# ent

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  antibodies 170 P aeruginosa Human gamma globulin 172 Escherichia coli Murine E5 LPS antibodies 174 Shistosoma mansoni Praziquantel Rabbit immune sera 175 Candida albicans Amphotericin B Human gamma globulin 137 Cryptococcus neoformans


id: cord-010570-ytv7dwr0
type: ORG
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  The National Institute of Child Health and Human Development Intravenous Immunoglobulin Study Group Intravenous


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  PER C6 cell grown influenza H7 virus vaccine Influenza vaccination coverage how well did we do in 2012 13


id: cord-001800-644lf8vn
type: WORK_OF_ART
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  Estimating the Potential Effects of a Vaccine Program Against an Emerging Influenza Pandemic United States


id: cord-001800-644lf8vn
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  influenza A H7N9 virus Population level antibody estimates to novel influenza A H7N9 Emergence of avian influenza A H7N9 virus


id: cord-288432-n2y9cunc
type: ORG
entity:
  Wuhan China Potential for International Spread Via Commercial Air Travel Modeling Impact of Temperature and Human Movement


id: cord-288432-n2y9cunc
type: EVENT
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  an Outbreak of Ebola Virus Disease Results from Community Engagement in Two Districts Uganda Forecast


id: cord-254183-98o0dssj
type: DISEASE
entity:
  human Tcell leukemia virus type 1 positive renal transplant recipients Human T cell leukemia virus type I


id: cord-278084-km04sz2s
type: CHEMICAL
entity:
  1 2 3 4 5 6 7 In this patient population these viruses cause upper respiratory tract infections URTIs


id: cord-278084-km04sz2s
type: DISEASE
entity:
  bone marrow transplant recipients the European perspective Community acquired respiratory syncytial virus and parainfluenza virus infections


id: cord-260274-c3586tp6
type: ORG
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  the International Severe Acute Respiratory and Emerging Infection Consortium ISARIC Clinical Characterization Protocol


id: cord-260274-c3586tp6
type: WORK_OF_ART
entity:
  Strengthening the Reporting of Observational Studies in Epidemiology STROBE Immortal Time Bias in Pharmacoepidemiology Comparison of the SpO2


id: cord-271014-xzpvupms
type: GGP
entity:
  A c c e p t e d M a n u s c r i p t 13 M a n u s c r i p t 15 A c c e p t e d M a n u s c r i p t 16


id: cord-271014-xzpvupms
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  the Departments of Clinical Immunology at Aarhus University Hospital Copenhagen University Hospital Odense University Hospital Zealand University Hospital


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type: WORK_OF_ART
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  A Phase II Randomized Double blind Placebo Controlled Trial of Presatovir for the Treatment of Respiratory Syncytial Virus Upper Respiratory Tract Infection


id: cord-007064-nepgttxf
type: CHEMICAL
entity:
  Catherine B Mullane Kathleen M Patron Roberto L Lee Dong Gun Hirsch Hans H Waghmare Alpana McKevitt Matt Jordan Robert Guo Ying German Polina Porter Danielle P Gossage David L Watkins Timothy R Marty Francisco M Chien Jason W Boeckh Michael title A


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type: WORK_OF_ART
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  The Use of Ebola Convalescent Plasma to Treat Ebola Virus Disease in Resource Constrained Settings A Perspective From the Field date 2016 01 01


id: cord-266808-wyuodzyt
type: GGP
entity:
  Antibodies A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p


id: cord-260457-m1jbpo5l
type: CELL_LINE
entity:
  Boca reverse GGG TGT TCC TGA TGA TAT GAG C and 150 nmol L Boca probe FAM CTG CGG CTC CTG CTC CTG TGA T TAMRA


id: cord-010578-uib9h1lb
type: GGP
entity:
  herpesviruses cytomegalovirus varicella zoster virus human herpesvirus 6 EBV early antigen nuclear antigen and VCA and herpes simplex virus 1


id: cord-010578-uib9h1lb
type: DISEASE
entity:
  herpes simplex virus 1 the respiratory viruses adenovirus respiratory syncytial virus coronavirus and parainfluenza viruses 1 2 and 3 measles virus parvovirus B19


id: cord-259471-lsdodl0a
type: WORK_OF_ART
entity:
  Hydroxychloroquine a Possible Postexposure Prophylaxis Drug to Limit the Transmission to Healthcare Workers


id: cord-280958-36ytqapi
type: DNA
entity:
  SH G intergenic region RSV SH G Forward TTAACATCCCACCATGCAAA RSV SH G Reverse GCATTTGCCCCAATGTTATT 2


id: cord-280958-36ytqapi
type: WORK_OF_ART
entity:
  The Lancet Global Health United States Centers for Disease Control and Prevention Interim Guidance Healthcare Professionals 2019


id: cord-280958-36ytqapi
type: ORG
entity:
  United States Centers for Disease Control and Prevention STANDARD OPERATING PROCEDURE FORMAT AND TEMPLATE Viral Transport Medium Essential


id: cord-280005-i9fp5rys
type: GGP
entity:
  A c c e p t e d M a n u s c r i p t 19 A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p t


id: cord-280005-i9fp5rys
type: WORK_OF_ART
entity:
  Treatment of COVID 19 Patients with Prolonged Post Symptomatic Viral Shedding with Leflunomide a Single Center Randomized Controlled Clinical Trial date 2020


id: cord-012511-fl5llkoj
type: PROTEIN
entity:
  Y21 N3 d31 N4 d41 3 669 000 1 8 3 997 000 0 7 9 402 100 Y12 N1 d12 N2 d22 3 914 000 0 7 3 517 000 1 These 2


id: cord-257553-479x7av6
type: GGP
entity:
  hepatitis B immunoglobulin 0 06 mL kg intramuscularly should be offered after injury and repeated in 1 month 4 Hepatitis B immunoglobulin


id: cord-288558-rthnj6wd
type: WORK_OF_ART
entity:
  Nasopharynx Is Associated with Diarrhea in Patients with Severe Acute Respiratory Syndrome date 2004


id: cord-258724-1qhen1bj
type: PROTEIN
entity:
  Cytokine Chemokine Growth Factor 45 Plex Human ProcartaPlex TM Panel 1 ThermoFisher Scientific details in Supplementary Appendix Cytokine


id: cord-258724-1qhen1bj
type: ORG
entity:
  China SARS CoV 2 Viral Load in Upper Respiratory Specimens of Infected Patients Detection of SARS CoV 2


id: cord-258724-1qhen1bj
type: WORK_OF_ART
entity:
  Treatment With Convalescent Plasma for Critically Ill Patients With Severe Acute Respiratory Syndrome Coronavirus 2 Infection Treatment of 5 Critically Ill Patients With COVID 19 With Convalescent Plasma Plasma


id: cord-290133-4ou7ubb4
type: ORG
entity:
  Board on Health Promotion and Disease Prevention Institute of Medicine Review of the Centers for Disease Control and Prevention


id: cord-007075-sl45z4i0
type: ORG
entity:
  Placebo Controlled Multicenter Study Evaluating Antiviral Effects Pharmacokinetics Safety and Tolerability of Presatovir


id: cord-273840-jjm7y07m
type: DNA
entity:
  ORF1a ATR HKU1 sens 5 AATGGCCTCTCGTATGTAT 3 ATR HKU1 antisense 5 TTACAAGTAACACAGAACGCA 3 The RT PCR products


id: cord-273840-jjm7y07m
type: DNA
entity:
  human coronavirus strain OC43 phylogenetic relationships to bovine and murine coronaviruses and influenza C virus Potential conflicts


id: cord-280954-wd89nka9
type: ORG
entity:
  Severe Morbidity and Mortality Associated With Respiratory Syncytial Virus Versus Influenza Infection


id: cord-252005-3ld5e7f5
type: WORK_OF_ART
entity:
  the USA Presymptomatic SARS CoV 2 Infections and Transmission in a Skilled Nursing Facility Characteristics of and Important Lessons From the Coronavirus Disease 2019


id: cord-278045-hr3r17mz
type: ORG
entity:
  DNA Development of Reverse Transcription Loop Mediated Isothermal Amplification Assays Targeting Severe Acute Respiratory Syndrome Coronavirus


id: cord-278045-hr3r17mz
type: WORK_OF_ART
entity:
  False Negative Tests for SARS CoV 2 Infection Challenges and Implications SARS CoV 2 Viral Load in Upper Respiratory Specimens of Infected Patients Sensitivity of Chest CT


id: cord-278045-hr3r17mz
type: WORK_OF_ART
entity:
  A Report of 1014 Cases Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease COVID 19 Temporal


id: cord-280571-ntgt5hy9
type: WORK_OF_ART
entity:
  Strengths and Weaknesses of FDA Approved Cleared Diagnostic Devices for the Molecular Detection of Respiratory Pathogens


id: cord-280571-ntgt5hy9
type: DISEASE
entity:
  influenza A H1N1 the specific hemagglutinin genes of seasonal influenza A H1 and seasonal influenza A


id: cord-280571-ntgt5hy9
type: DISEASE
entity:
  influenza A H1N1 pandemic laboratories must be able to respond immediately by rapidly expanding testing capabilities including sensitive and specific molecular diagnostics 43 At the onset of the Queens New York area 2009 influenza A H1N1 outbreak the NS LIJHS laboratories respiratory virus testing volume


id: cord-280571-ntgt5hy9
type: DISEASE
entity:
  influenza A virus and their value in health care management of institutionalized geriatric patients Why diagnose influenza


id: cord-294335-qnu19ru5
type: CELL_LINE
entity:
  Hubei China A Descriptive Cross Sectional Multicenter Study Enteric involvement in hospitalised patients with COVID 19 outside Wuhan Gender


id: cord-294335-qnu19ru5
type: PRODUCT
entity:
  Real Time RT PCR Diagnostic Panel Hospitalization Rates and Characteristics of Patients Hospitalized with Laboratory


id: cord-294335-qnu19ru5
type: DISEASE
entity:
  chest pain neurologic headache loss of taste or loss of smell and gastrointestinal nausea vomiting diarrhea


id: cord-294335-qnu19ru5
type: DISEASE
entity:
  aConstitutional fever chills muscle aches fatigue Upper respiratory runny nose nasal congestion sore


id: cord-294335-qnu19ru5
type: DISEASE
entity:
  chest pain Neurologic headache loss of taste loss of smell Gastrointestinal nausea diarrhea abdominal pain


id: cord-292094-vmsdhccp
type: ORG
entity:
  American Thoracic Society Centers for Disease Control and Prevention Infectious Diseases Society of America


id: cord-292094-vmsdhccp
type: DISEASE
entity:
  influenza A H5N1 World Health Organization Production of pilot lots of inactivated influenza vaccines from reassortants derived from avian influenza viruses interim biosafety assessment Avian influenza A H5N1 infection


id: cord-289598-t8upoq9a
type: GGP
entity:
  A c c e p t e d M a n u s c r i p t 14 M a n u s c r i p t M a n u s c r i p t 19 A c c e p t e d M a n u s c r i p t 21 A c c e p t e d M a n u s c r i p t


id: cord-294718-n3gx862b
type: ORG
entity:
  Detection of SARS CoV 2 in Different Types of Clinical Specimens Initial Guidance Management of Infants


id: cord-307660-onz6vfre
type: ORG
entity:
  Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome


id: cord-301066-62qe4fb0
type: CHEMICAL
entity:
  dNTP 5 5 mmol L MgCl 2 0 25 U of AmpErase UNG 0 8 mmol L each primer and 0 4 mmol L probe The primer sequences


id: cord-299720-f0ny4ur5
type: ORG
entity:
  Korea Ministry of Government Legislation Infectious Disease Control and Prevention Act World Health Organization Laboratory


id: cord-299720-f0ny4ur5
type: ORG
entity:
  Jeong Gu Nam Division of Respiratory Viruses Center of Infectious Disease Korea Centers for Disease Control and Prevention


id: cord-300013-6m1f4q5r
type: ORG
entity:
  the European Society of Clinical Microbiology and Infectious Diseases Thoracic Ultrasound Technique Applications and Interpretation International


id: cord-303330-zh8wzza5
type: ORG
entity:
  Impact of SARS CoV 2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease


id: cord-303330-zh8wzza5
type: DISEASE
entity:
  coronary artery disease congestive heart failure cerebrovascular disease hypertension chronic obstructive pulmonary disease COPD chronic kidney disease


id: cord-299499-66qh3r75
type: WORK_OF_ART
entity:
  Severe Acute Respiratory Syndrome Coronavirus 2 SARS CoV 2 and the Central Nervous System Adolescent


id: cord-307342-3gkiukh4
type: CELL_LINE
entity:
  Washington Post COVID 19 Contact Tracing We Can Live With A Roadmap and Recommendations Coronavirus recommendations ignored as case numbers rise The Washington Post A


id: cord-307342-3gkiukh4
type: GGP
entity:
  Businesses A c c e p t e d M a n u s c r i p t 12 A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p


id: cord-296588-q2716lda
type: ORG
entity:
  Alps Guidance for Risk Assessment and Public Health Management of Healthcare Personnel with Potential Exposure


id: cord-313427-6y4zvrmn
type: WORK_OF_ART
entity:
  Clinical Laboratories Understanding and Addressing Sources of Anxiety Among Health Care Professionals


id: cord-324007-hapzf0fl
type: WORK_OF_ART
entity:
  Diagnostic Testing or Empirical Therapy for Patients Hospitalized with Suspected Influenza What to Do


id: cord-299359-s8j78naz
type: WORK_OF_ART
entity:
  Influenza Vaccination Is Not Associated With Detection of Noninfluenza Respiratory Viruses in Seasonal Studies of Influenza Vaccine Effectiveness


id: cord-299359-s8j78naz
type: ORG
entity:
  the Advisory Committee on Immunization Practices ACIP Centers for Disease Control and Prevention CDC Prevention


id: cord-318458-jadk2qbm
type: GGP
entity:
  A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p


id: cord-318458-jadk2qbm
type: ORG
entity:
  the korean national health insurance system Information Technology Based Tracing Strategy in Response to


id: cord-318458-jadk2qbm
type: DISEASE
entity:
  diabetes ischemic heart disease congestive heart failure cerebrovascular disease hemiplegia dementia peripheral vascular disease liver disease


id: cord-318204-t024w7h6
type: GGP
entity:
  SARS CoV 2 8 51 52 53 This is particularly important because the positive or negative predictive value of a test


id: cord-318204-t024w7h6
type: GGP
entity:
  SARS CoV 2 A c c e p t e d M a n u s c r i p t 15 A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p


id: cord-312928-ef8hqs4s
type: DISEASE
entity:
  influenza respiratory syncytial virus and human metapneumovirus among infants and young children Genetic susceptibility to respiratory syncytial virus bronchiolitis


id: cord-305394-wwabxlgr
type: GGP
entity:
  SARS CoV 2 Polymerase preprint Mortality and causes of death in South Africa Findings from death notification Weight gain and integrase inhibitors


id: cord-326297-0r9pex1o
type: GGP
entity:
  A c c e p t e d M a n u s c r i p t 9 A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p t 16 A c c e p t e d M a n u s c r i p t 18 Figure 1


id: cord-331731-c2r0kfaz
type: WORK_OF_ART
entity:
  The Path to Cancer and Back Immune Modulation During Hepatitis C Virus Infection Progression to Fibrosis and Cancer


id: cord-336563-hwemigk7
type: ORG
entity:
  a Humanized Respiratory Syncytial Virus Monoclonal Antibody Reduces Hospitalization From Respiratory Syncytial Virus Infection


id: cord-336563-hwemigk7
type: ORG
entity:
  nCoV Pneumonia A Randomized Open Controlled Clinical Study to Evaluate the Efficacy of ASC09F and Ritonavir


id: cord-327862-zcg3baym
type: TAXON
entity:
  coronavirus HKV1 1 coronavirus 229E 2 coronavirus OC43 11 human rhinovirus enterovirus 4 human metapneumovirus 3 respiratory syncytial virus


id: cord-327862-zcg3baym
type: DISEASE
entity:
  respiratory viruses 4 coronavirus HKV1 1 coronavirus 229E 2 coronavirus OC43 11 human rhinovirus enterovirus 4 human metapneumovirus 3 respiratory syncytial virus 2 parainfluenza A c c e p t e d M a n u s c r i p t 5 type 1 virus 1 adenovirus No formation


id: cord-312797-hohzjx74
type: CELL_LINE
entity:
  Madin Darby canine kidney Vero African green monkey kidney human laryngeal carcinoma HEp 2 human foreskin fibroblast human rhabdomyosarcoma transformed human kidney 293 human lung adenocarcinoma A 549 and human colon adenocarcinoma HT 29 4 7


id: cord-312797-hohzjx74
type: PROTEIN
entity:
  nucleoprotein N phosphoprotein P matrix M protein fusion F protein transcription elongation factor RNA


id: cord-317948-svgguadm
type: WORK_OF_ART
entity:
  Different Types of Clinical Specimens Interim Infection Prevention and Control Recommendations for Patients with Confirmed Coronavirus Disease 2019


id: cord-325136-oyizfh2z
type: WORK_OF_ART
entity:
  A Language and Environment for Statistical Computing Estimate Time Varying Reproduction Numbers from Epidemic Curves


id: cord-329323-1cquorhs
type: GGP
entity:
  mellitus 8 9 10 11 12 13 14 hypertension 10 11 12 13 14 cardiovascular disease 8 9 10 14 obesity 10 11 13 14 and chronic lung disease 8 9 10


id: cord-329323-1cquorhs
type: ORG
entity:
  Emerging Infections Program Georgia Department of Health Veterans Affairs Medical Center CDC Division of Population Health US Department of Health and Human Services


id: cord-331930-w2055c42
type: ORG
entity:
  Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome date 2004


id: cord-333943-9d93na7s
type: CL
entity:
  platelet inhibitors dipeptidyl peptidase 4 inhibitors metformin insulin sulfonylurea sodium glucose cotransporter 2 inhibitors


id: cord-333943-9d93na7s
type: ORG
entity:
  a Resource for Health Research Strengths Limitations Applications and Strategies for Optimal Use of HIRA Data World Health Organization Laboratory


id: cord-340317-gwqy6u9x
type: WORK_OF_ART
entity:
  Using Serologic Testing to Assess the Effectiveness of Outbreak Control Efforts Serial PCR Testing and Cohorting of Positive SARS CoV


id: cord-340678-2e2s1gof
type: DISEASE
entity:
  coronaviruses entero rhinoviruses EV RV HMPV parainfluenza and RSV Coxsackie echovirus adenovirus and bocavirus


id: cord-340579-cvze15cj
type: ORG
entity:
  Coronavirus Pneumonia Emergency Response Epidemiology Team The Epidemiological Characteristics of an Outbreak of 2019


id: cord-322082-80ym2rsq
type: DISEASE
entity:
  influenza A H1N1 viruses 53 The previous prevailing dogma was that pandemic influenza was the result of the emergence of a new virus subtype However the subsequent global spread indicates that a pandemic is better defined by the global population s immunological susceptibility and antigenic distance of the new virus from other influenza viruses rather than rigid applications of virologic rules involving antigenic shift 54 The 2009 A H1N1 virus


id: cord-322082-80ym2rsq
type: DISEASE
entity:
  influenza A H1N1 virus strains Nonpharmaceutical influenza mitigation strategies US communities 1918 1920 pandemic The unidentified pandemic disease


id: cord-327069-vjlisnui
type: PROTEIN
entity:
  Orin S Baggett Henry C Brooks W Abdullah Feikin Daniel R Hammitt Laura L Howie Stephen R C Knoll Maria Deloria Kotloff Karen L Madhi


id: cord-351231-aoz5jbf1
type: ORG
entity:
  California World Health Organization Multicentre Collaborative Network for Severe Acute Respiratory Syndrome


id: cord-351231-aoz5jbf1
type: DISEASE
entity:
  influenza A H7N9 and influenza A H5N1 28 29 30 Both show high mortality rates but little evidence so far of that single critical mutation permitting attachment to the hemagglutinin antigen


id: cord-351314-atsuh8e2
type: ORG
entity:
  the U Centers for Disease Control and Prevention Evaluating and Reporting Persons Under Investigation PUI Centers for Disease Control and Prevention Interim Infection Prevention


id: cord-353103-sdij1d90
type: ORG
entity:
  Semin Arthritis Rheum Physiologically Based Pharmacokinetic Analyses Format and Content Guidance for Industry Predictive Performance of Physiologically Based Pharmacokinetic Models in Predicting Drug Drug Interactions Involving Enzyme Modulation Clinical


id: cord-353116-7t1prfkr
type: DNA
entity:
  interleukin IL 2 IL6 IL7 IL10 granulocyte colony stimulating factor GCSF tumor necrosis factor TNF alpha


id: cord-353116-7t1prfkr
type: GGP
entity:
  Angiotensin II receptor blockers A c c e p t e d M a n u s c r i p t A c c e p t e d M a n u s c r i p


id: cord-353116-7t1prfkr
type: ORG
entity:
  the Chinese Center for Disease Control and Prevention Clinical Characteristics of Coronavirus Disease 2019


id: cord-354877-n5du3bqt
type: DISEASE
entity:
  influenza B virus parainfluenza virus types 1 4 respiratory syncytial virus adenovirus and rhinovirus


id: cord-355734-pz64534w
type: DISEASE
entity:
  fever cough odynophagia dyspnea irritability diarrhea chest pain shivering headache myalgia arthralgia malaise rhinorrhea polypnea vomiting abdominal pain conjunctivitis cyanosis


id: cord-348178-6bjimde4
type: CELL_LINE
entity:
  Beijing Ditan Hospital Beijing Ditan Hospital s infectious diseases sewage system also has its own primary sewage decontamination system Decontamination and maintenance of the laboratory Because the gross spillage of potentially infectious materials during autopsy was inevitable we decontaminated the area after each autopsy The air was sterilized with UV light for 1 h surfaces and the floor


id: cord-348178-6bjimde4
type: ORG
entity:
  Geneva World Health Organization Centers for Disease Control and Prevention and National Institutes of Health World Health Organization WHO post


id: cord-348178-6bjimde4
type: ORG
entity:
  Beijing Science and Technology Research Committee Peoples Republic of China entitled Collaborative Investigation of the Immunopathology of SARS


id: cord-306495-o0ah1gj9
type: ORG
entity:
  mortality Characteristics of and Important Lessons From the Coronavirus Disease 2019 COVID 19 Outbreak


id: cord-341435-b36h69r1
type: ORG
entity:
  Age Severe Acute Respiratory Syndrome Coronavirus Infection Causes Neuronal Death in the Absence of Encephalitis in Mice Transgenic for Human ACE2 High


id: cord-340956-1t3o24u5
type: ORG
entity:
  United States Department of Agriculture Foreign Agricultural Services United States Department of Agriculture Foreign Agricultural Services


id: cord-340956-1t3o24u5
type: DISEASE
entity:
  influenza A viruses IAVs The sustained circulation of IAVs and often poor biosecurity provides great opportunity for swine IAVs


# bib

id: cord-001381-b0tlco4t
author: Howie, Stephen R. C.
date: 2014-09-01
txt: ./txt/cord-001381-b0tlco4t.txt
cache: ./cache/cord-001381-b0tlco4t.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4130311/
doi: 10.1093/cid/ciu384
summary:
  title: Etiology of Severe Childhood Pneumonia in The Gambia, West Africa, Determined by Conventional and Molecular Microbiological Analyses of Lung and Pleural Aspirate Samples Molecular analyses of lung aspirates from Gambian children with severe pneumonia detected pathogens more frequently than did culture and showed a predominance of bacteria, principally Streptococcus pneumoniae, >75% being of serotypes covered by current pneumococcal conjugate vaccines. influenzae), 16S rRNA PCR, multilocus sequence typing (MLST), molecular serotyping, and multiplex fast-track 33 PCR, all using standard methods (Supplementary Appendix 2) [2, [6] [7] [8] [9] [10] [11] [12] [13] , were performed at the MRC Unit in The Gambia, and multiplex MassTag PCR [14] was performed at Columbia University. This study also confirms that molecular methods are able to detect potential pathogens far more readily than culture and have a role in defining the etiology of pneumonia.

title:
  Etiology of Severe Childhood Pneumonia in The Gambia, West Africa, Determined by Conventional and Molecular Microbiological Analyses of Lung and Pleural Aspirate Samples

abstract:
  Molecular analyses of lung aspirates from Gambian children with severe pneumonia detected pathogens more frequently than did culture and showed a predominance of bacteria, principally Streptococcus pneumoniae, >75% being of serotypes covered by current pneumococcal conjugate vaccines. Multiple pathogens were detected frequently, notably Haemophilus influenzae (mostly nontypeable) together with S. pneumoniae.


id: cord-001800-644lf8vn
author: Biggerstaff, Matthew
date: 2015-05-01
txt: ./txt/cord-001800-644lf8vn.txt
cache: ./cache/cord-001800-644lf8vn.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4610126/
doi: 10.1093/cid/ciu1175
summary:
  For the second scenario, we clinical attack rate of the influenza pandemic is 20% and the overall case fatality ratio is 0.53% (high-severity scenario); 10 million doses (left) or 30 million doses (right) of vaccine are administered each week; the vaccination program begins 16 weeks after, 8 weeks after, the same week as, 8 weeks before, and 16 weeks before the first cases of a novel influenza virus occur in the United States; and the efficacy is "H1N1pmd09 monovalent vaccine-like." 2009 H1N1-like vaccine effectiveness: 2 doses of vaccine administered 3 weeks apart required to be fully effective (62% for persons aged <60 years and 43% for persons ≥60 years) in protecting against subclinical and clinical cases, hospitalizations, and deaths. For an influenza pandemic with a 30% overall cumulative attack rate and high-severity scenario, we estimated that a vaccination program beginning the same week as the pandemic started in the United States that administered 10 million doses of vaccine with the moderate VE per week could avert 260 000 hospitalizations and 32 000 deaths (6% reduction) (Tables 2 and 3 ; Figures 2 and 3) .

title:
  Estimating the Potential Effects of a Vaccine Program Against an Emerging Influenza Pandemic—United States

abstract:
  Background. Human illness from influenza A(H7N9) was identified in March 2013, and candidate vaccine viruses were soon developed. To understand factors that may impact influenza vaccination programs, we developed a model to evaluate hospitalizations and deaths averted considering various scenarios. Methods. We utilized a model incorporating epidemic curves with clinical attack rates of 20% or 30% in a single wave of illness, case hospitalization ratios of 0.5% or 4.2%, and case fatality ratios of 0.08% or 0.53%. We considered scenarios that achieved 80% vaccination coverage, various starts of vaccination programs (16 or 8 weeks before, the same week of, or 8 or 16 weeks after start of pandemic), an administration rate of 10 or 30 million doses per week (the latter rate is an untested assumption), and 2 levels of vaccine effectiveness (2 doses of vaccine required; either 62% or 80% effective for persons aged <60 years, and either 43% or 60% effective for persons aged ≥60 years). Results. The start date of vaccination campaigns most influenced impact; 141 000–2 200 000 hospitalizations and 11 000–281 000 deaths were averted when campaigns started before a pandemic, and <100–1 300 000 hospitalizations and 0–165 000 deaths were averted for programs beginning the same time as or after the introduction of the pandemic virus. The rate of vaccine administration and vaccine effectiveness did not influence campaign impact as much as timing of the start of campaign. Conclusions. Our findings suggest that efforts to improve the timeliness of vaccine production will provide the greatest impacts for future pandemic vaccination programs.


id: cord-002514-pp06m5xk
author: Venkatesan, Sudhir
date: 2017-05-15
txt: ./txt/cord-002514-pp06m5xk.txt
cache: ./cache/cord-002514-pp06m5xk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411393/
doi: 10.1093/cid/cix127
summary:
  title: Impact of Outpatient Neuraminidase Inhibitor Treatment in Patients Infected With Influenza A(H1N1)pdm09 at High Risk of Hospitalization: An Individual Participant Data Metaanalysis While evidence exists to support the effectiveness of neuraminidase inhibitors (NAIs) in reducing mortality when given to hospitalized patients with A(H1N1)pdm09 virus infection, the impact of outpatient treatment on hospitalization has not been clearly established. In patients with laboratory-confirmed or clinically diagnosed A(H1N1)pdm09 influenza, after adjustment for community-based antibiotic treatment and propensity score, the likelihood of hospital admission in patients with outpatient or community-based NAI treatment was 0.24 (95% CI, 0.20-0.30) when compared to no NAI treatment in the community (Table 2) . Our main findings ( Table 2) suggest that NAI treatment in the community for patients with severe pandemic influenza substantially reduced the likelihood of hospital admission due to influenza A(H1N1)pdm09. Effectiveness of neuraminidase inhibitors in reducing mortality in patients admitted to hospital with influenza A H1N1pdm09 virus infection: a meta-analysis of individual participant data

title:
  Impact of Outpatient Neuraminidase Inhibitor Treatment in Patients Infected With Influenza A(H1N1)pdm09 at High Risk of Hospitalization: An Individual Participant Data Metaanalysis

abstract:
  BACKGROUND. While evidence exists to support the effectiveness of neuraminidase inhibitors (NAIs) in reducing mortality when given to hospitalized patients with A(H1N1)pdm09 virus infection, the impact of outpatient treatment on hospitalization has not been clearly established. We investigated the impact of outpatient NAI treatment on subsequent hospitalization in patients with A(H1N1)pdm09 virus infection. METHODS. We assembled general community and outpatient data from 9 clinical centers in different countries collected between January 2009 and December 2010. We standardized data from each study center to create a pooled dataset and then used mixed-effects logistic regression modeling to determine the effect of NAI treatment on hospitalization. We adjusted for NAI treatment propensity and preadmission antibiotic use, including “study center” as a random intercept to account for differences in baseline hospitalization rate between centers. RESULTS. We included 3376 patients with influenza A(H1N1)pdm09, of whom 3085 (91.4%) had laboratory-confirmed infection. Eight hundred seventy-three patients (25.8%) received outpatient or community-based NAI treatment, 928 of 2395 (38.8%) with available data had dyspnea or respiratory distress, and hospitalizations occurred in 1705 (50.5%). After adjustment for preadmission antibiotics and NAI treatment propensity, preadmission NAI treatment was associated with decreased odds of hospital admission compared to no NAI treatment (adjusted odds ratio, 0.24; 95% confidence interval, 0.20–0.30). CONCLUSIONS. In a population with confirmed or suspected A(H1N1)pdm09 and at high risk of hospitalization, outpatient or community-based NAI treatment significantly reduced the likelihood of requiring hospital admission. These data suggest that community patients with severe influenza should receive NAI treatment.


id: cord-007047-7ty9mxa9
title: Implications of New Technology for Infectious Diseases Practice
author: Reller, L. Barth
date: 2006-11-15
txt: ./txt/cord-007047-7ty9mxa9.txt
cache: ./cache/cord-007047-7ty9mxa9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107913/
doi: 10.1086/508536
summary:
  Problems with currently available molecular assays include a lack of knowledge about the extent of microbial nucleic acid in "normal" hosts, concentration of agent material in small volume samples, lack of microbiologist expertise, lack of adequate reimbursement, and difficulty with validation based on conventional methods. Infectious diseases clinicians have relied on these expert workers, and Reliable molecular diagnostic tests are not readily available for many infectious agents Commercial tests should only be used for validated specimen types Transportation problems, low concentrations of infectious agent, primer binding site genetic changes, final assay volume, inhibition, contamination, nonspecific amplification, and operator error lead to false-negative and false-positive amplification results Genomic bacterial sequencing is subject to error because of sequence homology among different bacteria, database problems, and mutations A number of nucleic acid hybridization and amplification methods are now in use, including direct probe hybridization (AdvanDx FISH for Staphylococcus aureus [AdvanDx] and GenProbe for group A streptococci [GenProbe]), hybrid capture (Digene for human papillomavirus; Digene), PCR, branched-chain DNA (bDNA; Bayer Diagnostics), and transcription-mediated amplification (Probe-Tec for Chlamydia and N.

abstract:
  New assays for the diagnosis of infectious diseases—particularly those that use molecular technologies—will revolutionize infectious diseases practices, but the fulfillment of the promise is several years away. Problems with currently available molecular assays include a lack of knowledge about the extent of microbial nucleic acid in “normal” hosts, concentration of agent material in small volume samples, lack of microbiologist expertise, lack of adequate reimbursement, and difficulty with validation based on conventional methods. Clinicians must appreciate the shortcomings of new technology to use it effectively and appropriately. However, we are realizing tangible progress in our ability to detect new etiological agents; the availability of rapid, accurate diagnostic tests for previously difficult infections; and advances into new, human response—based paradigms for diagnostic testing.


id: cord-007049-02p8ug67
author: McGeer, Allison
date: 2004-07-15
txt: ./txt/cord-007049-02p8ug67.txt
cache: ./cache/cord-007049-02p8ug67.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107923/
doi: 10.1086/421784
abstract: nan
summary:
  In June 2003, the Centers for Disease Control and Prevention (CDC) surveyed members of the Infectious Disease Society of America Emerging Infections Network (EIN) about SARS preparedness in their hospitals. Of the 456 EIN members responding to the survey in this issue of Clinical Infectious Diseases [2] , 381 (83%) reported that patients with respiratory symptoms in their emergency department (ED) would be screened for a travel history. A careful assessment of exposures in SARS outbreaks, particularly those due to superspreading events and transmission despite compliance with isolation precautions, is needed to determine whether airborne spread occurs [10, [13] [14] [15] . At least 2 analyses of risks associated with health care worker infection despite the use of precautions now identify that 12 h of infection-control training and confidence that precautions would be protective are associated with substantial reductions in the risk of infection (Toronto SARS hospital investigation, unpublished data; Lau et al. Hospital preparedness for severe acute respiratory syndrome in the United States: views from a national survey of infectious diseases consultants

title:
  Let Him Who Desires Peace Prepare for War: United States Hospitals and Severe Acute Respiratory Syndrome Preparedness


id: cord-007050-ibmr5bev
author: Xu, Wei
date: 2013-09-15
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107925/
doi: 10.1093/cid/cit396
abstract: nan
title:
  Serological Investigation of Subclinical Influenza A(H7H9) Infection Among Healthcare and Non–Healthcare Workers in Zhejiang Province, China


id: cord-007064-nepgttxf
author: Chemaly, Roy F
date: 2019-12-03
txt: ./txt/cord-007064-nepgttxf.txt
cache: ./cache/cord-007064-nepgttxf.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108134/
doi: 10.1093/cid/ciz1166
summary:
  title: A Phase II, Randomized, Double-blind, Placebo-Controlled Trial of Presatovir for the Treatment of Respiratory Syncytial Virus Upper Respiratory Tract Infection in Hematopoietic-Cell Transplant Recipients This is the largest randomized, double blind, placebo-controlled clinical trial to date for the treatment of allogeneic and autologous HCT recipients with RSV URTIs. Presatovir treatment did not meet the coprimary endpoints of a greater time-weighted average change in the RSV viral load from Day 1 to 9 and the reduced development of LRTCs through Day 28, but was well tolerated, with a comparable safety profile relative to the placebo. In a post hoc analysis of patients with lymphopenia, the proportion who developed an LRTC through Day 28 was 51% lower following treatment with presatovir, as compared to the placebo; other post hoc analyses also indicated trends toward a treatment effect on LRTCs. The results suggest lessons for the design of future clinical trials of drugs for RSV or other respiratory viruses in transplant recipients or other immunocompromised patients.

title:
  A Phase II, Randomized, Double-blind, Placebo-Controlled Trial of Presatovir for the Treatment of Respiratory Syncytial Virus Upper Respiratory Tract Infection in Hematopoietic-Cell Transplant Recipients

abstract:
  BACKGROUND: Hematopoietic-cell transplant (HCT) recipients are at risk for severe respiratory syncytial virus (RSV) infection. We evaluated the RSV fusion inhibitor presatovir in a randomized, double-blind, Phase II trial in HCT recipients with RSV upper respiratory tract infections. METHODS: Patients were stratified by lymphopenia (<200/µL) and ribavirin use; were randomized, stratified by lymphopenia (<200/μL) and ribavirin use, to receive oral presatovir at 200 mg or a placebo on Days 1, 5, 9, 13, and 17, and were followed through Day 28. The coprimary efficacy endpoints were the time-weighted average change in the nasal RSV viral load between Days 1 and 9 and the proportion of patients developing lower respiratory tract complications (LRTCs) through Day 28. RESULTS: From 23 January 2015 to 16 June 2017, 189 patients were randomly assigned to treatment (96 to presatovir and 93 to the placebo). Presatovir treatment, compared with the placebo treatment, did not significantly affect (prespecified α = 0.01) a time-weighted average decline in the RSV viral load from Day 1 to 9 (treatment difference, −0.33 log(10) copies/mL; 95% confidence interval [CI] −.64 to −.02 log(10) copies/mL; P = .040) or the progression to LRTC (11.2% vs 19.5%, respectively; odds ratio, 0.50; 95% CI, .22–1.18; P = .11). In a post hoc analysis among patients with lymphopenia, presatovir decreased LRTC development by Day 28 (2/15 [13.3%] vs 9/14 [64.3%], respectively; P = .008), compared with the placebo. Adverse events were similar for patients receiving presatovir and the placebo. CONCLUSIONS: Presatovir had a favorable safety profile in adult HCT recipients with RSV but did not achieve the coprimary endpoints. Exploratory analyses suggest an antiviral effect among patients with lymphopenia. CLINICAL TRIALS REGISTRATION: NCT02254408; EUDRA-CT#2014-002474-36.


id: cord-007068-vcfs41eb
author: Moradi, Tony
date: 2019-10-22
txt: ./txt/cord-007068-vcfs41eb.txt
cache: ./cache/cord-007068-vcfs41eb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108168/
doi: 10.1093/cid/ciz1042
summary:
  We sought to determine whether an automated electronic medical record best practice alert (BPA) based on procalcitonin and respiratory polymerase chain reaction (PCR) results could help reduce inappropriate antibiotic use in patients with likely viral respiratory illness. In the study group, a BPA alerted providers of the diagnostic results suggesting viral infection and prompted them to reassess the need for antibiotics. CONCLUSIONS: The automated antimicrobial stewardship BPA effectively reduced antibiotic use and discharge prescribing rates when diagnostics suggested viral respiratory tract infection, without a higher rate for reinitiation of antibiotics after discontinuation. The aim of our study was to determine if antibiotic use could be reduced by deploying an automated antimicrobial stewardship provider alert that prompted antibiotic de-escalation if 3 criteria were met: PCT <0.25 ng/mL, virus detected on respiratory PCR, and active use of systemic antibiotics.

