Rare predicted loss-of-function variants of type I IFN immunity genes are associated with critical COVID-19 (preprint)

Background We previously reported inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity in 1-5% of unvaccinated patients with life-threatening COVID-19, and autoantibodies against type I IFN in another 15-20% of cases. Methods We report here a genome-wide rare variant burden association analysis in 3,269 unvaccinated patients with life-threatening COVID-19 (1,301 previously reported and 1,968 new patients), and 1,373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. A quarter of the patients tested had antibodies against type I IFN (234 of 928) and were excluded from the analysis. Results No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI:1.5-528.7, P=1.1x10-4), in analyses restricted to biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR=3.70 [95%CI:1.3-8.2], P=2.1x10-4). Adding the recently reported TYK2 COVID-19 locus strengthened this enrichment, particularly under a recessive model (OR=19.65 [95%CI:2.1-2635.4]; P=3.4x10-3). When these 14 loci and TLR7 were considered, all individuals hemizygous (n=20) or homozygous (n=5) for pLOF or bLOF variants were patients (OR=39.19 [95%CI:5.2-5037.0], P=4.7x10-7), who also showed an enrichment in heterozygous variants (OR=2.36 [95%CI:1.0-5.9], P=0.02). Finally, the patients 13 with pLOF or bLOF variants at these 15 loci were significantly younger (mean age [SD]=43.3 [20.3] years) than the other patients (56.0 [17.3] years; P=1.68x10-5). Conclusions Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie lifethreatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.

Multimodal deep learning for COVID-19 prognosis prediction in the emergency department: a bi-centric study. (preprint)

Clinical deterioration of COVID-19 patients is still a challenging event to predict in the emergency department (ED). The present study developed an artificial neural network using textual and tabular data from ED electronic medical reports. Predicted outcomes were 30-day mortality and ICU admission. Consecutive patients between February 20 and May 5, 2020, from Humanitas Research Hospital and San Raffaele Hospital, in the Milan area, were included. COVID-19 patients were 1296. Textual predictors were patient history, physical exam, and radiological reports. Tabular predictors were age, creatinine, C-reactive protein, hemoglobin, and platelet count. Tabular-textual model performance indices were compared to a model implementing only tabular data. For 30-day mortality, the combined model yielded slightly better performances than the tabular model, with AUC 0.84 ± 0.02, F-1 score 0.56 ± 0.04 and an MCC 0.44 ± 0.04. Tabular model performance was: AUC 0.84 ± 0.02, F-1 score 0.55 ± 0.03 and MCC 0.43 ± 0.04. As for ICU admission, the combined model was not superior to the tabular one.  The present data points to the effectiveness of a textual and tabular model for COVID-19 prognosis prediction. Also, it may support the ED physician in their decision-making process.

Salivary molecular testing for SARS-CoV-2: simplifying the diagnosis without losing accuracy (preprint)

Background Quantitative RT-PCR on NasoPharyngeal Swab (NPS) is still considered the standard for the diagnosis of SARS-CoV-2 infection, even if saliva has been evaluated in several studies as a possible alternative. The use of point of care (POC) platforms, providing highly specific results performed on saliva could simplify the diagnosis of COVID-19 and contribute to contain the spreading of SARS-CoV-2. Methods We assess the sensitivity and specificity of molecular testing performed on saliva in comparison to NPS using two different POC platforms (DiaSorin Simplexa™ and Cepheid Xpert®). NPS and saliva were collected prospectically from asymptomatic health care workers and mildly symptomatic patients. Moreover, the stability of saliva samples after storage at -80°C for up to 45 days was tested. Results The obtained results in comparison to NPS demonstrated for both DiaSorin Simplexa™ and Xpert® Xpress a specificity of 100% and a sensitivity of 90.24%. The overall agreement between the tests performed on saliva was 98%. A positive correlation in Ct values detected on saliva and on NPS was identified for all the targets shared by the tests in analysis (Orf1ab, E and N2). Both S Ct values and Orf1ab Ct values were not significantly different before and after the freezing in the tested saliva samples. Conclusion The obtained results demonstrated an overall performance of saliva comparable to NPS, confirming that RT-PCR performed using POCs on saliva could represent a valid public health solution for controlling SARS-CoV-2 pandemic.

