# bib

id: cord-333943-9d93na7s
author: Jeong, Han Eol
date: 2020-07-27
txt: ./txt/cord-333943-9d93na7s.txt
cache: ./cache/cord-333943-9d93na7s.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1056
doi: 10.1093/cid/ciaa1056
summary:
  title: Association between NSAIDs use and adverse clinical outcomes among adults hospitalized with COVID-19 in South Korea: A nationwide study BACKGROUND: Non-steroidal anti-inflammatory drugs (NSAIDs) may exacerbate COVID-19 and worsen associated outcomes by upregulating the enzyme that SARS-CoV-2 binds to enter cells. [1, 2] Concerns exist that the use of nonsteroidal anti-inflammatory drugs (NSAIDs) may exacerbate COVID-19 by upregulating angiotensin-converting enzyme 2 (ACE2) expressions, [3, 4] the enzyme which SARS-CoV-2 binds to enter cells. This cohort study therefore aimed to examine the association between NSAIDs use, compared to non-use, and worsened clinical outcomes among adults hospitalized with A c c e p t e d M a n u s c r i p t page | 5 COVID-19 using South Korea''s nationwide healthcare database containing all COVID-19 patients. To our knowledge, this is the first population-based study conducted using all hospitalized patients with COVID-19 to assess the association between NSAID use and COVID-19 related outcomes.

title:
  Association between NSAIDs use and adverse clinical outcomes among adults hospitalized with COVID-19 in South Korea: A nationwide study

abstract:
  BACKGROUND: Non-steroidal anti-inflammatory drugs (NSAIDs) may exacerbate COVID-19 and worsen associated outcomes by upregulating the enzyme that SARS-CoV-2 binds to enter cells. To our knowledge, no study has examined the association between NSAID use and the risk of COVID-19-related outcomes. METHODS: We conducted a cohort study using South Korea’s nationwide healthcare database, which contains data of all subjects who received a test for COVID-19 (n=69,793) as of April 8, 2020. We identified adults hospitalized with COVID-19, where cohort entry was the date of hospitalization. NSAIDs users were those prescribed NSAIDs in the 7 days before and including cohort entry and non-users were those not prescribed NSAIDs during this period. Our primary outcome was a composite of in-hospital death, intensive care unit admission, mechanical ventilation use, and sepsis; our secondary outcomes were cardiovascular complications and acute renal failure. We conducted logistic regression analysis to estimate odds ratio (OR) with 95% confidence intervals (CI) using inverse probability of treatment weighting to minimize confounding. RESULTS: Of 1,824 adults hospitalized with COVID-19 (mean age 49.0 years; female 59%), 354 were NSAIDs users and 1,470 were non-users. Compared with non-use, NSAIDs use was associated with increased risks of the primary composite outcome (OR 1.54 [95% CI 1.13-2.11]) but insignificantly associated with cardiovascular complications (1.54 [0.96-2.48]) or acute renal failure (1.45 [0.49-4.14]). CONCLUSION: While awaiting the results of confirmatory studies, we suggest NSAIDs be used with caution among patients with COVID-19 as the harms associated with their use may outweigh their benefits in this population.


id: cord-335038-q32ghvsv
author: Huang, Jiao
date: 2020-08-17
txt: ./txt/cord-335038-q32ghvsv.txt
cache: ./cache/cord-335038-q32ghvsv.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32803216/
doi: 10.1093/cid/ciaa1186
summary:
  title: Epidemiological, virological and serological features of COVID-19 cases in people living with HIV in Wuhan City: A population-based cohort study METHODS: This population-based cohort study identified all COVID-19 cases among the whole PLWH in Wuhan city, China, by April 16, 2020. Previous studies have found that PLWH with low CD4 cell count, high HIV viral load and not taking antiretroviral treatment have an increased risk of other respiratory infections [9] . This indicates that COVID-19 cases in PLWH may have delayed viral clearance for SARS-CoV-2 because of immunosuppression, although clinical improvement of COVID-19 in PLWH was not worse than that of individuals without HIV infection as described in the present study and other published studies [25, 32] . CD4 cell count and the risk of AIDS or death in HIV-Infected adults on combination antiretroviral therapy with a suppressed viral load: a longitudinal cohort study from COHERE

title:
  Epidemiological, virological and serological features of COVID-19 cases in people living with HIV in Wuhan City: A population-based cohort study

abstract:
  BACKGROUND: We aimed to describe the epidemiological, virological and serological features of coronavirus disease 2019 (COVID-19) cases in people living with HIV (PLWH). METHODS: This population-based cohort study identified all COVID-19 cases among the whole PLWH in Wuhan city, China, by April 16, 2020. The epidemiological, virological and serological features were analyzed based on the demographic data, temporal profile of nucleic acid test for SARS-CoV-2 during the disease, and SARS-CoV-2-specific IgM and IgG after recovery. RESULTS: From January 1 to April 16, 2020, 35 of 6001 PLWH have experienced COVID-19, with the cumulative incidence of COVID-19 to be 0.58% (95%CI: 0.42%-0.81%). Among the COVID-19 cases, 15 (42.86%) had severe illness, with 2 deaths. The incidence, case-severity and case-fatality of COVID-19 in PLWH were comparable to that in the entire population in Wuhan. 197 persons had cART discontinuation, of whom 4 persons experienced COVID-19. Risk factors for COVID-19 were age ≥50 years old and cART discontinuation. The median duration of SARS-CoV-2 viral shedding among confirmed COVID-19 cases in PLWH was 30 (IQR: 20-46) days. Cases with high HIV viral load (≥20 copies/ml) had lower IgM and IgG levels than those with low HIV viral load (<20 copies/ml) (median S/CO for IgM, 0.03 vs. 0.11, P<0.001; median S/CO for IgG, 10.16 vs. 17.04, P=0.069). CONCLUSIONS: Efforts need to maintain the persistent supply of antiretroviral treatment to elderly PLWH aged 50 years or above during the COVID-19 epidemic. The coinfection of HIV and SARS-CoV-2 might change the progression and prognosis of COVID-19 patients in PLWH.


id: cord-335691-lsuwsm43
title: The Burden of Community-Acquired Pneumonia in Seniors: Results of a Population-Based Study
author: Jackson, Michael L.
date: 2004-12-01
txt: ./txt/cord-335691-lsuwsm43.txt
cache: ./cache/cord-335691-lsuwsm43.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15578365/
doi: 10.1086/425615
summary:
  To estimate rates of community-acquired pneumonia and to identify risk factors for this disease, we conducted a large, population-based cohort study of persons aged ⩾65 years that included both hospitalizations and outpatient visits for pneumonia. In multivariate analysis, age, male sex, current smoking, diabetes mellitus, congestive heart failure, lung cancer, serious nonlung cancer, COPD, asthma without COPD, dementia, stroke, receipt of prednisone, use of home oxygen services, greater number of outpatient visits, and hospitalization for pneumonia in the year prior to the study start date were independently associated with risk of all CAP (table 3) . A population-based study involving 4175 elderly persons in Finland found that crude CAP rates did not differ between men and women and that male sex was not significantly associated with CAP after accounting for age and certain chronic medical conditions and risk factors, including asthma, receipt of immunosuppressive therapy, and heart disease [21] .

abstract:
  Background. Pneumonia is recognized as a leading cause of morbidity in seniors. However, the overall burden of this disease—and, in particular, the contribution of ambulatory cases to that burden—is not well defined. To estimate rates of community-acquired pneumonia and to identify risk factors for this disease, we conducted a large, population-based cohort study of persons aged ⩾65 years that included both hospitalizations and outpatient visits for pneumonia. Methods. The study population consisted of 46,237 seniors enrolled at Group Health Cooperative who were observed over a 3-year period. Pneumonia episodes presumptively identified by International Classification of Diseases, Ninth Revision, Clinical Modification codes assigned to medical encounters were validated by medical record review. Characteristics of participants were defined by administrative data sources. Results. The overall rate of community-acquired pneumonia ranged from 18.2 cases per 1000 person-years among persons aged 65–69 years to 52.3 cases per 1000 person-years among those aged ⩾85 years. In this population, 59.3% of all pneumonia episodes were treated on an outpatient basis. In multivariate analysis, risk factors for community-acquired pneumonia included age, male sex, chronic obstructive pulmonary disease, asthma, diabetes mellitus, congestive heart failure, and smoking. Conclusions. On the basis of these data, we estimate that roughly 915,900 cases of community-acquired pneumonia occur annually among seniors in the United States and that ∼1 of every 20 persons aged ⩾85 years will have a new episode of community-acquired pneumonia each year.


id: cord-335767-omm04fg5
title: Importance of Pediatric Inclusion in COVID-19 Therapeutic Trials
author: Raabe, Vanessa N
date: 2020-05-27
txt: ./txt/cord-335767-omm04fg5.txt
cache: ./cache/cord-335767-omm04fg5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa656
doi: 10.1093/cid/ciaa656
summary:
  Not only do children and the medical community lose out on opportunities to gain the highest level of clinical evidence for efficacy in a vulnerable population, but due to the lack of availability of pediatric trials, many children hospitalized for COVID-19 are receiving off-label use of therapeutic agents with unproven benefit against COVID-19. In addition to offering enhanced safety monitoring, enrollment of children in clinical trials ensures that parents and older children are fully informed of the potential risks and benefits associated with use of the therapeutic agent, a conversation often omitted when medications are prescribed off-label. Inclusion of children in these clinical trials is feasible under current regulations, provides direct benefit to pediatric trial participants from a safety perspective compared to off-label prescribing, and provides systematic collection of the highest quality of evidence for COVID-19 therapeutics in a vulnerable population where SARS-CoV-2 infection behaves differently from adults.

abstract:
  Pediatric patients are excluded from most coronavirus disease 2019 (COVID-19) therapeutic trials. We outline a rationale for the inclusion of children in COVID-19 therapeutic trials, which enabled us to include children of all ages in a therapeutic COVID-19 trial at our institution.


id: cord-335907-93gwmo0v
author: de Man, Peter
date: 2020-08-28
txt: ./txt/cord-335907-93gwmo0v.txt
cache: ./cache/cord-335907-93gwmo0v.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1270
doi: 10.1093/cid/ciaa1270
abstract: nan
summary:
  title: Outbreak of COVID-19 in a nursing home associated with aerosol transmission as a result of inadequate ventilation Recently, we were involved in an outbreak in a Dutch nursing home that was likely to be the result of aerosol transmission in a setting of inadequate ventilation. In total, 17 (81%) residents from one of the seven wards in a nursing home with psychogeriatric residents were diagnosed with COVID-19 as confirmed by RT-PCR ( Figure 1 ) [2] . To prevent and control COVID-19 infections all HCWs in this nursing home had been assigned to specific wards and did wear surgical masks during patient contacts since April 26, 2020 [4] . Because of the remarkable increase of COVID-19 infections in a very short time period despite the use of surgical masks, the ventilation system of the outbreak ward was investigated in addition to routine source and contact tracing. In this situation, low CO2 production by inactive nursing home patients might have limited the ventilation with outside air.

title:
  Outbreak of COVID-19 in a nursing home associated with aerosol transmission as a result of inadequate ventilation


id: cord-336563-hwemigk7
author: Bhimraj, Adarsh
date: 2020-04-27
txt: ./txt/cord-336563-hwemigk7.txt
cache: ./cache/cord-336563-hwemigk7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa478
doi: 10.1093/cid/ciaa478
summary:
  Given the rapidity of emerging literature, IDSA identified the need to develop living, frequently updated evidence-based guidelines to support patients, clinicians and other health-care professionals in their decisions about treatment and management of patients with COVID-19. Two RCTs of patients with confirmed COVID-19 with mild pneumonia (e.g., positive CT scan without oxygen requirement) or non-severe infection admitted to the hospital treated with hydroxychloroquine (HCQ) reported on mortality at 14 days, clinical progression (radiological progression on CT scan), clinical improvement, failure of virologic clearance (PCR), and adverse events (both) [11, 12] (Table 1 ). In addition, we identified four publications describing three trials of combination treatment with HCQ plus azithromycin (AZ) among hospitalized patients with COVID-19 reporting on the outcomes of mortality, failure of virologic clearance (assessed with PCR test), and adverse events (i.e., significant QT prolongation leading to treatment discontinuation) [13] [14] [15] [16] (Table 2) .

