# ent

id: cord-003565-14g33n7j
type: ORG
entity:
  Center for Biologics Evaluation Research and Review CBER and Committee for Medicinal Products for Human Use CHMP


id: cord-260257-phmd0u6d
type: ORG
entity:
  JAMA Health Forum2020 Detection of SARS CoV 2 RNA and Antibodies in Diverse Samples Protocol to Validate the Sufficiency of Provider


id: cord-002631-e6rc8mvu
type: WORK_OF_ART
entity:
  Metagenomic Sequencing of an Echovirus 30 Genome From Cerebrospinal Fluid of a Patient With Aseptic Meningitis


id: cord-001654-o2zfilcl
type: DISEASE
entity:
  influenza A H1N1 pdm09 Impact of neuraminidase inhibitor treatment on outcomes of public health importance during the 2009 2010 influenza A H1N1 pandemic


id: cord-252751-prock3co
type: ORG
entity:
  Gilead Sciences Inc Gilead Sciences Statement on Expanding Global Supply of Investigational Antiviral Remdesivir


id: cord-320511-qnxj7d9l
type: ORG
entity:
  Sharing All Influenza Data GISAID Diagnostic Procedures for Viral Rickettsial and Chlamydial Infections Profile


id: cord-279334-j0i9ozsz
type: CELL_LINE
entity:
  MERS CoV EC 50 175 IU mL However toxicities are substantial including severe cytopenias hepatotoxicity including fatality neuropsychiatric events and risk of developing fatal or life threatening ischemia or infection particularly when combined with ribavirin


id: cord-350767-6kc4hyzo
type: WORK_OF_ART
entity:
  Charting the Future of Infectious Disease Anticipating and Addressing the Supply and Demand Mismatch Factors Influencing Internal Medicine Resident Choice of Infectious Diseases or Other Specialties A National Cross


id: cord-334210-lhadzo7o
type: WORK_OF_ART
entity:
  Different Types of Clinical Specimens Comparison of Commercially Available and Laboratory Developed Assays


id: cord-333459-asem8xjz
type: PROTEIN
entity:
  Mallipattu S K Jawa R Moffit R Hajagos J Fries B Nachman S Gan T J Saltz M Saltz J Kaushansky K Skopicki H Abell Hart K Chaudhri I Deng J Garcia V Gayen S Kurc T Bolotova O Yoo J Dhaliwal S Nataraj N Sun S Tsai C Wang Y Abbasi S Abdullah R Ahmad S Bai K Bennett Guerrero E Chua A Gomes C Griffel M Kalogeropoulos A Kiamanesh D Kim N Koraishy F Lingham V Mansour M Marcos L Miller J Poovathor S Rubano J Rutigliano D Sands M Santora C Schwartz J Shroyer K Skopicki H Spitzer S Stopeck A Talamini M Tharakan M Vosswinkel J Wertheim W title Geospatial Distribution and Predictors of Mortality in Hospitalized Patients with COVID 19 A Cohort Study date 2020 09 14 journal Open Forum Infect Dis DOI 10 1093 ofid ofaa436 sha 41872fbc06f76b814df6c46b5b5f7844987386e1 doc_id 333459


id: cord-333459-asem8xjz
type: ORG
entity:
  Meta Analysis National Institutes of Health Association of Treatment With Hydroxychloroquine or Azithromycin With In Hospital Mortality in Patients


id: cord-305512-p5qchjva
type: DNA
entity:
  matrix M gene InfA F 5 GACCRATCCTGTCACCTCT GAC 3 InfA R 5 AGGGCATTYTGGACAAAKCGTCTA 3 InfA P 5 FAM TGCAGTCCTCGCTCACTGGGCACG MGB 3 RT PCR


id: cord-305512-p5qchjva
type: DISEASE
entity:
  influenza A viruses Supplementary Table S1 The obtained sequences were identical for samples SPC00384 SPC00394


id: cord-347255-fl9lur4h
type: GGP
entity:
  mellitus 9 10 9 9 Other 6 6 12 12 Kidney disorders 3 3 6 6 Immunosuppressed 17 18 17 17 Abbreviations BMI body mass index CHF congestive


id: cord-032268-oj94e8wo
type: WORK_OF_ART
entity:
  Cases Remdesivir for the Treatment of Covid 19 Preliminary Report Dexamethasone in Hospitalized Patients with Covid 19 Preliminary Report Development and Validation of a Clinical Risk Score to Predict the Occurrence of Critical Illness in Hospitalized Patients With COVID 19 Prediction for Progression Risk in Patients with COVID 19 Pneumonia


id: cord-032268-oj94e8wo
type: DISEASE
entity:
  fever dyspnea headache chills cough fatigue myalgia chest pain diarrhea abdominal pain confusion anosmia


id: cord-303935-qdehf6rb
type: ORG
entity:
  the United States Air Force 59th Medical Wing Science and Technology Air Education and Training Command Potential


id: cord-303935-qdehf6rb
type: DISEASE
entity:
  tympanic membranes gallop murmur abnormal rhythm for cardiac abnormal bowel sounds distended tender for abdominal these n


id: cord-274943-fn3m14cn
type: DISEASE
entity:
  respiratory syncytial virus human metapneumovirus parainfluenza viruses 1 4 influenza coronavirus bocavirus


id: cord-288044-ver1nrsz
type: WORK_OF_ART
entity:
  Airway Epithelial Derived Cytokines and Chemokines and Their Role in the Immune Response to Respiratory Syncytial Virus Infection Anti and Pro inflammatory Roles


id: cord-256130-zhlvvuj4
type: ORG
entity:
  European Organization for Research and Treatment of Cancer Invasive Fungal Infections Cooperative Group National Institute of Allergy and Infectious Diseases


id: cord-256130-zhlvvuj4
type: ORG
entity:
  the European Organization for Research and Treatment of Cancer Invasive Fungal Infections Cooperative Group


# bib

id: cord-001654-o2zfilcl
author: Laidler, Matthew R.
date: 2015-03-04
txt: ./txt/cord-001654-o2zfilcl.txt
cache: ./cache/cord-001654-o2zfilcl.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438907/
doi: 10.1093/ofid/ofv028
summary:
  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.

title:
  Statin Treatment and Mortality: Propensity Score-Matched Analyses of 2007–2008 and 2009–2010 Laboratory-Confirmed Influenza Hospitalizations

abstract:
  Background. Annual influenza epidemics are responsible for substantial morbidity and mortality. 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. Methods. 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). Results. Hazard ratios for death within the 30-day follow-up period were 0.41 (95% confidence interval [CI], .25–.68) for a matched sample from the 2007–2008 season and 0.77 (95% CI, .43–1.36) for a matched sample from the 2009 pandemic. Conclusions. The analysis suggests a protective effect against death from influenza among patients hospitalized in 2007–2008 but not during the pandemic. Sensitivity analysis indicates the findings for 2007–2008 may be influenced by unmeasured confounders. This analysis does not support using statins as an adjunct treatment for preventing death among persons hospitalized for influenza.


id: cord-002631-e6rc8mvu
author: Piantadosi, Anne
date: 2017-07-28
txt: ./txt/cord-002631-e6rc8mvu.txt
cache: ./cache/cord-002631-e6rc8mvu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534216/
doi: 10.1093/ofid/ofx138
summary:
  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

title:
  Metagenomic Sequencing of an Echovirus 30 Genome From Cerebrospinal Fluid of a Patient With Aseptic Meningitis and Orchitis

abstract:
  Enteroviruses cause a wide spectrum of clinical disease. In this study, we describe the case of a young man with orchitis and aseptic meningitis who was diagnosed with enterovirus infection. Using unbiased “metagenomic” massively parallel sequencing, we assembled a near-complete viral genome, the first use of this method for full-genome viral sequencing from cerebrospinal fluid. 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.


