#CT #Imaging of 3 Patients With #COVID19 #Pneumonia With Negative Virus Real-time Reverse-Transcription #PCR #Test (Clin Infect Dis., abstract)

[Source: Clinical Infectious Diseases, full page: (LINK). Abstract, edited.]

Computed Tomographic Imaging of 3 Patients With Coronavirus Disease 2019 Pneumonia With Negative Virus Real-time Reverse-Transcription Polymerase Chain Reaction Test

Junqing Xu, Ruodai Wu, Hua Huang, Weidong Zheng, Xinling Ren, Nashan Wu, Bin Ji, Yungang Lv, Yumeng Liu, Rui Mi

Clinical Infectious Diseases, ciaa207, https://doi.org/10.1093/cid/ciaa207

Published: 31 March 2020

 

Abstract

We reported computed tomographic (CT) imaging findings of 3 patients with coronavirus disease 2019 (COVID-19) pneumonia with initially negative results before CT examination and finally confirmed positive for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse-transcription polymerase chain reaction assay.

chest CT, covid-19 pneumonia, rt-PCR

Issue Section: Brief Report

Keywords: SARS-CoV-2; COVID-19; Radiology; Diagnostic tests.

—–

#SARS-CoV-2 #Testing: #Trials and #Tribulations (Am J Clin Pathol., summary)

[Source: American Journal of Clinical Pathology, full page: (LINK). Summary, edited.]

SARS-CoV-2 Testing: Trials and Tribulations

Ahmed Babiker, MD, Charlie W Myers, MD, Charles E Hill, MD, PhD, Jeannette Guarner, MD

American Journal of Clinical Pathology, aqaa052, https://doi.org/10.1093/ajcp/aqaa052

Published: 30 March 2020

Issue Section: Editorial

___

Coronavirus disease 2019 (COVID-19), the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), started in the Wuhan province of China and is now a pandemic that has caused a great number of deaths across the globe.1,2 The number of cases in the United States is increasing steadily, and the epidemic curve mimics the start of the infection in both China and Italy. Due to challenges associated with ramping up testing capacity, reliable estimates of the number of infections in the United States are not available. Multiple people, including Anthony Fauci, MD, Director of the National Institute of Allergy and Infectious Diseases, have stated that testing for COVID-19 has been problematic,3 with some dubbing the situation “testgate.” Below we will explore the evolution of tests in the United States, alternative tests, the logistics of increasing testing, and issues regarding laboratory staffing in response to the increased demands of testing.

(…)

___

Keywords: SARS-CoV-2; COVID-19; USA; Diagnostic tests.

—–

#Caution should be exercised for the #detection of #SARS‐CoV‐2, especially in the #elderly (J Med Virol., abstract)

[Source: Journal of Medical Virology, full page: (LINK). Abstract, edited.]

Caution should be exercised for the detection of SARS‐CoV‐2, especially in the elderly

YajunYuan,  Nan Wang,  Xueqing Ou

First published: 30 March 2020 | DOI:  https://doi.org/10.1002/jmv.25796

This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/jmv.25796

 

Abstract

In December 2019, a pneumonia outbreak, caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), was first identified in Wuhan, China and presented a major threat to public health. Nationwide, there were more than 70,000 confirmed cases, and 2500 deaths. Most patients were elderly, with severe disease. For acute respiratory infection, RT‐PCR is routinely used to detect causative viruses in respiratory secretions. Coronavirus RNA can be detected from nose and throat swabs, sputum and other lower respiratory tract secretions, blood and feces. Such specimens were examined by RT‐PCR. Three targets, RdRP, E and N genes were detected, indicating samples were positive for SARS‐CoV‐2]. After patient recovery, a chest CT examination, combined with SARS‐CoV‐2 RNA detection, confirmed diagnosis. However, some recovery patients with negative RNA tests turned RNA positive. The preliminary data is about 14% of discharged patients in Guangdong reported by the Guangdong Center for Disease Control (CDC). This is an important scientific issue. If samples are positive for SARS‐CoV‐2 RNA, patients should be managed according to infection source. Fortunately, there were no close contacts of second‐generation cases. We herein report six SARS‐CoV‐2 cases confirmed in our hospital, for the changes of results of SARS‐CoV‐2 RNA should attract attention. Most patients were elderly, with a low Geriatric Nutritional Risk Index (GNRI). However, the association of the phenomenon with aging and GNRI has not yet been reported in detail. Further investigations are necessary to confirm and improve these findings. Similarly, discharged patient follow‐up should be strengthened.

