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2.
Vaccine ; 39(48): 6969-6971, 2021 11 26.
Article in English | MEDLINE | ID: covidwho-1550124
3.
J Med Virol ; 93(12): 6551-6556, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1530181

ABSTRACT

Lineage B.1.617+, also known as G/452R.V3 and now denoted by WHO with the Greek letters δ and κ, is a recently described SARS-CoV-2 variant under investigation first identified in October 2020 in India. As of May 2021, three sublineages labeled as B.1.617.1 (κ), B.1.617.2 (δ), and B.1.617.3 have been already identified, and their potential impact on the current pandemic is being studied. This variant has 13 amino acid changes, three in its spike protein, which are currently of particular concern: E484Q, L452R, and P681R. Here, we report a major effect of the mutations characterizing this lineage, represented by a marked alteration of the surface electrostatic potential (EP) of the receptor-binding domain (RBD) of the spike protein. Enhanced RBD-EP is particularly noticeable in the B.1.617.2 (δ) sublineage, which shows multiple replacements of neutral or negatively charged amino acids with positively charged amino acids. We here hypothesize that this EP change can favor the interaction between the B.1.617+ RBD and the negatively charged ACE2, thus conferring a potential increase in the virus transmission.


Subject(s)
COVID-19/virology , SARS-CoV-2/pathogenicity , COVID-19/transmission , Humans , Mutation , Protein Structure, Tertiary , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Static Electricity
4.
Medicine (Baltimore) ; 100(41): e27418, 2021 Oct 15.
Article in English | MEDLINE | ID: covidwho-1501202

ABSTRACT

ABSTRACT: The occurrence of COVID-19 pandemic had a significant negative effect on health care systems over the last year. Health care providers were forced to focus mainly on COVID-19 patients, neglecting in many cases equally important diseases, both acute and chronic. Therefore, also screening and diagnostic strategies for HIV could have been significantly impaired.This retrospective, multicenter, observational study aimed at assessing the number and characteristics of new HIV/AIDS diagnoses during COVID-19 pandemic in Italy and compared characteristics of people living with HIV at diagnosis between pre- and post-COVID-19 era (2019 vs 2020).Our results showed a significant reduction of HIV diagnoses during pandemic. By contrast, people living with HIV during pandemic were older and were diagnosed in earlier stage of disease (considering CD4+ T cell count) compared to those who were diagnosed the year before. Moreover, there was a significant decrease of new HIV diagnoses among men who have sex with men, probably for the impact of social distancing and restriction applied by the Italian Government. Late presentation incidence, if numbers in 2020 were lower than those in 2019, is still an issue.Routinely performing HIV testing in patients with suspected SARS-CoV-2 infection is identifying and linking to care underdiagnosed people living with HIV earlier. Thus, combined tests (HIV and SARS-CoV-2) should be implemented in patients with SARS-CoV-2 symptoms overlapping HIV's ones. Lastly, our results lastly showed how urgent implementation of a national policy for HIV screening is necessary.


Subject(s)
Delivery of Health Care/organization & administration , HIV Infections/epidemiology , Mass Screening/statistics & numerical data , Adult , CD4 Lymphocyte Count/statistics & numerical data , COVID-19/epidemiology , Cross-Sectional Studies , Female , HIV Infections/diagnosis , Humans , Italy/epidemiology , Male , Mass Screening/organization & administration , Middle Aged , Pandemics , Retrospective Studies , Risk Factors , SARS-CoV-2
5.
Sci Rep ; 11(1): 21136, 2021 10 27.
Article in English | MEDLINE | ID: covidwho-1493228

