COVID 19 Special Collection
COVID-19 (SARS-CoV-2) Special Collection
Latest COVID-19 Articles
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Minireview
Immunologic testing for SARS-CoV-2 infection from the antigen perspective
Coronavirus disease 2019 (COVID-19) caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally as a severe pandemic. SARS-CoV-2 infection stimulates antigen-specific antibody responses. Multiple serologic tests have been developed for SARS-CoV-2. However, which antigens are most suitable for serological testing remains poorly understood. Specifically, which antigens have the highest sensitivity and specificity for serological testing and which have the least cross-reactivity with other coronaviruses are currently unknown. Previous studies have shown that the S1 domain of the spike (S) protein has very low cross-reactivity between epidemic coronaviruses and common human coronaviruses, whereas the S2 domain of the S protein, and the nucleocapsid protein (N protein) show low-level cross-reactivity. Therefore, S1 is considered more specific than the native homotrimer of the S protein, and the receptor-binding domain as an antigen to test patient antibodies is more sensitive than the native N protein. In addition, an increasing number of studies have used multi-antigen protein arrays to screen serum from convalescent patients with COVID-19. Antigen combinations demonstrated improved performance as compared to each individual antigen. For rapid antigen detection, the sensitivity of the test is higher in the first week of onset of the disease with high viral loads. Highly sensitive and specific immunological diagnostic methods for antibodies or those that directly detect viral antigens in clinical samples would be beneficial for the rapid and accurate diagnosis of SARS-CoV-2 infection.
Accepted Manuscript Posted 14 December 2020, JCM
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Research Article
Analytical Sensitivity of the Abbott BinaxNOW COVID-19 Ag CARD
Multiple rapid antigen tests for SARS-CoV-2 have recently received Emergency Use Authorization (EUA) from the United States Food and Drug Administration (FDA). Although less sensitive than molecular detection methods, rapid antigen testing offers the potential for cheap, quick, decentralized testing. Robust analytical sensitivity data in comparison to qRT-PCR is currently lacking for many rapid antigen tests. Here, we evaluated the analytical sensitivity of Abbott BinaxNOW COVID-19 Ag CARD using SARS-CoV-2 positive clinical specimens quantified by RT-ddPCR and multiple FDA EUA qRT-PCR platforms using RNA standards. Initial and confirmatory limits of detection for the BinaxNOW COVID-19 Ag CARD were determined to be equivalent to 4.04 – 8.06x104 copies/swab. We further confirmed this limit of detection with 72 additional clinical samples positive for SARS-CoV-2 in either phosphate-buffered saline or viral transport media.100% of samples with viral loads >40,000 copies/swab were detected by rapid antigen testing. These data indicate that the BinaxNOW COVID-19 Ag CARD has the approximate analytical sensitivity equivalent to a generic qRT-PCR CT of 29-30.
Accepted Manuscript Posted 11 December 2020, JCM
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Research Article
Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects
The development of an effective and durable SARS-CoV-2 vaccine is essential for combating the growing COVID-19 pandemic. The SARS-CoV-2 spike (S) glycoprotein is the main target of neutralizing antibodies elicited during virus infection or following vaccination. Knowledge of the spike glycoprotein evolution, function and interactions with host factors will help researchers to develop effective vaccine immunogens and treatments. Here we identify key features of the spike glycoprotein, including the furin cleavage site and the D614G natural mutation, that modulate viral cytopathic effects, infectivity and sensitivity to inhibition. We also identify two inhibitors of host metalloproteases that block S-mediated cell-cell fusion, a process that contributes to the destruction of the virus-infected cell.
Accepted Manuscript Posted 11 December 2020, JVI
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Research Article
Stapled Peptides Based on Human Angiotensin-Converting Enzyme 2 (ACE2) Potently Inhibit SARS-CoV-2 Infection In Vitro
SARS-CoV-2 is a novel virus with many unknowns. No vaccine or specific therapy is available yet to prevent and treat this deadly virus. Therefore, there is an urgent need to develop novel therapeutics. Structural studies revealed critical interactions between the binding site helix of the ACE2 receptor and SARS-CoV-2 receptor-binding domain (RBD). Therefore, targeting the entry pathway of SARS-CoV-2 is ideal for both prevention and treatment as it blocks the first step of the viral life cycle. We report the design of four double-stapled peptides, three of which showed potent antiviral activity in HT1080/ACE2 cells and human lung carcinoma cells, A549/ACE2. Most significantly, the active stapled peptides with antiviral activity against SARS-CoV-2 showed high α-helicity (60 to 94%). The most active stapled peptide, NYBSP-4, showed substantial resistance to degradation by proteolytic enzymes in human plasma. The lead stapled peptides are expected to pave the way for further optimization of a clinical candidate.
