The effect of early remdesivir administration in COVID-19 disease progression in hospitalised patients.

BACKGROUND: Antiviral drugs have become crucial in managing COVID-19, reducing complications and mortality. Remdesivir has emerged as an effective therapeutic drug for hospitalized patients at risk of disease progression, especially when alternative treatments are infeasible. While the recommended treatment duration of remdesivir extends up to 7 days post-symptom onset, this study examines how early remdesivir administration impacts clinical outcomes. METHODS: We conducted a retrospective analysis using clinical data from consecutively PCR confirmed SARS-CoV­2 adult patients (≥ 18 years) who received remdesivir during their hospitalization at the department of infectious diseases, Klinik Favoriten in Vienna. The data covered the period from July 1, 2021, to April 31, 2022. Patients were divided into two groups based on the timing of remdesivir administration: an early group (0-3 days since symptom onset) and a late group (≥ 4 days since symptom onset). The primary outcome was in-hospital disease progression, assessed using the WHO COVID-19 Clinical Progression Scale (≥ 1 point increase). Multivariable logistic regression, adjusted for age, sex, SARS-CoV­2 variant, and COVID-19 vaccination status, was used to assess clinical outcomes. RESULTS: In total 219 patients were included of whom 148 (67.6%) were in the early group and 71 (32.4%) were in the late group. The average age was 66.5 (SD: 18.0) years, 68.9% of the patients were vaccinated, and 72.6% had the Omicron virus variant. Late remdesivir administration was associated with a significantly higher probability of needing high-flow oxygen therapy (OR 2.52, 95% CI 1.40-4.52, p = 0.002) and ICU admission (OR 4.34, 95% CI 1.38-13.67, p = 0.012) after adjusting for confounders. In the late group there was a trend towards a higher risk of clinical worsening (OR 2.13, 95% CI 0.98-4.64, p = 0.056) and need for any oxygen therapy (OR 1.85, 95% CI 0.94-3.64, p = 0.074). CONCLUSION: Compared to patients who received remdesivir within the first 3 days after symptom onset, administering remdesivir after day 3 in hospitalized COVID-19 patients is associated with higher risk for complications, such as the need for high-flow oxygen therapy and ICU admission.

Genomic surveillance of SARS-CoV-2 evolution by a centralised pipeline and weekly focused sequencing, Austria, January 2021 to March 2023.

BackgroundThe COVID-19 pandemic was largely driven by genetic mutations of SARS-CoV-2, leading in some instances to enhanced infectiousness of the virus or its capacity to evade the host immune system. To closely monitor SARS-CoV-2 evolution and resulting variants at genomic-level, an innovative pipeline termed SARSeq was developed in Austria.AimWe discuss technical aspects of the SARSeq pipeline, describe its performance and present noteworthy results it enabled during the pandemic in Austria.MethodsThe SARSeq pipeline was set up as a collaboration between private and public clinical diagnostic laboratories, a public health agency, and an academic institution. Representative SARS-CoV-2 positive specimens from each of the nine Austrian provinces were obtained from SARS-CoV-2 testing laboratories and processed centrally in an academic setting for S-gene sequencing and analysis.ResultsSARS-CoV-2 sequences from up to 2,880 cases weekly resulted in 222,784 characterised case samples in January 2021-March 2023. Consequently, Austria delivered the fourth densest genomic surveillance worldwide in a very resource-efficient manner. While most SARS-CoV-2 variants during the study showed comparable kinetic behaviour in all of Austria, some, like Beta, had a more focused spread. This highlighted multifaceted aspects of local population-level acquired immunity. The nationwide surveillance system enabled reliable nowcasting. Measured early growth kinetics of variants were predictive of later incidence peaks.ConclusionWith low automation, labour, and cost requirements, SARSeq is adaptable to monitor other pathogens and advantageous even for resource-limited countries. This multiplexed genomic surveillance system has potential as a rapid response tool for future emerging threats.

Point-of-Care Method T2Bacteria®Panel Enables a More Sensitive and Rapid Diagnosis of Bacterial Blood Stream Infections and a Shorter Time until Targeted Therapy than Blood Culture.