title:
  Use of Procalcitonin and a Respiratory Polymerase Chain Reaction Panel to Reduce Antibiotic Use via an Electronic Medical Record Alert

abstract:
  BACKGROUND: Respiratory tract infections are often viral and but are frequently treated with antibiotics, providing a significant opportunity for antibiotic de-escalation in patients. We sought to determine whether an automated electronic medical record best practice alert (BPA) based on procalcitonin and respiratory polymerase chain reaction (PCR) results could help reduce inappropriate antibiotic use in patients with likely viral respiratory illness. METHODS: This multisite, pre–post, quasi-experimental study included patients 18 years and older with a procalcitonin level <0.25 ng/mL and a virus identified on respiratory PCR within 48 hours of each other, and 1 or more systemic antibiotics ordered. In the study group, a BPA alerted providers of the diagnostic results suggesting viral infection and prompted them to reassess the need for antibiotics. The primary outcome measured was total antibiotic-days of therapy. RESULTS: The BPA reduced inpatient antibiotic-days of therapy by a mean of 2.2 days compared with patients who met criteria but did not have the alert fire (8.0 vs 5.8 days, respectively, P < .001). The BPA also reduced the percentage of patients prescribed antibiotics on discharge (20% vs 47.8%, P < .001), whereas there was no difference in need for antibiotic escalation after initial discontinuation (7.6% vs 4.3%, P = .198). CONCLUSIONS: The automated antimicrobial stewardship BPA effectively reduced antibiotic use and discharge prescribing rates when diagnostics suggested viral respiratory tract infection, without a higher rate for reinitiation of antibiotics after discontinuation.


id: cord-007073-soov8q3q
author: Wang, Claire Y T
date: 2019-08-13
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108192/
doi: 10.1093/cid/ciz761
title:
  Parechovirus A Infections in Healthy Australian Children During the First 2 Years of Life: A Community-based Longitudinal Birth Cohort Study

abstract:
  BACKGROUND: Hospital-based studies identify parechovirus (PeV), primarily PeV-A3, as an important cause of severe infections in young children. However, few community-based studies have been published and the true PeV infection burden is unknown. We investigated PeV epidemiology in healthy children participating in a community-based, longitudinal birth cohort study. METHODS: Australian children (n = 158) enrolled in the Observational Research in Childhood Infectious Diseases (ORChID) study were followed from birth until their second birthday. Weekly stool and nasal swabs and daily symptom diaries were collected. Swabs were tested for PeV by reverse-transcription polymerase chain reaction and genotypes determined by subgenomic sequencing. Incidence rate, infection characteristics, clinical associations, and virus codetections were investigated. RESULTS: PeV was detected in 1423 of 11 124 (12.8%) and 17 of 8100 (0.2%) stool and nasal swabs, respectively. Major genotypes among the 306 infection episodes identified were PeV-A1 (47.9%), PeV-A6 (20.1%), and PeV-A3 (18.3%). The incidence rate was 144 episodes (95% confidence interval, 128–160) per 100 child-years. First infections appeared at a median age of 8 (interquartile range, 6.0–11.7) months. Annual seasonal peaks changing from PeV-A1 to PeV-A3 were observed. Infection was positively associated with age ≥6 months, summer season, nonexclusive breastfeeding at age <3 months, and formal childcare attendance before age 12 months. Sole PeV infections were either asymptomatic (38.4%) or mild (32.7%), while codetection with other viruses in stool swabs was common (64.4%). CONCLUSIONS: In contrast with hospital-based studies, this study showed that diverse and dynamically changing PeV genotypes circulate in the community causing mild or subclinical infections in children. Parechovirus can cause severe illnesses in children. However, studies focus mainly on hospitalized populations. True disease burden in the community remains largely unknown. From our community-based cohort, we found diverse parechovirus genotypes in the community, causing mild or subclinical infections in children.


id: cord-007075-sl45z4i0
author: Marty, Francisco M
date: 2019-12-03
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108198/
doi: 10.1093/cid/ciz1167
title:
  A Phase 2b, Randomized, Double-blind, Placebo-Controlled Multicenter Study Evaluating Antiviral Effects, Pharmacokinetics, Safety, and Tolerability of Presatovir in Hematopoietic Cell Transplant Recipients with Respiratory Syncytial Virus (RSV) Infection of the Lower Respiratory Tract

abstract:
  BACKGROUND: Presatovir significantly reduced nasal viral load, signs, and symptoms of respiratory syncytial virus (RSV) infection in a human challenge study. We evaluated presatovir in hematopoietic-cell transplant (HCT) recipients with RSV lower respiratory tract infection (LRTI). METHODS: Patients with confirmed RSV in upper and lower respiratory tract and new chest X-ray abnormalities were randomized (1:1), stratified by supplemental oxygen and ribavirin use, to receive oral presatovir 200 mg or placebo every 4 days for 5 doses. The primary endpoint was time-weighted average change in nasal RSV viral load through day 9. Secondary endpoints included supplemental oxygen-free days, incident respiratory failure requiring mechanical ventilation, and all-cause mortality. RESULTS: From January 31, 2015, to March 20, 2017, 60 patients from 17 centers were randomized (31 presatovir, 29 placebo); 59 received study treatment (50 allogeneic, 9 autologous HCT). In the efficacy population (29 presatovir, 28 placebo), presatovir treatment did not significantly reduce time-weighted average change in viral load (−1.12 vs −1.09 log(10) copies/mL; treatment difference −0.02 log(10) copies/mL, 95% confidence interval: −.62, .57; P = .94), median supplemental oxygen-free days (26 vs 28 days, P = .84), incident respiratory failure (10.3 vs 10.7%, P = .98), or all-cause mortality (0 vs 7.1%, P = .19) versus placebo. Adverse events were similar between arms (presatovir 80%, placebo 79%). Resistance-associated substitutions in RSV fusion protein emerged in 6/29 presatovir-treated patients. CONCLUSIONS: Presatovir treatment was well tolerated in HCT patients with RSV LRTI but did not improve virologic or clinical outcomes versus placebo. CLINICAL TRIALS REGISTRATION: www.clinicaltrials.gov, NCT02254421; EudraCT, #2014-002475-29


id: cord-007170-svsfu7fj
title: Infection with Borna Disease Virus: Molecular and Immunobiological Characterization of the Agent
author: Richt, J. A.
date: 1992-06-17
txt: ./txt/cord-007170-svsfu7fj.txt
cache: ./cache/cord-007170-svsfu7fj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109702/
doi: 10.1093/clinids/14.6.1240
summary:
  Studies on BDV may help to illuminate several important areas of neurobiology, including the mechanisms regulating the replication of a new type of RNA virus in the nuclei of neural cells, the neuroinvasiveness and neurotropism of such viruses, their T cell-mediated immunopathology, tolerance in newborn animals to persistent viral infection of the central nervous system, and behavioral diseases and eating disorders induced by such agents. Persistently infected MDCK (Madin-Darby canine kidney) cells are widely used in indirect immunofluorescence assays for the detection of BDV-specific antibodies in serum and CSF of affected animals and humans [18, 20] . The pathological changes in the brain and retina of BDVinfected animals resemble certain types of encephalitis and Most studies on the pathogenesis of BDV infection have involved experimentally inoculated Lewis rats. Although infection of newborn rats resulted in persistent viral replication in the CNS as well as in visceral organs, these animals developed no inflammatory response or signs of Borna disease.

abstract:
  Borna disease virus (BDV), which seems to be distinct from all other known viruses, exhibits a unique mechanism of pathogenesis. This review highlights several aspects of the biology of infection with this virus and summarizes the preliminary characterization of the agent. Studies on BDV may help to illuminate several important areas of neurobiology, including the mechanisms regulating the replication of a new type of RNA virus in the nuclei of neural cells, the neuroinvasiveness and neurotropism of such viruses, their T cell-mediated immunopathology, tolerance in newborn animals to persistent viral infection of the central nervous system, and behavioral diseases and eating disorders induced by such agents.


id: cord-007296-q9rn75qb
author: Muether, Philipp S.
date: 2001-11-01
txt: ./txt/cord-007296-q9rn75qb.txt
cache: ./cache/cord-007296-q9rn75qb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110240/
doi: 10.1086/322518
summary:
  Treatment with first-generation antihistamines reduces sneezing, rhinorrhea, nasal mucus weight, and, in some instances, cough in subjects with experimental or natural colds; however, treatment with second-generation antihistamines has not been effective for these complaints in trials in subjects with natural colds. The effectiveness of first-generation antihistamines in blocking sneezing in colds may be due primarily to neuropharmacological manipulation of histaminic and muscarinic receptors in the medulla. Also, treatment with first-generation antihistamines is highly effective in reducing sneezing in subjects with experimental and natural colds [3] [4] [5] . Therefore, it would be desirable to confirm the results of the natural cold studies by testing a second-generation antihistamine in the rhinovirus challenge model, which provides more precision in the measurement of sneezing. Although the study was originally designed to determine whether loratadine by down-regulating expression of intercellular adhesion molecule-1 (ICAM-1) on nasal epithelial cells reduces rhinovirus infection rates, it provides heretoforemissing information on the results of testing a second-generation antihistamine in the virus challenge mode.

title:
  Variant Effect of First- and Second-Generation Antihistamines as Clues to Their Mechanism of Action on the Sneeze Reflex in the Common Cold

abstract:
  Treatment with first-generation antihistamines reduces sneezing, rhinorrhea, nasal mucus weight, and, in some instances, cough in subjects with experimental or natural colds; however, treatment with second-generation antihistamines has not been effective for these complaints in trials in subjects with natural colds. This article reports the negative results of a clinical trial with loratadine, a second-generation antihistamine, in adults in the rhinovirus challenge model. This finding in the highly controlled setting of the challenge model confirms the earlier negative studies with second-generation antihistamines in natural colds. First-generation antihistamines block both histaminic and muscarinic receptors as well as passing the blood-brain barrier. Second-generation antihistamines mainly block histaminic receptors and do not pass the blood-brain barrier. The effectiveness of first-generation antihistamines in blocking sneezing in colds may be due primarily to neuropharmacological manipulation of histaminic and muscarinic receptors in the medulla.


id: cord-007321-7gi6xrci
title: Evaluation of New Anti-Infective Drugs for the Treatment of Respiratory Tract Infections
author: Chow, Anthony W.
date: 1992-11-17
txt: ./txt/cord-007321-7gi6xrci.txt
cache: ./cache/cord-007321-7gi6xrci.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110372/
doi: 10.1093/clind/15.supplement_1.s62
summary:
  These guidelines for the evaluation of drugs for the treatment of respiratory tract infections include acute streptococcal pharyngitis and tonsillitis, acute otitis media, acute and chronic sinusitis, acute exacerbations of chronic bronchitis, and acute infectious pneumonia (table 1). This is often the case in otitis media, sinusitis, and pneumonia, when the use of invasive procedures such as tympanocentesis, sinus puncture, or transtracheal aspiration to confirm microbial eradication in the patient who is improving clinically generally is considered unjustified. Patients eligible for study entrance are children or adults with symptomatic pharyngitis or tonsillitis of acute onset clinically consistent with infection with group A I3-hemolytic streptococci and from whom group A (3-hemolytic streptococci have been isolated in cultures of throat -swab specimen or for whom a rapid screening test has indicated the presence of streptococci.

abstract:
  These guidelines deal with the evaluation of anti-infective drugs for the treatment of respiratory tract infections. Five clinical entities are described: streptococcal pharyngitis and tonsillitis, otitis media, sinusitis, bronchitis, and pneumonia. A wide variety of microorganisms are potentially pathogenetic in these diseases; these guidelines focus on the bacterial infections. Inclusion of a patient in a trial of a new drug is based on the clinical entity, with the requirement that a reasonable attempt will be made to establish a specific microbial etiology. Microbiologic evaluation of efficacy requires isolation of the pathogen and testing for in vitro susceptibility. Alternatively, surrogate markers may be used to identify the etiologic agent. The efficacy of new drugs is evaluated with reference to anticipated response rates. Establishment of the microbial etiology of respiratory tract infections is hampered by the presence of “normal flora” of the nose, mouth, and pharynx, which may include asymptomatic carriage of potential pathogens. This issue is addressed for each category of infection described. For example, it is suggested that for initial phase 2 trials of acute otitis media and acute sinusitis tympanocentesis or direct sinus puncture be used to collect exudate for culture. Acute exacerbations of chronic bronchitis also present difficulties in the establishment of microbial etiology. These guidelines suggest that clinical trials employ an active control drug but leave open the possibility of a placebo-controlled trial. For pneumonia, the guidelines suggest the identification and enrollment of patients by the clinical type of pneumonia, e.g., atypical pneumonia or acute bacterial pneumonia, rather than by etiologic organism or according to whether it was community or hospital acquired. For each respiratory infection, the clinical response is judged as cure, failure, or indeterminate. Clinical improvement is not acceptable unless quantitative response measures can be applied.


id: cord-007325-g8ke9rfg
author: Koskiniemi, Marjaleena
date: 1993-08-17
txt: ./txt/cord-007325-g8ke9rfg.txt
cache: ./cache/cord-007325-g8ke9rfg.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110383/
doi: 10.1093/clinids/17.supplement_1.s52
summary:
  title: CNS Manifestations Associated with Mycoplasma pneumoniae Infections: Summary of Cases at the University of Helsinki and Review CNS manifestations appear in one of 1,000 patients with Mycoplasma pneumoniae-associated infections. Encephalitis is the most frequent manifestation, but cases of meningitis, myelitis, and polyradiculitis, as well as many other symptoms (e.g., coma, ataxia, psychosis, and stroke), have been reported. Besides encephalitis, adult patients had meningitis, myelitis, and polyradiculitis, two cases of each (figure 2). Central nervous system disease associated with Mycoplasma pneumoniae infection: report of five cases and review of the literature Central nervous system manifestations associated with serologically verified Mycoplasma pneumoniae infection Two fatal cases of meningoencephalitis associated with Mycoplasma pneumoniae infection Central nervous system disease associated with Mycoplasma pneumoniae infection Neurological manifestations and Mycoplasma pneumoniae infection A brainstem syndrome associated with Mycoplasma pneumoniae infection-a report of two cases Antibodies to brain and other tissues in cases of Mycoplasma pneumoniae infection

title:
  CNS Manifestations Associated with Mycoplasma pneumoniae Infections: Summary of Cases at the University of Helsinki and Review

abstract:
  CNS manifestations appear in one of 1,000 patients with Mycoplasma pneumoniae-associated infections. Encephalitis is the most frequent manifestation, but cases of meningitis, myelitis, and polyradiculitis, as well as many other symptoms (e.g., coma, ataxia, psychosis, and stroke), have been reported. The onset of these manifestations is usually acute, with lowered consciousness, convulsions, pareses, and other neurological signs. Severe, even fatal, cases are known. The pathophysiology of CNS manifestations is unknown. To our knowledge, M. pneumoniae has never been isolated from brain tissue, but instead it has been recovered from CSF specimens in at least seven cases. Besides direct invasion of M. pneumoniae into the brain, neurotoxic or autoimmune reaction within the brain tissue is suspected. At neuropathological examination, edema, demyelination, and microthrombi have been described. Improved diagnostic methods may reveal the pathophysiology of CNS manifestations associated with M. pneumoniae infection.


id: cord-010570-ytv7dwr0
title: Return to the Past: The Case for Antibody-Based Therapies in Infectious Diseases
author: Casadevall, Arturo
date: 1995-07-17
txt: ./txt/cord-010570-ytv7dwr0.txt
cache: ./cache/cord-010570-ytv7dwr0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197598/
doi: 10.1093/clinids/21.1.150
summary:
  In the preantibiotic era, passive antibody administration (serum therapy) was useful for the treatment of many infectious diseases. We briefly review the use of antibody-based therapy in the early 20th century and make the case for reintroducing passive antibody administration for the treatment ofinfectious diseases. Given the diminishing efficacy of existing antimicrobials because of widespread resistance and the difficulties of treating infections in immunosuppressed individuals, the reintroduction of antibody-based therapies is an option that should be given serious consideration. Thus, antibody therapy is still widely used in medicine, but its role in the treatment of infections is limited largely to viral and toxin neutralization and replacement therapy in patients with immunoglobulin deficiencies. In the past, serum therapy was effective against various pathogens despite the fact that immune sera contained only small amounts of specific antibody. Antibody-based therapies have traditionally been most effective in infections where viral and toxin neutralization modifies the course of the disease.

abstract:
  In the preantibiotic era, passive antibody administration (serum therapy) was useful for the treatment of many infectious diseases. The introduction of antimicrobial chemotherapy in the 1940s led to the rapid abandonment of many forms of passive antibody therapy. Chemotherapy was more effective and less toxic than antibody therapy. In this last decade of the 20th century the efficacy of antimicrobial chemotherapy is diminishing because of the rapidly escalating number of immunocompromised individuals, the emergence of new pathogens, the reemergence of old pathogens, and widespread development of resistance to antimicrobial drugs. This diminishment in the effectiveness of chemotherapy has been paralleled by advances in monoclonal antibody technology that have made feasible the generation of human antibodies. This combination of factors makes passive antibody therapy an option worthy of serious consideration. We propose that for every pathogen there exists an antibody that will modify the infection to the benefit of the host. Such antibodies are potential antimicrobial agents. Antibody-based therapies have significant advantages and disadvantages relative to standard chemotherapy. The reintroduction of antibody-based therapy would require major changes in the practices of infectious disease specialists.


id: cord-010578-uib9h1lb
title: Seroepidemiology of Chronic Fatigue Syndrome: A Case-Control Study
author: Mawle, Alison C.
date: 1995-12-17
txt: ./txt/cord-010578-uib9h1lb.txt
cache: ./cache/cord-010578-uib9h1lb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197952/
doi: 10.1093/clinids/21.6.1386
summary:
  We performed serological testing for a large number of infectious agents in 26 patients from Atlanta who had chronic fatigue syndrome (CFS) and in 50 controls matched by age, race, and sex. We performed serological testing for a large number of infectious agents in 26 patients from Atlanta who had chronic fatigue syndrome (CFS) and in 50 controls matched by age, race, and sex. We conducted serological tests for a large number of infectious agents as part of a case-control study assessing risk factors for CFS. Antibodies against human T-lymphotrophic virus types I and II were detected with an ELISA, and confirmatory testing was performed by western blotting [5] . All other agents tested were detected in ;;:::25% of CFS cases, and antibody levels were compared between cases and controls. Evidence for active Epstein-Barr virus infection in patients with persistent unexplained illness: elevated anti-early antigen antibodies

abstract:
  We performed serological testing for a large number of infectious agents in 26 patients from Atlanta who had chronic fatigue syndrome (CFS) and in 50 controls matched by age, race, and sex. We did not find any agent associated with CFS. In addition, we did not find elevated levels of antibody to any of a wide range of agents examined. In particular, we did not find elevated titers of antibody to any herpesvirus, nor did we find evidence of enteroviral exposure in this group of patients.


id: cord-010599-nwp2if8d
author: Hayden, Frederick G.
date: 2003-06-15
txt: ./txt/cord-010599-nwp2if8d.txt
cache: ./cache/cord-010599-nwp2if8d.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7199898/
doi: 10.1086/375069
summary:
  More recently, retrospective analysis of 2 phase II randomized, double-blind, placebo-controlled studies found that pleconaril treatment provided clinical benefit for colds due to picornaviruses in previously healthy adults [10] . Calculations indicated that enrollment of 1000 subjects in each study was required to detect a 25% relative difference between treatment groups in the proportion of picornavirus-infected subjects reaching the primary end point (or an estimated 2-day difference in median time) with 90% power (2-sided test at the 5% level of significance [20] ). Among the picornavirus-infected (ITT-I) population, the time to reach the primary end point of illness alleviation was significantly shorter among pleconaril-treated subjects than among placebo recipients in each study (figure 1). severity score was reduced by 19% over the duration of the study for pleconaril recipients (table 4) , who also experienced significant reductions from baseline in symptom severity scores by day 2 of treatment, compared with placebo recipients (figure 2).

title:
  Efficacy and Safety of Oral Pleconaril for Treatment of Colds Due to Picornaviruses in Adults: Results of 2 Double-Blind, Randomized, Placebo-Controlled Trials

abstract:
  The novel capsid-binding antiviral pleconaril inhibits in vitro replication of most rhinoviruses and enteroviruses. Oral pleconaril treatment was studied in 2 parallel randomized, double-blind, placebo-controlled trials. Among 1363 picornavirus-infected participants (65%) in the studies combined, the median time to alleviation of illness was 1 day shorter for pleconaril recipients than for placebo recipients (P > .001). Cold symptom scores and frequency of picornavirus cultured from nasal mucus specimens were lower among pleconaril recipients by day 2 of treatment. No treatment effects were seen in those without picornavirus infection. Pleconaril was associated with a higher incidence of nausea (6% vs. 4%) and diarrhea (9% vs. 7%) and with small increases in mean serum cholesterol levels and platelet counts, compared with baseline measurements. A subsequent 6-week prophylaxis study found that pleconaril induces cytochrome P-450 3A enzymes, which metabolize a variety of drugs, including ethinyl estradiol. Early pleconaril treatment was well tolerated and significantly reduced the duration and severity of colds due to picornaviruses in adults.


id: cord-011745-dbdtpojs
author: Thompson, Mark G.
date: 2013-12-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7314184/
doi: 10.1093/cid/cit551
title:
  Effectiveness of Nonadjuvanted Monovalent Influenza A(H1N1)pdm09 Vaccines for Preventing Reverse Transcription Polymerase Chain Reaction–Confirmed Pandemic Influenza Hospitalizations: Case-Control Study of Children and Adults at 10 US Influenza Surveillance Network Sites

abstract:
  During 2009–2010, we examined 217 patients hospitalized with laboratory-confirmed pandemic influenza in 9 Influenza Hospitalization Surveillance Network sites and 413 age- and community-matched controls and found that a single dose of monovalent nonadjuvanted influenza A(H1N1)pdm09 vaccine was 50% (95% confidence interval, 13%–71%) effective in preventing hospitalization associated with A(H1N1)pdm09 virus infection.


id: cord-012511-fl5llkoj
title: Standardizing Scenarios to Assess the Need to Respond to an Influenza Pandemic
author: Meltzer, Martin I.
date: 2015-05-01
txt: ./txt/cord-012511-fl5llkoj.txt
cache: ./cache/cord-012511-fl5llkoj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481578/
doi: 10.1093/cid/civ088
abstract: nan
summary:
  We were tasked to evaluate the 6 following interventions: invasive mechanical ventilators, influenza antiviral drugs for treatment (but not large-scale prophylaxis), influenza vaccines, respiratory protective devices for healthcare workers and surgical face masks for patients, school closings to reduce transmission, and airport-based screening to identify those ill with novel influenza virus entering the United States. To allow easy comparison between results (a specification), we standardized a risk space defined by using ranges of transmission and clinical severity from a previously published influenza severity assessment framework ( Figure 1 ) [5] . Standardized epidemiological curves-contact matrix: To model the 4 epidemic curves (Figure 2 ), we built a simple, nonprobabilistic (ie, deterministic) model in which we divided the population into 4 age groups (0-10, 11-20, 21-60, ≥61 years).


id: cord-015493-vf4et613
title: In the Literature
author: Deresinski, Stan
date: 2007-10-15
txt: ./txt/cord-015493-vf4et613.txt
cache: ./cache/cord-015493-vf4et613.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107829/
doi: 10.1086/522526
abstract: nan
summary:
  Tetracyclines as an oral treatment option for patients with community-onset methicillin-resistant Staphylococcus aureus skin and soft-tissue infections. Subgroup analysis that included only the 225 episodes in which incision and drainage were performed at presentation confirmed that blactam antibiotic therapy was significantly associated with treatment failure. These results are consistent with those of several other recent studies that have found that administration of an antibiotic that inhibits the growth of MRSA improves outcomes, even in patients who have undergone incision and drainage. For example, in a similar retrospective study of 531 episodes of community-acquired MRSA SSTI, most of which were treated with incision and drainage, Ruhe et al. Although Ruhe and colleagues provide evidence of the benefit of doxycyline for the treatment of SSTI due to antibioticsusceptible MRSA, alternative antibiotic choices may be considered. Prospective randomized trial of empiric therapy with trimethoprim-sulfamethoxazole or doxycycline for outpatient skin and soft tissue infections in an area of high prevalence of methicillin-resistant Staphylococcus aureus


id: cord-032234-pfr4l1v9
author: Poloni, Chad
date: 2020-06-04
txt: ./txt/cord-032234-pfr4l1v9.txt
cache: ./cache/cord-032234-pfr4l1v9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7499531/
doi: 10.1093/cid/ciaa664
abstract: nan
summary:
  The recently published study conducted in Wuhan, China, by Qin et al indicated dysregulation of the immune response specifically related to T lymphocytes, suggesting that they are highly involved in the pathophysiology of COVID-19 [1] . T-cell dysregulation is a major contributor to age-related changes of the immune system in the elderly, where T-cell responses become defective. Qin et al sought to characterize the T-lymphocyte responses in COVID-19, with aims to differentiate between nonsevere and severe cases. The Wuhan study also identified several differences in T-cell populations between the severe and nonsevere COVID-19 cases. This terminally differentiated T-cell population has been associated with immune dysregulation in the elderly and is further characterized by low CD28 and increased CD57 expression [9] . Improved characterization of terminally differentiated CD45RA + T cells, along with screening for IRP positivity, may be beneficial in identifying those with potential for severe COVID-19.

title:
  Evaluating Immune Dysregulation in Patients With COVID-19 Requires a More Accurate Definition of the CD45RA(+) T-cell Phenotype


id: cord-251945-v077hhgk
author: Titanji, Boghuma K
date: 2020-08-14
url: https://www.ncbi.nlm.nih.gov/pubmed/32797235/
doi: 10.1093/cid/ciaa1212
abstract: nan
title:
  Response to Correspondence: Baricitinib as Treatment of COVID-19 Friend or Foe of the Pancreas? Cerda-Contreras et.al


id: cord-252005-3ld5e7f5
title: Household Transmission of SARS-CoV-2 in the United States
author: Lewis, Nathaniel M
date: 2020-08-16
url: https://www.ncbi.nlm.nih.gov/pubmed/33185244/
doi: 10.1093/cid/ciaa1166
abstract:
  BACKGROUND: Although many viral respiratory illnesses are transmitted within households, the evidence base for SARS-CoV-2 is nascent. We sought to characterize SARS-CoV-2 transmission within US households and estimate the household secondary infection rate (SIR) to inform strategies to reduce transmission. METHODS: We recruited laboratory-confirmed COVID-19 patients and their household contacts in Utah and Wisconsin during March 22–April 25, 2020. We interviewed patients and all household contacts to obtain demographics and medical histories. At the initial household visit, 14 days later, and when a household contact became newly symptomatic, we collected respiratory swabs from patients and household contacts for testing by SARS-CoV-2 rRT-PCR and sera for SARS-CoV-2 antibodies testing by enzyme-linked immunosorbent assay (ELISA). We estimated SIR and odds ratios (OR) to assess risk factors for secondary infection, defined by a positive rRT-PCR or ELISA test. RESULTS: Thirty-two (55%) of 58 households had evidence of secondary infection among household contacts. The SIR was 29% (n = 55/188; 95% confidence interval [CI]: 23–36%) overall, 42% among children (<18 years) of the COVID-19 patient and 33% among spouses/partners. Household contacts to COVID-19 patients with immunocompromised conditions had increased odds of infection (OR: 15.9, 95% CI: 2.4–106.9). Household contacts who themselves had diabetes mellitus had increased odds of infection (OR: 7.1, 95% CI: 1.2–42.5). CONCLUSIONS: We found substantial evidence of secondary infections among household contacts. People with COVID-19, particularly those with immunocompromising conditions or those with household contacts with diabetes, should take care to promptly self-isolate to prevent household transmission.


id: cord-252423-ojmt4k2w
title: Monologue of a physician who tested persistently positive for COVID-19
author: Qu, Bing
date: 2020-05-11
txt: ./txt/cord-252423-ojmt4k2w.txt
cache: ./cache/cord-252423-ojmt4k2w.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa551
doi: 10.1093/cid/ciaa551
abstract: nan
summary:
  The COVID-19, as other new infectious diseases, has presented us unprecedented challenges and put us into huge dilemma. As a physician on clinical frontline, I had been treating patients actively and wishing them an early recovery, but never expecting that I would be infected. As in the early stage we knew little about COVID-19 and the possibility that someone with COVID-19 can transmit the virus even if they are not showing symptoms, many healthcare professionals were infected. According to a Press Conference of the WHO-China Joint Mission on COVID-19 on February 24, 3387 medical staff have been reported to be infected, among which over 90% were from Hubei province. Exploring the reasons for healthcare workers infected with novel coronavirus disease 2019 (COVID-19) in China Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China


id: cord-252761-ro5tj0tx
author: Marriott, Deborah
date: 2020-08-25
url: https://doi.org/10.1093/cid/ciaa1256
doi: 10.1093/cid/ciaa1256
title:
  Concomitant marked decline in prevalence of SARS-CoV-2 and other respiratory viruses among symptomatic patients following public health interventions in Australia: data from St Vincent’s Hospital and associated screening clinics, Sydney, NSW.

abstract:
  Our Australian hospital tested almost 22,000 symptomatic people over 11 weeks for SARS-CoV-2 in a multiplex PCR assay. Following travel bans and physical distancing, SARS-CoV-2 and other respiratory viruses diagnoses fell dramatically. Increasing rhinovirus diagnoses as social control measures were relaxed may indirectly indicate an elevated risk of COVID-19 resurgence


id: cord-254183-98o0dssj
title: Rare and Emerging Viral Infections in Transplant Recipients
author: Waggoner, Jesse J.
date: 2013-10-15
txt: ./txt/cord-254183-98o0dssj.txt
cache: ./cache/cord-254183-98o0dssj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/23839998/
doi: 10.1093/cid/cit456
summary:
  In this review, we first discuss viral diagnostics and the developing field of viral discovery and then focus on rare and emerging viruses in the transplant population: human T-cell leukemia virus type 1; hepatitis E virus; bocavirus; KI and WU polyomaviruses; coronaviruses HKU1 and NL63; influenza, H1N1; measles; dengue; rabies; and lymphocytic choriomeningitis virus. Detection and reporting of such rare pathogens in transplant recipients is critical to patient care and improving our understanding of posttransplant infections. In a multicenter review of 85 cases of acute HEV infection, 65.9% of the solid organ transplant (SOT) recipients developed chronic hepatitis of whom 14.3% developed cirrhosis. Cases of lymphocytic choriomeningitis virus (LCMV) transmitted through organ transplantation (4 clusters, including 14 cases and 11 deaths) document the ability of this pathogen to cause severe disease in the immunocompromised host [10, [49] [50] [51] . Human T-cell leukemia virus type I-associated myelopathy following living-donor liver transplantation

abstract:
  Emerging viral pathogens include newly discovered viruses as well as previously known viruses that are either increasing, or threatening to increase in incidence. While often first identified in the general population, they may affect transplant recipients, in whom their manifestations may be atypical or more severe. Enhanced molecular methods have increased the rate of viral discovery but have not overcome the problem of demonstrating pathogenicity. At the same time, improved clinical diagnostic methods have increased the detection of reemerging viruses in immunocompromised patients. In this review, we first discuss viral diagnostics and the developing field of viral discovery and then focus on rare and emerging viruses in the transplant population: human T-cell leukemia virus type 1; hepatitis E virus; bocavirus; KI and WU polyomaviruses; coronaviruses HKU1 and NL63; influenza, H1N1; measles; dengue; rabies; and lymphocytic choriomeningitis virus. Detection and reporting of such rare pathogens in transplant recipients is critical to patient care and improving our understanding of posttransplant infections.


id: cord-254458-bbcef8xt
title: Throat Wash Testing and COVID-19 Disease: Should We Put Our Money Where Our Mouth Is?
author: Ali, Farhana
date: 2020-04-30
txt: ./txt/cord-254458-bbcef8xt.txt
cache: ./cache/cord-254458-bbcef8xt.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32353114/
doi: 10.1093/cid/ciaa511
abstract: nan
summary:
  The tragedy that is the US aircraft carrier Theodore Roosevelt, in which 60 percent of the 600 sailors who tested positive for SARS-CoV-2 infection were asymptomatic, further highlights the need for accurate laboratory diagnostics for COVID-19 disease [2] . make the case that testing of throat wash samples may be more sensitive than testing of NP swabs for COVID-19 disease. Interestingly, there is biologic plausibility that a sample collected via the oral cavity (such as a throat wash) may yield higher results than a NP swab test based on a study by Xu et al. Finally, the authors'' detection of virus late in the patients'' clinical course emphasizes the uncertainty faced by policy makers as they try to determine the optimal length of isolation for an individual recovering from COVID-19 disease. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs


id: cord-256583-z3pd339v
author: Yen, Muh-Yong
date: 2015-03-01
url: https://www.ncbi.nlm.nih.gov/pubmed/25512433/
doi: 10.1093/cid/ciu978
abstract: nan
title:
  Traffic Control Bundling Is Essential for Protecting Healthcare Workers and Controlling the 2014 Ebola Epidemic


id: cord-257553-479x7av6
author: Kortepeter, Mark G.
date: 2010-12-01
txt: ./txt/cord-257553-479x7av6.txt
cache: ./cache/cord-257553-479x7av6.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1086/657115
doi: 10.1086/657115
summary:
  title: Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation This review provides practical advice for this special population of travelers, targeted to specific health care-related risks (needlestick, hemorrhagic fever viruses, severe viral respiratory disease, and tuberculosis), with suggestions for risk mitigation. Although no prophylaxis for hepatitis C virus (HCV) exposure exists, the needlestick transmission risk is lower (1.8%), and up to 20% of transmitted infections resolve spontaneously. The Centers for Disease Control and Prevention (CDC) recommends a 3-drug PEP regimen if the source patient is known to be infected with HIV and the source device is a hollow-bore needle or has visible blood contamination. During the pandemic, transmission to HCWs occurred after close, unprotected contact with symptomatic persons and was significantly mitigated once infection-control precautions were implemented; the degree of risk was related to the type and intensity of exposure (endotracheal intubation was significantly associated with contracting SARS) [27, 28] .

title:
  Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation

abstract:
  With the recent emphasis on funding and training opportunities for global health and humanitarian aid and the increased interest in the field, many health care workers and medical researchers are traveling from resource-replete to resource-limited settings. This type of travel brings unique disease risks not routinely considered for the business or vacationing traveler. This review provides practical advice for this special population of travelers, targeted to specific health care-related risks (needlestick, hemorrhagic fever viruses, severe viral respiratory disease, and tuberculosis), with suggestions for risk mitigation.


id: cord-258304-86gqxajw
title: Droplets and Aerosols generated by singing and the risk of COVID-19 for choirs
author: Bahl, Prateek
date: 2020-09-18
txt: ./txt/cord-258304-86gqxajw.txt
cache: ./cache/cord-258304-86gqxajw.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32945338/
doi: 10.1093/cid/ciaa1241
summary:
  title: Droplets and Aerosols generated by singing and the risk of COVID-19 for choirs The results of detailed particle tracking (in supplementary video) reveals that the maximum velocity of droplets expelled, specifically for certain syllables such as ''do'', ''fa'' and ''ti'', is approx. Figure 2c shows the velocity distribution of droplets that are visible while the subject was singing syllable ''sol'' & ''la'' and the direction in which these droplets are moving. Nevertheless, the droplets observed do not appear to be settling down rapidly and without adequate ventilation, these droplets can potentially saturate the indoor environment which can likely explain the very high attack rates of COVID-19 seen in choirs in the US and Europe (almost 87% in Skagit County, Washington) [1] . We note the present study only provides visual evidence of the droplets and aerosols expelled during singing and compare the associated velocities and directions with speaking and coughing.

abstract:
  Choral singing has become a major risk during COVID-19 pandemic due to high infection rates. Our visualisation and velocimetry results reveal that majority of droplets expelled during singing follow the ambient airflow pattern. These results points toward the possibility of COVID-19 spread by small airborne droplets during singing.


id: cord-258724-1qhen1bj
title: Viral dynamics and immune correlates of COVID-19 disease severity
author: Young, Barnaby E
date: 2020-08-28
url: https://www.ncbi.nlm.nih.gov/pubmed/32856707/
doi: 10.1093/cid/ciaa1280
abstract:
  BACKGROUND: Key knowledge gaps remain in the understanding of viral dynamics and immune response of SARS-CoV-2 infection. METHODS: We evaluated these characteristics and established their association with clinical severity in a prospective observational cohort study of 100 patients with PCR-confirmed SARS-CoV-2 infection (mean age 46 years, 56% male, 38% with comorbidities). Respiratory samples (n=74) were collected for viral culture, serum samples for measurement of IgM/IgG levels (n=30), and plasma samples for levels of inflammatory cytokines and chemokines (n=81). Disease severity was correlated with results from viral culture, serologic testing, and immune markers. RESULTS: 57 (57%) patients developed viral pneumonia, of whom 20 (20%) required supplemental oxygen including 12 (12%) invasive mechanical ventilation. Viral culture from respiratory samples was positive for 19 of 74 patients (26%). No virus was isolated when the PCR cycle threshold (Ct) value was >30 or >14 days after symptom onset. Seroconversion occurred at a median of 12.5 days (IQR 9-18) for IgM and 15.0 days (IQR 12-20) for IgG; 54/62 patients (87.1%) sampled at day 14 or later seroconverted. Severe infections were associated with earlier seroconversion and higher peak IgM and IgG levels. Levels of IP-10, HGF, IL-6, MCP-1, MIP-1α, IL-12p70, IL-18, VEGF-A, PDGF-BB and IL-1RA significantly correlated with disease severity. CONCLUSION: We found virus viability was associated with lower PCR Ct value in early illness. A stronger antibody response was associated with disease severity. The overactive proinflammatory immune signatures offers targets for host-directed immunotherapy which should be evaluated in randomised controlled trials.