11 December 2020, mBio
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Observation
Recombinant ACE2 Expression Is Required for SARS-CoV-2 To Infect Primary Human Endothelial Cells and Induce Inflammatory and Procoagulative Responses
SARS-CoV-2 infects pulmonary epithelial cells through ACE2 receptors and causes ARDS. COVID-19 causes progressive respiratory failure resulting from diffuse alveolar damage and systemic coagulopathy, thrombosis, and capillary inflammation that tie alveolar responses to EC dysfunction. This has prompted theories that SARS-CoV-2 directly infects ECs through ACE2 receptors, yet SARS-CoV-2 antigen has not been colocalized with ECs and prior studies indicate that ACE2 colocalizes with alveolar epithelial cells and vascular smooth muscle cells, not ECs. Here, we demonstrate that primary human ECs derived from lung, kidney, heart, brain, and umbilical veins require expression of recombinant ACE2 receptors in order to be infected by SARS-CoV-2. However, SARS-CoV-2 lytically infects ACE2-ECs and elicits procoagulative and inflammatory responses observed in COVID-19 patients. These findings suggest a novel mechanism of COVID-19 pathogenesis resulting from indirect EC activation, or infection of a small subset of ECs by an ACE2-independent mechanism, that transforms rationales and targets for therapeutic intervention.
11 December 2020, mBio
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Research Article
Multicenter Evaluation of the Clinical Performance and the Neutralizing Antibody Activity Prediction Properties of ten high throughput serological assays used in Clinical Laboratories
As the COVID-19 pandemic second wave is emerging, it is of the upmost importance to screen the population immunity in order to keep track of infected individuals. Consequently, SARS-CoV-2 immunoassays with high specificity and positive predictive values are needed to obtain an accurate epidemiological picture. As more data accumulate about the immune responses and the kinetics of neutralizing antibody (nAb) production in SARS-CoV-2 infected individuals, new applications are forecasted for serological assays such as nAb activity prediction in convalescent plasma from recovered patients. This multicenter study, involving six hospital centres, determined the baseline clinical performances, reproducibility and nAb level correlations of ten commercially available immunoassays. In addition, three lateral flow chromatography assays were evaluated as these devices can be used in logistically challenged area. All assays were evaluated using the same patient panels in duplicate thus enabling accurate comparison of the tests. Seven immunoassays examined in this study were shown to have excellent specificity (98 to 100%) and good to excellent positive predictive values (82 to 100%) when used in a low (5%) seroprevalence setting. We observed sensitivity values as low as 74% and as high as 95% at ≥15 days post symptom onset. The determination of optimized cut-off values through ROC curves analyses had a significant impact on the diagnostic resolution of several enzyme immunoassays by increasing the sensitivity significantly without a large trade-off in specificity. We found that Spike-based immunoassays seems to be better correlates of nAb activity. Finally, the results reported here will add up to the general knowledge of the inter-laboratory reproducibility of clinical performance parameters of immunoassays and provide new evidence about nAb activity prediction.
Accepted Manuscript Posted 10 December 2020, JCM
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Research Article
Variable sensitivity in molecular detection of SARS-CoV-2 in European Expert Laboratories: External Quality Assessment, June – July 2020
During the ongoing coronavirus disease 2019 (COVID-19) outbreak, robust detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key element for clinical management and to interrupt transmission chains. We organized an external quality assessment (EQA) of molecular detection of SARS-CoV-2 for European expert laboratories. An EQA panel composed of 12 samples, containing either SARS-CoV-2 at different concentrations to evaluate sensitivity or other respiratory viruses to evaluate specificity of SARS-CoV-2 testing, was distributed to 68 laboratories in 35 countries. Specificity samples included seasonal human coronaviruses hCoV-229E, hCoV-NL63 and hCoV-OC43, as well as MERS-CoV, SARS-CoV and human influenza virus A and B. Sensitivity was variable among laboratories, particularly for low concentration SARS-CoV-2 samples. Results indicated that performance was mostly independent of the selection of specific extraction or PCR methods.