id: cord-003565-14g33n7j
author: Frey, Sharon E
date: 2019-03-01
txt: ./txt/cord-003565-14g33n7j.txt
cache: ./cache/cord-003565-14g33n7j.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6446137/
doi: 10.1093/ofid/ofz107
summary:
  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

title:
  Safety and Immunogenicity of MF59-Adjuvanted Cell Culture–Derived A/H5N1 Subunit Influenza Virus Vaccine: Dose-Finding Clinical Trials in Adults and the Elderly

abstract:
  BACKGROUND: A/H5N1 influenza viruses have high pandemic potential; consequently, vaccines need to be produced rapidly. MF59® adjuvant reduces the antigen required per dose, allowing for dose sparing and more rapid vaccine availability. METHODS: Two multicenter, phase II trials were conducted to evaluate the safety and immunogenicity of an MF59-adjuvanted, cell culture–derived, A/H5N1 vaccine (aH5N1c) among 979 adult (18–64 years old) and 1393 elderly (≥65 years old) subjects. Participants were equally randomized to receive 2 full-dose (7.5 μg of hemagglutinin antigen per dose) or 2 half-dose aH5N1c vaccinations 3 weeks apart. Outcomes were based on Center for Biologics Evaluation Research and Review (CBER) and Committee for Medicinal Products for Human Use (CHMP) licensure criteria (titers ≥1:40 and seroconversions on day 43). Solicited reactions and adverse events were assessed (www.clinicaltrials.gov: NCT01776541 and NCT01766921). RESULTS: CBER and CHMP criteria were met by both age groups. CBER criteria for hemagglutination titers were met for the full-dose formulation. Solicited reaction frequencies tended to be higher in the full-dose group and were of mild to moderate intensity. No vaccine-related serious adverse events occurred. CONCLUSIONS: In adult and elderly participants, the full-dose aH5N1c vaccine formulation was well tolerated and met US and European licensure criteria for pandemic vaccines.


id: cord-010773-z2eogm18
author: Vora, Surabhi B
date: 2020-04-09
txt: ./txt/cord-010773-z2eogm18.txt
cache: ./cache/cord-010773-z2eogm18.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7221263/
doi: 10.1093/ofid/ofaa121
summary:
  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] .

title:
  Infectious Complications Following CD19 Chimeric Antigen Receptor T-cell Therapy for Children, Adolescents, and Young Adults

abstract:
  BACKGROUND: Infectious complications of chimeric antigen receptor (CAR) T-cell immunotherapy in children and young adults have not been well described. METHODS: Medical records of patients ≤26 years old receiving CD19 CAR T-cell infusion (CTI) at a single institution between 2014 and 2017 were reviewed. The number of infections per 100 days-at-risk (infection density) in the 90 days preceding and 0–28 and 29–90 days after CTI was calculated. Poisson regression and Cox analyses were utilized to identify risk factors for infections. RESULTS: Eighty-three patients received CTI during the study period. Most patients (98%) had refractory or relapsed acute lymphoblastic leukemia (ALL). Infections occurred in 54% of patients in the 90 days before CTI (infection density, 1.23) and in 40% of patients in the first 28 days following CTI (infection density, 2.89). Infection density decreased to 0.55 in the 29–90 days post-CTI. Most infections were bacteremias (39%) or respiratory viral infections (43%). 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. CONCLUSIONS: Infection rates in children and young adults receiving CD19 CAR T-cell therapy increase in the first month and then decline. Understanding types and timing of infections and contributing risk factors may help inform prophylactic and monitoring strategies. Specific attention should be given to patients with prior HCT, severe hypogammaglobulinemia, and severe CRS.


id: cord-032268-oj94e8wo
author: Kaeuffer, Charlotte
date: 2020-09-01
txt: ./txt/cord-032268-oj94e8wo.txt
cache: ./cache/cord-032268-oj94e8wo.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7499730/
doi: 10.1093/ofid/ofaa405
summary:
  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 ).

title:
  The BAS²IC score: a useful tool to identify patients at high risk of early progression to severe COVID-19

abstract:
  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. Using a cut-off of >6 points, the negative and positive predictive values were 87% and 49%, respectively.


id: cord-252305-rstxyofq
author: Tyan, Kevin
date: 2020-08-31
txt: ./txt/cord-252305-rstxyofq.txt
cache: ./cache/cord-252305-rstxyofq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32989420/
doi: 10.1093/ofid/ofaa396
summary:
  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.

title:
  Considerations for the Selection and Use of Disinfectants Against SARS-CoV-2 in a Healthcare Setting

abstract:
  Proper disinfection using adequate disinfecting agents will be necessary for infection control strategies against COVID-19. However, limited guidance exists on effective surface disinfectants or best practices for their use against SARS-CoV-2. We outlined a process of fully characterizing over 350 products on the EPA List N, including pH, method of delivery, indication for equipment sterilization, and purchase availability. 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. This resource guides the evaluation of ideal disinfectants amidst practical considerations posed by the COVID-19 pandemic.


id: cord-252751-prock3co
author: Kalligeros, Markos
date: 2020-08-06
txt: ./txt/cord-252751-prock3co.txt
cache: ./cache/cord-252751-prock3co.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/ofid/ofaa319
doi: 10.1093/ofid/ofaa319
summary:
  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.

title:
  Remdesivir Use Compared to Supportive Care in Hospitalized Patients with Severe COVID-19: A Single-Center Experience

abstract:
  BACKGROUND: The US Food and Drug Administration issued an Emergency Use Authorization for remdesivir use in patients with severe COVID-19. METHODS: We utilized data from two quaternary, acute care hospitals. The outcomes of interest were the impact of remdesivir on in-hospital death by day 28 as well as time to recovery, clinical improvement, and discharge. We utilized Cox proportional hazards models and stratified log-rank tests. RESULTS: 224 patients were included in the study. Median age was 59 years; 67.0% were male; 17/125 patients (13.6%) who received supportive care and 7/99 patients (7.1%) who received remdesivir died. The unadjusted risk for 28-day in-hospital death was lower for patients who received remdesivir compared to patients who received supportive care (HR 0.42; 95% CI: 0.16-1.08). Although this trend remained the same after adjusting for age, sex, race and oxygen requirements on admission (aHR 0.49; 95% CI: 0.19-1.28), as well as chronic comorbidities and use of corticosteroids (aHR 0.44; 95% CI: 0.16-1.23), it did not reach statistical significance. The use of remdesivir was not associated with an increased risk of acute kidney injury (AKI) and liver test abnormalities. Although not statistically significant, the rate ratios for time to recovery, clinical improvement, and discharge were higher in women and Black or African American patients. CONCLUSION: Patients on remdesivir had lower, albeit not significant, all-cause in hospital mortality, and the use of remdesivir did not increase the risk for AKI. Promising signals from this study need to be confirmed by future placebo-controlled randomized clinical trials.


id: cord-256130-zhlvvuj4
author: Nordén, Rickard
date: 2018-03-06
txt: ./txt/cord-256130-zhlvvuj4.txt
cache: ./cache/cord-256130-zhlvvuj4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29644247/
doi: 10.1093/ofid/ofy050
summary:
  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.