title:
  Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients with COVID-19

abstract:
  BACKGROUND: There are many pharmacologic therapies that are being used or considered for treatment of COVID-19. There is a need for frequently updated practice guidelines on their use, based on critical evaluation of rapidly emerging literature. OBJECTIVE: Develop evidence-based rapid guidelines intended to support patients, clinicians and other health-care professionals in their decisions about treatment and management of patients with COVID-19. METHODS: IDSA formed a multidisciplinary guideline panel of infectious disease clinicians, pharmacists, and methodologists with varied areas of expertise. Process followed a rapid recommendation checklist. The panel prioritized questions and outcomes. Then a systematic review of the peer-reviewed and grey literature was conducted. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to assess the certainty of evidence and make recommendations. RESULTS: The IDSA guideline panel agreed on 7 treatment recommendations and provided narrative summaries of other treatments undergoing evaluations. CONCLUSIONS: The panel expressed the overarching goal that patients be recruited into ongoing trials, which would provide much needed evidence on the efficacy and safety of various therapies for COVID-19, given that we could not make a determination whether the benefits outweigh harms for most treatments.


id: cord-337972-otfloo64
title: Mechanism of Fulminant Pulmonary Edema Caused by Enterovirus 71
author: Kao, Shang Jyh
date: 2004-06-15
txt: ./txt/cord-337972-otfloo64.txt
cache: ./cache/cord-337972-otfloo64.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15227628/
doi: 10.1086/421021
summary:
  Destruction of the medial, ventral, and caudal medulla may lead to sympathetic overactivation, causing blood to shift to the lungs. Destruction of the medial, ventral, and caudal medulla may lead to sympathetic overactivation, causing blood to shift to the lungs. Central sympathetic activation resulting in systemic vasoconstriction and the shift of blood volume to the pulmonary region of the circulatory system, as demonstrated in earlier findings from our laboratory, was used to explain centrogenic PE [2, 3] . In the present study, we report CNS lesions in patients associated with PE due to enterovirus infection. The present study also supports the contention that hyperglycemia, leukocytosis, and elevated protein levels in CSF are risk factors for the development of ARDS due to enterovirus infection [1, 2] . In this connection, we found that endogenous and exogenous nitric oxide reduced pulmonary hypertension but increased the capillary filtration coefficient and the extent of injury in an isolated rat''s lung that was subjected to ischemia and reperfusion [16] .

abstract:
  Pulmonary edema (PE) may occur with enterovirus 71 (EV71) infection. We monitored arterial pressure (AP) and heart rate (HR) in patients with EV71 infection and analyzed the variability of AP and HR. Sympathetic activity, AP, and HR increased with respiratory stress. Thereafter, parasympathetic activity increased with decreases in AP and HR. The lungs showed edema with inducible nitric oxide synthase (iNOS) expression. Destruction of the medial, ventral, and caudal medulla may lead to sympathetic overactivation, causing blood to shift to the lungs. The pathogenesis of PE may also involve iNOS and nitric oxide.


id: cord-338899-qt17jhg0
title: Clinical Features and Molecular Diagnosis of Chikungunya Fever from South India
author: Lakshmi, Vemu
date: 2008-05-01
txt: ./txt/cord-338899-qt17jhg0.txt
cache: ./cache/cord-338899-qt17jhg0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/18419449/
doi: 10.1086/529444
summary:
  Emergence or reemergence of severe arboviral hemorrhagic fevers caused by mosquitoborne viruses, such as dengue virus and Chikungunya (CHIK) virus, have been frequently reported in the Indian subcontinent in the past few years. We report clinical observations and laboratory investigations involving virus isolation methods and molecular assays performed for 296 clinically suspected cases of CHIK fever. Of particular interest was the applicability of a novel method of gene amplificatio called real-time loop-mediated isothermal amplifica tion (RT-LAMP) as a rapid, sensitive, and specifi real-time method to detect and quantify CHIK virus in the acute phase of the infection. All 132 patients who had clinically suspected CHIK virus but whose RT-PCR and RT-LAMP results were negative presented 17 days after the onset of fever; this may be the reason for the negative test results. The RT-LAMP allows rapid, realtime detection of CHIK virus in acute-phase serum samples, without requiring sophisticated equipment, and has potential usefulness for clinical diagnosis and surveillance of CHIK virus in developing countries.

abstract:
  An epidemic of Chikungunya fever of unprecedented magnitude occurred in many parts of India in early 2006 after an interval of 33 years, and there has been a resurgence in some parts of South India since June 2007. The article highlights clinical manifestations of infection and various molecular tests that were used for diagnoses of Chikungunya virus infection. Of particular interest is the real-time loop-mediated isothermal amplification (RT LAMP) assay, which is rapid and cost-effective and can be adopted at ill-equipped laboratories. Clinical symptoms were characterized by a triad of fever, rash, and severe rheumatic manifestations. RT LAMP identified 20 additional Chikungunya virus—positive cases, compared with reverse-transcriptase polymerase chain reaction. Chikungunya virus was isolated from 20 randomly selected samples. Genotyping of the virus isolates revealed that the East Central South African genotype of Chikungunya virus was the etiologic agent of this epidemic. Molecular diagnosis is an important tool to identify such new vectorborne viral illnesses.


id: cord-339004-49dkucxd
title: Severe Acute Respiratory Syndrome Beyond Amoy Gardens: Completing the Incomplete Legacy
author: Yu, Ignatius Tak-Sun
date: 2014-03-01
txt: ./txt/cord-339004-49dkucxd.txt
cache: ./cache/cord-339004-49dkucxd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/24319085/
doi: 10.1093/cid/cit797
summary:
  The temporal and spatial distributions of the 2003 severe acute respiratory syndrome (SARS) outbreak in Amoy Gardens of Hong Kong was reexamined using all confirmed cases. The temporal and spatial distributions of the 2003 severe acute respiratorysyndrome (SARS) outbreak in Amoy Gardens of Hong Kong was reexamined using all confirmed cases. In 2004, we analyzed the temporal and spatial distributions of the initial 187 cases in 7 blocks (A-G) of Amoy Gardens, a residential building complex with 19 buildings, where the largest community outbreak of SARS took place. Considering that cases in Telford Gardens and Tak Bo Garden with symptom onset during 24-29 March were most likely resulting from the common source originating in block E of Amoy Gardens, the distance of airborne transmission in that outbreak could be >200 m. In conclusion, the airborne spread in the largest community outbreak of SARS in 2003 actually extended beyond the Amoy Gardens and affected residential buildings >200 m from the source.

abstract:
  The temporal and spatial distributions of the 2003 severe acute respiratory syndrome (SARS) outbreak in Amoy Gardens of Hong Kong was reexamined using all confirmed cases. The outbreak actually extended to nearby residential complexes. Airborne spread was the most likely explanation, and the SARS coronavirus could have spread over a distance of 200 m.


id: cord-339859-anatn295
title: SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress
author: Paret, Michal
date: 2020-04-17
txt: ./txt/cord-339859-anatn295.txt
cache: ./cache/cord-339859-anatn295.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa452
doi: 10.1093/cid/ciaa452
summary:
  title: SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress We report two cases of SARS-CoV-2 infection (COVID-19) in infants presenting with fever in the absence of respiratory distress who required hospitalization for evaluation of possible invasive bacterial infections. The diagnoses resulted from routine isolation and real-time RT-PCR-based testing for SARS-CoV-2 for febrile infants in an outbreak setting. [2] [3] [4] Even in the setting of asymptomatic or mildly symptomatic infection, children may represent a source of SARS-CoV-2 spread in community or hospital settings, so understanding the spectrum of COVID-19 illness in infants, particularly regarding conditions that result in hospitalization, is crucial to establishment of effective infection control interventions. Vital signs and pertinent laboratory findings appear in the A real-time RT-PCR assay performed at the New York State Department of Health detected SARS-CoV-2 RNA in the patient''s NP sample.

abstract:
  We report two cases of SARS-CoV-2 infection (COVID-19) in infants presenting with fever in the absence of respiratory distress who required hospitalization for evaluation of possible invasive bacterial infections. The diagnoses resulted from routine isolation and real-time RT-PCR-based testing for SARS-CoV-2 for febrile infants in an outbreak setting.


id: cord-340317-gwqy6u9x
author: Dora, Amy V
date: 2020-08-28
txt: ./txt/cord-340317-gwqy6u9x.txt
cache: ./cache/cord-340317-gwqy6u9x.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32857830/
doi: 10.1093/cid/ciaa1286
summary:
  title: Using Serologic Testing to Assess the Effectiveness of Outbreak Control Efforts, Serial PCR Testing, and Cohorting of Positive SARS-CoV-2 Patients in a Skilled Nursing Facility Despite numerous outbreaks, the performance of serologic testing for SARS-CoV-2 in residents of skilled nursing facilities (SNF) is not well described; its utility in epidemiologic sero-surveillance studies and outbreak reporting is under evaluation. As our objective was to identify potentially missed cases of COVID-19 during serial surveillance testing, samples from residents with historically negative SARS-CoV-2 RT-PCR tests with DiaSorin IgG-positive results were re-tested on a second serologic testing platform (Abbott SARS-CoV-2 IgG Immunoassay) for IgG antibody specific to SARS-CoV-2 nucleocapsid. In a cohort of 150 nursing home residents tested for SARS-CoV-2 infection by RT-PCR, including 26 previously diagnosed with COVID-19, the sensitivity of the DiaSorin assay was 92% (24/26) and the specificity was 98% (122/124).

title:
  Using Serologic Testing to Assess the Effectiveness of Outbreak Control Efforts, Serial PCR Testing, and Cohorting of Positive SARS-CoV-2 Patients in a Skilled Nursing Facility

abstract:
  We characterized serology following a nursing home outbreak where residents were serially tested by RT-PCR and positive residents were cohorted. When tested 46-76 days later, 24/26 RT-PCR-positive residents were seropositive; none of the 124 RT-PCR-negative residents had confirmed seropositivity, supporting serial SARS-CoV-2 RT-PCR testing and cohorting in nursing homes.


id: cord-340579-cvze15cj
author: Dudley, Joseph P
date: 2020-03-31
txt: ./txt/cord-340579-cvze15cj.txt
cache: ./cache/cord-340579-cvze15cj.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa354
doi: 10.1093/cid/ciaa354
summary:
  There is a need to gain greater understanding of the highest risk populations for infection and serious disease from the SARS-CoV-2 virus to support the development and implementation of effective public health surveillance and mitigation efforts, and minimize the adverse effects of the current COVID-19 Pandemic in countries worldwide [1] . The reported data on confirmed cases and fatalities from the SARS-CoV-2 indicate highly significant The available epidemiological and observational data from the ROK suggests that reduced rates of compliance with social distancing and self-quarantine recommendations among different sectors of the population -especially the younger adult and juvenile age cohorts --may have a significant impact on the age-specific rates of morbidity and mortality within the population as a whole. Comparison of Age-Specific Morbidity and Mortality Rates Among Reported Confirmed Cases from China and Republic of Korea Figure 1

title:
  Disparities in Age-Specific Morbidity and Mortality from SARS-CoV-2 in China and the Republic of Korea

abstract:
  We analyzed age- and sex-specific morbidity and mortality data from SARS-COV-2 pandemic in China and Republic of Korea (ROK). Data from China exhibit a Gaussian distribution with peak morbidity in the 50-59 years cohort, while the ROK data have a bimodal distribution with highest morbidity in the 20-29 years cohort.


id: cord-340678-2e2s1gof
author: Skowronski, Danuta M
date: 2020-05-22
txt: ./txt/cord-340678-2e2s1gof.txt
cache: ./cache/cord-340678-2e2s1gof.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa626
doi: 10.1093/cid/ciaa626
summary:
  Influenza vaccine effectiveness against influenza and non-influenza respiratory viruses (NIRV) was assessed by test-negative design using historic datasets of the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN), spanning 2010-11 to 2016-17. Here, we use historic datasets of the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN) to assess the association between influenza vaccine and NIRV risk, notably seasonal coronaviruses. Conversely, influenza vaccine had no effect on non-influenza causes of ILI, with the likelihood of vaccination among NIRV cases relative to test-negative controls approaching unity. In combined NIRV analysis, relative to pan-negative controls, Wolff adjusted for age and excluded specimens that tested influenza-positive. We illustrate the impact of this bias in Supplementary_Material_3, where we have re-analyzed Wolff''s data as well as our own, comparing influenza vaccine effect against NIRV when influenza testpositive specimens are properly excluded (as per TND prerequisite) or improperly included (as per Wolff [4] ) within the control group.

title:
  Influenza vaccine does not increase the risk of coronavirus or other non-influenza respiratory viruses: retrospective analysis from Canada, 2010-11 to 2016-17

abstract:
  Influenza vaccine effectiveness against influenza and non-influenza respiratory viruses (NIRV) was assessed by test-negative design using historic datasets of the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN), spanning 2010-11 to 2016-17. Vaccine significantly reduced the risk of influenza illness by >40% with no effect on coronaviruses or other NIRV risk.


