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Petrillo M, Querci M, Brogna C, Ponti J, Cristoni S, Markov PV, Valsesia A, Leoni G, Benedetti A, Wiss T, Van den Eede G. Evidence of SARS-CoV-2 bacteriophage potential in human gut microbiota. F1000Res 2022. [DOI: 10.12688/f1000research.109236.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: In previous studies we have shown that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in vitro in bacterial growth medium, that the viral replication follows bacterial growth, and it is influenced by the administration of specific antibiotics. These observations are compatible with a ‘bacteriophage-like’ behaviour of SARS-CoV-2. Methods: We have further elaborated on these unusual findings and here we present the results of three different supplementary experiments: (1) an electron-microscope analysis of samples of bacteria obtained from a faecal sample of a subject positive to SARS-CoV-2; (2) mass spectrometric analysis of these cultures to assess the eventual de novo synthesis of SARS-CoV-2 spike protein; (3) sequencing of SARS-CoV-2 collected from plaques obtained from two different gut microbial bacteria inoculated with supernatant from faecal microbiota of an individual positive to SARS-CoV-2. Results: Immuno-labelling with Anti-SARS-CoV-2 nucleocapsid protein antibody confirmed presence of SARS-CoV-2 both outside and inside bacteria. De novo synthesis of SARS-CoV-2 spike protein was observed, as evidence that SARS-CoV-2 RNA is translated in the bacterial cultures. In addition, phage-like plaques were spotted on faecal bacteria cultures after inoculation with supernatant from faecal microbiota of an individual positive to SARS-CoV-2. Bioinformatic analyses on the reads obtained by sequencing RNA extracted from the plaques revealed nucleic acid polymorphisms, suggesting different replication environment in the two bacterial cultures. Conclusions: Based on these results we conclude that, in addition to its well-documented interactions with eukaryotic cells, SARS-CoV-2 may act as a bacteriophage when interacting with at least two bacterial species known to be present in the human microbiota. If the hypothesis proposed, i.e., that under certain conditions SARS-CoV-2 may multiply at the expense of human gut bacteria, is further substantiated, it would drastically change the model of acting and infecting of SARS-CoV-2, and most likely that of other human pathogenic viruses.
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Pu R, Liu S, Ren X, Shi D, Ba Y, Huo Y, Zhang W, Ma L, Liu Y, Yang Y, Cheng N. The screening value of RT-LAMP and RT-PCR in the diagnosis of COVID-19: systematic review and meta-analysis. J Virol Methods 2022; 300:114392. [PMID: 34856308 PMCID: PMC8629515 DOI: 10.1016/j.jviromet.2021.114392] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 11/28/2021] [Accepted: 11/28/2021] [Indexed: 02/08/2023]
Abstract
The purpose of this systematic review is to evaluate the test accuracy of reverse-transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription-PCR (RT-PCR) for the diagnosis of coronavirus disease 2019 (COVID-19). We comprehensively searched PUBMED, Web of Science, the Cochrane Library, the Chinese National Knowledge Infrastructure, and the Chinese Biomedical Literature Service System until September 1, 2021. We included clinical studies assessing the sensitivity and specificity of RT-PCR and RT-LAMP using respiratory samples. Thirty-three studies were included with 9360 suspected cases of SARS-CoV-2 infection. The RT-PCR or other comprehensive diagnostic method was defined as the reference method. The results showed that the overall pooled sensitivity of RT-PCR and RT-LAMP was 0.96 (95 % CI, 0.93-0.98) and 0.92 (95 % CI, 0.85-0.96), respectively. RT-PCR and RT-LAMP had a 0.06 (95 % CI, 0.04-0.08) and 0.12 (95 % CI, 0.06-0.16) false-negative rates (FNR), respectively. Moreover, subgroup analysis showed mixed sampling and multiple target gene diagnosis methods had better diagnostic value than single-site sampling and a single target gene. The sensitivity and FNR were also significantly affected by the reference method. Comparing RT-LAMP with established suboptimal RT-PCR may exaggerate the performance of RT-LAMP. RT-PCR and RT-LAMP showed high values in the diagnosis of COVID-19, but there was still a FNR of about 6%-12%.