Thromboembolism risk among patients with diabetes/stress hyperglycemia and COVID-19 (preprint)

A bstract Purpose Individuals with diabetes/stress hyperglycemia carry an increased risk for adverse clinical outcome in case of SARS-CoV-2 infection. The purpose of this study was to evaluate whether this risk is, at least in part, modulated by an increase of thromboembolic complications. Methods We prospectively followed 180 hospitalized patients with confirmed COVID-19 pneumonia admitted to the Internal Medicine Units of San Raffaele Hospital. Data from 11 out of 180 patients were considered incomplete and excluded from the analysis. We analysed inflammation, tissue damage biomarkers, hemostatic parameters, thrombotic events (TEs) and clinical outcome according to the presence of diabetes/stress hyperglycemia. Results Among 169 patients, 51 (30.2%) had diabetes/stress hyperglycemia. Diabetes/stress hyperglycemia and fasting blood glucose (FBG) were associated with increased inflammation and tissue damage circulating markers, higher D-dimer levels, increased prothrombin time and lower antithrombin III activity. Forty-eight venous and 10 arterial TEs were identified in 49 (29%) patients. Diabetes/stress hyperglycemia (HR 2.71, p=0.001), fasting blood glucose (HR 4.32, p<0.001) and glucose variability (HR 1.6, p < 0.009) were all associated with an increased risk of thromboembolic complication. TEs significantly increased the risk for an adverse clinical outcome only in the presence of diabetes/stress hyperglycemia (HR 3.05, p=0.01) or fasting blood glucose ≥ 7 mmol/l (HR 3.07, p=0.015). Conclusions Thromboembolism risk is higher among patients with diabetes/stress hyperglycemia and COVID-19 pneumonia and is associated to poor clinical outcome. In case of SARS-Cov-2 infection patients with diabetes/stress hyperglycemia could be considered for a more intensive prophylactic anticoagulation regimen.

Dysglyceamia after COVID-19 pneumonia: a six-month cohort study. (preprint)

Aim. The aim of this study was to understand whether the dysglyceamia associated with SARS-CoV-2 infection persists or reverts when the viral infection resolves. Methods. We analyzed fasting blood glucose (FBG) after hospital discharge in a cohort of 621 adult cases with suspected COVID-19 pneumonia. Results. At admission,, 18.8% of the patients in our cohort had pre-existing diabetes, 9.3% fasting glucose in the diabetes range without a prior diagnosis (DFG), 26% impaired fasting glucose (IFG), 44.9% normal fasting glucose (NFG), while 2% had no FBG available. FBG categories were similarly distributed in the 71 patients without confirmed COVID-19 pneumonia. During follow up (median time 6 month) FBG was available for 321 out of the 453 (70.9%) surviving patients and showed a trend to a marginal increase [from 97 (87–116) to 100 (92–114) mg/dL; p = 0.071]. Transitions between FBG categories was analysed in subjects without pre-existing diabetes (265 out of 321). We identified three groups: i) patients who maintained or improved FBG during follow-up [Group A, n = 185; from 100 (86–109) to 94 (88–99) mg/dL; p < 0.001]; ii) patients who moved from the NFG to IFG category [Group B, n = 66: from 89 (85–96) to 106 (102–113) mg/dl; p < 0.001]; iii) patients who maintained or reached DFG during follow-up [Group C, n = 14: from 114 (94–138) to 134 (126–143) mg/dl; p = 0.035]. Male sex and ICU admission during the hospitalization were more prevalent in Group C compared to Group A or B. Conclusions. Six months after the SARS-CoV-2 infection DFG was evident in only few patients who experienced severe COVID-19 pneumonia.

