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Article ; Online: Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays.

Fung, Becky / Gopez, Allan / Servellita, Venice / Arevalo, Shaun / Ho, Coral / Deucher, Anne / Thornborrow, Ed / Chiu, Charles / Miller, Steve

Journal of clinical microbiology

2020 Volume 58, Issue 9

Abstract: Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material ... ...

Abstract	Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material quantified with droplet digital PCR. Limits of detection ranged from ≤10 to 74 copies/ml for commercial high-throughput laboratory analyzers (Roche Cobas, Abbott m2000, and Hologic Panther Fusion) and 167 to 511 copies/ml for sample-to-answer (DiaSorin Simplexa, GenMark ePlex) and point-of-care instruments (Abbott ID NOW). The CDC assay yielded limits of detection ranging from 85 to 499 copies/ml, depending on the extraction method and thermocycler used. These results can help to inform the assay choice for testing approaches to manage the current COVID-19 outbreak.
MeSH term(s)	Betacoronavirus/genetics ; COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques/methods ; Clinical Laboratory Techniques/statistics & numerical data ; Coronavirus Infections/diagnosis ; Coronavirus Infections/epidemiology ; Humans ; Limit of Detection ; Molecular Diagnostic Techniques/methods ; Molecular Diagnostic Techniques/statistics & numerical data ; Pandemics ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/epidemiology ; RNA, Viral/analysis ; RNA, Viral/genetics ; SARS-CoV-2
Chemical Substances	RNA, Viral
Keywords	covid19
Language	English
Publishing date	2020-08-24
Publishing country	United States
Document type	Comparative Study ; Journal Article
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.01535-20
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Article ; Online: Predicting severe outcomes in Covid-19 related illness using only patient demographics, comorbidities and symptoms.

Ryan, Charles / Minc, Alexa / Caceres, Juan / Balsalobre, Alexandra / Dixit, Achal / Ng, Becky KaPik / Schmitzberger, Florian / Syed-Abdul, Shabbir / Fung, Christopher

The American journal of emergency medicine

2020 Volume 45, Page(s) 378–384

Abstract: Objective: Development of a risk-stratification model to predict severe Covid-19 related illness, using only presenting symptoms, comorbidities and demographic data.: Materials and methods: We performed a case-control study with cases being those ... ...

Abstract	Objective: Development of a risk-stratification model to predict severe Covid-19 related illness, using only presenting symptoms, comorbidities and demographic data. Materials and methods: We performed a case-control study with cases being those with severe disease, defined as ICU admission, mechanical ventilation, death or discharge to hospice, and controls being those with non-severe disease. Predictor variables included patient demographics, symptoms and past medical history. Participants were 556 patients with laboratory confirmed Covid-19 and were included consecutively after presenting to the emergency department at a tertiary care center from March 1, 2020 to April 21, 2020 RESULTS: Most common symptoms included cough (82%), dyspnea (75%), and fever/chills (77%), with 96% reporting at least one of these. Multivariable logistic regression analysis found that increasing age (adjusted odds ratio [OR], 1.05; 95% confidence interval [CI], 1.03-1.06), dyspnea (OR, 2.56; 95% CI: 1.51-4.33), male sex (OR, 1.70; 95% CI: 1.10-2.64), immunocompromised status (OR, 2.22; 95% CI: 1.17-4.16) and CKD (OR, 1.76; 95% CI: 1.01-3.06) were significant predictors of severe Covid-19 infection. Hyperlipidemia was found to be negatively associated with severe disease (OR, 0.54; 95% CI: 0.33-0.90). A predictive equation based on these variables demonstrated fair ability to discriminate severe vs non-severe outcomes using only this historical information (AUC: 0.76). Conclusions: Severe Covid-19 illness can be predicted using data that could be obtained from a remote screening. With validation, this model could possibly be used for remote triage to prioritize evaluation based on susceptibility to severe disease while avoiding unnecessary waiting room exposure.
MeSH term(s)	Aged ; COVID-19/epidemiology ; Case-Control Studies ; Comorbidity ; Female ; Hospitalization/statistics & numerical data ; Humans ; Male ; Middle Aged ; Pandemics ; Retrospective Studies ; Risk Factors ; SARS-CoV-2 ; Tertiary Care Centers ; Triage/methods ; Triage/statistics & numerical data ; United States/epidemiology
Keywords	covid19
Language	English
Publishing date	2020-09-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	605890-5
ISSN	1532-8171 ; 0735-6757
ISSN (online)	1532-8171
ISSN	0735-6757
DOI	10.1016/j.ajem.2020.09.017
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Article ; Online: COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme.