BACKGROUND: Rapid diagnosis and identification of pathogens are pivotal for appropriate therapy of blood stream infections. The T2Bacteria®Panel, a culture-independent assay for the detection of Escherichia coli, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa in blood, was evaluated under real-world conditions as a point-of-care method including patients admitted to the internal medicine ward due to suspected blood stream infection. METHODS: Patients were assigned to two groups (standard of care-SOC vs. T2). In the SOC group 2 × 2 blood culture samples were collected, in the T2 group the T2Bacteria®Panel was performed additionally for pathogen identification. RESULTS: A total of 94 patients were included. Pathogens were detected in 19 of 50 patients (38%) in the T2 group compared to 16 of 44 patients (36.4%) in the SOC group. The median time until pathogen detection was significantly shorter in the T2 group (4.5 h vs. 60 h, p < 0.001), as well as the time until targeted therapy (antibiotic with the narrowest spectrum and maximal effectiveness) (6.4 h vs. 42.2 h, p = 0.043). CONCLUSIONS: The implementation of the T2Bacteria®Panel for patients with sepsis leads to an earlier targeted antimicrobial therapy resulting in earlier sufficient treatment and decreased excessive usage of broad-spectrum antimicrobials.

Is the T2MR Candida Panel a suitable alternative to the SeptiFast for the rapid diagnosis of candidemia in routine clinical practice?

OBJECTIVES: The diagnosis of invasive Candida infection remains challenging because of tests with slow turnaround times or mediocre performance. T2magnetic resonance imaging is a new diagnostic tool. We investigated the diagnostic accuracy of the T2Candida panel (T2) in comparison with blood culture (BC) and the SeptiFast (SF) for the detection of five different Candida species among high-risk intensive care unit patients with suspected candidemia. METHODS: We analysed blood samples collected from patients with suspected candidemia (177 samples from 138 patients) from August 2018 to April 2020. Blood samples were collected and analysed concurrently by BC, SF, and T2Candida. Subsequently, based on clinical and microbiological findings, patient samples were assigned to specific risk categories (proven, probable, and no candidemia). RESULTS: Twenty-two samples from 17 patients were classified as proven candidemia, and 15 samples from 14 patients were classified as probable candidemia. A sensitivity of 68.2% (95% CI, 45-86%) was observed for the BC and the SF, and a sensitivity of 63.6% (95% CI, 41-83%) was observed for the T2 when only cases with proven candidemia were evaluated. For proven and probable candidemia, the sensitivity was 40.5% (95% CI, 23-58%) for BC, 81.1% (95% CI, 65-92%) for SF, and 73.0% (95% CI, 56-86%) for T2. DISCUSSION: The diagnostic performance of SF and T2 was similar. For samples with proven/probable candidemia, SF and T2 had a higher sensitivity compared to BC. Used in conjunction with other diagnostic methods, T2 can replace the no longer available SF for the diagnosis of candidemia, enabling the timely initiation of targeted antifungal therapy.

Randomized controlled study to evaluate the safety and clinical impact of percutaneous auricular vagus nerve stimulation in patients with severe COVID-19.

Introduction: A severe course of COVID-19 is characterized by a hyperinflammatory state resulting in acute respiratory distress syndrome or even multi-organ failure along a derailed sympatho-vagal balance. Methods: In this prospective, randomized study, we evaluate the hypothesis that percutaneous minimally invasive auricular vagus nerve stimulation (aVNS) is a safe procedure and might reduce the rate of clinical complications in patients with severe course of COVID-19. In our study, patients with SARS-CoV-2 infection admitted to the intensive care unit with moderate-to-severe acute respiratory distress syndrome, however without invasive ventilation yet, were included and following randomization assigned to a group receiving aVNS four times per 24 h for 3 h and a group receiving standard of care (SOC). Results: A total of 12 patients were included (six in the aVNS and six in the SOC group). No side effects in aVNS were reported, especially no significant pain at device placement or during stimulation at the stimulation site or significant headache or bleeding after or during device placement or lasting skin irritation. There was no significant difference in the aVNS and SOC groups between the length of stay in the intensive care unit and at the hospital, bradycardia, delirium, or 90-day mortality. In the SOC group, five of six patients required invasive mechanical ventilation during their stay at hospital and 60% of them venovenous extracorporeal membrane oxygenation, compared to three of six patients and 0% in the aVNS group (p = 0.545 and p = 0.061). Discussion: Vagus nerve stimulation in patients with severe COVID-19 is a safe and feasible method. Our data showed a trend to a reduction of progression to the need of invasive ventilation and venovenous extracorporeal membrane oxygenation which encourages further research with larger patient samples.