id: cord-340956-1t3o24u5
title: High Risk of Influenza Virus Infection Among Swine Workers: Examining a Dynamic Cohort in China
author: Borkenhagen, Laura K
date: 2019-09-01
txt: ./txt/cord-340956-1t3o24u5.txt
cache: ./cache/cord-340956-1t3o24u5.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31504322/
doi: 10.1093/cid/ciz865
summary:
  Despite elevated titers, among the 187 study subjects for whom we had complete follow-up, participants working at swine CAFOs had significantly greater odds of seroconverting against both the swine H1N1 (odds ratio [OR] 19.16, 95% confidence interval [CI] 3.55–358.65) and swine H3N2 (OR 2.97, 95% CI 1.16–8.01) viruses, compared to unexposed and non-CAFO swine workers with less intense swine exposure. Conversely, higher odds of seroconversion against swine H3N2 virus were observed among the unexposed (OR 2.27, 95% CI 1.43-3.60) and CAFO-exposed (OR 1.98, 95% CI 1.11-3.42), when compared to the non-CAFO swine workers; the unexposed participants had higher geometric mean MN titers, compared to the other 2 groups, for all time points (Table 3) . In this report, we present the first 24 months of data from a 5-year prospective, cohort study of IAV among participants exposed and unexposed to swine in China.

abstract:
  BACKGROUND: China is thought to be a hotspot for zoonotic influenza virus emergence, yet there have been few prospective studies examining the occupational risks of such infections. METHODS: We present the first 2 years of data collected from a 5-year, prospective, cohort study of swine-exposed and -unexposed participants at 6 swine farms in China. We conducted serological and virological surveillance to examine evidence for swine influenza A virus infection in humans. RESULTS: Of the 658 participants (521 swine-exposed and 137 swine-unexposed), 207 (31.5%) seroconverted against at least 1 swine influenza virus subtype (swine H1N1 or H3N2). Swine-exposed participants’ microneutralization titers, especially those enrolled at confined animal feeding operations (CAFOs), were higher against the swine H1N1 virus than were other participants at 12 and 24 months. Despite elevated titers, among the 187 study subjects for whom we had complete follow-up, participants working at swine CAFOs had significantly greater odds of seroconverting against both the swine H1N1 (odds ratio [OR] 19.16, 95% confidence interval [CI] 3.55–358.65) and swine H3N2 (OR 2.97, 95% CI 1.16–8.01) viruses, compared to unexposed and non-CAFO swine workers with less intense swine exposure. CONCLUSIONS: While some of the observed increased risk against swine viruses may have been explained by exposure to human influenza strains, study data suggest that even with elevated preexisting antibodies, swine-exposed workers were at high risk of infection with enzootic swine influenza A viruses.


id: cord-341359-c34gyuv6
title: Clinical Outcomes of Coronavirus Disease 2019 With Evidence-based Supportive Care
author: Larson, Derek T
date: 2020-05-30
txt: ./txt/cord-341359-c34gyuv6.txt
cache: ./cache/cord-341359-c34gyuv6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32472675/
doi: 10.1093/cid/ciaa678
summary:
  This retrospective study of an institutional cohort including 135 patients with confirmed COVID-19 demonstrates positive outcomes when organizational standards of care consist of evidence-based supportive therapies. Following widespread use of therapeutic agents with limited data to support their use, calls were made to focus on the evidence-based care that has been the foundation of modern medical therapy for most acute respiratory viral infections [7, 8] . Our study is the first report of COVID-19 outcomes when institutional standards of care consist solely of known evidence-based practices of supportive care. Of those diagnosed with COVID-19, 21 (15.6%) had severe enough disease to necessitate hospitalization and 6 (4.4%) required care in the ICU. Our study demonstrates favorable outcomes for patients with mild to moderately severe COVID-19 disease when evidence-based supportive care is considered the institutional standard.

abstract:
  Calls for adherence to evidence-based medicine have emerged during the initial wave of the COVID-19 pandemic but reports of outcomes are lacking. This retrospective study of an institutional cohort including 135 patients with confirmed COVID-19 demonstrates positive outcomes when organizational standards of care consist of evidence-based supportive therapies.


id: cord-341435-b36h69r1
title: Loss of Taste and Smell as Distinguishing Symptoms of COVID-19
author: Dawson, Patrick
date: 2020-06-21
txt: ./txt/cord-341435-b36h69r1.txt
cache: ./cache/cord-341435-b36h69r1.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa799
doi: 10.1093/cid/ciaa799
summary:
  In a household study, loss of taste and/or smell was the fourth most reported symptom (26/42; 62%) among COVID-19 case-patients and had the highest positive predictive value (83%; 95% CI: 55–95%) among household contacts. This investigation provided an opportunity to identify household COVID-19 cases and describe their symptom profiles, including loss of taste and smell, prior to diagnosis. Among the 64 household members of COVID-19 index cases, loss of taste and/or smell was reported by 12 individuals, of whom 10 were positive for SARS-CoV-2. The positive predictive value (PPV) of any loss of taste and/or smell (83%, 95% CI: 55-95%) was higher than for fever (subjective or measured) and cough, two of the three classic symptoms, and equal to the third, shortness of breath (83%, 95% CI: 44-97%) ( Table 1 ). In the absence of confirmatory laboratory testing, CSTE criteria for a probable COVID-19 case now include loss of taste and/or smell in conjunction with other non-classic symptoms (3).

abstract:
  In a household study, loss of taste and/or smell was the fourth most reported symptom (26/42; 62%) among COVID-19 case-patients and had the highest positive predictive value (83%; 95% CI: 55–95%) among household contacts. Olfactory and taste dysfunctions should be considered for COVID-19 case identification and testing prioritization.


id: cord-341838-lkz8ro90
title: Clinical features and outcomes of HIV patients with coronavirus disease 2019
author: Gervasoni, Cristina
date: 2020-05-14
txt: ./txt/cord-341838-lkz8ro90.txt
cache: ./cache/cord-341838-lkz8ro90.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa579
doi: 10.1093/cid/ciaa579
summary:
  The aim of this retrospective study was to describe the clinical characteristics and outcomes of HIVinfected patients with a probable/proven diagnosis of SARS-CoV-2 infection who have been regularly followed up by our hospital. As in the general population, the large majority of our patients were males, but their mean age was nearly 10 years lower than that observed in HIV-negative COVID-19 patients. 16 Furthermore, the findings of this study document favourable outcomes in HIV patients treated mainly with integrase inhibitors (11% protease inhibitors), which apparently indicates that antiretroviral therapy does not play a key role, A c c e p t e d M a n u s c r i p t 8 although a potentially protective effect of tenofovir cannot be ruled out given its recently reported effect against SARS-CoV-2 RNA-dependent RNA polymerase. In conclusion, our findings suggest that HIV-positive patients with SARS-CoV-2 infection are not at greater risk of severe disease or death than HIV-negative patients.

abstract:
  Little is known about the clinical outcomes of HIV patients infected with SARS-CoV-2. We describe 47 patients referred to our hospital between 21 February and 16 April 2020 with proven/probable COVID-19, 45 (96%) of whom fully recovered and two died.


id: cord-343827-jo61t3m0
title: Direct evidence of active SARS-CoV-2 replication in the intestine
author: Qian, Qun
date: 2020-07-08
txt: ./txt/cord-343827-jo61t3m0.txt
cache: ./cache/cord-343827-jo61t3m0.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa925
doi: 10.1093/cid/ciaa925
summary:
  We investigated the presence of virions and pathological changes in surgical rectal tissues of a clinically confirmed COVID-19 patient with rectal adenocarcinoma. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens, but not in samples collected on 37 day after discharge. Notably, coincidence with rectal tissues of surgical specimens tested nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Notably, fecal samples remained positive for SARS-CoV-2 RNA nearly 5 weeks after the viral clearance from the upper respiratory tract in COVID-19 patients [8] . To clarify the above questions, we performed a retrospective study to detect the presence of SARS-CoV-2 virions and determine the pathological changes in rectal tissues of this patient. Samples of rectal tissues, succus entericus and intestinal mucosa of ileostomy, and rectal mucosa were tested for SARS-CoV-2 nucleic acid using qRT-PCR.

abstract:
  BACKGROUND: Currently, there is no direct evidence to prove the active SARS-CoV-2 replication in the intestinal tract and relevant pathological changes in the colon and rectum. We investigated the presence of virions and pathological changes in surgical rectal tissues of a clinically confirmed COVID-19 patient with rectal adenocarcinoma. METHODS: Here, the clinical data were collected during hospitalization and follow-up of this patient. Quantitative RT-PCR was performed on the rectal tissue specimens obtained from surgical resection, succus entericus and intestinal mucosa of ileostomy, and rectal mucosa during follow-up after recovery. Ultrathin sections of surgical samples were observed for SARS-CoV-2 virions using electron microscopy. Histopathological examination was performed using hematoxylin-eosin stain. Immunohistochemical analysis and immunofluorescence were carried out on rectal tissues to evaluate the distribution of SARS-CoV-2 antigen, and immune cell infiltrations. RESULTS: The patient had fever and cough on day 3 postoperatively, was diagnosed with COVID-19 on day 7, and was discharged from the hospital on day 41. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens, but not in samples collected on 37 day after discharge. Notably, coincidence with rectal tissues of surgical specimens tested nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Moreover, abundant lymphocytes and macrophages (some are SARS-CoV-2 positive) infiltrating the lamina propria were found with no significant mucosal damage. CONCLUSIONS: We firstly reported that direct evidence of the active SARS-CoV-2 replication in the patient's rectum during the incubation period, which might explain SARS-CoV-2 fecal-oral transmission.


id: cord-344038-20n74z3o
title: Sequential analysis of viral load in a neonate and her mother infected with SARS-CoV-2
author: Han, Mi Seon
date: 2020-04-16
txt: ./txt/cord-344038-20n74z3o.txt
cache: ./cache/cord-344038-20n74z3o.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32297925/
doi: 10.1093/cid/ciaa447
summary:
  In this study, we described the clinical manifestation of COVID-19 in a neonate and her mother, and further analyzed the viral load kinetics of SARS-CoV-2 in clinical specimens from different sources. The neonate was febrile and SARS-CoV-2 RNA was detected in all of her clinical specimens, with high viral loads in the respiratory and stool samples. Her mother had mild symptoms with SARS-CoV-2 RNA detected in the respiratory and stool specimens at low titers. An interesting finding in this study is that SARS-CoV-2 RNA was detected in all of the neonate''s clinical specimens, including blood, urine, stool, and saliva along with the upper respiratory tract specimens. In comparison, although exposed to the same infection source, only the mother''s respiratory and stool specimens were positive for SARS-CoV-2 and at a much lower viral load. Recent studies have reported that SARS-CoV-2 RNA could be detected in different types of clinical specimens other than respiratory tract samples [9] .

abstract:
  We report changes in viral load over time in a 27-day old neonate with COVID-19 who presented with fever, cough, and vomiting. SARS-CoV-2 RNA was detected in the nasopharynx, oropharynx, stool, saliva, plasma, and urine. The highest viral RNA copies in nasopharynx decreased over time while viral load in stool remained high.


id: cord-345045-nlui9d6e
author: Zahn, Matthew
date: 2019-07-15
txt: ./txt/cord-345045-nlui9d6e.txt
cache: ./cache/cord-345045-nlui9d6e.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciy888
doi: 10.1093/cid/ciy888
summary:
  Unfortunately, much of this work is undercompensated despite the proven efficacy of public health interventions such as hospital acquired infection prevention, antimicrobial stewardship, disease surveillance, and outbreak response. Here, we examine compensation data for ID physicians compared to their value in population and public health settings and suggest policy recommendations to address the pay disparities that exist between cognitive and procedural specialties that prevent more medical students and residents from entering the field. In 2015, 8515 ID physicians were practicing in the United States [5] , often combining clinical care with work as educators, epidemiologists, public health leaders, antimicrobial stewardship or infection prevention and control directors, researchers, administrators, and policymakers. Further, the work of ID physicians provides broader public protection against infectious threats through community and healthcare facility-based infection control and prevention activities, surveillance, outbreak response, and other public health activities.

title:
  Infectious Diseases Physicians: Improving and Protecting the Public’s Health: Why Equitable Compensation Is Critical

abstract:
  Infectious diseases (ID) physicians play a crucial role in public health in a variety of settings. Unfortunately, much of this work is undercompensated despite the proven efficacy of public health interventions such as hospital acquired infection prevention, antimicrobial stewardship, disease surveillance, and outbreak response. The lack of compensation makes it difficult to attract the best and the brightest to the field of ID, threatening the future of the ID workforce. Here, we examine compensation data for ID physicians compared to their value in population and public health settings and suggest policy recommendations to address the pay disparities that exist between cognitive and procedural specialties that prevent more medical students and residents from entering the field. All ID physicians should take an active role in promoting the value of the subspecialty to policymakers and influencers as well as trainees.