Interferon β-1a (IFNβ-1a) in COVID-19 patients (INTERCOP): study protocol for a randomized controlled trial. (preprint)

Background: Pharmacological therapies of proven efficacy in coronavirus disease 2019 (COVID-19) are still lacking. We have identified IFNβ-1a as the most promising drug to be repurposed for COVID-19. The rationale relies on the evidence of IFNβ anti-viral activity in vitro against SARS-CoV-2 and animal models resembling SARS-CoV-2 infection and on a recent clinical trial where IFNβ was indicated as the key component of a successful therapeutic combination. Methods: This is a randomized, controlled, open-label, monocentric, phase II trial (INTERCOP trial). 126 patients with positive swab detection of SARS-CoV-2, radiological signs of pneumonia, and mild-to-moderate disease will be randomized 2:1 to IFNβ-1a in addition to standard of care vs standard of care alone. No other anti-viral drugs will be used as part of the regimens, both in the control and the intervention arms. IFNβ-1a will be administered subcutaneously at the dose of 44 mcg (equivalent to 12 million international units) three times per week, at least 48 hours apart, for a total of two weeks. The primary outcome is the time to negative conversion of SARS-CoV-2 nasopharyngeal swabs. Secondary outcomes include improvement or worsening in a clinical severity score measured on a 7-point ordinal scale (including transfer to intensive care unit and death), oxygen- and ventilator-free days, mortality, changes in pulmonary computed tomography severity score, hospital stay duration, reduction of viral load measured on nasopharyngeal swabs, number of serious adverse events, changes in biochemical markers of organ dysfunction. Exploratory outcomes include blood cell counts, cytokine and inflammatory profile, peripheral mRNA expression profiles of interferon-stimulated genes, antibodies to SARS-CoV-2 and to IFNβ-1a. INTERCOP is the first study to specifically investigate the clinical benefits of IFNβ-1a in COVID-19 patients.Discussion: Potential implications of this trial are multifaceted: should the primary outcome be fulfilled and the treatment be safe, one may envisage that IFNβ-1a be used to reduce the infectivity of patients with mild-to moderate disease. In case IFNβ-1a reduced the duration of hospital stay and/or ameliorated the clinical status, it may become a cornerstone of COVID-19 treatment.Trial registration: EudraCT 2020-002458-25. Registered on May 11, 2020ClinicalTrials.gov Identifier: NCT04449380

Viral Clearance After Early Corticosteroid Treatment In Patients With Moderate Or Severe Covid-19 (preprint)

The aim of this study was to evaluate the impact of early treatment with corticosteroids on SARS-CoV-2 clearance in hospitalized COVID-19 patients.Retrospective analysis on patients admitted to the San Raffaele Hospital (Milan, Italy) with moderate/severe COVID-19 and availability of at least two nasopharyngeal swabs.The primary outcome was the time to nasopharyngeal swab negativization.A multivariable Cox model was fitted to determine factors associated with nasopharyngeal swab negativization.Of 280 patients included, 59 (21.1%) patients were treated with steroids.Differences observed between steroid users and non-users included the proportion of patients with a baseline PaO2/FiO2 ≤200 mmHg (45.8% vs 34.4% in steroids and non-steroids users, respectively; p=0.023) or ≤100 mmHg (16.9% vs 12.7%; p=0.027), and length of hospitalization (20 vs 14 days; p<0.001).Time to negativization of nasopharyngeal swabs was similar in steroid and non-steroid users (p=0.985).According to multivariate analysis, SARS-CoV-2 clearance was associated with age ≤70 years, a shorter duration of symptoms at admission, a baseline PaO2/FiO2 >200 mmHg, and a lymphocyte count at admission >1.0*109/L. SARS-CoV-2 clearance was not associated with corticosteroid use.Our study shows that delayed SARS-CoV-2 clearance in moderate/severe COVID-19 is associated with older age and a more severe disease, but not with early use of corticosteroids