plan for Novel Coronavirus on 27 February 2020 in anticipation of a pandemic. Subsequently, the World Health Organization declared COVID-19 to be a Public Health Emergency of International Concern followed by a pandemic on 30 January 2020 and 11 March 2020, respectively. Laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, is key in identifying infected persons to guide timely public health actions of contact tracing and patient isolation to limit transmission of infection. This article aims to provide a comprehensive overview of current laboratory diagnostic methods for SARS-CoV-2, including nucleic acid testing, serology, rapid antigen detection and antibody tests, virus isolation and whole genome sequencing. The relative advantages and disadvantages of the different diagnostic tests are presented, as well as their value in different clinical, infection control and public health contexts. We also describe the challenges in the provision of SARS-CoV-2 diagnostics in Australia, a country with a relatively low COVID-19 incidence in the first pandemic wave but in which prevalence could rapidly change.
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Affiliation(s)
- T Gulholm
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, NSW, Australia.
| | - K Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - J Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - S C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead, NSW, Australia
| | - W Rawlinson
- NSW Health Pathology, Serology and Virology Division, Prince of Wales Hospital, Randwick, NSW, Australia; Virology Research Laboratory, Prince of Wales Hospital, University of New South Wales, Randwick, NSW, Australia; School of Medical Sciences and School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Kensington, NSW, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Kensington, NSW, Australia
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20
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Coronavirus testing in women attending antenatal care. Women Birth 2020; 34:473-476. [PMID: 33092997 PMCID: PMC7538116 DOI: 10.1016/j.wombi.2020.09.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/18/2020] [Accepted: 09/30/2020] [Indexed: 01/08/2023]
Abstract
Background Universal screening has been proposed as a strategy to identify asymptomatic individuals infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and mitigate transmission. Aim To investigate the rate of positive tests among pregnant women in Melbourne, Australia. Methods We performed a cross-sectional prevalence study at three maternity hospitals (one tertiary referral hospital and two secondary maternities) in Melbourne, Australia. SARS-CoV-2 testing was offered to all pregnant women attending face-to-face antenatal visits and to those attending the hospital with symptoms of possible coronavirus disease, between 6th and 19th of May 2020. Testing was performed by multiplex-tandem polymerase chain reaction (PCR) on combined oropharyngeal and nasopharyngeal swabs. The primary outcome was the proportion of positive SARS-CoV-2 tests. Findings SARS-CoV-2 testing was performed in 350 women, of whom 19 had symptoms of possible COVID-19. The median maternal age was 32 years (IQR 28–35 years), and the median gestational age at testing was 33 weeks and four days (IQR 28 weeks to 36 weeks and two days). All 350 tests returned negative results (p̂ = 0%, 95% CI 0–1.0%). Conclusion In a two-week period of low disease prevalence, the rate of asymptomatic coronavirus infection among pregnant women in Australia during the study period was negligible, reflecting low levels of community transmission.
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Impact of on-site compared to off-site testing for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) on duration of isolation and resource utilization. Infect Control Hosp Epidemiol 2020; 42:1004-1006. [PMID: 32829737 PMCID: PMC8245332 DOI: 10.1017/ice.2020.433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Rapid detection and isolation of coronavirus disease 2019 (COVID-19) patients is the only means of reducing hospital transmission. We describe the impact of implementation of on-site severe acute respiratory coronavirus virus 2 (SARS-CoV-2) reverse-transcription polymerase chain reaction (RT-PCR) testing on reducing turnaround time, isolation duration, pathology test ordering, and antibiotic use in patients who do not have COVID-19.
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22
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Bird P, Badhwar V, Fallon K, Kwok KO, Tang JW. High SARS-CoV-2 infection rates in respiratory staff nurses and correlation of COVID-19 symptom patterns with PCR positivity and relative viral loads. J Infect 2020; 81:452-482. [PMID: 32562793 PMCID: PMC7299866 DOI: 10.1016/j.jinf.2020.06.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/14/2020] [Accepted: 06/15/2020] [Indexed: 11/18/2022]
Affiliation(s)
- Paul Bird
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Vinay Badhwar
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Karlie Fallon
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Kin On Kwok
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region; Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region; Shenzhen Research Institute of The Chinese University of Hong Kong, Shenzhen, China
| | - Julian W Tang
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom; Respiratory Sciences, University of Leicester, Leicester, United Kingdom
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23
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Stanley K. AusDiagnostics SARS-CoV-2 kits shown to be more sensitive than reference laboratory test. J Clin Virol 2020; 129:104485. [PMID: 32526675 PMCID: PMC7274083 DOI: 10.1016/j.jcv.2020.104485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/02/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Keith Stanley
- AusDiagnostics Pty Ltd, 290-292 Coward Street, Mascot, NSW, 2020, Australia.
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