id: cord-346502-x2b0ao3q
author: Arabi, Yaseen M
date: 2019-06-25
txt: ./txt/cord-346502-x2b0ao3q.txt
cache: ./cache/cord-346502-x2b0ao3q.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciz544
doi: 10.1093/cid/ciz544
summary:
  BACKGROUND: The objective of this study was to evaluate the effect of ribavirin and recombinant interferon (RBV/rIFN) therapy on the outcomes of critically ill patients with Middle East respiratory syndrome (MERS), accounting for time-varying confounders. We evaluated the association of RBV/rIFN with 90-day mortality and MERS coronavirus (MERS-CoV) RNA clearance using marginal structural modeling to account for baseline and time-varying confounders. After adjusting for baseline and time-varying confounders using a marginal structural model, RBV/rIFN was not associated with changes in 90-day mortality (adjusted odds ratio, 1.03 [95% confidence interval {CI}, .73–1.44]; P = .87) or with more rapid MERS-CoV RNA clearance (adjusted hazard ratio, 0.65 [95% CI, .30–1.44]; P = .29). The objective of this study was to examine the effect of RBV/ rIFN therapy in a large cohort of critically ill patients with MERS on the 90-day mortality and MERS-CoV RNA clearance by accounting for baseline and time-varying confounders.

title:
  Ribavirin and Interferon Therapy for Critically Ill Patients With Middle East Respiratory Syndrome: A Multicenter Observational Study

abstract:
  BACKGROUND: The objective of this study was to evaluate the effect of ribavirin and recombinant interferon (RBV/rIFN) therapy on the outcomes of critically ill patients with Middle East respiratory syndrome (MERS), accounting for time-varying confounders. METHODS: This is a retrospective cohort study of critically ill patients with laboratory-confirmed MERS from 14 hospitals in Saudi Arabia diagnosed between September 2012 and January 2018. We evaluated the association of RBV/rIFN with 90-day mortality and MERS coronavirus (MERS-CoV) RNA clearance using marginal structural modeling to account for baseline and time-varying confounders. RESULTS: Of 349 MERS patients, 144 (41.3%) patients received RBV/rIFN (RBV and/or rIFN-α2a, rIFN-α2b, or rIFN-β1a; none received rIFN-β1b). RBV/rIFN was initiated at a median of 2 days (Q1, Q3: 1, 3 days) from intensive care unit admission. Crude 90-day mortality was higher in patients with RBV/rIFN compared to no RBV/rIFN (106/144 [73.6%] vs 126/205 [61.5%]; P = .02]. After adjusting for baseline and time-varying confounders using a marginal structural model, RBV/rIFN was not associated with changes in 90-day mortality (adjusted odds ratio, 1.03 [95% confidence interval {CI}, .73–1.44]; P = .87) or with more rapid MERS-CoV RNA clearance (adjusted hazard ratio, 0.65 [95% CI, .30–1.44]; P = .29). CONCLUSIONS: In this observational study, RBV/rIFN (RBV and/or rIFN-α2a, rIFN-α2b, or rIFN-β1a) therapy was commonly used in critically ill MERS patients but was not associated with reduction in 90-day mortality or in faster MERS-CoV RNA clearance.


id: cord-348036-yub2cqz6
title: Obesity in patients younger than 60 years is a risk factor for Covid-19 hospital admission
author: Lighter, Jennifer
date: 2020-04-09
txt: ./txt/cord-348036-yub2cqz6.txt
cache: ./cache/cord-348036-yub2cqz6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32271368/
doi: 10.1093/cid/ciaa415
abstract: nan
summary:
  title: Obesity in patients younger than 60 years is a risk factor for Covid-19 hospital admission Covid-19 disease, caused by SARS-CoV-2 infection includes a spectrum of illness; from asymptomatic infection [2] to severe pneumonia characterized by acute respiratory injury in about 20% of patients presenting to medical care [3] . A c c e p t e d M a n u s c r i p t years were 2.2 (95% CI 1.7-2.9, p<.0001) and 3.6 (95% CI 2.5-5.3, p=<.0001) times more likely to be admitted to acute and critical care compared to patients in the same age category who had BMI <30. Though patients aged <60 years are generally considered a lower risk group of Covid-19 disease severity, based on data from our institution, obesity appears to be a previously unrecognized risk factor for hospital admission and need for critical care.


id: cord-348144-t0chpsuh
title: Carbohydrate Moieties as Vaccine Candidates
author: Lucas, Alexander H.
date: 2005-09-01
txt: ./txt/cord-348144-t0chpsuh.txt
cache: ./cache/cord-348144-t0chpsuh.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16080094/
doi: 10.1086/432582
summary:
  We discuss the cellular basis of carbohydrate immunity, newly identified glycotope processing pathways and recognition capabilities, and the synthetic and microarray technologies that are being developed that will permit new experimental approaches to carbohydrate vaccine development and the exploration of the interaction of the immune system with self and nonself glycans. It has long been known that bactericidal and/or opsonic antibodies directed against capsular polysaccharide (PS) glycotopes protect against invasive diseases caused by encapsulated bacteria, and, accordingly, vaccine development has focused on the elicitation of these antibody specificities. Purified microbial PS vaccines have been in use for 140 years, but they have proven to be variably immunogenic and variably efficacious in protecting susceptible populations against invasive meningococcal, pneumococcal, and Haemophilus influenzae type b (Hib) diseases [1, 2] . Significant variation in serotype-specific immunogenicity of the sevenvalent Streptococcus pneumoniae capsular polysaccharide-CRM197 conjugate vaccine occurs despite vigorous T cell help induced by the carrier protein

abstract:
  Carbohydrate epitopes or glycotopes are structurally diverse, occur in a variety of chemical contexts, and are present on the surfaces of cells in the body and on the surfaces of pathogens. These various structures and modes of presentation affect how they are perceived and processed by the body and dictate the outcome of the immune response directed against them. This review focuses on mechanisms of carbohydrate immunity, with an emphasis on carbohydrate vaccines that have been or are being developed for protection against encapsulated bacterial pathogens. We discuss the cellular basis of carbohydrate immunity, newly identified glycotope processing pathways and recognition capabilities, and the synthetic and microarray technologies that are being developed that will permit new experimental approaches to carbohydrate vaccine development and the exploration of the interaction of the immune system with self and nonself glycans.


id: cord-348178-6bjimde4
author: Li, Ling
date: 2005-09-15
txt: ./txt/cord-348178-6bjimde4.txt
cache: ./cache/cord-348178-6bjimde4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16107979/
doi: 10.1086/432720
summary:
  title: Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects A specially designed biosafety level 3 (BSL-3) autopsy laboratory was constructed and divided into a clean area, a semicontaminated area, a contaminated area, and 2 buffer zones. Our experience suggests that BSL-3 laboratory operating principles should be among the special requirements for performing autopsies of contaminated bodies and that they can safeguard the clinicians and the environment involved in these procedures. According to the guidelines of World Health Organization and the Centers for Disease Control and Prevention (CDC) in the United States, SARS-CoV fulfills the criteria for a biohazard group 3 pathogen. The biosafety of our BSL-3 autopsy laboratory has been ensured in 4 ways: through the design of the facility, use of PPE, decontamination, and administrative regulation. Interim laboratory biosafety guidelines for handling and processing specimens associated with severe acute respiratory syndrome (SARS)

title:
  Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects

abstract:
  Background. During the outbreak of the emergent severe acute respiratory syndrome (SARS) infection, >30% of the ∼8000 infected persons were health care workers. The highly infectious nature of SARS coronavirus (SARS-CoV) compelled our pathologists to consider biosafety issues in the autopsy room and for tissue processing procedures. Methods. A specially designed biosafety level 3 (BSL-3) autopsy laboratory was constructed and divided into a clean area, a semicontaminated area, a contaminated area, and 2 buffer zones. High-efficiency particulate air filters were placed in the air supply and exhaust systems. Laminar air flow was from the clean areas to the less clean areas. The negative pressures of the contaminated, semicontaminated, and clean areas were approximately -50 pa, -25 pa, and -5 pa, respectively. Personal protective equipment, including gas mask, impermeable protective clothing, and 3 layers of gloves worn during autopsies; the equipment was decontaminated before it was allowed to exit the facility. Strict BSL-3 practices were followed. Results. When a given concentration of particulate sarin simulant was introduced into the contaminated area, it could not be detected in either the semicontaminated area or clean area, and particles >0.3 μm in size were not detected in the exhaust air. A total of 16 complete postmortem examinations for probable and suspected SARS were performed during a 2-month period. Of these, 7 reported confirmed cases of SARS. None of the 23 pathologists and technicians who participated in these autopsies was infected with SARS-CoV. Conclusions. Our experience suggests that BSL-3 laboratory operating principles should be among the special requirements for performing autopsies of contaminated bodies and that they can safeguard the clinicians and the environment involved in these procedures.


id: cord-348350-pac9ha4q
title: Hydroxychloroquine in COVID-19 patients: what still needs to be known about the kinetics
author: Martin-Blondel, G
date: 2020-05-11
txt: ./txt/cord-348350-pac9ha4q.txt
cache: ./cache/cord-348350-pac9ha4q.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32392332/
doi: 10.1093/cid/ciaa558
summary:
  Different dosage regimens of hydroxychloroquine are used to manage COVID-19 patients, without information on the pharmacokinetics in this population.Blood samples (n=101) were collected from 57 COVID-19 patients for 7 days and concentrations were compared with simulated kinetic profiles.Hydroxychloroquine exposure is low and cannot be predicted by other populations. Because of the severity of COVID-19 and the pharmacokinetics of hydroxychloroquine in SLE patients [5] , a loading dose was rapidly included in the new hospital regimens to optimize drug distribution in tissues and more precisely in the lungs. For each regimen applied at the Toulouse University Hospital, an example of the expected kinetic profiles for a body weight of 80 kg (the median weight in our population) are presented in Figure 1 with the corresponding serum concentration for each patient.

abstract:
  Different dosage regimens of hydroxychloroquine are used to manage COVID-19 patients, without information on the pharmacokinetics in this population.Blood samples (n=101) were collected from 57 COVID-19 patients for 7 days and concentrations were compared with simulated kinetic profiles.Hydroxychloroquine exposure is low and cannot be predicted by other populations.


id: cord-348392-e35cd9sg
title: Multi-Inflammatory Syndrome in Children related to SARS-CoV-2 in Spain
author: Moraleda, Cinta
date: 2020-07-25
txt: ./txt/cord-348392-e35cd9sg.txt
cache: ./cache/cord-348392-e35cd9sg.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32710613/
doi: 10.1093/cid/ciaa1042
summary:
  Some clusters of children with a multisystem inflammatory syndrome associated with SARS-CoV-2 infection (MIS-C) have been reported. MIS-C is a potentially severe condition that presents in children with recent SARS-CoV-2 infection. This is a case series of children with MIS-C associated with SARS-CoV-2 enrolled in the Epidemiological Study of COVID-19 in Children of the Spanish Society of Pediatrics (EPICO-AEP), from March 1 st to June 1 st, 2020. Inclusion criteria included positivity in real-time polymerase chain reaction (RT-PCR) positive, IgM or IgG in lateral-flow rapid test, ELISA or immuno chemiluminescence serology (see Table 1 ), or severe disease suggestive of MIS-C and recent household contact with a confirmed patient with COVID-19. In this registry, entry criteria was COVID-19 disease, differently from the previous reports that include patient without SARS-CoV-2 1,3 . MIS-C is a potentially severe condition that presents in some children after SARS-CoV-2 infection.

abstract:
  Some clusters of children with a multisystem inflammatory syndrome associated with SARS-CoV-2 infection (MIS-C) have been reported. We describe the epidemiological and clinical features of children with MIS-C in Spain. MIS-C is a potentially severe condition that presents in children with recent SARS-CoV-2 infection.


