cord-001654-o2zfilcl	2015	The use of immunomodulatory agents such as statins to target host inflammatory responses in influenza virus infection has been suggested as an adjunct treatment, especially during pandemics, when antiviral quantities are limited or vaccine production can be delayed. We used population-based, influenza hospitalization surveillance data, propensity score-matched analysis, and Cox regression to determine whether there was an association between mortality (within 30 days of a positive influenza test) and statin treatment among hospitalized cohorts from 2 influenza seasons (October 1, 2007 to April 30, 2008 and September 1, 2009 to April 31, 2010). A study by Vandermeer et al [23] , using data from a populationbased influenza surveillance system, found a protective effect of statin use on mortality among patients hospitalized with laboratory-confirmed influenza during the 2007-2008 influenza season. We used Cox proportional hazards models with robust standard errors, stratified on matched pairs, to determine the effect of statin treatment on mortality within 30 days of a positive influenza test.
cord-002631-e6rc8mvu	2017	title: Metagenomic Sequencing of an Echovirus 30 Genome From Cerebrospinal Fluid of a Patient With Aseptic Meningitis and Orchitis We found that the genome belonged to the subgroup echovirus 30, which is a common cause of aseptic meningitis but has not been previously reported to cause orchitis. We found that the genome belonged to the subgroup echovirus 30, which is a common cause of aseptic meningitis but has not been previously reported to cause orchitis. Given the relatively unusual presentation of orchitis and meningitis, we performed metagenomic sequencing to obtain additional genomic information about the particular strain of enterovirus and to identify any potential copathogens including mumps virus. We performed metagenomic sequencing and enterovirus genome assembly using methods developed and validated by our group [1, 2] . We performed metagenomic analysis of all sequencing reads from this patient''s CSF and identified enterovirus; no other pathogen, including mumps virus, was found. Aseptic meningitis and orchitis associated with echovirus 6 infection
cord-003565-14g33n7j	2019	We evaluated the immunogenicity and safety of an MF59adjuvanted, cell culture-derived, H5N1 subunit influenza virus vaccine in 2 phase II studies; vaccine was administered as either a full-or half-dose formulation to healthy adult or elderly subjects. In conclusion, two 7.5-μg doses of a cell culture-derived, MF59-adjuvanted H5N1 vaccine administered 3 weeks apart were well tolerated and highly immunogenic, raised no safety concerns, and induced robust antibody responses in adult and elderly subjects that met all the immunogenicity criteria required for pandemic vaccine licensure by both the US and European regulatory authorities. A randomised, single-blind, dose-range study to assess the immunogenicity and safety of a cell-culture-derived A/H1N1 influenza vaccine in adult and elderly populations Assessment of the immunogenicity and safety of varying doses of an MF59®-adjuvanted cell culture-derived A/H1N1 pandemic influenza vaccine in Japanese paediatric, adult and elderly subjects
cord-010773-z2eogm18	2020	Pre-CTI risk factors associated with infection included prior hematopoietic cell transplantation (HCT), immunoglobulin G (IgG) level <400 mg/dL, and lymphodepletion other than cyclophosphamide plus fludarabine; post-CTI risk factors included higher-severity CRS and IgG <400 mg/dL. Finally, these patients often develop cytokine release syndrome (CRS) following CTI, which may require treatment with anti-interleukin 6 (IL-6) therapies (eg, tocilizumab), steroids, and admission to the intensive care unit (ICU), with associated increased risk for immunosuppression and nosocomial infections [8] [9] [10] . This study is the first in-depth description of the frequency, type, severity, and risk factors for infections following CD-19 CAR T-cell therapy in children, adolescents, and young adults. In a study of adult CTI recipients, the median time to neutrophil recovery was 6 days, but prolonged cytopenias have been demonstrated previously, even in patients with MRD-negative remission after CAR T-cell therapy [3, 7, 11, 21] .
cord-032268-oj94e8wo	2020	We developed a score, based on easily accessible data (age, sex, BMI, dyspnea and inflammatory parameters), to predict the risk of rapid progression to severe disease in hospitalized patients with COVID-19. In a previous multicenter study involving 1,045 hospitalized patients with confirmed COVID-19, we identified several independent risk factors, such as advanced age, obesity and inflammation, associated with the early development of severe disease [3] . In the present study, we aimed to develop a practical score for estimating the risk of rapid progression to severe disease in a cohort of patients hospitalized for COVID-19. [SD], 16), and 612 patients (58.6%) were men (supplementary Table 1 Based on previously identified prognostic factors [3] , we then defined a prognostic BAS²IC score including BMI, age, sex, shortness of breath and inflammatory parameters to screen patients at a risk of developing early severe disease (Table 1 ).