id: cord-259243-1lkzcslx
author: Álvarez-Aragón, Luis Miguel
date: 2020-04-08
txt: ./txt/cord-259243-1lkzcslx.txt
cache: ./cache/cord-259243-1lkzcslx.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa402
doi: 10.1093/cid/ciaa402
abstract: nan
summary:
  title: Inquiring into Benefits of Independent Activation of Non-Classical Renin-Angiotensin System in the Clinical Prognosis and Reduction of COVID-19 mortality We have read with great interest the elegant manuscript by Hanff et al [1] proposing a very interesting association between the classical renin-angiotensin system (RAS) and angiotensinconverting enzyme 2 (ACE2) dysregulation present in cardiovascular disease (CVD) and the high mortality index in patients with CVD and coronavirus disease 2019 (COVID-19). On the one hand, it will decrease the proinflammatory effect of Angiotensin II with its subsequent benefit on decreasing the risk of acute respiratory distress syndrome (ARDS) observed in these patients, and on the other hand, it will increase ACE2 expression and therefore the virulence of SARS-Cov2. In addition, in vitro studies in human renal cells treated with SLGT2 inhibitors have shown an increment in Angiotensin(1-7) due to the independent activation of the non-classical RES, leading to important anti-inflammatory and anti-M a n u s c r i p t fibrotic effects [6, 7] .

title:
  Inquiring into Benefits of Independent Activation of Non-Classical Renin-Angiotensin System in the Clinical Prognosis and Reduction of COVID-19 mortality


id: cord-259471-lsdodl0a
author: Pagliano, Pasquale
date: 2020-03-24
url: https://www.ncbi.nlm.nih.gov/pubmed/32211764/
doi: 10.1093/cid/ciaa320
abstract: nan
title:
  Is Hydroxychloroquine a Possible Postexposure Prophylaxis Drug to Limit the Transmission to Healthcare Workers Exposed to Coronavirus Disease 2019?


id: cord-260274-c3586tp6
title: Tocilizumab for treatment of mechanically ventilated patients with COVID-19
author: Somers, Emily C
date: 2020-07-11
txt: ./txt/cord-260274-c3586tp6.txt
cache: ./cache/cord-260274-c3586tp6.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa954
doi: 10.1093/cid/ciaa954
summary:
  CONCLUSIONS: In this cohort of mechanically ventilated COVID-19 patients, tocilizumab was associated with lower mortality despite higher superinfection occurrence. At our institution, IL-6 blockade with tocilizumab is considered for patients with severe COVID-19 and suspected hyperinflammation based on rapidly worsening respiratory status and elevated inflammatory markers, with the majority of usage occurring in patients requiring mechanical ventilation. Using our COVID-19 Rapid Response Registry infrastructure, we performed an observational study of outcomes in patients with COVID-19 requiring mechanical ventilation, comparing those treated with tocilizumab with those who were not. In this observational, controlled study of patients with severe COVID-19 necessitating mechanical ventilation, receipt of tocilizumab was independently associated with improved survival. To date, the risk of superinfection in mechanically ventilated patients with severe COVID-19 remains poorly described and the incremental risk associated with a single dose of tocilizumab is not well characterized.

abstract:
  BACKGROUND: Severe COVID-19 can manifest in rapid decompensation and respiratory failure with elevated inflammatory markers, consistent with cytokine release syndrome for which IL-6 blockade is approved treatment. METHODS: We assessed effectiveness and safety of IL-6 blockade with tocilizumab in a single-center cohort of patients with COVID-19 requiring mechanical ventilation. The primary endpoint was survival probability post-intubation; secondary analyses included an ordinal illness severity scale integrating superinfections. Outcomes in patients who received tocilizumab compared to tocilizumab-untreated controls were evaluated using multivariable Cox regression with propensity score inverse probability weighting (IPTW). RESULTS: 154 patients were included, of whom 78 received tocilizumab and 76 did not. Median follow-up was 47 days (range 28-67). Baseline characteristics were similar between groups, although tocilizumab-treated patients were younger (mean 55 vs. 60 years), less likely to have chronic pulmonary disease (10% vs. 28%), and had lower D-dimer values at time of intubation (median 2.4 vs. 6.5 mg/dL). In IPTW-adjusted models, tocilizumab was associated with a 45% reduction in hazard of death [hazard ratio 0.55 (95% CI 0.33, 0.90)] and improved status on the ordinal outcome scale [odds ratio per 1-level increase: 0.58 (0.36, 0.94)]. Though tocilizumab was associated with an increased proportion of patients with superinfections (54% vs. 26%; p<0.001), there was no difference in 28-day case fatality rate among tocilizumab-treated patients with versus without superinfection [22% vs. 15%; p=0.42]. Staphylococcus aureus accounted for ~50% of bacterial pneumonia. CONCLUSIONS: In this cohort of mechanically ventilated COVID-19 patients, tocilizumab was associated with lower mortality despite higher superinfection occurrence.


id: cord-260457-m1jbpo5l
title: Human Bocavirus and Acute Wheezing in Children
author: Allander, Tobias
date: 2007-04-01
txt: ./txt/cord-260457-m1jbpo5l.txt
cache: ./cache/cord-260457-m1jbpo5l.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17342639/
doi: 10.1086/512196
summary:
  We investigated the presence of human bocavirus by quantitative polymerase chain reaction of nasopharyngeal aspirate specimens and selected serum samples obtained from 259 children (median age, 1.6 years) who had been hospitalized for acute expiratory wheezing. Human bocavirus DNA was frequently detected in serum specimens obtained from patients with acute wheezing, suggesting systemic infection. Results suggest a model for bocavirus infection in which high viral loads are potentially associated with respiratory symptoms and low viral loads indicate asymptomatic shedding. Of the 293 children who were randomized, 259 children (median age, 1.6 years; range, 3 months to 15 years) who had sufficient sample material available for complete virus diagnostic evaluation (nasopharyngeal aspirate specimens were used for PCR [for 16 viruses], virus culture [for 9 viruses], and antigen detection [for 7 viruses]; acute-and convalescent-phase serum samples were used for serologic testing [for 7 viruses]) were included in the present study.

abstract:
  Background. Human bocavirus is a newly discovered parvovirus. It has been detected primarily in children with acute lower respiratory tract infection, but its occurrence, clinical profile, and role as a causative agent of respiratory tract disease are not clear. Methods. We investigated the presence of human bocavirus by quantitative polymerase chain reaction of nasopharyngeal aspirate specimens and selected serum samples obtained from 259 children (median age, 1.6 years) who had been hospitalized for acute expiratory wheezing. The samples were analyzed for 16 respiratory viruses by polymerase chain reaction, virus culture, antigen detection, and serological assays. Results. At least 1 potential etiologic agent was detected in 95% of children, and >1 agent was detected in 34% of children. Human bocavirus was detected in 49 children (19%). A large proportion of the cases were mixed infections with other viruses, but human bocavirus was the only virus detected in 12 children (5%). High viral loads of human bocavirus were noted mainly in the absence of other viral agents, suggesting a causative role for acute wheezing. In addition, infections that had uncertain clinical relevance and low viral loads were prevalent. Human bocavirus DNA was frequently detected in serum specimens obtained from patients with acute wheezing, suggesting systemic infection. Conclusions. Human bocavirus is prevalent among children with acute wheezing and can cause systemic infection. Results suggest a model for bocavirus infection in which high viral loads are potentially associated with respiratory symptoms and low viral loads indicate asymptomatic shedding. Therefore, quantitative polymerase chain reaction analysis may be important for additional studies of human bocavirus.


id: cord-260630-vvpzp73r
title: Etiologies of Acute Respiratory Tract Infections
author: Mandell, Lionel A.
date: 2005-08-15
txt: ./txt/cord-260630-vvpzp73r.txt
cache: ./cache/cord-260630-vvpzp73r.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16028159/
doi: 10.1086/432019
abstract: nan
summary:
  In this issue of Clinical Infectious Diseases, there are 2 articles that provide us with some insight into the various etiologic agents that can cause acute respiratory tract infection (ARTI) in general practice patients in The Netherlands [1] and into the significance of the human metapneumovirus (hMPV) in patients with community-acquired pneumonia (CAP) and exacerbations of chronic obstructive pulmonary disease (COPD) in Quebec, Canada [2] . The objectives of the Dutch study were to estimate the incidence of influenza-like illnesses (ILIs) and of other ARTIs in patients visiting their general practitioners (to determine the etiologic agents) and to test the hypothesis that asymptomatic persons with subclinical infection may act as sources of transmission [1] . Nose and throat swab specimens were obtained from case patients and control subjects, and viral cultures and PCR tests were performed for detection of adenovirus, coronavirus, enterovirus, hMPV, influenza virus, parainfluenza virus, rhinovirus, and respiratory syncytial virus (RSV), as well as for Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Chlamydophila psittaci.


id: cord-260779-riw5xs3j
author: van Griensven, Johan
date: 2016-01-01
txt: ./txt/cord-260779-riw5xs3j.txt
cache: ./cache/cord-260779-riw5xs3j.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26261205/
doi: 10.1093/cid/civ680
summary:
  The clinical evaluation of convalescent plasma (CP) for the treatment of Ebola virus disease (EVD) in the current outbreak, predominantly affecting Guinea, Sierra Leone, and Liberia, was prioritized by the World Health Organization in September 2014. The World Health Organization (WHO) guidelines recommend both convalescent whole blood (CWB) and CP for use against Ebola virus disease (EVD) [12] . Blood transfusion is routinely done in all 3 high-transmission countries involved in the current EVD outbreak; however, plasma has numerous advantages in these settings. Use of convalescent whole blood or plasma collected from patients recovered from Ebola virus disease for transfusion, as an empirical treatment during outbreaks. Treatment of Ebola hemorrhagic fever with blood transfusions from convalescent patients. Clinical trial to evaluate the efficacy and safety of convalescent plasma for Ebola treatment (EVD001). Acute respiratory distress syndrome after convalescent plasma use: treatment of a patient with Ebola virus disease Large-scale convalescent blood and plasma transfusion therapy for Ebola virus disease

title:
  The Use of Ebola Convalescent Plasma to Treat Ebola Virus Disease in Resource-Constrained Settings: A Perspective From the Field

abstract:
  The clinical evaluation of convalescent plasma (CP) for the treatment of Ebola virus disease (EVD) in the current outbreak, predominantly affecting Guinea, Sierra Leone, and Liberia, was prioritized by the World Health Organization in September 2014. In each of these countries, nonrandomized comparative clinical trials were initiated. The Ebola-Tx trial in Conakry, Guinea, enrolled 102 patients by 7 July 2015; no severe adverse reactions were noted. The Ebola-CP trial in Sierra Leone and the EVD001 trial in Liberia have included few patients. Although no efficacy data are available yet, current field experience supports the safety, acceptability, and feasibility of CP as EVD treatment. Longer-term follow-up as well as data from nontrial settings and evidence on the scalability of the intervention are required. CP sourced from within the outbreak is the most readily available source of anti-EVD antibodies. Until the advent of effective antivirals or monoclonal antibodies, CP merits further evaluation.


id: cord-261270-jkm9c5yv
title: National French survey of COVID-19 symptoms in people aged 70 and over
author: Annweiler, Cédric
date: 2020-06-18
txt: ./txt/cord-261270-jkm9c5yv.txt
cache: ./cache/cord-261270-jkm9c5yv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa792
doi: 10.1093/cid/ciaa792
summary:
  The following symptoms observed within the first 72 hours of SARS-CoV-2 infection (i.e., 72h from suspicion, possibly before diagnostic confirmation by RT-PCR test) were collected for each patient using yes/no questions: general signs (sudden deterioration of general condition, temperature, blood pressure), respiratory signs (cough, polypnea), ear nose and throat (ENT) signs (rhinorrhea, odynophagia, otalgia, conjunctivitis, dysgeusia or ageusia, anosmia), gastrointestinal signs (diarrhea, nausea or vomiting) and geriatric syndromes (falls, hypo or overactive delirium, altered consciousness). This national French survey shows that older adults with COVID-19 exhibit a paucisymptomatic clinical picture with less than 3 signs during the first 72h of the infection, generally combining general and respiratory signs (e.g. hyperthermia and cough) with peculiarities that should alert the clinician (e.g. sudden deterioration of general condition, diarrhea, lymphopenia, and/or geriatric syndromes including falls and delirium).

abstract:
  The objective of this national French survey was to determine the COVID-19 semiology in seniors(n=353; mean,84.7±7.0y). 57.8% of patients exhibited ≤3symptoms, including thermal dysregulation(83.6%), cough(58.9%), asthenia(52.7%), polypnea(39.9%), gastrointestinal signs(24.4%). Patients≥80y exhibited falls(P=0.002) and asthenia(P=0.002). Patients with neurocognitive disorders exhibited delirium(P<0.001) and altered consciousness(P=0.001). Clinical peculiarities of COVID-19 were reported in seniors.


id: cord-264660-tfktgy57
title: It’s True Even in a Pandemic: Children are Not Merely Little Adults
author: Creech, C Buddy
date: 2020-05-30
txt: ./txt/cord-264660-tfktgy57.txt
cache: ./cache/cord-264660-tfktgy57.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa680
doi: 10.1093/cid/ciaa680
abstract: nan
summary:
  In this issue of CID, Mehta et al (CID PAPER) provide a systematic review of pediatric COVID-19, evaluating the available literature to date to glean characteristics of disease and transmission. The authors report that children represent only 5% or less of diagnosed COVID cases and the data available at the time of review suggest that children are less likely to develop either severe pneumonia or the laboratory alterations commonly associated with severe disease, such as lymphopenia and elevated inflammatory markers. The authors also report that intrauterine transmission appears to be extremely uncommon and that newborns born to infected mothers are likely to experience either asymptomatic disease or mild disease. Taken together, it would appear that children experience a very different response to SARS-CoV-2 infection than adults and raises the hypothesis that dysregulated host responses may be the primary driver of disease severity.


id: cord-265006-m1dmgcd1
author: Kow, Chia Siang
date: 2020-08-08
txt: ./txt/cord-265006-m1dmgcd1.txt
cache: ./cache/cord-265006-m1dmgcd1.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1167
doi: 10.1093/cid/ciaa1167
abstract: nan
summary:
  In fact, we are aware of the publication of few systematic reviews and metaanalyses [2] [3] [4] [5] [6] [7] [8] which included these observational studies with questionable quality to determine the association between renin-angiotensin system (RAS) inhibitors use, including angiotensin converting enzyme (ACE) inhibitors and angiotensin receptor blockers (ARBs), and mortality/severity of COVID-19. A systematic review and meta-analysis to evaluate the clinical outcomes in COVID-19 patients on angiotensin-converting enzyme inhibitors or angiotensin receptor blockers ACEI/ARB use and risk of infection or severity or mortality of COVID-19: A systematic review and meta-analysis Outcomes of renin-angiotensin-aldosterone system blockers in patients with COVID-19: a systematic review and meta-analysis The use of renin angiotensin system inhibitor on mortality in patients with coronavirus disease 2019 (COVID-19): A systematic review and meta-analysis

title:
  Do the meta-analyses provide a clean bill of health to the use of renin-angiotensin system inhibitors in COVID-19?


id: cord-265242-y8t37p0b
title: Expression of Lymphocytes and Lymphocyte Subsets in Patients with Severe Acute Respiratory Syndrome
author: Cui, Wei
date: 2003-09-15
url: https://www.ncbi.nlm.nih.gov/pubmed/12955652/
doi: 10.1086/378587
abstract:
  In a cohort of 38 patients with severe acute respiratory syndrome (SARS), we observed leukopenia in 47% of patients, lymphopenia in 84%, and T lymphopenia in 95%. CD4(+) T lymphocyte levels were reduced in 100% of patients, CD8(+) T lymphocyte levels were reduced in 87%, B lymphocyte levels were reduced in 76%, and natural killer cell levels were reduced in 55%. Our data suggested that these patients' immune systems were impaired during the course of SARS. The absolute counts of lymphocyte subsets demonstrated a clinical significance for patients with SARS.


id: cord-266150-wox7pnkr
author: Torres, Juan Pablo
date: 2020-07-10
txt: ./txt/cord-266150-wox7pnkr.txt
cache: ./cache/cord-266150-wox7pnkr.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa955
doi: 10.1093/cid/ciaa955
summary:
  Once these forms were signed, a copy was emailed to participants for their records and they were directed to a secure survey that i) asked basic demographic questions, ii) requested information on any previous RT-PCR test for SARS-CoV-2 and potential contact with any Covid-19 positive cases, and iii) asked about symptoms experienced since the outbreak (date and duration in days of each symptom). Among students, antibody positive children were younger, had a higher PCR positivity rate (in those who underwent PCR testing during the outbreak), and were more likely to self-report contact with one or more confirmed cases, as compared to seronegative children ( Table 2 ). Overall, PCR testing and contact history was significantly higher in staff compared to students, which in addition to the higher antibody positivity observed in this study, support the more significant role of adults within the outbreak, in proportion to the overall population.

title:
  SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study

abstract:
  BACKGROUND: A SARS-CoV-2 outbreak affecting 52 people from a large school community in Santiago, Chile was identified (March 12), nine days after the first country case. We assessed the magnitude of the outbreak and the role students and staff played using a self-administered antibody detection test and survey. METHODS: The school was closed on March 13, and the entire community was placed under quarantine. We implemented a home-delivery, self-administered, IgG/IgM antibody test and survey to a classroom stratified sample of students and all staff from May 4-19. We aimed to determine overall seroprevalence rates by age group, reported symptoms, contact exposure and to explore dynamics of transmission. RESULTS: Antibody positivity rates were 9.9% (95%CI: 8.2-11.8) for 1,009 students and 16.6% (95%CI: 12.1-21.9) for 235 staff. Among students, positivity was associated with younger age (P=0.01), lower grade level (P=0.05), prior RT-PCR positivity (P=0.03), and history of contact with a confirmed case (P<0.001). Among staff, positivity was higher in teachers (P=0.01) and in those previously RT-PCR positive (P<0.001). Excluding RT-PCR positive individuals, antibody positivity was associated with fever in adults and children (P=0.02; P=0.002), abdominal pain in children (P=0.001), and chest pain in adults (P=0.02). Within antibody positive individuals, 40% of students and 18% of staff reported no symptoms (P=0.01). CONCLUSIONS: Teachers were more affected during the outbreak and younger children were at higher infection risk, likely because index case(s) were teachers and/or parents from preschool. Self-administered antibody testing, supervised remotely, proved to be a suitable and rapid tool. Our study provides useful information for school re-openings.


id: cord-266232-2ctfmjb8
title: Alterations in smell or taste – Classic COVID-19?
author: Trubiano, Jason A
date: 2020-05-28
txt: ./txt/cord-266232-2ctfmjb8.txt
cache: ./cache/cord-266232-2ctfmjb8.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa655
doi: 10.1093/cid/ciaa655
abstract: nan
summary:
  A c c e p t e d M a n u s c r i p t Dear Editor, There are increased reports of loss of smell (anosmia) and taste (ageusia) in patients with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causing coronavirus disease 2019 , in particular in the setting of mild disease. Luers and colleagues described from a retrospective adult cohort of confirmed SARS-CoV-2 from Germany (n = 72) that 74% of patients reported anosmia and 69% ageusia [7] . prior to this also described from a retrospective cohort study of COVID-19 patients interviewed 5-6 days post diagnosis that 64.4% reported alternations in taste or smell [1] . It is important for clinicians to realize that ansomia and ageusia are likely to be commonly reported symptoms in other upper respiratory tract infections, when appropriately asked (8.9% of our COVID-19 test negative group) [3, 8] . Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study


id: cord-266696-w9sb038q
title: Is the Immune System Impaired in Patients with Severe Acute Respiratory Syndrome?
author: Zhou, Yi-Hua
date: 2004-03-15
txt: ./txt/cord-266696-w9sb038q.txt
cache: ./cache/cord-266696-w9sb038q.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/14999642/
doi: 10.1086/382081
abstract: nan
summary:
  [1] recently described pronounced lymphopenia and low counts of CD4 + cells, CD8 + cells, and B cells in patients with severe acute respiratory syndrome (SARS). Low counts of both CD4 + and CD8 + cells in the peripheral circulation do not always indicate that the immune system is impaired: redistribution of lymphocytes among peripheral and secondary lymphoid organs and migration of these cells to inflamed tissues caused by infections may also result in lymphopenia. We believe that Zhou and Chen [1] need more data to support their conclusion that the immune function of B cells in our patients appeared not to be impaired because specific anti-SARS-CoV could be detected as early as 10 days after the onset of illness. Is the immune system impaired in patients with severe acute respiratory syndrome The clinical pathology of severe acute respiratory syndrome (SARS): a report from China


id: cord-266775-4npowkkz
author: Xu, Jun
date: 2005-10-15
txt: ./txt/cord-266775-4npowkkz.txt
cache: ./cache/cord-266775-4npowkkz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16163626/
doi: 10.1086/444461
summary:
  In the present study, we isolated a SARS coronavirus strain from a brain tissue specimen obtained from a patient with SARS with significant central nervous symptoms. In the present study, we isolated a SARS-CoV strain from a brain tissue specimen obtained during autopsy from a patient with SARS who became severely sick and showed significant central nervous symptoms during the course of his illness. Immunohistochemistry stains for N protein of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) in a specimen of brain tissue obtained from the patient with SARS during autopsy. With regard to the superinfection with invasive Aspergillus in the brain and other organs of the patient, we think that severe immunodepression resulting from the damage to the immune system induced by SARS-CoV infection, combined with high-dosage treatment with a corticosteroid, provided access for conditional pathogens, causing a superinfection with invasive Aspergillus in multiple organs [24] .

title:
  Detection of Severe Acute Respiratory Syndrome Coronavirus in the Brain: Potential Role of the Chemokine Mig in Pathogenesis

abstract:
  Background. Previous studies have shown that common human coronavirus might be neurotropic, although it was first isolated as a pathogen of the respiratory tract. We noticed that a few patients with severe acute respiratory syndrome (SARS) experienced central nervous symptoms during the course of illness. In the present study, we isolated a SARS coronavirus strain from a brain tissue specimen obtained from a patient with SARS with significant central nervous symptoms. Methods. Using transmission electronic microscopy and nested reverse transcription–polymerase chain reaction, the causative pathogen was identified in cultures of a brain tissue specimen obtained from the patient with SARS. Histopathologic examination of the brain tissue was performed using the methods of immunohistochemistry analysis and double immunofluorescence staining. Fifteen cytokines and chemokines were detected in the blood of the patient with SARS by means of a bead-based multiassay system. Results. A fragment specific for SARS human coronavirus was amplified from cultures of the brain suspension, and transmission electronic microscopy revealed the presence of an enveloped virus morphologically compatible with a coronavirus isolated in the cultures. Pathologic examination of the brain tissue revealed necrosis of neuron cells and broad hyperplasia of gliocytes. Immunostaining demonstrated that monokine induced by interferon-Γ (Mig) was expressed in gliocytes with the infiltration of CD68(+) monocytes/macrophages and CD3(+) T lymphocytes in the brain mesenchyme. Cytokine/chemokine assay revealed that levels of interferon-Γ–inducible protein 10 and Mig in the blood were highly elevated, although the levels of other cytokines and chemokines were close to normal. Conclusions. This study provides direct evidence that SARS human coronavirus is capable of infecting the central nervous system, and that Mig might be involved in the brain immunopathology of SARS.


id: cord-266808-wyuodzyt
author: Nagler, Arielle R
date: 2020-06-28
txt: ./txt/cord-266808-wyuodzyt.txt
cache: ./cache/cord-266808-wyuodzyt.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa867
doi: 10.1093/cid/ciaa867
summary:
  title: Early Results from SARS-CoV-2 PCR testing of Healthcare Workers at an Academic Medical Center in New York City Over the following eight weeks three groups were tested: 1) symptomatic staff with fever or respiratory illness; 2) asymptomatic employees with self-reported exposure to COVID-19 which included any degree or duration of contact with an individual who had a documented COVID-19 infection in the work place or in the community; and 3) all employees who were returning to work in services that had been suspended during the epidemic''s peak. Positivity rates amongst all groups of employees being tested including symptomatic employees, asymptomatic employees with self-reported exposure to COVID-19, and employees being screened for returning work declined over time ( Figure 1 ). Thus during this testing program, most NYULH employees had continued exposure to COVID patients, yet A c c e p t e d M a n u s c r i p t employees still demonstrated sharp declines in COVID infection rates.

title:
  Early Results from SARS-CoV-2 PCR testing of Healthcare Workers at an Academic Medical Center in New York City

abstract:
  COVID-19 RT-PCR employee-testing was implemented across NYU Langone. Over eight-weeks, 14,764 employees were tested: 33% of symptomatic employees, 8% of asymptomatic employees reporting COVID-19 exposure, 3% of employees returning to work were positive. Positivity rates declined over time possibly reflecting the importance of community transmission and efficacy of PPE.


id: cord-266820-exl36jt3
title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin
author: Rivera, Frida
date: 2020-08-19
txt: ./txt/cord-266820-exl36jt3.txt
cache: ./cache/cord-266820-exl36jt3.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1225
doi: 10.1093/cid/ciaa1225
summary:
  title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin We aim to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties in Wisconsin. This study aims to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties with markedly different rates of COVID-19. From April 6, 2020 to June 04, 2020, a total of 11,654 asymptomatic patients were tested for SARS-CoV-2, and 61 (0.52%) were positive [Froedtert Health, 38; UW Health, 23]. During the study period, we observed a low prevalence of asymptomatic SARS-CoV-2 infections in these two academic health systems in South Wisconsin. This low prevalence of asymptomatic infections has been recently reported in other areas with high COVID-19 rates, such as Boston and Philadelphia [4, 5] ; however, these two studies included pregnant women and children. In contrast, two hospitals in New York City reported a prevalence of SARS-CoV-2 asymptomatic infections of 14% among women admitted for delivery.

abstract:
  SARS-CoV-2 asymptomatic infections may play a critical role in disease transmission. We aim to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties in Wisconsin. The SARS-CoV-2 prevalence was 1% or lower at both systems despite the higher incidence of COVID-19 in Milwaukee county


id: cord-268233-ibxufjrv
title: Seroconversion rate and diagnostic accuracy of serological tests for COVID-19
author: Nagappa, Bharathnag
date: 2020-05-30
txt: ./txt/cord-268233-ibxufjrv.txt
cache: ./cache/cord-268233-ibxufjrv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa676
doi: 10.1093/cid/ciaa676
abstract: nan
summary:
  We read the recent article by Zhao J et al which studied the antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 [1] . However in results, the authors have mentioned that only 112 out of 173 participants tested positive for RNA over complete duration of the study, which contradicts the methodology. Third, Antibody tests in this study population should be interpreted cautiously since 1) there is plausibility to have cross reaction to antibodies related to other corona virus strains and 2) also diseases caused by other corona virus present with similar symptoms as COVID-19, and symptomatic patients might have antibodies which may lead to increased false positivity rate. Therefore present study should carefully interpret the serological tests and sensitivity should be calculated only in participants tested positive for RNA. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019


id: cord-268809-plgip4h6
author: Bielecki, Michel
date: 2020-06-29
url: https://doi.org/10.1093/cid/ciaa889
doi: 10.1093/cid/ciaa889
title:
  Social distancing alters the clinical course of COVID-19 in young adults: A comparative cohort study

abstract:
  BACKGROUND: Social distancing and stringent hygiene seem effective in reducing the number of transmitted virus particles, and therefore the infectivity, of coronavirus disease 2019 (COVID-19) and could alter the mode of transmission of the disease. However, it is not known if such practices can change the clinical course in infected individuals. METHODS: We prospectively studied an outbreak of COVID-19 in Switzerland among a population of 508 predominantly male soldiers with a median age of 21 years. We followed the number of infections in two spatially separated cohorts with almost identical baseline characteristics with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) before and after implementation of stringent social distancing. RESULTS: Of the 354 soldiers infected prior to the implementation of social distancing, 30% fell ill from COVID-19. While no soldier in a group of 154, in which infections appeared after implementation of social distancing, developed COVID-19 despite the detection of viral RNA in the nose and virus-specific antibodies within this group. CONCLUSIONS: Social distancing not only can slow the spread of SARS-CoV-2 in a cohort of young, healthy adults but can also prevent the outbreak of COVID-19 while still inducing an immune response and colonizing nasal passages. Viral inoculum during infection or mode of transmission may be key factors determining the clinical course of COVID-19.


id: cord-269455-pkjov371
author: Faust, Jeremy Samuel
date: 2020-05-30
url: https://www.ncbi.nlm.nih.gov/pubmed/32472126/
doi: 10.1093/cid/ciaa639
abstract: nan
title:
  Towards a better case fatality estimate for SARS-CoV-2 during the early phase of the United States outbreak


id: cord-269973-sntnmqqd
title: Unique SARS-CoV-2 clusters causing a large COVID-19 outbreak in Hong Kong
author: To, Kelvin Kai-Wang
date: 2020-08-05
txt: ./txt/cord-269973-sntnmqqd.txt
cache: ./cache/cord-269973-sntnmqqd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32756996/
doi: 10.1093/cid/ciaa1119
summary:
  However, the number of COVID-19 cases remained relatively low due to the early implementation of stringent public health measures, including border control, voluntary community-wide wearing of face masks, hand hygiene and social distancing, prompt isolation of suspected cases, and testing and quarantine of close contacts and travelers from epidemic areas [2, 3] . Spike protein D614G mutation was not found in any genomes during the first wave, which mainly involved travelers from mainland China or other parts of Asia, or the linked local cases. The majority of genomes from locally-acquired cases (91%) during this third wave belong to a cluster HK1, a unique cluster within the GR clade, which is characterized by 4 non-synonymous mutations (nsp3 A85V, nsp15 A231V, spike protein S12F, NP A12G) and 1 synonymous mutation (NP C29144T). Two unique SARS-CoV-2 clusters have been identified during this large summer outbreak in Hong Kong shortly after the easing of social distancing policies.

abstract:
  After two months of relative quiescence, a large COVID-19 outbreak occurred in Hong Kong in July 2020 after gradual relaxation of social distancing policy. Two unique SARS-CoV-2 phylogenetic clusters have been identified among locally-acquired cases, with most genomes belonging to cluster HK1 which is phylogenetically related to SARS-CoV-2 reported overseas.


id: cord-271014-xzpvupms
title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors
author: Erikstrup, Christian
date: 2020-06-25
txt: ./txt/cord-271014-xzpvupms.txt
cache: ./cache/cord-271014-xzpvupms.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa849
doi: 10.1093/cid/ciaa849
summary:
  title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors The objective was to perform nationwide real-time seroprevalence surveying among blood donors as a tool to estimate previous SARS-CoV-2 infections and the population based IFR. We have initiated real-time nationwide anti-SARS-CoV-2 seroprevalence surveying of blood donations as a tool in monitoring the epidemic. Thus, numbers of patients tested positive for SARS-CoV-2, admitted to hospital, needing respiratory assistance or deceased from coronavirus disease 2019 (COVID-19) are updated on a daily basis. The objective of this study is to perform a seroprevalence survey among blood donors as a tool in the monitoring of the SARS-CoV-2 epidemic. In this survey of SARS-CoV-2 antibodies in Danish blood donors we found a seroprevalence of 1.9 (CI: 0.8-2.3) adjusted for the assay performance and a low IFR of 89/100,000 (CI: 72-211). The ratio between estimated antibody-positive individuals and confirmed COVID-19 cases is expected given the targeted early Danish SARS-CoV-2 testing strategy.

abstract:
  BACKGROUND: The pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has tremendous consequences for our societies. Knowledge of the seroprevalence of SARS-CoV-2 is needed to accurately monitor the spread of the epidemic and to calculate the infection fatality rate (IFR). These measures may help the authorities to make informed decisions and adjust the current societal interventions. The objective was to perform nationwide real-time seroprevalence surveying among blood donors as a tool to estimate previous SARS-CoV-2 infections and the population based IFR. METHODS: Danish blood donors aged 17–69 years giving blood April 6 to May 3 were tested for SARS-CoV-2 immunoglobulin M and G antibodies using a commercial lateral flow test. Antibody status was compared between geographical areas and an estimate of the IFR was calculated. The seroprevalence was adjusted for assay sensitivity and specificity taking the uncertainties of the test validation into account when reporting the 95% confidence intervals (CI). RESULTS: The first 20,640 blood donors were tested and a combined adjusted seroprevalence of 1.9% (CI: 0.8-2.3) was calculated. The seroprevalence differed across areas. Using available data on fatalities and population numbers a combined IFR in patients younger than 70 is estimated at 89 per 100,000 (CI: 72-211) infections. CONCLUSIONS: The IFR was estimated to be slightly lower than previously reported from other countries not using seroprevalence data. The IFR is likely several fold lower than the current estimate. We have initiated real-time nationwide anti-SARS-CoV-2 seroprevalence surveying of blood donations as a tool in monitoring the epidemic.


id: cord-271269-0gimxteg
author: Gourtsoyannis, John
date: 2020-05-31
url: https://www.ncbi.nlm.nih.gov/pubmed/32474587/
doi: 10.1093/cid/ciaa685
abstract: nan
title:
  COVID-19: Possible reasons for the increased prevalence of Olfactory and Gustatory dysfunction observed in European studies


id: cord-272956-0yumc7em
author: Gnavi, Roberto
date: 2020-05-22
txt: ./txt/cord-272956-0yumc7em.txt
cache: ./cache/cord-272956-0yumc7em.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa634
doi: 10.1093/cid/ciaa634
summary:
  Exposure to agents acting on the renin-angiotensin system was not associated with a risk increase of COVID-19 infection in 2 Italian matched case-control studies, 1 nested in hypertensive patients and the other in patients with cardiovascular diseases or diabetes. Consequently, patients treated with ACE inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs), in particular those with diabetes or cardiovascular disease, should be considered at higher risk of developing severe coronavirus disease 2019 (COVID-19) infection (CVi), and of experiencing unfavorable outcomes [2, 3] . As, to the best of our knowledge, a relationship between ACEI or ARB treatments and increased risk of CVi has never been demonstrated [8] , the aim of the present study was to determine whether an association exists between therapies based on agents acting on the RAAS and CVi in 2 populations at greater risk of being diagnosed with SARS-CoV-2 infection: hypertensive patients and patients who were affected by a cardio-cerebrovascular disease.

title:
  Therapy With Agents Acting on the Renin-Angiotensin System and Risk of Severe Acute Respiratory Syndrome Coronavirus 2 Infection

abstract:
  Exposure to agents acting on the renin-angiotensin system was not associated with a risk increase of COVID-19 infection in 2 Italian matched case-control studies, 1 nested in hypertensive patients and the other in patients with cardiovascular diseases or diabetes.


id: cord-273839-oasgagpc
title: Diagnosis and Management of Group A Streptococcal Pharyngitis: A Practice Guideline
author: Bisno, Alan L.
date: 1997-09-17
txt: ./txt/cord-273839-oasgagpc.txt
cache: ./cache/cord-273839-oasgagpc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/9314443/
doi: 10.1086/513768
summary:
  Except under special circumstances, neither repeated bacteri-Evidence ologic testing (culture or RADT) of patients who have success-We reviewed a large number of clinical trials of diagnostic fully completed a course of antimicrobial therapy nor routine and treatment strategies for group A streptococcal pharyngitis. ple, studies of treatment were evaluated for randomization, A small percentage of patients will have recurrences of acute blinding, use of streptococcal typing to differentiate treatment pharyngitis that are associated with throat cultures (or RADTs) failures from new infections, duration and timing of follow-up positive for group A streptococci within a short period following examinations, and statistical power [1, 2] . Such tests are appropriate for streptococci in the upper respiratory tract and for the confirmation of the clinical diagnosis of acute streptococcal pharyngitis use by microbiology laboratory personnel, but most physicians who perform throat cultures would find it difficult to justify [12] (category A, grade II).

abstract:
  This is the second in a series of practice guidelines commissioned by the Infectious Diseases Society of America through its Practice Guidelines Committee. The purpose of these guidelines is to provide assistance to clinicians when making decisions on treating the conditions specified in each guideline. The targeted providers are pediatricians, family practitioners, and internists. The targeted patients and setting for the acute pharyngitis guideline are pediatric, adolescent, and adult outpatients with a complaint of sore throat. Funding was provided by the IDSA. Panel members represented experts in adult and pediatric infectious diseases. The guidelines are evidence-based. A standard ranking system was used for the strength of the recommendations and the quality of the evidence cited in the literature reviewed. The document has been subjected to external review by peer reviewers as well as by the Practice Guidelines Committee and was approved by the IDSA Council. An executive summary, algorithms, and tables highlight the major recommendations. Indicators of quality will assist in guideline implementation. The guideline will be listed on the IDSA home page at http://www.idsociety.org.


id: cord-273840-jjm7y07m
title: Detection of the New Human Coronavirus HKU1: A Report of 6 Cases
author: Vabret, Astrid
date: 2006-03-01
url: https://www.ncbi.nlm.nih.gov/pubmed/16447108/
doi: 10.1086/500136
abstract:
  Background. Human coronavirus HKU1 (HCoV-HKU1), a new group 2 coronavirus, was first characterized in 2005 from 2 adults with pneumonia in Hong Kong, China. To the best of our knowledge, there is no other report to date about the detection of this new virus. We report a molecular method allowing for the detection of HCoV-HKU1 and also report the clinical presentation of 6 infected patients. Methods. We screened 141 specimens (135 nasal samples and 6 stool samples) received in February and March 2005 in our laboratory and obtained from 135 hospitalized patients (61.5% of whom were <5 years old and 34.1% of whom were >20 years old) for HCoV-HKU1. Results. HCoV-HKU1 was detected in 6 (4.4%) of the 135 nasal specimens and in 2 (33.3%) of the 6 stool samples; the positive samples were obtained from 6 patients (5 children and 1 adult). The clinical presentation of these 6 patients was as follows: 3 were admitted to the hospital for acute enteric disease resulting in severe dehydration associated with upper respiratory symptoms; 1 had fever, otitis, and febrile seizure; 1 had a sample obtained to investigate failure to thrive; and 1 had a sample obtained for exploration of X-linked agammaglobulinemia and hyperleucocytosis. Conclusion. HCoV-HKU1 can be detected in respiratory and stool samples from children and adults in a part of the world other than Hong Kong. Our results suggest that HCoV-HKU1 could be associated with respiratory and enteric diseases, and its detection can be related to a persistent asymptomatic infection in patients with poor underlying conditions.