id: cord-348478-ho89o8mj
title: SARS-CoV-2 pandemic : Time to revive the cyclophilin inhibitor alisporivir
author: Pawlotsky, Jean-Michel
date: 2020-05-15
txt: ./txt/cord-348478-ho89o8mj.txt
cache: ./cache/cord-348478-ho89o8mj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32409832/
doi: 10.1093/cid/ciaa587
summary:
  This Viewpoint summarizes the strong scientific arguments supporting the use of alisporivir, a non-immunosuppressive analogue of cyclosporine A with potent cyclophilin inhibition properties that has reached Phase 3 clinical development, for the treatment of COVID-19. They include the strong cyclophilin dependency of the lifecycle of many coronaviruses, including SARS-CoV and MERS-CoV, and preclinical data showing strong antiviral and cytoprotective properties of alisporivir in various models of coronavirus infection, including SARS-CoV-2. It has indeed been shown that the lifecycles of human coronaviruses 229E (HCoV-229E) and NL-63 (HCoV-NL63), responsible for mild respiratory infections in humans, of feline infectious peritonitis coronavirus (FPIV), responsible for a fatal disease in cats, and of SARS-CoV were highly dependent on cyclophilin A (and possibly also cyclophilin B for FPIV) [18] [19] [20] [21] [22] . Human coronavirus NL63 replication is cyclophilin A-dependent and inhibited by non-immunosuppressive cyclosporine Aderivatives including alisporivir Inhibition of SARS-CoV-2 infection by the cyclophilin inhibitor Alisporivir (Debio 025)

abstract:
  December 2019 saw the emergence of a new epidemic of pneumonia of varying severity, called COVID-19, caused by a newly identified coronavirus, SARS-CoV-2. No therapeutic option is available to treat this infection that has already killed more than 235,000 people worldwide. This Viewpoint summarizes the strong scientific arguments supporting the use of alisporivir, a non-immunosuppressive analogue of cyclosporine A with potent cyclophilin inhibition properties that has reached Phase 3 clinical development, for the treatment of COVID-19. They include the strong cyclophilin dependency of the lifecycle of many coronaviruses, including SARS-CoV and MERS-CoV, and preclinical data showing strong antiviral and cytoprotective properties of alisporivir in various models of coronavirus infection, including SARS-CoV-2. Alisporivir should be tested without delay on both virological and clinical endpoints in patients with or at-risk of severe forms of SARS-CoV-2 infection.


id: cord-349070-bqv03u2e
author: Jiang, Shih Sheng
date: 2004-01-15
txt: ./txt/cord-349070-bqv03u2e.txt
cache: ./cache/cord-349070-bqv03u2e.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/14699465/
doi: 10.1086/380841
summary:
  title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction In most of the cases, we and others have found that the single-step real time RT-PCR methods (as suggested by the World Health Organization [WHO] ; available at http://www.who.int/csr/sars/diagnostic tests/en/) could specifically detect SARS-CoV but were unable to proficiently detect !10 copies of virus per test, suggesting that the conventional RT-PCR assay may actually yield falsenegative results. In contrast, the second-round amplification by nested real-time PCR proficiently generated a signal of SARS-CoV DNA without apparent background, compared with no detectable signal for the negative control samples ( figure 1A ). After 25 cycles of first-round amplification and 25 cycles of nested PCR amplification, our assay could detect a theoretical single copy of extracted viral RNA (figure 1A), suggesting its superior sensitivity for detection of SARS-CoV.

title:
  Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction

abstract:
  A quantitative, real-time, nested polymerase chain reaction (PCR) method, combining the high sensitivity of nested PCR with time-saving real-time instrumentation, was developed for large-scale screening for severe acute coronavirus (SARS) coronavirus. Forty-six clinical specimens were analyzed by this method, and results were compared with those obtained by conventional, single-round, real-time reverse-transcriptase PCR (RT-PCR) performed in parallel. Of the 17 positive results, 2 identified by our method were not detected by single-round, real-time RT-PCR, which suggests that real-time nested PCR has the potential for increased sensitivity, leading to earlier detection of SARS.


id: cord-349556-k312qkvh
author: Roldán-Santiago, Ernesto
date: 2020-09-18
txt: ./txt/cord-349556-k312qkvh.txt
cache: ./cache/cord-349556-k312qkvh.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1422
doi: 10.1093/cid/ciaa1422
summary:
  title: SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 After a FNAP we demonstrate that SARS-CoV-2 is found in lymph nodes (LNs) even in mild disease along with a strong expansion of terminally differentiated effector memory CD4+T-cells , a cell population that is practically absent in LN. Naive or central memory cells, which are the two main CD4+ subsets that are usually detected in normal or reactive LN that are or are not infected by EBV (Fig. 1B) , switched almost completely to effector memory and especially to T EMRA T-cells (Fig. 1A) . The findings strongly suggest that the enlarged LN was a consequence of EBV rather than SARS-CoV-2 infection, but this co-infection was an excellent opportunity to assess the presence of coronavirus in LNs from patients with mild symptoms. This case suggests that virus reaches LNs , regardless of disease severity.The other relevant finding of this study is an unexpected expansion of CD4+ T EMRA in the patient''s cervical LN.

title:
  SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19

abstract:
  A woman with mild Covid-19 developed cervical adenopathy, being diagnosed of Epstein−Barr virus infectious mononucleosis. After a FNAP we demonstrate that SARS-CoV-2 is found in lymph nodes (LNs) even in mild disease along with a strong expansion of terminally differentiated effector memory CD4+T-cells , a cell population that is practically absent in LN.


id: cord-349566-zx9kt144
author: de Alencar, Julio Cesar Garcia
date: 2020-09-23
txt: ./txt/cord-349566-zx9kt144.txt
cache: ./cache/cord-349566-zx9kt144.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1443
doi: 10.1093/cid/ciaa1443
summary:
  title: Double-blind, randomized, placebo-controlled trial with N-acetylcysteine for treatment of severe acute respiratory syndrome caused by COVID-19 There is still no robust experimental confirmation for this fact; however, increased serum AngII levels have been reported in patients with severe Covid-19 cases [7] and enhanced expression of ACE2 in adults, compared to children, has been advocated to cause the difference of disease prevalence in these age ranges [8] . Therefore, we designed a double-blind, placebo-controlled, randomized clinical trial to determine whether NAC (in doses used to treat acute liver failure), is able to protect alveolar cells and avoid respiratory failure in patients with severe acute respiratory syndrome caused by (confirmed or suspect) Covid-19. This is a double-blind, randomized, placebo-controlled trial to assess the effectiveness and safety of intravenous NAC to prevent respiratory failure in patients with confirmed or suspect severe Covid-19.

title:
  Double-blind, randomized, placebo-controlled trial with N-acetylcysteine for treatment of severe acute respiratory syndrome caused by COVID-19

abstract:
  BACKGROUND: A local increase in angiotensin 2 after inactivation of angiotensin-converting enzyme 2 by SARS-CoV-2 may induce a redox imbalance in alveolar epithelium cells, causing apoptosis, increased inflammation and, consequently, impaired gas exchange. We hypothesized that N-acetylcysteine (NAC) administration could restore this redox homeostasis and suppress unfavorable evolution in Covid-19 patients. OBJECTIVE: To determine whether NAC in high doses can avoid respiratory failure in patients with Covid-19. METHODS: It was a double-blind, randomized, placebo-controlled, unicentric trial, conducted at the Emergency Department of Hospital das Clínicas, São Paulo, Brazil. We enrolled 135 patients with severe Covid-19 (confirmed or suspected), with an oxyhemoglobin saturation of less than 94% or respiratory rate higher than 24 breaths/min. Patients were randomized to receive NAC 21 g (approximately 300 mg/kg) for 20 hours, or dextrose 5%. Primary endpoint was the need for mechanical ventilation. Secondary endpoints were time of mechanical ventilation, admission to ICU, time in ICU, and mortality. RESULTS: Baseline characteristics were very similar in the two groups, with no significant difference in age, sex, comorbidities, medicines taken, and disease severity. Also, groups were similar in laboratory tests and chest CT scan findings. Sixteen patients (23.9%) in the Placebo group were submitted to endotracheal intubation and mechanical ventilation, compared to 14 patients (20.6%) in the NAC group (p=0.675). No difference was observed in secondary endpoints. CONCLUSION: Administration of NAC in high doses did not affect the evolution of severe Covid-19.


id: cord-350338-lcsa06gm
author: Wang, Kun
date: 2020-05-03
txt: ./txt/cord-350338-lcsa06gm.txt
cache: ./cache/cord-350338-lcsa06gm.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa538
doi: 10.1093/cid/ciaa538
summary:
  title: Clinical and laboratory predictors of in-hospital mortality in patients with COVID-19: a cohort study in Wuhan, China We then validated these models by randomly collecting COVID-19 patients in the Infection department of Union Hospital in Wuhan from January 1, 2020, to February 20, 2020. The laboratory model developed with age, high-sensitivity C-reactive protein (hsCRP), peripheral capillary oxygen saturation (SpO2), neutrophil and lymphocyte count, D-dimer, aspartate aminotransferase (AST) and glomerular filtration rate (GFR) had a significantly stronger discriminatory power than the clinical model (p=0.0157), with AUC of 0.98 (95% CI, 0.92-0.99); threshold, -2.998; sensitivity, 100.00%; specificity, 92.82% and NPV, 100.00%. We developed a clinical model and laboratory model for predicting the in-hospital mortality of COVID-19 patients, the AUCs (95% CI) were 0.88 (0.80, 0.95) and 0.98 (0.92, 0.99) in training cohort, and 0.83 (0.68, 0.93) and 0.88 (0.77, 0.95) in validation cohort, respectively. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China

title:
  Clinical and laboratory predictors of in-hospital mortality in patients with COVID-19: a cohort study in Wuhan, China

abstract:
  BACKGROUND: This study aimed to develop mortality-prediction models for patients with Coronavirus disease 2019 (COVID-19). METHODS: The training cohort were consecutive patients with COVID-19 in the First People’s Hospital of Jiangxia District in Wuhan from January 7, 2020 to February 11, 2020. We selected baseline clinical and laboratory data through the stepwise Akaike information criterion and ensemble XGBoost model to build mortality-prediction models. We then validated these models by randomly collecting COVID-19 patients in the Infection department of Union Hospital in Wuhan from January 1, 2020, to February 20, 2020. RESULTS: 296 patients with COVID-19 were enrolled in the training cohort, 19 of whom died during hospitalization and 277 were discharged from the hospital. The clinical model developed with age, history of hypertension and coronary heart disease showed AUC of 0.88 (95% CI, 0.80-0.95); threshold, -2.6551; sensitivity, 92.31%; specificity, 77.44% and negative predictive value (NPV), 99.34%. The laboratory model developed with age, high-sensitivity C-reactive protein (hsCRP), peripheral capillary oxygen saturation (SpO2), neutrophil and lymphocyte count, D-dimer, aspartate aminotransferase (AST) and glomerular filtration rate (GFR) had a significantly stronger discriminatory power than the clinical model (p=0.0157), with AUC of 0.98 (95% CI, 0.92-0.99); threshold, -2.998; sensitivity, 100.00%; specificity, 92.82% and NPV, 100.00%. In the subsequent validation cohort (N=44), the AUCs (95% CI) were 0.83 (0.68, 0.93) and 0.88 (0.75, 0.96) for clinical model and laboratory model, respectively. CONCLUSIONS: We developed two predictive models for the in-hospital mortality of patients with COVID-19 in Wuhan and validated in patients from another center.


id: cord-350686-q2bu7o4i
title: Pool size selection when testing for SARS-CoV-2
author: Bilder, Christopher R
date: 2020-06-16
txt: ./txt/cord-350686-q2bu7o4i.txt
cache: ./cache/cord-350686-q2bu7o4i.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa774
doi: 10.1093/cid/ciaa774
abstract: nan
summary:
  title: Pool size selection when testing for SARS-CoV-2 M a n u s c r i p t Dear Editor-Pooling samples has been proposed in multiple articles as an efficient way to test for SARS-CoV-2 [1] [2] [3] [4] . They concluded that "this pooling method can be applied immediately in current clinical testing laboratories." However, this research [1] and similar research of others [2] [3] missed answering a very important question: How does one choose the most efficient pool size relative to SARS-CoV-2 prevalence in samples? The efficiencies from pooling samples occur when pools test negative. For example, the most efficient pool size is four samples when prevalence is 10% (calculation to be discussed shortly). By changing the size to 32 samples in our example, only 3% of the pools will test negative. Pooling of samples for testing for SARS-CoV-2 in asymptomatic people


id: cord-350972-0n4dumgg
author: Sing, Chor-Wing
date: 2020-07-16
txt: ./txt/cord-350972-0n4dumgg.txt
cache: ./cache/cord-350972-0n4dumgg.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa992
doi: 10.1093/cid/ciaa992
summary:
  title: Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors Results showed that high-dose glucocorticoids greatly increased long-term risk of avascular necrosis, but not other major diseases. Hong Kong had an outbreak of severe acute respiratory syndrome (SARS; caused by SARS-CoV-1) in 2003, resulting in 1,755 cases and 299 deaths 3 Short course of very-high-dose (VHD) glucocorticoids was used for the treatment of SARS, especially to prevent cytokine storm. To understand the long-term consequences of VHD glucocorticoids, we studied the clinical outcomes of SARS survivors after 17 years. We identified SARS survivors using an electronic medical record database, Clinical Data Analysis and Reporting System (CDARS) of the Hong Kong Hospital Authority, the details of which have been described elsewhere. In this retrospective study of SARS survivors with 17 years of follow-up, a short-course use of VHD glucocorticoids was not associated with major diseases except AVN.