cord-252305-rstxyofq	2020	We then developed a streamlined set of guidelines to help rapidly evaluate and select suitable disinfectants from List N, including practicality, efficacy, safety, and cost/availability. While this list appears extensive, it lacks guidance or discussion of practical concerns that must be taken into consideration when selecting a disinfectant during this pandemic, including efficacy, practicality, safety profile, and availability. Some products on List N do not have an emerging viral pathogen claim but have been included because they 1) demonstrate efficacy against another human coronavirus similar to SARS-CoV-2 or 2) are EPA-approved against select viruses that are harder-to-kill [5] . The publication of the EPA List N was an important step in providing a resource for selecting disinfectants against SARS-CoV-2 and can be more easily operationalized in healthcare settings when supplemented with additional data on safety, practicality, and availability.
cord-252751-prock3co	2020	To be considered eligible for trial inclusion, patients had to meet the following criteria: 1) Currently hospitalized, aged ≥ 18 years, 2) SARS-CoV-2 infection confirmed by PCR test ≤ 4 days before trial enrollment 3) SpO2 ≤ 94% on room air or requiring supplemental oxygen at screening 4) Presence of radiographic evidence of pulmonary infiltrates. For each patient we extracted the following information: age, sex, race, ethnicity, days from onset of symptoms, imaging results, weight, vital signs and laboratory values (both on admission and during hospitalization), preexisting medical conditions, admission to the intensive care unit (ICU), use of mechanical ventilation, use of systemic corticosteroids [12] , hospitalization outcome (death or discharge) and incidence of acute kidney injury (AKI) using the KDIGO criteria [13] . In order to provide a cohesive assessment of the efficacy of remdesivir, we compared the clinical outcomes of patients who were hospitalized with severe COVID-19 (requiring supplemental oxygen and having abnormal imaging findings) and received either remdesivir or supportive care.
cord-256130-zhlvvuj4	2018	Here, we evaluated quantification of torque teno virus (TTV) and Epstein-Barr virus (EBV) as biomarkers for defining the net state of immunosuppression in lung-transplanted patients. The aim of the present study was to evaluate levels of TTV and EBV in relation to the frequency of infectious events and acute rejections over time in a prospective manner in a single-center cohort of lung-transplanted patients. The total nucleic acid content was isolated from serum or whole blood samples and analyzed for TTV-, EBV-, and CMV-DNA load by real-time PCR. Comparison of TTV-and EBV-DNA levels in lung transplant recipients who received either Tacrolimus-or Cyclosporinebased therapy revealed that Cyclosporine-treated patients had significantly lower TTV-DNA levels in serum at month 6 post-LTx and onwards, compared with the Tacrolimustreated patients (Figure 1 ). However, we found no association between either TTV-or EBV-DNA load and infectious events or acute rejections, which suggests a limited clinical applicability as biomarkers predicting short-term outcomes related to the net state of immunosuppression.
cord-256195-1hmzgwrw	2020	2 In the United States, where a racially and ethnically diverse population has been exposed to infection in the setting of known racial and ethnic health disparities, 14 several news reports have suggested that ethnic and racial minorities, especially Latinx and non-Latin African American individuals, may bear a higher burden of disease during the COVID-19 pandemic. We used medical records available from the largest not-for-profit healthcare system in Massachusetts to examine the association between age, race and ethnicity, reported preexisting comorbidities, and the need for hospitalization and ICU admission in a large study population of COVID-19 positive patients. First, analysis of our large study population confirmed our firsthand clinical experience and showed indeed that Latinx and African American patients are at higher risk of being hospitalized and admitted to ICU level of care with COVID-19, than White patients.
