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BackgroundWhilst timely clinical characterisation of infections caused by novel SARS-CoV-2 variants is necessary for evidence-based policy response, individual-level data on infecting variants are typically only available for a minority of patients and settings. MethodsHere, we propose an innovative approach to study changes in COVID-19 hospital presentation and outcomes after the Omicron variant emergence using publicly available population-level data on variant relative frequency to infer SARS-CoV-2 variants likely responsible for clinical cases. We apply this method to data collected by a large international clinical consortium before and after the emergence of the Omicron variant in different countries. ResultsOur analysis, that includes more than 100,000 patients from 28 countries, suggests that in many settings patients hospitalised with Omicron variant infection less often presented with commonly reported symptoms compared to patients infected with pre-Omicron variants. Patients with COVID-19 admitted to hospital after Omicron variant emergence had lower mortality compared to patients admitted during the period when Omicron variant was responsible for only a minority of infections (odds ratio in a mixed-effects logistic regression adjusted for likely confounders, 0.67 [95% confidence interval 0.61 - 0.75]). Qualitatively similar findings were observed in sensitivity analyses with different assumptions on population-level Omicron variant relative frequencies, and in analyses using available individual-level data on infecting variant for a subset of the study population. ConclusionsAlthough clinical studies with matching viral genomic information should remain a priority, our approach combining publicly available data on variant frequency and a multi-country clinical characterisation dataset with more than 100,000 records allowed analysis of data from a wide range of settings and novel insights on real-world heterogeneity of COVID-19 presentation and clinical outcome.
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As the COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to spread around the globe, effective vaccination protocols are under deployment. Alternatively, the use of convalescent plasma (CP) therapy relies on the transfer of the immunoglobulin repertoire of a donor that has recovered from the disease as a means of passive vaccination. While the lack of an effective antiviral treatment inadvertently increases the interest in CP products, initial clinical evaluation on COVID-19 patients revealed that critical factors determining the outcome of CP therapy need to be defined clearly if clinical efficacy is to be expected. Measurement of neutralizing activity against SARS-CoV-2 using wildtype virus presents a reliable functional assay but the availability of suitable BSL3 facilities for virus culture restricts its applicability. Instead, the use of pseudovirus particles containing elements from the SARS-CoV-2 virus is widely applied to determine the activity of CP or other neutralizing agents such as monoclonal antibodies. In this study, we present our approach to optimize GFP-encoding lentiviral particles pseudotyped with the SARS-CoV-2 Spike and Membrane proteins for use in neutralization assays. Our results show the feasibility of pseudovirus production using a C-terminal truncated Spike protein which is greatly enhanced by the incorporation of the D614G mutation. Moreover, we report that the use of Sodium Butyrate during lentiviral vector production dramatically increases pseudovirus titers. Analysis of CP neutralizing activity against particles pseudotyped with wildtype or D614G mutant Spike protein in the presence or absence the M protein revealed differential activity in CP samples that did not necessarily correlate with the amount of anti-SARS-CoV-2 antibodies. Our results indicate that the extent of neutralizing activity in CP samples depends on the quality rather than the quantity of the humoral immune responses and varies greatly between donors. Functional screening of neutralizing activity using pseudovirus-based neutralization assays must be accepted as a critical tool for choosing CP donors if clinical efficacy is to be maximized.
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BackgroundCoronavirus disease 2019 (COVID-19) quickly spread worldwide to become a pandemic. This study aimed to define the predictors of critical illness development within 28 days postadmission. MethodsWe conducted a prospective cohort study including 477 PCR-positive COVID-19 patients admitted to a tertiary care hospital in Istanbul from March 12 to May 12, 2020. The development of critical illness, e.g., invasive mechanical ventilation and/or death, was followed for a period of 28 days postadmission. Demographic characteristics, number of comorbidities, illness severity at admission defined by the WHO scale, vital signs, laboratory findings and period of admission to the hospital were independent variables. Cox proportional hazards analysis was performed, and the C-index was calculated. ResultsThe median (IQR) age of the cohort was 55.0 (44.0-67.0) years, and 50.1% were male. The most common presenting symptoms were cough, dyspnea and fatigue. Overall, 65.2% of the patients had at least one comorbidity. Hydroxychloroquine was given to 99.2% of the patients. Critical illness developed in 45 (9.4%; 95% CI: 7.0%-12.4%) patients. In the multivariable analysis, age (HR: 1.05, p<0.001), number of comorbidities (HR: 1.33, p=0.02), procalcitonin [≥]0.25 {micro}g/L (HR: 2.12, p=0.03) and LDH [≥]350 U/L (HR: 2.04, p=0.03) were independently associated with critical illness development. The WHO scale on admission was the strongest predictor of critical illness (HR: 4.15, p<0.001). Prognosis improved within the study period (p<0.05). The C-index of the model was 0.92. ConclusionsAge, comorbidity number, WHO scale, LDH and procalcitonin were independently associated with critical illness development. Mortality from COVID-19 seems to be decreasing as the pandemic advances. summaryWe analyzed 477 confirmed COVID-19 patients for the development of critical illness, e.g., invasive mechanical ventilation and/or death within 28 days postadmission. Age, comorbidity number, WHO scale, LDH and procalcitonin were independently associated with critical illness development.
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A better understanding of the innate and adaptive cells in the COVID-19 disease caused by the SARS-CoV-2 coronavirus is a necessity for the development of effective treatment methods and vaccines. We studied phenotypic features of innate and adaptive immune cells, oxidative burst, phagocytosis and apoptosis. One hundred and three patients with COVID-19 grouped according to their clinical features as mild (35%), moderate (40.8%), and severe (24.3%) were included in the study. Monocytes from all COVID-19 patients were CD16+ pro-inflammatory monocytes. Neutrophils were mature and functional. No defect has been found in ROS production of monocytes and neutrophils as well as no defect in their apoptosis. As bridging cells of the innate and adaptive immune system; the percentage of NK cells was in normal range whereas the percentages of CD3-CD8+CD56+ innate lymphoid and CD3+CD56+ NK like T cells were found to be high in the severe cases of COVID-19. Although absolute numbers of all lymphocyte subsets were low and showed a tendency for a gradual decrease in accord with the disease progression, in all COVID-19 patients, the lymphocyte subset with the most decreased absolute number was B lymphocytes, followed by CD4 + T cells in the severe cases. The percentages of suppressive, CD3+CD4-CD8-; HLA-DR+CD3+ and CD28-CD8+ cells were found to be significantly increased. Importantly, we demonstrated spontaneous caspase-3 activation and increased lymphocyte apoptosis. Altogether our data suggest that SARS-CoV-2 primarily affects lymphocytes not innate cells. So that, it may interrupt the cross-talk between adaptive and innate immune systems.