Immunoglobulin G production in COVID-19 - associations with age, outcome, viral persistence, inflammation and pro-thrombotic markers.

Age represents the major risk factor for fatal disease outcome in coronavirus disease (COVID-19) due to age-related changes in immune responses. On the one hand lymphocyte counts continuously decline with advancing age, on the other hand somatic hyper-mutations of B-lymphocytes and levels of class-switched antibodies diminish, resulting in lower neutralizing antibody titers. To date the impact of age on immunoglobulin G (IgG) production in response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is unknown. Therefore, we investigated the impact of age on the onset of IgG production and its association with outcome, viral persistence, inflammatory and thrombotic markers in consecutive, hospitalized COVID-19 patients admitted to the Clinic Favoriten (Vienna, Austria) between April and October 2020 that fulfilled predefined inclusion criteria. Three different IgGs against SARS-CoV-2 (spike protein S1, nucleocapsid (NC), and the spike protein receptor binding domain (RBD)) were monitored in plasma of 97 patients upon admission and three times within the first week followed by weekly assessment during their entire hospital stay. We analyzed the association of clinical parameters including C-reactive protein (CRP), D-dimer levels and platelet count as well as viral persistence with the onset and concentration of different anti-SARS-CoV-2 specific IgGs. Our data demonstrate that in older individuals anti-SARS-CoV-2 IgG production increases earlier after symptom onset and that deceased patients have the highest amount of antibodies against SARS-CoV-2 whereas intensive care unit (ICU) survivors have the lowest titers. In addition, anti-SARS-CoV-2 IgG concentrations are not associated with curtailed viral infectivity, inflammatory or thrombotic markers, suggesting that not only serological memory but also other adaptive immune responses are involved in successful viral killing and protection against a severe COVID-19 infection.

Tocilizumab vs. baricitinib in hospitalized severe COVID-19 patients: results from a real-world cohort.

BACKGROUND: Tocilizumab and baricitinib are recommended treatment options for hospitalized COVID-19 patients requiring oxygen support. Literature about its efficacy and safety in a head-to-head comparison is scarce. METHODS: Hospitalized COVID-19 patients requiring oxygen were treated with tocilizumab or baricitinib additionally to dexamethasone. Tocilizumab was available from February till the 19th of September 2021 and baricitinib from 21st of September. The primary outcome was in-hospital mortality. Secondary outcome parameters were progression to mechanical ventilation (MV), length-of-stay (LOS) and potential side effects. RESULTS: 159 patients (tocilizumab 68, baricitinib 91) with a mean age of 60.5 years, 64% male were included in the study. Tocilizumab patients were admitted 1 day earlier, were in a higher WHO category at the time of inclusion and had a higher CRP level on admission and treatment initiation. Patients receiving Tocilizumab were treated with remdesivir more often and only patients in the baricitinib group were treated with monoclonal antibodies. Other characteristics did not differ significantly. In-hospital mortality (18% vs. 11%, p = 0.229), progression to MV (19% vs. 11%, p = 0.173) and LOS (13 vs. 12 days, p = 0.114) did not differ between groups. Side effects were equally distributed between groups, except ALAT elevation which was significantly more often observed in the tocilizumab group (43% vs. 25%, p = 0.021). CONCLUSIONS: In-hospital mortality, progression to MV and LOS were not significantly different in patients treated with tocilizumab or baricitinib additionally to standard of care. Both drugs seem equally effective but further head-to-head trials are needed.

The Role of Bacterial and Fungal Superinfection in Critical COVID-19.