Fasching, Clare L / Servellita, Venice / McKay, Bridget / Nagesh, Vaishnavi / Broughton, James P / Sotomayor-Gonzalez, Alicia / Wang, Baolin / Brazer, Noah / Reyes, Kevin / Streithorst, Jessica / Deraney, Rachel N / Stanfield, Emma / Hendriks, Carley G / Fung, Becky / Miller, Steve / Ching, Jesus / Chen, Janice S / Chiu, Charles Y

Journal of clinical microbiology

2022 Volume 60, Issue 7, Page(s) e0026122

Abstract: Laboratory tests for the accurate and rapid identification of SARS-CoV-2 variants can potentially guide the treatment of COVID-19 patients and inform infection control and public health surveillance efforts. Here, we present the development and ... ...

Abstract	Laboratory tests for the accurate and rapid identification of SARS-CoV-2 variants can potentially guide the treatment of COVID-19 patients and inform infection control and public health surveillance efforts. Here, we present the development and validation of a rapid COVID-19 variant DETECTR assay incorporating loop-mediated isothermal amplification (LAMP) followed by CRISPR-Cas12 based identification of single nucleotide polymorphism (SNP) mutations in the SARS-CoV-2 spike (S) gene. This assay targets the L452R, E484K/Q/A, and N501Y mutations, at least one of which is found in nearly all major variants. In a comparison of three different Cas12 enzymes, only the newly identified enzyme CasDx1 was able to accurately identify all targeted SNP mutations. An analysis pipeline for CRISPR-based SNP identification from 261 clinical samples yielded a SNP concordance of 97.3% and agreement of 98.9% (258 of 261) for SARS-CoV-2 lineage classification, using SARS-CoV-2 whole-genome sequencing and/or real-time RT-PCR as test comparators. We also showed that detection of the single E484A mutation was necessary and sufficient to accurately identify Omicron from other major circulating variants in patient samples. These findings demonstrate the utility of CRISPR-based DETECTR as a faster and simpler diagnostic method compared with sequencing for SARS-CoV-2 variant identification in clinical and public health laboratories.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Testing ; CRISPR-Cas Systems ; Clinical Laboratory Techniques/methods ; Humans ; Mutation ; SARS-CoV-2/genetics ; Sensitivity and Specificity
Language	English
Publishing date	2022-06-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/jcm.00261-22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Predicting severe outcomes in Covid-19 related illness using only patient demographics, comorbidities and symptoms

Ryan, Charles / Minc, Alexa / Caceres, Juan / Balsalobre, Alexandra / Dixit, Achal / Ng, Becky KaPik / Schmitzberger, Florian / Syed-Abdul, Shabbir / Fung, Christopher

The American Journal of Emergency Medicine ; ISSN 0735-6757

2020

Keywords	Emergency Medicine ; General Medicine ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
DOI	10.1016/j.ajem.2020.09.017
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Oral antibiotics perturbation on gut microbiota after prostate biopsy.

Li, Joseph Kai Man / Wang, Lynn Lin / Lau, Becky Su Yan / Tse, Ryan Tsz Hei / Cheng, Carol Ka Lo / Leung, Steven Chi Ho / Wong, Christine Yim Ping / Tsui, Stephen Kwok Wing / Teoh, Jeremy Yuen Chun / Chiu, Peter Ka Fung / Ng, Chi Fai

Frontiers in cellular and infection microbiology

2022 Volume 12, Page(s) 959903

Abstract: Introduction: The use of antibiotics may induce the changes in gut microbiota. Previous studies have shown conflicting results on whether the changed gut microbiota by antibiotics can be recovered. Our study aims to investigate whether the gut ... ...

Abstract	Introduction: The use of antibiotics may induce the changes in gut microbiota. Previous studies have shown conflicting results on whether the changed gut microbiota by antibiotics can be recovered. Our study aims to investigate whether the gut microbiota could be recovered after a single dose of oral co-amoxiclav before transrectal ultrasound-guided transperineal prostate biopsy (TPPBx) in 5 weeks' time. Methods: Fifteen patients with elevated serum prostate-specific antigen (PSA) were recruited to provide pre-antibiotic and post-antibiotic fecal samples. The V4 region of 16S rRNA was sequenced. Analysis was performed by QIIME2. Alpha- and beta-diversities were analyzed, as well as the differential enrichment by Linear discriminant analysis Effect Size (LEfSe) analysis. Results: Both the alpha- and beta-diversities of the pre- and post-antibiotic fecal samples were significantly different. Genera that are associated with alleviation of inflammation were enriched in the pre-antibiotic fecal samples, while the inflammation-associated genera were more enriched in the post-antibiotic fecal samples. Conclusion: A single dose of oral co-amoxiclav before TPPBx could have led to a change of gut microbiota that cannot be recovered in 5 weeks' time. Microbiome studies on prostate cancer patients should be cautioned on the use of post-prostate biopsy fecal sampling. Further studies should be conducted for the impact on gut microbiome for TPPBx alone.
MeSH term(s)	Amoxicillin-Potassium Clavulanate Combination/pharmacology ; Anti-Bacterial Agents/pharmacology ; Biopsy ; Feces ; Gastrointestinal Microbiome ; Humans ; Inflammation/pathology ; Male ; Prostate ; RNA, Ribosomal, 16S/genetics
Chemical Substances	Anti-Bacterial Agents ; RNA, Ribosomal, 16S ; Amoxicillin-Potassium Clavulanate Combination (74469-00-4)
Language	English
Publishing date	2022-08-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2022.959903
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays

Fung, Becky / Gopez, Allan / Servellita, Venice / Arevalo, Shaun / Ho, Coral / Deucher, Anne / Thornborrow, Ed / Chiu, Charles / Miller, Steve

J. clin. microbiol

Abstract	Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material quantified with droplet digital PCR. Limits of detection ranged from ≤10 to 74 copies/ml for commercial high-throughput laboratory analyzers (Roche Cobas, Abbott m2000, and Hologic Panther Fusion) and 167 to 511 copies/ml for sample-to-answer (DiaSorin Simplexa, GenMark ePlex) and point-of-care instruments (Abbott ID NOW). The CDC assay yielded limits of detection ranging from 85 to 499 copies/ml, depending on the extraction method and thermocycler used. These results can help to inform the assay choice for testing approaches to manage the current COVID-19 outbreak.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #638997
Database	COVID19

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Article ; Online: Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays

Fung, Becky / Gopez, Allan / Servellita, Venice / Arevalo, Shaun / Ho, Coral / Deucher, Anne / Thornborrow, Ed / Chiu, Charles / Miller, Steve

Journal of Clinical Microbiology

2020 Volume 58, Issue 9

Abstract: ABSTRACT Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material ... ...

Abstract	ABSTRACT Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material quantified with droplet digital PCR. Limits of detection ranged from ≤10 to 74 copies/ml for commercial high-throughput laboratory analyzers (Roche Cobas, Abbott m2000, and Hologic Panther Fusion) and 167 to 511 copies/ml for sample-to-answer (DiaSorin Simplexa, GenMark ePlex) and point-of-care instruments (Abbott ID NOW). The CDC assay yielded limits of detection ranging from 85 to 499 copies/ml, depending on the extraction method and thermocycler used. These results can help to inform the assay choice for testing approaches to manage the current COVID-19 outbreak.
Keywords	Microbiology (medical) ; covid19
Language	English
Publisher	American Society for Microbiology
Publishing country	us
Document type	Article ; Online
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/jcm.01535-20
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays.

Fung, Becky / Gopez, Allan / Servellita, Venice / Arevalo, Shaun / Ho, Coral / Deucher, Anne / Thornborrow, Ed / Chiu, Charles / Miller, Steve

Journal of clinical microbiology, vol 58, iss 9

2020

Abstract	Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material quantified with droplet digital PCR. Limits of detection ranged from ≤10 to 74 copies/ml for commercial high-throughput laboratory analyzers (Roche Cobas, Abbott m2000, and Hologic Panther Fusion) and 167 to 511 copies/ml for sample-to-answer (DiaSorin Simplexa, GenMark ePlex) and point-of-care instruments (Abbott ID NOW). The CDC assay yielded limits of detection ranging from 85 to 499 copies/ml, depending on the extraction method and thermocycler used. These results can help to inform the assay choice for testing approaches to manage the current COVID-19 outbreak.
Keywords	Humans ; Pneumonia ; Viral ; Coronavirus Infections ; RNA ; Clinical Laboratory Techniques ; Molecular Diagnostic Techniques ; Limit of Detection ; Pandemics ; Betacoronavirus ; SARS-CoV-2 ; Microbiology ; Biological Sciences ; Agricultural and Veterinary Sciences ; Medical and Health Sciences ; covid19
Publishing date	2020-08-24
Publisher	eScholarship, University of California
Publishing country	us
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Predicting severe outcomes in Covid-19 related illness using only patient demographics, comorbidities and symptoms

Ryan, Charles / Minc, Alexa / Caceres, Juan / Balsalobre, Alexandra / Dixit, Achal / Ng, Becky KaPik / Schmitzberger, Florian / Syed-Abdul, Shabbir / Fung, Christopher

Am. j. emerg. med

Abstract: OBJECTIVE: Development of a risk-stratification model to predict severe Covid-19 related illness, using only presenting symptoms, comorbidities and demographic data. MATERIALS AND METHODS: We performed a case-control study with cases being those with ... ...