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Affiliation(s)
- Ruiyang Pu
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, PR China
| | - Sha Liu
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, PR China
| | - Xiaoyu Ren
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, PR China
| | - Dian Shi
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, PR China
| | - Yupei Ba
- Institute of Epidemiology and Statistics, School of Public Health, Lanzhou University, Lanzhou, Gansu, PR China
| | - Yanbei Huo
- Institute of Epidemiology and Statistics, School of Public Health, Lanzhou University, Lanzhou, Gansu, PR China
| | - Wenling Zhang
- Institute of Epidemiology and Statistics, School of Public Health, Lanzhou University, Lanzhou, Gansu, PR China
| | - Lingling Ma
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, PR China
| | - Yanyan Liu
- Institute of Epidemiology and Statistics, School of Public Health, Lanzhou University, Lanzhou, Gansu, PR China
| | - Yan Yang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, PR China
| | - Ning Cheng
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, PR China.
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Luong AD, Buzid A, Vashist SK, Luong JHT. Perspectives on electrochemical biosensing of COVID-19. CURRENT OPINION IN ELECTROCHEMISTRY 2021; 30:100794. [PMID: 34250313 PMCID: PMC8254385 DOI: 10.1016/j.coelec.2021.100794] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Rapid detection of human coronavirus disease 2019, termed as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or COVID-19 infection, is urgently needed for containment strategy owing to its unprecedented spreading. Novel biosensors can be deployed in remote clinical settings without central facilities for infection screening. Electrochemical biosensors serve as analytical tools for rapid detection of viral structure proteins, mainly spike (S) and nucleocapsid (N) proteins, human immune responses, reactive oxygen species, viral ribonucleic acid, polymerase chain reaction by-products, and other potential biomarkers. The development of point-of-care testing devices is challenging due to the requirement of extensive validation, a time-consuming and expensive step. Together with specific biorecognition molecules, nanomaterial-based biosensors have emerged for the fast detection of early viral infections.
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Affiliation(s)
- Albert D Luong
- Department of Surgery, Jacobs School of Medicine, University of Buffalo, Buffalo, NY, 14215, USA
| | - Alyah Buzid
- Department of Chemistry, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa, 31982, Saudi Arabia
| | - Sandeep K Vashist
- Pictor Pvt. Ltd., 24 Balfour Road Parnell, Auckland, 1052, New Zealand
| | - John H T Luong
- Innovative Chromatography Group, Irish Separation Science Cluster (ISSC), School of Chemistry and Analytical & Biological Chemistry Research Facility (ABCRF), University College Cork, College Road, Cork, T12 YN60, Ireland
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4
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Design of a population-based longitudinal cohort study of SARS-CoV-2 incidence and prevalence among adults in the San Francisco Bay Area. Ann Epidemiol 2021; 67:81-100. [PMID: 34800659 PMCID: PMC8596645 DOI: 10.1016/j.annepidem.2021.11.001] [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: 05/26/2021] [Revised: 09/16/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022]
Abstract
Purpose We describe the design of a longitudinal cohort study to determine SARS-CoV-2 incidence and prevalence among a population-based sample of adults living in six San Francisco Bay Area counties. Methods Using an address-based sample, we stratified households by county and by census-tract risk. Risk strata were determined by using regression models to predict infections by geographic area using census-level sociodemographic and health characteristics. We disproportionately sampled high and medium risk strata, which had smaller population sizes, to improve precision of estimates, and calculated a desired sample size of 3400. Participants were primarily recruited by mail and were followed monthly with PCR testing of nasopharyngeal swabs, testing of venous blood samples for antibodies to SARS-CoV-2 spike and nucleocapsid antigens, and testing of the presence of neutralizing antibodies, with completion of questionnaires about socio-demographics and behavior. Estimates of incidence and prevalence will be weighted by county, risk strata and sociodemographic characteristics of non-responders, and will take into account laboratory test performance. Results We enrolled 3842 adults from August to December 2020, and completed follow-up March 31, 2021. We reached target sample sizes within most strata. Conclusions Our stratified random sampling design will allow us to recruit a robust general population cohort of adults to determine the incidence of SARS-CoV-2 infection. Identifying risk strata was unique to the design and will help ensure precise estimates, and high-performance testing for presence of virus and antibodies will enable accurate ascertainment of infections.