title:
  Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors

abstract:
  Use of high-dose glucocorticoids for coronavirus disease 2019 (COVID-19; caused by SARS-CoV-2) is controversial because of safety concerns. We examined long-term consequences in severe acute respiratory syndrome (SARS; caused by SARS-CoV-1) survivors. Results showed that high-dose glucocorticoids greatly increased long-term risk of avascular necrosis, but not other major diseases.


id: cord-351231-aoz5jbf1
title: Why Infectious Diseases
author: Bartlett, John G.
date: 2014-09-15
txt: ./txt/cord-351231-aoz5jbf1.txt
cache: ./cache/cord-351231-aoz5jbf1.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciu441
doi: 10.1093/cid/ciu441
summary:
  The value of the infectious disease practitioner is now magnified by the crisis of antibiotic resistance, the expanding consequences of international travel, the introduction of completely new pathogen diagnostics, and healthcare reform with emphasis on infection prevention and cost in dollars and lives. The point is that epidemics are the domain of infectious diseases and public health, with the expectation for management or prevention of outbreaks with requirements for detection, reporting, isolation, and case management. This began with a patient transferred from a New York City hospital with a KPC infection and became the source of an institutional outbreak that required extraordinary efforts to control, including a wall constructed to isolate cases, removal of plumbing (as a possible source), use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) molecular diagnostics to detect cases and carriers, hydrogen peroxide room aerosols, and "whole house" surveillance cultures. The new healthcare system should value infectious disease expertise based on its important role in addressing resistance and costs associated with nosocomial infections.

abstract:
  Infectious diseases is a broad discipline that is almost unique in contemporary medicine with its ability to cure and prevent disease, to identify specific disease causes (microbes), and to deal with diverse, sometimes massive outbreaks. The value of the infectious disease practitioner is now magnified by the crisis of antibiotic resistance, the expanding consequences of international travel, the introduction of completely new pathogen diagnostics, and healthcare reform with emphasis on infection prevention and cost in dollars and lives. Infectious disease careers have great personal rewards to the practitioner based on these observations. It is unfortunate that we have been so effective in our work, but relatively ineffective in convincing the healthcare system of this value.


id: cord-351314-atsuh8e2
author: Bryson-Cahn, Chloe
date: 2020-03-12
txt: ./txt/cord-351314-atsuh8e2.txt
cache: ./cache/cord-351314-atsuh8e2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32166310/
doi: 10.1093/cid/ciaa256
summary:
  Safe evaluation of persons for suspected infection with a special pathogen (including SARS-CoV-2) in the traditional healthcare environment is costly and resource intensive. It requires specialized rooms, use of personal protective equipment (PPE), monitored donning and doffing, logistically-complicated patient transportation from the community to the healthcare facility and back (typically through emergency medical services), and appropriate decontamination of transport and hospital environments. 4 The patient is evaluated by the physician, who gathers a focused history and All involved HAT members complete a daily log including temperature and respiratory and gastrointestinal symptom reporting through employee health for 14 days or until SARS-CoV-2 testing returns negative from the index visit. This model benefits both the public health and clinical healthcare systems by increasing safety and efficiency while reducing the costs and complexity of SARS-CoV-2 testing for patients who do not require emergency evaluation or hospitalization.

title:
  A Novel Approach for a Novel Pathogen: using a home assessment team to evaluate patients for 2019 novel coronavirus (SARS-CoV-2)

abstract:
  Thousands of people in the United States have required testing for SARS-CoV-2. Evaluation for a special pathogen is resource intensive. We report an innovative approach to home assessment that, in collaboration with public health, enables safe evaluation and specimen collection outside the healthcare setting, avoiding unnecessary exposures and resource utilization.


id: cord-351348-lzo0dz7z
title: Alterations of the Gut Microbiota in Patients with COVID-19 or H1N1 Influenza
author: Gu, Silan
date: 2020-06-04
txt: ./txt/cord-351348-lzo0dz7z.txt
cache: ./cache/cord-351348-lzo0dz7z.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32497191/
doi: 10.1093/cid/ciaa709
summary:
  METHODS: We conducted a cross-sectional study of 30 COVID-19 patients, 24 influenza A (H1N1) patients, and 30 matched healthy controls (HC) to identify differences in the gut microbiota by 16S ribosomal RNA (rRNA) gene V3-V4 region sequencing. Previous studies indicated that the intestinal flora was closely related to respiratory virus infection and could affect the occurrence and development of diseases through the gut-lung axis [13] . The analysis of group similarities indicated that differences in richness, diversity, A c c e p t e d M a n u s c r i p t and structure of the gut microbiota were not significantly different between general and severe COVID-19 patients (ANOSIM, p=0.426; Supplementary Figure S1 ), indicating that the experimental design was adequate. The gut microbiota signature of COVID-19 and H1N1 patients was analyzed to assess correlations between disease characteristics and the microbiome.

abstract:
  BACKGROUND: Coronavirus disease 2019 (COVID-19) is an emerging serious global health problem. Gastrointestinal symptoms are common in COVID-19 patients, and SARS-CoV-2 RNA has been detected in stool specimens. However, the relationship between the gut microbiome and disease remains to be established. METHODS: We conducted a cross-sectional study of 30 COVID-19 patients, 24 influenza A (H1N1) patients, and 30 matched healthy controls (HC) to identify differences in the gut microbiota by 16S ribosomal RNA (rRNA) gene V3-V4 region sequencing. RESULTS: Compared with HC, COVID-19 patients had significantly reduced bacterial diversity, a significantly higher relative abundance of opportunistic pathogens, such as Streptococcus, Rothia, Veillonella and Actinomyces, and a lower relative abundance of beneficial symbionts. Five biomarkers showed high accuracy for distinguishing COVID-19 patients from HC with an area under the curve (AUC) up to 0.89. Patients with H1N1 displayed lower diversity and different overall microbial composition compared with COVID-19 patients. Seven biomarkers were selected to distinguish the two cohorts with an AUC of 0.94. CONCLUSION: The gut microbial signature of patients with COVID-19 was different from that of H1N1 patients and HC. Our study suggests the potential value of the gut microbiota as a diagnostic biomarker and therapeutic target for COVID-19, but further validation is needed.


id: cord-351589-32kd9vva
title: Pneumocystis Jirovecii Pneumonia and SARS-CoV-2 Co-Infection in newly diagnosed HIV-1 infection
author: Mang, Sebastian
date: 2020-07-01
txt: ./txt/cord-351589-32kd9vva.txt
cache: ./cache/cord-351589-32kd9vva.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa906
doi: 10.1093/cid/ciaa906
abstract: nan
summary:
  title: Pneumocystis Jirovecii Pneumonia and SARS-CoV-2 Co-Infection in newly diagnosed HIV-1 infection We report the case of a 52-year-old male from our intensive care unit (ICU) who developed acute respiratory failure due to Covid-19, Pneumocystis jirovecii Pneumonia (PJP) and newly diagnosed HIV, stage 3 [2] . He deteriorated further despite escalated pressure-controlled invasive ventilation and was finally transferred to our intensive care unit on 13 th May, 2020, for possible initiation of extracorporeal membrane oxygenation (ECMO). As a potential sign for subacute manifestation, airway changes, pleural changes, fibrosis, and nodules were present (Figure 1 Over the next two weeks, his state improved significantly. Why Aren''t People Living with HIV at Higher Risk for Developing Severe Coronavirus Disease 2019 (COVID-19) Radiological findings from 81 patients with COVID-19 pneumonia in Wuhan, China: a descriptive study. Coronavirus Disease 2019 (COVID-19) CT Findings: A Systematic Review and Meta-analysis


id: cord-352837-a29d5dkv
author: Hirsch, Hans H
date: 2019-04-01
txt: ./txt/cord-352837-a29d5dkv.txt
cache: ./cache/cord-352837-a29d5dkv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciy663
doi: 10.1093/cid/ciy663
abstract: nan
summary:
  Given the technical and bioinformatic advances as well as the declining laboratory costs, the application of deep sequencing to identify etiologic agents in clinical samples has been approached in different pathologies, including those caused by community-acquired respiratory viruses (CARVs). With these caveats in mind, and given the significant global burden of viral respiratory tract disease in the very young and the very old [10] [11] [12] oropharyngeal (NP/OP) samples of SARI cases were identified through a national surveillance study conducted by the Uganda Virus Research Institute from 2010 through 2015. Taken together, this report from resource-limiting settings is also of relevance for resource-rich countries and raises the question about how to best expand current first-or second-line testing for respiratory viral pathogens including CMV, parvovirus B19, and measles, and how to move to more deep sequencing virome analysis and comprehensive metagenomics in the near future.

title:
  Spatiotemporal Virus Surveillance for Severe Acute Respiratory Infections in Resource-limited Settings: How Deep Need We Go?


id: cord-352899-bt2xg0ha
author: Van Kerkhove, Maria D.
date: 2016-10-15
txt: ./txt/cord-352899-bt2xg0ha.txt
cache: ./cache/cord-352899-bt2xg0ha.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciw478
doi: 10.1093/cid/ciw478
abstract: nan
summary:
  authors: Van Kerkhove, Maria D.; Peiris, Malik J. Researchers in Korea have recently published studies [4, 5] evaluating environmental and/or air contamination by MERS-CoV and should be commended for their efforts to evaluate the hospital outbreaks in their country. To fully understand the possible role of environmental contamination, including the possible detection of MERS-CoV in the air, additional studies must be conducted to see whether these results can be replicatedfor example, in hospitals in the Middle East where patients with MERS-CoV are treated, to evaluate virus persistence in hospital environments. A more complete understanding of the results of environmental and air contamination studies will have important implications for the application of infection prevention and control measures [8] currently used in hospitals treating patients with MERS-CoV, possibly leading to more detailed recommendations. Environmental contamination and viral shedding in MERS patients during MERS-CoV outbreak in South Korea Middle East respiratory syndrome coronavirus (MERS-CoV)

title:
  Interpreting Results From Environmental Contamination Studies of Middle East Respiratory Syndrome Coronavirus


id: cord-353103-sdij1d90
author: Yao, Xueting
date: 2020-03-09
txt: ./txt/cord-353103-sdij1d90.txt
cache: ./cache/cord-353103-sdij1d90.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32150618/
doi: 10.1093/cid/ciaa237
summary:
  title: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Using the PBPK models, hydroxychloroquine concentrations in lung fluid were simulated under 5 different dosing regimens to explore the most effective regimen whilst considering the drug''s safety profile. Based on PBPK models results, a loading dose of 400 mg twice daily of hydroxychloroquine sulfate given orally, followed by a maintenance dose of 200 mg given twice daily for 4 days is recommended for SARS-CoV-2 infection, as it reached three times the potency of chloroquine phosphate when given 500 mg twice daily 5 days in advance. In this study we aimed to: (i) investigate the antiviral and prophylactic activity of hydroxychloroquine and chloroquine in vitro, (ii) build a PBPK model for hydroxychloroquine and chloroquine using data from literature, and, (iii) predict drug concentrations under different dosing regimens using the developed PBPK models.

title:
  In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

abstract:
  BACKGROUND: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) first broke out in Wuhan (China) and subsequently spread worldwide. Chloroquine has been sporadically used in treating SARS-CoV-2 infection. Hydroxychloroquine shares the same mechanism of action as chloroquine, but its more tolerable safety profile makes it the preferred drug to treat malaria and autoimmune conditions. We propose that the immunomodulatory effect of hydroxychloroquine also may be useful in controlling the cytokine storm that occurs late-phase in critically ill SARS-CoV-2 infected patients. Currently, there is no evidence to support the use of hydroxychloroquine in SARS-CoV-2 infection. METHODS: The pharmacological activity of chloroquine and hydroxychloroquine was tested using SARS-CoV-2 infected Vero cells. Physiologically-based pharmacokinetic models (PBPK) were implemented for both drugs separately by integrating their in vitro data. Using the PBPK models, hydroxychloroquine concentrations in lung fluid were simulated under 5 different dosing regimens to explore the most effective regimen whilst considering the drug’s safety profile. RESULTS: Hydroxychloroquine (EC(50)=0.72 μM) was found to be more potent than chloroquine (EC(50)=5.47 μM) in vitro. Based on PBPK models results, a loading dose of 400 mg twice daily of hydroxychloroquine sulfate given orally, followed by a maintenance dose of 200 mg given twice daily for 4 days is recommended for SARS-CoV-2 infection, as it reached three times the potency of chloroquine phosphate when given 500 mg twice daily 5 days in advance. CONCLUSIONS: Hydroxychloroquine was found to be more potent than chloroquine to inhibit SARS-CoV-2 in vitro.