Abstract	OBJECTIVE: Development of a risk-stratification model to predict severe Covid-19 related illness, using only presenting symptoms, comorbidities and demographic data. MATERIALS AND METHODS: We performed a case-control study with cases being those with severe disease, defined as ICU admission, mechanical ventilation, death or discharge to hospice, and controls being those with non-severe disease. Predictor variables included patient demographics, symptoms and past medical history. Participants were 556 patients with laboratory confirmed Covid-19 and were included consecutively after presenting to the emergency department at a tertiary care center from March 1, 2020 to April 21, 2020 RESULTS: Most common symptoms included cough (82%), dyspnea (75%), and fever/chills (77%), with 96% reporting at least one of these. Multivariable logistic regression analysis found that increasing age (adjusted odds ratio [OR], 1.05; 95% confidence interval [CI], 1.03-1.06), dyspnea (OR, 2.56; 95% CI: 1.51-4.33), male sex (OR, 1.70; 95% CI: 1.10-2.64), immunocompromised status (OR, 2.22; 95% CI: 1.17-4.16) and CKD (OR, 1.76; 95% CI: 1.01-3.06) were significant predictors of severe Covid-19 infection. Hyperlipidemia was found to be negatively associated with severe disease (OR, 0.54; 95% CI: 0.33-0.90). A predictive equation based on these variables demonstrated fair ability to discriminate severe vs non-severe outcomes using only this historical information (AUC: 0.76). CONCLUSIONS: Severe Covid-19 illness can be predicted using data that could be obtained from a remote screening. With validation, this model could possibly be used for remote triage to prioritize evaluation based on susceptibility to severe disease while avoiding unnecessary waiting room exposure.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #754024
Database	COVID19

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Article ; Online: Serum hepatitis B core-related antigen predicts hepatocellular carcinoma in hepatitis B e antigen-negative patients.

Liang, Lilian Yan / Wong, Vincent Wai-Sun / Toyoda, Hidenori / Tse, Yee-Kit / Yip, Terry Cheuk-Fung / Yuen, Becky Wing-Yan / Tada, Toshifumi / Kumada, Takashi / Lee, Hye-Won / Lui, Grace Chung-Yan / Chan, Henry Lik-Yuen / Wong, Grace Lai-Hung

Journal of gastroenterology

2020 Volume 55, Issue 9, Page(s) 899–908

Abstract: Background: Hepatitis B core-related antigen (HBcrAg) is a novel serum viral marker. Recent studies showed that its level correlates with the risk of hepatocellular carcinoma (HCC) in patients with chronic hepatitis B (CHB). We aimed to evaluate the ... ...

Abstract	Background: Hepatitis B core-related antigen (HBcrAg) is a novel serum viral marker. Recent studies showed that its level correlates with the risk of hepatocellular carcinoma (HCC) in patients with chronic hepatitis B (CHB). We aimed to evaluate the accuracy of serum HBsAg and HBcrAg levels at baseline to predict HCC. Methods: 1400 CHB patients who received nucleos(t)ide analogues (NA) treatment since December 2005 were included. Their stored serum samples at baseline were retrieved to measure HBsAg and HBcrAg levels. The primary endpoint was the cumulative incidence of HCC. Results: 85 (6.1%) patients developed HCC during a mean (± SD) follow-up duration of 45 ± 20 months. Serum HBcrAg level above 2.9 log10 U/mL at baseline was an independent factor for HCC in hepatitis B e antigen (HBeAg)-negative patients by multivariable analysis (adjusted hazard ratio 2.13, 95% CI 1.10-4.14, P = 0.025). HBcrAg above 2.9 log Conclusion: Serum HBcrAg level predicts the risk of HCC accurately in NA-treated HBeAg-negative CHB patients.
MeSH term(s)	Adult ; Aged ; Antiviral Agents/administration & dosage ; Carcinoma, Hepatocellular/epidemiology ; Carcinoma, Hepatocellular/virology ; Cohort Studies ; Female ; Follow-Up Studies ; Hepatitis B Core Antigens/blood ; Hepatitis B Surface Antigens/blood ; Hepatitis B e Antigens/blood ; Hepatitis B, Chronic/complications ; Hepatitis B, Chronic/drug therapy ; Humans ; Liver Neoplasms/epidemiology ; Liver Neoplasms/virology ; Male ; Middle Aged ; Predictive Value of Tests ; Prospective Studies ; Retrospective Studies
Chemical Substances	Antiviral Agents ; Hepatitis B Core Antigens ; Hepatitis B Surface Antigens ; Hepatitis B e Antigens
Language	English
Publishing date	2020-06-17
Publishing country	Japan
Document type	Journal Article
ZDB-ID	1186495-3
ISSN	1435-5922 ; 0944-1174
ISSN (online)	1435-5922
ISSN	0944-1174
DOI	10.1007/s00535-020-01700-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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