COVID 19 Special Collection
COVID-19 (SARS-CoV-2) Special Collection
Latest COVID-19 Articles
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Research Article
Performance Characteristics of BinaxNOW COVID-19 Antigen Card for Screening Asymptomatic Individuals in a University Setting
We compared the performance of the Abbott BinaxNOW COVID-19 Antigen Card to a standard RT-PCR assay (ThermoFisher TaqPath COVID-19 Combo Kit) for the detection of SARS-CoV-2 in 2,645 asymptomatic students presenting for screening at the University of Utah. SARS-CoV-2 RNA was detected in 1.7% of the study participants by RT-PCR. BinaxNOW identified 24 infections but missed 21 infections that were detected by RT-PCR. The analytical sensitivity (positive agreement) and analytical specificity (negative agreement) for the BinaxNOW was 53.3% and 100%, respectively when compared against the RT-PCR assay. The median cycle threshold (Ct) value in the specimens that had concordant positive BinaxNOW antigen result was significantly lower compared to those that were discordant (Ct 17.6 vs. 29.6; p < 0.001). In individuals with presumably high viral loads (Ct < 23.0), a 95.8% positive agreement was observed between the RT-PCR assay and BinaxNOW. Due to the possibility of false negative results, caution must be taken when utilizing rapid antigen testing for screening asymptomatic individuals.
Accepted Manuscript Posted 28 January 2021, JCM; Final Article Posted 19 March 2021
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Genome Sequences
Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq
The coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an Iraqi patient was sequenced for the first-time using Illumina MiSeq technology. There was a D614G mutation in the spike protein-coding sequence. This report is valuable for better understanding the spread of the virus in Iraq.
28 January 2021, MRA
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Genome Sequences
Genome Sequences of 10 SARS-CoV-2 Viral Strains Obtained by Nanopore Sequencing of Nasopharyngeal Swabs in Malta
The genome sequences of 10 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains from Sliema, Malta, were obtained by Nanopore sequencing using the amplicon sequencing approach developed by the Artic Network. The assembled genomes were analyzed with Pangolin software and assigned to the B.1 lineage, which is widely circulating in Europe.
28 January 2021, MRA
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Genome Sequences
Genome Sequence of a SARS-CoV-2 VUI 202012/01 Strain Identified from a Patient Returning from London, England, to the Apulia Region of Italy
The coding-complete sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was obtained from a sample from a 25-year-old female returning to the Apulia region of Italy from England. The characterized strain showed all of the spike protein mutations defining SARS-CoV-2 VUI 202012/01, as well as other mutations in the spike protein and in other genomic regions.
28 January 2021, MRA
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Minireview
Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: A Systematic Review and Meta-analysis
Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval October 1st, 2020) for comparative studies of alternative specimen types [saliva, oropharyngeal (OP), and nasal (NS) swabs] versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in sub-groups. The QUADAS 2 tool was used to assess bias. From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives [NS (82%, 95% CI: 73-90%), OP (84%, 95% CI: 57-100%), saliva (88%, 95% CI: 81 – 93%)] than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90-100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield. NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric vs. adult, late vs. early in disease course) and head-to-head studies of sampling strategies are urgently needed.
Accepted Manuscript Posted 27 January 2021, JCM; Final Article Posted 20 April 2021
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Editorial
Is the patient infected with SARS-CoV-2?
The US Food and Drug Administration currently uses the nasopharyngeal swab specimen as the reference standard for evaluation of SARS-CoV-2 assays. We propose that the patient-infected status algorithm is a superior way to classify whether an individual is infected or not infected.