This article is protected by copyright. All rights reserved.

Keywords: SARS-CoV-2; COVID-19; Diagnostic tests.

—–

Quantitative #Detection and #Viral #Load Analysis of #SARS-CoV-2 in Infected Patients (Clin Infect Dis., abstract)

[Source: Clinical Infectious Diseases, full page: (LINK). Abstract, edited.]

Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients

Fengting Yu, Liting Yan, Nan Wang, Siyuan Yang, Linghang Wang, Yunxia Tang, Guiju Gao, Sa Wang, Chengjie Ma, Ruming Xie, Fang Wang, Chianru Tan, Lingxiang Zhu, Yong Guo, Fujie Zhang

Clinical Infectious Diseases, ciaa345, https://doi.org/10.1093/cid/ciaa345

Published: 28 March 2020

 

Abstract

Background

Coronavirus disease 2019 (COVID-19) has become a public health emergency. The widely used reverse transcription PCR (RT-PCR) method has limitations for clinical diagnosis and treatment.

Methods

A total of 323 samples from 76 COVID-19 confirmed patients were analyzed by droplet digital PCR (ddPCR) and RT-PCR based two target genes (ORF1ab and N). Nasal swabs, throat swabs, sputum, blood, and urine were collected. Clinical and imaging data were obtained for clinical staging.

Results

In 95 samples tested positive by both methods, the cycle threshold (Ct) of RT-PCR was highly correlated with the copy numbed of ddPCR (ORF1ab gene, R2 = 0.83; N gene, R2 = 0.87). 4 (4/161) negative and 41 (41/67) single-gene positive samples tested by RT-PCR were positive according to ddPCR with viral load ranging from 11.1 to 123.2 copies/test. Then the viral load of respiratory samples was compared and the average viral load in sputum (17429 ± 6920 copies/test) was found to be significantly higher than in throat swabs (2552 ± 1965 copies/test, p < 0.001) and nasal swabs (651 ± 501 copies/test, p < 0.001). Furthermore, the viral load in the early and progressive stages were significantly higher than that in the recovery stage (46800 ± 17272 vs 1252 ± 1027, p < 0.001) analyzed by sputum samples.

Conclusions

Quantitative monitoring of viral load in lower respiratory tract samples helps to evaluate disease progression, especially in cases of low viral load.

COVID-19, SARS-CoV-2, RT-PCR, ddPCR, Viral load

Issue Section: Major Article

This content is only available as a PDF.

Author notes F.Y., L.Y., N.W. contributed equally to this study.

© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: SARS-CoV-2; COVID-19; Diagnostic tests.

—–

#Report from the American Society for Microbiology #COVID19 International #Summit, 23 March 2020: Value of #Diagnostic #Testing for #SARS–CoV-2/COVID-19 (MBio, summary)

[Source: Mbio, full page: (LINK). Summary, edited.]

Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19

Robin Patel, Esther Babady, Elitza S. Theel, Gregory A. Storch, Benjamin A. Pinsky, Kirsten St. George, Tara C. Smith, Stefano Bertuzzi

DOI: 10.1128/mBio.00722-20

 

GUEST EDITORIAL

As we enter the second quarter of the COVID-19 pandemic, with testing for severe acute respiratory syndrome coronavirus 2 (SARS–CoV-2) increasingly available (though still limited and/or slow in some areas), we are faced with new questions and challenges regarding this novel virus. When to test? Whom to test? What to test? How often to test? And, what to do with test results? Since SARS–CoV-2 is a new virus, there is little evidence to fall back on for test utilization and diagnostic stewardship (1). Several points need to be considered to begin answering of these questions; specifically, what types of tests are available and under which circumstances are they useful? This understanding can help guide the use of testing at the local, regional, state, and national levels and inform those assessing the supply chain to ensure that needed testing is and continues to be available. Here, we explain the types of tests available and how they might be useful in the face of a rapidly changing and never-before-experienced situation. There are two broad categories of SARS–CoV-2 tests: those that detect the virus itself and those that detect the host’s response to the virus. Each will be considered separately.

(…)

Keywords: SARS-CoV-2; COVID-19; Diagnostic tests.