id: cord-273956-mruywa71
author: Mathers, Amy J
date: 2020-07-10
txt: ./txt/cord-273956-mruywa71.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa958
doi: 10.1093/cid/ciaa958
abstract: nan
summary:
  title: The practical challenges of making clinical use of the quantitative value for SARS-CoV-2 viral load across several dynamics As the numbers of patients infected with SARS-CoV-2 continues to increase in the United States so does access diagnostic molecular testing especially for hospitalized patients. However, interpreting a low Ct value at the time of hospital admission can A c c e p t e d M a n u s c r i p t only be applied for prognosis of patients in this context while learning about the natural history of a novel infection. As most laboratory reports are not context aware this may mean that additional information for interpretation of the Ct value may need to be amended to the report so that we can use this valuable data to understand how it can help us care for patients infected with SARS-CoV-2.

title:
  The practical challenges of making clinical use of the quantitative value for SARS-CoV-2 viral load across several dynamics


id: cord-275349-b35pt3mo
title: The Emergence of Baricitinib: A Story of Tortoises Versus Hares
author: Lenz, Heinz-Josef
date: 2020-07-06
txt: ./txt/cord-275349-b35pt3mo.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa940
doi: 10.1093/cid/ciaa940
abstract: nan
summary:
  The artificial intelligence algorithms predicted that baricitinib would inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of cells [2] , (an effect later confirmed in human liver spheroids) [3] , combined with its better-known anti-inflammatory properties. Consequently, the combined potential antiviral and anti-inflammatory effects of this dually acting drug could be ideal for halting the progression of the disease in hospitalized patients, when taken for a limited duration. This new paper in the journal extends the previous published reports of baricitinib treatment in mild-tomoderate COVID19 patients and provides further evidence that baricitinib could be a potential treatment for unwell hospitalized patients with this disease, independent of severity. One would be advised to remain vigilant of such signals reflecting thromboembolic or infection risk in randomized controlled trials testing a variety of immunomodulatory therapies in COVID-19 patients, either alone or in combination, especially in view of associations between clots and SARS-CoV-2 infection [10] .


id: cord-275454-an8xvow3
author: Clark, Andrew E
date: 2020-09-28
url: https://www.ncbi.nlm.nih.gov/pubmed/32986122/
doi: 10.1093/cid/ciaa1145
abstract: nan
title:
  Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Screening With Specimen Pools: Time to Swim, or Too Deep for Comfort?


id: cord-276995-b003vcdc
author: Wiese, Andrew D
date: 2020-06-20
txt: ./txt/cord-276995-b003vcdc.txt
cache: ./cache/cord-276995-b003vcdc.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa834
doi: 10.1093/cid/ciaa834
abstract: nan
summary:
  And while novel surveillance systems have been implemented to monitor SARS-CoV-2 activity, pre-existing surveillance systems have the advantage of allowing comparison to trends in prior years to assess the impact of social distancing measures on the activity of influenza and other respiratory pathogens. In this issue of the journal, Hyunju Lee and colleagues describe the use of national influenza surveillance data to assess the impact of social distancing measures, implemented in response to the SARS-CoV-2 pandemic, on seasonal influenza activity in Korea. [1] [2] [3] In this study, investigators compared the A c c e p t e d M a n u s c r i p t While surveillance data are helpful to identify abnormal activity of certain diseases of public health interest, and to demonstrate the impact of major interventions, such as implementation of social distancing measures, it is important to understand the limitations and strengths of specific surveillance systems.

title:
  Social distancing measures: evidence of interruption of seasonal influenza activity and early lessons of the SARS-CoV-2 pandemic


id: cord-277307-wabruzfs
title: Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel
author: Gu, Wei
date: 2020-05-21
txt: ./txt/cord-277307-wabruzfs.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa599
doi: 10.1093/cid/ciaa599
summary:
  In San Francisco, we validated a qRT-PCR test to detect SARS-CoV-2 infection from nasopharyngeal swab samples based on the EUA (Emergency Use Authorization)approved US CDC assay 3 . Those who did not have a recent travel history, a close contact who was COVID-19 positive, or were not a frontline healthcare worker were categorized as community transmission with an unknown source of infection and comprised 39% of cases. Viruses in the G clade comprise most of the genomes sequenced from patients in Europe 8, 9 , but notably have also been identified in the vast majority of cases associated with the New York SARS-CoV-2 outbreak in March to April of 2020, which occurred after the timeline of this study 11, 12 Viruses from two additional travel-associated cases from Europe (UC43) and New York (UC41) were mapped to other clades circulating in Europe (Figure 2) . Sequencing identifies multiple, early introductions of SARS-CoV2 to New York City Region

abstract:
  In early-to-mid March 2020, 20 of 46 (43%) COVID-19 cases at a tertiary care hospital in San Francisco, California were travel-related. Cases were significantly associated with travel to Europe or New York (odds ratio 32.9). Viral genomes recovered from 9 of 12 (75%) cases co-clustered with lineages circulating in Europe.


id: cord-277410-lt19mijb
title: Epidemiological Correlates of PCR Cycle Threshold Values in the Detection of SARS-CoV-2
author: Salvatore, Phillip P
date: 2020-09-28
url: https://www.ncbi.nlm.nih.gov/pubmed/32986120/
doi: 10.1093/cid/ciaa1469
abstract:
  BACKGROUND: Detection of SARS-CoV-2 infection has principally been performed through the use of real-time reverse-transcription PCR (rRT-PCR) testing. Results of such tests can be reported as cycle threshold (Ct) values, which may provide semi-quantitative or indirect measurements of viral load. Previous reports have examined temporal trends in Ct values over the course of a SARS-CoV-2 infection. METHODS: Using testing data collected during a prospective household transmission investigation of outpatient and mild COVID-19 cases, we examined the relationship between Ct values of the viral RNA N1 target and demographic, clinical, and epidemiological characteristics collected through participant interviews and daily symptom diaries. RESULTS: We found Ct values are lowest (corresponding to higher viral RNA concentration) soon after symptom onset and are significantly correlated with time elapsed since onset (p<0.001); within 7 days after symptom onset, the median Ct value was 26.5 compared with a median Ct value of 35.0 occurring 21 days after onset. Ct values were significantly lower among participants under 18 years of age (p=0.01) and those reporting upper respiratory symptoms at the time of sample collection (p=0.001) and were higher among participants reporting no symptoms (p=0.05). CONCLUSIONS: These results emphasize the importance of early testing for SARS-CoV-2 among individuals with symptoms of respiratory illness and allows cases to be identified and isolated when their viral shedding may be highest.


id: cord-277611-3iynrfzq
title: Risk factors for SARS-CoV-2 detection in blood of critically ill patients
author: Buetti, Niccolò
date: 2020-09-02
txt: ./txt/cord-277611-3iynrfzq.txt
cache: ./cache/cord-277611-3iynrfzq.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1315
doi: 10.1093/cid/ciaa1315
abstract: nan
summary:
  In their multivariate analysis the authors showed that SARS-CoV-2 RNAaemia was strongly associated with the clinical class, with higher level RNAaemia among critically ill patients. Therefore, we conducted a similar study using prospectively collected data at the Bichat University Hospital, France, in order to identify risk factors for SARS-CoV-2 detection in blood in critically ill intubated patients. In order to identify risk factors for SARS-CoV-2 detection in blood, we used univariable and multivariable mixed-effect logistic models for clustered data (PROC GLIMMIX of SAS) and we adjusted for the time between symptoms'' onset and date of sampling. Using univariable mixed-effect models after adjusting for the time interval between onset of symptoms and date of sampling, we showed that immunosuppression (OR 12.16, 95% CI 1.74-84.93, p=0.013) and chronic renal failure (OR 5.98, A c c e p t e d M a n u s c r i p t 3 95% CI 1.14-31.35, p=0.035) increased the risk for SARS-CoV-2 detection in blood (Table) .


id: cord-277788-6ls21tkr
author: Nelson, Brian C
date: 2020-08-09
url: https://www.ncbi.nlm.nih.gov/pubmed/32772069/
doi: 10.1093/cid/ciaa1163
title:
  Clinical Outcomes Associated with Methylprednisolone in Mechanically Ventilated Patients with COVID-19

abstract:
  BACKGROUND: The efficacy and safety of methylprednisolone in mechanically ventilated patients with acute respiratory distress syndrome due to coronavirus disease 2019 (COVID-19) are unclear. In this study, we evaluated the association between use of methylprednisolone and key clinical outcomes. METHODS: Clinical outcomes associated with the use of methylprednisolone were assessed in an unmatched, case-control study; a subset of patients also underwent propensity-score matching. Patients were admitted between March 1 and April 12, 2020. The primary outcome was ventilator-free days by 28 days after admission. Secondary outcomes included extubation, mortality, discharge, positive cultures, and hyperglycemia. RESULTS: A total of 117 patients met inclusion criteria. Propensity matching yielded a cohort of 42 well-matched pairs. Groups were similar except for hydroxychloroquine and azithromycin use, which were more common in patients who did not receive methylprednisolone. Mean ventilator free-days were significantly higher in patients treated with methylprednisolone (6.21±7.45 versus 3.14±6.22; P = 0.044). The probability of extubation was also increased in patients receiving methylprednisolone (45% versus 21%; P = 0.021), and there were no significant differences in mortality (19% versus 36%; P = 0.087). In a multivariable linear regression analysis, only methylprednisolone use was associated with higher number of ventilator-free days (P = 0.045). The incidence of positive cultures and hyperglycemia were similar between groups. CONCLUSIONS: Methylprednisolone was associated with increased ventilator-free days and higher probability of extubation in a propensity-score matched cohort. Randomized, controlled studies are needed to further define methylprednisolone use in patients with COVID-19.


id: cord-278045-hr3r17mz
title: Mass screening of asymptomatic persons for SARS-CoV-2 using saliva
author: Yokota, Isao
date: 2020-09-25
url: https://doi.org/10.1093/cid/ciaa1388
doi: 10.1093/cid/ciaa1388
abstract:
  BACKGROUND: COVID-19 has rapidly evolved to become a global pandemic due largely to the transmission of its causative virus through asymptomatic carriers. Detection of SARS-CoV-2 in asymptomatic people is an urgent priority for the prevention and containment of disease outbreaks in communities. However, few data are available in asymptomatic persons regarding the accuracy of PCR testing. Additionally, although self-collected saliva has significant logistical advantages in mass screening, its utility as an alternative specimen in asymptomatic persons is yet to be determined. METHODS: We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using nasopharyngeal swabs (NPS) and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. RESULTS: In this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. The true concordance probability between the nasopharyngeal and saliva tests was estimated at 0.998 (90%CI:0.996-0.999) on the estimated airport prevalence at 0.3%. In positive individuals, viral load was highly correlated between NPS and saliva. CONCLUSION: Both nasopharyngeal and saliva specimens had high sensitivity and specificity. Self-collected saliva is a valuable specimen to detect SARS-CoV-2 in mass screening of asymptomatic persons.


id: cord-278084-km04sz2s
title: Respiratory Virus Infections in Adults with Hematologic Malignancies: A Prospective Study
author: Martino, Rodrigo
date: 2003-01-01
txt: ./txt/cord-278084-km04sz2s.txt
cache: ./cache/cord-278084-km04sz2s.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/12491194/
doi: 10.1086/344899
summary:
  On multivariate analysis, the only variable that predicted progression to pneumonia in patients with an upper respiratory tract infection was the presence of respiratory syncytial virus, whereas lymphocytopenia had a nonsignificant trend. We performed a prospective 2-year study to assess the role of respiratory virus infections in the pathogenesis of URTI and LRTI and risk factors for severe LRTI in an adult clinical hematology department. All adult patients with a hematologic malignancy (including HSCT recipients) who had signs and symptoms of a URTI or LRTI in the inpatient and outpatient settings underwent a detailed clinical evaluation, and samples from the upper and/or lower respiratory tracts were screened for the presence of respiratory viruses. A first episode of infection was defined as the period during which the patient had symptoms of URTI and/ or LRTI, regardless of whether a respiratory virus was isolated.

abstract:
  During a 2-year period, 157 consecutive episodes of respiratory virus infections that occurred in 130 patients with upper or lower respiratory tract infection were analyzed for respiratory viruses. A respiratory virus was identified in 75 episodes (48%), and several viruses were found in 13 episodes: there were a total of 56 influenza A virus infections, 14 respiratory syncytial virus infections, 8 adenovirus infections, 8 infections with parainfluenza virus types 1 or 3, and 7 enterovirus infections. On multivariate analysis, the only variable that predicted progression to pneumonia in patients with an upper respiratory tract infection was the presence of respiratory syncytial virus, whereas lymphocytopenia had a nonsignificant trend. Also, among the 38 patients who had pneumonia at any time during the episode, both respiratory syncytial virus and lymphocytopenia were commonly found. For both epidemiological and therapeutic considerations, frequent screening for respiratory viruses should be incorporated into the routine diagnostic study of patients with hematologic malignancies.


id: cord-278259-pbnnp9i1
author: Choi, Eun Hwa
date: 2006-09-01
url: https://www.ncbi.nlm.nih.gov/pubmed/16886150/
doi: 10.1086/506350
title:
  The Association of Newly Identified Respiratory Viruses with Lower Respiratory Tract Infections in Korean Children, 2000–2005

abstract:
  Background. This study was performed to evaluate the associations of newly recognized viruses, namely, human metapneumovirus (hMPV), human coronavirus (HCoV)–NL63, and human bocavirus (HBoV) with lower respiratory tract infections (LRTIs) in previously healthy children. Methods. To determine the prevalences of 11 viruses—respiratory syncytial virus (RSV), adenovirus, rhinovirus, parainfluenza viruses (PIVs) 1 and 3, influenza viruses A and B, hMPV, HCoV, HCoV-NL63, and HBoV—among infants or children with LRTIs, in association with their epidemiologic characteristics, we performed multiplex reverse-transcriptase polymerase chain reaction on nasopharyngeal aspirates obtained from 515 children 5 years old with LRTIs during the period 2000–2005. Results. Viruses were identified in 312 (60.6%) of the 515 patients. RSV was detected in 122 (23.7%), HBoV in 58 (11.3%), adenovirus in 35 (6.8%), PIV-3 in 32 (6.2%), rhinovirus in 30 (5.8%), hMPV in 24 (4.7%), influenza A in 24 (4.7%), PIV-1 in 9 (1.7%), influenza B in 9 (1.7%), and HCoV-NL63 in 8 (1.6%). Coinfections with 2 viruses were observed in 36 patients (11.5%). Twenty-two patients (37.9%) infected with HBoV had a coinfection. Bronchiolitis was frequently diagnosed in patients who tested positive for RSV, PIV-3, or rhinovirus, whereas influenza A, PIV-1, and HCoV-NL63 were commonly found in patients with croup. The age distributions of patients with viral infections differed; notably, RSV was responsible for 77% of LRTIs that occurred in infants 3 months old. The number of hMPV infections peaked between February and April, whereas the number of HCoV-NL63 infections peaked between April and May. Conclusions. This study describes the features of LRTIs associated with newly identified viruses in children, compared with those associated with known viruses. Additional investigations are required to define the role of HBoV in LRTI.


id: cord-279550-7u2hksxm
title: Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection
author: Wang, Kai
date: 2020-08-03
url: https://doi.org/10.1093/cid/ciaa1143
doi: 10.1093/cid/ciaa1143
abstract:
  BACKGROUND: Coronavirus disease 2019 (COVID-19) is a global pandemic with no licensed vaccine or specific antiviral agents for therapy. Little is known about the longitudinal dynamics of SARS-CoV-2-specific neutralizing antibodies (NAbs) in COVID-19 patients. METHODS: Blood samples (n=173) were collected from 30 COVID-19 patients over a 3-month period after symptom onset and analyzed for SARS-CoV-2-specific NAbs, using the lentiviral pseudotype assay, coincident with the levels of IgG and proinflammatory cytokines. RESULTS: SARS-CoV-2-specific NAb titers were low for the first 7–10 d after symptom onset and increased after 2–3 weeks. The median peak time for NAbs was 33 d (IQR 24–59 d) after symptom onset. NAb titers in 93·3% (28/30) of the patients declined gradually over the 3-month study period, with a median decrease of 34·8% (IQR 19·6–42·4%). NAb titers increased over time in parallel with the rise in IgG antibody levels, correlating well at week 3 (r = 0·41, p & 0·05). The NAb titers also demonstrated a significant positive correlation with levels of plasma proinflammatory cytokines, including SCF, TRAIL, and M-CSF. CONCLUSIONS: These data provide useful information regarding dynamic changes in NAbs in COVID-19 patients during the acute and convalescent phases.


id: cord-279828-es498qul
author: Boulle, Andrew
date: 2020-08-29
txt: ./txt/cord-279828-es498qul.txt
cache: ./cache/cord-279828-es498qul.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32860699/
doi: 10.1093/cid/ciaa1198
summary:
  We used Cox-proportional hazards models adjusted for age, sex, location and comorbidities to examine the association between HIV, tuberculosis and COVID-19 death from 1 March-9 June 2020 among (i) public sector "active patients" (≥1 visit in the 3 years before March 2020), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases. We conducted a cohort study using de-identified data from the Western Cape Provincial Health Data Centre (WCPHDC) of public sector patients aged ≥20 years with documented sex and not known to have died before March 1, 2020 (before the first diagnosed COVID-19 case in South Africa, and several weeks before the first documented COVID-19 death) and included all follow up through June 9, 2020. We used Cox-proportional hazards models adjusted for age, sex and other comorbidities to examine the association between HIV, tuberculosis and COVID-19 death among (i) all public sector patients with ≥1 health visit in the 3 years before March 1, 2020 (considered "active patients"), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases.

title:
  Risk factors for COVID-19 death in a population cohort study from the Western Cape Province, South Africa

abstract:
  BACKGROUND: Risk factors for COVID-19 death in sub-Saharan Africa and the effects of HIV and tuberculosis on COVID-19 outcomes are unknown. METHODS: We conducted a population cohort study using linked data from adults attending public sector health facilities in the Western Cape, South Africa. We used Cox-proportional hazards models adjusted for age, sex, location and comorbidities to examine the association between HIV, tuberculosis and COVID-19 death from 1 March-9 June 2020 among (i) public sector “active patients” (≥1 visit in the 3 years before March 2020), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases. We calculated the standardized mortality ratio (SMR) for COVID-19 comparing HIV positive vs. negative adults using modelled population estimates. RESULTS: Among 3,460,932 patients (16% HIV positive), 22,308 were diagnosed with COVID-19, of whom 625 died. COVID-19 death was associated with male sex, increasing age, diabetes, hypertension and chronic kidney disease. HIV was associated with COVID-19 mortality (adjusted hazard ratio [aHR] 2.14; 95% confidence interval [CI] 1.70-2.70), with similar risks across strata of viral load and immunosuppression. Current and previous tuberculosis were associated with COVID-19 death (aHR [95%CI] 2.70 [1.81-4.04] and 1.51 [1.18-1.93] respectively). The SMR for COVID-19 death associated with HIV was 2.39 (95%CI 1.96-2.86); population attributable fraction 8.5% (95%CI 6.1-11.1). CONCLUSION: While our findings may over-estimate HIV- and tuberculosis-associated COVID-19 mortality risks due to residual confounding, both HIV and current tuberculosis were independently associated with increased COVID-19 mortality. The associations between age, sex and other comorbidities and COVID-19 mortality were similar to other settings.


id: cord-279932-bilr71ay
author: Plotkin, Stanley A
date: 2020-07-16
txt: ./txt/cord-279932-bilr71ay.txt
cache: ./cache/cord-279932-bilr71ay.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32674139/
doi: 10.1093/cid/ciaa1013
abstract: nan
summary:
  A number of people, including Nguyen et al [1] in this issue and others [2] [3] [4] [5] [6] [7] elsewhere, have proposed the use of human challenge trials as a way of confirming the protective ability of candidate vaccines, in order to allow emergency use in high-risk groups and to facilitate the way to eventual licensure and use in the general population. The idea behind human challenge trials is to recruit young, healthy volunteers who have the lowest chance of serious disease, who would be given vaccine candidates and then be challenged with SARS-CoV-2 in order to determine whether the vaccines protect. Aside from the ethical issues, the principal objection to human challenge trials with SARS-CoV-2 is the absence of a reliable rescue medication for the treatment of serious disease. Evaluating use cases for human challenge trials in accelerating SARS-CoV-2 vaccine development

title:
  The Value of Human Challenges in Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Development


id: cord-280005-i9fp5rys
author: Wang, Mengmei
date: 2020-09-21
txt: ./txt/cord-280005-i9fp5rys.txt
cache: ./cache/cord-280005-i9fp5rys.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32955081/
doi: 10.1093/cid/ciaa1417
summary:
  title: Treatment of COVID-19 Patients with Prolonged Post-Symptomatic Viral Shedding with Leflunomide -a Single-Center, Randomized, Controlled Clinical Trial CONCLUSIONS: In COVID-19 patients with prolonged PCR positivity, no benefit in terms of the duration of viral shedding was observed with the combined treatment of leflunomide and IFN α-2a beyond IFN α-2a alone. Based on that background, we conducted a prospective randomized, controlled, open-label trial, to evaluate the efficacy and safety of oral leflunomide to treat hospitalized COVID-19 patients with prolonged post-symptomatic viral shedding. Fifty eligible patients were randomly assigned to a combination treatment group that received leflunomide (50 mg, q12h, three consecutive times, orally; then 20 mg, once a day for 8 days; a total course of 10 days) plus nebulized IFN -2a (3 million IU each time, adding 2 ml of sterilized water, atomization inhalation twice daily for 10 days), or to a control group that received nebulized IFN -2a This was an open-label, prospective randomized, controlled trial, which was conducted at East Campus, Renmin Hospital of Wuhan University.

title:
  Treatment of COVID-19 Patients with Prolonged Post-Symptomatic Viral Shedding with Leflunomide -- a Single-Center, Randomized, Controlled Clinical Trial

abstract:
  OBJECTIVE: To evaluate the efficacy and safety of leflunomide, an approved dihydroorotate dehydrogenase inhibitor, to treat COVID-19 patients with prolonged post-symptomatic viral shedding. METHODS: We conducted a prospective, randomized, controlled, open-label trial involving hospitalized adult COVID-19 patients with prolonged PCR positivity. Patients were randomly assigned to receive either leflunomide (50 mg, q12h, three consecutive times, orally; then 20 mg, once daily for 8 days), in addition to nebulized interferon alpha 2a (IFN α-2a, 3 million IU each time, twice daily for 10 days), or nebulized IFN α-2a alone for 10 days. The primary end point was the duration of viral shedding. RESULTS: A total of 50 COVID-19 patients with prolonged PCR positivity were randomized into 2 groups; 26 were assigned to the leflunomide group, and 24 were assigned to the interferon alone group. Treatment with leflunomide was not associated with a difference from the interferon alone group in the duration of viral shedding (hazard ratio for negative RT-PCR, 0.70; 95% confidence interval, 0.391-1.256; P=0.186). In addition, the patients given leflunomide did not have a substantially shorter length of hospital stay than patients treated with interferon alone, with median (IQRs) durations of 29.0 (19.3-47.3) days and 33.0 (29.3-42.8) days, respectively, P=0.170. Two leflunomide recipients were unable to complete the full 10-day course of administration due to adverse events. CONCLUSIONS: In COVID-19 patients with prolonged PCR positivity, no benefit in terms of the duration of viral shedding was observed with the combined treatment of leflunomide and IFN α-2a beyond IFN α-2a alone.


id: cord-280571-ntgt5hy9
author: Ginocchio, Christine C.
date: 2011-05-01
url: https://doi.org/10.1093/cid/cir046
doi: 10.1093/cid/cir046
title:
  Strengths and Weaknesses of FDA-Approved/Cleared Diagnostic Devices for the Molecular Detection of Respiratory Pathogens

abstract:
  The rapid, sensitive, and specific identification of the microbial etiological characteristics of respiratory tract infections enhances the appropriate use of both antibiotics and antiviral agents and reduces the risk of nosocomial transmission. This article reviews the current nucleic acid amplification tests approved by the U.S. Food and Drug Administration (FDA) for the detection of respiratory pathogens. In addition, Emergency Use Authorization tests for the detection of 2009 influenza A H1N1 are discussed. The advantages and limitations of the current FDA-approved/cleared tests are reviewed.


id: cord-280763-4bnv2t3f
author: Piñana, José Luis
date: 2019-06-01
txt: ./txt/cord-280763-4bnv2t3f.txt
cache: ./cache/cord-280763-4bnv2t3f.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciy792
doi: 10.1093/cid/ciy792
summary:
  METHODS: In this prospective, cross-sectional study, we retrospectively analyzed the effect of inactivated trivalent influenza vaccination on the prevalence of influenza RVI in a consecutive cohort of 136 allo-HSCT adult recipients who developed 161 RVI over 5 flu seasons (from 2013 to 2018). The influenza virus has a significant impact on morbidity and mortality in allogeneic hematopoietic stem cell transplantation patients (allo-HSCT), leading to complications ranging from self-limited upper-respiratory tract infections to life-threatening or fatal pneumonias [1] [2] [3] [4] . We conducted a prospective, cross-sectional, observational epidemiological study of community-acquired respiratory virus (CARV) respiratory tract disease (RTD) in allo-HSCT recipients who developed upper RTD (URTD) and/or lower RTD (LRTD) symptoms after transplant. In this study, we report the prevalence of influenza RTD according to the vaccination status over 5 consecutive influenza seasons in a consecutive series of allo-HSCT recipients with virologically-documented respiratory virus infections (RVIs).

title:
  Clinical Effectiveness of Influenza Vaccination After Allogeneic Hematopoietic Stem Cell Transplantation: A Cross-sectional, Prospective, Observational Study

abstract:
  BACKGROUND: Vaccination is the primary method for preventing influenza respiratory virus infection (RVI). Although the influenza vaccine is able to achieve serological responses in some allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients, its clinical benefits are still uncertain. METHODS: In this prospective, cross-sectional study, we retrospectively analyzed the effect of inactivated trivalent influenza vaccination on the prevalence of influenza RVI in a consecutive cohort of 136 allo-HSCT adult recipients who developed 161 RVI over 5 flu seasons (from 2013 to 2018). Respiratory viruses in upper– and/or lower–respiratory tract specimens were tested using multiplex polymerase chain reaction panel assays. RESULTS: Overall, we diagnosed 74 episodes (46%) of influenza RVI in 70 allo-HSCT recipients. Influenza RVI occurred in 51% of the non-vaccinated compared to 36% of the vaccinated recipients (P = .036). A multivariate analysis showed that influenza vaccination was associated with a lower prevalence of influenza RVI (odds ratio [OR] 0.39, P = .01). A multivariate risk factor analysis of lower–respiratory tract disease (LRTD) identified 2 conditions associated with the probability of influenza RVI progression: influenza vaccination (OR 0.12, 95% confidence interval [CI] 0.014–1, P = .05) and a high-risk immunodeficiency score (OR 36, 95% CI 2.26–575, P = .011). Influenza vaccination was also associated with a lower likelihood of an influenza-related hospital admission (14% vs 2%, P = .04). CONCLUSIONS: This study shows that influenza vaccination may have a clinical benefit in allo-HSCT recipients with virologically-confirmed RVI, in terms of a lower influenza RVI prevalence, slower LRTD progression, and lower likelihood of hospital admission.


id: cord-280915-yk872yaz
title: Infant Outcomes Following Maternal Infection with SARS-CoV-2: First Report from the PRIORITY Study
author: Flaherman, Valerie J
date: 2020-09-18
txt: ./txt/cord-280915-yk872yaz.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1411
doi: 10.1093/cid/ciaa1411
summary:
  In a prospective U.S. registry of 263 infants born to mothers testing positive or negative for SARS-CoV-2, SARS-CoV-2 status was not associated with birth weight, difficulty breathing, apnea or upper or lower respiratory infection through 8 weeks of age. Currently, national and international guidelines for management of infants born to mothers with SARS-CoV-2 [6] [7] [8] are based on limited data without outcomes reported past the neonatal period. To address this urgent need, we report here early findings from infants born to mothers enrolled in the PRegnancy CoronavIrus Outcomes RegIsTrY (PRIORITY), an ongoing nationwide study of pregnant or recently pregnant women who have confirmed or suspected SARS-CoV-2. Among 263 initial infants enrolled in the PRIORITY study, adverse outcomes, including preterm birth, NICU admission, and respiratory disease did not differ between those born to mothers testing positive for SARS-CoV-2 and those born to mothers testing negative.

abstract:
  Infant outcomes after maternal SARS-CoV-2 infection are not well-described. In a prospective U.S. registry of 263 infants born to mothers testing positive or negative for SARS-CoV-2, SARS-CoV-2 status was not associated with birth weight, difficulty breathing, apnea or upper or lower respiratory infection through 8 weeks of age.


id: cord-280954-wd89nka9
author: Ackerson, Bradley
date: 2019-07-15
url: https://www.ncbi.nlm.nih.gov/pubmed/30452608/
doi: 10.1093/cid/ciy991
title:
  Severe Morbidity and Mortality Associated With Respiratory Syncytial Virus Versus Influenza Infection in Hospitalized Older Adults

abstract:
  BACKGROUND: Respiratory syncytial virus (RSV) is an important cause of serious respiratory illness in older adults. Comparison of RSV and influenza infection in hospitalized older adults may increase awareness of adult RSV disease burden. METHODS: Hospitalized adults aged ≥60 years who tested positive for RSV or influenza between 1 January 2011 and 30 June 2015 were identified from Kaiser Permanente Southern California electronic medical records. Baseline characteristics, comorbidities, utilization, and outcomes were compared. RESULTS: The study included 645 RSV- and 1878 influenza-infected hospitalized adults. Patients with RSV were older than those with influenza (mean, 78.5 vs 77.4 years; P = .035) and more likely to have congestive heart failure (35.3% vs 24.5%; P < .001) and chronic obstructive pulmonary disease (COPD) (29.8% vs 24.3%; P = .006) at baseline. In adjusted analyses, RSV infection was associated with greater odds of length of stay ≥7 days (odds ratio [OR] = 1.5; 95% confidence interval [CI], 1.2–1.8; P < .001); pneumonia (OR = 2.7; 95% CI, 2.2–3.2; P < .001); intensive care unit admission (OR = 1.3; 95% CI, 1.0–1.7; P = .023); exacerbation of COPD (OR = 1.7; 95% CI, 1.3–2.4; P = .001); and greater mortality within 1 year of admission (OR = 1.3; 95% CI, 1.0–1.6; P = .019). CONCLUSIONS: RSV infection may result in greater morbidity and mortality among older hospitalized adults than influenza. Increased recognition of adult RSV disease burden will be important in the evaluation and use of new RSV vaccines and antivirals.


id: cord-280958-36ytqapi
author: Decker, Summer J
date: 2020-09-10
txt: ./txt/cord-280958-36ytqapi.txt
cache: ./cache/cord-280958-36ytqapi.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1366
doi: 10.1093/cid/ciaa1366
summary:
  BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, can be detected in respiratory samples by Real-time Reverse Transcriptase (RT)-PCR or other molecular methods. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at three clinical sites (n=291) using three SARS-CoV-2 EUA tests: a modified version of the CDC Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel and two commercial automated formats, Roche Cobas and NeuMoDx. RESULTS: The cycle threshold (C(t)) values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (p=0.152 and p=0.092), with the RNase P target performing significantly better in the 3DP swabs (p & 0.001). Given the need for widespread testing, 3DP swabs printed on-site are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits.

title:
  3D Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for COVID-19 testing

abstract:
  BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, can be detected in respiratory samples by Real-time Reverse Transcriptase (RT)-PCR or other molecular methods. Accessibility of diagnostic testing for COVID-19 has been limited by intermittent shortages of supplies required for testing, including flocked nasopharyngeal (FLNP) swabs. METHODS: We developed a 3D-printed nasopharyngeal (3DP) swab as a replacement of the FLNP swab. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at three clinical sites (n=291) using three SARS-CoV-2 EUA tests: a modified version of the CDC Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel and two commercial automated formats, Roche Cobas and NeuMoDx. RESULTS: The cycle threshold (C(t)) values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (p=0.152 and p=0.092), with the RNase P target performing significantly better in the 3DP swabs (p & 0.001). The C(t) values showed no significant differences between swabs for both viral gene targets in the Roche cobas assay (p=0.05 and p=0.05) as well as the NeuMoDx assay (p=0.401 and p=0.484). The overall clinical correlation of COVID-19 diagnosis between all methods was 95.88% (Kappa 0.901). CONCLUSIONS: 3DP swabs were equivalent to standard FLNP in three testing platforms for SARS-CoV-2. Given the need for widespread testing, 3DP swabs printed on-site are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits.


id: cord-281418-mvgp6qfv
author: Soccal, P. M.
date: 2010-07-15
url: https://doi.org/10.1086/653529
doi: 10.1086/653529
title:
  Upper and Lower Respiratory Tract Viral Infections and Acute Graft Rejection in Lung Transplant Recipients

abstract:
  Background. Lung transplant recipients are frequently exposed to respiratory viruses and are particularly at risk for severe complications. The aim of this study was to assess the association among the presence of a respiratory virus detected by molecular assays in bronchoalveolar lavage (BAL) fluid, respiratory symptoms, and acute rejection in adult lung transplant recipients. Methods. Upper (nasopharyngeal swab) and lower (BAL) respiratory tract specimens from 77 lung transplant recipients enrolled in a cohort study and undergoing bronchoscopy with BAL and transbronchial biopsies were screened using 17 different polymerase chain reaction—based assays. Results. BAL fluid and biopsy specimens from 343 bronchoscopic procedures performed in 77 patients were analyzed. We also compared paired nasopharyngeal and BAL fluid specimens collected in a subgroup of 283 cases. The overall viral positivity rate was 29.3% in the upper respiratory tract specimens and 17.2% in the BAL samples (P < .001). We observed a significant association between the presence of respiratory symptoms and positive viral detection in the lower respiratory tract (P = .012). Conversely, acute rejection was not associated with the presence of viral infection (odds ratio, 0.41; 95% confidence interval, 0.20–0.88). The recovery of lung function was significantly slower when acute rejection and viral infection were both present. Conclusions. A temporal relationship exists between acute respiratory symptoms and positive viral nucleic acid detection in BAL fluid from lung transplant recipients. We provide evidence suggesting that respiratory viruses are not associated with acute graft rejection during the acute phase of infection.


id: cord-281726-s1o5l7ns
title: Temporal-Spatial Analysis of Severe Acute Respiratory Syndrome among Hospital Inpatients
author: Yu, Ignatius T. S.
date: 2005-05-01
url: https://www.ncbi.nlm.nih.gov/pubmed/15825024/
doi: 10.1086/428735
abstract:
  Background. We report the temporal-spatial spread of severe acute respiratory syndrome (SARS) among inpatients in a hospital ward during a major nosocomial outbreak and discuss possible mechanisms for the outbreak. Methods. All inpatients who had stayed in the same ward as the initial index case patient for any duration before isolation were recruited into a cohort and followed up to document the occurrence of SARS. The normalized concentration of virus-laden aerosols at different locations of the ward was estimated by use of computational fluid dynamics modeling. The attack rates in the various subgroups stratified by bed location were calculated. Multivariate Cox proportional hazards regression was used to document important risk factors. Results. The overall attack rate of SARS was 41% (30 of 74 subjects). It was 65%, 52%, and 18% in the same bay, adjacent bay, and distant bays, respectively (P = .001). Computation fluid dynamics modeling indicated that the normalized concentration of virus-laden aerosols was highest in the same bay and lowest in the distant bays. Cox regression indicated that staying in the ward on 6 or 10 March entailed higher risk, as well as staying in the same or adjacent bays. The epidemic curve showed 2 peaks, and stratified analyses by bed location suggested >1 generation of spread. Conclusions. The temporal-spatial spread of SARS in the ward was consistent with airborne transmission, as modeled by use of computational fluid dynamics. Infected health care workers likely acted as secondary sources in the latter phase of the outbreak.


id: cord-282539-skzosh6u
author: Casadevall, Arturo
date: 2020-08-17
url: https://www.ncbi.nlm.nih.gov/pubmed/32805024/
doi: 10.1093/cid/ciaa1213
abstract: nan
title:
  Implications of Coronavirus Disease 2019 (COVID-19) Antibody Dynamics for Immunity and Convalescent Plasma Therapy


id: cord-283780-h4lwzpl9
author: Zhang, John J Y
date: 2020-05-14
txt: ./txt/cord-283780-h4lwzpl9.txt
cache: ./cache/cord-283780-h4lwzpl9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32407459/
doi: 10.1093/cid/ciaa576
summary:
  title: Risk Factors of Severe Disease and Efficacy of Treatment in Patients Infected with COVID-19: A Systematic Review, Meta-Analysis and Meta-Regression Analysis We conducted a systematic review and meta-analysis of all published studies up to March 15, 2020 which reported COVID-19 clinical features and/or treatment outcomes. To address this gap in the literature, we conducted a systematic review, meta-analysis and meta-regression to 1) investigate the predictive value of laboratory investigations for severe disease and adverse outcomes, and 2) evaluate the efficacy of antivirals and corticosteroids for COVID-19. Among the patients with antiviral use reported in our meta-analysis, overall rates of mortality, ICU admission and ARDS were 5.7%, 11.8% and 20.2%, respectively. Our meta-analysis suggested that the use of corticosteroids is associated with disease severity (ICU admission) and higher ARDS rates. To the best of our knowledge, this is the first systematic review and meta-analysis of COVID-19 to describe specific laboratory predictors of severe disease and adverse outcomes.