cord-258113-mnou31j3	2020	title: Clinical Characteristics of Patients Infected With the Novel 2019 Coronavirus (SARS-Cov-2) in Guangzhou, China CONCLUSIONS: Most of the patients infected with SARS-CoV-2 in Guangzhou, China are not severe cases and patients with older age, male, and decreased albumin level were more likely to develop into severe ones. [5] studied the clinical features of 99 patients with COVID-19 and found that SARS-Cov-2 was more likely to infect older men with comorbidities and to lead to acute respiratory distress syndrome (ARDS). Among all patients, univariate analysis indicated that age, sex, imported disease, incubation period, interval between hospital admission and symptom onset, any coexisting medical condition, leukocyte count, neutrophil count, lymphocyte count, PCT, LDH, CK, ALB, AST, and D-dimer were associated with disease severity. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series
cord-259969-q65k590s	2020	We describe a 43-year-old patient with coronavirus disease 2019 who developed a bullous hemorrhagic rash that progressed to necrotic lesions. Small blood vessel occlusion by microthrombi, which has been described in patients with coronavirus disease 2019 (COVID-19) [1] , could not be demonstrated. Under suspicion of a SARS-CoV-2-induced cutaneous vasculitis, the patient was treated with prednisolone at 0.5 mg per kilogram. Variable and heterogenous skin manifestations in patients with COVID-19 have been described that appear before, during, and after the disease [2] . However, other groups have described skin manifestations in up to 20% of COVID patients [4, 5] . However, our case demonstrates a small/medium-sized vessel vasculitis with involvement of mucous membranes as the cause of skin manifestations in a patient with COVID-19 that appeared late in the disease. Cutaneous manifestations in patients with COVID-19: a preliminary review of an emerging issue
cord-260257-phmd0u6d	2020	METHODS: A cross-sectional, online survey in the United States measured willingness to seek testing if feeling ill under different specimen collection scenarios: home-based saliva, home-based swab, drive-through facility swab, and clinic-based swab. 8, 9 Calls for home-based specimen collection or drive-through specimen collection models to address SARS-CoV-2 virus test scale-up have cogently argued that these approaches have the benefit of (1) avoiding burdening hospitals at a critical time, (2) avoiding potential nosocomial infections (the risk of acquiring disease from clinical or laboratory settings), (3) likely lowering costs, and (4) potentially achieving rapid scale-up due to laboratory centralization. We conducted an online survey to assess patient willingness to use the following SARS-CoV-2 testing modalities for clinical care: home-based specimen collection, drive-through testing, and clinic-based testing. Across a diverse sample of 1,435 participants, one-third more persons reported that they would be willing to collect specimens at home for SARS-CoV-2 testing if they experienced illness, compared to clinic-based testing.
cord-261619-31jk1vh6	2020	Drive-through coronavirus disease 2019 screening can evaluate large numbers of patients while reducing healthcare exposures and personal protective equipment use. Mitigation of the coronavirus disease 2019 (COVID-19) pandemic requires increased access to testing for its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1] . During the current pandemic, drive-through screening has processed large volumes of patients more efficiently than conventional in-clinic assessment, while reducing potential healthcare exposures and personal protective equipment (PPE) use [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] . The electronic medical record was reviewed (1) for comorbid conditions in positive cases and (2) for additional SARS-CoV-2 testing and BAMC hospital admission within 14 days of screening for all patients. Nonetheless, the median time from screening to admission suggests that some patients requiring additional medical evaluation may have reported to the drive-through. However, none of the screen-only patients later tested positive or were hospitalized for COVID-19 within 14 days.
cord-267023-w5ig7mrl	2017	We integrated case-based modules, group learning activities, smartphone applications (apps), decision support tools, and prescription audit and feedback into curricula of the medical school, medicine residency program, infectious diseases (ID) fellowship program, and hospital medicine program operations. In a 2013 follow-up multicenter survey of fourth year medical students, 90% desired further education on antimicrobial prescribing, but only 40% were familiar with the role of antimicrobial stewardship (AS) in promoting judicious antimicrobial use and preventing multidrug resistance [3, 4] . It consists of 5 educational strategies designed to bridge perceived learning gaps and lay the foundation for best practices in stewardship and infection prevention in medical students, postgraduate trainees, and mature clinicians. The majority used a quasi-experimental, before-and-after study design with preand postintervention knowledge assessment questions, surveys of learners, or chart review with post-antibiotic prescription audit as methods of evaluation.
cord-268662-mw8ec7u2	2020	
cord-268975-xzdh8yum	2020	The sample size was chosen to allow for sufficient power to analyze likely differences between subgroups such as confirmed cases, A c c e p t e d M a n u s c r i p t people with a history of recent contact with COVID19 They needed to answer questions about their basic information, the perception of the COVID-19 outbreak, recent preventive or avoidance behaviors, and self-reported mental health scales. The survey also asked people seven questions about preventive behaviors (public mask-wearing, increases in handwashing and the frequency, surface sterilization) and avoidance behaviors (such as avoid crowded places or public transport or people with contact history, personal protective, and social distancing behavior, urge their family members or friends for these The perception of the COVID-19 outbreak includes the severity of the disease, the attitude towards the disease, information, support, the worries of being infected and for their families.