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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.
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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
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Lui DTW, Fung MMH, Chiu KWH, Lee CH, Chow WS, Lee ACH, Tam AR, Pang P, Ho TY, Fong CHY, Loong CHN, Wong WW, Lee CYY, Law CY, To KKW, Lam CW, Tan KCB, Woo YC, Hung IFN, Lam KSL, Lang BHH. Higher SARS-CoV-2 viral loads correlated with smaller thyroid volumes on ultrasound among male COVID-19 survivors. Endocrine 2021; 74:205-214. [PMID: 34467467 PMCID: PMC8408037 DOI: 10.1007/s12020-021-02855-2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/19/2021] [Indexed: 11/28/2022]
Abstract
PURPOSE Thyroid dysfunction, including thyroiditis, is well recognized in COVID-19 patients. We evaluated thyroid ultrasonographic features among COVID-19 survivors, which are less well known. METHODS Adult COVID-19 survivors without known thyroid disorders who attended dedicated COVID-19 clinic underwent thyroid ultrasonography and assessment of thyroid function and autoimmunity. Adults admitted for acute non-thyroidal surgical problems and negative for COVID-19 were recruited as control. SARS-CoV-2 viral load (VL) was presented as the inverse of cycle threshold values from the real-time reverse transcription-polymerase chain reaction of the respiratory specimen on admission. RESULTS In total, 79 COVID-19 patients and 44 non-COVID-19 controls were included. All abnormal thyroid function tests during acute COVID-19 recovered upon follow-up. Thyroid ultrasonography was performed at a median of 67 days after acute COVID-19. The median thyroid volume was 9.73 mL (IQR: 7.87-13.70). In multivariable linear regression, SARS-CoV-2 VL on presentation (standardized beta -0.206, p = 0.042) inversely correlated with thyroid volume, in addition to body mass index at the time of ultrasonography (p < 0.001). Sex-specific analysis revealed similar results among men but not women. Eleven COVID-19 patients (13.9%) had ultrasonographic changes suggestive of thyroiditis, comparable to non-COVID-19 patients (p = 0.375). None of these 11 patients had isolated low thyroid-stimulating hormone levels suggestive of thyroiditis at initial admission or the time of ultrasonography. CONCLUSIONS Higher SARS-CoV-2 VL on presentation were associated with smaller thyroid volumes, especially in men. Further research is suggested to investigate this possible direct viral effect of SARS-CoV-2 on the thyroid gland. There was no increased rate of ultrasonographic features suggestive of thyroiditis in COVID-19 survivors.
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Affiliation(s)
- David Tak Wai Lui
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Matrix Man Him Fung
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Keith Wan Hang Chiu
- Department of Diagnostic Radiology, The University of Hong Kong, Hong Kong, China
| | - Chi Ho Lee
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Wing Sun Chow
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Alan Chun Hong Lee
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Anthony Raymond Tam
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Polly Pang
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Tip Yin Ho
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Carol Ho Yi Fong
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Connie Hong Nin Loong
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Wade Wei Wong
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Cassandra Yuen Yan Lee
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Chun Yiu Law
- Division of Chemical Pathology, Queen Mary Hospital, Hong Kong, China
| | - Kelvin Kai Wang To
- Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Ching Wan Lam
- Department of Pathology, The University of Hong Kong, Hong Kong, China
| | - Kathryn Choon Beng Tan
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Yu Cho Woo
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Ivan Fan Ngai Hung
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Karen Siu Ling Lam
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Brian Hung Hin Lang
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China.
