Miracle-dz/UniFAR-FTUs huggingface dataset:
No evidence of clinical efficacy of hydroxychloroquine in patients hospitalized for COVID-19 infection with oxygen requirement: results of a study using routinely collected data to emulate a target trial

Background Treatments are urgently needed to prevent respiratory failure and deaths from coronavirus disease 2019 (COVID-19). Hydroxychloroquine (HCQ) has received worldwide attention because of positive results from small studies. Methods We used data collected from routine care of all adults in 4 French hospitals with documented SARS-CoV-2 pneumonia and requiring oxygen ≥ 2 L/min to emulate a target trial aimed at assessing the effectiveness of HCQ at 600 mg/day. The composite primary endpoint was transfer to intensive care unit (ICU) within 7 days from inclusion and/or death from any cause. Analyses were adjusted for confounding factors by inverse probability of treatment weighting. Results This study included 181 patients with SARS-CoV-2 pneumonia; 84 received HCQ within 48 hours of admission (HCQ group) and 97 did not (no-HCQ group). Initial severity was well balanced between the groups. In the weighted analysis, 20.2% patients in the HCQ group were transferred to the ICU or died within 7 days vs 22.1% in the no-HCQ group (16 vs 21 events, relative risk [RR] 0.91, 95% CI 0.47-1.80). In the HCQ group, 2.8% of the patients died within 7 days vs 4.6% in the no-HCQ group (3 vs 4 events, RR 0.61, 95% CI 0.13-2.89), and 27.4% and 24.1%, respectively, developed acute respiratory distress syndrome within 7 days (24 vs 23 events, RR 1.14, 95% CI 0.65-2.00). Eight patients receiving HCQ (9.5%) experienced electrocardiogram modifications requiring HCQ discontinuation. Interpretation These results do not support the use of HCQ in patients hospitalised for documented SARS-CoV-2-positive hypoxic pneumonia.
Urinalysis, but not blood biochemistry, detects the early renal-impairment in patients with COVID-19

Background: In December 2019, a novel coronavirus (SARS-CoV-2) caused infectious disease, termed COVID-19, outbroke in Wuhan, China. COVID-19 patients manifested as lung injury with complications in other organs, such as liver, heart, gastrointestinal tract, especially for severe cases. However, whether COVID-19 causes significant acute kidney injury (AKI) remained controversial. Methods: We retrospectively analyzed the clinical characteristics, urine and blood routine tests and other laboratory parameters of hospitalized COVID-19 patients in Wuhan Union Hospital. Findings: 178 patients, admitted to Wuhan Union hospital from February 02 to February 29, 2020, were included in this study. No patient (0 [0%]) presented increased serum creatinine (Scr), and 5 (2.8%) patients showed increased blood urea nitrogen (BUN), indicating few cases with kidney dysfunction. However, for patients (83) with no history of kidney disease who received routine urine test upon hospitalization, 45 (54.2%) patients displayed abnormality in urinalysis, such as proteinuria, hematuria and leukocyturia, while none of the patients was recorded to have acute kidney injury (AKI) throughout the study. Meanwhile, the patients with abnormal urinalysis usually had worse disease progression reflecting by laboratory parameters presentations, including markers of liver injury, inflammation, and coagulation. Conclusion: Many patients manifested by abnormal urinalysis on admission, including proteinuria or hematuria. Our results revealed that urinalysis is better in unveiling potential kidney impairment of COVID-19 patients than blood chemistry test and urinalysis could be used to reflect and predict the disease severity. We therefore recommend pay more attention in urinalysis and kidney impairment in COVID-19 patients.
Liver injury is associated with severe coronavirus disease 2019 (COVID‐19) infection: A systematic review and meta‐analysis of retrospective studies