Accepted Manuscript Posted 26 January 2021, JCM; Final Article Posted 19 March 2021
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Research Article
Pooling of Nasopharyngeal (NP) Swab Samples to Overcome Global Shortage of rRT-PCR COVID-19 Test Kits
The global outbreak and rapid spread of SARS-CoV-2 created an urgent need for large scale testing of populations. There is a demand for high throughput testing protocols that can be used for efficient and rapid testing of clinical specimens. We evaluated a pooled-PCR protocol for testing nasopharyngeal swabs using known positive/negative and untested clinical samples that were assigned to pools of 5 or 10. Six-hundred and thirty (630) samples were used in this study. Individual positive samples with Ct values as high as 33 could be consistently detected when pooled with 4 negative samples (pool of 5) and individual positive samples with Ct values up to 31 could be consistently detected when pooled with 9 negative samples (pool of 10). Pooling of up to 5 samples can be employed in laboratories for the diagnosis of COVID-19 for efficient utilization of resources, rapid screening of a greater number of people, and faster reporting of test results.
Accepted Manuscript Posted 26 January 2021, JCM; Final Article Posted 19 March 2021
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Research Article
A New SARS CoV-2 Dual Purpose Serology Test: Highly Accurate Infection Tracing and Neutralizing Antibody Response Detection
Many SARS CoV-2 serology tests have proven to be less accurate than expected and do not assess antibody function as neutralizing, correlating with protection from reinfection. A new assay technology measuring the interaction of purified SARS CoV-2 spike protein receptor binding domain (RBD) with the extracellular domain of the human ACE2 receptor detects these important antibodies. This cPassTM surrogate virus neutralization test (sVNT) when compared directly with eight SARS CoV-2 IgG serology and two live cell neutralization tests gives similar or improved accuracy for qualitative delineation between positive and negative individuals in a fast, scalable and high throughput assay. The combined data support cPassTM sVNT as a tool for highly accurate SARS CoV-2 immunity surveillance of infected/recovered and/or vaccinated individuals, as well as drug and convalescent donor screening. The data also prevue a novel application for cPassTM sVNT in calibrating the stringency of live cell neutralization tests and its use in longitudinal testing of recovered and/or vaccinated patients.
Accepted Manuscript Posted 26 January 2021, JCM; Final Article Posted 19 March 2021
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Research Article
Time-evolution of SARS-CoV-2 in wastewater during the first pandemic wave of COVID-19 in the metropolitan area of Barcelona
Water-based epidemiology (WBE) is a valuable early warning tool for tracking the circulation of the virus among the population, including not only symptomatic patients, but also asymptomatic, presymptomatic and misdiagnosed carriers, which represent a high proportion of the infected population. In the specific case of Barcelona, wastewater surveillance anticipated several weeks not only the original COVID-19 pandemic wave, but also the onset of the second wave. In addition, SARS-CoV-2 occurrence in wastewater evidenced the efficacy of the adopted lockdown measures on the circulation of the virus.
Accepted Manuscript Posted 22 January 2021, AEM; Final Article Posted 11 March 2021
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Research Article
Quantitative measurement of anti-SARS-CoV-2 antibodies: Analytical and clinical evaluation
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus Disease 2019 (COVID-19). While molecular-based testing is used to diagnose COVID-19, serologic testing of antibodies specific to SARS-CoV-2 is used to detect past infection. While most serologic assays are qualitative, a quantitative serologic assay was recently developed that measures antibodies against the S protein, the target of vaccines. Quantitative antibody determination may help determine antibody titer, facilitate longitudinal monitoring of the antibody response, including antibody response to vaccines. We evaluated the quantitative Roche Elecsys® Anti-SARS-CoV-2 S assay. Specimens from 167 PCR-positive patients and 103 control specimens were analyzed using the Elecsys® Anti-SARS-CoV-2 S assay on the cobas e411 (Roche Diagnostics). Analytical evaluation included assessing linearity, imprecision, and analytical sensitivity. Clinical evaluation included assessing clinical sensitivity, specificity, cross-reactivity, positive predictive value (PPV), negative predictive value (NPV), and serial sampling from the same patient. The Elecsys® Anti-SARS-CoV-2 S assay exhibited highest sensitivity of 84.0% 15-30 days post-PCR positivity, no cross-reactivity, specificity and PPV of 100%, and NPV between 98.3%-99.8% ≥14 days post-PCR positivity, depending on the seroprevalence estimate. Imprecision was <2% at 9.06 U/mL across 6 days, the negative QC was consistently negative (<0.40 U/mL), the manufacturer’s claimed limit of quantitation of 0.40 U/mL was verified, and linearity across the analytical measuring range was observed, except at the low end (<20 U/mL). Lastly antibody response showed high inter-individual variation in level and time of peak antibody titre and trends over time.
