COVID 19 Special Collection
COVID-19 (SARS-CoV-2) Special Collection
Latest COVID-19 Articles
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Letter to the Editor
Comparison of Copan Eswab and FLOQswab for COVID-19 PCR diagnosis: working around a supply shortage
On March 16th 2020, WHO Director-General stated “You cannot fight a fire blindfolded. And we cannot stop this [COVID-19] pandemic if we don't know who is infected. We have a simple message for all countries: test, test, test. Test every suspected case.”...
Accepted Manuscript Posted 15 April 2020, Final Article Posted 26 May, 2020, JCM
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Opinion/Hypothesis
Repurposing Didanosine as a Potential Treatment for COVID-19 Using Single-Cell RNA Sequencing Data
As of today (7 April 2020), more than 81,000 people around the world have died from the coronavirus disease 19 (COVID-19) pandemic. There is no approved drug or vaccine for COVID-19, although more than 10 clinical trials have been launched to test potential drugs. In an urgent response to this pandemic, I developed a bioinformatics pipeline to identify compounds and drug candidates to potentially treat COVID-19. This pipeline is based on publicly available single-cell RNA sequencing (scRNA-seq) data and the drug perturbation database “Library of Integrated Network-Based Cellular Signatures” (LINCS). I developed a ranking score system that prioritizes these drugs or small molecules. The four drugs with the highest total score are didanosine, benzyl-quinazolin-4-yl-amine, camptothecin, and RO-90-7501. In conclusion, I have demonstrated the utility of bioinformatics for identifying drugs than can be repurposed for potentially treating COVID-19 patients.
14 April 2020, mSystems
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Research Article
Clinical evaluation of the cobas SARS-CoV-2 test and a diagnostic platform switch during 48 hours in the midst of the COVID-19 pandemic
Laboratories are currently witnessing extraordinary demand globally for sampling devices, reagents, consumables, and diagnostic instruments needed for timely diagnosis of SARS-CoV-2 infection. To meet diagnostic needs as the pandemic grows, the US Food and Drug Administration (FDA) recently granted several commercial SARS-CoV-2 tests Emergency Use Authorization (EUA), but manufacturer-independent evaluation data are scarce. We performed the first manufacturer-independent evaluation of the fully automated sample-to-result two-target test cobas 6800 SARS-CoV-2 (cobas) (Roche Molecular Systems, Branchburg, NJ), which received US FDA EUA on March 12, 2020. The comparator was a standardized 3-hour SARS-CoV-2 protocol, consisting of RNA extraction using an automated portable instrument, followed by a two-target RT-PCR, which our laboratory has routinely used since January 2020 (Corman VM et al. EuroSurveill 25 (3):2000045). Cobas and the comparator showed overall agreement of 98.1% and a kappa value of 0.95 on an in-house validation panel consisting of 217 well-characterized retrospective samples. Immediate prospective head-to-head comparative evaluation followed on 502 samples, and the diagnostic approaches showed overall percent agreement of 99.6% and a kappa value of 0.98. A good correlation (r2 = 0.96) between cycle threshold values for SARS-CoV-2 specific targets obtained by cobas and the comparator was observed. Our results showed that cobas is a reliable assay for qualitative detection of SARS-CoV-2 in nasopharyngeal swab samples collected in the UTM-RT system. Under the extraordinary circumstances that laboratories are facing worldwide, a safe diagnostic platform switch is feasible in only 48 hours and in the midst of the COVID-19 pandemic if carefully planned and executed.
Accepted Manuscript Posted 10 April 2020, Final Article Posted 26 May, 2020, JCM
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Research Article
A method to prevent SARS-CoV-2 IgM false positives in gold immunochromatography and enzyme-linked immunosorbent assays
Objective: To investigate the interference factors that lead to false-positive novel coronavirus (SARS-CoV-2) IgM detected using gold immunochromatography assay (GICA) and enzyme-linked immunosorbent assay (ELISA) and the corresponding solutions...
Accepted Manuscript Posted 10 April 2020, Final Article Posted 26 May, 2020, JCM
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Research Article
Comparative Performance of SARS-CoV-2 Detection Assays using Seven Different Primer/Probe Sets and One Assay Kit
Nearly 400,000 people worldwide are known to have been infected with SARS-CoV-2 beginning in December 2019. The virus has now spread to over 168 countries including the United States, where the first cluster of cases was observed in the Seattle metropolitan area in Washington. Given the rapid increase in the number of cases in many localities, the availability of accurate, high-throughput SARS-CoV-2 testing is vital to efforts to manage the current public health crisis. In the course of optimizing SARS-CoV-2 testing performed by the University of Washington Clinical Virology Lab (UW Virology Lab), we evaluated assays using seven different primer/probe sets and one assay kit. We found that the most sensitive assays were those that used the E-gene primer/probe set described by Corman et al. (Eurosurveillance 25 (3), 2020, https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045) and the N2 set developed by the CDC (Division of Viral Diseases, Centers for Disease Control and Prevention, 2020, https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-primer-probes.pdf). All assays tested were found to be highly specific for SARS-CoV-2, with no cross-reactivity with other respiratory viruses observed in our analyses regardless of the primer/probe set or kit used. These results will provide valuable information to other clinical laboratories who are actively developing SARS-CoV-2 testing protocols at a time when increased testing capacity is urgently needed worldwide.
