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1.
Clin Infect Dis ; 74(3): 521-524, 2022 02 11.
Article in English | MEDLINE | ID: covidwho-1684544

ABSTRACT

During COVID-19 lockdown, the in-hospital number of HIV indicator conditions decreased disproportionally compared with other non-COVID-19 diseases, which was accompanied by reduced HIV testing rates, number and proportion of positive HIV tests, and new HIV referrals, with more late presentation after lockdown cessation, indicating a significantly impacted HIV care continuum.


Subject(s)
COVID-19 , HIV Infections , Communicable Disease Control , Continuity of Patient Care , HIV , HIV Infections/drug therapy , HIV Infections/epidemiology , Hospitals , Humans , SARS-CoV-2
2.
PLoS One ; 16(11): e0259165, 2021.
Article in English | MEDLINE | ID: covidwho-1581791

ABSTRACT

The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry (MS) based proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was estimated to be in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics.


Subject(s)
COVID-19/diagnosis , Proteomics , SARS-CoV-2/isolation & purification , Viral Proteins/isolation & purification , Animals , COVID-19/pathology , COVID-19/virology , Chlorocebus aethiops , Humans , Mass Spectrometry , Nucleocapsid/genetics , Nucleocapsid/isolation & purification , Phosphoproteins/genetics , Phosphoproteins/isolation & purification , Proteome/genetics , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , Sputum/virology , Vero Cells , Viral Proteins/genetics
3.
J Virol Methods ; 300: 114397, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1540816

ABSTRACT

Here we describe a SARS-CoV-2 variant with diminished amplification of the ORF ORF1ab target in the Cobas® dual-target SARS-CoV-2 assay resulting in a discrepancy of Ct-values (Ct-value 20.7 for the E-gene and Ct-value 30.2 for ORF1ab). Five unique nucleotide mutations were identified in ORF1ab: C11450A (nsp10) C14178T (RdRp), G15006T (RdRp), G18394T (Hel), and G20995T (Hel). This case highlights the importance of surveillance of genomic regions used in molecular diagnostics and the importance of the public release of target regions used to update commercial and in-house developed SARS-CoV-2 PCR tests. This work underpins the importance of using dual-targets in molecular diagnostic assays to limit the change of false-negative results due to primer and/or probe mismatches.


Subject(s)
COVID-19 , SARS-CoV-2 , Diagnostic Tests, Routine , Humans , RNA, Viral , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity
4.
Int J Infect Dis ; 107: 34-36, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1300796

ABSTRACT

This report describes the first heart transplantation recipient with acute biventricular heart failure symptoms caused by a post-myocarditis state, late after a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. No other viral pathogens could be detected. Computed tomography angiography did not show cardiac allograft vasculopathy, and myocardial biopsy demonstrated no clinically relevant rejection. Subsequent cardiovascular magnetic resonance imaging revealed extensive epicardial delayed enhancement without myocardial edema. Heart failure medication was initiated and an implantable cardioverter defibrillator was implanted (due to non-sustained ventricular tachycardias), leading to a partial recovery of the ejection fraction. Further studies are needed to investigate the number of heart transplant recipients with myocardial damage after a SARS-CoV-2 infection.


Subject(s)
COVID-19/complications , Heart Transplantation/adverse effects , Myocarditis/etiology , SARS-CoV-2 , Heart Failure/etiology , Humans , Middle Aged
5.
Nat Commun ; 12(1): 3189, 2021 05 27.
Article in English | MEDLINE | ID: covidwho-1246368

ABSTRACT

In a randomized clinical trial of 86 hospitalized COVID-19 patients comparing standard care to treatment with 300mL convalescent plasma containing high titers of neutralizing SARS-CoV-2 antibodies, no overall clinical benefit was observed. Using a comprehensive translational approach, we unravel the virological and immunological responses following treatment to disentangle which COVID-19 patients may benefit and should be the focus of future studies. Convalescent plasma is safe, does not improve survival, has no effect on the disease course, nor does plasma enhance viral clearance in the respiratory tract, influence SARS-CoV-2 antibody development or serum proinflammatory cytokines levels. Here, we show that the vast majority of patients already had potent neutralizing SARS-CoV-2 antibodies at hospital admission and with comparable titers to carefully selected plasma donors. This resulted in the decision to terminate the trial prematurely. Treatment with convalescent plasma should be studied early in the disease course or at least preceding autologous humoral response development.