cord-270703-c8mv2eve	2018	We implemented a real-time report to distribute respiratory pathogen data for our 8-hospital system to anyone with an Internet connection and a web browser. We implemented a real-time report to distribute respiratory pathogen data for our 8-hospital system to anyone with an Internet connection and a web browser. To address these local needs in a major US metropolitan area, our clinical microbiology laboratory implemented an online dashboard to distribute respiratory pathogen data for our 8-hospital system to clinicians, epidemiologists, infection control practitioners, system leadership, and the public. Development of this report began in the Fall 2017, before the respiratory virus season, during which influenza reached an epidemic status across the United States that resulted in supply shortages, testing difficulties, and a widespread public health crisis [4, 5] . In summary, our microbiology laboratory implemented a near real-time Internet report to distribute respiratory pathogen data for our 8-hospital system to clinicians, hospital epidemiologists, infection control committees, system leadership, and the public.
cord-274943-fn3m14cn	2017	
cord-279334-j0i9ozsz	2020	
cord-282862-kve6fa49	2020	
cord-288044-ver1nrsz	2020	We found significant differences between the groups with favorable and unfavorable clinical evolution, suggesting the value of the early detection of TNFα, CCL2/MCP-1, CCL3/MIP-1 A c c e p t e d M a n u s c r i p t alpha mRNA in nasopharyngeal swab samples, and the predictive value of CCL2/MCP-1 for the COVID-19 clinical outcome. The objective of this study was to explore the early expression of TNF-alpha, CCL2/MCP-1, CCL3/MIP-1 alpha, IL-10, and TGFβ, previously associated with the uncontrolled cytokines response in the ARDS pathogenesis produced by human pathogenic coronaviruses, thereby taking advantage of the nasopharyngeal swab sample, mandatory for diagnosis of COVID-19 diagnosis in Cuban suspected cases. To determine the possible association of early gene expression of immune mediators in nasopharyngeal swab sample with the clinical evolution, we studied patients with a mild or severe COVID-19 clinical picture, and asymptomatic subjects.
cord-296890-08kqtw8s	2019	Specimens were examined at our collaborating institutions with a panel of molecular assays for viral pathogens including influenza A (IAV), IBV, ICV, and IDV, human adenovirus (AdV), human enterovirus (EV), human coronavirus (CoV), respiratory syncytial virus subtype A (RSV-A) or RSV-B, and parainfluenza virus (PIV) types 1–4. One study of respiratory samples collected from children living in Kuala Lumpur under 5 years of age between 1982 and 2008 found that 26.4% of the samples were positive by immunofluorescence assays and viral cultures for viral pathogens, with a prevalence of 18.6% for respiratory syncytial virus (RSV), 3.5% for parainfluenza viruses (PIVs), 2.9% for influenza viruses, and 1.37% for adenovirus [10] . The overall objective of this study was to examine the viral etiology of and risk factors for pneumonia among patients admitted to Sibu and Kapit Hospitals between June 2017 and May 2018 and, in doing so, to assist Malaysian collaborators with setting up sustainable real-time molecular assays for viral respiratory pathogens.
cord-303091-jky6jlrl	2020	We identified patients with coronavirus disease 2019 (COVID-19) in a telemedicine clinic who requested ongoing follow-up calls 6 weeks after symptom onset. We seek to describe the persistent symptoms experienced by patients with mild COVID-19 by reviewing records of those who requested follow-up VOMC care for greater than the planned 21 days and more than 6 weeks beyond symptom onset. Chart review included: (1) verification of patient demographics and comorbidities documented at VOMC intake visit, (2) verification of symptom onset dates, (3) review of follow-up notes during the 6 th week of symptoms, (4) review of return to work advice/disability letters, and (5) review of final notes for health status at time of VOMC discharge. For patients who required additional medical evaluation after the acute period (defined as an in-person or telemedicine visit at least 3 weeks into illness), we reviewed evaluation notes, diagnostics, and final diagnoses (including "alternate diagnoses" and "contributing diagnoses" based on provider documentation).