BACKGROUND: The range of reported rates of bacterial and fungal superinfections in patients with a severe course of COVID-19 is wide, suggesting a lack of standardised reporting. METHODS: The rates of bacterial and fungal superinfection were assessed using predefined criteria to differentiate between infection and contamination. RESULTS: Overall, 117 patients admitted to the Intensive Care Unit due to severe COVID-19 were included. Overall, 55% of patients developed a superinfection and 13.6% developed a fungal superinfection (5.9% candidemia and 7.7% CAPA). The rate of ventilator-associated pneumonia was 65.2%. If superinfection was detected, the length of hospital stay was significantly longer and the mortality was especially increased if candidemia was detected. An increased risk of superinfection was observed in patients with pre-existing diabetes mellitus or chronic heart failure. The presence of immunomodulating therapy did not seem to have an impact on the frequency of superinfections. CONCLUSION: Increased awareness of high superinfection rates, fungal infections in particular, in patients suffering from severe COVID-19 is necessary.

Early administration of remdesivir may reduce mortality in hospitalized COVID-19 patients : A propensity score matched analysis.

BACKGROUND: Remdesivir is the only antiviral agent approved for the treatment of hospitalized coronavirus disease 2019 (COVID-19) patients requiring supplemental oxygen. Studies show conflicting results regarding its effect on mortality. METHODS: In this single center observational study, we included adult hospitalized COVID-19 patients. Patients who were treated with remdesivir were compared to controls. Remdesivir was administered for 5 days. To adjust for any imbalances in our cohort, a propensity score matched analysis was performed. The aim of our study was to analyze the effect of remdesivir on in-hospital mortality and length of stay (LOS). RESULTS: After propensity score matching, 350 patients (175 remdesivir, 175 controls) were included in our analysis. Overall, in-hospital mortality was not significantly different between groups remdesivir 5.7% [10/175] vs. control 8.6% [15/175], hazard ratio 0.50, 95% confidence interval (CI) 0.22-1.12, p = 0.091. Subgroup analysis showed a significant reduction of in-hospital mortality in patients who were treated with remdesivir ≤ 7 days of symptom onset remdesivir 4.2% [5/121] vs. control 10.4% [13/125], hazard ratio 0.26, 95% CI 0.09 to 0.75, p = 0.012 and in female patients remdesivir 2.9% [2/69] vs. control 12.2% [9/74], hazard ratio 0.18 95%CI 0.04 to 0.85, p = 0.03. Patients in the remdesivir group had a significantly longer LOS (11 days vs. 9 days, p = 0.046). CONCLUSION: Remdesivir did not reduce in-hospital mortality in our whole propensity score matched cohort, but subgroup analysis showed a significant mortality reduction in female patients and in patients treated within ≤ 7 days of symptom onset. Remdesivir may reduce mortality in patients who are treated in the early stages of illness.

Comparison of clinical characteristics among patients infected with alpha vs. delta SARS-CoV-2 variants.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone different molecular changes, sprouting genetic variants of the original wildtype. Clinical comparisons between patients infected with alpha versus delta are scarce. METHODS: In this retrospective observational study, adult patients hospitalized with coronavirus disease 2019 (COVID-19) due to confirmed SARS-CoV­2 alpha or delta infection were included. Patient characteristics, virologic and laboratory parameters, as well as the clinical course were compared in patients infected with alpha vs. delta variants. RESULTS: A total of 106 patients infected with alpha and 215 patients infected with delta were included. Patients infected with the delta variant were admitted to hospital earlier after symptom onset (6 vs. 7 days, p < 0.001). Blood levels of C­reactive protein (43.3 vs. 62.9 mg/l, p = 0.02) and neutrophil count (3.81 vs. 4.53 G/l, p = 0.06) were lower in delta patients. Furthermore, at hospital admission cycle threshold (CT) values were significantly lower in patients infected with the delta variant (22.3 vs. 24.9, p < 0.001). Patients infected with the delta variant needed supplemental oxygen less often during disease course (50% vs. 64%, p = 0.02). Furthermore, there was a statistically non-significant trend towards a lower ICU admission rate among delta patients (16% vs. 24%, p = 0.08) CONCLUSION: Patients diagnosed with the delta variant were admitted to the hospital earlier, had a less severe course of disease and a higher viral replication on admission. This may provide a window of opportunity for antivirals in the hospital setting.

Percutaneous Auricular Vagus Nerve Stimulation Reduces Inflammation in Critical Covid-19 Patients.