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Kanwar N, Banerjee D, Sasidharan A, Abdulhamid A, Larson M, Lee B, Selvarangan R, Liesman RM. Comparison of diagnostic performance of five molecular assays for detection of SARS-CoV-2. Diagn Microbiol Infect Dis 2021; 101:115518. [PMID: 34481324 PMCID: PMC8343369 DOI: 10.1016/j.diagmicrobio.2021.115518] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 12/01/2022]
Abstract
We compared the performance of the Abbott Real Time SARS-CoV-2 assay (Abbott assay), Aptima™ SARS-CoV-2 assay (Aptima assay), BGI Real-Time SARS-CoV-2 assay (BGI assay), Lyra® SARS-CoV-2 assay (Lyra assay), and DiaSorin Simplexa™ COVID assay for SARS-CoV-2 detection. Residual nasopharyngeal samples (n = 201) submitted for routine SARS-CoV-2 testing by Simplexa assay during June-July 2020 and January 2021 were salvaged. Aliquots were tested on other assays and compared against the CDC 2019-nCoV Real-Time RT-PCR assay. Viral load in positive samples was determined by droplet digital PCR. Among 201 samples, 99 were positive and 102 were negative by the CDC assay. The Aptima and Abbott assays exhibited the highest positive percent agreement (PPA) at 98.9% while the BGI assay demonstrated the lowest PPA of 89.9% with 10 missed detections. Negative percent agreement for all 5 platforms was comparable, ranging from 96.1% to 100%. The performance of all five assays was comparable.
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Affiliation(s)
- Neena Kanwar
- Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, MO, USA; School of Medicine, University of Missouri- Kansas City, MO, USA
| | - Dithi Banerjee
- Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, MO, USA; School of Medicine, University of Missouri- Kansas City, MO, USA
| | - Anjana Sasidharan
- Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, MO, USA
| | - Ayah Abdulhamid
- Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, MO, USA
| | - Marissa Larson
- Department of Pathology and Laboratory Medicine, University of Kansas Health System, Kansas City, KS, USA
| | - Brian Lee
- School of Medicine, University of Missouri- Kansas City, MO, USA; Division of Health Services and Outcomes Research, Children's Mercy, Kansas City, MO, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, MO, USA; School of Medicine, University of Missouri- Kansas City, MO, USA; Department of Pathology and Laboratory Medicine, University of Kansas Health System, Kansas City, KS, USA.
| | - Rachael M Liesman
- Department of Pathology and Laboratory Medicine, University of Kansas Health System, Kansas City, KS, USA.
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Meng Z, Guo S, Zhou Y, Li M, Wang M, Ying B. Applications of laboratory findings in the prevention, diagnosis, treatment, and monitoring of COVID-19. Signal Transduct Target Ther 2021; 6:316. [PMID: 34433805 PMCID: PMC8386162 DOI: 10.1038/s41392-021-00731-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
The worldwide pandemic of coronavirus disease 2019 (COVID-19) presents us with a serious public health crisis. To combat the virus and slow its spread, wider testing is essential. There is a need for more sensitive, specific, and convenient detection methods of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Advanced detection can greatly improve the ability and accuracy of the clinical diagnosis of COVID-19, which is conducive to the early suitable treatment and supports precise prophylaxis. In this article, we combine and present the latest laboratory diagnostic technologies and methods for SARS-CoV-2 to identify the technical characteristics, considerations, biosafety requirements, common problems with testing and interpretation of results, and coping strategies of commonly used testing methods. We highlight the gaps in current diagnostic capacity and propose potential solutions to provide cutting-edge technical support to achieve a more precise diagnosis, treatment, and prevention of COVID-19 and to overcome the difficulties with the normalization of epidemic prevention and control.