ABSTRACT

The COVID-19 pandemic is impressively challenging the healthcare system. Several prognostic models have been validated but few of them are implemented in daily practice. The objective of the study was to validate a machine-learning risk prediction model using easy-to-obtain parameters to help to identify patients with COVID-19 who are at higher risk of death. The training cohort included all patients admitted to Fondazione Policlinico Gemelli with COVID-19 from March 5, 2020, to November 5, 2020. Afterward, the model was tested on all patients admitted to the same hospital with COVID-19 from November 6, 2020, to February 5, 2021. The primary outcome was in-hospital case-fatality risk. The out-of-sample performance of the model was estimated from the training set in terms of Area under the Receiving Operator Curve (AUROC) and classification matrix statistics by averaging the results of fivefold cross validation repeated 3-times and comparing the results with those obtained on the test set. An explanation analysis of the model, based on the SHapley Additive exPlanations (SHAP), is also presented. To assess the subsequent time evolution, the change in paO2/FiO2 (P/F) at 48 h after the baseline measurement was plotted against its baseline value. Among the 921 patients included in the training cohort, 120 died (13%). Variables selected for the model were age, platelet count, SpO2, blood urea nitrogen (BUN), hemoglobin, C-reactive protein, neutrophil count, and sodium. The results of the fivefold cross-validation repeated 3-times gave AUROC of 0.87, and statistics of the classification matrix to the Youden index as follows: sensitivity 0.840, specificity 0.774, negative predictive value 0.971. Then, the model was tested on a new population (n = 1463) in which the case-fatality rate was 22.6%. The test model showed AUROC 0.818, sensitivity 0.813, specificity 0.650, negative predictive value 0.922. Considering the first quartile of the predicted risk score (low-risk score group), the case-fatality rate was 1.6%, 17.8% in the second and third quartile (high-risk score group) and 53.5% in the fourth quartile (very high-risk score group). The three risk score groups showed good discrimination for the P/F value at admission, and a positive correlation was found for the low-risk class to P/F at 48 h after admission (adjusted R-squared = 0.48). We developed a predictive model of death for people with SARS-CoV-2 infection by including only easy-to-obtain variables (abnormal blood count, BUN, C-reactive protein, sodium and lower SpO2). It demonstrated good accuracy and high power of discrimination. The simplicity of the model makes the risk prediction applicable for patients in the Emergency Department, or during hospitalization. Although it is reasonable to assume that the model is also applicable in not-hospitalized persons, only appropriate studies can assess the accuracy of the model also for persons at home.


Subject(s)
COVID-19/mortality , Machine Learning , Pandemics , SARS-CoV-2 , Aged , Aged, 80 and over , Blood Cell Count , Blood Chemical Analysis , COVID-19/blood , Cohort Studies , Female , Hospital Mortality , Humans , Male , Middle Aged , Models, Statistical , Multivariate Analysis , Oxygen/blood , Pandemics/statistics & numerical data , ROC Curve , Risk Factors , Rome/epidemiology
6.
Biomolecules ; 11(10)2021 10 10.
Article in English | MEDLINE | ID: covidwho-1463549

ABSTRACT

Among the more recently identified SARS-CoV-2 Variants of Interest (VOI) is the Lambda variant, which emerged in Peru and has rapidly spread to South American regions and the US. This variant remains poorly investigated, particularly regarding the effects of mutations on the thermodynamic parameters affecting the stability of the Spike protein and its Receptor Binding Domain. We report here an in silico study on the potential impact of the Spike protein mutations on the immuno-escape ability of the Lambda variant. Bioinformatics analysis suggests that a combination of shortening the immunogenic epitope loops and the generation of potential N-glycosylation sites may be a viable adaptation strategy, potentially allowing this emerging viral variant to escape from host immunity.


Subject(s)
Epitopes/genetics , SARS-CoV-2/genetics , Epitopes/immunology , Humans , SARS-CoV-2/immunology
7.
EClinicalMedicine ; 27: 100553, 2020 Oct.
Article in English | MEDLINE | ID: covidwho-1385448