Covid-19 is an infectious disease associated with cytokine storms and derailed sympatho-vagal balance leading to respiratory distress, hypoxemia and cardiovascular damage. We applied the auricular vagus nerve stimulation to modulate the parasympathetic nervous system, activate the associated anti-inflammatory pathways, and reestablish the abnormal sympatho-vagal balance. aVNS is performed percutaneously using miniature needle electrodes in ear regions innervated by the auricular vagus nerve. In terms of a randomized prospective study, chronic aVNS is started in critical, but not yet ventilated Covid-19 patients during their stay at the intensive care unit. The results show decreased pro-inflammatory parameters, e.g. a reduction of CRP levels by 32% after 1 day of aVNS and 80% over 7 days (from the mean 151.9 mg/dl to 31.5 mg/dl) or similarly a reduction of TNFalpha levels by 58.1% over 7 days (from a mean 19.3 pg/ml to 8.1 pg/ml) and coagulation parameters, e.g. reduction of DDIMER levels by 66% over 7 days (from a mean 4.5 µg/ml to 1.5 µg/ml) and increased anti-inflammatory parameters, e.g. an increase of IL-10 levels by 66% over 7 days (from the mean 2.7 pg/ml to 7 pg/ml) over the aVNS duration without collateral effects. aVNS proved to be a safe clinical procedure and could effectively supplement treatment of critical Covid-19 patients while preventing devastating over-inflammation.

Rapid Detection of Bacterial and Fungal Pathogens Using the T2MR versus Blood Culture in Patients with Severe COVID-19.

A high rate of bacterial and fungal superinfections was reported in critically ill patients with COVID-19. However, diagnosis can be challenging. The aim of this study is to evaluate the sensitivity and the clinical utility of the point-of-care method T2 magnetic resonance (T2MR) with the gold standard: the blood culture. T2MR can potentially detect five different Candida species and six common bacteria (so-called "ESKAPE" pathogens including Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Acinet`obacter baumanii, Pseudomonas aeruginosa, and Enterococcus faecium). If superinfection was suspected in patients with COVID-19 admitted to the intensive care unit, blood culture and two panels of T2MR were performed. Eighty-five diagnostic bundles were performed in 60 patients in total. T2MR detected an ESKAPE pathogen in 9 out of 85 (10.6%) samples, compared to BC in 3 out of 85 (3.5%). A Candida species was detected in 7 of 85 (8.2%) samples of T2MR compared to 1 out of 85(1.2%) in blood culture. The mean time to positive test result in samples with concordant positive results was 4.5 h with T2MR and 52.5 h with blood culture. The additional use of T2MR enables a highly sensitive and rapid detection of ESKAPE and Candida pathogens. IMPORTANCE Coronavirus disease 2019 (COVID-19) has led to a high number of deaths since the beginning of the pandemic worldwide. One of the reasons is the high number of bacterial and fungal superinfections in patients suffering from critical disease. However, diagnosis is often challenging. In this study we could show that the additional use of the culture-independent method T2MR did not only show a much higher detection rate of bacterial and fungal pathogens but also a significantly shorter time until detection and therapy change compared to the gold standard: the blood culture. The implementation of T2MRin the care of patients with severe course of COVID-19 might lead to an earlier sufficient antimicrobial therapy and as a result lower mortality and less use of broad-spectrum unnecessary therapy reducing the risk of resistance development.

A Rapid, Highly Sensitive and Open-Access SARS-CoV-2 Detection Assay for Laboratory and Home Testing.

RT-qPCR-based diagnostic tests play important roles in combating virus-caused pandemics such as Covid-19. However, their dependence on sophisticated equipment and the associated costs often limits their widespread use. Loop-mediated isothermal amplification after reverse transcription (RT-LAMP) is an alternative nucleic acid detection method that overcomes these limitations. Here, we present a rapid, robust, and sensitive RT-LAMP-based SARS-CoV-2 detection assay. Our 40-min procedure bypasses the RNA isolation step, is insensitive to carryover contamination, and uses a colorimetric readout that enables robust SARS-CoV-2 detection from various sample types. Based on this assay, we have increased sensitivity and scalability by adding a nucleic acid enrichment step (Bead-LAMP), developed a version for home testing (HomeDip-LAMP), and identified open-source RT-LAMP enzymes that can be produced in any molecular biology laboratory. On a dedicated website, rtlamp.org (DOI: 10.5281/zenodo.6033689), we provide detailed protocols and videos. Our optimized, general-purpose RT-LAMP assay is an important step toward population-scale SARS-CoV-2 testing.