title:
  Risk Factors of Severe Disease and Efficacy of Treatment in Patients Infected with COVID-19: A Systematic Review, Meta-Analysis and Meta-Regression Analysis

abstract:
  The coronavirus disease 2019 (COVID-19) pandemic spread globally in the beginning of 2020. At present, predictors of severe disease and the efficacy of different treatments are not well-understood. We conducted a systematic review and meta-analysis of all published studies up to March 15, 2020 which reported COVID-19 clinical features and/or treatment outcomes. 45 studies reporting 4203 patients were included. Pooled rates of intensive care unit (ICU) admission, mortality and acute respiratory distress syndrome (ARDS) were 10.9%, 4.3% and 18.4%, respectively. On meta-regression, ICU admission was predicted by raised leukocyte count (p<0.0001), raised alanine aminotransferase (p=0.024), raised aspartate transaminase (p=0.0040), elevated lactate dehydrogenase (LDH) (p<0.0001) and increased procalcitonin (p<0.0001). ARDS was predicted by elevated LDH (p<0.0001), while mortality was predicted by raised leukocyte count (p=0.0005) and elevated LDH (p<0.0001). Treatment with lopinavir-ritonavir showed no significant benefit in mortality and ARDS rates. Corticosteroids were associated with a higher rate of ARDS (p=0.0003).


id: cord-283788-04gwxo4b
title: Comparing Nasopharyngeal and Mid-Turbinate Nasal Swab Testing for the Identification of SARS-CoV-2
author: Pinninti, Swetha
date: 2020-06-29
url: https://www.ncbi.nlm.nih.gov/pubmed/32596725/
doi: 10.1093/cid/ciaa882
abstract:
  Testing of paired mid-turbinate (MT) nasal and nasopharyngeal (NP) swabs, collected by trained personnel from 40 patients with COVID-19 showed more NP (76/95, 80%) than MT swabs tested positive (61/95, 64%; p=0.02). Among samples collected a week after study enrollment, fewer MT than NP samples were positive (45% vs 76%; p=0.001).


id: cord-284782-51mbq7qb
title: Care for the psychological status of frontline medical staff fighting against COVID-19
author: Huang, Jing
date: 2020-04-03
txt: ./txt/cord-284782-51mbq7qb.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32246142/
doi: 10.1093/cid/ciaa385
abstract: nan
summary:
  key: cord-284782-51mbq7qb authors: Huang, Jing; Liu, Fangkun; Teng, Ziwei; Chen, Jindong; Zhao, Jingping; Wang, Xiaoping; Wu, Renrong title: Care for the psychological status of frontline medical staff fighting against COVID-19 cord_uid: 51mbq7qb Besides, a total of 6, 097 medical workers from different provinces in China were in Hubei province to assist in the COVID-19 by Jan 30, 2020 2 . For example, the emergency medical team from the Second Xiangya Hospital is able to set up field hospitals and ambulances to help and serve the With the increasing spreading of the virus worldwide, COVID-19 outbreak is now becoming a pandemic. None of the authors has any potential conflicts of interest to disclose. Timely mental health care for the 2019 novel coronavirus outbreak is urgently needed The immediate psychological and occupational impact of the 2003 SARS outbreak in a teaching hospital Protecting Health Care Workers during the COVID-19 Coronavirus Outbreak -Lessons from Taiwan''s SARS response


id: cord-285403-h8ahn8fw
title: Origin and Evolution of the 2019 Novel Coronavirus
author: Zhang, Liangsheng
date: 2020-02-03
txt: ./txt/cord-285403-h8ahn8fw.txt
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url: https://www.ncbi.nlm.nih.gov/pubmed/32011673/
doi: 10.1093/cid/ciaa112
abstract: nan
summary:
  To the Editor-The 2019 novel coronavirus disease (2019-nCoV or COVID-19) recently reported from Wuhan (China), which has cases in Thailand, Japan, South Korea, and the United States, has been confirmed as a new coronavirus [1] . Based on our phylogenomic analysis of the recently released genomic data of 2019-nCoV, we showed that the 2019-nCoV is most closely related to 2 severe acute respiratory syndrome (SARS)-like CoV sequences that were isolated in bats during 2015 to 2017 [2] , suggesting that the bats'' CoV and the human 2019-nCoV share a recent common ancestor ( Figure 1A) . This market also sells wild animals or mammals, which were likely intermediate hosts of 2019-nCoV, which originated from bat hosts ( Figure 1B ). The 2019-nCoVs have long branches (0.09) for the 2 isolated in the phylogenomic tree ( Figure 1A) , indicating that the 2019-nCoVs likely share bat hosts. There were 3 genotypes present in samples from Guangdong province, indicating that the 6 strains were infected from different places in Wuhan.


id: cord-287676-qh7zeyyx
author: Angoulvant, François
date: 2020-06-03
url: https://www.ncbi.nlm.nih.gov/pubmed/32492117/
doi: 10.1093/cid/ciaa710
title:
  COVID-19 pandemic: Impact caused by school closure and national lockdown on pediatric visits and admissions for viral and non-viral infections, a time series analysis

abstract:
  A time series analysis of 871,543 pediatric emergency visits revealed that the COVID-19 lockdown and school closure were associated with a significant decrease in infectious diseases disseminated through airborne or fecal-oral transmissions: common cold, gastro-enteritis, bronchiolitis, acute otitis. No change was found for urinary tract infections.


id: cord-287923-ev93r09i
title: Infection Prevention and Control in Asia: Current Evidence and Future Milestones
author: Apisarnthanarak, Anucha
date: 2017-05-15
txt: ./txt/cord-287923-ev93r09i.txt
cache: ./cache/cord-287923-ev93r09i.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28475784/
doi: 10.1093/cid/cix071
abstract: nan
summary:
  This issue of Clinical Infectious Diseases focuses on 3 key themes of infection prevention and control in healthcare settings across the Asia-Pacific regions: (1) epidemiology and evidence to support prevention and control interventions, (2) enhancements to infection prevention and control in healthcare settings, and (3) practices associated with the containment of emerging infectious diseases and outbreaks. We thank the Infectious Diseases Association of Thailand for its partial sponsorship of this issue and share our hope that the collective experience from the study contributors reporting work in this issue will serve as a 2017 platform for improvement in the science and practice of infection prevention in the Asia-Pacific region and in other resource-limited settings. This article appears as part of the supplement "Infection Prevention in Asia Pacific, " sponsored by the Infectious Diseases Association of Thailand (IDAT) with additional author sponsorship.


id: cord-288432-n2y9cunc
author: Liu, Kun
date: 2020-04-17
txt: ./txt/cord-288432-n2y9cunc.txt
cache: ./cache/cord-288432-n2y9cunc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32302377/
doi: 10.1093/cid/ciaa422
summary:
  BACKGROUND: The unprecedented outbreak of 2019-nCoV pneumonia infection in Wuhan City caused global concern, the outflowing population from Wuhan was believed to be a main reason for the rapid and large-scale spread of the disease, so the government implemented a city closure measure to prevent its transmission considering the large amount of travelling before the Chinese New Year. METHODS: Based on the daily reported new cases and the population movement data between January 1 and 31, we examined the effects of population outflow from Wuhan on the geographical expansion of the infection in other provinces and cities of China, as well as the impacts of the city closure in Wuhan in different scenarios of closing dates. Thus, we conducted this study with the following objectives: 1) to evaluate the impacts of the population movement on the spatial transmission of the 2019-nCoV cases at the provincial and city levels in China; 2) to estimate the potential outbreak risk at areas with the population outflowed from Wuhan; 3) to evaluate the effectiveness of the city closure measures on the epidemic control.

title:
  Population movement, city closure in Wuhan and geographical expansion of the 2019-nCoV pneumonia infection in China in January 2020

abstract:
  BACKGROUND: The unprecedented outbreak of 2019-nCoV pneumonia infection in Wuhan City caused global concern, the outflowing population from Wuhan was believed to be a main reason for the rapid and large-scale spread of the disease, so the government implemented a city closure measure to prevent its transmission considering the large amount of travelling before the Chinese New Year. METHODS: Based on the daily reported new cases and the population movement data between January 1 and 31, we examined the effects of population outflow from Wuhan on the geographical expansion of the infection in other provinces and cities of China, as well as the impacts of the city closure in Wuhan in different scenarios of closing dates. RESULTS: We observed a significantly positive association between population movement and the number of the 2019-nCoV cases. The spatial distribution of cases per unit outflow population indicated that some areas with large outflow population might have been underestimated for the infection, such as Henan and Hunan provinces. Further analysis revealed that if the city closure policy was implemented two days earlier, 1420 (95% CI: 1059, 1833) cases could have been prevented, and if two days later, 1462 (95% CI: 1090, 1886) more cases would be possible. CONCLUSIONS: Our findings suggest that population movement might be one important trigger for the transmission of 2019-nCoV infection in China, and the policy of city closure is effective to control the epidemic.


id: cord-288558-rthnj6wd
author: Cheng, V. C. C.
date: 2004-02-15
url: https://www.ncbi.nlm.nih.gov/pubmed/14765337/
doi: 10.1086/382681
title:
  Viral Replication in the Nasopharynx Is Associated with Diarrhea in Patients with Severe Acute Respiratory Syndrome

abstract:
  The role of severe acute respiratory syndrome (SARS) coronavirus as an enteric pathogen was investigated in a cohort of 142 patients with SARS who were treated with a standard treatment protocol. Data from daily hematological, biochemical, radiological, and microbiological investigations were prospectively collected, and the correlation of these findings with diarrhea was retrospectively analyzed. Sixty-nine patients (48.6%) developed diarrhea at a mean (± standard deviation [SD]) of 7.6 ± 2.6 days after the onset of symptoms. The diarrhea was most severe at a mean (±SD) of 8.8 ± 2.4 days after onset, with a maximum frequency of 24 episodes per day (median, 5 episodes; range, 3–24 episodes). A higher mean virus load in nasopharyngeal specimens obtained on day 10 after the onset of symptoms was significantly associated with the occurrence of diarrhea (3.1 log(10) vs. 1.8 log(10) copies/mL; P = .01) and mortality (6.2 vs. 1.7 log(10) copies/mL; P < .01). However, diarrhea was not associated with mortality. The lung and the gastrointestinal tract may react differently to SARS coronavirus infection. Additional investigation of the role of SARS coronavirus in the pathogenesis of diarrhea in patients with SARS should be conducted.


id: cord-289247-qc3to2xj
title: Whole nucleocapsid protein of SARS-CoV-2 may cause false positive results in serological assays
author: Yamaoka, Yutaro
date: 2020-05-23
txt: ./txt/cord-289247-qc3to2xj.txt
cache: ./cache/cord-289247-qc3to2xj.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa637
doi: 10.1093/cid/ciaa637
abstract: nan
summary:
  The nucleocapsid protein (NP) of SARS-CoV-2 is one of the widely used antigens in serodiagnostics of the novel Coronavirus disease . They have generated recombinant whole nucleocapsid protein (rNP) of SARS-CoV-2 using Escherichia coli expression system and used it to develop an enzyme linked immunosorbent assay (ELISA) to detect anti-SARS-CoV-2 antibodies in plasma. Although the amino acid sequences of the entire nucleocapsid proteins (NP) of SARS-CoV and other common Coronaviruses are dissimilar to that of SARS-CoV-2 [1] , the conserved residues at the Nterminal domain of NP show a high degree of similarity (Figure-1A) . Evaluation of inapparent nosocomial severe acute respiratory syndrome coronavirus infection in Vietnam by use of highly specific recombinant truncated nucleocapsid protein-based enzyme-linked immunosorbent assay Novel Immunoglobulin M Capture Enzyme-Linked Immunosorbent Assay for Diagnosis of Severe Acute Respiratory Syndrome Coronavirus Infection Development of Monoclonal Antibody and Diagnostic Test for Middle East Respiratory Syndrome Coronavirus Using Cell-Free Synthesized Nucleocapsid Antigen


id: cord-289598-t8upoq9a
author: Yoon, Jane C
date: 2020-09-08
url: https://doi.org/10.1093/cid/ciaa1340
doi: 10.1093/cid/ciaa1340
title:
  COVID-19 Prevalence among People Experiencing Homelessness and Homelessness Service Staff during Early Community Transmission in Atlanta, Georgia, April–May 2020

abstract:
  BACKGROUND: In response to reported COVID-19 outbreaks among people experiencing homelessness (PEH) in other U.S. cities, we conducted multiple, proactive, facility-wide testing events for PEH living sheltered and unsheltered and homelessness service staff in Atlanta, Georgia. We describe SARS-CoV-2 prevalence and associated symptoms and review shelter infection prevention and control (IPC) policies METHODS: PEH and staff were tested for SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR) during April 7–May 6, 2020. A subset of PEH and staff was screened for symptoms. Shelter assessments were conducted concurrently at a convenience sample of shelters using a standardized questionnaire RESULTS: Overall, 2,875 individuals at 24 shelters and nine unsheltered outreach events underwent SARS-CoV-2 testing and 2,860 (99.5%) had conclusive test results. SARS-CoV-2 prevalence was 2.1% (36/1,684) among PEH living sheltered, 0.5% (3/628) among PEH living unsheltered, and 1.3% (7/548) among staff. Reporting fever, cough, or shortness of breath in the last week during symptom screening was 14% sensitive and 89% specific for identifying COVID-19 cases compared with RT-PCR. Prevalence by shelter ranged 0%–27.6%. Repeat testing 3–4 weeks later at four shelters documented decreased SARS-CoV-2 prevalence (0%–3.9%). Nine of 24 shelters completed shelter assessments and implemented IPC measures as part of the COVID-19 response CONCLUSIONS: PEH living in shelters experienced higher SARS-CoV-2 prevalence compared with PEH living unsheltered. Facility-wide testing in congregate settings allowed for identification and isolation of COVID-19 cases and is an important strategy to interrupt SARS-CoV-2 transmission


id: cord-290133-4ou7ubb4
title: Rethinking Smallpox
author: Weiss, Martin M.
date: 2004-12-01
url: https://www.ncbi.nlm.nih.gov/pubmed/15578369/
doi: 10.1086/425745
abstract:
  The potential consequences of a competently executed smallpox attack have not been adequately considered by policy makers. The possibility of release of an aerosolized and/or bioengineered virus must be anticipated and planned for. The transmission and infectivity of variola virus are examined. Arguments for and against pre-event vaccination are offered. The likely morbidity and mortality that would ensue from implementation of a mass pre-event vaccination program, within reasonable boundaries, are known. The extent of contagion that could result from an aerosolized release of virus is unknown and may have been underestimated. Pre-event vaccination of first responders is urged, and voluntary vaccination programs should be offered to the public. Two defenses against a vaccine-resistant, engineered variola virus are proposed for consideration. Methisazone, an overlooked drug, is reported to be effective for prophylaxis only. The extent of reduction in the incidence of smallpox with use of this agent is uncertain. It is useless for treatment of clinical smallpox. N-100 respirators (face masks) worn by uninfected members of the public may prevent transmission of the virus.


id: cord-291286-diwigcy9
author: De Schutter, Iris
date: 2011-06-15
url: https://www.ncbi.nlm.nih.gov/pubmed/21628484/
doi: 10.1093/cid/cir235
title:
  Microbiology of Bronchoalveolar Lavage Fluid in Children With Acute Nonresponding or Recurrent Community-Acquired Pneumonia: Identification of Nontypeable Haemophilus influenzae as a Major Pathogen

abstract:
  Background. Precise etiologic diagnosis in pediatric community-acquired pneumonia (CAP) remains challenging. Methods. We conducted a retrospective study of CAP etiology in 2 groups of pediatric patients who underwent flexible bronchoscopy (FOB) with bronchoalveolar lavage (BAL); children with acute nonresponsive CAP (NR-CAP; n = 127) or recurrent CAP (Rec-CAP; n = 123). Procedural measures were taken to limit contamination risk and quantitative bacterial culture of BAL fluid (significance cutoff point, ≥10(4) colony-forming units/mL) was used. Blood culture results, serological test results, nasopharyngeal secretion findings, and pleural fluid culture results were also assessed, where available. Results. An infectious agent was detected in 76.0% of cases. In 51.2% of infections, aerobic bacteria were isolated, of which 75.0%, 28.9%, and 13.3% were Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae, respectively. Most (97.9%) of the H. influenzae strains were nontypeable (NTHi). H. influenzae was detected in 26.0% of NR-CAP cases and 51.2% of Rec-CAP cases, whereas Mycoplasma pneumoniae was the predominant pathogen in the NR-CAP group (accounting for 34.9% of cases) but not in the Rec-CAP group (19.3%). Viruses were found in 30.4% of cases, with respiratory syncytial virus, parainfluenzaviruses, and influenzaviruses detected most frequently. Mixed infections were found in 18.9% of NR-CAP cases and 30.1% of Rec-CAP cases. Conclusions. A variety of microorganisms were isolated with frequent mixed infection. NTHi was one of the major pathogens found, especially in association with recurrent CAP, possibly because of improved detection with the FOB with BAL procedure. This suggests that the burden of pediatric CAP could be reduced by addressing NTHi as a major causative pathogen.


id: cord-291363-re45w37d
author: Sanville, Bradley
date: 2020-03-30
txt: ./txt/cord-291363-re45w37d.txt
cache: ./cache/cord-291363-re45w37d.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32227197/
doi: 10.1093/cid/ciaa347
abstract: nan
summary:
  title: A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States The current novel coronavirus (SARS CoV2) outbreak, which was identified in December 2019 in Wuhan, Hubei, China has spread rapidly causing a significant public health crisis worldwide 1 . Two healthcare workers in contact with the patient at the outside hospital have subsequently tested positive for SARS CoV2. Overall, these reviews note a case fatality rate of 1.40-3.46%, though this may be considerably lower when accounting for a likely large number of mild or asymptomatic patients that were not tested 6, 9, 10 DeWit and colleagues from the NIH, Gilead, and Columbia University successfully treated rhesus macaques against a model of MERS 13 . As noted in a recent editorial, diagnosis becomes even more difficult considering the likelihood of a large number of mild or asymptomatic patients who are not formally identified with a SARS CoV2 infection 18, 19 .

title:
  A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States


id: cord-291726-8670s4st
author: Che, Xiao-yan
date: 2006-07-01
txt: ./txt/cord-291726-8670s4st.txt
cache: ./cache/cord-291726-8670s4st.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16758408/
doi: 10.1086/504943
summary:
  Seventeen serum specimens were collected from 4 index case patients who exhibited recurrence of SARS with laboratory-confirmed SARS-CoV infection in Guangzhou City, China, from 22 December 2003 through 30 January 2004. The findings of these 2 assays had been validated previously with the use of serum specimens obtained from patients with serologically confirmed SARS, and the sensitivity and specificity of the N antigen-capture ELISA were documented [4] [5] [6] . Although none of the 4 index case patients showed evidence of secondary spread of the infection [1] , the direct detection of SARS-CoV N protein by the highly sensitive CIA a Serum samples in a serial 2-fold dilution (from 10-fold to 5120-fold). However, in the 2003-2004 community outbreak of SARS, none of the 4 index case patients with confirmed SARS had severe illness, and they all seemed to have acquired infection with SARS-CoV directly from animals.

title:
  A Patient with Asymptomatic Severe Acute Respiratory Syndrome (SARS) and Antigenemia from the 2003–2004 Community Outbreak of SARS in Guangzhou, China

abstract:
  An asymptomatic case of severe acute respiratory syndrome (SARS) occurred early in 2004, during a community outbreak of SARS in Guangzhou, China. This was the first time that a case of asymptomatic SARS was noted in an individual with antigenemia and seroconversion. The asymptomatic case patient and the second index case patient with SARS in the 2003–2004 outbreak both worked in the same restaurant, where they served palm civets, which were found to carry SARS-associated coronaviruses. Epidemiological information and laboratory findings suggested that the findings for the patient with asymptomatic infection, together with the findings from previously reported serological analyses of handlers of wild animals and the 4 index case patients from the 2004 community outbreak, reflected a likely intermediate phase of animal-to-human transmission of infection, rather than a case of human-to-human transmission. This intermediate phase may be a critical stage for virus evolution and disease prevention.


id: cord-292094-vmsdhccp
author: Mandell, Lionel A.
date: 2007-03-01
txt: ./txt/cord-292094-vmsdhccp.txt
cache: ./cache/cord-292094-vmsdhccp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17278083/
doi: 10.1086/511159
abstract: nan
summary:
  Severity-of-illness scores, such as the CURB-65 criteria (confusion, uremia, respiratory rate, low blood pressure, age 65 years or greater), or prognostic models, such as the Pneumonia Severity Index (PSI), can be used to identify patients with CAP who may be candidates for outpatient treatment. A respiratory fluoroquinolone should be used for penicillin-allergic patients.) Increasing resistance rates have suggested that empirical therapy with a macrolide alone can be used only for the treat-ment of carefully selected hospitalized patients with nonsevere disease and without risk factors for infection with drug-resistant pathogens. Advantages include the high specificity, the ability of some assays to distinguish between influenza A and B, the rapidity with which the results can be obtained, the possibly reduced use of antibacterial agents, and the utility of establishing this diagnosis for epidemiologic purposes, especially in hospitalized patients who may require infection control precautions.

title:
  Infectious Diseases Society of America/American Thoracic Society Consensus Guidelines on the Management of Community-Acquired Pneumonia in Adults


id: cord-292372-kn27ghlv
author: de Chaisemartin, Clément
date: 2020-08-23
txt: ./txt/cord-292372-kn27ghlv.txt
cache: ./cache/cord-292372-kn27ghlv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1223
doi: 10.1093/cid/ciaa1223
summary:
  Instead, this paper takes advantage of a rare nationwide natural experiment that took place in Sweden in 1975, where discontinuation of newborns BCG vaccination led to a dramatic fall of the BCG coverage rate, thus allowing us to estimate the BCG''s effect without the biases associated with cross-country comparisons. found that countries with universal Bacillus Calmette-Guérin (BCG) childhood vaccination policies tend to be less affected by the COVID-19 pandemic, in terms of their number of cases and deaths [7] . In this study, we took advantage of a change in vaccination policy in Sweden to investigate the link between BCG vaccination in infancy and Covid-19 cases, hospitalizations and deaths, using a regression discontinuity approach. For instance, this study estimates the effect of universal BCG vaccination for individuals born around April 1st 1975, who are in their mid-forties during the COVID-19 pandemic, and cannot be generalized to the entire population.

title:
  BCG vaccination in infancy does not protect against COVID-19. Evidence from a natural experiment in Sweden

abstract:
  BACKGROUND: The Bacille Calmette-Guérin (BCG) tuberculosis vaccine has immunity benefits against respiratory infections. Accordingly, it has been hypothesized to have a protective effect against COVID-19. Recent research found that countries with universal BCG childhood vaccination policies tend to be less affected by the COVID-19 pandemic. However, such ecological studies are biased by numerous confounders. Instead, this paper takes advantage of a rare nationwide natural experiment that took place in Sweden in 1975, where discontinuation of newborns BCG vaccination led to a dramatic fall of the BCG coverage rate, thus allowing us to estimate the BCG’s effect without the biases associated with cross-country comparisons. METHODS: Numbers of COVID-19 cases and hospitalizations were recorded for birth cohorts born just before and just after 1975, representing 1,026,304 and 1,018,544 individuals, respectively. We used regression discontinuity to assess the effect of BCG vaccination on Covid-19 related outcomes. This method used on such a large population allows for a high precision that would be hard to achieve using a randomized controlled trial. RESULTS: The odds ratio for Covid-19 cases and Covid-19 related hospitalizations were 1·0005 (CI95: [0·8130-1·1881]) and 1·2046 (CI95: [0·7532-1·6560]), allowing us to reject fairly modest effects of universal BCG vaccination. We can reject with 95% confidence that universal BCG vaccination reduces the number of cases by 19% and the number of hospitalizations by 25%. CONCLUSIONS: While the effect of a recent vaccination must be evaluated, we provide strong evidence that receiving the BCG vaccine at birth does not have a protective effect against COVID-19 among middle-aged individuals.


id: cord-292546-un0blb3w
author: Dandachi, Dima
date: 2020-09-09
txt: ./txt/cord-292546-un0blb3w.txt
cache: ./cache/cord-292546-un0blb3w.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1339
doi: 10.1093/cid/ciaa1339
summary:
  BACKGROUND: People with HIV (PWH) may have numerous risk factors for acquiring Coronavirus disease-19 (COVID-19) and developing severe outcomes, but current data are conflicting. [12] [13] [14] [15] Some of these studies reported that PWH with COVID-19 had similar clinical characteristics and comparable risk of severe disease to the general population. Study variables included patient demographics, HIV-associated variables, underlying medical problems, COVID-19 clinical presentation as reported by patients, laboratory values, treatment, and clinical outcomes. In a multivariable analysis, older age, lower CD4 count, chronic lung disease, hypertension, and high comorbidity burden were significantly associated with severe outcomes (Table 4) . As reported in multiple other studies in people without HIV, we found that age, chronic lung disease, and comorbidity burden were associated with increased rates of severe outcomes. In addition, among HIV-specific factors, we found that a lower CD4 count (< 200 cells/mm3) was associated with poor outcomes, including higher hospitalization rates, lower ICU-free survival, and overall survival.

title:
  Characteristics, Comorbidities, and Outcomes in a Multicenter Registry of Patients with HIV and Coronavirus Disease-19

abstract:
  BACKGROUND: People with HIV (PWH) may have numerous risk factors for acquiring Coronavirus disease-19 (COVID-19) and developing severe outcomes, but current data are conflicting. METHODS: Healthcare providers enrolled consecutively by non-random sampling PWH with lab-confirmed COVID-19, diagnosed at their facilities between April 1st and July 1st, 2020. De-identified data were entered into an electronic Research Electronic Data Capture (REDCap). The primary endpoint was severe outcome, defined as a composite endpoint of intensive care unit (ICU) admission, mechanical ventilation, or death. The secondary outcome was the need for hospitalization. RESULTS: 286 patients were included; the mean age was 51.4 years (SD, 14.4), 25.9% were female, and 75.4% were African-American or Hispanic. Most patients (94.3%) were on antiretroviral therapy (ART), 88.7% had HIV virologic suppression, and 80.8% had comorbidities. Within 30 days of positive SARS-CoV-2 testing, 164 (57.3%) patients were hospitalized, and 47 (16.5%) required ICU admission. Mortality rates were 9.4% (27/286) overall, 16.5% (27/164) among those hospitalized, and 51.5% (24/47) among those admitted to an ICU. The primary composite endpoint occurred in 17.5% (50/286) of all patients and 30.5% (50/164) of hospitalized patients. Older age, chronic lung disease, and hypertension were associated with severe outcomes. A lower CD4 count (<200 cells/mm³) was associated with the primary and secondary endpoints. There was no association between the antiretroviral regimen or lack of viral suppression and predefined outcomes. CONCLUSION: Severe clinical outcomes occurred commonly in PWH and COVID-19. The risk for poor outcomes was higher in those with comorbidities and lower CD4 cell counts, despite HIV viral suppression.


id: cord-294335-qnu19ru5
author: Yousaf, Anna R
date: 2020-07-28
txt: ./txt/cord-294335-qnu19ru5.txt
cache: ./cache/cord-294335-qnu19ru5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1072
doi: 10.1093/cid/ciaa1072
summary:
  We assessed symptoms reported by household contacts on the collection date of their first RT-PCRpositive NP specimen (Figure 1 , Subset A), and categorized symptoms as constitutional (fever, chills, myalgia, or fatigue), upper respiratory (runny nose, nasal congestion, or sore throat), lower respiratory (cough, difficulty breathing, shortness of breath, wheezing, or chest pain), neurologic (headache, loss of taste, or loss of smell), and gastrointestinal (nausea/vomiting, diarrhea, or abdominal pain). We identified and prospectively followed household contacts who were asymptomatic at the time they initially tested positive for SARS-CoV-2 by PCR ( Figure 1 , Subset B) to see if they developed symptoms during the study period. The symptom profiles and demographic characteristics of our cohort of SARS-CoV-2 RT-PCR positive household contacts differ from those described in inpatient populations [3] [4] [5] 12] .

title:
  A prospective cohort study in non-hospitalized household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time

abstract:
  BACKGROUND: Improved understanding of SARS-CoV-2 spectrum of disease is essential for clinical and public health interventions. There are limited data on mild or asymptomatic infections, but recognition of these individuals is key as they contribute to viral transmission. We describe the symptom profiles from individuals with mild or asymptomatic SARS-CoV-2 infection. METHODS: From March 22 to April 22, 2020 in Wisconsin and Utah, we enrolled and prospectively observed 198 household contacts exposed to SARS-CoV-2. We collected and tested nasopharyngeal (NP) specimens by RT-PCR two or more times during a 14-day period. Contacts completed daily symptom diaries. We characterized symptom profiles on the date of first positive RT-PCR test and described progression of symptoms over time. RESULTS: We identified 47 contacts, median age 24 (3-75) years, with detectable SARS-CoV-2 by RT-PCR. The most commonly reported symptoms on the day of first positive RT-PCR test were upper respiratory (n=32, 68%) and neurologic (n=30, 64%); fever was not commonly reported (n=9, 19%). Eight (17%) individuals were asymptomatic at the date of first positive RT-PCR collection; two (4%) had preceding symptoms that resolved and six (13%) subsequently developed symptoms. Children less frequently reported lower respiratory symptoms (age <18: 21%, age 18-49: 60%, age 50+ years: 69%; p=0.03). CONCLUSIONS: Household contacts with lab-confirmed SARS-CoV-2 infection reported mild symptoms. When assessed at a single time-point, several contacts appeared to have asymptomatic infection; however, over time all developed symptoms. These findings are important to inform infection control, contact tracing, and community mitigation strategies.


id: cord-294558-cqa58db8
author: Wang, Yubo
date: 2020-05-22
txt: ./txt/cord-294558-cqa58db8.txt
cache: ./cache/cord-294558-cqa58db8.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa629
doi: 10.1093/cid/ciaa629
summary:
  BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, resulting in the coronavirus disease COVID-19) is highly transmissible among people. METHODS: We identified close contacts of confirmed COVID-19 cases in northeast Chongqing who were RT-PCR+ yet remained asymptomatic throughout their infections. In December 2019 a novel coronavirus, which was later named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused a large outbreak of infectious disease, designated COVID-19. Symptomatic COVID-19 patients and asymptomatic cases are both a source of infection and patients in the incubation period can transmit SARS-CoV-2 to other persons [7] [8] [9] [10] . Epidemiological data collection was achieved by interviewing each patient and their family members, including the dates and times of close contact with (working together, living or gathering) or to exposure individuals from the affected area (not only Wuhan) with confirmed or suspected SARS-CoV-2 infection.

title:
  Characterization of an asymptomatic cohort of SARS-COV-2 infected individuals outside of Wuhan, China

abstract:
  BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, resulting in the coronavirus disease COVID-19) is highly transmissible among people. Asymptomatic infections are also an important source of infection. Here, we aimed to further clarify the epidemiologic and clinical characteristics of asymptomatic SARS-CoV-2 infections. METHODS: We identified close contacts of confirmed COVID-19 cases in northeast Chongqing who were RT-PCR+ yet remained asymptomatic throughout their infections. We stratified this cohort by normal versus abnormal findings on chest CT, and compared the strata regarding comorbidities, demographics, laboratory findings, viral transmission and other factors. RESULTS: Between January and March, 2020, we identified and hospitalized 279 RT-PCR+ contacts of COVID-19 patients. Of these, 63 (23%) remained asymptomatic until discharge; 29 had abnormal and 34 had normal chest CT findings. The mean cohort age was 39.3 years, and 87.3% had no comorbidities. Mean time to diagnosis after close contact with a COVID-19 index patient was 16.0 days (range 1 to 29), and 13.4 days and 18.7 days for those with abnormal and normal CT findings, respectively (p < 0.05). Nine subjects (14.3%) transmitted the virus to others; 4 and 5 were in the abnormal and normal CT strata, respectively. The median length of nucleic acid turning negative in asymptomatic COVID-19 patients was 13 days, compared to 10.4 days in those with normal chest CT (p < 0.05). CONCLUSIONS: A portion of these asymptomatic individuals, with and without abnormal chest CT scans, were capable of transmitting the virus to others. Given the frequency and potential infectiousness of asymptomatic infections, testing of traced contacts is essential. Studies of the impact of treatment on asymptomatic RT-PCR+ individuals on disease progression and transmission should be undertaken.


id: cord-294718-n3gx862b
author: Tam, Patrick C K
date: 2020-05-30
txt: ./txt/cord-294718-n3gx862b.txt
cache: ./cache/cord-294718-n3gx862b.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa673
doi: 10.1093/cid/ciaa673
summary:
  title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) Although RNA has been detected in various clinical samples, no reports to date have documented SARS-CoV-2 in human milk. This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk. The first sampling of human milk occurred five days following maternal symptom onset with no episodes of breastfeeding in those five days prior to collection of the sample. An additional six samples of human milk were collected with one further sample demonstrating detectable SARS-COV-2 RNA (Figure 1 ). These samples continued to have detectable RNA sixty-six days following infant symptom onset (Figure 1 ). To our knowledge, this is the first case of detectable SARS-CoV-2 RNA from human milk in a patient with COVID-19.

title:
  Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19)

abstract:
  SARS-CoV-2 is a novel coronavirus and causative pathogen to the pandemic illness COVID-19. Although RNA has been detected in various clinical samples, no reports to date have documented SARS-CoV-2 in human milk. This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk.


id: cord-294853-8b0s5w4u
author: Nolen, Leisha D
date: 2020-09-05
txt: ./txt/cord-294853-8b0s5w4u.txt
cache: ./cache/cord-294853-8b0s5w4u.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1328
doi: 10.1093/cid/ciaa1328
summary:
  title: Impact of Social Distancing and Travel Restrictions on non-COVID-19 Respiratory Hospital Admissions in Young Children in Rural Alaska Hospitalizations due to non-COVID-19 respiratory illnesses decreased dramatically after social distancing was implemented in a high-risk population in rural Alaska. People in the remote Yukon-Kuskokwim Delta (YKD) region of Alaska have a high burden of respiratory illnesses, with up to ten times the rate of infant hospitalization for pneumonia compared to the general US population [4] and the highest reported rates of infant RSV hospitalization in the United States, reaching 259 per 1,000 We compared the total, ARI, and RSV hospitalization rate in YKD children <3 years in the first 5 months of 2020 to the previous ten respiratory illness seasons. One limitation of our study is the inability to distinguish what proportion of the decline in ARI hospitalizations in YKD children is due to avoidance of care versus a decrease in circulation of respiratory pathogens secondary to the health mandates.

title:
  Impact of Social Distancing and Travel Restrictions on non-COVID-19 Respiratory Hospital Admissions in Young Children in Rural Alaska

abstract:
  Hospitalizations due to non-COVID-19 respiratory illnesses decreased dramatically after social distancing was implemented in a high-risk population in rural Alaska. Our data from the past ten respiratory seasons show that this decline is unprecedented. This demonstrates the potential secondary benefits of implementing social distancing and travel restrictions on respiratory illnesses.


id: cord-295270-6ptaxg74
title: Response to Correspondence: Baricitinib – Impact on COVID-19 Coagulopathy? Jorgensen et. al.
author: Titanji, Boghuma K
date: 2020-08-14
txt: ./txt/cord-295270-6ptaxg74.txt
cache: ./cache/cord-295270-6ptaxg74.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32797226/
doi: 10.1093/cid/ciaa1210
abstract: nan
summary:
  authors: Titanji, Boghuma K; Farley, Monica M; Schinazi, Raymond F; Marconi, Vincent C Baricitinib through its immunomodulatory effects as highlighted by Jorgensen et.al may in fact be beneficial in terms of reducing coagulopathy in patients with COVID-19, which is thought to be primarily mediated by hyper-inflammation and endothelial damage. All of the cohort studies of baricitinib for COVID-19 treatment led to significant decline in inflammatory M a n u s c r i p t markers for patients who received the drug 2,3,8 . Regarding baricitinib, ACTT2 should provide clarity on the VTE issue in the near future and its role in the treatment of COVID-19 in moderate to severe patients. Ruxolitinib in treatment of severe coronavirus disease 2019 (COVID-19): A multicenter, single-blind, randomized controlled trial Use of Baricitinib in patients with moderate and severe COVID-19 Vincent Marconi and Raymond F Schinazi are partially funded by -Emory University Center for AIDS Research (AI050409).


id: cord-295525-emrwcx0m
title: Consistent Detection of 2019 Novel Coronavirus in Saliva
author: To, Kelvin Kai-Wang
date: 2020-02-12
txt: ./txt/cord-295525-emrwcx0m.txt
cache: ./cache/cord-295525-emrwcx0m.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32047895/
doi: 10.1093/cid/ciaa149
summary:
  The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. We have previously demonstrated that saliva has a high concordance rate of greater than 90% with nasopharyngeal specimens in the detection of respiratory viruses, including coronaviruses [5, 6] . A patient is considered to have laboratory-confirmed infection if 2019-nCoV was detected in their nasopharyngeal or sputum specimens. For patient K, the first saliva specimen collected on the day of hospital admission tested negative. The use of saliva is preferred over nasopharyngeal or oropharyngeal specimens for serial viral load monitoring because this would reduce the discomfort to the patient and reduce the health hazards to healthcare workers during repeated sampling. Our results have demonstrated the potential for saliva to be a noninvasive specimen type for the diagnosis and viral load monitoring of 2019-nCoV.

abstract:
  The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. Serial saliva viral load monitoring generally showed a declining trend. Live virus was detected in saliva by viral culture. Saliva is a promising noninvasive specimen for diagnosis, monitoring, and infection control in patients with 2019-nCoV infection.