—–

#Stability #Issues of #RTPCR #Testing of #SARS‐CoV‐2 for Hospitalized Patients Clinically Diagnosed with #COVID19 (J Med Virol., abstract)

[Source: Journal of Medical Virology, full page: (LINK). Abstract, edited.]

Stability Issues of RT‐PCR Testing of SARS‐CoV‐2 for Hospitalized Patients Clinically Diagnosed with COVID‐19

Yafang Li, Lin Yao,  Jiawei Li,  Lei Chen,  Yiyan Song,  Zhifang Cai,  Chunhua Yang

First published: 26 March 2020 | DOI:  https://doi.org/10.1002/jmv.25786

This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/jmv.25786

 

Abstract

In this study, we collected a total of 610 hospitalized patients from Wuhan between Feb 2, 2020, and Feb 17, 2020. We reported a potentially high false negtive rate of RT‐PCR testing for SARS‐CoV‐2 in the 610 hospitalized patients clinically diagnosed with COVID‐19 during the 2019 outbreak. We also found that the RT‐PCR results from several tests at different points were variable from the same patients during the course of diagnosis and treatment of these patients. Our results indicate that in addition to the emphasis on RT‐PCR testing, clinical indicators such as CT images should also be used not only for diagnosis and treatment but also for isolation, recovery/discharge and transferring for hospitalized patients clinically diagnosed with COVID‐19 during the current epidemic. These results suggested the urgent needs for standard of procedures(SOP) of sampling from different anatomic sites, sample transportation, optimization of RT‐PCR, serology diagnosis/screening for SARS‐CoV‐2 infection, and distinct diagnosis from other respiratory diseases such as fluenza infections as well.

This article is protected by copyright. All rights reserved.

Keywords: SARS-CoV-2; COVID-19; Diagnostic tests.

—–

#Epidemiological and #Clinical #Predictors of #COVID19 (Clin Infect Dis., abstract)

[Source: Clinical Infectious Diseases, full page: (LINK). Abstract, edited.]

Epidemiological and Clinical Predictors of COVID-19

Yinxiaohe Sun, Vanessa Koh, Kalisvar Marimuthu, Oon Tek Ng, Barnaby Young, Shawn Vasoo, Monica Chan, Vernon J M Lee, Partha P De, Timothy Barkham …

Clinical Infectious Diseases, ciaa322, https://doi.org/10.1093/cid/ciaa322

Published: 25 March 2020

 

Abstract

Background

Rapid identification of COVID-19 cases, which is crucial to outbreak containment efforts, is challenging due to the lack of pathognomonic symptoms and in settings with limited capacity for specialized nucleic acid-based reverse transcription polymerase chain reaction (PCR) testing.

Methods

This retrospective case-control study involves subjects (7 to 98 years) presenting at the designated national outbreak screening centre and tertiary care hospital in Singapore for SARS-CoV-2 testing from January 26 to February 16, 2020. COVID-19 status was confirmed by PCR testing of sputum, nasopharyngeal swabs or throat swabs. Demographic, clinical, laboratory and exposure-risk variables ascertainable at presentation were analyzed to develop an algorithm for estimating the risk of COVID-19. Model development used Akaike’s information criterion in a stepwise fashion to build logistic regression models, which were then translated into prediction scores. Performance was measured using receiver operating characteristics curves, adjusting for over-confidence using leave-out-one cross validation.

Results

The study population included 788 subjects, of whom 54 (6.9%) were SARS-CoV-2 positive and 734 (93.1%) were SARS-CoV-2 negative. The median age was 34 years and 407 (51.7%) were female. Using leave-out-one cross validation, all the models incorporating clinical tests (Models 1, 2 and 3) performed well with areas under the receiver operating characteristics curve (AUC) of 0.91, 0.88 and 0.88 respectively. In comparison, Model 4 had an AUC of 0.65.

Conclusions

Rapidly ascertainable clinical and laboratory data could identify individuals at high risk of COVID-19 and enable prioritization of PCR-testing and containment efforts. Basic laboratory test results were crucial to prediction models.

COVID-19, SARS-CoV-2, Risk factors, Prediction model

Issue Section: Major Article

This content is only available as a PDF.

Author notes: These authors contributed equally to the manuscript

© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: SARS-CoV-2; COVID-19; Diagnostic tests.

—–