Evaluation of Five Commercial SARS-CoV-2 Antigen Tests in a Clinical Setting.

BACKGROUND: Point-of-care antigen tests (AgTs) for the detection of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) enable the rapid testing of infected individuals and are easy-to-use. However, there are few studies evaluating their clinical use. OBJECTIVE: The present study aimed to evaluate and compare the clinical performance characteristics of various commercial SARS-CoV-2 AgTs. DESIGN: The sensitivity of five AgTs, comprising four rapid antigen tests (RAT; AMP Rapid Test SARS-CoV-2 Ag, NADAL COVID-19 Antigen Rapid Test, CLINITEST Rapid COVID-19 Antigen Test, and Roche SARS-CoV-2 Rapid Antigen Test) and one sandwich chemiluminescence immunoassay (CLIA; LIAISON SARS-CoV-2 Assay), were evaluated in 300 nasopharyngeal (NP) swabs. Reverse transcriptase (RT) polymerase chain reaction (PCR) was used as a reference method. PARTICIPANTS: NP swabs were collected from patients admitted to hospital due to COVID-19. KEY RESULTS: Sensitivities of the AgTs ranged from 64.9 to 91.7% for samples with RT-PCR cycle threshold (Ct) values lower than 30 and were 100% for cycle threshold (Ct) values lower than 20. The highest sensitivity was observed for CLINITEST Rapid COVID-19 Antigen Test, and Roche SARS-CoV-2 rapid antigen test. Multivariate analysis using time from symptom onset and the Ct value for AgT sensitivity showed an inverse correlation. Further, the female sex was an independent factor of lower RAT sensitivity. CONCLUSIONS: Antigen tests from NP swab samples show high sensitivity in patients with a Ct value < 20. The best clinical sensitivity can be obtained using AgTs within the first 6 days after symptom onset.

Sensitivity and Specificity of SARS-CoV-2 Rapid Antigen Detection Tests Using Oral, Anterior Nasal, and Nasopharyngeal Swabs: a Diagnostic Accuracy Study.

The objective of our study was to evaluate the sensitivity and specificity of rapid antigen detection tests versus those of reverse transcriptase PCR (RT-PCR) using oral, anterior nasal, and nasopharyngeal swabs. The underlying prospective, diagnostic case-control-type accuracy study included 87 hospitalized and nonhospitalized participants in a positive and a negative sample cohort between 16 March and 14 May 2021 in two hospitals in Vienna. SARS-CoV-2 infection status was confirmed by RT-PCR. Participants self-performed one oral and one anterior nasal swab for the rapid antigen test, immediately followed by two nasopharyngeal swabs for the rapid antigen test and RT-PCR by the investigator. Test results were read after 15 min, and participants completed a questionnaire in the meantime. Test parameters were calculated based on the evaluation of 87 participants. The overall sensitivity of rapid antigen detection tests versus that of RT-PCR with oral, anterior nasal, and nasopharyngeal samples was 18.18% (95% confidence interval [CI] 8.19% to 32.71%), 63.04% (95% CI 47.55% to 76.79%), and 73.33% (95% CI 58.06% to 85.4%), respectively. All sampling methods had a test specificity of 100% regardless of the cycle threshold (CT) value. Rapid antigen detection tests using self-collected anterior nasal swabs proved to be as sensitive as and more tolerable than professionally collected nasopharyngeal swabs for CT values up to 30 determined by RT-PCR. This finding illustrates the reliability of tests obtained by adequate self-collected anterior nasal specimen. Sensitivity was dependent upon the CT value for each sampling method. While the main advantage of rapid antigen detection tests is the immediate availability of results, PCR should be preferred in crucial settings wherever possible. IMPORTANCE Rapid antigen detection devices for SARS-CoV-2 represent a valuable tool for monitoring the spread of infection. However, the reliability of the tests depends largely on the test performance and the respective sampling method. Nasopharyngeal swabs mark the gold standard for sample collection in suspected respiratory tract infections but are unsuitable for widespread application, as they must be performed by medically trained personnel. With the underlying study, the head-to-head test performance and the usability of self-collected samples for SARS-CoV-2 detection using rapid antigen detection devices were evaluated. The results confirm similar sensitivity of self-collected anterior nasal swabs to that of professionally collected nasopharyngeal swabs for patients with a CT of < 30 determined by RT-PCR.