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Affiliation(s)
- Zirui Meng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Shuo Guo
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Mengjiao Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
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Yip CCY, Leung KH, Ng ACK, Chan KH, To KKW, Chan JFW, Hung IFN, Cheng VCC, Sridhar S. Comparative evaluation of a dual-target real-time RT-PCR assay for COVID-19 diagnosis and assessment of performance in pooled saliva and nasopharyngeal swab samples. Expert Rev Mol Diagn 2021; 21:741-747. [PMID: 34014785 PMCID: PMC8182820 DOI: 10.1080/14737159.2021.1933445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 05/19/2021] [Indexed: 11/05/2022]
Abstract
OBJECTIVES Sensitive molecular diagnostic assays are essential for COVID-19 diagnosis. We evaluated the Hecin Scientific SARS-CoV-2 nucleic acid test kit, a dual-target real-time RT-PCR assay targeting the SARS-CoV-2 N and ORF1ab genes. METHODS The Hecin test kit's diagnostic performance in detecting SARS-CoV-2 RNA was compared to the LightMix Modular SARS and Wuhan CoV E-gene kit (TIB Molbiol) and an in-house single-tube nested real-time RT-PCR using 296 clinical specimens, 11 proficiency testing samples, and 30 low-positive deep throat saliva and nasopharyngeal swab (NPS) samples pooled into negative samples in ratios of 1:5, 1:10, and 1:30. RESULTS The limit-of-detection of the Hecin test kit was around 500 dC/mL for the N and ORF1ab targets. Sensitivity and specificity of the Hecin test kit were 98.1% (95% CI: 93.4-99.8%) and 100% (98.1-100%), respectively, when measured against the reference method. The Hecin test kit showed fair sensitivity (80%) in low-positive NPS samples pooled in ratios of 1:5 and 1:10. Its performance in pooled samples could be dramatically improved by adjusting the assay Ct cutoff. CONCLUSION The Hecin test kit enables sensitive and specific detection of SARS-CoV-2 in clinical samples and pooled samples.
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Affiliation(s)
- Cyril C. Y. Yip
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Kit-Hang Leung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Anthony C. K. Ng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kwok-Hung Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kelvin K. W. To
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jasper F. W Chan
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ivan F. N. Hung
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Vincent C. C. Cheng
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Siddharth Sridhar
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
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Ulhaq ZS, Soraya GV. The diagnostic accuracy of seven commercial molecular in vitro SARS-CoV-2 detection tests: a rapid meta-analysis. Expert Rev Mol Diagn 2021; 21:733-740. [PMID: 34015984 PMCID: PMC8171007 DOI: 10.1080/14737159.2021.1933449] [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: 02/16/2021] [Accepted: 05/19/2021] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To compare the accuracy parameters of seven commercial molecular in vitro diagnostic tests for detecting SARS-CoV-2. METHODS Studies evaluating the accuracy of seven different commercial molecular diagnostic tests for detecting SARS-CoV-2 (Cepheid Xpert Xpress SARS-CoV-2 test, Simplexa COVID-19 Direct, Abbott ID NOW COVID-19, Cobas SARS-CoV-2, Allplex 2019-nCoV Assay, Panther Fusion SARS-CoV-2, and BioFire COVID-19 Test) were included. The quality of the included studies was assessed using the QUADAS-2 checklist. A bivariate random-effects regression model was implemented. RESULTS Meta-analysis of 12 included studies showed that the performances of commercial COVID-19 molecular in vitro diagnostic tests were high, with a summary sensitivity of 95.9% (95% CI 93.9-97.2%, I2 = 60.22%) and specificity of 97.2% (95% CI 95.5-98.3%, I2 = 56.66%). Among seven evaluated tests, the Abbott ID NOW COVID-19 and Simplexa COVID-19 Direct displayed lower sensitivity (91.6%, 95% CI 80.5-96.6% and 92%, 95% CI 86.2-95.5, respectively). CONCLUSION All evaluated tests showed good accuracy. However, the slightly lower sensitivity observed in the Abbott ID Now COVID-19 and Simplexa COVID-19 Direct should be considered when deciding on a test platform. Moreover, the diagnostic accuracy of COVID-19 commercial diagnostic tests should be weighed against their ease of use and speed.