id: cord-295940-siy32dj7
author: Saito, Makoto
date: 2020-04-02
txt: ./txt/cord-295940-siy32dj7.txt
cache: ./cache/cord-295940-siy32dj7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32241023/
doi: 10.1093/cid/ciaa377
abstract: nan
summary:
  title: Gargle lavage as a safe and sensitive alternative to swab samples to diagnose COVID-19: a case report in Japan Moreover, the sensitivity for virus detection is low with these swabs; viral load is reportedly higher in sputum samples. 3 Here we report a case in which gargle lavage samples yielded a positive PCR result. Additional gargle lavage samples and oropharyngeal swabs were collected and tested on Days 8 and 9 and found to be positive, with a slightly higher amount of viral genome in the gargle lavage sample (Supplement Figure 3) . For other respiratory pathogens, gargle lavage samples have been reported to be more sensitive than throat swabs. 1 Gargle lavage thus offers a safer and possibly more sensitive alternative or additional option for diagnosing COVID-19. SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Comparison of gargle samples and throat swab samples for the detection of respiratory pathogens

title:
  Gargle lavage as a safe and sensitive alternative to swab samples to diagnose COVID-19: a case report in Japan


id: cord-296588-q2716lda
title: Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19
author: Hanson, Kimberly E
date: 2020-06-16
txt: ./txt/cord-296588-q2716lda.txt
cache: ./cache/cord-296588-q2716lda.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32556191/
doi: 10.1093/cid/ciaa760
summary:
  OBJECTIVE: The IDSA''s goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. It is important to note as well, that not all specimens were collected from the same patient at the same time, the time of collection from symptom onset was not provided in all studies and various approaches for establishing SARS-CoV-2 positivity were used to define positive results (i.e., clinical evaluation, detection different gene targets versus nucleic acid sequencing). While NP swab collection is widely used and the primary specimen type for commercial direct SARS-CoV-2 test platforms, based on current available evidence, clinical practice, and availability of testing resources, the panel believes there are comparable alternative methods for sampling the nasal passages.

abstract:
  BACKGROUND: Accurate molecular diagnostic tests are necessary for confirming a diagnosis of coronavirus disease 2019 (COVID-19). Direct detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acids in respiratory tract specimens informs patient, healthcare institution and public health level decision-making. The numbers of available SARS-CoV-2 nucleic acid detection tests are rapidly increasing, as is the COVID-19 diagnostic literature. Thus, the Infectious Diseases Society of America (IDSA) recognized a significant need for frequently updated systematic reviews of the literature to inform evidence-based best practice guidance. OBJECTIVE: The IDSA’s goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. In addition, we provide a conceptual framework for understanding molecular diagnostic test performance, discuss the nuance of test result interpretation in a variety of practice settings, and highlight important unmet research needs in the COVID-19 diagnostic testing space. METHODS: IDSA convened a multidisciplinary panel of infectious diseases clinicians, clinical microbiologists, and experts in systematic literature review to identify and prioritize clinical questions and outcomes related to the use of SARS-CoV-2 molecular diagnostics. Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to assess the certainty of evidence and make testing recommendations. RESULTS: The panel agreed on 15 diagnostic recommendations. CONCLUSIONS: Universal access to accurate SARS-CoV-2 nucleic acid testing is critical for patient care, hospital infection prevention and the public response to the COVID-19 pandemic. Information on the clinical performance of available tests is rapidly emerging, but the quality of evidence of the current literature is considered low to very low. Recognizing these limitations, the IDSA panel weighed available diagnostic evidence and recommends nucleic acid testing for all symptomatic individuals suspected of having COVID-19. In addition, testing is recommended for asymptomatic individuals with known or suspected contact with a COVID-19 case. Testing asymptomatic individuals without known exposure is suggested when the results will impact isolation/quarantine/personal protective equipment (PPE) usage decisions, dictate eligibility for surgery, or inform administration of immunosuppressive therapy. Ultimately, prioritization of testing will depend on institutional-specific resources and the needs of different patient populations.


id: cord-296631-43z3ee8m
title: ACE inhibitors/ARB use and COVID-19. Time to change practice or keep gathering data?
author: de Feria, Alejandro
date: 2020-07-04
txt: ./txt/cord-296631-43z3ee8m.txt
cache: ./cache/cord-296631-43z3ee8m.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa819
doi: 10.1093/cid/ciaa819
abstract: nan
summary:
  This mechanism of entry, in combination with the findings of the previously mentioned risk factors, raised concerns that angiotensin-converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARBs) could increase both the susceptibility and severity of SARS CoV-2 infection. An international, multicenter study which included electronic records from 169 hospitals in 11 countries on three continents again confirmed that advanced age (>65), heart failure, coronary disease, and hypertension (among other factors) increased risk for in hospital mortality with COVID-19, but ACEi/ARB therapy showed no harm [4] . In contrast to these findings, early studies out of China suggested that ARB therapy may improve clinical outcomes in COVID-19 infection [5, 6] . The current study is unique in that it focuses on patients with "severe COVID" disease and found that chronic ACE inhibitor and ARB use was associated with an increased risk of acute kidney injury, as well as a signal for a dosage effect.


id: cord-297239-or6h6p9p
title: Influenza Among Afebrile and Vaccinated Healthcare Workers
author: Ridgway, Jessica P.
date: 2015-06-01
txt: ./txt/cord-297239-or6h6p9p.txt
cache: ./cache/cord-297239-or6h6p9p.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25733370/
doi: 10.1093/cid/civ163
summary:
  To prevent transmission of influenza from healthcare workers (HCWs) to patients, many hospitals exclude febrile HCWs from working, but allow afebrile HCWs with respiratory symptoms to have contact with patients. During the 2013–2014 influenza season at our hospital, an influenza-positive HCW with respiratory symptoms but no fever was linked to a case of possible healthcare-associated influenza in a patient. In accordance with the CDC''s guidelines, our hospital''s routine sick policy at the time prohibited febrile HCWs from working, but not those with respiratory symptoms in the absence of fever. Given the risk of influenza transmission to patients from afebrile employees with influenza, we implemented a temporary mandatory influenza-testing policy for all HCWs with respiratory symptoms. To prevent healthcare-associated influenza, hospitals should consider more stringent infection control measures for HCWs with respiratory symptoms, even if no fever is present.

abstract:
  Background. To prevent transmission of influenza from healthcare workers (HCWs) to patients, many hospitals exclude febrile HCWs from working, but allow afebrile HCWs with respiratory symptoms to have contact with patients. During the 2013–2014 influenza season at our hospital, an influenza-positive HCW with respiratory symptoms but no fever was linked to a case of possible healthcare-associated influenza in a patient. Therefore, we implemented a temporary policy of mandatory influenza testing for HCWs with respiratory symptoms. Methods. From 3 January through 28 February 2014, we tested HCWs with respiratory symptoms for influenza and other respiratory pathogens by polymerase chain reaction of flocked nasopharyngeal swabs. HCWs also reported symptoms and influenza vaccination status, and underwent temperature measurement. We calculated the proportion of influenza-positive HCWs with fever and prior influenza vaccination. Results. Of 449 HCWs, 243 (54%) had a positive test for any respiratory pathogen; 34 (7.6%) HCWs tested positive for influenza. An additional 7 HCWs were diagnosed with influenza by outside physicians. Twenty-one (51.2%) employees with influenza had fever. Among influenza-infected HCWs, 20 had previously received influenza vaccination, 18 had declined the vaccine, and 3 had unknown vaccination status. There was no significant difference in febrile disease among influenza-infected employees who had received the influenza vaccine and those who had not received the vaccine (45% vs 61%; P = .32). Conclusions. Nearly half of HCWs with influenza were afebrile prior to their diagnosis. HCWs with respiratory symptoms but no fever may pose a risk of influenza transmission to patients and coworkers.


id: cord-297612-swc2pitd
author: Nosyk, Bohdan
date: 2020-04-27
txt: ./txt/cord-297612-swc2pitd.txt
cache: ./cache/cord-297612-swc2pitd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32339245/
doi: 10.1093/cid/ciaa501
summary:
  title: Contact tracing for COVID-19: An opportunity to reduce health disparities and End the HIV/AIDS Epidemic in the US We argue that COVID-19 contact tracing may provide a unique opportunity to also conduct widespread HIV testing, among other health promotion activities. M a n u s c r i p t Massive SARS-CoV2 testing and contact tracing at a scale and speed never before seen have been proposed as critical components of a COVID-19 public health strategy that could, in theory, safely allow us to relax social distancing measures and begin to bring back the world we left behind before a cure or effective vaccine is delivered. Aside from the potentially profound health benefits of a combination implementation approach, pairing COVID-19 contact tracing with testing for HIV may serve to offset the immense costs of such an approach.

title:
  Contact tracing for COVID-19: An opportunity to reduce health disparities and End the HIV/AIDS Epidemic in the US

abstract:
  SARS-CoV2 testing and contact tracing have been proposed as critical components of a safe and effective COVID-19 public health strategy. We argue that COVID-19 contact tracing may provide a unique opportunity to also conduct widespread HIV testing, among other health promotion activities.


id: cord-298539-yncda1us
title: New measures for COVID-19 response: a lesson from the Wenzhou experience
author: Ruan, Linhui
date: 2020-04-03
txt: ./txt/cord-298539-yncda1us.txt
cache: ./cache/cord-298539-yncda1us.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa386
doi: 10.1093/cid/ciaa386
summary:
  This is the result of the more than 90,000 people who return to Wenzhou from Wuhan during On January 17 when the first case of COVID-19 was confirmed, the Wenzhou New Coronavirus Pneumonia Prevention and Control Committee launched emergency epidemic prevention and control measures, which in general consisted of two phases. The main measures included (1) centralizing the confirmed and suspected patients in designated hospitals for treatment, (2) identifying and investigating all returnees from Wuhan using a big data network and persuading them to undergo 14-day home quarantine, and (3) centralizing and medically observing individuals who had been exposed to a confirmed COVID-19 patient. However, the numbers of new cases in these cities were meaningfully reduced after implementation of most aggressive social distancing and quarantining measures, which was similar to Wenzhou second-phase measures on February 10 ( Figure 1A) .

abstract:
  As the outbreak of COVID-19 has spread globally, determining how to prevent the spread is of paramount importance. We reported the effectiveness of different responses of four affected cities in preventing the COVID-19 spread. We expect Wenzhou anti-COVID-19 measures may provide experience for cities around the world that are experiencing this epidemic.


id: cord-299274-gnbp7so5
author: Bodkin, Claire
date: 2020-06-08
txt: ./txt/cord-299274-gnbp7so5.txt
cache: ./cache/cord-299274-gnbp7so5.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32511704/
doi: 10.1093/cid/ciaa743
summary:
  title: Pandemic Planning in Homeless Shelters: A pilot study of a COVID-19 testing and support program to mitigate the risk of COVID-19 outbreaks in congregate settings We tested 104 residents and 141 staff for COVID-19 who failed daily symptom screening in homeless shelters in Hamilton, Canada. The objective of this report is to describe our experience with shelter facility restructuring, daily symptom screening and rapid testing to mitigate the risk of COVID-19 in the homeless shelter setting in Hamilton, Ontario, Canada. Between March 17 and April 30, 2020, COVID-19 testing was performed on all shelter residents and staff who failed daily screening for potential COVID-19 related symptoms as well as staff and residents identified as close contacts of positive cases. We have thus far been successful in preventing large outbreaks in the shelter setting despite identifying positive cases in both staff and residents.

title:
  Pandemic Planning in Homeless Shelters: A pilot study of a COVID-19 testing and support program to mitigate the risk of COVID-19 outbreaks in congregate settings

abstract:
  We tested 104 residents and 141 staff for COVID-19 who failed daily symptom screening in homeless shelters in Hamilton, Canada. We detected one resident (1%), seven staff (5%) and one case of secondary spread. Shelter restructuring to allow physical distancing, testing and isolation can decrease outbreaks in shelters.


id: cord-299359-s8j78naz
author: Sundaram, Maria E.
date: 2013-09-15
txt: ./txt/cord-299359-s8j78naz.txt
cache: ./cache/cord-299359-s8j78naz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/23748138/
doi: 10.1093/cid/cit379
summary:
  We investigated the association between influenza infection, vaccination, and detection of other respiratory viruses among children <5 years old and adults ≥50 years old with acute respiratory illness who participated in seasonal studies of influenza vaccine effectiveness. This could theoretically contribute to overestimation of true VE (ie, bias away from the null); therefore, a key assumption of the test-negative control design of influenza vaccine effectiveness studies is that the proportion of noninfluenza viral illness does not differ by influenza vaccination status [9] . The goals of this study were to determine if influenza vaccination is associated with detection of noninfluenza respiratory viruses and to determine if vaccine effectiveness estimates differ when different control groups are used in the analysis. For participants in these age groups, multiplex reverse transcription polymerase chain reaction (RT-PCR) testing was subsequently performed to detect other respiratory viruses, providing an opportunity to investigate the relationship between influenza vaccination and infection with other viral pathogens.

title:
  Influenza Vaccination Is Not Associated With Detection of Noninfluenza Respiratory Viruses in Seasonal Studies of Influenza Vaccine Effectiveness

abstract:
  Background. The test-negative control study design is the basis for observational studies of influenza vaccine effectiveness (VE). Recent studies have suggested that influenza vaccination increases the risk of noninfluenza respiratory virus infection. Such an effect could create bias in VE studies using influenza-negative controls. We investigated the association between influenza infection, vaccination, and detection of other respiratory viruses among children <5 years old and adults ≥50 years old with acute respiratory illness who participated in seasonal studies of influenza vaccine effectiveness. Methods. Nasal/nasopharyngeal samples collected from 2004–2005 through 2009–2010 were tested for 19 respiratory virus targets using a multiplex reverse-transcription polymerase chain reaction (RT-PCR) platform. Vaccination status was determined using a validated registry. Adjusted odds ratios for influenza and vaccination status were calculated using three different control groups: influenza-negative, other respiratory virus positive, and pan-negative. Results. Influenza was detected in 12% of 2010 children and 20% of 1738 adults. Noninfluenza respiratory viruses were detected in 70% of children and 38% of adults without influenza. The proportion vaccinated did not vary between virus-positive controls and pan-negative controls in children (P = .62) or adults (P = .33). Influenza infection was associated with reduced odds of vaccination, but adjusted odds ratios differed by no more than 0.02 when the analysis used influenza-negative or virus-positive controls. Conclusions. Influenza vaccination was not associated with detection of noninfluenza respiratory viruses. Use of influenza-negative controls did not generate a biased estimate of vaccine effectiveness due to an effect of vaccination on other respiratory virus infections.


id: cord-299499-66qh3r75
title: Reconsidering assumptions of adolescent and young adult SARS-CoV-2 transmission dynamics
author: Guilamo-Ramos, Vincent
date: 2020-09-07
txt: ./txt/cord-299499-66qh3r75.txt
cache: ./cache/cord-299499-66qh3r75.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32894747/
doi: 10.1093/cid/ciaa1348
summary:
  In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adult specific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescents and young adults (AYA), who are between the ages of 10 and 24 years, account for approximately 20% of the total population in the United States (US), but the extent to which AYA contribute to forward transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not fully understood. In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adultspecific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescent and young adult-specific data Furthermore, behavioral factors unique to AYA may increase the risk of forward transmission of SARS-CoV-2 relative to both younger children and older adults.

abstract:
  Evidence regarding the important role of adolescents and young adults (AYA) in accelerating and sustaining coronavirus disease 2019 (COVID-19) outbreaks is growing. Furthermore, data suggest two known factors that contribute to high severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmissibility—presymptomatic transmission and asymptomatic case presentations—may be amplified in AYA. However, AYA have not been prioritized as a key population in the public health response to the COVID-19 pandemic. Policy decisions that limit public health attention on AYA and are driven by the assumption of insignificant forward transmission from AYA pose a risk to inadvertently reinvigorate local transmission dynamics. In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adult specific considerations for future COVID-19 control measures, and provide applied programmatic suggestions.


id: cord-299720-f0ny4ur5
author: Kim, Seung Woo
date: 2017-03-01
txt: ./txt/cord-299720-f0ny4ur5.txt
cache: ./cache/cord-299720-f0ny4ur5.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27940937/
doi: 10.1093/cid/ciw768
summary:
  title: Risk Factors for Transmission of Middle East Respiratory Syndrome Coronavirus Infection During the 2015 Outbreak in South Korea Transmission heterogeneity was observed during the 2015 Korean outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Transmission heterogeneity was a significant characteristic of the 2015 South Korean outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection [1] . Epidemiological reports from the outbreak were evaluated to collect data regarding basic demographic characteristics, medical history, MERS-CoV exposure, symptoms and their onset date(s), sampling date(s), contact history, and post-exposure infection control. In the univariate analyses, transmission was associated with underlying respiratory disease, Ct value, interval from symptom onset to diagnosis, number of contacts, and pre-isolation hospitalization or ER visits. It appears that both host infectivity and the number of contacts influenced MERS-CoV transmission, whereas super-spreading events were mostly associated with a greater likelihood of encountering other people under diverse environmental conditions.

title:
  Risk Factors for Transmission of Middle East Respiratory Syndrome Coronavirus Infection During the 2015 Outbreak in South Korea

abstract:
  BACKGROUND. Transmission heterogeneity was observed during the 2015 Korean outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Only 22 of 186 cases transmitted the infection, and 5 super-spreading events caused 150 transmissions. We investigated the risk factors for MERS-CoV transmission. METHODS. Epidemiological reports were used to classify patients as nonspreaders, spreaders, or those associated with a super-spreading event (5 or more transmissions). Logistic regression analyses were used to evaluate the factors for MERS-CoV transmission. RESULTS. Compared to nonspreaders, spreaders exhibited a longer interval from symptom onset to isolation (7 days vs 3 days) and more frequent pre-isolation pneumonia diagnoses (68.2% vs 17.1%). Spreaders also exhibited higher values for pre-isolation contacts (149 vs 17.5), pre-isolation hospitalization (68.2% vs 16.5%), and emergency room (ER) visits (50% vs 7.3%). Spreaders exhibited lower cycle thresholds for the upE and ORF1a genes (22.7 vs 27.2 and 23.7 vs 27.9, respectively). In multivariate analysis, transmission was independently associated with the cycle threshold (odds ratio [OR], 0.84; 95% confidence interval [CI], 0.75–0.96) and pre-isolation hospitalization or ER visits (OR, 6.82; 95% CI, 2.06–22.84). The super-spreading events exhibited higher values for pre-isolation contacts (777 vs 78), pre-isolation ER visits (100% vs 35.3%), and doctor shopping (100% vs 47.1%) compared to non-super-spreading events. CONCLUSIONS. These findings indicate that transmission is determined by host infectivity and the number of contacts, whereas super-spreading events were determined by the number of contacts and hospital visits. These relationships highlight the importance of rapidly enforcing infection control measures to prevent outbreaks.


id: cord-300013-6m1f4q5r
author: Brahier, Thomas
date: 2020-09-17
txt: ./txt/cord-300013-6m1f4q5r.txt
cache: ./cache/cord-300013-6m1f4q5r.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32940646/
doi: 10.1093/cid/ciaa1408
summary:
  This study describes and compares LUS characteristics between patients with different clinical outcomes METHODS: Prospective observational study of PCR-confirmed COVID-19 adults with symptoms of lower respiratory tract infection in the emergency department (ED) of Lausanne University Hospital. We describe and compare early LUS findings (acquired within 24hours of presentation to the ED) between patient groups based on their outcome at 7 days after inclusion: 1) outpatients, 2) hospitalised and 3) intubated/death. Median normalized LUS score had a good level of discrimination between outpatients and others with area under the ROC of 0.80 (95% CI 0.68-0.92) CONCLUSIONS: Systematic LUS has potential as a reliable, cheap and easy-to-use triage tool for the early risk stratification in COVID-19 patients presenting in EDs Despite the potential of LUS as a cheap, portable and accessible point-of-care triage tool in acute respiratory disease (especially in low resource settings), a multinational consensus recently stated that the lack of studies limited specific recommendations for the management of COVID-19 patients (27) .

title:
  Lung ultrasonography for risk stratification in patients with COVID-19: a prospective observational cohort study

abstract:
  BACKGROUND: Point-of-care lung ultrasound (LUS) is a promising pragmatic risk stratification tool in COVID-19. This study describes and compares LUS characteristics between patients with different clinical outcomes METHODS: Prospective observational study of PCR-confirmed COVID-19 adults with symptoms of lower respiratory tract infection in the emergency department (ED) of Lausanne University Hospital. A trained physician recorded LUS images using a standardized protocol. Two experts reviewed images blinded to patient outcome. We describe and compare early LUS findings (acquired within 24hours of presentation to the ED) between patient groups based on their outcome at 7 days after inclusion: 1) outpatients, 2) hospitalised and 3) intubated/death. Normalized LUS score was used to discriminate between groups RESULTS: Between March 6 and April 3 2020, we included 80 patients (17 outpatients, 42 hospitalized and 21 intubated/dead). 73 patients (91%) had abnormal LUS (70% outpatients, 95% hospitalised and 100% intubated/death; p=0.003). The proportion of involved zones was lower in outpatients compared with other groups (median 30% [IQR 0-40%], 44% [31-70%] and 70% [50-88%], p<0.001). Predominant abnormal patterns were bilateral and multifocal spread thickening of the pleura with pleural line irregularities (70%), confluent B lines (60%) and pathologic B lines (50%). Posterior inferior zones were more often affected. Median normalized LUS score had a good level of discrimination between outpatients and others with area under the ROC of 0.80 (95% CI 0.68-0.92) CONCLUSIONS: Systematic LUS has potential as a reliable, cheap and easy-to-use triage tool for the early risk stratification in COVID-19 patients presenting in EDs


id: cord-300411-ppcdkfxq
author: Xu, Xiao-Ke
date: 2020-06-18
txt: ./txt/cord-300411-ppcdkfxq.txt
cache: ./cache/cord-300411-ppcdkfxq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32556265/
doi: 10.1093/cid/ciaa790
summary:
  title: Reconstruction of Transmission Pairs for novel Coronavirus Disease 2019 (COVID-19) in mainland China: Estimation of Super-spreading Events, Serial Interval, and Hazard of Infection METHODS: A unique database with detailed demographic characteristics, travel history, social relationships, and epidemiological timelines for 1,407 transmission pairs that formed 643 transmission clusters in mainland China was reconstructed from 9,120 COVID-19 confirmed cases reported during January 15 February 29, 2020. CONCLUSIONS: Non-negligible frequency of super-spreading events, short serial intervals, and a higher risk of being infected outside of households for male people of working age indicate a significant barrier to the identification and management of COVID-19 cases, which requires enhanced non-pharmaceutical interventions to mitigate this pandemic. We have built a line-list database with detailed demographic information, travel history, epidemiological timelines, and social relationships for 1,407 transmission pairs that formed 643 transmission clusters in mainland China outside Hubei Province.

title:
  Reconstruction of Transmission Pairs for novel Coronavirus Disease 2019 (COVID-19) in mainland China: Estimation of Super-spreading Events, Serial Interval, and Hazard of Infection

abstract:
  BACKGROUND: Knowledge on the epidemiological features and transmission patterns of COVID-19 is accumulating. Detailed line-list data with household settings can advance the understanding of COVID-19 transmission dynamics. METHODS: A unique database with detailed demographic characteristics, travel history, social relationships, and epidemiological timelines for 1,407 transmission pairs that formed 643 transmission clusters in mainland China was reconstructed from 9,120 COVID-19 confirmed cases reported during January 15 - February 29, 2020. Statistical model fittings were used to identify the super-spreaders and estimate serial interval distributions. Age and gender-stratified hazard of infection were estimated for household versus non-household transmissions. RESULTS: There were 34 primary cases identified as super-spreaders, with 5 super-spreading events occurred within households. Mean and standard deviation of serial intervals were estimated as 5.0 (95% CrI: 4.4, 5.5) and 5.2 (95% CrI: 4.9, 5.7) days for household transmissions and 5.2 (95% CrI: 4.6, 5.8) and 5.3 (95% CrI: 4.9, 5.7) days for non-household transmissions, respectively. Hazard of being infected outside of households is higher for age between 18 and 64 years, whereas hazard of being infected within households is higher for young and old people. CONCLUSIONS: Non-negligible frequency of super-spreading events, short serial intervals, and a higher risk of being infected outside of households for male people of working age indicate a significant barrier to the identification and management of COVID-19 cases, which requires enhanced non-pharmaceutical interventions to mitigate this pandemic.


id: cord-300550-l28tadhn
title: Olfactory and Gustatory Dysfunction in Coronavirus Disease 19 (COVID-19)
author: Luers, Jan C
date: 2020-05-01
txt: ./txt/cord-300550-l28tadhn.txt
cache: ./cache/cord-300550-l28tadhn.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa525
doi: 10.1093/cid/ciaa525
summary:
  In this cross-sectional study, two-thirds of European patients with polymerase chain reaction confirmed COVID-19 reported olfactory and gustatory dysfunction, indicating the significance of this history in the early diagnostics. First of all, patients were asked for the onset of fever, cough, sore throat, rhinitis, muscle aches, headache, diarrhea, reduced olfaction, and a reduced sense of taste during COVID-19. To investigate factors related to reduced olfaction as well as to a reduced sense of taste two general linear models were used with explanatory variables of age, gender, TNSS, fever, cough, sore throat, rhinitis, and headache, respectively. In addition, fever, cough, sore throat, rhinitis, headache, and TNSS were also not associated with reduced olfaction or reduced sense of taste (p ≥ 0.05, respectively). Our study shows for the first time that both olfactory and gustatory dysfunction is very common in COVID-19 patients, with olfactory dysfunction even leveling the symptom ''cough'' at > 70%.

abstract:
  Coronavirus-disease-2019 (COVID-19) caused by the severe-acute-respiratory-syndrome-coronavirus-2 (SARS-CoV-2) shows a rapid spread over-the-world. Given scarce resources, non-laboratory diagnostics is crucial. In this cross-sectional study, two-thirds of European patients with polymerase chain reaction confirmed COVID-19 reported olfactory and gustatory dysfunction, indicating the significance of this history in the early diagnostics.


id: cord-301066-62qe4fb0
author: Chiu, Susan S.
date: 2005-06-15
txt: ./txt/cord-301066-62qe4fb0.txt
cache: ./cache/cord-301066-62qe4fb0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15909257/
doi: 10.1086/430301
summary:
  In 2001 and 2002, we performed prospective clinical and virological studies of children (age, р18 years) with acute respiratory tract infection who were admitted to Queen Mary Hospital (Hong Kong, China). We studied a systematic sample of children (age, р18 years) with acute respiratory infection admitted to Queen Mary Hospital during the period from August 2001 to March 2002. One child with HCoV-NL63 upper respiratory tract infection had positive results of only the consensus primer PCR, so no viral load could be measured. We documented that human coronavirus infection was a significant cause of hospitalization for children aged р18 years, accounting for 4.4% of all admissions for acute respiratory infections. A previous study showed that 8.2% of children aged !18 months who were admitted to a Chicago, Illinois, hospital with lower respiratory tract diseases had serological evidence of HCoV-229E or HCoV-OC43 infection [13] .

title:
  Human Coronavirus NL63 Infection and Other Coronavirus Infections in Children Hospitalized with Acute Respiratory Disease in Hong Kong, China

abstract:
  Background. Human coronavirus NL63 (HCoV-NL63) is a recently discovered human coronavirus found to cause respiratory illness in children and adults that is distinct from the severe acute respiratory syndrome (SARS) coronavirus and human coronaviruses 229E (HCoV-229E) and OC43 (HCoV-OC43). Methods. We investigated the role that HCoV-NL63, HCoV-OC43, and HCoV-229E played in children hospitalized with fever and acute respiratory symptoms in Hong Kong during the period from August 2001 through August 2002. Results. Coronavirus infections were detected in 26 (4.4%) of 587 children studied; 15 (2.6%) were positive for HCoV-NL63, 9 (1.5%) were positive for HCoV-OC43, and 2 (0.3%) were positive for HCoV-229E. In addition to causing upper respiratory disease, we found that HCoV-NL63 can present as croup, asthma exacerbation, febrile seizures, and high fever. The mean age (± standard deviation [SD]) of the infected children was 30.7 ± 19.8 months (range, 6–57 months). The mean maximum temperature (±SD) for the 12 children who were febrile was 39.3°C ± 0.9°C, and the mean total duration of fever (±SD) for all children was 2.6 ± 1.2 days (range, 1–5 days). HCoV-NL63 infections were noted in the spring and summer months of 2002, whereas HCoV-OC43 infection mainly occurred in the fall and winter months of 2001. HCoV-NL63 viruses appeared to cluster into 2 evolutionary lineages, and viruses from both lineages cocirculated in the same season. Conclusions. HCoV-NL63 is a significant pathogen that contributes to the hospitalization of children, and it was estimated to have caused 224 hospital admissions per 100,000 population aged ⩽6 years each year in Hong Kong.


id: cord-303240-tv1ta3z5
author: Althoff, Keri N
date: 2020-06-11
txt: ./txt/cord-303240-tv1ta3z5.txt
cache: ./cache/cord-303240-tv1ta3z5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa757
doi: 10.1093/cid/ciaa757
abstract: nan
summary:
  M a n u s c r i p t As the pandemic in the US continues to evolve, data from contact tracing can continue to inform our understanding about SARS-CoV-2 transmission and guide the public health response. Contact tracing that includes home-based molecular and/or serologic specimen collection to trigger isolation and quarantine may be especially critical when both testing and physical distancing are necessary to achieve the public health goals of epidemic control and mitigation of community transmission. "re-opening"), and test and trace strategies will again be deployed to facilitate epidemic control and interruption of SARS-CoV-2 transmission via isolation and quarantine. Test and trace initiatives will yield equally important information in the current phase of the epidemic as communities begins to "re-open." The contact tracers who will continue to log endless hours to protect the health of the population against COVID-19, and subsequently the stability of our healthcare systems, should be supported and commended.

title:
  Contact tracing: Essential to the public health response and our understanding of the epidemiology of COVID-19


id: cord-303330-zh8wzza5
author: Magleby, Reed
date: 2020-06-30
txt: ./txt/cord-303330-zh8wzza5.txt
cache: ./cache/cord-303330-zh8wzza5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa851
doi: 10.1093/cid/ciaa851
summary:
  In two studies of hospitalized patients in China, those with severe presentations of COVID-19 had higher viral loads than those with mild presentations, but the impact of SARS-CoV-2 viral load on the risk of intubation or death was not evaluated [10, 11] . We hypothesized that assessing SARS-CoV-2 viral load by analyzing Ct values from an initial NP swab sample could be a clinically valuable tool to identify patients at highest risk of intubation and death and provide insights into the pathogenesis of COVID-19. We therefore conducted this retrospective analysis of SARS-CoV-2 viral loads on admission, clinical presentations, and outcomes at two affiliated New York City hospitals using a high-throughput RT-PCR assay. In conclusion, we found that admission SARS-CoV-2 viral loads, as determined by Ct values that are generated with standard-of-care diagnostic assays, are independently associated with intubation and death among hospitalized patients with COVID-19.

title:
  Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019

abstract:
  BACKGROUND: Patients hospitalized with coronavirus disease 2019 (COVID-19) frequently require mechanical ventilation and have high mortality rates, but the impact of viral burden on these outcomes is unknown. METHODS: We conducted a retrospective cohort study of patients hospitalized with COVID-19 from March 30 to April 30, 2020 at two hospitals in New York City. SARS-CoV-2 viral load was assessed using cycle threshold (Ct) values from a reverse transcription-polymerase chain reaction assay applied to nasopharyngeal swab samples. We compared patient characteristics and outcomes among patients with high, medium, and low admission viral loads and assessed whether viral load was independently associated with risk of intubation and in-hospital mortality. RESULTS: We evaluated 678 patients with COVID-19. Higher viral load was associated with increased age, comorbidities, smoking status, and recent chemotherapy. In-hospital mortality was 35.0% with a high viral load (Ct<25; n=220), 17.6% with a medium viral load (Ct 25-30; n=216), and 6.2% with a low viral load (Ct>30; n=242; P<0.001). The risk of intubation was also higher in patients with a high viral load (29.1%), compared to those with a medium (20.8%) or low viral load (14.9%; P<0.001). High viral load was independently associated with mortality (adjusted odds ratio [aOR] 6.05; 95% confidence interval [CI]: 2.92-12.52; P<0.001) and intubation (aOR 2.73; 95% CI: 1.68-4.44; P<0.001) in multivariate models. CONCLUSIONS: Admission SARS-CoV-2 viral load among hospitalized patients with COVID-19 independently correlates with the risk of intubation and in-hospital mortality. Providing this information to clinicians could potentially be used to guide patient care.


id: cord-303603-4mi64bgm
author: Martínez-Urbistondo, Diego
date: 2020-07-04
txt: ./txt/cord-303603-4mi64bgm.txt
cache: ./cache/cord-303603-4mi64bgm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32621739/
doi: 10.1093/cid/ciaa910
abstract: nan
summary:
  title: Early Combination of Tocilizumab and Corticosteroids: An Upgrade in Anti-inflammatory Therapy for Severe Coronavirus Disease (COVID) In our experience, the early administration of corticosteroids associated to tocilizumab, according to the previously published recommendations by the Spanish Ministry of Health [6] , may solve this high failure rate. In the HM Sanchinarro Hospital, a 200 bed teaching institution, we consecutively and ambispectively collected the outcome of 136 patients who received tocilizumab plus corticosteroids to treat severe COVID, defined as a SpO2/FiO2 <325 with bilateral pneumonia and a clinical diagnosis of infection by SARS-CoV-2. Generalized linear and Cox regression models, adjusted by age, sex, interaction between age and sex, CCI, time from onset to admission, dose of corticosteroids and tocilizumab and C-reactive protein and D-dimer levels at anti-inflammatory therapy administration, showed benefit in the use of ET in COVID patients (Relative Risk, 0.18, P = .01, and Hazard Ratio, 0.13, P = .01, respectively).

title:
  Early Combination of Tocilizumab and Corticosteroids: An Upgrade in Anti-inflammatory Therapy for Severe Coronavirus Disease (COVID)


id: cord-303968-ikr6eeov
title: Towards Optimization of Hydroxychloroquine Dosing in Intensive Care Unit COVID-19 Patients
author: Perinel, Sophie
date: 2020-04-07
txt: ./txt/cord-303968-ikr6eeov.txt
cache: ./cache/cord-303968-ikr6eeov.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32255489/
doi: 10.1093/cid/ciaa394
summary:
  Apart from the ongoing clinical evaluation of the efficacy of HCQ, little information is available concerning the modalities of administration of this drug for Intensive Care Unit (ICU) patients, especially in the context of COVID-19. M a n u s c r i p t Treatment Patients received 200 mg of oral HCQ, three times daily, as suggested by a recent study [9] . To more clearly understand HCQ PK and the effect of the dosing regimen, a simulation based on a PK population study in patients with rheumatoid arthritis was performed [2] . In this study, we demonstrated that the 200 mg three times daily dosing regimen is inappropriate to reach a supposed target blood level of 1 -2 mg/L in this population. This regimen could constitute an appropriate option, although the results of our study suggest that 800 mg once daily on the first day can more rapidly reach therapeutic levels in ICU patients.

abstract:
  Hydroxychloroquine (HCQ) appears to be a promising treatment for COVID-19. However, all ongoing clinical trials with HCQ use different dosing regimens, resulting on various concentrations PK studies are therefore needed to define the optimal dosing regimen.


id: cord-304487-ycvu5l5f
title: A glimpse into the origins of genetic diversity in SARS-CoV-2
author: Wertheim, Joel O
date: 2020-03-04
txt: ./txt/cord-304487-ycvu5l5f.txt
cache: ./cache/cord-304487-ycvu5l5f.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32129842/
doi: 10.1093/cid/ciaa213
abstract: nan
summary:
  Evolution tinkers with these viruses in bats, and the epidemiological consequences are seen both in pathogenic zoonotic diseases (e.g., SARS, MERS, and COVID-19) and in the less-virulent circulating coronaviruses causing common colds. Molecular epidemiology can use the genetic variation of SARS-CoV-2 to trace its history and better understand clusters of transmission. However, deep-sequencing of viral genomes from 7 patients (including this probable transmission pair), the authors detect substantial variation in the number and frequency of minority variants within different individuals. The evolutionary history of MERS-CoV in its intermediate host, camels, is littered with recombination events [6] . However, as the number of infections increases and the circulating viruses become more genetically distinct, natural selection will become more efficient, making viral adaptation more of a possibility. For now, SARS-CoV-2 genetic variation is likely evolutionarily inconsequential and will be more important for facilitating molecular epidemiology in tracing the origins of novel clusters of viral infection.


id: cord-305394-wwabxlgr
title: COVID-19: First data from Africa
author: Venter, W D Francois
date: 2020-08-31
txt: ./txt/cord-305394-wwabxlgr.txt
cache: ./cache/cord-305394-wwabxlgr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32865552/
doi: 10.1093/cid/ciaa1293
abstract: nan
summary:
  This data is from an ongoing surveillance cohort that has previously generated rich data on disease patterns in the Western Cape, and currently continues to provide near real-time updates on the impact of PCR-confirmed SARS-CoV-2 on factors ranging from death to oxygen consumption within hospitals. Key strengths of the paper include a dataset covering over 3 million healthcare users in the Western Cape Province, and the use of both hospitalized and nonhospitalized cases and deaths Davies'' data shows similar mortality risk factors, including age, sex, diabetes (especially uncontrolled diabetes), hypertension and renal disease to other cohorts from richer countries. For South Africa, a sigh of relief at a relatively small increase in mortality in HIV and TB should be quickly tempered; diabetes was the second commonest cause of death in the country pre-COVID-19, and most patients in the country have poor glucose control, a major risk factor from Davies'' data (7) .