Accepted Manuscript Posted 22 January 2021, JCM; Final Article Posted 19 March 2021
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Research Article
A Scalable, Easy-to-Deploy, Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic Material
The COVID-19 pandemic has created massive demand for widespread, distributed tools for detecting SARS-CoV-2 genetic material. The hurdles to scalable testing include reagent and instrument accessibility, availability of highly trained personnel, and large upfront investment. Here we showcase an orthogonal pipeline we call CREST (Cas13-based, Rugged, Equitable, Scalable Testing) that addresses some of these hurdles. Specifically, CREST pairs commonplace and reliable biochemical methods (PCR) with low-cost instrumentation, without sacrificing detection sensitivity. By taking advantage of simple fluorescence visualizers, CREST allows for a binary interpretation of results. CREST may provide a point-of-care solution to increase the distribution of COVID-19 surveillance.
Accepted Manuscript Posted 21 January 2021, JCM; Final Article Posted 19 March 2021
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Commentary
Lessons in public (mis)communication about the laboratory from the COVID-19 pandemic
The COVID-19 pandemic has put the clinical laboratory in the spotlight. The news media is regularly seeking out interviews with microbiologists, infectious disease specialists, and pathologists. Increased public exposure offers opportunities to improve how laboratory professionals communicate our insights. We can emphasize what is new, unusual, or controversial about our knowledge, utilize social media effectively, and improve relationships with journalists by understanding their workflow and traditions. While public engagement has risks and must be considerate of institutional policies, it also validates our value to patients, policy-makers, and employers.
Accepted Manuscript Posted 21 January 2021, JCM; Final Article Posted 19 March 2021
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Letter to the Editor
A novel point mutation in the N gene of SARS-CoV-2 may affect the detection of the virus by RT-qPCR
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, laboratory testing to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription PCR (RT-qPCR) has played a central role in mitigating the spread of the virus....
Accepted Manuscript Posted 20 January 2021, JCM; Final Article Posted 19 March 2021
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Research Article
Comparison of Subgenomic and Total RNA in SARS-CoV-2 Challenged Rhesus Macaques
Developing therapeutic and prophylactic countermeasures for the SARS-CoV-2 virus is a public health priority. During challenge studies, respiratory viruses are delivered and sampled from the same anatomical location. It is therefore important to distinguish actively replicating virus from input challenge virus. The most common assay for detecting SARS-CoV-2 virus, reverse transcription polymerase chain reaction (RT-PCR) targeting nucleocapsid total RNA, cannot distinguish neutralized input virus from replicating virus. In this study, we assess SARS-CoV-2 subgenomic RNA as a potential measure of replicating virus in rhesus macaques.
Accepted Manuscript Posted 20 January 2021, JVI
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Research Article
Interplay of Antibody and Cytokine Production Reveals CXCL13 as a Potential Novel Biomarker of Lethal SARS-CoV-2 Infection
The SARS-CoV-2 pandemic is continuing to impact the global population, and knowledge of the immune response to COVID-19 is still developing. This study assesses the interplay of different parts of the immune system during COVID-19 disease. We demonstrate that COVID-19 patients produce antibodies to three proteins of the COVID-19 virus (SARS-CoV-2) and identify many other immunological proteins that are involved during infection. The data suggest that one of these proteins (CXCL13) may be a novel biomarker for severe COVID-19 that can be readily measured in blood. This information combined with our broad-scale analysis of immune activity during COVID-19 provides new information on the immunological response throughout the course of disease and identifies a novel potential marker for assessing disease severity.
20 January 2021, mSphere