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Affiliation(s)
- Zulvikar Syambani Ulhaq
- Department of Biochemistry, Faculty of Medicine and Health Science, Maulana Malik Ibrahim State Islamic University of Malang, Malang, Indonesia
| | - Gita Vita Soraya
- Department of Biochemistry, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
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11
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Anderson G, Liu JL, Esparza TJ, Voelker BT, Hofmann ER, Goldman ER. Single-Domain Antibodies for the Detection of SARS-CoV-2 Nucleocapsid Protein. Anal Chem 2021; 93:7283-7291. [PMID: 33955213 PMCID: PMC8117401 DOI: 10.1021/acs.analchem.1c00677] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/22/2021] [Indexed: 12/19/2022]
Abstract
The goal of this work was to develop recombinantly expressed variable domains derived from camelid heavy-chain antibodies known as single-domain antibodies (sdAbs) directed against the SARS-CoV-2 nucleocapsid protein for incorporation into detection assays. To achieve this, a llama was immunized using a recombinant SARS-CoV-2 nucleocapsid protein and an immune phage-display library of variable domains was developed. The sdAbs selected from this library segregated into five distinct sequence families. Three of these families bind to unique epitopes with high affinity, low nM to sub-nM KD, as determined by surface plasmon resonance. To further enhance the utility of these sdAbs for the detection of nucleocapsid protein, homobivalent and heterobivalent genetic fusion constructs of the three high-affinity sdAbs were prepared. The effectiveness of the sdAbs for the detection of nucleocapsid protein was evaluated using MagPlex fluid array assays, a multiplexed immunoassay on color-coded magnetic microspheres. Using the optimal bivalent pair, one immobilized on the microsphere and the other serving as the biotinylated recognition reagent, a detection limit as low as 50 pg/mL of recombinant nucleocapsid and of killed virus down to 1.28 × 103 pfu/mL was achieved. The sdAbs described here represent immune reagents that can be tailored to be optimized for a number of detection platforms and may one day aid in the detection of SARS-CoV-2 to assist in controlling the current pandemic.
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Affiliation(s)
- George
P. Anderson
- Center
for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Jinny L. Liu
- Center
for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Thomas J. Esparza
- Laboratory
of Functional and Molecular Imaging, The
National Institute of Neurological Disorders and Stroke Intramural
Research Program, Bethesda, Maryland 20892, United States
- Henry
M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland 20892, United States
| | - Bruce T. Voelker
- Chemical
Biological Center, U.S. Army Combat Capabilities
Development Command, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - E. Randal Hofmann
- Chemical
Biological Center, U.S. Army Combat Capabilities
Development Command, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
- EXCET,
Inc., 6225 Brandon Avenue
#360, Springfield, Virginia 22150, United States
| | - Ellen R. Goldman
- Center
for Biomolecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
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12
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Yiannoutsos CT, Halverson PK, Menachemi N. Bayesian estimation of SARS-CoV-2 prevalence in Indiana by random testing. Proc Natl Acad Sci U S A 2021; 118:e2013906118. [PMID: 33441450 PMCID: PMC7865174 DOI: 10.1073/pnas.2013906118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
From 25 to 29 April 2020, the state of Indiana undertook testing of 3,658 randomly chosen state residents for the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, the agent causing COVID-19 disease. This was the first statewide randomized study of COVID-19 testing in the United States. Both PCR and serological tests were administered to all study participants. This paper describes statistical methods used to address nonresponse among various demographic groups and to adjust for testing errors to reduce bias in the estimates of the overall disease prevalence in Indiana. These adjustments were implemented through Bayesian methods, which incorporated all available information on disease prevalence and test performance, along with external data obtained from census of the Indiana statewide population. Both adjustments appeared to have significant impact on the unadjusted estimates, mainly due to upweighting data in study participants of non-White races and Hispanic ethnicity and anticipated false-positive and false-negative test results among both the PCR and antibody tests utilized in the study.