Subject(s)
Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/immunology , COVID-19/therapy , Cytokines/blood , SARS-CoV-2/immunology , Aged , Antibodies, Neutralizing/blood , Antibodies, Viral/blood , Blood Donors , COVID-19/blood , COVID-19/virology , Disease Progression , Female , Hospitalization , Humans , Immunization, Passive , Immunoglobulin G/blood , Kaplan-Meier Estimate , Male , Middle Aged , Spike Glycoprotein, Coronavirus/immunology , Treatment Outcome
6.
J Infect Dis ; 223(9): 1512-1521, 2021 05 20.
Article in English | MEDLINE | ID: covidwho-1238201

ABSTRACT

Lower respiratory tract (LRT) disease induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can deteriorate to acute respiratory distress syndrome (ARDS). Because the release of neutrophil extracellular traps (NETs) is implicated in ARDS pathogenesis, we investigated the presence of NETs and correlates of pathogenesis in blood and LRT samples of critically ill patients with COVID-19. Plasma NET levels peaked early after intensive care unit admission and were correlated with the SARS-CoV-2 RNA load in sputum and levels of neutrophil-recruiting chemokines and inflammatory markers in plasma samples. The baseline plasma NET quantity was correlated with disease severity but was not associated with soluble markers of thrombosis or with development of thrombosis. High NET levels were present in LRT samples and persisted during the course of COVID-19, consistent with the detection of NETs in bronchi and alveolar spaces in lung tissue from deceased patient with COVID-19. Thus, NETs are produced and retained in the LRT of critically ill patients with COVID-19 and could contribute to SARS-CoV-2-induced ARDS disease.


Subject(s)
Bronchoalveolar Lavage Fluid/virology , COVID-19/complications , COVID-19/pathology , Extracellular Traps/virology , Respiratory Distress Syndrome/etiology , Respiratory Distress Syndrome/pathology , SARS-CoV-2 , Adult , Aged , Biomarkers , Chemokines/blood , Cohort Studies , Computed Tomography Angiography , Critical Illness , Enzyme-Linked Immunosorbent Assay , Female , Humans , Immunohistochemistry , Male , Middle Aged , Netherlands/epidemiology , Prospective Studies , Severity of Illness Index , Thrombosis/virology , Viral Load
7.
Nat Commun ; 12(1): 267, 2021 01 11.
Article in English | MEDLINE | ID: covidwho-1019818

ABSTRACT

Key questions in COVID-19 are the duration and determinants of infectious virus shedding. Here, we report that infectious virus shedding is detected by virus cultures in 23 of the 129 patients (17.8%) hospitalized with COVID-19. The median duration of shedding infectious virus is 8 days post onset of symptoms (IQR 5-11) and drops below 5% after 15.2 days post onset of symptoms (95% confidence interval (CI) 13.4-17.2). Multivariate analyses identify viral loads above 7 log10 RNA copies/mL (odds ratio [OR] of 14.7 (CI 3.57-58.1; p < 0.001) as independently associated with isolation of infectious SARS-CoV-2 from the respiratory tract. A serum neutralizing antibody titre of at least 1:20 (OR of 0.01 (CI 0.003-0.08; p < 0.001) is independently associated with non-infectious SARS-CoV-2. We conclude that quantitative viral RNA load assays and serological assays could be used in test-based strategies to discontinue or de-escalate infection prevention and control precautions.


Subject(s)
COVID-19/diagnosis , COVID-19/virology , SARS-CoV-2 , Virus Shedding , Aged , COVID-19 Testing , Female , Humans , Male , Middle Aged , Multivariate Analysis , Odds Ratio , RNA, Viral , Respiratory System/virology , Viral Load
9.
Nat Commun ; 11(1): 3436, 2020 07 06.
Article in English | MEDLINE | ID: covidwho-630511

ABSTRACT

The world is entering a new era of the COVID-19 pandemic in which there is an increasing call for reliable antibody testing. To support decision making on the deployment of serology for either population screening or diagnostics, we present a detailed comparison of serological COVID-19 assays. We show that among the selected assays there is a wide diversity in assay performance in different scenarios and when correlated to virus neutralizing antibodies. The Wantai ELISA detecting total immunoglobulins against the receptor binding domain of SARS CoV-2, has the best overall characteristics to detect functional antibodies in different stages and severity of disease, including the potential to set a cut-off indicating the presence of protective antibodies. The large variety of available serological assays requires proper assay validation before deciding on deployment of assays for specific applications.


Subject(s)
Antibodies, Viral/blood , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Serologic Tests/standards , Antibodies, Neutralizing/blood , Betacoronavirus , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques , Enzyme-Linked Immunosorbent Assay , High-Throughput Screening Assays , Humans , Luminescent Measurements , Neutralization Tests , Pandemics , SARS-CoV-2 , Sensitivity and Specificity
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