title:
  Quantification of Torque Teno Virus and Epstein-Barr Virus Is of Limited Value for Predicting the Net State of Immunosuppression After Lung Transplantation

abstract:
  BACKGROUND: Major hurdles for survival after lung transplantation are rejections and infectious complications. Adequate methods for monitoring immune suppression status are lacking. 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. METHODS: This prospective single-center study included 98 patients followed for 2 years after transplantation. Bacterial infections, fungal infections, viral respiratory infections (VRTI), cytomegalovirus (CMV) viremia, and acute rejections, as well as TTV and EBV levels, were monitored. RESULTS: The levels of torque teno virus DNA increased rapidly after transplantation, likely due to immunosuppressive treatment. A modest increase in levels of Epstein-Barr virus DNA was also observed after transplantation. There were no associations between either TTV or EBV and infectious events or acute rejection, respectively, during follow-up. When Tacrolimus was the main immunosuppressive treatment, TTV DNA levels were significantly elevated 6–24 months after transplantation as compared with Cyclosporine treatment. CONCLUSIONS: Although replication of TTV, but not EBV, appears to reflect the functionality of the immune system, depending on the type of immunosuppressive treatment, quantification of TTV or EBV as biomarkers has limited potential for defining the net state of immune suppression.


id: cord-256195-1hmzgwrw
author: Izzy, Saef
date: 2020-09-01
txt: ./txt/cord-256195-1hmzgwrw.txt
cache: ./cache/cord-256195-1hmzgwrw.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33088846/
doi: 10.1093/ofid/ofaa401
summary:
  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.

title:
  Characteristics and outcomes of Latinx patients with COVID-19 in comparison to other ethnic and racial groups

abstract:
  BACKGROUND: There is limited understating of the impact of COVID-19 on the Latinx population. We hypothesized that Latinx patients would be more likely to be hospitalized and admitted to the ICU than White patients. METHODS: We analyzed all patients with COVID-19 in 12 Massachusetts hospitals between February 1 and April 14, 2020. We examined the association between race, ethnicity, age, reported comorbidities, and hospitalization and intensive care unit (ICU) admission using multivariable regression. RESULTS: Of 5190 COVID-19 patients, 29% were hospitalized; 33% required ICU and 4.3% died. 46% of patients were White, 25% Latinx, 14% African American, and 3% Asian American. Ethnicity and race were significantly associated with hospitalization. More Latinx and African American patients in the younger age groups were hospitalized than whites. Latinx and African Americans disproportionally required ICU, with 39% of hospitalized Latinx patients requiring ICU compared to 33% of African Americans, 24% of Asian Americans, and 30% of Whites (p&0.007). Within each ethnic and racial group, age and male gender were independently predictive of hospitalization. Previously reported pre-existing comorbidities contributed to the need for hospitalization in all racial and ethnic groups (p&0.05). However, the observed disparities were less likely related to reported comorbidities, with Latinx and African American patients being admitted at twice the rate of Whites, regardless of such comorbidities. CONCLUSIONS: Latinx and African American patients with COVID-19 have higher rates of hospitalization and ICU admission than White patients. The etiologies of such disparities are likely multifactorial and cannot be explained only by reported comorbidities.


id: cord-258113-mnou31j3
author: Wang, Yaping
date: 2020-05-19
txt: ./txt/cord-258113-mnou31j3.txt
cache: ./cache/cord-258113-mnou31j3.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/ofid/ofaa187
doi: 10.1093/ofid/ofaa187
summary:
  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

title:
  Clinical Characteristics of Patients Infected With the Novel 2019 Coronavirus (SARS-Cov-2) in Guangzhou, China

abstract:
  BACKGROUND: The clinical manifestations and factors associated with the severity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections outside of Wuhan are not clearly understood. METHODS: All laboratory-confirmed cases with SARS-Cov-2 infection who were hospitalized and monitored in Guangzhou Eighth People’s Hospital were recruited from January 20 to February 10. RESULTS: A total of 275 patients were included in this study. The median patient age was 49 years, and 63.6% had exposure to Wuhan. The median virus incubation period was 6 days. Fever (70.5%) and dry cough (56.0%) were the most common symptoms. A decreased albumin level was found in 51.3% of patients, lymphopenia in 33.5%, and pneumonia based on chest computed tomography in 86%. Approximately 16% of patients (n = 45) had severe disease, and there were no deaths. Compared with patients with nonsevere disease, those with severe disease were older, had a higher frequency of coexisting conditions and pneumonia, and had a shorter incubation period (all P < .05). There were no differences between patients who likely contacted the virus in Wuhan and those who had no exposure to Wuhan. Multivariate logistic regression analysis indicated that older age, male sex, and decreased albumin level were independently associated with disease severity. 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.


id: cord-259969-q65k590s
title: Cutaneous Vasculitis in a Patient With COVID-19
author: Kösters, Katrin
date: 2020-10-05
txt: ./txt/cord-259969-q65k590s.txt
cache: ./cache/cord-259969-q65k590s.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/ofid/ofaa474
doi: 10.1093/ofid/ofaa474
summary:
  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

abstract:
  We describe a 43-year-old patient with coronavirus disease 2019 who developed a bullous hemorrhagic rash that progressed to necrotic lesions. Histopathology confirmed a vasculitis of small- and medium-sized cutaneous vessels.


id: cord-260257-phmd0u6d
author: Siegler, Aaron J
date: 2020-06-30
txt: ./txt/cord-260257-phmd0u6d.txt
cache: ./cache/cord-260257-phmd0u6d.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/ofid/ofaa269
doi: 10.1093/ofid/ofaa269
summary:
  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.

title:
  Willingness to seek laboratory testing for SARS-CoV-2 with home, drive-through, and clinic-based specimen collection locations

abstract:
  BACKGROUND: SARS-CoV-2 virus testing for persons with COVID-19 symptoms, and contact tracing for those testing positive, will be critical to successful epidemic control. Willingness of persons experiencing symptoms to seek testing may determine the success of this strategy. 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. Instructions clarified that home-collected specimens would be mailed to a laboratory for testing. We presented similar willingness questions regarding testing during follow-up care. RESULTS: Of 1435 participants, comprising a broad range of sociodemographic groups, 92% were willing to test with a home saliva specimen, 88% with home swab, 71% with drive-through swab, and 60% with clinic collected swab. Moreover, 68% indicated they would be more likely to get tested if there was a home testing option. There were no significant differences in willingness items across sociodemographic variables or for those currently experiencing COVID-19 symptoms. Results were nearly identical for willingness to receive testing for follow-up COVID-19 care. CONCLUSIONS: We observed a hierarchy of willingness to test for SARS-CoV-2, ordered by the degree of contact required. Home specimen collection options could result in up to one-third more symptomatic persons seeking testing, facilitating contact tracing and optimal clinical care. Remote specimen collection options may ease supply chain challenges and decrease the likelihood of nosocomial transmission. As home specimen collection options receive regulatory approval, they should be scaled rapidly by health systems.


id: cord-261619-31jk1vh6
title: Outcomes of Coronavirus Disease 2019 Drive-Through Screening at an Academic Military Medical Center
author: Lindholm, David A
date: 2020-07-17
txt: ./txt/cord-261619-31jk1vh6.txt
cache: ./cache/cord-261619-31jk1vh6.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/ofid/ofaa306
doi: 10.1093/ofid/ofaa306
summary:
  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.

abstract:
  Drive-through coronavirus disease 2019 screening can evaluate large numbers of patients while reducing healthcare exposures and personal protective equipment use. We describe the characteristics of screened individuals as well as drive-through process and outcome measures. Optimal drive-through screening involves rapid turnaround of test results and linkage to follow-up care.


id: cord-267023-w5ig7mrl
author: Nori, Priya
date: 2017-07-20
txt: ./txt/cord-267023-w5ig7mrl.txt
cache: ./cache/cord-267023-w5ig7mrl.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28748196/
doi: 10.1093/ofid/ofx117
summary:
  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.