Evaluation of RT-qPCR of mouthwash and buccal swabs for detection of SARS-CoV-2 in children and adults.

BACKGROUND: The use of nasopharyngeal (NP) swabs as a specimen collection method to diagnose SARS-CoV-2 infection is frequently perceived as uncomfortable by patients and requires trained personnel. In this study, detection rate of SARS-CoV-2 in mouthwash samples and buccal swabs were compared in both children and adults. MATERIAL AND METHODS: In patients admitted to hospital with confirmed COVID-19 within the previous 72 hours, NP and buccal swabs as well as mouthwash samples were collected. RT-qPCR was performed on all samples. RESULTS: In total, 170 samples were collected from 155 patients (137 adults and 18 children). Approximately 91.7% of the collected NP swabs were positive in RT-PCR compared to 63.1% of mouthwash samples and 42.4% of buccal swabs. Compared to NP swabs, the sensitivity of using mouthwash was 96.3% and 65.4% for buccal swabs in NP swab samples with a CT value <25. With increasing CT values, sensitivity decreased in both mouthwash and buccal swabs. The virus load was highest during the first week of infection, with a continuous decline observed in all three collection methods over time. DISCUSSION: Mouthwash presents an alternative collection method for detecting SARS-CoV-2 in the case of unfeasible NP swab sampling. Buccal swabs should not be used due to their low sensitivity.

Detection of bacteria via multiplex PCR in respiratory samples of critically ill COVID-19 patients with suspected HAP/VAP in the ICU.

BACKGROUND: Critically ill Coronavirus disease 2019 (COVID-19) patients have high rates of bacterial superinfection. Multiplex polymerase chain reaction panels may be able to provide useful information about the incidence and spectrum of bacteria causing superinfections. METHODS: In this retrospective observational study we included all COVID-19 positive patients admitted to our intensive care unit with suspected hospital-acquired pneumonia/ventilator-associated pneumonia (HAP/VAP) in whom the BioFire® Pneumonia Panel (PP) was performed from tracheal aspirate or bronchoalveolar lavage fluid for diagnostic purposes. The aim of our study was to analyze the spectrum of pathogens detected with the PP. RESULTS: In this study 60 patients with a median age of 62.5 years were included. Suspected VAP was the most frequent (48/60, 80%) indication for performing the PP. Tracheal aspirate was the predominant sample type (50/60, 83.3%). The PP led to a negative, monomicrobial and polymicrobial result in 36.7%, 35% and 28.3% of the patients, respectively. The three most detected bacteria were Staphylococcus aureus (13/60, 21.7%), Klebsiella pneumoniae (12/60, 20%) and Haemophilus influenzae (9/60, 15%). Neither atypical bacteria nor resistance genes were detected. Microbiological culture of respiratory specimens was performed in 36 (60%) patients concomitantly. The PP and microbiological culture yielded a non-concordant, partial concordant and completely concordant result in 13.9% (5/36), 30.6% (11/36) and 55.6% (20/36) of the analyzed samples, respectively. CONCLUSION: In critically ill COVID-19 patients with suspected HAP/VAP results of the PP and microbiological culture methods were largely consistent. In our cohort, S. aureus and K. pneumoniae were the most frequently detected organisms. A higher diagnostic yield may be achieved if both methods are combined.

Platelet Phenotype Analysis of COVID-19 Patients Reveals Progressive Changes in the Activation of Integrin αIIbß3, F13A1, the SARS-CoV-2 Target EIF4A1 and Annexin A5.