Aim: The Coronavirus disease 2019 (COVID-19) outbreak is a major threat to human beings. Lung injury has been reported as the major outcome of COVID-19 infection. However, liver damage has also been considered to occur in severe cases. Current meta-analysis of retrospective studies was done to summarize available findings on the association between liver injury and severity of COVID-19 infection. Methods: Online databases including PubMed, Scopus, Web of Science and Cochrane Library were searched to detect relevant publications up to 1 April 2020, using relevant keywords. To pool data, a fixed- or random-effects model was used depending on the heterogeneity between studies. Furthermore, publication bias test and sensitivity analysis were also done. Results: In total, 20 retrospective studies with 3,428 COVID-19 infected patients (severe cases = 1,455 and mild cases = 1,973), were included in this meta-analysis. Higher serum levels of Aspartate aminotransferase (weighted mean difference = 8.84 U/L, 95% CI = 5.97 to 11.71, P<0.001), Alanine aminotransferase (weighted mean difference = 7.35 U/L, 95% CI = 4.77 to 9.93, P<0.001), total Bilirubin (weighted mean difference = 2.30 mmol/L, 95% CI = 1.24 to 3.36, P<0.001) and lower serum levels of Albumin (weighted mean difference = -4.24 g/L, 95% CI = -6.20 to -2.28, P<0.001), were associated with a significant increase in the severity of COVID-19 infection. Conclusions: The incidence of liver injury seems to be higher in patients with severe COVID-19 infection. This finding could help physicians to identify patients with poor prognosis at an early stage.
Clinical efficacy of intravenous immunoglobulin therapy in critical ill patients with COVID‐19: a multicenter retrospective cohort study

Coronavirus disease 2019 (COVID‐19) outbreak is a major challenge all over the world, without acknowledged treatment. Intravenous immunoglobulin (IVIG) has been recommended to treat critical coronavirus disease 2019 (COVID‐19) patients in a few reviews, but the clinical study evidence on its efficacy in COVID‐19 patients was lacking.
Epidemiological characteristics of COVID-19: a systematic review and meta-analysis

Abstract Our understanding of the Coronavirus disease 2019 (COVID-19) continues to evolve and there are many unknowns about its epidemiology. This study aims to synthesise case fatality rate (CFR) among confirmed COVID-19 patients, incubation period and time from onset of COVID-19 symptoms to first medical visit, intensive care unit (ICU) admission, recovery, and death. We searched MEDLINE, Embase, Google Scholar, and bibliographies of relevant articles from 01 December 2019 to 11 March 2020 without any language restrictions. Quantitative studies that recruited people with confirmed COVID-19 diagnosis were included. Two independent reviewers extracted the data. Out of 1675 non-duplicate studies, 43 were included in the meta-analysis. The pooled mean incubation period was 5.68 (99% confidence interval [CI]: 4.78, 6.59) days. The pooled mean number of days from the onset of COVID-19 symptoms to first clinical visit was 4.92 (95% CI: 3.95, 5.90), ICU admission was 9.84 (95% CI: 8.78, 10.90), recovery was 18.55 (95% CI: 13.69, 23.41), and death was 15.93 (95% CI: 13.07, 18.79). Pooled CFR among confirmed COVID-19 patients was 0.02 (95% CI: 0.02, 0.03). We found that the incubation period and lag between the onset of symptoms and first clinical visit for COVID-19 are longer than other respiratory viral infections including Middle East respiratory syndrome and severe acute respiratory syndrome; however, the current policy of 14 days of mandatory quarantine for everyone potentially exposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) might be too conservative. Longer quarantine periods might be more justified for extreme cases.
Comparison of Transmissibility of Coronavirus Between Symptomatic and Asymptomatic Patients: Reanalysis of the Ningbo COVID-19 Data

We investigate the transmissibility of coronavirus for symptomatic and asymptomatic patients using the Ningbo Covid-19 data1. Through more in-depth and comprehensive statistical analysis, we conclude that there is no difference in the transmission rates of coronavirus between the symptomatic and asymptomatic patients, which is consistent with the original findings in Chen et al.1
A survey-based study on the knowledge, attitude, and the practices pertaining to the 2019 novel Corona Virus infection amongst undergraduate medical students in India