title:
  Developing Interactive Antimicrobial Stewardship and Infection Prevention Curricula for Diverse Learners: A Tailored Approach

abstract:
  BACKGROUND. To impart principles of antimicrobial stewardship (AS) and infection prevention and control (IPC), we developed a curriculum tailored to the diverse aptitudes of learners at our medical center. METHODS. 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. Interventions were implemented in 2012–2016 using a quasi-experimental before-and-after study design, and this was assessed using pre- and postintervention surveys or audit of antibiotic prescriptions. RESULTS. Over 180 medical students participated in the AS and IPC seminars. After smartphone app introduction, 69% reported using the app as their preferred source of antibiotic information. Approximately 70% of students felt comfortable prescribing antibiotics for a known infection compared with 40% at baseline (P = .02), and approximately 83% were able to identify the appropriate personal protective equipment for specific scenarios. Approximately 99% agreed that they have a role in promoting patient safety and preventing healthcare-associated infections as medical students. At 20 months, appropriateness of trainee antibiotic prescriptions increased by 20% (P < .01). Almost all ID fellows indicated that the AS and IPC seminar was a vital training supplement. Uptake of internist antibiotic recommendations using AS decision support tools was approximately 70%. CONCLUSIONS. All 5 interventions addressed learning objectives and knowledge gaps and are applicable across a range of environments. Evaluating long-term impact of our curriculum is the focus of future study.


id: cord-268662-mw8ec7u2
title: Prolonged low-dose methylprednisolone in patients with severe COVID-19 pneumonia
author: Salton, Francesco
date: 2020-09-12
url: https://www.ncbi.nlm.nih.gov/pubmed/33072814/
doi: 10.1093/ofid/ofaa421
abstract:
  BACKGROUND: In hospitalized patients with COVID-19 pneumonia, progression to acute respiratory failure requiring invasive mechanical ventilation (MV) is associated with significant morbidity and mortality. Severe dysregulated systemic inflammation is the putative mechanism. We hypothesize that early prolonged methylprednisolone (MP) treatment could accelerate disease resolution, decreasing the need for ICU and mortality. METHODS: We conducted a multicenter, observational study to explore the association between exposure to prolonged, low-dose, MP treatment and need for ICU referral, intubation or death within 28 days (composite primary endpoint) in patients with severe COVID-19 pneumonia admitted to Italian respiratory high-dependency units. Secondary outcomes were invasive MV-free days and changes in C-reactive protein (CRP) levels. RESULTS: Findings are reported as MP (n=83) vs. control (n=90). The composite primary endpoint was met by 19 vs. 40 [adjusted hazard ratio (HR) 0.41; 95% confidence interval (CI): 0.24-0.72]. Transfer to ICU and need for invasive MV was necessary in 15 vs. 27 (p=0.07) and 14 vs. 26 (p=0.10), respectively. By day 28, the MP group had fewer deaths (6 vs. 21, adjusted HR=0.29; 95% CI: 0.12-0.73) and more days off invasive MV (24.0 ± 9.0 vs. 17.5 ± 12.8; p=0.001). Study treatment was associated with rapid improvement in PaO(2):FiO(2) and CRP levels. The complication rate was similar for the two groups (p=0.84). CONCLUSION: In patients with severe COVID-19 pneumonia, early administration of prolonged MP treatment was associated with a significantly lower hazard of death (71%) and decreased ventilator dependence. Treatment was safe and did not impact viral clearance. A large RCT (RECOVERY trial) has been performed that validates these findings. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov NCT04323592


id: cord-268975-xzdh8yum
title: Public behavior change, perceptions, depression, and anxiety in relation to the COVID-19 outbreak
author: Huang, Jing
date: 2020-07-03
txt: ./txt/cord-268975-xzdh8yum.txt
cache: ./cache/cord-268975-xzdh8yum.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/ofid/ofaa273
doi: 10.1093/ofid/ofaa273
summary:
  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.

abstract:
  BACKGROUND: The COVID-19 has spread rapidly and world-widely, which elicits public panic and psychological problems. Public protective behaviors and perception play crucial roles in controlling the spread of illness and psychological status. METHODS: We conducted a cross-sectional online survey in the hardest-hit Hubei province and other areas in China affected by COVID-19 outbreak. Questions about their basic information, the perception of the COVID-19 outbreak, recent preventive or avoidance behaviors, and self-reported mental health scales including the Patient Health Questionnaire (PHQ-9) and Self-Rating Anxiety Scale (SAS) were included. Binary logistic regressions were used to investigate the association between personal variables/perceptions and psychological distress. RESULTS: 6,261 people were included for analysis, with 3,613 (57.7%) in Hubei province (1,743 in Wuhan). A majority of people have adopted preventive and avoidance behaviors. People from Hubei, with contact history, and people who or whose family members were infected had much higher depression or anxiety prevalence. Providing truthful and sufficient information, informing the public about the severity of the disease, and perceptions that the outbreak will be control by protective behaviors were associated with lower depression and anxiety prevalence. CONCLUSIONS: Assessing the public response, perception, and psychological burden during the outbreak may help improve public health recommendations and deliver timely psychological intervention. Further researches can focus on the psychological status of a specialized group to identify ways for better support based on public response and psychological demand.


id: cord-270703-c8mv2eve
author: Christensen, Paul A
date: 2018-11-30
txt: ./txt/cord-270703-c8mv2eve.txt
cache: ./cache/cord-270703-c8mv2eve.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30619910/
doi: 10.1093/ofid/ofy322
summary:
  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.

title:
  Real-time Communication With Health Care Providers Through an Online Respiratory Pathogen Laboratory Report

abstract:
  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. Real-time access to accurate regional laboratory observation data during an epidemic influenza season can guide diagnostic and therapeutic strategies.


id: cord-274943-fn3m14cn
title: Febrile Rhinovirus Illness During Pregnancy Is Associated With Low Birth Weight in Nepal
author: Philpott, Erin K
date: 2017-04-06
url: https://www.ncbi.nlm.nih.gov/pubmed/28584855/
doi: 10.1093/ofid/ofx073
abstract:
  BACKGROUND: Adverse birth outcomes, including low birth weight (LBW), defined as <2500 grams, small-for-gestational-age (SGA), and prematurity, contribute to 60%–80% of infant mortality worldwide and may be related to infections during pregnancy. The aim of this study was to assess whether febrile human rhinovirus (HRV) illness is associated with adverse birth outcomes. METHODS: Active household-based weekly surveillance was performed for respiratory illness episodes in pregnant women as part of a community-based, prospective, randomized trial of maternal influenza immunization in rural Nepal. Rhinovirus (HRV) febrile illness episodes were defined as fever plus cough, sore throat, runny nose, and/or myalgia with HRV detected on mid-nasal swab. Multivariate regression analysis evaluated the association between febrile HRV respiratory illness and adverse birth outcomes. RESULTS: Overall, 96 (3%) of 3693 pregnant women had HRV-positive febrile respiratory illnesses. Infants born to pregnant women with HRV febrile illness had a 1.6-fold increased risk of being LBW compared with those with non-HRV febrile illness (28 of 96 [38%] vs 109 of 458 [24%]; relative risk [RR], 1.6; 95% confidence interval [CI], 1.1–2.3). No difference in risk of LBW was observed between infants born to mothers with non-HRV febrile respiratory illness and those without respiratory illness during pregnancy (109 of 458 [24%] vs 552 of 2220 [25%], respectively; RR, 1.0; 95% CI, 0.8–1.2). CONCLUSIONS: Febrile illness due to rhinovirus during pregnancy was associated with increased risk of LBW in a rural South Asian population. Interventions to reduce the burden of febrile respiratory illness due to rhinovirus during pregnancy may have a significant impact on LBW and subsequent infant mortality.