id: cord-353116-7t1prfkr
title: Predictors for Severe COVID-19 Infection
author: Bhargava, Ashish
date: 2020-05-30
txt: ./txt/cord-353116-7t1prfkr.txt
cache: ./cache/cord-353116-7t1prfkr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32472676/
doi: 10.1093/cid/ciaa674
summary:
  BACKGROUND: COVID-19 is a pandemic disease caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In multivariable logistic regression analysis, risk factors for severe infection included pre-existing renal disease (odds ratio [OR], 7.4; 95% CI 2.5-22.0), oxygen requirement at hospitalization (OR, 2.9; 95% CI, 1.3-6.7), acute renal injury (OR, 2.7; 95% CI 1.3-5.6) and initial CRP (OR,1.006; 95% CI, 1.001-1.01). CONCLUSIONS: Acute or pre-existing renal disease, supplemental oxygen at the time of hospitalization and initial CRP were independent predictors for the development of severe COVID-19 infections. The most common symptoms at the onset of illness in the studied cohort were cough (141 including higher white blood cell counts, lower lymphocyte and platelet counts, and increased C-reactive protein (CRP) levels compared with those patients with non-severe infection. In our study we report pre-existing renal disease, supplemental oxygen requirement at admission, acute renal insufficiency, and initial CRP value as independent predictors of severe COVID-19 infections.

abstract:
  BACKGROUND: COVID-19 is a pandemic disease caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Predictors for severe COVID-19 infection have not been well defined. Determination of risk factors for severe infection would enable identifying patients who may benefit from aggressive supportive care and early intervention. METHODS: We conducted a retrospective observational study of 197 patients with confirmed COVID-19 infection admitted to a tertiary academic medical center. RESULTS: Of 197 hospitalized patients, the mean (SD) age of the cohort was 60.6 (16.2) years, 103 (52.3%) were male and 156 (82.1%) were black. Severe COVID-19 infection was noted in 74 (37.6%) patients, requiring intubation. Patients aged above 60 were significantly more likely to have severe infection. Patients with severe infection were significantly more likely to have diabetes, renal disease, chronic pulmonary disease and had significantly higher white blood cell counts, lower lymphocyte counts, and increased C-reactive protein (CRP) compared to patients with non-severe infection. In multivariable logistic regression analysis, risk factors for severe infection included pre-existing renal disease (odds ratio [OR], 7.4; 95% CI 2.5-22.0), oxygen requirement at hospitalization (OR, 2.9; 95% CI, 1.3-6.7), acute renal injury (OR, 2.7; 95% CI 1.3-5.6) and initial CRP (OR,1.006; 95% CI, 1.001-1.01). Race, age and socioeconomic status were not identified as independent predictors. CONCLUSIONS: Acute or pre-existing renal disease, supplemental oxygen at the time of hospitalization and initial CRP were independent predictors for the development of severe COVID-19 infections. Every 1 unit increase in CRP increased the risk of severe disease by 0.06%.


id: cord-353342-2n6kqyeo
author: Corman, Victor M.
date: 2016-02-15
txt: ./txt/cord-353342-2n6kqyeo.txt
cache: ./cache/cord-353342-2n6kqyeo.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26565003/
doi: 10.1093/cid/civ951
summary:
  title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Quantitative data, such as viral loads and antibody titers, could enable comparisons with related diseases, in particular, severe acute respiratory syndrome (SARS), for which studies of natural history were conducted in the aftermath of the 2002-2003 epidemic [7] . DISCUSSION We studied quantitative viral excretion and serum antibody kinetics of a substantial group of hospitalized patients infected with MERS-CoV. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays

title:
  Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection

abstract:
  Background. The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. Essential features of the natural history of disease are poorly understood. Methods. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Antibodies and serum neutralizing activities were determined over the course of disease. Results. One hundred ninety-nine LRT samples collected during the 3 weeks following diagnosis yielded virus RNA in 93% of tests. Average (maximum) viral loads were 5 × 10(6) (6 × 10(10)) copies/mL. Viral loads (positive detection frequencies) in 84 URT samples were 1.9 × 10(4) copies/mL (47.6%). Thirty-three percent of all 108 serum samples tested yielded viral RNA. Only 14.6% of stool and 2.4% of urine samples yielded viral RNA. All seroconversions occurred during the first 2 weeks after diagnosis, which corresponds to the second and third week after symptom onset. Immunoglobulin M detection provided no advantage in sensitivity over immunoglobulin G (IgG) detection. All surviving patients, but only slightly more than half of all fatal cases, produced IgG and neutralizing antibodies. The levels of IgG and neutralizing antibodies were weakly and inversely correlated with LRT viral loads. Presence of antibodies did not lead to the elimination of virus from LRT. Conclusions. The timing and intensity of respiratory viral shedding in patients with MERS closely matches that of those with severe acute respiratory syndrome. Blood viral RNA does not seem to be infectious. Extrapulmonary loci of virus replication seem possible. Neutralizing antibodies do not suffice to clear the infection.


id: cord-353862-7xe3fvd5
title: Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study
author: Li, Na
date: 2020-03-30
txt: ./txt/cord-353862-7xe3fvd5.txt
cache: ./cache/cord-353862-7xe3fvd5.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32249918/
doi: 10.1093/cid/ciaa352
summary:
  METHODS: We conducted a case-control study to compare clinical characteristics, maternal and neonatal outcomes of pregnant women with and without COVID-19 pneumonia. An earlier study by Chen et al reported nine pregnant women with COVID-19 pneumonia, who took cesarean section in a tertiary hospital of Wuhan [8] . To date, none of previous studies have investigated the adverse effects of COVID-19 infection on pregnancy, by comparing maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia to those without pneumonia. Similar to two previous reports of nine and one pregnant women with confirmed COVID-19 infection [8, 22] , we did not find any evidence to support the vertical transmission of SARS-CoV-2 from mother to fetus via placenta or during cesarean section. Second, we collected the data of sixteen pregnant women with laboratory confirmed COVID-19 pneumonia and eighteen suspected cases with typical CT imaging.

abstract:
  BACKGROUND: The ongoing epidemics of coronavirus disease 2019 (COVID-19) have caused serious concerns about its potential adverse effects on pregnancy. There are limited data on maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia. METHODS: We conducted a case-control study to compare clinical characteristics, maternal and neonatal outcomes of pregnant women with and without COVID-19 pneumonia. RESULTS: During January 24 to February 29, 2020, there were sixteen pregnant women with confirmed COVID-19 pneumonia and eighteen suspected cases who were admitted to labor in the third trimester. Two had vaginal delivery and the rest took cesarean section. Few patients presented respiratory symptoms (fever and cough) on admission, but most had typical chest CT images of COVID-19 pneumonia. Compared to the controls, COVID-19 pneumonia patients had lower counts of white blood cells (WBC), neutrophils, C-reactive protein (CRP), and alanine aminotransferase (ALT) on admission. Increased levels of WBC, neutrophils, eosinophils, and CRP were found in postpartum blood tests of pneumonia patients. There were three (18.8%) and three (16.7%) of the mothers with confirmed or suspected COVID-19 pneumonia had preterm delivery due to maternal complications, which were significantly higher than the control group. None experienced respiratory failure during hospital stay. COVID-19 infection was not found in the newborns and none developed severe neonatal complications. CONCLUSION: Severe maternal and neonatal complications were not observed in pregnant women with COVID-19 pneumonia who had vaginal delivery or caesarean section. Mild respiratory symptoms of pregnant women with COVID-19 pneumonia highlight the need of effective screening on admission.


id: cord-354009-1ek4s8oe
title: Spatiotemporal Characteristics of COVID-19 Epidemic in the United States
author: Wang, Yun
date: 2020-07-08
txt: ./txt/cord-354009-1ek4s8oe.txt
cache: ./cache/cord-354009-1ek4s8oe.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa934
doi: 10.1093/cid/ciaa934
summary:
  We characterized the dynamics of COVID-19 epidemic through detecting weekly hotspots of newly confirmed cases using Spatial and Space-Time Scan Statistics and quantifying the trends of incidence of COVID-19 by county characteristics using the Joinpoint analysis. The results would enhance our understanding of small area-based spatiotemporal dynamics of COVID-19 outbreak, thus help inform multilevel strategies to control the spread of coronavirus and appropriate allocations of public health and healthcare resources in the United States. To identify the characteristics of counties with a high burden of COVID-19, we examined county-level geographic and sociodemographic factors, including rural-urban context, distance to the nearest core airport, population density, percentage of non-white minority population, percentage of population 65 years or older, and percentage of population below the federal poverty line.

abstract:
  BACKGROUND: A range of near-real-time online/mobile mapping dashboards and applications have been used to track the COVID-19 pandemic worldwide. It remains unknown about small area-based spatiotemporal patterns of COVID-19 in the United States. METHODS: We obtained county-based counts of COVID-19 cases confirmed in the United States from January 22 to May 13, 2020 (N=1,386,050). We characterized the dynamics of COVID-19 epidemic through detecting weekly hotspots of newly confirmed cases using Spatial and Space-Time Scan Statistics and quantifying the trends of incidence of COVID-19 by county characteristics using the Joinpoint analysis. RESULTS: Along with the national plateau reached in early April, COVID-19 incidence significantly decreased in the Northeast (estimated weekly percentage changes [EWPC]: -16.6%), but remained increasing in the Midwest, South and West Regions (EWPCs: 13.2%, 5.6%, and 5.7%, respectively). Higher risks of clustering and incidence of COVID-19 were consistently observed in metropolitan vs rural counties, counties closest to core airports, most populous counties, and counties with highest proportion of racial/ethnic minority counties. However, geographic differences in the incidence have shrunk since early April, driven by a significant decrease in the incidence in these counties (EWPC range: -2.0% – -4.2%) and a consistent increase in other areas (EWPC range: 1.5% – 20.3%). CONCLUSIONS: To substantially decrease the nationwide incidence of COVID-19, strict social distancing measures should be continuously implemented, especially in geographic areas with increasing risks, including rural areas. Spatiotemporal characteristics and trends of COVID-19 should be considered in decision-making on the timeline of re-opening for states and localities.


id: cord-354011-v9t2b2ca
title: Circulation of Respiratory Viruses Among Pilgrims During the 2012 Hajj Pilgrimage
author: Benkouiten, Samir
date: 2013-10-01
txt: ./txt/cord-354011-v9t2b2ca.txt
cache: ./cache/cord-354011-v9t2b2ca.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/23839997/
doi: 10.1093/cid/cit446
summary:
  We performed a prospective survey among a cohort of pilgrims departing from Marseille, France, to Mecca in the Kingdom of Saudi Arabia (KSA) for the 2012 Hajj season. This study suggests a rapid acquisition of respiratory viruses among pilgrims during their stay in the KSA, most notably rhinovirus, and highlights the potential of spreading these infections in the pilgrims'' home countries upon their return. This study, including sample collection and laboratory methods, was conducted among a cohort of pilgrims departing from Marseille, France, to Mecca in the KSA for the 2012 Hajj season. Each sample was tested for the following viruses by real-time reverse transcription polymerase chain reaction (rRT-PCR): influenza A (FLUA) [11] , influenza B (FLUB) [11] , influenza C (FLUC), and A/2009/H1N1 [12] viruses; human respiratory syncytial virus A and B (RSVB) [13] ; human metapneumovirus (HMPV) [14] ; human rhinovirus (HRV) [15] ; MS2 bacteriophage; human adenovirus (HAdV) [16] ; and human enterovirus (HEV) [17] .

abstract:
  Background. The Hajj is the oldest and largest annual mass gathering in the world and may increase the risk of spread of respiratory viruses. Methods. We performed a prospective survey among a cohort of pilgrims departing from Marseille, France, to Mecca in the Kingdom of Saudi Arabia (KSA) for the 2012 Hajj season. Nasal swabs were collected from participants and tested for 11 respiratory viruses by real-time reverse transcription polymerase chain reaction. Results. Of 165 participants sampled before departing to the KSA, 8 (4.8%) were positive for at least 1 virus (5 rhinovirus, 1 influenza C, 1 adenovirus, and 1 enterovirus). Seventy symptomatic pilgrims underwent additional nasal swabs during their pilgrimage in the KSA, of which 27 (38.6%) were positive for at least 1 virus (19 rhinovirus, 6 influenza A, 1 influenza C, 1 respiratory syncytial virus B, 1 metapneumovirus, 1 adenovirus, and 1 enterovirus). This was significantly higher than the 4.8% who were positive before departing for the KSA (P < .001). Of 154 pilgrims sampled before leaving the KSA, 17 (11%) were positive for at least 1 virus (13 rhinovirus, 3 adenovirus, 2 influenza B, and 1 enterovirus), which was also significantly higher than the percentage of positive pilgrims (4.8%), before departing for the KSA (P = .040). Conclusions. This study suggests a rapid acquisition of respiratory viruses among pilgrims during their stay in the KSA, most notably rhinovirus, and highlights the potential of spreading these infections in the pilgrims' home countries upon their return.