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Affiliation(s)
- Constantin T Yiannoutsos
- Department of Biostatistics, Indiana University Fairbanks School of Public Health, Indianapolis, IN 46202;
| | - Paul K Halverson
- Department of Health Policy and Management, Indiana University Fairbanks School of Public Health, Indianapolis, IN 46202
| | - Nir Menachemi
- Department of Health Policy and Management, Indiana University Fairbanks School of Public Health, Indianapolis, IN 46202
- Regenstrief Institute, Inc., Indianapolis, IN 46202
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13
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Shen H, Forgacs D, Chapla D, Moremen KW, Wells L, Hamer SA, Tompkins SM, Ross TM, Rouphael N, Edupuganti S, Collins MH, Tarleton RL. A flexible, pan-species, multi-antigen platform for the detection and monitoring of SARS-CoV-2-specific antibody responses. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.01.20.21249279. [PMID: 33532799 PMCID: PMC7852250 DOI: 10.1101/2021.01.20.21249279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The SARS-CoV-2 pandemic and the vaccination effort that is ongoing has created an unmet need for accessible, affordable, flexible and precise platforms for monitoring the induction, specificity and maintenance of virus-specific immune responses. Herein we validate a multiplex (Luminex-based) assay capable of detecting SARS-CoV-2-specific antibodies irrespective of host species, antibody isotype, and specimen type (e.g. plasma, serum, saliva or blood spots). The well-established precision of Luminex-based assays provides the ability to follow changes in antibody levels over time to many antigens, including multiple permutations of the most common SARS-CoV-2 antigens. This platform can easily measure antibodies known to correlate with neutralization activity as well as multiple non-SARS-CoV-2 antigens such as vaccines (e.g. Tetanus toxoid) or those from frequently encountered agents (influenza), which serve as stable reference points for quantifying the changing SARS-specific responses. All of the antigens utilized in our study can be made in-house, many in E. coli using readily available plasmids. Commercially sourced antigens may also be incorporated and newly available antigen variants can be rapidly produced and integrated, making the platform adaptable to the evolving viral strains in this pandemic.
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Affiliation(s)
- Huifeng Shen
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens GA, USA
| | - David Forgacs
- Center for Vaccines and Immunology, University of Georgia, Athens GA, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens GA, USA
| | - Kelley W. Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens GA, USA
- Department of Biochemistry, University of Georgia, Athens GA, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens GA, USA
- Department of Biochemistry, University of Georgia, Athens GA, USA
| | - Sarah A. Hamer
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station TX, USA
| | - Stephen M. Tompkins
- Center for Vaccines and Immunology, University of Georgia, Athens GA, USA
- Department of Infectious Diseases, University of Georgia, Athens GA, USA
| | - Ted M. Ross
- Center for Vaccines and Immunology, University of Georgia, Athens GA, USA
- Department of Infectious Diseases, University of Georgia, Athens GA, USA
| | - Nadine Rouphael
- Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Decatur, Georgia, USA
| | - Srilatha Edupuganti
- Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Decatur, Georgia, USA
| | - Matthew H. Collins
- Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Decatur, Georgia, USA
| | - Rick L. Tarleton
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens GA, USA
- Department of Cellular Biology, University of Georgia, Athens GA, USA
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14
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Rezaei M, Razavi Bazaz S, Zhand S, Sayyadi N, Jin D, Stewart MP, Ebrahimi Warkiani M. Point of Care Diagnostics in the Age of COVID-19. Diagnostics (Basel) 2020; 11:E9. [PMID: 33374612 PMCID: PMC7822494 DOI: 10.3390/diagnostics11010009] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 12/20/2022] Open
Abstract
The recent outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its associated serious respiratory disease, coronavirus disease 2019 (COVID-19), poses a major threat to global public health. Owing to the lack of vaccine and effective treatments, many countries have been overwhelmed with an exponential spread of the virus and surge in the number of confirmed COVID-19 cases. Current standard diagnostic methods are inadequate for widespread testing as they suffer from prolonged turn-around times (>12 h) and mostly rely on high-biosafety-level laboratories and well-trained technicians. Point-of-care (POC) tests have the potential to vastly improve healthcare in several ways, ranging from enabling earlier detection and easier monitoring of disease to reaching remote populations. In recent years, the field of POC diagnostics has improved markedly with the advent of micro- and nanotechnologies. Due to the COVID-19 pandemic, POC technologies have been rapidly innovated to address key limitations faced in existing standard diagnostic methods. This review summarizes and compares the latest available POC immunoassay, nucleic acid-based and clustered regularly interspaced short palindromic repeats- (CRISPR)-mediated tests for SARS-CoV-2 detection that we anticipate aiding healthcare facilities to control virus infection and prevent subsequent spread.