id: cord-279334-j0i9ozsz
title: Coronavirus Disease 2019 Treatment: A Review of Early and Emerging Options
author: McCreary, Erin K
date: 2020-03-23
url: https://doi.org/10.1093/ofid/ofaa105
doi: 10.1093/ofid/ofaa105
abstract:
  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread across the globe resulting in a pandemic. At the time of this review, COVID-19 has been diagnosed in more than 200 000 patients and associated with over 8000 deaths (Centers for Disease Control and Prevention, World Health Organization). On behalf of the Society of Infectious Diseases Pharmacists, we herein summarize the current evidence as of March 18, 2020 to provide guidance on potential COVID-19 treatment options. It is important to caution readers that new data emerges daily regarding clinical characteristics, treatment options, and outcomes for COVID-19. Optimized supportive care remains the mainstay of therapy, and the clinical efficacy for the subsequent agents is still under investigation. Antimicrobial stewardship programs, including infectious diseases pharmacists and physicians, are at the forefront of COVID-19 emergency preparedness. We encourage all readers to continue to assess clinical data as it emerges and share their experience within our community in a well-controlled, adequately powered fashion.


id: cord-282862-kve6fa49
author: Pastick, Katelyn A
date: 2020-08-13
url: https://www.ncbi.nlm.nih.gov/pubmed/32929403/
doi: 10.1093/ofid/ofaa350
title:
  A Systematic Review of Treatment and Outcomes of Pregnant Women with COVID-19 – A Call for Clinical Trials

abstract:
  BACKGROUND: Data pertaining to COVID-19 in pregnancy are limited; to better inform clinicians, we collated data from COVID-19 cases in pregnancy and summarized clinical trials enrolling this population. METHODS: We performed a systematic literature review of PubMed/MEDLINE to identify cases of COVID-19 in pregnancy or the postpartum period and associated outcomes. We then evaluated the proportion of COVID-19 clinical trials (from Clinicaltrials.gov) excluding pregnant or breastfeeding persons (both through June 29(th), 2020). RESULTS: We identified 11,308 published cases of COVID-19 in pregnancy. Of those reporting disease severity, 21% (416/1999) were severe/critical. Maternal and neonatal survival were reassuring (98% [10437/10597] and 99% [1155/1163], respectively). Neonatal disease was rare with only 41 possible cases of infection reported in the literature. Of 2351 ongoing COVID-19 therapeutic clinical trials, 1282 were enrolling persons of reproductive age and 65% (829/1282) excluded pregnant persons. Pregnancy was an exclusion criterion for 69% (75/109) of chloroquine/hydroxychloroquine, 80% (28/35) of lopinavir/ritonavir, and 48% (44/91) of convalescent plasma studies. We identified 48 actively recruiting or completed drug trials reporting inclusion of this population. CONCLUSIONS: There are limited published reports of COVID-19 in pregnancy despite more than 14 million cases worldwide. To date, clinical outcomes appear reassuring, but data related to important long-term outcomes are missing or not yet reported. The large number of clinical trials excluding pregnant persons, despite interventions with safety data in pregnancy, is concerning. In addition to observational cohort studies, pregnancy specific adaptive clinical trials could be designed to identify safe and effective treatments.


id: cord-288044-ver1nrsz
author: Sierra, Beatriz
date: 2020-09-03
txt: ./txt/cord-288044-ver1nrsz.txt
cache: ./cache/cord-288044-ver1nrsz.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/ofid/ofaa407
doi: 10.1093/ofid/ofaa407
summary:
  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.

title:
  Association of early nasopharyngeal immune markers with COVID-19 clinical outcome: predictive value of CCL2/MCP-1

abstract:
  Early recognition of severe forms of COVID-19 is essential for an opportune and effective intervention, reducing life risk complications. An altered inflammatory immune response seems to be associated to COVID-19´s pathogenesis and progression to severity. Here we demonstrated the utility of the early nasopharyngeal swab sample for detection of the early expression of immune markers and the potential value of CCL2/MCP-1 in predicting disease outcome


id: cord-296890-08kqtw8s
author: Toh, Teck-Hock
date: 2019-02-13
txt: ./txt/cord-296890-08kqtw8s.txt
cache: ./cache/cord-296890-08kqtw8s.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/ofid/ofz074
doi: 10.1093/ofid/ofz074
summary:
  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.

title:
  High Prevalence of Viral Infections Among Hospitalized Pneumonia Patients in Equatorial Sarawak, Malaysia

abstract:
  BACKGROUND: Although pneumonia is a known cause of morbidity and mortality in Sarawak, Malaysia, the etiology and epidemiology of pneumonia are not well described in this equatorial region. Routine clinical diagnostics for pneumonia etiology at government hospitals in Sarawak had historically involved only bacterial diagnostics. Viral diagnostics were only obtained through outside consultations. METHODS: From June 15, 2017 to May 14, 2018, we collected nasopharyngeal swabs from 600 patients of all ages older than 1 month hospitalized with pneumonia at Sibu and Kapit Hospitals. 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. RESULTS: Of 599 samples examined, 288 (48%) had molecular evidence of 1 or more respiratory viruses. Overall, the most prevalent virus detected was RSV-A (14.2%) followed by AdV (10.4%) and IAV (10.4%), then RSV-B (6.2%), EV (4.2%), IBV (2.2%), PIV-3 (1.7%), CoV (1.0%), PIV-1 (1.0%), PIV-4 (0.7%), and PIV-2 (0.2%). No specimens were confirmed positive for ICV or IDV. CONCLUSIONS: The high prevalence of viruses detected in this study suggest that respiratory viruses may be responsible for considerable morbidity in equatorial regions such as Sarawak. Access to viral diagnostics are very necessary for medical staff to determine appropriate pneumonia treatments.


id: cord-303091-jky6jlrl
title: Characterization of prolonged COVID-19 symptoms in an outpatient telemedicine clinic
author: Cellai, Michele
date: 2020-09-12
txt: ./txt/cord-303091-jky6jlrl.txt
cache: ./cache/cord-303091-jky6jlrl.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33117851/
doi: 10.1093/ofid/ofaa420
summary:
  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).

abstract:
  We identified patients with coronavirus disease 2019 (COVID-19) in a telemedicine clinic who requested ongoing follow-up calls 6 weeks after symptom onset. In this group, respiratory symptoms are the most common complaints, asthma and lung disease are frequent comorbidities, and patients often have not returned to work or usual activity.


id: cord-303935-qdehf6rb
author: Yun, Heather C.
date: 2015-09-01
url: https://doi.org/10.1093/ofid/ofv120
doi: 10.1093/ofid/ofv120
title:
  Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine

abstract:
  Background. Adenovirus (Ad) has long been the predominant cause of acute respiratory illness (ARI) in military trainees. In 2011, live oral Ad vaccines for serotypes 4 and 7 were reintroduced into US basic military training populations. This study evaluated the impact on clinical presentations and other respiratory pathogens. Methods. The Center for Advanced Molecular Detection at Joint Base San Antonio-Lackland prospectively collects demographic, clinical, and polymerase chain reaction data from respiratory specimens (throat swab and nasal wash) among Air Force trainees presenting for care of ARI. Results. From June 2008 to August 2013, 2660 trainees enrolled and were tested for selected respiratory pathogens. Post-vaccine introduction (VI), reported systemic symptoms were less frequent, including fever (38% vs 94%) and myalgia (37% vs 67%; P < .01). Median temperature and heart rate decreased (98.4 vs 101.3°F, 81 vs 96 beats per minute; P < .01). Ad detection decreased for all Ad (3% vs 68%), Ad4 (1% vs 70%), 7 (0% vs 8%), 14 (0% vs 5%), and 3 (0.1% vs 2%); P < .01). Rhinovirus and cases with no pathogen identified increased in frequency (35% vs 18%, 51% vs 14%; P < .01). Conclusions. Acute respiratory illness in military trainees post-VI is associated with decreased severity of systemic symptoms and reduced fever and heart rate. Marked reductions in frequency of Ad serotypes are seen, including those in the vaccine, with no serotype shift. However, detection of several other respiratory pathogens, most notably rhinovirus, is observed in increasing proportions, and a majority are now undiagnosed clinical syndromes.