ABSTRACT

Background: Interleukin-6 signal blockade showed preliminary beneficial effects in treating inflammatory response against SARS-CoV-2 leading to severe respiratory distress. Herein we describe the outcomes of off-label intravenous use of Sarilumab in severe SARS-CoV-2-related pneumonia. Methods: 53 patients with SARS-CoV-2 severe pneumonia received intravenous Sarilumab; pulmonary function improvement or Intensive Care Unit (ICU) admission rate in medical wards, live discharge rate in ICU treated patients and safety profile were recorded. Sarilumab 400 mg was administered intravenously on day 1, with eventual additional infusion based on clinical judgement, and patients were followed for at least 14 days, unless previously discharged or dead. Findings: Of the 53 SARS-CoV-2pos patients receiving Sarilumab, 39(73·6%) were treated in medical wards [66·7% with a single infusion; median PaO2/FiO2:146(IQR:120-212)] while 14(26·4%) in ICU [92·6% with a second infusion; median PaO2/FiO2: 112(IQR:100-141.5)].Within the medical wards, 7(17·9%) required ICU admission, 4 of whom were re-admitted to the ward within 5-8 days. At 19 days median follow-up, 89·7% of medical inpatients significantly improved (46·1% after 24 h, 61·5% after 3 days), 70·6% were discharged from the hospital and 85·7% no longer needed oxygen therapy. Within patients receiving Sarilumab in ICU, 64·2% were discharged from ICU to the ward and 35·8% were still alive at the last follow-up. Overall mortality rate was 5·7%. Interpretation: IL-6R inhibition appears to be a potential treatment strategy for severe SARS-CoV-2 pneumonia and intravenous Sarilumab seems a promising treatment approach showing, in the short term, an important clinical outcome and good safety.

9.
Commun Biol ; 4(1): 489, 2021 04 21.
Article in English | MEDLINE | ID: covidwho-1387493

ABSTRACT

We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulation of multiple SARS-CoV-2 lineages over time, which were linked to multiple importations and characterized by large transmission clusters concomitant with a high number of infections. Subsequent implementation of a three-phase nationwide lockdown strategy greatly reduced infection numbers and hospitalizations. Yet we present evidence of sustained viral spread among sporadic clusters acting as "hidden reservoirs" during summer 2020. Mathematical modelling shows that increased mobility among residents eventually catalyzed the coalescence of such clusters, thus driving up the number of infections and initiating a new epidemic wave. Our results suggest that the efficacy of public health interventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.


Subject(s)
COVID-19/transmission , Communicable Disease Control/methods , Genome, Viral/genetics , Mutation , Public Health/methods , SARS-CoV-2/genetics , COVID-19/epidemiology , COVID-19/virology , Geography , Humans , Italy/epidemiology , Pandemics , Phylogeny , Public Health/trends , SARS-CoV-2/classification , SARS-CoV-2/physiology
10.
J Healthc Eng ; 2021: 5556207, 2021.
Article in English | MEDLINE | ID: covidwho-1314165

ABSTRACT

The efficacy of hydroxychloroquine (HCQ) in treating SARS-CoV-2 infection is harshly debated, with observational and experimental studies reporting contrasting results. To clarify the role of HCQ in Covid-19 patients, we carried out a retrospective observational study of 4,396 unselected patients hospitalized for Covid-19 in Italy (February-May 2020). Patients' characteristics were collected at entry, including age, sex, obesity, smoking status, blood parameters, history of diabetes, cancer, cardiovascular and chronic pulmonary diseases, and medications in use. These were used to identify subtypes of patients with similar characteristics through hierarchical clustering based on Gower distance. Using multivariable Cox regressions, these clusters were then tested for association with mortality and modification of effect by treatment with HCQ. We identified two clusters, one of 3,913 younger patients with lower circulating inflammation levels and better renal function, and one of 483 generally older and more comorbid subjects, more prevalently men and smokers. The latter group was at increased death risk adjusted by HCQ (HR[CI95%] = 3.80[3.08-4.67]), while HCQ showed an independent inverse association (0.51[0.43-0.61]), as well as a significant influence of cluster∗HCQ interaction (p < 0.001). This was driven by a differential association of HCQ with mortality between the high (0.89[0.65-1.22]) and the low risk cluster (0.46[0.39-0.54]). These effects survived adjustments for additional medications in use and were concordant with associations with disease severity and outcome. These findings suggest a particularly beneficial effect of HCQ within low risk Covid-19 patients and may contribute to clarifying the current controversy on HCQ efficacy in Covid-19 treatment.