id: cord-306495-o0ah1gj9
author: Haidar, Ghady
date: 2020-08-11
txt: ./txt/cord-306495-o0ah1gj9.txt
cache: ./cache/cord-306495-o0ah1gj9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32780792/
doi: 10.1093/cid/ciaa1193
abstract: nan
summary:
  Thus, while morbidity and mortality related to COVID-19 in SOT recipients are substantial, A c c e p t e d M a n u s c r i p t 3 they appear to be driven by age and underlying medical conditions and unaffected by immunosuppression, corroborating the results of other studies in the general population. The study included only 30 lung transplant recipients was therefore unable to assess whether mortality in these patients is greatest (as is the case with sepsis [3] ), or whether COVID-19 precipitates acute or chronic lung allograft rejection. Furthermore, since all laboratory testing was done as standard of care, the study could not evaluate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viremia or the duration of SARS-CoV-2 PCR positivity, which may be longer than that of non-transplant patients.

title:
  COVID-19, organ transplantation, and the nuances of immunomodulation: lessons learned and what comes next


id: cord-307342-3gkiukh4
title: Why contact tracing efforts have failed to curb COVID-19 transmission in much of the U.S
author: Clark, Eva
date: 2020-08-06
txt: ./txt/cord-307342-3gkiukh4.txt
cache: ./cache/cord-307342-3gkiukh4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32761123/
doi: 10.1093/cid/ciaa1155
summary:
  By late April 2020, public discourse in the U.S. had shifted toward the idea of using more targeted case-based mitigation tactics (e.g., contact tracing) to combat COVID-19 transmission while allowing for the safe "re-opening" of society, in an effort to reduce the social, economic, and political ramifications associated with stricter approaches. This viewpoint offers a discussion of why testing-tracing efforts failed to sufficiently mitigate COVID-19 across much of the nation, with the hope that such deliberation will help the U.S. public health community better plan for the future. Partly for this reason, our nation rushed to espouse the idea of targeted, case-based COVID-19 management [3] [4] [5] [6] , focusing on expanded testing and contact tracing, while disregarding several major obstacles that set us apart from countries that succeeded in mounting a timely, targeted response.

abstract:
  By late April 2020, public discourse in the U.S. had shifted toward the idea of using more targeted case-based mitigation tactics (e.g., contact tracing) to combat COVID-19 transmission while allowing for the safe “re-opening” of society, in an effort to reduce the social, economic, and political ramifications associated with stricter approaches. Expanded tracing-testing efforts were touted as a key solution that would allow for a precision approach, thus preventing economies from having to shut down again. However, it is now clear that many regions of the U.S. were unable to mount robust enough testing-tracing programs to prevent major resurgences of disease. This viewpoint offers a discussion of why testing-tracing efforts failed to sufficiently mitigate COVID-19 across much of the nation, with the hope that such deliberation will help the U.S. public health community better plan for the future.


id: cord-307497-wtfvoifb
title: Predictors of refractory Coronavirus disease (COVID-19) pneumonia
author: Abu-Raya, Bahaa
date: 2020-04-09
txt: ./txt/cord-307497-wtfvoifb.txt
cache: ./cache/cord-307497-wtfvoifb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32271373/
doi: 10.1093/cid/ciaa409
abstract: nan
summary:
  In addition, refractory COVID-19 patients were more likely to receive oxygen, mechanical ventilation, expectorant, adjunctive treatment including corticosteroids, antiviral drugs and immune enhancers when compared to general COVID-19 patients. The authors have further attempted to explore predictive factors for refractory COVID-19 using a multivariate analysis showing that male sex, anorexia on admission and being afebrile are independent risk factors for the development of a refractory disease. Furthermore, out of this analysis the authors have found that patients with refractory COVID-19 were more likely to receive oxygen, expectorant, corticosteroids, lopinavir/ritonavir and immune enhancer. In their paper, the authors compared categorical and continuous variables between the two groups of patients and these variables that differed significantly between the two groups were included in the multivariate regression analysis. In their paper, the authors included the treatment introduced at the time of patient admission and/or hospitalization in the multivariate analysis aiming to identify independent risk factors for refractory COVID-19.


id: cord-307660-onz6vfre
title: Use of Baricitinib in Patients with Moderate and Severe COVID-19
author: Titanji, Boghuma K
date: 2020-06-29
txt: ./txt/cord-307660-onz6vfre.txt
cache: ./cache/cord-307660-onz6vfre.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa879
doi: 10.1093/cid/ciaa879
summary:
  Coronavirus Infectious Disease-19 (COVID-19), caused by Severe Acute Respiratory Virus Syndrome Coronavirus-2 (SARS-CoV-2) has led to over 8 million confirmed infections worldwide with an estimated global mortality of 5.6% as of June 17 th 2020 1 . Patients had laboratory confirmed COVID-19, diagnosed by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) testing of oropharyngeal, nasopharyngeal or tracheal aspirate samples and were treated at the discretion of the medical team with a combination of hydroxychloroquine and baricitinib if they fulfilled at least one of the following criteria: 1) evidence of pneumonia on lung imaging and requiring supplemental oxygen on admission or development of a new oxygen requirement during the course of their hospitalization 2) moderate disease requiring hospitalization (e.g., severe diarrhea requiring volume resuscitation, encephalopathy, evidence of end-A c c e p t e d M a n u s c r i p t organ damage); 3) elevated or rising inflammatory markers during hospitalization.

abstract:
  Cytokine storm and hyperinflammation are associated with increased mortality in COVID-19. In this small uncontrolled cohort of patients with moderate-severe COVID-19, treatment with baricitinib plus hydroxychloroquine was associated with recovery in 11 of 15 patients. Baricitinib for the treatment of COVID-19 should be further investigated in randomized controlled clinical trials.


id: cord-307770-1igydu3y
author: Rawson, Timothy M
date: 2020-05-02
txt: ./txt/cord-307770-1igydu3y.txt
cache: ./cache/cord-307770-1igydu3y.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32358954/
doi: 10.1093/cid/ciaa530
summary:
  title: Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing Articles presenting clinical data for patients with coronavirus infection (defined as SARS-1, MERS, SARS-COV-2, and other coronavirus) and bacterial/fungal co-infection reported in English, Mandarin, or Italian were included. CONCLUSIONS: Despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial/fungal co-infection. In terms of antimicrobial prescribing bacterial/fungal co-infection of the respiratory tract; some patients presenting to hospital with SARS-COV-2 infection have a clinical phenotype that is not dissimilar from atypical bacterial pneumonia. [13] We performed a review of the medical literature to explore commonly reported bacterial/fungal co-infections in patients admitted to hospital with coronavirus lower respiratory tract infections. It is not clear whether these patients were in critical or nonSelection of empiric antimicrobial therapy for respiratory bacterial/fungal co-infection and recommendations for duration of treatment require several considerations.

title:
  Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing

abstract:
  BACKGROUND: To explore and describe the current literature surrounding bacterial/fungal co-infection in patients with coronavirus infection. METHODS: MEDLINE, EMBASE, and Web of Science were searched using broad based search criteria relating to coronavirus and bacterial co-infection. Articles presenting clinical data for patients with coronavirus infection (defined as SARS-1, MERS, SARS-COV-2, and other coronavirus) and bacterial/fungal co-infection reported in English, Mandarin, or Italian were included. Data describing bacterial/fungal co-infections, treatments, and outcomes were extracted. Secondary analysis of studies reporting antimicrobial prescribing in SARS-COV-2 even in the absence of co-infection was performed. RESULTS: 1007 abstracts were identified. Eighteen full texts reported bacterial/fungal co-infection were included. Most studies did not identify or report bacterial/fungal coinfection (85/140;61%). 9/18 (50%) studies reported on COVID-19, 5/18 (28%) SARS-1, 1/18 (6%) MERS, and 3/18 (17%) other coronavirus. For COVID-19, 62/806 (8%) patients were reported as experiencing bacterial/fungal co-infection during hospital admission. Secondary analysis demonstrated wide use of broad-spectrum antibacterials, despite a paucity of evidence for bacterial coinfection. On secondary analysis, 1450/2010 (72%) of patients reported received antimicrobial therapy. No antimicrobial stewardship interventions were described. For non-COVID-19 cases bacterial/fungal co-infection was reported in 89/815 (11%) of patients. Broad-spectrum antibiotic use was reported. CONCLUSIONS: Despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial/fungal co-infection. Generation of prospective evidence to support development of antimicrobial policy and appropriate stewardship interventions specific for the COVID-19 pandemic are urgently required.


id: cord-309091-te15ahvw
title: A Case of Early Re-infection with SARS-CoV-2
author: Larson, Derek
date: 2020-09-19
txt: ./txt/cord-309091-te15ahvw.txt
cache: ./cache/cord-309091-te15ahvw.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32949240/
doi: 10.1093/cid/ciaa1436
abstract: nan
summary:
  A c c e p t e d M a n u s c r i p t 3 Dear Editor, It is with great interest that we read the first report of re-infection from SARS-CoV-2, which represented an important data point in the ongoing COVID-19 pandemic [1] [2] [3] . 42-year-old healthy male military healthcare provider presented with cough, subjective fever, and myalgias on 21 March following a workplace COVID-19 exposure and tested positive by SARS-CoV-2 RT-PCR ( Figure 1 ). The SARS-CoV-2 genome from the re-infection sample was deposited in NCBI GenBank under Accession The identification of specific products, scientific instrumentation, or organization is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the author, DoD, or any component agency. COVID-19 re-infection by a phylogenetically distinct SARScoronavirus-2 strain confirmed by whole genome sequencing Persistent positivity and fluctuations of SARS-CoV-2 RNA in clinically-recovered COVID-19 patients Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus


id: cord-310390-7pkbd3kg
author: Han, Xiaoyu
date: 2020-03-30
txt: ./txt/cord-310390-7pkbd3kg.txt
cache: ./cache/cord-310390-7pkbd3kg.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa271
doi: 10.1093/cid/ciaa271
summary:
  title: Novel Coronavirus Pneumonia (COVID-19) Progression Course in 17 Discharged Patients: Comparison of Clinical and Thin-Section CT Features During Recovery BACKGROUND: To retrospectively analyze the evolution of clinical features and thin-section CT imaging of novel coronavirus pneumonia (COVID-19) in 17 discharged patients. Hence, this study aimed to analyze the serial thin-section CT changes of 17 discharged patients with COVID-19, and to compare the progression trend of imaging pattern and clinical parameters. The standard for survive and discharge of patients was according to the guideline of Diagnosis and Treatment of Pneumonia Caused by SARS-COV-2 (trial sixth version) published by the China Ministry of Health [22] , which include: temperature returning to normal for more than 3 days, both the clinical and chest imaging showing significant improvement, and two consecutive respiratory pathogen nucleic acid tests turning negative (the interval at least 24 hours).

title:
  Novel Coronavirus Pneumonia (COVID-19) Progression Course in 17 Discharged Patients: Comparison of Clinical and Thin-Section CT Features During Recovery

abstract:
  BACKGROUND: To retrospectively analyze the evolution of clinical features and thin-section CT imaging of novel coronavirus pneumonia (COVID-19) in 17 discharged patients. METHODS: Serial thin-section CT scans of 17 discharged patients with COVID-19 were obtained during recovery. Longitudinal changes of clinical parameters and CT pattern were documented in all patients during 4 weeks since admission. CT score was used to evaluate the extent of the disease. RESULTS: There was a marked improvement of fever, lymphocytes count, C-reactive protein and erythrocyte sedimentation rate within the first two weeks since admission. However, the mean CT score rapidly increased from the 1(st) to 3(rd) week, with a top score of 8.2 obtained in the 2(nd) week. During the 1(st) week, the main CT pattern was ground-glass opacities (GGO,76.5%). The frequency of GGO (52.9%) decreased in the 2(nd) week. Consolidation and mixed patterns (47.0%) were noted in the 2(nd) week. Thereafter, consolidations generally dissipated into GGO and the frequency of GGO increased in the 3(rd) week (76.5%) and 4(th) week (71.4%). Opacities were mainly located in the peripheral (76.5%), subpleural (47.1%) zones of the lungs, and presented as focal (35.3%) or multifocal (29.4%) in the 1(st) week and became more diffuse in the 2(nd) (47.1%) and 3(rd )week (58.8%), then showed reduced extent in 4(th )week (50%). CONCLUSIONS: The progression course of CT pattern was later than the clinical parameters within the first two weeks since admission; however, there was a synchronized improvement in both clinical and radiologic features in the 4(th) week.


id: cord-310476-mhm7r3qc
title: 2019 novel coronavirus is undergoing active recombination
author: Yi, Huiguang
date: 2020-03-04
txt: ./txt/cord-310476-mhm7r3qc.txt
cache: ./cache/cord-310476-mhm7r3qc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32130405/
doi: 10.1093/cid/ciaa219
abstract: nan
summary:
  The single origin of 2019-nCov indicates a persistent animal to human transmission is unlikely, otherwise, multiple nodes with above characteristics should be observed. To quantify the significance of recombination over recurring sequencing error/mutations, Phi [6] and Max Chi-squared tests [7] in the software PhiPack [8] were performed. It showed p-values of 0.03 and 0.005 for Phi and Max Chi-squared, respectively, indicating the presence of recombinants in 2019-nCoV population. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event


id: cord-312797-hohzjx74
title: Human Metapneumovirus: A New Player among Respiratory Viruses
author: Hamelin, Marie-Ève
date: 2004-04-01
txt: ./txt/cord-312797-hohzjx74.txt
cache: ./cache/cord-312797-hohzjx74.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15034830/
doi: 10.1086/382536
summary:
  Despite the fact that prospective and case-control studies have been limited, the epidemiology and clinical manifestations associated with hMPV have been found to be reminiscent of those of the human respiratory syncytial virus, with most severe respiratory tract infections occurring in infants, elderly subjects, and immunocompromised hosts. In addition, studies have shown that hMPV is not a new pathogen, with serological evidence of human infection dating from 1958 in The Netherlands [4] and viral isolation for the past 10-20 years in Europe and Canada [4, 7] . Symptoms of both upper and lower respiratory tract infections have been associated with hMPV in young children, although most reports are biased towards description of the most severe symptomatology in hospitalized subjects. Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups

abstract:
  The human metapneumovirus (hMPV) is a newly described member of the Paramyxoviridae family belonging to the Metapneumovirus genus. Since its initial description in 2001, hMPV has been reported in most parts of the world and isolated from the respiratory tract of subjects from all age groups. Despite the fact that prospective and case-control studies have been limited, the epidemiology and clinical manifestations associated with hMPV have been found to be reminiscent of those of the human respiratory syncytial virus, with most severe respiratory tract infections occurring in infants, elderly subjects, and immunocompromised hosts. Additional research is needed to define the pathogenesis of this viral infection and the host's specific immune response.


id: cord-312905-8xlt92pl
title: Asymptomatic and Presymptomatic Infectors: Hidden Sources of COVID-19 Disease
author: Li, Guanjian
date: 2020-04-09
txt: ./txt/cord-312905-8xlt92pl.txt
cache: ./cache/cord-312905-8xlt92pl.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa418
doi: 10.1093/cid/ciaa418
abstract: nan
summary:
  At the time of writing this paper, the authors claimed that "evidence regarding transmission from individuals with asymptomatic infection or mild illness is limited", but that the current evidence may need an update. Recently, two epidemiological studies on COVID-19 have reported that typically asymptomatic carriers transmit the virus to close contacts, resulting in aggregated infection of symptomatic COVID-19 diseases [2, 3] . This study used a prospective design to follow up the viral load and clinical manifestations of 2147 close contacts of symptomatic and asymptomatic COVID-19 cases. The authors suggested that the transmission ability of asymptomatic individuals should not be ignored. First Mildly Ill, Non-Hospitalized Case of Coronavirus Disease 2019 (COVID-19) Without Viral Transmission in the United States Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing The epidemiological characteristics of infection in close contacts of COVID-19 in Ningbo city


id: cord-312928-ef8hqs4s
title: Viral Upper Respiratory Tract Infection and Otitis Media Complication in Young Children
author: Chavanet, Pascal
date: 2008-03-15
txt: ./txt/cord-312928-ef8hqs4s.txt
cache: ./cache/cord-312928-ef8hqs4s.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1086/528686
doi: 10.1086/528686
abstract: nan
summary:
  title: Viral Upper Respiratory Tract Infection and Otitis Media Complication in Young Children [1] conducted a large, longitudinal observational study of children with upper respiratory infection and examined for otitis complicationeither acute otitis media or otitis media with effusion. Indeed, in this study, the rate of respiratory syncitial virus infection was found to be low, probably as a result of the method used (conventional assays, type of molecular technique, RT-PCR vs. In this study, children aged !1 year and those who attended day care centers had a greater risk of acquiring upper respiratory tract infection and otitis media, compared with older children and those who were cared for at home. This article is important, especially because the rate of complications of otitis in upper respiratory tract infection was longitudinally studied. Viral upper respiratory tract infection and otitis media complication in young children Rates of hospitalisation for influenza, respiratory syncytial virus and human metapneumovirus among infants and young children


id: cord-313427-6y4zvrmn
author: Mani, Nandita S
date: 2020-06-16
txt: ./txt/cord-313427-6y4zvrmn.txt
cache: ./cache/cord-313427-6y4zvrmn.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32548613/
doi: 10.1093/cid/ciaa761
summary:
  Using data from these testing centers, we report the prevalence of SARS-CoV-2 infection among symptomatic employees and describe the clinical characteristics and outcomes among employees with COVID-19. Multiple factors have been reported to contribute to the risk of infections in HCWs, including lack of awareness during the early weeks of the outbreak, inadequate personal protective equipment (PPE) supply and training, insufficient rapid diagnostic testing for COVID-19, long work hours in high-risk environments, and ongoing community spread and household exposures. [12] [13] [14] A c c e p t e d M a n u s c r i p t Early and high-throughput testing for SARS-CoV-2 among symptomatic employees is essential to prevent nosocomial transmission of COVID-19 to patients, minimize clusters among HCWs, and maintain staffing during the pandemic. HCWs. 16 Here we describe the approach to establishing high-throughput employee testing centers, the prevalence of infections among symptomatic frontline versus non-frontline staff, and clinical outcomes associated with COVID-19 in these employees.

title:
  Prevalence of COVID-19 Infection and Outcomes Among Symptomatic Healthcare Workers in Seattle, Washington

abstract:
  BACKGROUND: Healthcare workers (HCW) serving on the front lines of the coronavirus disease 2019 (COVID-19) pandemic have been at increased risk for infection due to SARS-CoV-2 in some settings. Healthcare-acquired infection has been reported in similar epidemics, but there are limited data on the prevalence of COVID-19 among HCWs and their associated clinical outcomes in the United States. METHODS: We established two high-throughput employee testing centers in Seattle, Washington with drive-through and walk-through options for symptomatic employees in the University of Washington Medicine system and its affiliated organizations. Using data from these testing centers, we report the prevalence of SARS-CoV-2 infection among symptomatic employees and describe the clinical characteristics and outcomes among employees with COVID-19. RESULTS: Between March 12 and April 23, a total of 3,477 symptomatic employees were tested for COVID-19 at two employee testing centers; 185 (5.3%) employees tested positive for COVID-19. The prevalence of SARS-CoV-2 was similar when comparing frontline HCWs (5.2%) to non-frontline staff (5.5%). Among 174 positive employees reached for follow-up at least 14 days after diagnosis, 6 reported COVID-related hospitalization; all recovered. CONCLUSIONS: During the study period, we observed that the prevalence of positive SARS-CoV-2 tests among symptomatic HCWs was comparable to that of symptomatic non-frontline staff. Reliable and rapid access to testing for employees is essential to preserve the health, safety, and availability of the healthcare workforce during this pandemic and to facilitate the rapid return of SARS-CoV-2 negative employees to work.


id: cord-313499-8ijbesl8
title: Role of serology in the COVID-19 pandemic
author: Stowell, Sean
date: 2020-05-01
txt: ./txt/cord-313499-8ijbesl8.txt
cache: ./cache/cord-313499-8ijbesl8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32357206/
doi: 10.1093/cid/ciaa510
abstract: nan
summary:
  In this issue of Clinical Infections Diseases, F Xiang et al present a serologic study of 85 nucleic acid test (NAT) SARS-CoV-2 positive patients and 24 NAT negative patients who had symptoms suspicious for COVID-19 1 . Serological testing consisted of an enzyme linked immunosorbent assay designed to detect IgM and IgG antibodies against the N protein of SARS-CoV-2. In patients with suspected COVID-19 who tested NAT negative, IgM antibodies were detected in 87.5% and IgG was present in 70.8%. In the case of COVID-19, while serological analysis may be helpful in examining exposure, such approaches can be more challenging to interpret in patients with acute infection. Despite these considerations, the results of this manuscript suggest repeat serological testing may be informative in the acute setting, especially in patients who continue to follow a COVID-19-like disease course despite NAT negativity. Additional testing, such as NAT testing, may be warranted in serological positive individuals to determine potential risk for infecting others.


id: cord-313617-hh7lccet
title: Covid-19 and People with HIV Infection: Outcomes for Hospitalized Patients in New York City
author: Sigel, Keith
date: 2020-06-28
txt: ./txt/cord-313617-hh7lccet.txt
cache: ./cache/cord-313617-hh7lccet.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa880
doi: 10.1093/cid/ciaa880
summary:
  We collected data on baseline clinical characteristics, laboratory values, HIV infection status, COVID-19 treatment, and outcomes from this group and matched comparators (one PWH to up to five patients by age, sex, race/ethnicity and calendar week of infection). INTERPRETATION: We found no differences in adverse outcomes associated with HIV infection for hospitalized COVID-19 patients compared to a demographically similar patient group. We then compared differences in time to death to assess disease trajectory for hospitalized patients by HIV status by fitting unadjusted cumulative incidence function curves with hospital discharge as a competing risk. [7] To compare cumulative incidence of death by HIV status accounting for potential confounding factors we then fit a multivariable survival model using Fine-Grey competing risk methods, including demographics, COVID-19 severity, comorbid conditions and laboratory values that differed by HIV status.

abstract:
  BACKGROUND: There have been limited data regarding the clinical impact of COVID-19 disease on people with HIV (PWH). In this study we compared outcomes for PWH with COVID-19 disease to a matched comparison group. DESIGN: We identified 88 PWH hospitalized with laboratory confirmed COVID-19 in our hospital system in New York between March 12 and April 23, 2020. We collected data on baseline clinical characteristics, laboratory values, HIV infection status, COVID-19 treatment, and outcomes from this group and matched comparators (one PWH to up to five patients by age, sex, race/ethnicity and calendar week of infection). We compared baseline clinical characteristics and outcomes (death, mechanical ventilation, hospital discharge) for these two groups, as well as cumulative incidence of death by HIV status. RESULTS: Patients did not differ significantly by HIV status by age, sex or race/ethnicity due to the matching algorithm. PWH hospitalized with COVID-19 had high proportions of HIV virologic control on antiretroviral therapy. PWH had greater proportions of smoking (p<0.001) and comorbid illness than demographically similar uninfected comparators. There was no difference in COVID-19 severity on admission by HIV status (p=0.15). Poor outcomes for hospitalized PWH were frequent but similar to proportions in comparators; 18% required mechanical ventilation and ultimately 21% died during follow-up (compared with 23% and 20% respectively). There was similar cumulative incidence of death over time by HIV status (p=0.94). INTERPRETATION: We found no differences in adverse outcomes associated with HIV infection for hospitalized COVID-19 patients compared to a demographically similar patient group.


id: cord-313693-qmkrn7pr
title: Possible Role of Aerosol Transmission in a Hospital Outbreak of Influenza
author: Wong, Bonnie C. K.
date: 2010-11-15
txt: ./txt/cord-313693-qmkrn7pr.txt
cache: ./cache/cord-313693-qmkrn7pr.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1086/656743
doi: 10.1086/656743
summary:
  Airflow measurements were conducted, and concentrations of hypothetical virus-laden aerosols at different ward locations were estimated using computational fluid dynamics modeling. A major nosocomial outbreak of severe acute respiratory syndrome (SARS) occurred at PWH in 2003 [15, 23] ; since then, all patients hospitalized with acute febrile respiratory illnesses are put on droplet precautions; if influenza is confirmed, the patients will be isolated or cohorted in designated wards [21, 22] . Dispersion of the hypothetical virus-laden aerosols, originated from the index patient''s bed through the entire ward, was analyzed by computational fluid dynamics (CFD) method. In clinical studies, virus-laden particles less than 5-6 mm (ie, within the respirable aerosol fraction) have been detected in exhaled breaths of patients with influenza and in the air sampled from an acute healthcare setting during seasonal peak [19, 35, 36] . In conclusion, our findings suggest a possible role of aerosol transmission of influenza in an acute ward setting.

abstract:
  Background. We examined the role of aerosol transmission of influenza in an acute ward setting. Methods. We investigated a seasonal influenza A outbreak that occurred in our general medical ward (with open bay ward layout) in 2008. Clinical and epidemiological information was collected in real time during the outbreak. Spatiotemporal analysis was performed to estimate the infection risk among patients. Airflow measurements were conducted, and concentrations of hypothetical virus-laden aerosols at different ward locations were estimated using computational fluid dynamics modeling. Results. Nine inpatients were infected with an identical strain of influenza A/H3N2 virus. With reference to the index patient's location, the attack rate was 20.0% and 22.2% in the “same” and “adjacent” bays, respectively, but 0% in the “distant” bay (P=.04). Temporally, the risk of being infected was highest on the day when noninvasive ventilation was used in the index patient; multivariate logistic regression revealed an odds ratio of 14.9 (95% confidence interval, 1.7–131.3; P=.015). A simultaneous, directional indoor airflow blown from the “same” bay toward the “adjacent” bay was found; it was inadvertently created by an unopposed air jet from a separate air purifier placed next to the index patient's bed. Computational fluid dynamics modeling revealed that the dispersal pattern of aerosols originated from the index patient coincided with the bed locations of affected patients. Conclusions. Our findings suggest a possible role of aerosol transmission of influenza in an acute ward setting. Source and engineering controls, such as avoiding aerosol generation and improving ventilation design, may warrant consideration to prevent nosocomial outbreaks.


id: cord-314025-h9gj814e
title: Survival of Severe Acute Respiratory Syndrome Coronavirus
author: Lai, Mary Y. Y.
date: 2005-10-01
txt: ./txt/cord-314025-h9gj814e.txt
cache: ./cache/cord-314025-h9gj814e.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16142653/
doi: 10.1086/433186
summary:
  SARS-CoV GVU6109 can survive for 4 days in diarrheal stool samples with an alkaline pH, and it can remain infectious in respiratory specimens for >7 days at room temperature. Soon after the isolation of SARS-CoV in our laboratory, we were able to perform a survival study of the virus, and partial results were reported on the World Health Organization Communicable Disease Surveillance and Response Web site on SARS [6] . Here, we provide a full report of our study of the survival characteristics of SARS-CoV in different clinical sample matrices, as well as on various environmental surfaces in the laboratory and hospital. The present study demonstrates that SARS-CoV can survive in respiratory samples for 5 days at room temperature and for up to 3 weeks at 4ЊC. Our present data show that, at a high concentration of virus (10 6 TCID 50 / mL), SARS-CoV can survive for 4-5 days at room temperature in both respiratory and diarrheal stool samples.

abstract:
  Background. The primary modes of transmission of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) appear to be direct mucus membrane contact with infectious droplets and through exposure to formites. Knowledge of the survival characteristics of the virus is essential for formulating appropriate infection-control measures. Methods. Survival of SARS-CoV strain GVU6109 was studied in stool and respiratory specimens. Survival of the virus on different environmental surfaces, including a laboratory request form, an impervious disposable gown, and a cotton nondisposable gown, was investigated. The virucidal effects of sodium hypochlorite, house detergent, and a peroxygen compound (Virkon S; Antec International) on the virus were also studied. Results. SARS-CoV GVU6109 can survive for 4 days in diarrheal stool samples with an alkaline pH, and it can remain infectious in respiratory specimens for >7 days at room temperature. Even at a relatively high concentration (10(4) tissue culture infective doses/mL), the virus could not be recovered after drying of a paper request form, and its infectivity was shown to last longer on the disposable gown than on the cotton gown. All disinfectants tested were shown to be able to reduce the virus load by >3 log within 5 min. Conclusions. Fecal and respiratory samples can remain infectious for a long period of time at room temperature. The risk of infection via contact with droplet-contaminated paper is small. Absorbent material, such as cotton, is preferred to nonabsorptive material for personal protective clothing for routine patient care where risk of large spillage is unlikely. The virus is easily inactivated by commonly used disinfectants.


id: cord-314489-e5r5s5ee
title: The SARS-CoV-2 epidemic in Zimbabwe: Quo vadis?
author: Katsidzira, Leolin
date: 2020-05-11
txt: ./txt/cord-314489-e5r5s5ee.txt
cache: ./cache/cord-314489-e5r5s5ee.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32392333/
doi: 10.1093/cid/ciaa552
summary:
  The trajectory, and impact of the SARS-CoV-2 pandemic in sub-Saharan Africa is unclear, but it is seemingly varied between different countries, with most reporting low numbers. Using Zimbabwe as an example, we argue that the magnitude, and impact of the epidemic in most of sub-Saharan Africa is likely to be smaller than anticipated, with a reduced morbidity and mortality. This case strongly influenced the subsequent response to COVID-19 by both the government, and the private healthcare industry in Zimbabwe, and played a pivotal role in raising public awareness. There is a link between the volume of international flights, and the magnitude of the SARS-CoV-2 epidemic in sub-Saharan Africa [7, 11] . A potential source of higher than anticipated mortality from COVID-19 disease in sub-Saharan Africa is the high burden of HIV infection [5] . Moreover, considerable progress has It remains unclear whether complete lockdowns are the most ideal method to limit the spread of SARS-CoV-2 in sub-Saharan Africa [22] .

abstract:
  The trajectory, and impact of the SARS-CoV-2 pandemic in sub-Saharan Africa is unclear, but it is seemingly varied between different countries, with most reporting low numbers. We use the situation in Zimbabwe to build an argument that the epidemic is likely to be attenuated in some countries with similar socio-economic and cultural structures. However, even an attenuated epidemic may overwhelm weak health systems, emphasising the importance of prevention. These prevention strategies should be tailored to the unique social and cultural networks of individual countries which may facilitate the spread of SARS-CoV 2. It is also equally important to maintain services for the major infectious diseases in the region such as tuberculosis and malaria. A breakdown of treatment and prevention services for these conditions may even overshadow the projected morbidity and mortality from COVID-19.


id: cord-315180-itvc86cv
author: Hollingsworth, T Déirdre
date: 2018-06-15
txt: ./txt/cord-315180-itvc86cv.txt
cache: ./cache/cord-315180-itvc86cv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciy284
doi: 10.1093/cid/ciy284
summary:
  In 2012, the World Health Organization set ambitious targets for eliminating many of these diseases as a public health problem by 2020, an aspiration that was supported by donations of treatments, intervention materials, and funding committed by a broad partnership of stakeholders in the London Declaration on NTDs. Alongside these efforts, there has been an increasing role for quantitative analysis and modeling to support the achievement of these goals through evaluation of the likely impact of interventions, the factors that could undermine these achievements, and the role of new diagnostics and treatments in reducing transmission. This article acts as an introduction for a special issue that aims to increase the accessibility of the results so far by summarizing insights from NTD models and identifying key themes for the control of these diseases. The modeling summarized in this issue highlights the value of vector control in reducing the infectiousness of all infected individuals, as well as the value of increasing diagnosis rates (Table 1) .

title:
  Counting Down the 2020 Goals for 9 Neglected Tropical Diseases: What Have We Learned From Quantitative Analysis and Transmission Modeling?

abstract:
  The control of neglected tropical diseases (NTDs) has received huge investment in recent years, leading to large reductions in morbidity. In 2012, the World Health Organization set ambitious targets for eliminating many of these diseases as a public health problem by 2020, an aspiration that was supported by donations of treatments, intervention materials, and funding committed by a broad partnership of stakeholders in the London Declaration on NTDs. Alongside these efforts, there has been an increasing role for quantitative analysis and modeling to support the achievement of these goals through evaluation of the likely impact of interventions, the factors that could undermine these achievements, and the role of new diagnostics and treatments in reducing transmission. In this special issue, we aim to summarize those insights in an accessible way. This article acts as an introduction to the special issue, outlining key concepts in NTDs and insights from modeling as we approach 2020.


id: cord-315356-9zf2h0xr
author: Apisarnthanarak, Anucha
date: 2007-11-15
txt: ./txt/cord-315356-9zf2h0xr.txt
cache: ./cache/cord-315356-9zf2h0xr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17968831/
doi: 10.1086/522538
summary:
  In developing countries, health care worker preparedness training should address the modes of avian influenza transmission and specify how to implement appropriate infection-control strategies to prevent and control the spread of avian influenza. Pandemic influenza preparedness plans must include health care administrative support, mechanisms to rapidly create temporary isolation facilities, systems to restrict access to exposed health care workers, and plans to involve specialists to screen and identify cases early, to provide for continuous monitoring to ensure adherence to optimal infection-control practices, and to provide regular feedback to health care workers Given the experience of severe acute respiratory syndrome (SARS) outbreaks, which occurred in both designated "SARS hospitals" and "non-SARS hospitals" [40] [41] [42] , global preparedness plans should facilitate administrative, fiscal, and infrastructure support for routine occupational health and safety programs for HCWs, appropriate infection-control expertise, and infrastructure in health care settings, available PPE for HCWs, and epidemiological resources for the prevention and control of emerging infectious diseases.

title:
  Issues Relevant to the Adoption and Modification of Hospital Infection-Control Recommendations for Avian Influenza (H5N1 Infection) in Developing Countries

abstract:
  The reemergence of avian influenza (H5N1 infection) has heightened concern for a potential human influenza pandemic. Recommendations regarding preparation for a global avian influenza pandemic are available, and it is imperative that health care workers participate in preparedness planning and training. In developing countries, health care worker preparedness training should address the modes of avian influenza transmission and specify how to implement appropriate infection-control strategies to prevent and control the spread of avian influenza. We provide evidence for avian influenza transmission methods and identify prevention strategies relevant to infection control for hospitals in developing countries. Pandemic influenza preparedness plans must include health care administrative support, mechanisms to rapidly create temporary isolation facilities, systems to restrict access to exposed health care workers, and plans to involve specialists to screen and identify cases early, to provide for continuous monitoring to ensure adherence to optimal infection-control practices, and to provide regular feedback to health care workers


id: cord-316970-n2dly3oa
title: COVID-19: The New Caledonia experience
author: Kerbaj, Jad
date: 2020-05-16
txt: ./txt/cord-316970-n2dly3oa.txt
cache: ./cache/cord-316970-n2dly3oa.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa600
doi: 10.1093/cid/ciaa600
summary:
  Every passenger with fever or cough was hospitalized in the Centre Hospitalier Territorial CHT (the main island''s hospital, reference center in Infectious Diseases) and tested by SARS-CoV-2 reverse transcriptase Polymerase Chain Reaction (RT-PCR). On February 10, screening by SARS-CoV-2 RT-PCR started for all patients hospitalized for an Influenza like illness or a severe acute respiratory infection (SARI). All close contact to person confirmed with COVID-19 infection were isolated in a quarantine facility for 14 days. Iceland has quickly considered all travels outside the island as high risk, has done a large population screening and important tracking of SARS-A c c e p t e d M a n u s c r i p t 6 CoV-2 infections, associating these measures with quarantine, self-isolation and social distancing (8) . The surveillance, quarantine measures, the hospitalization of all detected COVID-19 positive patients and the rapid lockdown had probably an impact on stopping the spread.

abstract:
  New Caledonia is a French associated territory in the South Pacific Ocean. While COVID-19 is expanding over the world, we seem to be well preserved with a total of 18 documented cases. We report the measures implemented on our island that probably helped containing an epidemic spread.


id: cord-317092-5qba9jiq
title: Lessons from COVID-19 in children: Key hypotheses to guide preventative and therapeutic strategies
author: Singh, Tulika
date: 2020-05-08
txt: ./txt/cord-317092-5qba9jiq.txt
cache: ./cache/cord-317092-5qba9jiq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32382748/
doi: 10.1093/cid/ciaa547
summary:
  The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), reveals a peculiar trend of milder disease and lower case fatality in children compared to adults. Understanding differences in children''s immunity, host cellular factors required for virus replication, and physiology can provide insights into the correlates of protection from SARS-CoV-2 and other CoVs. In this review, we summarize current pediatric-specific knowledge on clinical disease, transmission, risks for severe disease, protective immunity, and novel therapies and vaccines in trial. 38 For example, a regulator of lung morphogenesis that is lower in childhood, nuclear factor kappa-light-chainenhancer of activated B cells (NF-b), plays a pathologic role in inflammatory diseases and should be evaluated as a protective host factor in pediatric versus adult SARS-CoV-2 infections. In this review, we evaluated recent reports on the pathology and immunity to SARS-CoV-2 infection and offered several hypotheses for how these features may differ in children versus adults, and how they may differentially modulate disease in these populations.

abstract:
  The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), reveals a peculiar trend of milder disease and lower case fatality in children compared to adults. Consistent epidemiologic evidence of reduced severity of infection in children across different populations and countries suggests there are underlying biologic differences between children and adults that mediate differential disease pathogenesis. This presents a unique opportunity to learn about disease modifying host factors from pediatric populations. Our review summarizes the current knowledge of pediatric clinical disease, role in transmission, risks for severe disease, protective immunity, as well as novel therapies and vaccine trials for children. We then define key hypotheses and areas for future research that can use the pediatric model of disease, transmission, and immunity to develop preventive and therapeutic strategies for people of all age groups.


id: cord-317823-ztawznod
title: Statewide Interventions and Covid-19 Mortality in the United States: An Observational Study
author: Yehya, Nadir
date: 2020-07-08
txt: ./txt/cord-317823-ztawznod.txt
cache: ./cache/cord-317823-ztawznod.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32634828/
doi: 10.1093/cid/ciaa923
summary:
  Historical analysis of the 1918-1919 influenza pandemic during the second wave of infections that examined 43 cities in the United States demonstrated an association between earlier school closures and bans on public gatherings with lower mortality [5] . Therefore, we assessed the association between the timing of emergency declarations and school closures, two specific statewide distancing measures, and subsequent Covid-19 mortality. Second, because deaths per million is a common method to compare localities, we provide an analysis testing the association between deaths per million at the state level after multivariable adjustment relative to timing of emergency declarations or statewide school closures. States implementing emergency declarations or school closures later in the course of the pandemic experienced higher Covid-19 mortality, with each day of delay increasing mortality risk 5 to 6%.