id: cord-305512-p5qchjva
author: Alghamdi, Abdulaziz
date: 2019-09-30
url: https://doi.org/10.1093/ofid/ofz370
doi: 10.1093/ofid/ofz370
title:
  Molecular Evidence of Influenza A Virus Circulation in African Dromedary Camels Imported to Saudi Arabia, 2017–2018

abstract:
  Little is known about influenza A viruses in dromedaries. Here, we detected influenza A viral RNA in 11 specimens (1.7 %) out of 665 nasal swabs collected from dromedaries between 2017 and 2018 in Saudi Arabia. Positive samples were detected only in imported camels from Sudan and Djibouti but not local ones. Partial genome sequencing indicates a close relationship to 2009–2019 human/swine influenza A H1N1 isolates from different countries, suggesting possible interspecies transmission. Taken together, dromedaries could represent a potentially unrecognized permissive host for these viruses, highlighting the need for enhanced surveillance in animals to aid implementation of one-health strategies.


id: cord-310807-p5cb6idp
title: Human Coronavirus-HKU1 Infection Among Adults in Cleveland, Ohio
author: Kanwar, Anubhav
date: 2017-03-25
url: https://www.ncbi.nlm.nih.gov/pubmed/28616442/
doi: 10.1093/ofid/ofx052
abstract:
  BACKGROUND. Human coronaviruses (CoV) have been long recognized as a common cause of respiratory tract disease including severe respiratory tract illness. Coronavirus-HKU1 has been described predominantly among children less than 5 years of age in the United States with few studies characterizing the disease spectrum among adults. METHODS. Nasopharyngeal specimens of patients with respiratory symptoms were analyzed for CoV-HKU1 by NxTAG Respiratory Pathogen Panel multiplex assay from February 7, 2016 to April 30, 2016. Epidemiologic, clinical, and laboratory data were collected on adults (patients >18 years) whose samples screened positive. RESULTS. Of 832 adult respiratory specimens screened, 13 (1.6%) cases of CoV-HKU1 were identified. Adults age ranged between 23 and 75 years and 6 (46%) were males. All of whom had 1 or more respiratory symptoms, and 5 (38%) also reported 1 or more gastrointestinal symptoms. Eleven (85%) reported history of smoking and 5 (38%) used inhaled steroids. Seven (54%) required hospitalization, 5 (71%) of these needed supplemental oxygen, and 2 (29%) were admitted to intensive care. Median length of hospitalization was 5 days. Eight (62%) received antibiotics despite identification of CoV-HKU1. Infectious work-up in 1 patient who died did not reveal any other pathogen. In 2 (15%) CoV-HKU1-positive adults, the only viral coinfection detected was influenza A. CONCLUSIONS. Coronavirus-HKU1 accounted for 1.6% of adult respiratory infections and should be considered in differential diagnosis of severe respiratory illnesses among adults.


id: cord-310872-2z1wnj63
title: Alignment With Market Forces: The “Re-Whithering” of Infectious Diseases
author: Spellberg, Brad
date: 2020-06-20
txt: ./txt/cord-310872-2z1wnj63.txt
cache: ./cache/cord-310872-2z1wnj63.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/ofid/ofaa245
doi: 10.1093/ofid/ofaa245
summary:
  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.

abstract:
  Given constant emergence of new infectious threats, infectious diseases (ID) should be one of the most attractive medical specialties to students and trainees. Yet, ID Fellowship programs continue to not fill in the match, and ID remains among the lowest paid specialties. 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. Einstein said, “Continuing to do the same thing over and over and expecting a different result is the definition of insanity.” We must move towards alignment with market forces, to benefit our patients, society, and our colleagues.


id: cord-311082-sspcz9t6
author: Chen, Shi
date: 2020-08-07
txt: ./txt/cord-311082-sspcz9t6.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32851113/
doi: 10.1093/ofid/ofaa333
summary:
  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.

title:
  Four Challenges Associated With Current Mathematical Modeling Paradigm of Infectious Diseases and Call for a Shift

abstract:
  Mathematical models are critical tools to characterize COVID-19 dynamics and take action accordingly. 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. Therefore, these challenges made the current SEIR modeling paradigm less practical to handle the complex COVID-19 and future pandemics. Novel and more reliable data sources and alternative modeling paradigms are needed to address these issues.


id: cord-314517-n1yj2zdy
author: Huang, Dayong
date: 2020-08-31
txt: ./txt/cord-314517-n1yj2zdy.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1093/ofid/ofaa400
doi: 10.1093/ofid/ofaa400
summary:
  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.

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

abstract:
  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. Availability of accessible personal protective equipment (PPE) is vital to effective care and prevention. METHODS: We conducted a cross-sectional survey from February 24-28, 2020 to assess COVID-19 preparedness among health workers. In addition, we assessed trends from search engine web crawling and text-mining data trending over the Sina Weibo platform from January 1 to March 3, 2020. Data were abstracted on Chinese outbreak preparedness. RESULTS: In the survey, we engaged 6,350 persons, of whom 1,065 agreed to participate and after an eligibility logic check, 1,052 participated (16.6%). We accessed 412 internet posts as to PPE availability. 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. Health workers with more confidence in their abilities to respond were those with more faith in their institution’s response capacities. Elements of readiness included having airborne infection isolation room, visitor control procedures, training in precautions and PPE use. Both survey and web post assessments suggested that health workers in need were unable to reliably obtain PPE. CONCLUSION: Health workers’ self-confidence depends on perceived institutional readiness. Failure to maintain available PPE inventory for emerging infectious diseases preparedness suggests a failure to learn key lessons from the 2003-2004 SARS outbreak in China.


id: cord-320511-qnxj7d9l
title: The antibody response to SARS-CoV-2 infection
author: Hueston, Linda
date: 2020-08-27
url: https://doi.org/10.1093/ofid/ofaa387
doi: 10.1093/ofid/ofaa387
abstract:
  BACKGROUND: Testing for SARS-CoV-2-specific antibodies has become an important tool, complementing nucleic acid tests (NATs) for diagnosis and for determining the prevalence of COVID-19 in population serosurveys. The magnitude and persistence of antibody responses are critical for assessing the duration of immunity. METHODS: A SARS-CoV-2-specific immunofluorescent antibody (IFA) assay for IgG, IgA and IgM was developed, and prospectively evaluated by comparison to the reference standard of NAT on respiratory tract samples from individuals with suspected COVID-19. Neutralizing antibody responses were measured in a subset of samples using a standard microneutralization assay. RESULTS: 2753 individuals were eligible for the study (126 NAT positive, prevalence 4·6%). The median ‘window period’ from illness onset to appearance of antibody was 10·2 days (range 5·8 – 14·4). The sensitivity and specificity of either SARS-CoV-2 IgG, IgA or IgM when collected 14 days or more after symptom onset was 91·3% (95% CI 84·9-95·6) and 98·9% (98·4-99·3), respectively. The negative predictive value was 99·6% (99·3-99·8). The positive predictive value of detecting any antibody class was 79·9% (73·3-85·1); this increased to 96·8% (90·7-99·0) for the combination of IgG and IgA. CONCLUSIONS: Measurement of SARS-CoV-2-specific antibody by IFA is an accurate method to diagnose COVID-19. Serological testing should be incorporated into diagnostic algorithms for SARS-CoV-2 infection to identify additional cases where NAT was not performed, and resolve cases where false-negative and false-positive NATs are suspected. The majority of individuals develop robust antibody responses following infection, but the duration of these responses and implications for immunity remain to be established.