Background. In the light of recent outbreak of COVID19 Pandemic for which is there no specific treatment, prevention and awareness is the only key to overcome an adversity of such magnitude. Thus, we aimed to understand the knowledge, attitude and practices of undergraduate medical students pertaining to infection with the COVID19. Methods. An electronic survey developed using an online cloud-based website (Survey Monkey) was served to undergraduate medical students. Participants had a week to voluntarily complete the 8 minute long questionnaire. Descriptive statistics and figures were obtained from surveymonkey.com. Results. Of 2507 invitees across six medical colleges in India, 616 (24.6%) responded. Most undergraduates (age 21.5 years, 46.1% males) were undergoing internship (16.7%) or final year undergraduate training (54.1%). Knowledge regarding viral transmission, clinical-radiologic features, laboratory diagnosis and treatment was adequate among most students (Fig 1). However, the understanding of the incubation period and time to symptoms was less than satisfactory (Supplementary Table 1). Nearly three-fourths 461 (74.8%) were aware of the COVID-19 specific precautions. While their universities had advised most regarding hand hygiene, social distancing, symptom identification, and high-risk groups, fewer were advised to avoid staying back in hostels or drug prevention. Nearly 70% were reluctant to attend clinics from fear of getting infected or passing on to others. Most students read about COVID-19 regularly, and social media accounts of medical journals were the primary 78.9% source. Conclusion. Most medical students are aware of the basics of COVID19 infection and act as a potential reservoir to fill the gaps in Healthcare services should the need arise.
Ultra-High-Resolution CT Follow-Up in Patients with Imported Early-Stage Coronavirus Disease 2019 (COVID-19) Related Pneumonia

Background: An ongoing outbreak of mystery pneumonia in Wuhan was caused by coronavirus disease 2019 (COVID-19). The infectious disease has spread globally and become a major threat to public health. Purpose: We aim to investigate the ultra-high-resolution CT (UHR-CT) findings of imported COVID-19 related pneumonia from the initial diagnosis to early-phase follow-up. Methods: This retrospective study included confirmed cases with early-stage COVID-19 related pneumonia imported from the epicenter. Initial and early-phase follow-up UHR-CT scans (within 5 days) were reviewed for characterizing the radiological findings. The normalized total volumes of ground-glass opacities (GGOs) and consolidations were calculated and compared during the radiological follow-up by artificial-intelligence-based methods. Results: Eleven patients (3 males and 8 females, aged 32-74 years) with confirmed COVID-19 were evaluated. Subpleural GGOs with inter/intralobular septal thickening were typical imaging findings. Other diagnostic CT features included distinct margins (8/11, 73%), pleural retraction or thickening (7/11, 64%), intralesional vasodilatation (6/11, 55%). Normalized volumes of pulmonary GGOs (p=0.003) and consolidations (p=0.003) significantly increased during the CT follow-up. Conclusions: The abnormalities of GGOs with peripleural distribution, consolidated areas, septal thickening, pleural involvement and intralesional vasodilatation on UHR-CT indicate the diagnosis of COVID-19. COVID-19 cases could manifest significantly progressed GGOs and consolidations with increased volume during the early-phase CT follow-up.
Timing of antiviral treatment initiation is critical to reduce SARS-Cov-2 viral load

We modeled the viral dynamics of 13 untreated patients infected with SARS-CoV-2 to infer viral growth parameters and predict the effects of antiviral treatments. In order to reduce peak viral load by more than 2 logs, drug efficacy needs to be greater than 80% if treatment is administered after symptom onset; an efficacy of 50% could be sufficient if treatment is initiated before symptom onset. Given their pharmacokinetic/pharmacodynamic properties, current investigated drugs may be in a range of 20-70% efficacy. They may help control virus if administered very early, but may not have a major effect in severe patients.
Understanding Economic and Health Factors Impacting the Spread of COVID-19 Disease