Subject(s)
Antimalarials/adverse effects , Antimalarials/therapeutic use , COVID-19/drug therapy , COVID-19/mortality , Hospital Mortality , Hydroxychloroquine/adverse effects , Hydroxychloroquine/therapeutic use , Aged , Aged, 80 and over , COVID-19/physiopathology , Cluster Analysis , Female , Humans , Italy , Male , Middle Aged , Retrospective Studies , SARS-CoV-2/drug effects , Severity of Illness Index , Treatment Outcome
11.
Front Med (Lausanne) ; 8: 639970, 2021.
Article in English | MEDLINE | ID: covidwho-1285307

ABSTRACT

Background: Protease inhibitors have been considered as possible therapeutic agents for COVID-19 patients. Objectives: To describe the association between lopinavir/ritonavir (LPV/r) or darunavir/cobicistat (DRV/c) use and in-hospital mortality in COVID-19 patients. Study Design: Multicenter observational study of COVID-19 patients admitted in 33 Italian hospitals. Medications, preexisting conditions, clinical measures, and outcomes were extracted from medical records. Patients were retrospectively divided in three groups, according to use of LPV/r, DRV/c or none of them. Primary outcome in a time-to event analysis was death. We used Cox proportional-hazards models with inverse probability of treatment weighting by multinomial propensity scores. Results: Out of 3,451 patients, 33.3% LPV/r and 13.9% received DRV/c. Patients receiving LPV/r or DRV/c were more likely younger, men, had higher C-reactive protein levels while less likely had hypertension, cardiovascular, pulmonary or kidney disease. After adjustment for propensity scores, LPV/r use was not associated with mortality (HR = 0.94, 95% CI 0.78 to 1.13), whereas treatment with DRV/c was associated with a higher death risk (HR = 1.89, 1.53 to 2.34, E-value = 2.43). This increased risk was more marked in women, in elderly, in patients with higher severity of COVID-19 and in patients receiving other COVID-19 drugs. Conclusions: In a large cohort of Italian patients hospitalized for COVID-19 in a real-life setting, the use of LPV/r treatment did not change death rate, while DRV/c was associated with increased mortality. Within the limits of an observational study, these data do not support the use of LPV/r or DRV/c in COVID-19 patients.

12.
Pathog Glob Health ; 115(7-8): 456-466, 2021.
Article in English | MEDLINE | ID: covidwho-1269474

ABSTRACT

Background: Hydroxychloroquine (HCQ) was proposed as potential treatment for COVID-19, but its association with mortality is unclear. We reviewed published literature for evidence of an association between HCQ (with or without azithromycin (AZM)) and total mortality in COVID-19 patients.Methods: Articles were retrieved until April 29th, 2021 by searching in seven databases. Data were combined using the general-variance-based method.Results: A total of 25 cohort studies (N=41,339 patients) and 11 randomized clinical trials (RCTs; N=8,709) were found. The use of HCQ was not associated with mortality in meta-analysis of RCTs (pooled risk ratio (PRR): 1.08, 95%CI: 0.97-1.20; I2=0%), but it was associated with 20% lower mortality risk (PRR=0.80, 95%CI: 0.69-0.93; I2=80%) in pooling of cohort studies. The negative association with mortality was mainly apparent by pooling cohort studies that used lower doses of HCQ (≤400 mg/day; PRR=0.69, 95%CI: 0.57-0.87). Use of HCQ+AZM (11 studies) was associated with 25% non-statistically significant lower mortality risk (PPR=0.75; 0.51-1.10; P=0.15). Use of HCQ was not associated with severe adverse events (PRR=1.12, 95%CI: 0.88-1.44; I2=0%).Conclusions: HCQ use was not associated with mortality in COVID-19 patients in pooling results from RCTs (high level of certainty of evidence), but it was associated with 20% mortality reduction when findings from observational studies were combined (low level of certainty of evidence). The reduction of mortality was mainly apparent in observational studies where lower doses of HCQ were used. These findings might help disentangling the debate on HCQ use in COVID-19.