id: cord-321000-3jd2gn73
author: Karra, Nour
date: 2020-08-13
url: https://doi.org/10.1093/ofid/ofaa355
doi: 10.1093/ofid/ofaa355
title:
  A Case of Hemophagocytic Lymphohistiocytosis Associated With Mediterranean Spotted Fever in a Healthy 29-Year-Old Female

abstract:
  A 29-year-old female presented with fever, headache, and epigastric pain. Though her initial presentation was benign and nonspecific, she soon developed a full-blown cytokine storm with disseminated intravascular coagulation. She was diagnosed with hemophagocytosis secondary to Rickettsia conorii infection. A good outcome was achieved thanks to prompt diagnosis and proper treatment.


id: cord-322524-bq9ok8h1
author: Belongia, Edward A
date: 2018-11-27
url: https://www.ncbi.nlm.nih.gov/pubmed/30619907/
doi: 10.1093/ofid/ofy316
title:
  Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old

abstract:
  BACKGROUND: The epidemiology and burden of respiratory syncytial virus (RSV) illness are not well defined in older adults. METHODS: Adults ≥60 years old seeking outpatient care for acute respiratory illness were recruited from 2004–2005 through 2015–2016 during the winter seasons. RSV was identified from respiratory swabs by multiplex polymerase chain reaction. Clinical characteristics and outcomes were ascertained by interview and medical record abstraction. The incidence of medically attended RSV was estimated for each seasonal cohort. RESULTS: RSV was identified in 243 (11%) of 2257 enrollments (241 of 1832 individuals), including 121 RSV type A and 122 RSV type B. The RSV clinical outcome was serious in 47 (19%), moderate in 155 (64%), and mild in 41 (17%). Serious outcomes included hospital admission (n = 29), emergency department visit (n = 13), and pneumonia (n = 23) and were associated with lower respiratory tract symptoms during the enrollment visit. Moderate outcomes included receipt of a new antibiotic prescription (n = 144; 59%), bronchodilator/nebulizer (n = 45; 19%), or systemic corticosteroids (n = 28; 12%). The relative risk of a serious outcome was significantly increased in persons aged ≥75 years (vs 60–64 years) and in those with chronic obstructive pulmonary disease or congestive heart failure. The average seasonal incidence was 139 cases/10 000, and it was significantly higher in persons with cardiopulmonary disease compared with others (rate ratio, 1.89; 95% confidence interval, 1.44–2.48). CONCLUSIONS: RSV causes substantial outpatient illness with lower respiratory tract involvement. Serious outcomes are common in older patients and those with cardiopulmonary disease.


id: cord-326642-kc85pev4
author: Cohen, Adam L.
date: 2015-09-19
url: https://www.ncbi.nlm.nih.gov/pubmed/26566534/
doi: 10.1093/ofid/ofv139
title:
  Parainfluenza Virus Infection Among Human Immunodeficiency Virus (HIV)-Infected and HIV-Uninfected Children and Adults Hospitalized for Severe Acute Respiratory Illness in South Africa, 2009–2014

abstract:
  Background. Parainfluenza virus (PIV) is a common cause of acute respiratory tract infections, but little is known about PIV infection in children and adults in Africa, especially in settings where human immunodeficiency virus (HIV) prevalence is high. Methods. We conducted active, prospective sentinel surveillance for children and adults hospitalized with severe acute respiratory illness (SARI) from 2009 to 2014 in South Africa. We enrolled controls (outpatients without febrile or respiratory illness) to calculate the attributable fraction for PIV infection. Respiratory specimens were tested by multiplex real-time reverse-transcription polymerase chain reaction assay for parainfluenza types 1, 2, and 3. Results. Of 18 282 SARI cases enrolled, 1188 (6.5%) tested positive for any PIV type: 230 (19.4%) were type 1; 168 (14.1%) were type 2; 762 (64.1%) were type 3; and 28 (2.4%) had coinfection with 2 PIV types. After adjusting for age, HIV serostatus, and respiratory viral coinfection, the attributable fraction for PIV was 65.6% (95% CI [confidence interval], 47.1–77.7); PIV contributed to SARI among HIV-infected and -uninfected children <5 years of age and among individuals infected with PIV types 1 and 3. The observed overall incidence of PIV-associated SARI was 38 (95% CI, 36–39) cases per 100 000 population and was highest in children <1 year of age (925 [95% CI, 864–989] cases per 100 000 population). Compared with persons without HIV, persons with HIV had an increased relative risk of PIV hospitalization (9.4; 95% CI, 8.5–10.3). Conclusions. Parainfluenza virus causes substantial severe respiratory disease in South Africa among children <5 years of age, especially those that are infected with HIV.


id: cord-327609-no58ucyq
author: Murkey, Jamie A.
date: 2017-06-13
url: https://www.ncbi.nlm.nih.gov/pubmed/28721353/
doi: 10.1093/ofid/ofx121
title:
  Hepatitis E Virus–Associated Meningoencephalitis in a Lung Transplant Recipient Diagnosed by Clinical Metagenomic Sequencing

abstract:
  Hepatitis E virus (HEV) infection uncommonly causes chronic hepatitis and neurologic disease. We describe a case of genotype 3a HEV meningoencephalitis diagnosed by metagenomic next-generation sequencing, illustrating the power of an unbiased molecular approach to microbial testing and the first reported case of HEV infection presumably acquired through lung transplantation.


id: cord-333459-asem8xjz
author: Mallipattu, S K
date: 2020-09-14
txt: ./txt/cord-333459-asem8xjz.txt
cache: ./cache/cord-333459-asem8xjz.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/ofid/ofaa436
doi: 10.1093/ofid/ofaa436
summary:
  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 ).

title:
  Geospatial Distribution and Predictors of Mortality in Hospitalized Patients with COVID-19: A Cohort Study

abstract:
  BACKGROUND: The global Coronavirus Disease 2019 (COVID-19) pandemic offers the opportunity to assess how hospitals managed the care of hospitalized patients with varying demographics and clinical presentation. The goal of this study is to demonstrate the impact of densely populated residential areas on hospitalization and to identify predictors of length of stay and mortality in hospitalized patients with COVID-19 in one of the hardest hit counties internationally. METHODS: This is a single-center cohort study of 1325 sequentially hospitalized patients with COVID-19 in New York between March 2, 2020 to May 11, 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 the remaining active study patients. RESULTS: The median age of the study cohort was 62 years (IQR - 49-75), and more than half were male (57%) with history of hypertension (60%), obesity (41%), and diabetes (42%). Geographic residence of the study patients was disproportionately associated with areas of higher population density (r(s)=0.235, p=0.004), with noted “hot spots” in the region. Study patients were predominantly hypertensive (MAP>90mmHg (670, 51%)) on presentation with lymphopenia (590, 55%), hyponatremia (411, 31%), and kidney dysfunction (eGFR&60ml/min/1.73m (2) (381, 29%)). Of the patients with a disposition (1188/1325), 15% (182/1188) required IMV and 21% (250/1188) developed acute kidney injury. In patients on IMV, median hospital length of stay in survivors (22 days; 16.5-29.5) was significantly longer than non-survivors (15 days; 10-23.75), but this was not due to prolonged time on the ventilator. The overall mortality in all hospitalized patients was 15% and in patients receiving IMV was 48%, which is predicted to minimally rise from 48% to 49% based on logistic regression models constructed to project the disposition in the remaining patients on the ventilator. Acute kidney injury during hospitalization (OR(E)=3.23) was the strongest predictor of mortality in patients requiring IMV. CONCLUSIONS: This is the first study to collectively utilize the demographics, clinical characteristics and hospital course of COVID-19 patients to identify predictors of poor outcomes that can be used for resource allocation in future waves of the pandemic.


