COVID 19 Special Collection
COVID-19 (SARS-CoV-2) Special Collection
Latest COVID-19 Articles
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Genome Sequences
Coding-Complete Genome Sequences of Two SARS-CoV-2 Isolates from Egypt
This report announces the complete genome sequences of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolates detected in Egypt. The isolates were obtained from oropharyngeal swab specimens from two Egyptians in Upper and Lower Egypt. Sequence analysis showed mutations that differentiate Egyptian strains from the reference strain 2019-nCoV WHU01.
28 May 2020, MRA
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Research Article
Comparison of two commercial molecular tests and a laboratory-developed modification of the CDC 2019-nCoV RT-PCR assay for the detection of SARS-CoV-2
We compared the ability of 2 commercial molecular amplification assays [RealTime SARS-CoV-2 on the m2000 (Abbott) (abbreviated ACOV) and ID NOW™ COVID-19 (Abbott) (abbreviated IDNOW)] and a laboratory-developed test [modified CDC 2019-nCoV RT-PCR assay with RNA extraction by eMag® (bioMérieux) and amplification on QuantStudio™ 6 or ABI 7500 Real-Time PCR System (Life Technologies) (abbreviated CDC COV)] to detect SARS-CoV-2 RNA in upper respiratory tract specimens. Discrepant results were adjudicated by medical record review. 200 nasopharyngeal swab specimens in viral transport medium (VTM) were collected from symptomatic patients between March 27 and April 9, 2020. Results were concordant for 167 specimens (83.5% overall agreement), including 94 positive and 73 negative specimens. The ACOV assay yielded 33 additional positive results, 25 of which were also positive by the CDC COV assay but not by the IDNOW assay. In a follow-up evaluation, 97 patients for whom a dry nasal swab specimen yielded negative results by IDNOW had a paired nasopharyngeal swab specimen collected in VTM and tested by the ACOV assay; SARS-CoV-2 RNA was detected in 13 (13.4%) of these specimens. Medical record review deemed all discrepant results to be true positives. The IDNOW test was the easiest to perform and provided a result in the shortest time, but detected fewer cases of COVID-19. The ACOV assay detected more cases of COVID-19 than CDC COV or IDNOW assays.
Accepted Manuscript Posted 27 May 2020, JCM; Final Article Posted 23 July 2020
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Letter to the Editor
Patients with Common Cold Coronaviruses Tested Negative for IgG Antibody to SARS-CoV-2
The need for accurate antibody testing in patients following symptomatic or asymptomatic infections with SARS-CoV-2 is well documented....
Accepted Manuscript Posted 27 May 2020, JCM; Final Article Posted 23 July 2020
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Research Article
Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens
Several point-of-care (POC) molecular tests have received emergency use authorization (EUA) from the Food and Drug Administration (FDA) for diagnosis of SARS-CoV-2. The test performance characteristics of the Accula (Mesa Biotech) SARS-CoV-2 POC test need to be evaluated to inform its optimal use.
Accepted Manuscript Posted 27 May 2020, JCM; Final Article Posted 23 July 2020
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Letter to the Editor
Test Agreement Between Roche Cobas 6800 and Cepheid GeneXpert Xpress SARS-CoV-2 Assays at High Cycle Threshold Ranges
The SARS-CoV-2 pandemic has changed the face of the globe and upended the daily lives of billions....
Accepted Manuscript Posted 22 May 2020, JCM; Final Article Posted 23 July 2020
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Letter to the Editor
COVID-19 Interference with Renin-Angiotensin System in the Context of Heart Failure
Novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (coronavirus disease 2019 [COVID-19] pandemic) attacks the host cells modulating the local renin-angiotensin (RAS) system....
22 May 2020, mBio
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Research Article
Antiviral Efficacies of FDA-Approved Drugs against SARS-CoV-2 Infection in Ferrets
The SARS-CoV-2 pandemic continues to spread worldwide, with rapidly increasing numbers of mortalities, placing increasing strain on health care systems. Despite serious public health concerns, no effective vaccines or therapeutics have been approved by regulatory agencies. In this study, we tested the FDA-approved drugs lopinavir-ritonavir, hydroxychloroquine sulfate, and emtricitabine-tenofovir against SARS-CoV-2 infection in a highly susceptible ferret infection model. While most of the drug treatments marginally reduced clinical symptoms, they did not reduce virus titers, with the exception of emtricitabine-tenofovir treatment, which led to diminished virus titers in nasal washes at 8 dpi. Further, the azathioprine-treated immunosuppressed ferrets showed delayed virus clearance and low SN titers, resulting in a prolonged infection. As several FDA-approved or repurposed drugs are being tested as antiviral candidates at clinics without sufficient information, rapid preclinical animal studies should proceed to identify therapeutic drug candidates with strong antiviral potential and high safety prior to a human efficacy trial.
22 May 2020, mBio
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Research Article
Replication of SARS-CoV-2 in human respiratory epithelium
SARS-CoV-2 emerged by the end of 2019 to rapidly spread in 2020. At present, it is of utmost importance to understand the virus biology and to rapidly assess the potential of existing drugs and develop new active compounds. While some animal models for such studies are under development, most of the research is carried out in the Vero E6 cells. Here, we propose fully differentiated human airway epithelium cultures as a model for studies on the SARS-CoV-2.
Accepted Manuscript Posted 20 May 2020, JVI; Final Article Posted 16 July 2020
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Letter to the Editor
Stability of SARS-CoV-2 in PBS for Molecular Detection
RNA viruses often require “cold-chains” of transportation to prevent the breakdown of genetic material....