13.
Thromb Haemost ; 121(8): 1054-1065, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1112023

ABSTRACT

INTRODUCTION: A hypercoagulable condition was described in patients with coronavirus disease 2019 (COVID-19) and proposed as a possible pathogenic mechanism contributing to disease progression and lethality. AIM: We evaluated if in-hospital administration of heparin improved survival in a large cohort of Italian COVID-19 patients. METHODS: In a retrospective observational study, 2,574 unselected patients hospitalized in 30 clinical centers in Italy from February 19, 2020 to June 5, 2020 with laboratory-confirmed severe acute respiratory syndrome coronavirus-2 infection were analyzed. The primary endpoint in a time-to event analysis was in-hospital death, comparing patients who received heparin (low-molecular-weight heparin [LMWH] or unfractionated heparin [UFH]) with patients who did not. We used multivariable Cox proportional-hazards regression models with inverse probability for treatment weighting by propensity scores. RESULTS: Out of 2,574 COVID-19 patients, 70.1% received heparin. LMWH was largely the most used formulation (99.5%). Death rates for patients receiving heparin or not were 7.4 and 14.0 per 1,000 person-days, respectively. After adjustment for propensity scores, we found a 40% lower risk of death in patients receiving heparin (hazard ratio = 0.60; 95% confidence interval: 0.49-0.74; E-value = 2.04). This association was particularly evident in patients with a higher severity of disease or strong coagulation activation. CONCLUSION: In-hospital heparin treatment was associated with a lower mortality, particularly in severely ill COVID-19 patients and in those with strong coagulation activation. The results from randomized clinical trials are eagerly awaited to provide clear-cut recommendations.


Subject(s)
Anticoagulants/therapeutic use , COVID-19/complications , Heparin, Low-Molecular-Weight/therapeutic use , Heparin/therapeutic use , Thrombophilia/etiology , Thrombophilia/prevention & control , Aged , Blood Coagulation/drug effects , COVID-19/blood , COVID-19/drug therapy , Female , Hospital Mortality , Humans , Italy/epidemiology , Male , Middle Aged , Retrospective Studies , Survival Analysis , Thrombophilia/blood
15.
J Med Virol ; 92(10): 2232-2237, 2020 10.
Article in English | MEDLINE | ID: covidwho-935129

ABSTRACT

Italy is the first western country suffering heavy severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and disease impact after coronavirus disease-2019 pandemia started in China. Even though the presence of mutations on spike glycoprotein and nucleocapsid in Italian isolates has been reported, the potential impact of these mutations on viral transmission has not been evaluated. We have compared SARS-CoV-2 genome sequences from Italian patients with virus sequences from Chinese patients. We focussed upon three nonsynonymous mutations of genes coding for S(one) and N (two) viral proteins present in Italian isolates and absent in Chinese ones, using various bioinformatics tools. Amino acid analysis and changes in three-dimensional protein structure suggests the mutations reduce protein stability and, particularly for S1 mutation, the enhanced torsional ability of the molecule could favor virus binding to cell receptor(s). This theoretical interpretation awaits experimental and clinical confirmation.


Subject(s)
COVID-19/epidemiology , COVID-19/transmission , Coronavirus Nucleocapsid Proteins/chemistry , Genome, Viral , Pandemics , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/chemistry , Amino Acid Substitution , COVID-19/pathology , COVID-19/virology , China/epidemiology , Coronavirus Nucleocapsid Proteins/genetics , Evolution, Molecular , Humans , Italy/epidemiology , Models, Molecular , Molecular Epidemiology , Mutation , Phosphoproteins/chemistry , Phosphoproteins/genetics , Phylogeny , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , SARS-CoV-2/classification , Severity of Illness Index , Spike Glycoprotein, Coronavirus/genetics , Travel , Virus Replication
16.
Preprint | SSRN | ID: ppcovidwho-748

ABSTRACT

Background: SARS-2-CoV is a new coronavirus that has spread globally, infecting more than 150000 people, and being declared pandemic by the WHO. We provide here