cord-303935-qdehf6rb	2015	
cord-305512-p5qchjva	2019	
cord-310807-p5cb6idp	2017	
cord-310872-2z1wnj63	2020	Approximately 35 years after Dr. Petersdorf first asked the question, we find ourselves once again wondering, "Whither Infectious Diseases?" To answer this question, and align with predominant US market forces, ID experts should push for the following: (1) restrictions regarding utilization of ID diagnostics and antimicrobial agents; (2) pay-for-performance measures regarding antimicrobial prescribing rates; and (3) healthcare reform as called for by the American College of Physicians to move away from fee-for-service medicine. Infectious diseases practitioners may be better at diagnosing and treating infections than those who practice other specialties, but to what financial advantage to healthcare systems that hang on by their fingernails with operating margins under 2% [16, 17] ? First, ID practitioners have unique expertise in the diagnosis and treatment of infections, which can lead to less antimicrobial resistance and superinfections, better outcomes, and lower cost for patients and health systems.
cord-311082-sspcz9t6	2020	We identified 4 major challenges associated with the current modeling paradigm (SEIR) that hinder the efforts to accurately characterize the emerging COVID-19 and future epidemics. These challenges included (1) lack of consistent definition of "case"; (2) discrepancy between patient-level clinical insights and population-level modeling efforts; (3) lack of adequate inclusion of individual behavioral and social influence; and (4) allowing little flexibility of including new evidence and insights when our knowledge evolved rapidly during the pandemic. Researchers, clinicians, and public health officials rely on mathematical models to characterize and predict the COVID-19 epidemic, derive critical epidemiological metrics (eg, the basic reproduction number R 0 ), evaluate various intervention strategies, and optimize resource needs [2] . The SEIR modeling paradigm is less practical to handle the complicated clinical, public health, and social system of the COVID-19 pandemic.
cord-314517-n1yj2zdy	2020	title: Social media survey and web posting assessment of the COVID-19 response in China: Health worker attitudes towards preparedness and personal protective equipment shortages BACKGROUND: Understanding health worker awareness, attitudes, and self-confidence in the workplace can inform local and global responses towards emerging infectious threats, like COVID-19 pandemic response. Health workers satisfied with current preparedness to address COVID-19 were more likely to be female, to obtain knowledge about the SARS-CoV-2 outbreak from government organizations, and to consider their hospital prepared for the outbreak management. They cannot function effectively if they lack personal protective equipment (PPE), essential to ensure continuity of healthcare services during a public health emergency and to avoiding nosocomial acquisitions 5 A c c e p t e d M a n u s c r i p t 6 As of April 4, 2020, 60 Chinese health workers have died, of whom 22 (36.7%) were confirmed dead of COVID-19, according to reports by China Central Television.
cord-320511-qnxj7d9l	2020	
cord-321000-3jd2gn73	2020	
cord-322524-bq9ok8h1	2018	
cord-326642-kc85pev4	2015	
cord-327609-no58ucyq	2017	
cord-333459-asem8xjz	2020	Geospatial distribution of study patients'' residence relative to population density in the region were mapped and data analysis included hospital length of stay, need and duration of invasive mechanical ventilation (IMV), and mortality. Logistic regression models were constructed to predict discharge dispositions in our patient population (excluding patients that remained actively hospitalized at the end of the study period)-one model used only variables available at the beginning of an encounter to predict overall outcomes and a second model included more variables in an attempt to find associations with outcomes in mechanically ventilated patients. In patients who received IMV, only age 65 years, male gender, comorbidities (hypertension, heart failure), need for kidney replacement therapy, and acute kidney injury during hospitalization were significantly associated with increased mortality in the univariate analysis (Supplemental Table 5 ).
cord-334210-lhadzo7o	2020	
cord-347255-fl9lur4h	2019	Secondary outcomes included the proportion of patients with a respiratory pathogen identified by the FilmArray Respiratory Panel test or any other upper respiratory pathogen diagnostic test ordered by the physician; the proportion of patients with a laboratory-confirmed influenza diagnosis; the proportion of patients receiving appropriate anti-influenza treatment or prescription in the ED by an emergency medicine clinician (composite rate of anti-influenza treatment in positive patients and nonuse of anti-influenza treatment in negative patients); the proportion of patients discharged home from the ED vs hospital admission; the proportion of patients with all-cause or respiratory illness-related repeat ED visit, hospital or ICU admission, or death within 30 days; clinician adherence to guidelines for the treatment of patients with influenza (recommendations for use of antivirals only); length of ED stay; length of hospital stay; time to influenza test results; and time to other respiratory pathogen test results. Thus, we conducted a randomized clinical trial of the FilmArray RP vs usual care in ED patients with signs or symptoms of upper respiratory infection or influenza-like illness.
cord-350557-7i7122zi	2020	
cord-350767-6kc4hyzo	2020	
cord-351022-8y43jhmu	2020