Accepted Manuscript Posted 15 May 2020, JCM; Final Article Posted 23 July 2020
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Letter to the Editor
Saliva as an Alternate Specimen Source for Detection of SARS-CoV-2 in Symptomatic Patients Using Cepheid Xpert Xpress SARS-CoV-2
Among the many facets of the SARS-CoV-2 pandemic is the unprecedented pressure it has placed on different points of the supply chain for hospital systems worldwide such as collection devices for the diagnosis of COVID-19....
Accepted Manuscript Posted 15 May 2020, JCM; Final Article Posted 23 July 2020
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Genome Sequences
Complete Genome Sequences of SARS-CoV-2 Strains Detected in Malaysia
We sequenced four severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Malaysia during the second wave of infection and found unique mutations which suggest local evolution. Circulating Malaysian strains represent introductions from different countries, particularly during the first wave of infection. Genome sequencing is important for understanding local epidemiology.
14 May 2020, MRA
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Research Article
Bacteremia and Blood Culture Utilization During COVID-19 Surge in New York City
A surge of patients with coronavirus disease 2019 (COVID-19) presenting to New York City hospitals in March 2020 led to a sharp increase blood culture utilization, which overwhelmed the capacity of automated blood culture instruments. We sought to evaluate the utilization and diagnostic yield of blood cultures during the COVID-19 pandemic to determine prevalence and common etiologies of bacteremia, and to inform a diagnostic approach to relieve blood culture overutilization. We performed a retrospective cohort analysis of 88,201 blood cultures from 28,011 patients at a multicenter network of hospitals within New York City to evaluate order volume, positivity rate, time to positivity, and etiologies of positive cultures in COVID-19. Ordering volume increased by 34.8% in the second half of March 2020 compared to the first half of the month. The rate of bacteremia was significantly lower among COVID-19 patients (3.8%) than COVID-19 negative patients (8.0%) and those not tested (7.1%), p < 0.001. COVID-19 patients had a high proportion of organisms reflective of commensal skin microbiota, reducing the bacteremia rate to 1.6% when excluded. More than 98% of all positive cultures were detected within 4 days of incubation. Bloodstream infections are very rare for COVID-19 patients, which supports the judicious use of blood cultures in the absence of compelling evidence for bacterial co-infection. Clear communication with ordering providers is necessary to prevent overutilization of blood cultures during patient surges, and laboratories should consider shortening the incubation period from 5 days to 4 days, if necessary, to free additional capacity.
Accepted Manuscript Posted 13 May 2020, JCM; Final Article Posted 23 July 2020
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Research Article
Large-scale, in-house production of viral transport media to support SARS-CoV-2 PCR testing in a multi-hospital healthcare network during the COVID-19 pandemic
The COVID-19 pandemic has severely disrupted worldwide supplies of viral transport media (VTM) due to widespread demand for SARS-CoV-2 RT-PCR testing. In response to this ongoing shortage, we began production of VTM in-house in support of diagnostic testing in our hospital network. As our diagnostic laboratory was not equipped for reagent production, we took advantage of space and personnel that became available due to closure of the research division of our medical center. We utilized a formulation of VTM described by the CDC that was simple to produce, did not require filtration for sterilization, and used reagents that were available from commercial suppliers. Performance of VTM was evaluated by several quality assurance measures. Based on Ct values of spiking experiments, we found that our VTM supported highly consistent amplification of the SARS-CoV-2 target (coefficient of variation = 2.95%) using the Abbott RealTime SARS-CoV-2 EUA assay on the Abbott m2000 platform. VTM was also found to be compatible with multiple swab types and, based on accelerated stability studies, able to maintain functionality for at least four months at room temperature. We further discuss how we met logistical challenges associated with large-scale VTM production in a crisis setting including use of staged, assembly line for VTM transport tube production.
Accepted Manuscript Posted 13 May 2020, JCM; Final Article Posted 23 July 2020
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Letter to the Editor
Evaluation of a rapid diagnostic assay for detection of SARS CoV-2 antigen in nasopharyngeal swab
Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the virus causing causing Coronavirus disease 2019 (COVID-19) was reported for the first time in Wuhan (Hubei, China) in December 2019 (1, 2) and has become a major public health concern all over the world....
Accepted Manuscript Posted 13 May 2020, JCM; Final Article Posted 23 July 2020
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Research Article
Comparison of SARS-CoV-2 spike protein binding to ACE2 receptors from human, pets, farm animals, and putative intermediate hosts
SARS-CoV-2 is threatening people worldwide and there are no drugs or vaccines available to mitigate its spread. The origin of the virus is still unclear and whether pets and livestock can be infected and transmit SARS-CoV-2 are important and unknown scientific questions. Effective binding to the host receptor ACE2 is the first prerequisite for infection of cells and determines the host range. Our analysis provides a framework for the prediction of potential hosts of SARS-CoV-2. We found that ACE2 from species known to support SARS-CoV-2 infection tolerate many amino acid changes indicating that the species barrier might be low. An exception are dogs and especially pigs, which, however, revealed relatively low ACE2 expression levels in the respiratory tract. Monitoring of animals is necessary to prevent the generation of a new coronavirus reservoir. Finally, our analysis also showed that SARS-CoV-2 may not be specifically adapted to any of its putative intermediate hosts.
Accepted Manuscript Posted 13 May 2020, JVI; Final Article Posted 16 July 2020