Accepted Manuscript Posted 8 April 2020, Final Article Posted 26 May, 2020, JCM
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Letter to the Editor
International expansion of a novel SARS-CoV-2 mutant
RNA viruses such as coronavirus are rapidly evolving pathogens that can accumulate considerable genetic diversity in relatively short time periods...
Accepted Manuscript Posted 8 April 2020, JVI
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Research Article
Single-Dose, Intranasal Immunization with Recombinant Parainfluenza Virus 5 Expressing Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Spike Protein Protects Mice from Fatal MERS-CoV Infection
MERS-CoV causes lethal infection in humans, and there is no vaccine. Our work demonstrates that PIV5 is a promising vector for developing a MERS vaccine. Furthermore, success of PIV5-based MERS vaccine can be employed to develop a vaccine for emerging CoVs such as SARS-CoV-2, which causes COVID-19.
7 April 2020, mBio
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Minireview
2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission
With the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that results in coronavirus disease 2019 (COVID-19), corporate entities, federal, state, county, and city governments, universities, school districts, places of worship, prisons, health care facilities, assisted living organizations, daycares, homeowners, and other building owners and occupants have an opportunity to reduce the potential for transmission through built environment (BE)-mediated pathways. Over the last decade, substantial research into the presence, abundance, diversity, function, and transmission of microbes in the BE has taken place and revealed common pathogen exchange pathways and mechanisms. In this paper, we synthesize this microbiology of the BE research and the known information about SARS-CoV-2 to provide actionable and achievable guidance to BE decision makers, building operators, and all indoor occupants attempting to minimize infectious disease transmission through environmentally mediated pathways. We believe this information is useful to corporate and public administrators and individuals responsible for building operations and environmental services in their decision-making process about the degree and duration of social-distancing measures during viral epidemics and pandemics.
7 April 2020, mSystems
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Commentary
The Laboratory Diagnosis of COVID-19 Infection: Current Issues and Challenges
The COVID-19 outbreak has had a major impact on clinical microbiology laboratories in the past several months. This commentary covers current issues and challenges for the laboratory diagnosis of infections caused by SARS-CoV-2. In the pre-analytical stage, collecting the proper respiratory tract specimen at the right time from the right anatomic site is essential for a prompt and accurate molecular diagnosis of COVID-19. Appropriate measures are required to keep laboratory staff safe while producing reliable test results. In the analytic stage, real-time RT-PCR assays remain the molecular test of choice for the etiologic diagnosis of SARS-CoV-2 infection while antibody-based techniques are being introduced as supplemental tools. In the postanalytical stage, testing results should be carefully interpreted using both molecular and serological findings. Finally, random access, integrated devices available at the point of care with scalable capacities will facilitate the rapid and accurate diagnosis and monitoring of SARS-CoV-2 infections and greatly assist in the control of this outbreak.
Accepted Manuscript Posted 3 April 2020, Final Article Posted 26 May, 2020, JCM
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Letter to the Editor
A pandemic in times of global tourism: superspreading and exportation of COVID-19 cases from a ski area in Austria
On January 7, 2020, the World Health Organization (WHO) announced a novel coronavirus to be the cause of unclear pneumonia cases in China...
Accepted Manuscript Posted 3 April 2020, Final Article Posted 26 May, 2020, JCM
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Letter to the Editor
Isolation and full-length genome characterization of SARS-CoV-2 from COVID-19 cases in Northern Italy
In December 2019, the novel coronavirus Severe Acquired Respiratory Syndrome SARS-CoV-2 emerged in the city of Wuhan in the Hubei province, People's Republic of China, as the etiologic agent of coronavirus disease 2019 (COVID-19), which has hence spread worldwide causing a global pandemic (1-3)...
Accepted Manuscript Posted 1 April 2020, Final Article Posted 18 May, 2020, JVI
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Research Article
Computational inference of selection underlying the evolution of the novel coronavirus, SARS-CoV-2
Coronaviruses are dangerous zoonotic pathogens: in the last two decades three coronaviruses have crossed the species barrier and caused human epidemics. One of these is the recently emerged SARS-CoV-2. We investigated how, since its divergence from a closely related bat virus, natural selection shaped the genome of SARS-CoV-2. We found that distinct coding regions in the SARS-CoV-2 genome evolve under different degrees of constraint and are consequently more or less prone to tolerate amino acid substitutions. In practical terms, the level of constraint provides indications about which proteins/protein regions are better suited as possible targets for the development of antivirals or vaccines. We also detected limited signals of positive selection in three viral ORFs. However, we warn that, in the absence of knowledge about the chain of events that determined the human spill-over, these signals should not be necessarily interpreted as evidence of an adaptation to our species.
Accepted Manuscript Posted 1 April 2020, JVI
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Letter to the Editor
Evaluation of saline, phosphate buffered saline and minimum essential medium as potential alternatives to viral transport media for SARS-CoV-2 testing
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of coronavirus disease-19 (COVID-19), has caused a global pandemic since being discovered in late 2019...
Accepted Manuscript Posted 30 March 2020, Final Article Posted 26 May, 2020 JCM
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Research Article
Evaluation of Nucleocapsid and Spike Protein-based ELISAs for detecting antibodies against SARS-CoV-2
Background: At present, PCR-based nucleic acid detection cannot meet the demands for coronavirus infectious disease (COVID-19) diagnosis...
Accepted Manuscript Posted 30 March 2020, Final Article Posted 26 May, 2020, JCM
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Editorial
Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19
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.
26 March 2020, mBio