Background: The fatal consequences of an infection with severe acute respiratory syndrome coronavirus 2 are not only caused by severe pneumonia, but also by thrombosis. Platelets are important regulators of thrombosis, but their involvement in the pathogenesis of COVID-19 is largely unknown. The aim of this study was to determine their functional and biochemical profile in patients with COVID-19 in dependence of mortality within 5-days after hospitalization. Methods: The COVID-19-related platelet phenotype was examined by analyzing their basal activation state via integrin αIIbß3 activation using flow cytometry and the proteome by unbiased two-dimensional differential in-gel fluorescence electrophoresis. In total we monitored 98 surviving and 12 non-surviving COVID-19 patients over 5 days of hospital stay and compared them to healthy controls (n = 12). Results: Over the observation period the level of basal αIIbß3 activation on platelets from non-surviving COVID-19 patients decreased compared to survivors. In line with this finding, proteomic analysis revealed a decrease in the total amount of integrin αIIb (ITGA2B), a subunit of αIIbß3, in COVID-19 patients compared to healthy controls; the decline was even more pronounced for the non-survivors. Consumption of the fibrin-stabilizing factor coagulation factor XIIIA (F13A1) was higher in platelets from COVID-19 patients and tended to be higher in non-survivors; plasma concentrations of the latter also differed significantly. Depending on COVID-19 disease status and mortality, increased amounts of annexin A5 (ANXA5), eukaryotic initiation factor 4A-I (EIF4A1), and transaldolase (TALDO1) were found in the platelet proteome and also correlated with the nasopharyngeal viral load. Dysregulation of these proteins may play a role for virus replication. ANXA5 has also been identified as an autoantigen of the antiphospholipid syndrome, which is common in COVID-19 patients. Finally, the levels of two different protein disulfide isomerases, P4HB and PDIA6, which support thrombosis, were increased in the platelets of COVID-19 patients. Conclusion: Platelets from COVID-19 patients showed significant changes in the activation phenotype, in the processing of the final coagulation factor F13A1 and the phospholipid-binding protein ANXA5 compared to healthy subjects. Additionally, these results demonstrate specific alterations in platelets during COVID-19, which are significantly linked to fatal outcome.

Age Related Differences in Monocyte Subsets and Cytokine Pattern during Acute COVID-19-A Prospective Observational Longitudinal Study.

The COVID-19 pandemic drastically highlighted the vulnerability of the elderly population towards viral and other infectious threats, illustrating that aging is accompanied by dysregulated immune responses currently summarized in terms like inflammaging and immunoparalysis. To gain a better understanding on the underlying mechanisms of the age-associated risk of adverse outcome in individuals experiencing a SARS-CoV-2 infection, we analyzed the impact of age on circulating monocyte phenotypes, activation markers and inflammatory cytokines including interleukin 6 (IL-6), IL-8 and tumor necrosis factor (TNF) in the context of COVID-19 disease progression and outcome in 110 patients. Our data indicate no age-associated differences in peripheral monocyte counts or subset composition. However, age and outcome are associated with differences in monocyte activation status. Moreover, a distinct cytokine pattern of IL-6, IL-8 and TNF in elderly survivors versus non-survivors, which consolidates over the time of hospitalization, suggests that older patients with adverse outcomes experience an inappropriate immune response, reminiscent of an inflammaging driven immunoparalysis. Our study underscores the value, necessity and importance of longitudinal monitoring in elderly COVID-19 patients, as dynamic changes after symptom onset can be observed, which allow for a differentiated insight into confounding factors that impact the complex pathogenesis following an infection with SARS-CoV-2.

Adverse Outcome in COVID-19 Is Associated With an Aggravating Hypo-Responsive Platelet Phenotype.

Thromboembolic complications are frequently observed in Coronavirus disease 2019 (COVID-19). While COVID-19 is linked to platelet dysregulation, the association between disease outcome and platelet function is less clear. We prospectively monitored platelet activation and reactivity in 97 patients during the first week of hospitalization and determined plasma markers of platelet degranulation and inflammation. Adverse outcome in COVID-19 was associated with increased basal platelet activation and diminished platelet responses, which aggravated over time. Especially GPIIb/IIIa responses were abrogated, pointing toward impeded platelet aggregation. Moreover, platelet-leukocyte aggregate formation was diminished, pointing toward abrogated platelet-mediated immune responses in COVID-19. No general increase in plasma levels of platelet-derived granule components could be detected, arguing against platelet exhaustion. However, studies on platelets from healthy donors showed that plasma components in COVID-19 patients with unfavorable outcome were at least partly responsible for diminished platelet responses. Taken together this study shows that unfavorable outcome in COVID-19 is associated with a hypo-responsive platelet phenotype that aggravates with disease progression and may impact platelet-mediated immunoregulation.