17.
J Patient Saf ; 16(4): e299-e302, 2020 12.
Article in English | MEDLINE | ID: covidwho-780592

ABSTRACT

BACKGROUND: On May 12, 2020, a symposium titled "Liability of healthcare professionals and institutions during COVID-19 pandemic" was held in Italy with the participation of national experts in malpractice law, hospital management, legal medicine, and clinical risk management. The symposium's rationale was the highly likely inflation of criminal and civil proceedings concerning alleged errors committed by health care professionals and decision makers during the COVID-19 pandemic. Its aim was to identify and discuss the main issues of legal and medicolegal interest and thus to find solid solutions in the spirit of preparedness planning. METHODS: There were 5 main points of discussion: (A) how to judge errors committed during the pandemic because of the application of protocols and therapies based on no or weak evidence of efficacy, (B) whether hospital managers can be considered liable for infected health care professionals who were not given adequate personal protective equipment, (C) whether health care professionals and institutions can be considered liable for cases of infected inpatients who claim that the infection was transmitted in a hospital setting, (D) whether health care institutions and hospital managers can be considered liable for the hotspots in long-term care facilities/care homes, and (E) whether health care institutions and hospital managers can be considered liable for the worsening of chronic diseases. RESULTS AND CONCLUSION: Limitation of the liability to the cases of gross negligence (with an explicit definition of this term), a no-fault system with statal indemnities for infected cases, and a rigorous methodology for the expert witnesses were proposed as key interventions for successfully facing future proceedings.


Subject(s)
Health Personnel/legislation & jurisprudence , Legislation, Hospital , Liability, Legal , Pandemics/legislation & jurisprudence , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus Infections/epidemiology , Humans , Italy/epidemiology , Pneumonia, Viral/epidemiology , SARS-CoV-2
18.
Nutr Metab Cardiovasc Dis ; 30(11): 1899-1913, 2020 10 30.
Article in English | MEDLINE | ID: covidwho-759219

ABSTRACT

BACKGROUND AND AIMS: There is poor knowledge on characteristics, comorbidities and laboratory measures associated with risk for adverse outcomes and in-hospital mortality in European Countries. We aimed at identifying baseline characteristics predisposing COVID-19 patients to in-hospital death. METHODS AND RESULTS: Retrospective observational study on 3894 patients with SARS-CoV-2 infection hospitalized from February 19th to May 23rd, 2020 and recruited in 30 clinical centres distributed throughout Italy. Machine learning (random forest)-based and Cox survival analysis. 61.7% of participants were men (median age 67 years), followed up for a median of 13 days. In-hospital mortality exhibited a geographical gradient, Northern Italian regions featuring more than twofold higher death rates as compared to Central/Southern areas (15.6% vs 6.4%, respectively). Machine learning analysis revealed that the most important features in death classification were impaired renal function, elevated C reactive protein and advanced age. These findings were confirmed by multivariable Cox survival analysis (hazard ratio (HR): 8.2; 95% confidence interval (CI) 4.6-14.7 for age ≥85 vs 18-44 y); HR = 4.7; 2.9-7.7 for estimated glomerular filtration rate levels <15 vs ≥ 90 mL/min/1.73 m2; HR = 2.3; 1.5-3.6 for C-reactive protein levels ≥10 vs ≤ 3 mg/L). No relation was found with obesity, tobacco use, cardiovascular disease and related-comorbidities. The associations between these variables and mortality were substantially homogenous across all sub-groups analyses. CONCLUSIONS: Impaired renal function, elevated C-reactive protein and advanced age were major predictors of in-hospital death in a large cohort of unselected patients with COVID-19, admitted to 30 different clinical centres all over Italy.


Subject(s)
Betacoronavirus , Cardiovascular Diseases/etiology , Coronavirus Infections/mortality , Hospital Mortality , Machine Learning , Pneumonia, Viral/mortality , Adolescent , Adult , Age Factors , Aged , Aged, 80 and over , C-Reactive Protein/analysis , COVID-19 , Female , Glomerular Filtration Rate , Humans , Male , Middle Aged , Pandemics , Retrospective Studies , Risk Factors , SARS-CoV-2 , Survival Analysis , Young Adult
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