The rapid spread of the Coronavirus 2019 disease (COVID-19) had drastically impacted life all over the world. While some economies are actively recovering from this pestilence, others are experiencing fast and consistent disease spread, compelling governments to impose social distancing measures that have put a halt on routines, especially in densely-populated areas. Aiming at bringing more light on key economic and public health factors affecting the disease spread, this initial study utilizes a quantitative statistical analysis based on the most recent publicly-available COVID-19 datasets. The study had shown and explained multiple significant relationships between the COVID-19 data and other country-level statistics. We have also identified and statistically profiled four major country-level clusters with relation to different aspects of COVID-19 development and country-level economic and health indicators. Specifically, this study has identified potential COVID-19 under-reporting traits as well as various economic factors that impact COVID-19 Diagnosis, Reporting, and Treatment. Based on the country clusters, we have also described the four disease development scenarios, which are tightly knit to country-level economic and public health factors. Finally, we have highlighted the potential limitation of reporting and measuring COVID-19 and provided recommendations on further in-depth quantitative research.
COVID-19 global pandemic planning: Decontamination and reuse processes for N95 respirators

Coronavirus disease 2019 (COVID-19) is an illness caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease was first identified as a cluster of respiratory illness in Wuhan City, Hubei Province, China, in December 2019, and has rapidly spread across the globe to greater than 200 countries. Healthcare providers are at an increased risk for contracting the disease due to occupational exposure and require appropriate personal protective equipment (PPE), including N95 respirators. The rapid worldwide spread of high numbers of COVID-19 cases has facilitated the need for a substantial supply of PPE that is largely unavailable in many settings, thereby creating critical shortages. Creative solutions for the decontamination and safe reuse of PPE to protect our frontline healthcare personnel are essential. Here, we describe the development of a process that began in late February 2020 for selecting and implementing the use of hydrogen peroxide vapor (HPV) as viable method to reprocess N95 respirators. Since pre-existing HPV decontamination chambers were not available, we optimized the sterilization process in an operating room after experiencing initial challenges in other environments. Details are provided about the prioritization and implementation of processes for collection and storage, pre-processing, HPV decontamination, and post-processing of filtering facepiece respirators. Important lessons learned from this experience include, developing an adequate reserve of PPE for effective reprocessing and distribution, and identifying a suitable location with optimal environmental controls (i.e. operating room). Collectively, information presented here provides a framework for other institutions considering decontamination procedures for N95 respirators. Impact statement There is a critical shortage of personal protective equipment (PPE) around the globe. This article describes the safe collection, storage, and decontamination of N95 respirators using hydrogen peroxide vapor (HPV). This article is unique because it describes the HPV process in an operating room, and is therefore, a deployable method for many healthcare settings. Results presented here offer creative solutions to the current PPE shortage.
Impact of COVID-19 on psychiatric assessment in emergency and outpatient settings measured using electronic health records

Importance: As with other traumatic events, pandemics such as coronavirus-19 (COVID-19) may precipitate or exacerbate psychiatric symptoms such as anxiety and depression, while potentially interfering with health systems' capacity to treat such symptoms. Objective: To quantify the impact of increasing COVID-19 infection on extent of psychiatric assessment across 5 Eastern Massachusetts hospitals. Design: In silico cohort using narrative clinical notes generated between 1/2/2020 and 3/25/2020 Setting: Emergency department and outpatient settings from 2 academic medical centers and 3 community hospitals Participants: All individuals age 13 and older presenting to emergency department or outpatient clinics Main Outcome or Measure: Documentation of psychiatric symptoms reflecting depression, anxiety, psychosis, or suicide, and documentation of violence, was drawn from previously-validated term lists. Results: A total of 2,483,159 outpatient and 205,957 emergency department visit notes were analyzed. Instances of notes referencing depression or anxiety decreased 75-81% in outpatient settings with onset of coronavirus in March 2019, and by 44-45% in emergency departments. In adjusted logistic regression, presence of individual psychiatric symptoms in outpatient notes was associated with significant decreases in likelihood of coronavirus testing (for depression, OR=0.636, 95% CI 0.606-0.667). Conversely, presence of violence in an emergency department note was associated with greater likelihood of testing (OR=1.487, 95% CI 1.249-1.761). Conclusions and Relevance: Documentation of psychiatric symptoms in both outpatient and emergency department settings diminished sharply in the context of increasing coronavirus infection in Massachusetts, suggesting that efforts to provide additional resources to manage psychiatric symptoms will be needed. Funding: none.
Prevalence and Factors Associated with Depression and Anxiety of Hospitalized Patients with COVID-19