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Affiliation(s)
- Meysam Rezaei
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
- SUStech-UTS Joint Research Centre for Biomedical Materials & Devices, Southern University of Science and Technology, Shenzhen 518055, China
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
| | - Sareh Zhand
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
| | - Nima Sayyadi
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University Sydney, Sydney, NSW 2109, Australia
| | - Dayong Jin
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
- SUStech-UTS Joint Research Centre for Biomedical Materials & Devices, Southern University of Science and Technology, Shenzhen 518055, China
| | - Martin P. Stewart
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
- SUStech-UTS Joint Research Centre for Biomedical Materials & Devices, Southern University of Science and Technology, Shenzhen 518055, China
- Institute of Molecular Medicine, Sechenov University, 119991 Moscow, Russia
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15
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Axell-House DB, Lavingia R, Rafferty M, Clark E, Amirian ES, Chiao EY. The estimation of diagnostic accuracy of tests for COVID-19: A scoping review. J Infect 2020; 81:681-697. [PMID: 32882315 PMCID: PMC7457918 DOI: 10.1016/j.jinf.2020.08.043] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 08/27/2020] [Indexed: 12/28/2022]
Abstract
OBJECTIVES To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. METHODS We conducted a systematic search of English-language articles published December 31, 2019-June 19, 2020. Studies of any design that performed tests on ≥10 patients and reported or inferred correlative statistics were included. Studies were evaluated using elements of the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) guidelines. RESULTS We conducted a narrative and tabular synthesis of studies organized by their reference standard strategy or comparative agreement method, resulting in six categorizations. Critical study details were frequently unreported, including the mechanism for patient/sample selection and researcher blinding to results, which lead to concern for bias. CONCLUSIONS Current studies estimating test performance characteristics have imperfect study design and statistical methods for the estimation of test performance characteristics of SARS-CoV-2 tests. The included studies employ heterogeneous methods and overall have an increased risk of bias. Employing standardized guidelines for study designs and statistical methods will improve the process for developing and validating rRT-PCR and NAAT for the diagnosis of COVID-19.
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Affiliation(s)
- Dierdre B. Axell-House
- Section of Infectious Diseases, Department of Internal Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Richa Lavingia
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA,School of Social Sciences, Rice University, MS 272, 5620 Greenbriar Dr, Houston, TX 77005, USA,UTHealth School of Public Health, Houston, TX, USA
| | - Megan Rafferty
- School of Social Sciences, Rice University, MS 272, 5620 Greenbriar Dr, Houston, TX 77005, USA,UTHealth School of Public Health, Houston, TX, USA
| | - Eva Clark
- Section of Infectious Diseases, Department of Internal Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA,Houston HSR&D IQuESt, Michael E. DeBakey VA Medical Center, 2450 Holcombe Blvd, Houston, TX, 77021, USA
| | - E. Susan Amirian
- School of Social Sciences, Rice University, MS 272, 5620 Greenbriar Dr, Houston, TX 77005, USA
| | - Elizabeth Y. Chiao
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1155 Pressler St., Unit 1340, Houston, TX 77030, USA,Corresponding author
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16
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The case for routine screening for SARS-CoV-2 before surgery. Can J Anaesth 2020; 67:1315-1320. [PMID: 32495121 PMCID: PMC7268956 DOI: 10.1007/s12630-020-01730-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/24/2020] [Indexed: 01/09/2023] Open
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