id: cord-354265-udt2spoe
title: Menopause status and COVID-19
author: Gersh, Felice
date: 2020-09-23
txt: ./txt/cord-354265-udt2spoe.txt
cache: ./cache/cord-354265-udt2spoe.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32968797/
doi: 10.1093/cid/ciaa1447
abstract: nan
summary:
  A c c e p t e d M a n u s c r i p t Dear Editor, We greatly appreciate the publication of this important research article, for its exploration of the connection of estradiol levels and menopausal status with outcomes from infections with SARS-CoV-2 in women. We advocate for the use of physiologically dosed human-identical transdermal estradiol as hormone replacement, combined with human-identical cyclic progesterone, in appropriate recently menopausal women. (8) Given the potential for serious negative effects ensuing from a state of estradiol deficiency, heightened by the COVID-19 pandemic, not only should appropriate postmenopausal women be considered for hormone replacement therapy, but women being treated with aromatase inhibitors and estrogen receptor antagonists should be counseled on the risks and benefits of those drugs, personalized in each case, in light of the findings of this study. Potential influence of menstrual status and sex hormones on female SARS-CoV-2 infection: A cross-sectional study from Multicentre in Wuhan


id: cord-354877-n5du3bqt
title: Rapid Antigen Tests for Diagnosis of Pandemic (Swine) Influenza A/H1N1
author: Vasoo, Shawn
date: 2009-10-01
txt: ./txt/cord-354877-n5du3bqt.txt
cache: ./cache/cord-354877-n5du3bqt.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/19725784/
doi: 10.1086/644743
summary:
  During the period from 1 May 2009 through 2 June 2009, a convenience sample of 84 positive, nonduplicate nasopharyngeal specimens were tested using 3 different rapid antigen test kits: BD Directigen EZ Flu A+B test (Becton Dickinson), BinaxNOW Influenza A&B (Inverness Medical), and QuickVue Influenza A+B Test (Quidel). Patient charts were reviewed, if available, for potential factors that may have been associated with rapid antigen test result; these included patient age, duration of symptoms before presentation, inpatient or emergency department versus outpatient status, and the median number of RT-PCR fluorescence intensity (MFI) units. Because of the widespread interest regarding the clinical performance of rapid antigen tests for detection of pandemic influenza A/H1N1 virus, we used a convenience sample of positive specimens to allow for a quick yet relatively accurate assessment of these tests.

abstract:
  We found that the sensitivities of 3 rapid influenza antigen tests for pandemic influenza A/H1N1 virus were low to moderate: BD Directigen EZ Flu A+B test (Becton Dickinson), 46.7%; BinaxNOW Influenza A&B (Inverness Medical), 38.3%; and QuickVue Influenza A+B Test (Quidel), 53.3%. A patient with influenza-like illness who has a negative rapid antigen test result should undergo further testing using reverse-transcription polymerase chain reaction.


id: cord-354943-wxhbwcfr
title: Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19)
author: Guo, Li
date: 2020-03-21
txt: ./txt/cord-354943-wxhbwcfr.txt
cache: ./cache/cord-354943-wxhbwcfr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32198501/
doi: 10.1093/cid/ciaa310
summary:
  METHODS: The host humoral response against SARS-CoV-2, including IgA, IgM, and IgG response, was examined by using an ELISA-based assay on the recombinant viral nucleocapsid protein. The positive detection rate is significantly increased (98.6%) when combining IgM ELISA assay with PCR for each patient compared with a single qPCR test (51.9%). Western blot analysis showed that there was no cross-reactivity of SARS-CoV-2 rNP with human plasma positive for IgG antibodies against NL63, 229E, OC43, and HKU1. The antibody levels were then evaluated in the plasma samples of CCs and PCs. The appearance of IgM, IgA, and IgG antibodies against SARS-CoV-2 was positive as early as day 1 after the symptom onset ( Figure 3A) . These results suggest that IgM ELISA can increase the positive detection rate when combined with the PCR method and can be used for the early diagnosis of COVID-19 infections.

abstract:
  BACKGROUND: The emergence of coronavirus disease 2019 (COVID-19) is a major healthcare threat. The current method of detection involves a quantitative polymerase chain reaction (qPCR)–based technique, which identifies the viral nucleic acids when present in sufficient quantity. False-negative results can be achieved and failure to quarantine the infected patient would be a major setback in containing the viral transmission. We aim to describe the time kinetics of various antibodies produced against the 2019 novel coronavirus (SARS-CoV-2) and evaluate the potential of antibody testing to diagnose COVID-19. METHODS: The host humoral response against SARS-CoV-2, including IgA, IgM, and IgG response, was examined by using an ELISA-based assay on the recombinant viral nucleocapsid protein. 208 plasma samples were collected from 82 confirmed and 58 probable cases (qPCR negative but with typical manifestation). The diagnostic value of IgM was evaluated in this cohort. RESULTS: The median duration of IgM and IgA antibody detection was 5 (IQR, 3–6) days, while IgG was detected 14 (IQR, 10–18) days after symptom onset, with a positive rate of 85.4%, 92.7%, and 77.9%, respectively. In confirmed and probable cases, the positive rates of IgM antibodies were 75.6% and 93.1%, respectively. The detection efficiency by IgM ELISA is higher than that of qPCR after 5.5 days of symptom onset. The positive detection rate is significantly increased (98.6%) when combining IgM ELISA assay with PCR for each patient compared with a single qPCR test (51.9%). CONCLUSIONS: The humoral response to SARS-CoV-2 can aid in the diagnosis of COVID-19, including subclinical cases.


id: cord-355618-7kfxc2w1
title: The VACCINES Act, Deciphering Vaccine Hesitancy in the Time of COVID19
author: McAteer, John
date: 2020-04-13
txt: ./txt/cord-355618-7kfxc2w1.txt
cache: ./cache/cord-355618-7kfxc2w1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32282038/
doi: 10.1093/cid/ciaa433
abstract: nan
summary:
  In his statement of support 7 , the WHO Director-General Dr. Tedros Ghebreyesus asserted that "These online efforts must be matched by tangible steps by governments and the health sector to promote trust in vaccination and respond to the needs and concerns of parents." In order to adequately respond to these needs and concerns, which differ depending on the cultural, societal, and personal beliefs of a particular region, the WHO recommends that each country take steps to develop an understanding of vaccine hesitancy at a local level on an ongoing basis 8 . In recognition of these missed opportunities and in response to declining immunization rates and increasing national skepticism on the safety of vaccines, Congress has introduced bipartisan legislation to expand research into vaccine hesitancy. The bipartisan VACCINES Act is an important step in supporting evidence-based research into vaccine hesitancy. Association between vaccine refusal and vaccine-preventable diseases in the United States: a review of measles and pertussis


id: cord-355734-pz64534w
author: Antonio-Villa, Neftali Eduardo
date: 2020-09-28
txt: ./txt/cord-355734-pz64534w.txt
cache: ./cache/cord-355734-pz64534w.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32986819/
doi: 10.1093/cid/ciaa1487
summary:
  Physicians had higher risk for hospitalization and for severe outcomes compared with nurses and other HCWs. CONCLUSIONS: We report a high prevalence of SARS-CoV-2 infection in HCWs in Mexico City. The situation in Mexico is complex, given that SARS-CoV-2 infections coexist with a high prevalence of comorbidities associated with COVID-19 complications in a large proportion of patients, including HCWs. Furthermore, healthcare systems within Mexico are highly fragmented and quality of care and the ability to protect HCWs within each institution is highly heterogeneous due to structural inequalities, which overall could increase the disparities in risk among HCWs within marginalized communities (7) . Our results also show that comorbidities in HCWs, particularly those related to chronic noncommunicable diseases (e.g., diabetes, obesity and arterial hypertension), and the presentation of severe respiratory symptoms at the time of clinical assessment, increases the risk of adverse COVID-19 outcomes.

title:
  Health-care workers with COVID-19 living in Mexico City: clinical characterization and related outcomes

abstract:
  BACKGROUND: Health-care workers (HCWs) could be at increased occupational risk for SARS-CoV-2 infection. Information regarding prevalence and risk factors for adverse outcomes in HCWs is scarce in Mexico. Here, we aimed to explore prevalence of SARS-CoV-2, symptoms, and risk factors associated with adverse outcomes in HCWs in Mexico City. METHODS: We explored data collected by the National Epidemiological Surveillance System in Mexico City. All cases underwent real-time RT-PCR test. We explored outcomes related to severe COVID-19 in HCWs and the diagnostic performance of symptoms to detect SARS-CoV-2 infection in HCWs. RESULTS: As of July 5 (th), 2020, 35,095 HCWs were tested for SARS-CoV-2 and 11,226 were confirmed (31.9%). Overall, 4,322 were nurses (38.5%), 3,324 physicians (29.6%), 131 dentists (1.16%) and 3,449 laboratory personnel and other HCWs (30.8%). After follow-up, 1,009 HCWs required hospitalization (9.00%), 203 developed severe outcomes (1.81%), and 93 required mechanical-ventilatory support (0.82%). Lethality was recorded in 226 (2.01%) cases. Symptoms associated with SARS-CoV-2 positivity were fever, cough, malaise, shivering, myalgias at evaluation but neither had significant predictive value. We also identified 341 asymptomatic SARS-CoV-2 infections (3.04%). Older HCWs with chronic non-communicable diseases, pregnancy, and severe respiratory symptoms were associated with higher risk for adverse outcomes. Physicians had higher risk for hospitalization and for severe outcomes compared with nurses and other HCWs. CONCLUSIONS: We report a high prevalence of SARS-CoV-2 infection in HCWs in Mexico City. No symptomatology can accurately discern HCWs with SARS-CoV-2 infection. Particular attention should focus on HCWs with risk factors to prevent adverse outcomes and reduce infection risk.


id: cord-356084-621qzpqd
author: Qu, Jiuxin
date: 2020-04-27
txt: ./txt/cord-356084-621qzpqd.txt
cache: ./cache/cord-356084-621qzpqd.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa489
doi: 10.1093/cid/ciaa489
summary:
  title: Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) We profiled the serological responses to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and spike (S) glycoprotein. In this study, we investigated the humoral immunity of hospitalized patients, analyzed the profile of IgG and IgM antibodies against the SARS-CoV-2 in 41 COVID-19 patients between three and 43 days of their illness. Li et al., reported that both IgG and IgM antibody levels increased to detectable levels from the second week of illness in 20 SARS-CoV patients [5] . found that acute lung injury in Chinese macaques caused by SARS-CoV could be mediated by higher anti-spike IgG [9] , and we detected high levels of IgG antibody in critical patients. Longitudinal profile of immunoglobulin G (IgG), IgM, and IgA antibodies against the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in patients with pneumonia due to the SARS coronavirus

title:
  Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

abstract:
  We profiled the serological responses to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and spike (S) glycoprotein. The majority of the patients developed robust antibody responses between 17 and 23 days after illness onset. Delayed, but stronger antibody responses were observed in critical patients.


id: cord-356316-ui11jr2h
author: Patel, Monita R
date: 2020-06-16
txt: ./txt/cord-356316-ui11jr2h.txt
cache: ./cache/cord-356316-ui11jr2h.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa759
doi: 10.1093/cid/ciaa759
summary:
  Among 146 nasopharyngeal (NP) and oropharyngeal (OP) swab pairs collected ≤7 days since illness onset, CDC real-time RT-PCR SARS-CoV-2 assay diagnostic results were 95.2% concordant. Current US Centers for Disease Control and Prevention (CDC) guidelines identify nasopharyngeal (NP) and oropharyngeal (OP) swabs as acceptable upper respiratory specimens to test for presence of SARS-CoV-2 ribonucleic acid (RNA) (1) . Overall, among persons with specimens collected early in the illness course, SARS-CoV-2 RNA diagnostic results were highly concordant between OP and NP swabs. Current Infectious Diseases Society of America Guidelines specifically recommend collection of NP, mid-turbinate or nasal swabs rather than OP swabs alone for all symptomatic persons; our findings suggest this recommendation may be particularly relevant for persons later in the illness course and who may have lower amount of SARS-CoV-2 viral RNA (7). Together, our findings support CDC guidelines that identify NP and OP swabs as acceptable specimens for SARS-CoV-2 RNA testing; but suggest that NP swab may comparatively be a more sensitive specimen type for testing persons later in the illness course.

title:
  Performance of oropharyngeal swab testing compared to nasopharyngeal swab testing for diagnosis of COVID-19 —United States, January-February 2020

abstract:
  Among 146 nasopharyngeal (NP) and oropharyngeal (OP) swab pairs collected ≤7 days since illness onset, CDC real-time RT-PCR SARS-CoV-2 assay diagnostic results were 95.2% concordant. However, NP swab Ct values were lower (indicating more virus) in 66.7% of concordant-positive pairs, suggesting NP swabs may more accurately detect amount of SARS-CoV-2.