Objective: The 2019 coronavirus disease (COVID-19) epidemic has raised international concern. Mental health is becoming an issue that cannot be ignored in our fight against it. This study aimed to explore the prevalence and factors linked to anxiety and depression in hospitalized patients with COVID-19. Methods: A total of 144 patients diagnosed with COVID-19 were included in this study. We assessed depression and anxiety symptoms using the Hospital Anxiety and Depression Scale (HADS), and social support using the Perceived Social Support Scale (PSSS) among patients at admission. Multivariate linear regression analyses were performed to identify factors associated with symptoms of anxiety and depression. Results: Of the 144 participants, 34.72% and 28.47% patients with COVID-19 had symptoms of anxiety or depression, respectively. The bivariate correlations showed that less social support was correlated with more anxious (r=-0.196, p<0.05) and depressive (r=-0.360，p<0.05) symptoms among patients with COVID-19. The multiple linear regression analysis showed that gender (β=1.446, p=0.034), age (β=0.074, p=0.003), oxygen saturation (β =-2.140, p=0.049), and social support (β =-1.545, p=0.017) were associated with anxiety for COVID-19 patients. Moreover, age (β=0.084, p=0.001), family infection with SARS-CoV-2 (β =1.515, p=0.027) and social support (β =-2.236, p＜0.001) were the factors associated with depression. Conclusion: Hospitalized patients with COVID-19 presented features of anxiety and depression. Mental concern and appropriate intervention are essential parts of clinical care for those who are at risk.
The phenotypic changes of γδ T cells in COVID‐19 patients

A novel pneumonia‐associated respiratory syndrome named coronavirus disease‐2019 (COVID‐19), which was caused by SARS‐CoV‐2，broke out in Wuhan, China, in the end of 2019. Unfortunately, there is no specific antiviral agent or vaccine available to treat SARS‐CoV‐2 infections. The information regarding the immunological characteristics in COVID‐19 patients remains limited. Here, we collected the blood samples from 18 healthy donors (HD) and 38 COVID‐19 patients to analyze changes on γδ T cell population. In comparison with HD, the γδ T cell percentage decreased, while the activation marker CD25 expression increased in response to SARS‐CoV‐2 infection. Interestingly, the CD4 expression was upregulated in γδ T cells reflecting the occurrence of a specific effector cell population, which may serve as a biomarker for the assessment of SARS‐CoV‐2 infection.
Fast SARS-CoV-2 detection by RT-qPCR in preheated nasopharyngeal swab samples

Objectives The gold-standard COVID-19 diagnosis relies on detecting SARS-CoV-2 using RNA purification and one-step retrotranscription and quantitative PCR (RT-qPCR). Based on the urgent need for high-throughput screening, we tested the performance of three alternative, simple and affordable protocols to rapidly detect SARS-CoV-2, bypassing the long and tedious RNA extraction step and reducing the time to viral detection. Methods We evaluated three methods based on direct nasopharyngeal swab viral transmission medium (VTM) heating before the RT-qPCR: a) direct without additives; b) in a formamide-EDTA (FAE) buffer, c) in a RNAsnapTM buffer. Results Although with a delay in cycle threshold compared to the gold-standard, we found consistent results in nasopharyngeal swab samples that were subject to a direct 70°C incubation for 10 min. Conclusions Our findings provide valuable options to overcome any supply chain issue and help to increase the throughput of diagnostic tests, thereby complementing standard diagnosis.
Analysing Recovery From Pandemics by Learning Theory: The Case of CoVid-19

We present a method for predicting the recovery time from infectious diseases outbreaks such as the recent CoVid-19 virus. The approach is based on the theory of learning from errors, specifically adapted to the control of the virus spread by reducing infection rates using countermeasures such as medical treatment, isolation, social distancing etc. When these are effective, the infection rate, after reaching a peak, declines following what we call the Universal Recovery Curve. We use presently available data from many countries to make actual predictions of the recovery trend and time needed for securing minimum infection rates in the future. We claim that the trend of decline is direct evidence of learning about risk reduction, also in this case of the pandemic.