id: cord-334210-lhadzo7o
author: Lepak, Alexander J
date: 2020-08-27
url: https://doi.org/10.1093/ofid/ofaa388
doi: 10.1093/ofid/ofaa388
title:
  Utility of Repeat Nasopharyngeal SARS-CoV-2 RT-PCR Testing and Refinement of Diagnostic Stewardship Strategies at a Tertiary Care Academic Center in a low Prevalence Area of the United States

abstract:
  BACKGROUND: Multiple factors have led to an extremely high volume of SARS-CoV-2 RT-PCR testing. Concerns exist about sensitivity and false-negative SARS-CoV-2 RT-PCR testing results. We describe a retrospective observational study examining the utility of repeat nasopharyngeal (NP) SARS-CoV-2 RT-PCR testing at an academic center in a low prevalence setting. METHODS: All patients within our health system with >1 NP SARS-CoV-2 RT-PCR test result were included. SARS-CoV-2 RT-PCR testing was performed according to one of four validated assays. Key clinical and demographic data was collected including whether the patient was inpatient or outpatient at time of the test and whether the test was performed as part of a person under investigation (PUI) for possible COVID-19 or for asymptomatic screening. RESULTS: A total of 660 patients had >1 NP SARS-CoV-2 PCR test performed. The initial test was negative in 638. There were only 6 negative-to-positive conversions (0.9%). All 6 were outpatients undergoing a PUI work-up 5-17 days after an initial negative result. In >260 inpatients with repeat testing, we found no instances of negative-to-positive conversion including those undergoing PUI or asymptomatic evaluation. CONCLUSIONS: In a low prevalence area, repeat inpatient testing after an initial negative result, using a highly analytically sensitive SARS-CoV-2 RT-PCR, failed to demonstrate negative-to-positive conversion. The clinical sensitivity of NP RT-PCR testing may be higher than previously believed. These results have helped shape diagnostic stewardship guidelines, in particular guidance to decrease repeated testing in the inpatient setting to optimize test utilization and preserve resources.


id: cord-347255-fl9lur4h
author: May, Larissa
date: 2019-11-05
txt: ./txt/cord-347255-fl9lur4h.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32128326/
doi: 10.1093/ofid/ofz481
summary:
  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.

title:
  Rapid Multiplex Testing for Upper Respiratory Pathogens in the Emergency Department: A Randomized Controlled Trial

abstract:
  BACKGROUND: Acute upper respiratory tract infections are a common cause of emergency department (ED) visits and often result in unnecessary antibiotic treatment. METHODS: We conducted a randomized clinical trial to evaluate the impact of a rapid, multipathogen respiratory panel (RP) test vs usual care (control). Patients were eligible if they were ≥12 months old, had symptoms of upper respiratory infection or influenza-like illness, and were not on antibiotics. The primary outcome was antibiotic prescription; secondary outcomes included antiviral prescription, disposition, and length of stay (ClinicalTrials.gov# NCT02957136). RESULTS: Of 191 patients enrolled, 93 (49%) received RP testing; 98 (51%) received usual care. Fifty-three (57%) RP and 7 (7%) control patients had a virus detected and reported during the ED visit (P = .0001). Twenty (22%) RP patients and 33 (34%) usual care patients received antibiotics during the ED visit (–12%; 95% confidence interval, –25% to 0.4%; P = .06/0.08); 9 RP patients received antibiotics despite having a virus detected. The magnitude of antibiotic reduction was greater in children (–19%) vs adults (–9%, post hoc analysis). There was no difference in antiviral use, length of stay, or disposition. CONCLUSIONS: Rapid RP testing was associated with a trend toward decreased antibiotic use, suggesting a potential benefit from more rapid viral tests in the ED. Future studies should determine if specific groups are more likely to benefit from testing and evaluate the relative cost and effectiveness of broad testing, focused testing, and a combined diagnostic and antimicrobial stewardship approach.


id: cord-350557-7i7122zi
author: Rawlings, Stephen A
date: 2020-08-07
url: https://www.ncbi.nlm.nih.gov/pubmed/32875005/
doi: 10.1093/ofid/ofaa325
title:
  No Evidence of SARS-CoV-2 Seminal Shedding Despite SARS-CoV-2 Persistence in the Upper Respiratory Tract

abstract:
  RNA viruses (eg, Zika, Ebola, HIV) are often shed in male genital secretions. We evaluated the presence and level of SARS-CoV-2 RNA in semen, nasal secretion, and saliva collected after confirmed infection. SARS-CoV-2 RNA was not detected in semen 6–17 days after the onset of symptoms despite concomitant shedding in oral secretions.


id: cord-350767-6kc4hyzo
title: The Pandemic Academy: Reflections of Infectious Diseases Fellows During COVID-19
author: Beh, Darius L L
date: 2020-06-25
url: https://doi.org/10.1093/ofid/ofaa256
doi: 10.1093/ofid/ofaa256
abstract:
  The COVID-19 pandemic has taken over the world at an unprecedented scale. As Infectious Diseases fellows, this has come straight into the heart of our specialty and created a unique impact on our training progress and perspective. Here, we reflect on our early experiences during the first three months of battling COVID-19 in Singapore and glean some lessons for this pandemic and beyond.


id: cord-351022-8y43jhmu
author: Schwartz, Carmela
date: 2020-09-01
url: https://doi.org/10.1093/ofid/ofaa384
doi: 10.1093/ofid/ofaa384
title:
  A dynamic response to exposures of healthcare workers to newly diagnosed COVID-19 patients or hospital personnel, in order to minimize cross transmission and need for suspension from work during the outbreak

abstract:
  BACKGROUND: During the corona virus disease (COVID-19) epidemic, many healthcare workers (HCWs) were exposed to infected persons, leading to suspension from work. We describe a dynamic response to exposures of HCWs at the Hadassah Hospital, Jerusalem, to minimize the need for suspension from work. METHODS: We performed an epidemiological investigation following each exposure to a newly diagnosed COVID-19 patient or HCW; close contacts were suspended from work. During the course of the epidemic, we adjusted our isolation criteria according to the timing of exposure related to symptoms onset, use of personal protective equipment and duration of exposure. In parallel, we introduced universal masking and performed periodic SARS-CoV-2 screening for all hospital personnel. We analyzed the number of HCWs suspended weekly from work and those who subsequently acquired infection. RESULTS: In the 51 investigations conducted during March-May 2020, we interviewed 1095 HCWs and suspended 400 (37%) from work, most of them, 251 (63%), during the first two weeks of the outbreak. The median duration of exposure was 30 minutes (IQR, 15-120). Only 5/400 (1.3%) developed infection, all in the first two weeks of the epidemic. After introduction of universal masking and despite loosening the isolation criteria, none of the exposed HCWs developed COVID-19. CONCLUSIONS: Relatively short exposures of HCWs, even if only either the worker or the patient wore a mask, probably poses a very low risk for infection. This allows us to perform strict follow-up of exposed HCWs in these exposures, combined with repeated testing, instead of suspension from work.