Accepted Manuscript Posted 9 December 2020, JCM
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Research Article
Multi-center Evaluation of the Cepheid Xpert® Xpress SARS-CoV-2/Flu/RSV Test
With the approach of respiratory virus season in the Northern Hemisphere, clinical microbiology and public health laboratories will need rapid diagnostic assays to distinguish SARS-CoV-2 from influenza and respiratory syncytial virus (RSV) infections for diagnosis and surveillance. In this study, the clinical performance of the Xpert® Xpress SARS-CoV-2/Flu/RSV test (Cepheid, Sunnyvale, CA, USA) for nasopharyngeal swab specimens was evaluated in four centers: Johns Hopkins Medical Microbiology Laboratory, Northwell Health Laboratories, NYC Public Health Laboratory, and Los Angeles County/University of Southern California (LAC+USC) Medical Center. A total of 319 nasopharyngeal swab specimens, positive for SARS-CoV-2 (n = 75), influenza A (n = 65), influenza B (n = 50), RSV (n = 38), or negative (n = 91) by the standard of care nucleic acid amplification tests at each site were tested using the Cepheid panel test. The overall positive percent agreement for the SARS-CoV-2 target was 98.7% (n= 74/75) and the negative agreement was 100% (n= 91) with all other analytes showing 100% total agreement (n= 153). Standard of care tests to which the Cepheid panel was compared included the Cepheid Xpert Xpress SARS-CoV-2, Cepheid Xpert Xpress Flu/RSV, the GenMark ePlex respiratory panel, the BioFire Respiratory panels 2.1 and v1.7, the DiaSorin Simplexa COVID-19 Direct, and the Hologic Panther Fusion SARS-CoV-2 assays. The Xpert Xpress SARS-CoV-2/Flu/RSV test showed high sensitivity and accuracy for all analytes included in the test. This test will provide a valuable clinical diagnostic and public health solution for detecting and differentiating SARS-CoV-2, influenza A and B, and RSV infections during the current respiratory virus season.
Accepted Manuscript Posted 9 December 2020, JCM
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Research Article
A Fast and Accessible Method for the Isolation of RNA, DNA, and Protein to Facilitate the Detection of SARS-CoV-2
Management of the COVID-19 pandemic requires widespread SARS-CoV-2 testing. A main limitation for widespread SARS-CoV-2 testing is the global shortage of essential supplies, among these, RNA extraction kits. The need for commercial RNA extraction kits places a bottleneck on tests that detect SARS-CoV-2 genetic material, including PCR-based reference tests. Here we propose an alternative method we call PEARL (Precipitation Enhanced Analyte RetrievaL) that addresses this limitation. PEARL uses a lysis solution that disrupts cell membranes and viral envelopes while simultaneously providing conditions suitable for alcohol-based precipitation of RNA, DNA, and proteins. PEARL is a fast, low-cost, and simple method that uses common laboratory reagents and offers comparable performance to commercial RNA extraction kits. PEARL offers an alternative method to isolate host and pathogen nucleic acids and proteins to streamline the detection of DNA and RNA viruses, including SARS-CoV-2.
Accepted Manuscript Posted 8 December 2020, JCM
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Letter to the Editor
Favipiravir and the Need for Early Ambulatory Treatment of COVID-19
The commentary by McCullough emphasizes the urgent need for early ambulatory therapy of COVID-19 (1).…
Accepted Manuscript Posted 7 December 2020, AAC
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Letter to the Editor
Evidence-Based Guidelines Should Be Used to Inform COVID-19 Management
A recent commentary by McCullough (1) includes a recommended COVID treatment algorithm that is outdated and parts of which are contradicted by high quality trial data.…
Accepted Manuscript Posted 7 December 2020, AAC
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Research Article
Frequency of Positive Aspergillus Tests in COVID-19 Patients in Comparison to Other Patients with Pulmonary Infections Admitted to the ICU
The aim of this study was to describe the frequency of positive Aspergillus tests in COVID-19 patients and investigate the association between COVID-19 and a positive Aspergillus test result. We compared the proportion of positive Aspergillus tests in COVID-19 patients admitted to the ICU for > 24 hours with two control groups; patients with community acquired pneumonia with 1. a PCR confirmed influenza infection (considered as ‘positive’ control since the link between influenza and invasive aspergillosis has been established), and 2. Streptococcus pneumoniae pneumonia (in whom positive Aspergillus tests are mostly considered as colonisation). During the study period, 92 COVID-19 patients (mean age (SD) 62(14) years, 76.1% males), 48 influenza (55(14), 56.2% males), and 65 pneumococcal pneumonia (58 (15), 63,1% males) patients were identified. Any positive Aspergillus test from any respiratory sample was found in 10.9% of the COVID-19 patients, 6.2% of the patients with pneumococcal pneumonia and 22.9% of those infected with influenza. A positive culture or PCR or galactomannan test on bronchoalveolar lavage fluid (BAL) only was found in 5.4% of COVID-19 patients, which was lower than in patients with influenza (18.8%) and comparable to pneumococcal pneumonia group (4.6%). Using logistic regression analysis, the odds ratio, OR (95% CI) for a positive Aspergillus test on BAL fluid for COVID19 patients was 1.2 (0.3 to 5.1, p=0.8) compared to the pneumococcal pneumonia group while it was 0.2 (0.1 to 0.8, p=0.02) compared with influenza group. This difference remained significant when corrected for age and sex. In conclusion, in COVID19 patients, the prevalence of a positive aspergillus test was comparable to patients with admitted for pneumococcal pneumonia but substantially lower than what we observed in patients with influenza.
Accepted Manuscript Posted 4 December 2020, JCM
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Research Article
Identification of HLA-A*02:01-restricted candidate epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2 that may be natural targets of CD8+ T cell recognition in vivo
For the development of vaccines based on SARS-CoV-2-specific cytotoxic T lymphocytes (CTLs), we attempted to identify HLA-A*02:01-restricted CTL epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2. Out of 82 peptides predicted on bioinformatics, 54 peptides showed good binding affinities to HLA-A*02:01. Using HLA-A*02:01 transgenic mice, 18 in 54 peptides were found to be CTL epitopes in the intracellular cytokine staining assay. Out of 18 peptides, 10 peptides were chosen for the following analyses because of their high responses. To identify dominant epitopes, mice were immunized with liposomes containing the mixture of the 10 peptides. Some peptides were shown to be statistically predominant. Surprisingly, all immunized mice did not show the same reaction pattern to the 10 peptides. There were three reaction patterns, suggesting the existence of an immunodominance hierarchy following peptide vaccination, which may provide us more variations in the epitope selection for designing CTL-based COVID-19 vaccines.
Accepted Manuscript Posted 2 December 2020, JVI
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Research Article
The global and local distribution of RNA structure throughout the SARS-CoV-2 genome
The RNA genome of SARS-CoV-2 is among the largest and most complex viral genomes, and yet its RNA structural features remain relatively unexplored. Since RNA elements guide function in most RNA viruses, and they represent potential drug targets, it is essential to chart the architectural features of SARS-CoV-2 and pinpoint regions that merit focused study. Here we show that RNA folding stability of SARS-CoV-2 genome is exceptional among viral genomes and we develop a method to directly compare levels of predicted secondary structure across SARS-CoV-2 domains. Remarkably, we find that coding regions display the highest structural propensity in the genome, forming motifs that differ between the genomic and subgenomic contexts. Our approach provides an attractive strategy to rapidly screen for candidate structured regions based on base pairing potential and provides a readily interpretable roadmap to guide functional studies of RNA viruses and other pharmacologically relevant RNA transcripts.
Accepted Manuscript Posted 2 December 2020, JVI
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Research Article
Pooled Saliva Specimens for SARS-CoV-2 Testing
We evaluated saliva (SAL) specimens for SARS-CoV-2 RT-PCR testing by comparison of 459 prospectively paired nasopharyngeal (NP) or mid-turbinate (MT) swabs from 449 individuals with the aim of using saliva for asymptomatic screening. Samples were collected in a drive-through car line for symptomatic individuals (N=380) and in the emergency department (ED) (N=69). The percent positive and negative agreement of saliva compared to nasopharyngeal swab were 81.1% (95% CI: 65.8% – 90.5%) and 99.8% (95% CI: 98.7% – 100%), respectively. The percent positive agreement increased to 90.0% (95% CI: 74.4% – 96.5%) when considering only samples with moderate to high viral load (Cycle threshold (Ct) for the NP <=34). Pools of five saliva specimens were also evaluated on three platforms: bioMérieux NucliSENS easyMAG with ABI 7500Fast (CDC assay), Hologic Panther Fusion®, and Roche COBAS® 6800. The average loss of signal upon pooling was 2-3 Ct values across the platforms. The sensitivity of detecting a positive specimen in a pool compared with testing individually was 94%, 90%, and 94% for CDC 2019-nCoV Real-Time RT-PCR, Panther Fusion® SARS-CoV-2 assay, and cobas® SARS-CoV-2 test respectively, with decreased sample detection trending with lower viral load. We conclude that although pooled saliva testing, as collected in this study, is not quite as sensitive as NP/MT testing, saliva testing is adequate to detect individuals with higher viral loads in an asymptomatic screening program, does not require swabs or viral transport media for collection, and may help to improve voluntary screening compliance for those individuals averse to various forms of nasal collections.
Accepted Manuscript Posted 1 December 2020, JCM