abstract:
  BACKGROUND: Social distancing is encouraged to mitigate viral spreading during outbreaks. However, the association between distancing and patient-centered outcomes in Covid-19 has not been demonstrated. In the United States social distancing orders are implemented at the state level with variable timing of onset. Emergency declarations and school closures were two early statewide interventions. METHODS: To determine whether later distancing interventions were associated with higher mortality, we performed a state-level analysis in 55,146 Covid-19 non-survivors. We tested the association between timing of emergency declarations and school closures with 28-day mortality using multivariable negative binomial regression. Day 1 for each state was set to when they recorded ≥ 10 deaths. We performed sensitivity analyses to test model assumptions. RESULTS: At time of analysis, 37 of 50 states had ≥ 10 deaths and 28 follow-up days. Both later emergency declaration (adjusted mortality rate ratio [aMRR] 1.05 per day delay, 95% CI 1.00 to 1.09, p=0.040) and later school closure (aMRR 1.05, 95% CI 1.01 to 1.09, p=0.008) were associated with more deaths. When assessing all 50 states and setting day 1 to the day a state recorded its first death, delays in declaring an emergency (aMRR 1.05, 95% CI 1.01 to 1.09, p=0.020) or closing schools (aMRR 1.06, 95% CI 1.03 to 1.09, p<0.001) were associated with more deaths. Results were unchanged when excluding New York and New Jersey. CONCLUSIONS: Later statewide emergency declarations and school closure were associated with higher Covid-19 mortality. Each day of delay increased mortality risk 5 to 6%.


id: cord-317940-yg91bsmm
author: Chalumeau, Martin
date: 2005-08-01
txt: ./txt/cord-317940-yg91bsmm.txt
cache: ./cache/cord-317940-yg91bsmm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16007520/
doi: 10.1086/431762
summary:
  title: Transmission of Panton-Valentine Leukocidin–Producing Staphylococcus aureus to a Physician during Resuscitation of a Child We report the first case of transmission of Panton-Valentine leukocidin–producing Staphylococcus aureus to a physician during the resuscitation of an infant with fatal pneumonia. We report the first case of transmission of Panton-Valentine leukocidin-producing Staphylococcus aureus to a physician during the resuscitation of an infant with fatal pneumonia. Severe respiratory diseases, in immunocompetent infants, and chronic furunculosis have been associated with Staphylococcus aureus strains producing Panton-Valentine leukocidin (PVL), a cytotoxin that causes leukocyte destruction and tissue necrosis [1] . S. aureus strains susceptible to methicillin were isolated from samples from the physician and from 5 other health care workers. aureus isolates from the infant (S1) and the physician (S2) but not from the isolates from the other health care workers. aureus strain from a patient to a health care worker during resuscitation.

title:
  Transmission of Panton-Valentine Leukocidin–Producing Staphylococcus aureus to a Physician during Resuscitation of a Child

abstract:
  We report the first case of transmission of Panton-Valentine leukocidin–producing Staphylococcus aureus to a physician during the resuscitation of an infant with fatal pneumonia. The physician exhibited numerous furuncles. This case highlights the necessity for health care workers to protect themselves against transmission of infectious diseases from patient to care giver.


id: cord-317948-svgguadm
title: Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients
author: Xiao, Ai Tang
date: 2020-04-19
txt: ./txt/cord-317948-svgguadm.txt
cache: ./cache/cord-317948-svgguadm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32306036/
doi: 10.1093/cid/ciaa460
summary:
  title: Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients To date, an outbreak of infectious diseases--coronavirus disease 2019 (COVID-19) associated with Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) continues in Wuhan, China and threatens countries such as Korea, Italy, Iraq and Japan, etc. Currently no study reported the viral dynamics of SARS-CoV-2 infection in a long observation period. Therefore, we collected clinical specimens from 56 COVID-19 patients and reported the results of SARS-CoV-2 detection during the disease course. If two consecutive negative results were achieved, the period between symptoms onset and the date of first negative RT-PCR test result was defined as viral nucleic acid conversion time. In first 3 weeks after symptoms onset, majority results of RT-PCR for SARS-CoV-2 were positive. [14] [15] [16] This preliminary study has found evidence of the dynamic profile of SARS-CoV-2 in non-ICU COVID-19 patients during disease course.

abstract:
  A novel coronavirus (COVID-19) pandemic threatens the world. Here, we first studied the dynamics profile of SARS-CoV-2 from 56 recovered COVID-19 patients. We found virus shedding was up to 6 weeks after onset of symptoms. Prolonged observation period is necessary for older patients.


id: cord-318204-t024w7h6
title: The Laboratory Diagnosis of COVID-19-- Frequently-Asked Questions
author: Fang, Ferric C
date: 2020-06-08
txt: ./txt/cord-318204-t024w7h6.txt
cache: ./cache/cord-318204-t024w7h6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32511679/
doi: 10.1093/cid/ciaa742
summary:
  As communities attempt to re-open following periods of shutdown, the detection of both SARS-CoV-2 and specific antibodies recognizing the virus will become increasingly important as a means to assess infection and immunity in individuals and communities. In view of the less than ideal sensitivity of an NP swab to detect SARS-CoV-2 infection, it may be useful to repeat testing in a patient in whom the clinical suspicion is high (32) . Although the primary use of serologic tests is to determine prior exposure to SARS-CoV-2, the detection of specific antibodies may support the diagnosis of COVID-19 in a patient with a high clinical suspicion but negative PCR tests (57-59). Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Early detection of SARS-CoV-2 antibodies in COVID-19 patients as a serologic marker of infection

abstract:
  Diagnostic testing has played and will continue to play a major role in the COVID-19 pandemic. The ability to detect the SARS-CoV-2 coronavirus in respiratory secretions is essential to determine when an individual is infected and potentially infectious to others. Viral detection is used for the identification, management and isolation of individual patients. Viral detection is also used to determine when the virus has entered a community and how rapidly it is spreading. As communities attempt to re-open following periods of shutdown, the detection of both SARS-CoV-2 and specific antibodies recognizing the virus will become increasingly important as a means to assess infection and immunity in individuals and communities. Here we discuss questions commonly asked by clinicians about COVID-19 diagnostic testing.


id: cord-318358-glbr8kxh
title: COVID-19 and the RAAS
author: Naik, George O A
date: 2020-06-20
txt: ./txt/cord-318358-glbr8kxh.txt
cache: ./cache/cord-318358-glbr8kxh.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa818
doi: 10.1093/cid/ciaa818
abstract: nan
summary:
  Further to Thomas Hanff et al [1] timely call for epidemiological and clinical investigations of COVID-19 infectious disease, measurements of the renin angiotensin aldosterone system (RAAS) components, as sub-studies would be insightful of this pandemic. Angiotensin-converting enzyme 2 (ACE 2) participates in the coronavirus (SARS-CoV-2) cell entry. Drugs that block RAAS also affect ACE 2 expression: it is down regulated by renin inhibition (RI) and up regulated by angiotensin-converting enzyme inhibitors (ACEIs), angiotensin receptor blockers (ARBs) (1) and mineralocorticoid receptor antagonists (MRAs) [2] . Such perturbations would also indirectly influence other RAAS components, and the coordination between circulating and local tissue expressions, as shown in Figure 1 ACE 2 is distributed throughout the body and is abundantly expressed in the lung, small intestine, and in blood vessels of many organs including the brain, heart, kidney and testis [4] . Mineralocorticoid receptor blocker increases angiotensin-converting enzyme 2 activity in congestive heart failure patients


id: cord-318458-jadk2qbm
author: Jung, Chan-Young
date: 2020-08-25
txt: ./txt/cord-318458-jadk2qbm.txt
cache: ./cache/cord-318458-jadk2qbm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32841322/
doi: 10.1093/cid/ciaa1257
summary:
  METHODS: We examined the association between BMI level and the risk of COVID-19 infection in a nationwide case-control study comprised of 3,788 case patients confirmed with COVID-19 between January 24 and April 9, 2020 and 15,152 controls matched by age and sex, who were aged 20 years or more and underwent National Health Insurance Service (NHIS) health examinations between 2015−2017, using data from the Korean NHIS with linkage to the Korea Centers for Disease Control and Prevention data. In multivariable logistic regression models adjusted for sociodemographic, comorbidity, laboratory and medication data, there was a graded association between higher BMI levels and higher risk of COVID-19 infection; compared to normal weight individuals, the adjusted ORs in the overweight and obese individuals were 1.13 (95% CI, 1.03-1.25) and 1.26 (95% CI, 1.15-1.39), respectively.

title:
  Association between Body Mass Index and Risk of COVID-19: A Nationwide Case-Control Study in South Korea

abstract:
  BACKGROUND: Increased body mass index (BMI) has been associated with higher risk of severe coronavirus disease 2019 (COVID-19) infections. However, whether obesity is a risk factor for contracting COVID-19 has been hardly investigated so far. METHODS: We examined the association between BMI level and the risk of COVID-19 infection in a nationwide case-control study comprised of 3,788 case patients confirmed with COVID-19 between January 24 and April 9, 2020 and 15,152 controls matched by age and sex, who were aged 20 years or more and underwent National Health Insurance Service (NHIS) health examinations between 2015−2017, using data from the Korean NHIS with linkage to the Korea Centers for Disease Control and Prevention data. Our primary exposure of interest was BMI level categorized into four groups; &18.5 (underweight), 18.5-22.9 (normal weight), 23-24.9 (overweight), and ≥25 kg/m (2) (obese). RESULTS: Of the entire 18,940 study population, 11,755 (62.1%) were women, and the mean (SD) age of the study participants was 53.7 (13.8) years. In multivariable logistic regression models adjusted for sociodemographic, comorbidity, laboratory and medication data, there was a graded association between higher BMI levels and higher risk of COVID-19 infection; compared to normal weight individuals, the adjusted ORs in the overweight and obese individuals were 1.13 (95% CI, 1.03-1.25) and 1.26 (95% CI, 1.15-1.39), respectively. This association was robust across age and sex subgroups. CONCLUSIONS: Higher BMI levels were associated with higher risk of contracting COVID-19.


id: cord-318615-uhh3owcx
title: Antibody Detection and Dynamic Characteristics in Patients with COVID-19
author: Xiang, Fei
date: 2020-04-19
txt: ./txt/cord-318615-uhh3owcx.txt
cache: ./cache/cord-318615-uhh3owcx.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32306047/
doi: 10.1093/cid/ciaa461
summary:
  METHODS: The antibodies against SARS-CoV-2 were detected by an enzyme-linked immunosorbent assay (ELISA) based on the recombinant nucleocapsid protein of SARS-CoV-2 in patients with confirmed or suspected COVID-19 at 3-40 days after symptom onset. Here, we detected dynamics characteristics and magnitude of antibody response in patients with COVID-19, and evaluated serodiagnostic value of ELISA-based IgM, IgG tests for COVID-19 pneumonia. Detection of IgM and IgG Antibody on Different Periods (Table 2.) We evaluated specificity of IgM and IgG antibodies based on ELISA from 216 serum sample of 85 confirmed COVID-19 pneumonia patients. To evaluate the diagnostic potential of serological IgM and IgG antibodies detection, 66 patients with confirmed COVID-19 pneumonia were evaluated and compare to standard RT-PCR assays. * Specific IgM and IgG antibodies against SARS-CoV-2 from 216 serum samples of 85 confirmed COVID-19 pneumonia cases were tested with ELISA.

abstract:
  BACKGROUND: The corona virus disease 2019 (COVID-19) caused by the corona virus 2 (SARS-CoV-2) has been rapidly spreading nationwide and abroad. A serologic test to identify antibody dynamics and response to SARS-CoV-2 was developed. METHODS: The antibodies against SARS-CoV-2 were detected by an enzyme-linked immunosorbent assay (ELISA) based on the recombinant nucleocapsid protein of SARS-CoV-2 in patients with confirmed or suspected COVID-19 at 3-40 days after symptom onset. The gold standard for COVID-19 diagnosis was nucleic acid testing for SARS-CoV-2 by RT-PCR. The serodiagnostic power of the specific IgM and IgG antibodies against SARS-CoV-2 was investigated in terms of sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and consistency rate. RESULTS: The seroconversion of specific IgM and IgG antibodies were observed as early as the 4(th) day after symptom onset. In the confirmed patients with COVID-19, sensitivity, specificity, PPV, NPV, and consistency rate of IgM were 77.3% (51/66), 100%, 100%, 80.0%, and 88.1%, and those of IgG were 83.3.3% (55/66), 95.0%, 94.8%, 83.8%, and 88.9 %. In patients with suspected COVID-19, sensitivity, specificity, PPV, NPV, and consistency rate of IgM were 87.5% (21/24), 100%, 100%, 95.2%, and 96.4%, and those of IgG were 70.8% (17/24), 96.6%, 85.0%, 89.1%, and 88.1%. Both antibodies performed well in serodiagnosis for COVID-19 rely on great specificity. CONCLUSIONS: The antibodies against SARS-CoV-2 can be detected in the middle and later stage of the illness. Antibody detection may play an important role in the diagnosis of COVID-19 as complement approach for viral nucleid acid assays.


id: cord-320562-zvsf3va0
title: Tuberculosis Elimination in the Era of COVID-19: A Moving Target
author: Dookie, Navisha
date: 2020-09-14
txt: ./txt/cord-320562-zvsf3va0.txt
cache: ./cache/cord-320562-zvsf3va0.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1400
doi: 10.1093/cid/ciaa1400
abstract: nan
summary:
  In this issue, Liu and colleagues describe the impact of a temporary disruption in health services due to COVID-19 mitigation measures on diagnosis and treatment of TB in the Jiangsu province of China. Thus, the resulting decline in case notifications is likely an unintended consequence of limited access to health care services during the pandemic. resulting from limited access to diagnosis and treatment, could potentially escalate TB related mortality have a lasting impact on TB burden. Thus, disruption to health care services will likely result in short term escalation in TB mortality and postlockdown surge in TB case notification, followed by a sustained increase in TB incidence and mortality over the next several years, with long-term consequences on TB elimination. The potential impact of the covid-19 response on tuberculosis in high-burden countries: a modelling analysis Potential impact of the COVID-19 pandemic on HIV, tuberculosis, and malaria in low-income and middle-income countries: a modelling study


id: cord-321603-lbbsnriv
title: Comparing nasopharyngeal swab and early morning saliva for the identification of SARS-CoV-2
author: Rao, Mohan
date: 2020-08-06
txt: ./txt/cord-321603-lbbsnriv.txt
cache: ./cache/cord-321603-lbbsnriv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1156
doi: 10.1093/cid/ciaa1156
summary:
  The aim of this study was to compare patient-performed testing based on a morning saliva sample with the current standard testing method, healthcare worker-collected sampling via a nasopharyngeal swab (NPS). METHODS: This was a prospective single center study which recruited 217 asymptomatic adult male participants in a COVID-19 quarantine center who had tested positive for SARS-CoV-2 8-10 days prior isolation. The current standard sampling techniques such as NPS and OPS used for surveillance and serial monitoring of infected patients are exposing healthcare workers to SARS-CoV-2 virus and other unknown pathogens via aerosols from swabbing and jeopardizing physical distancing. This prospective single center diagnostic study was conducted among 217 individuals who were tested positive for SARS-CoV-2 via NPS at a COVID-19 quarantine center, MAEPS. Nevertheless, we had 72 individuals with their saliva specimen tested positive for SARS-CoV-2 while they were test negative for nasopharyngeal swab. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs.

abstract:
  BACKGROUND: The ideal SARs-CoV-2 testing method would be accurate and also be patient-performed to reduce exposure to healthcare workers. The aim of this study was to compare patient-performed testing based on a morning saliva sample with the current standard testing method, healthcare worker-collected sampling via a nasopharyngeal swab (NPS). METHODS: This was a prospective single center study which recruited 217 asymptomatic adult male participants in a COVID-19 quarantine center who had tested positive for SARS-CoV-2 8-10 days prior isolation. Paired NPS and saliva specimens were collected and processed within 5 hours of sample collection. Real time reverse transcriptase polymerase chain reaction (RT-PCR) targeting Envelope (E) and RNA-dependent RNA polymerase (RdRp) genes was performed and the results were compared. RESULTS: Overall, 160 of the 217 (74%) participants tested positive for Covid-19 based on saliva, NPS, or both testing methods. The detection rate for SARS-CoV-2 was higher in saliva compared to NPS testing (93.1%, 149/160 vs 52.5%, 84/160, p<0.001). The concordance between the two tests was 45.6% (virus was detected in both saliva and NPS in 73/160), while 47.5% were discordant (87/160 tested positive for one while negative for the other). The Ct values for E and RdRp genes were significantly lower in saliva specimens compared to NP swab specimens. CONCLUSIONS: Our findings demonstrate that saliva is a better alternative specimen for detection of SARS-CoV-2. Taking into consideration, the simplicity of specimen collection, shortage of PPE and the transmissibility of the virus, saliva could enable self-collection for an accurate SARS-CoV-2 surveillance testing.


id: cord-321873-9l9zp6gm
title: The duration of viral shedding of discharged patients with severe COVID-19
author: Zhou, Bo
date: 2020-04-17
txt: ./txt/cord-321873-9l9zp6gm.txt
cache: ./cache/cord-321873-9l9zp6gm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32302000/
doi: 10.1093/cid/ciaa451
summary:
  title: The duration of viral shedding of discharged patients with severe COVID-19 However, little studies have focused on clinical characteristics of discharged patients with severe COVID-19, especially the duration of viral shedding. The RT-PCR tests were performed on throat swabs following a previously described method 3 Moreover, another study displayed that four patients with COVID-19 who met the criteria for hospital discharge in China had positive RT-PCR test results 5 to 13 days later 6 , suggesting that recovered patients might still be virus carriers. Based on the results, we did not observe shortening of viral shedding time in the above groups, so it implied that all patients with severe COVID-19 should complete adequate course of treatment, regardless of sex and age. Clinical features of patients infected with 2019 novel coronavirus in Wuhan Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study

abstract:
  The 2019 coronavirus disease (COVID-19) has drawn global intensive attention(1-3). Most of studies paid attention to epidemiological, clinical, and radiological features of inpatients with COVID-19(1-3). However, little studies have focused on clinical characteristics of discharged patients with severe COVID-19, especially the duration of viral shedding.


id: cord-322082-80ym2rsq
title: Lessons From Influenza Pandemics of the Last 100 Years
author: Monto, Arnold S
date: 2020-03-01
txt: ./txt/cord-322082-80ym2rsq.txt
cache: ./cache/cord-322082-80ym2rsq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31420670/
doi: 10.1093/cid/ciz803
summary:
  Since this was the first true pandemic since 1918, there was immediate concern about its potential impact and great relief when it was found to resemble seasonal influenza with morbidity highest in children and mortality at the extremes of age [26, 27] (Figure 3 ). However, the new A(H3N2) virus completely replaced the previous subtype, and its variants, more than 50 years later, have been responsible for the greatest proportion of mortality from influenza viruses. In the United States, there was particular attention directed to nonpharmaceutical interventions, a result of the recognition that pandemic-specific vaccines would be available relatively late and that influenza-specific antiviral drugs, while important, would be limited in quantity. " The latter issue has been made worse by the repeated recognition of the pandemic potential of different avian influenza virus variants that have infected humans [63] [64] [65] .

abstract:
  Seasonal influenza is an annual occurrence, but it is the threat of pandemics that produces universal concern. Recurring reports of avian influenza viruses severely affecting humans have served as constant reminders of the potential for another pandemic. Review of features of the 1918 influenza pandemic and subsequent ones helps in identifying areas where attention in planning is critical. Key among such issues are likely risk groups and which interventions to employ. Past pandemics have repeatedly underscored, for example, the vulnerability of groups such as pregnant women and taught other lessons valuable for future preparedness. While a fundamental difficulty in planning for the next pandemic remains their unpredictability and infrequency, this uncertainty can be mitigated, in part, by optimizing the handling of the much more predictable occurrence of seasonal influenza. Improvements in antivirals and novel vaccine formulations are critical in lessening the impact of both pandemic and seasonal influenza.


id: cord-322204-kc7dy2za
author: Khalil, Asma
date: 2020-08-08
txt: ./txt/cord-322204-kc7dy2za.txt
cache: ./cache/cord-322204-kc7dy2za.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32770224/
doi: 10.1093/cid/ciaa893
abstract: nan
summary:
  title: SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results Universal healthcare worker (HCW) testing is potentially useful in ameliorating workforce depletion and reducing asymptomatic spread of SARS-CoV-2. Nasopharyngeal swab polymerase chain reaction (RT-PCR) can diagnose only current or recent infection; testing for antibody responses against SARS-CoV-2 could enhance the ability to expedite reinstatement of services, while ensuring patient and staff safety. Tests are now available for immunoglobulin (Ig) G against the SARS-CoV-2 nucleocapsid protein; the Abbott SARS-CoV-2 IgG ELISA is reported to have high specificity We previously reported that 32% of HCW testing positive for SARS-CoV-2 on nasopharyngeal swab were asymptomatic at the time. 2 Symptomatic and asymptomatic SARS-CoV-2 positive adults have similar viral loads and infectious virus isolation. Of those testing positive for SARS-CoV-2 IgG, 39% had an earlier negative nasopharyngeal swab. 5 Both symptomatic and asymptomatic infections were associated with SARS-COV-2 IgG antibodies, as were 10% of

title:
  SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results


id: cord-322448-s04e6po9
title: Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia
author: Gadsby, Naomi J.
date: 2016-04-01
txt: ./txt/cord-322448-s04e6po9.txt
cache: ./cache/cord-322448-s04e6po9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26747825/
doi: 10.1093/cid/civ1214
summary:
  Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. The development of multiplex real-time polymerase-chain reaction (PCR) assays currently enables a respiratory specimen to be rapidly screened for a wide range of viral and atypical bacterial pathogens in a small number of reactions [10] [11] [12] [13] [14] [15] . As our study focused on testing sputum by molecular methods, our high level of pathogen detection for typical bacteria may not be directly comparable to results from other recent studies in hospitalized adult CAP.

abstract:
  Background. The frequent lack of a microbiological diagnosis in community-acquired pneumonia (CAP) impairs pathogen-directed antimicrobial therapy. This study assessed the use of comprehensive multibacterial, multiviral molecular testing, including quantification, in adults hospitalized with CAP. Methods. Clinical and laboratory data were collected for 323 adults with radiologically-confirmed CAP admitted to 2 UK tertiary care hospitals. Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Bacterial loads were also calculated for 8 bacterial pathogens. Appropriate pathogen-directed therapy was retrospectively assessed using national guidelines adapted for local antimicrobial susceptibility patterns. Results. Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Haemophilus influenzae and Streptococcus pneumoniae were the main agents detected, along with a wide variety of typical and atypical pathogens. Viruses were present in 30% of cases; 82% of these were codetections with bacteria. Most (85%) patients had received antimicrobials in the 72 hours before admission. Of these, 78% had a bacterial pathogen detected by PCR but only 32% were culture-positive (P < .0001). Molecular testing had the potential to enable de-escalation in number and/or spectrum of antimicrobials in 77% of patients. Conclusions. Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. It also has the potential to enable early de-escalation from broad-spectrum empirical antimicrobials to pathogen-directed therapy.


id: cord-322650-q8inhgtr
author: Fung, Yin-Wan Wendy
date: 2004-08-15
txt: ./txt/cord-322650-q8inhgtr.txt
cache: ./cache/cord-322650-q8inhgtr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15356838/
doi: 10.1086/422887
abstract: nan
summary:
  title: Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection In conclusion, voriconazole is highly active against Aspergillus species, but additional studies are needed to confirm that our low drug concentrations result from the method of sampling and not from poor efficacy of this molecule in the CSF. In early 2003, a novel severe acute respiratory syndrome (SARS) coronavirus (CoV) [1] spread around the world; ultimately, more than 8000 patients in 32 countries contracted SARS, many of whom died. The ERT method clearly demonstrated the presence of SARS CoV in all samples obtained from the patient on 16 June (table 1) , which was 1 day before his transfer to WTSH. More studies will be necessary to determine the infectivity status of patients who have ERT results positive for SARS CoV. Severe acute respiratory syndrome (SARS): laboratory diagnostic tests

title:
  Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection


id: cord-323125-qtlevnbt
author: Al Hosani, Farida Ismail
date: 2019-02-01
txt: ./txt/cord-323125-qtlevnbt.txt
cache: ./cache/cord-323125-qtlevnbt.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciy503
doi: 10.1093/cid/ciy503
summary:
  BACKGROUND: Although there is evidence of person-to-person transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) in household and healthcare settings, more data are needed to describe and better understand the risk factors and transmission routes in both settings, as well as the extent to which disease severity affects transmission. METHODS: A seroepidemiological investigation was conducted among MERS-CoV case patients (cases) and their household contacts to investigate transmission risk in Abu Dhabi, United Arab Emirates. In this investigation, we use serological detection of MERS-CoV antibodies to evaluate if asymptomatic or mildly ill case patients had detectable MERS-CoV antibodies, estimate transmission rates from known cases to their household contacts, and identify potential risk factors. For each MERS-CoV case identified in the investigation, clinical information, including symptoms, was collected using the International Severe Acute Respiratory and Emerging Infection Consortium form, which was filled out in real time by healthcare providers and subsequently verified by retrospective chart review.

title:
  Serologic Follow-up of Middle East Respiratory Syndrome Coronavirus Cases and Contacts—Abu Dhabi, United Arab Emirates

abstract:
  BACKGROUND: Although there is evidence of person-to-person transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) in household and healthcare settings, more data are needed to describe and better understand the risk factors and transmission routes in both settings, as well as the extent to which disease severity affects transmission. METHODS: A seroepidemiological investigation was conducted among MERS-CoV case patients (cases) and their household contacts to investigate transmission risk in Abu Dhabi, United Arab Emirates. Cases diagnosed between 1 January 2013 and 9 May 2014 and their household contacts were approached for enrollment. Demographic, clinical, and exposure history data were collected. Sera were screened by MERS-CoV nucleocapsid protein enzyme-linked immunosorbent assay and indirect immunofluorescence, with results confirmed by microneutralization assay. RESULTS: Thirty-one of 34 (91%) case patients were asymptomatic or mildly symptomatic and did not require oxygen during hospitalization. MERS-CoV antibodies were detected in 13 of 24 (54%) case patients with available sera, including 1 severely symptomatic, 9 mildly symptomatic, and 3 asymptomatic case patients. No serologic evidence of MERS-CoV transmission was found among 105 household contacts with available sera. CONCLUSIONS: Transmission of MERS-CoV was not documented in this investigation of mostly asymptomatic and mildly symptomatic cases and their household contacts. These results have implications for clinical management of cases and formulation of isolation policies to reduce the risk of transmission.


id: cord-324007-hapzf0fl
author: McGeer, Allison J.
date: 2009-01-01
txt: ./txt/cord-324007-hapzf0fl.txt
cache: ./cache/cord-324007-hapzf0fl.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1086/591852
doi: 10.1086/591852
summary:
  In a retrospective study of adult patients with influenza who were admitted to the Prince of Wales Hospital in Hong Kong during the 2004-2005 influenza season with fever and respiratory and systemic symptoms, a clinically and statistically significant reduction in length of hospital stay was associated with treatment with oseltamivir [14] . The accumulating evidence suggests that, for patients with acute cardiorespiratory illness requiring hospital admission during influenza season, consideration should be given to either prompt laboratory diagnostic testing and treatment for influenza virus-infected patients or empirical antiviral therapy for influenza. The best choice is made on a case-by-case basis and depends on the severity of illness in the patient being admitted (since earlier therapy for pneumonia is more effective), the probability of influenza virus infection in the individual patient, and the sensitivity of the rapid diagnostic tests available.

title:
  Diagnostic Testing or Empirical Therapy for Patients Hospitalized with Suspected Influenza: What to Do?

abstract:
  Accumulating evidence supports the use of specific diagnostic tests and antiviral therapies for seriously ill patients with influenza. Among available diagnostic tests, reverse-transcriptase polymerase chain reaction is faster than culture and more sensitive than commercial antigen assays. Current neuraminidase inhibitors were approved on the basis of their efficacy in ambulatory patients, but seriously ill patients who receive these agents are less likely to die, even when treatment is initiated >48 h after symptom onset. For patients hospitalized with suspected influenza, it is unclear which circumstances warrant diagnostic testing and which warrant the use of empirical therapy. Rapid antigen assays may reduce the unnecessary use of other tests and medications but are relatively insensitive, thus eliminating many patients with influenza as candidates for treatment. Empirical antiviral therapy ensures that all patients receive treatment promptly, at a cost equivalent to that of diagnostic tests alone, but results in the receipt of treatment by many patients without influenza. For patients hospitalized with suspected influenza, clinicians need to combine these approaches in order to optimize patient care.


id: cord-324307-2zbm4iwn
title: A Well Infant With Coronavirus Disease 2019 With High Viral Load
author: Kam, Kai-qian
date: 2020-02-28
txt: ./txt/cord-324307-2zbm4iwn.txt
cache: ./cache/cord-324307-2zbm4iwn.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa201
doi: 10.1093/cid/ciaa201
summary:
  A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. Two specific real-time reverse-transcription polymerase chain reaction (rRT-PCR) methods, targeting the N and ORF1ab genes, were designed to detect the presence of SARS-CoV-2 in clinical samples. A nasopharyngeal specimen taken on admission and tested by rRT-PCR confirmed the diagnosis of COVID-19 infection with low cycle threshold (N gene, 15.57; Orf1ab gene, 13.73), suggesting high viral load. On day 2 of admission, he was found to be viremic with detection of SARS-CoV-2 in his blood sample via rRT-PCR. Repeat testing of his urine on day 9 of admission was negative, but his stool sample became positive for SARS-CoV-2. Similar to reports of adult COVID-19, we confirm the detection of SARS-CoV-2 RNA in the stool of our infant.

abstract:
  A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. This case highlights the difficulties in establishing the true incidence of COVID-19, as asymptomatic individuals can excrete the virus. These patients may play important roles in human-to-human transmission in the community.


id: cord-324607-rpwccvqi
title: Core Minimal Datasets to Advance Clinical Research for Priority Epidemic Diseases
author: Rojek, Amanda M
date: 2020-02-15
txt: ./txt/cord-324607-rpwccvqi.txt
cache: ./cache/cord-324607-rpwccvqi.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciz760
doi: 10.1093/cid/ciz760
summary:
  Among the noteworthy successes of vaccine trials, and the commendable efforts to implement clinical treatment trials during Ebola outbreaks, we should also focus on strengthening the collection and curation of epidemiological and observational data that can improve the conception and design of clinical research. Table 1 identifies some key domains that could contribute to a core minimal dataset that informs clinical trial design for each priority pathogen. While these data have their most important benefits in improving patient management (through better recognition of disease complications and informing supportive care) and public health control, patient-based data are also used to determine key parameters for clinical trials, such as the inclusion criteria, the nature and rate of clinically relevant outcomes, and potential confounders. A systematic review and meta-analysis of patient data from the west Africa (2013-16) Ebola virus disease epidemic

abstract:
  The Ebola virus disease outbreak in west Africa has prompted significant progress in responding to the clinical needs of patients affected by emerging infectious disease outbreaks. Among the noteworthy successes of vaccine trials, and the commendable efforts to implement clinical treatment trials during Ebola outbreaks, we should also focus on strengthening the collection and curation of epidemiological and observational data that can improve the conception and design of clinical research.


id: cord-324707-9ld73wv1
title: Hydroxychloroquine for Early Treatment of Adults with Mild Covid-19: A Randomized-Controlled Trial
author: Mitjà, Oriol
date: 2020-07-16
txt: ./txt/cord-324707-9ld73wv1.txt
cache: ./cache/cord-324707-9ld73wv1.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1009
doi: 10.1093/cid/ciaa1009
summary:
  Study outcomes were the reduction of viral RNA load in nasopharyngeal swabs up to 7 days after treatment start, patient disease progression using the WHO scale up to 28 days, and time to complete resolution of symptoms. Adult patients aged 18 years or more were eligible if they had mild symptoms of Covid-19 (i.e., fever, acute cough, shortness of breath, sudden olfactory or gustatory loss, or influenza-like-illness) for less than five days before enrollment, were non-hospitalized, and had a positive PCR test for SARS-CoV-2 in the baseline nasopharyngeal swab. We estimated that a sample size of 280 patients would provide the trial with 80% power to detect a difference of 0.5 log 10 in the mean reduction of SARS-CoV-2 viral load at a two-sided significance level of α = 0.05, assuming an expected standard deviation of 1.5 [23] .

abstract:
  BACKGROUND: No therapeutics have yet been proven effective for the treatment of mild-illness caused by SARS-CoV-2. We aimed to determine whether early treatment with hydroxychloroquine (HCQ) would be more efficacious than no-treatment for outpatients with mild Covid-19. METHODS: We conducted a multicenter, open label, randomized controlled trial in Catalonia (Spain) between March 17, and May 26, 2020. Eligible Covid-19 cases were non-hospitalized adult patients with recently confirmed SARS-CoV-2 infection and less than five days of symptoms. Patients were assigned to receive HCQ (800 mg on day 1, followed by 400 mg once daily for 6 days) or no antiviral treatment (not-placebo controlled). Study outcomes were the reduction of viral RNA load in nasopharyngeal swabs up to 7 days after treatment start, patient disease progression using the WHO scale up to 28 days, and time to complete resolution of symptoms. Adverse events were assessed up to 28 days. RESULTS: A total of 293 patients were eligible for intention-to-treat analysis: 157 in the control arm and 136 in the intervention arm. The mean age was 41.6 years (SD 12.6), mean viral load at baseline was 7.90 (SD 1.82) Log(10) copies/mL, and median time from symptom onset to randomization was 3 days. No significant differences were found in the mean reduction of viral load at day 3 (-1.41 vs. -1.41 Log(10) copies/mL in the control and intervention arm, respectively; difference 0.01 [95% CI -0.28;0.29]) or at day 7 (-3.37 vs. -3.44; d –0.07 [-0.44;0.29]). This treatment regimen did not reduce risk of hospitalization (7.1%, control vs. 5.9%, intervention; RR 0.75 [0.32;1.77]) nor shortened the time to complete resolution of symptoms (12 days, control vs. 10 days, intervention; p = 0.38). No relevant treatment-related AEs were reported. CONCLUSIONS: In patients with mild Covid-19, no benefit was observed with HCQ beyond the usual care.


id: cord-325068-j1lfq60o
title: Coronavirus 229E-Related Pneumonia in Immunocompromised Patients
author: Pene, Frédéric
date: 2003-10-01
txt: ./txt/cord-325068-j1lfq60o.txt
cache: ./cache/cord-325068-j1lfq60o.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/13130404/
doi: 10.1086/377612
summary:
  The results of inoculation tests performed with HUH7 cells were also positive, revealing corona-like particles that were subsequently identified as coronavirus 229E by RT-PCR performed on both culture supernatant and BAL fluid specimens. However, respiratory symptoms only appeared after completion of antiviral treatment and improvement of skin eruptions, and both viral culture and PCR for VZV performed on BAL fluid specimens were negative. The prevalence of coronavirus pulmonary infections among immunocompromised patients is unknown, and it is probably largely underestimated in the absence of the routine performance of sensitive cell culture, RT-PCR, or electron microscopy on BAL fluid specimens. Thus, only 1 case of coronavirus-associated pneumonia was previously described in an immunocompromised patient following autologous bone marrow transplantation, with the diagnosis based on the presence of viral particles in BAL fluid specimens [22] .

abstract:
  Coronaviruses strains 229E and OC43 have been associated with various respiratory illnesses ranging from the self-resolving common cold to severe pneumonia. Although chronic underlying conditions are major determinants of severe respiratory virus infections, few data about coronavirus-related pneumonia in immunocompromised patients are available. Here we report 2 well-documented cases of pneumonia related to coronavirus 229E, each with a different clinical presentation. Diagnosis was made on the basis of viral culture and electron microscopy findings that exhibited typical crown-like particles and through amplification of the viral genome by reverse transcriptase—polymerase chain reaction. On the basis of this report, coronaviruses should be considered as potential causative microorganisms of pneumonia in immunocompromised patients.


id: cord-325136-oyizfh2z
title: The first 100 days of SARS-CoV-2 control in Vietnam
author: Pham, Quang Thai
date: 2020-08-01
txt: ./txt/cord-325136-oyizfh2z.txt
cache: ./cache/cord-325136-oyizfh2z.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1130
doi: 10.1093/cid/ciaa1130
summary:
  METHODS: Clinical and demographic data on the first 270 SARS-CoV-2 infected cases and the timing and nature of Government control measures, including numbers of tests and quarantined individuals, were analysed. Data from 270 SARS-CoV-2-confirmed cases to May 1 st 2020 included their age, gender, nationality, dates of symptom onset (if any), entry to the country and quarantine (if any), hospital admission and discharge, and the results of RT-PCR tests. The epidemic timeline for Vietnam, including the numbers quarantined and hospitalised, tests performed, cases confirmed, population movements, and the timing and nature of major Government-led control measures are summarised in Figure 1 . Entry of airline passengers into Vietnam from Wuhan city and elsewhere in China was monitored and progressively limited ( Table 1) After further measures to prevent entry of infected international travellers (Table 1) Forty-three percent (89/208) of discharged cases never developed symptoms, and this was not significantly associated with age, gender, nationality, or origin of infection (imported or domestically-acquired).

abstract:
  BACKGROUND: One hundred days after SARS-CoV-2 was first reported in Vietnam on January 23(rd), 270 cases were confirmed, with no deaths. We describe the control measures used by the Government and their relationship with imported and domestically-acquired case numbers, with the aim of identifying the measures associated with successful SARS-CoV-2 control. METHODS: Clinical and demographic data on the first 270 SARS-CoV-2 infected cases and the timing and nature of Government control measures, including numbers of tests and quarantined individuals, were analysed. Apple and Google mobility data provided proxies for population movement. Serial intervals were calculated from 33 infector-infectee pairs and used to estimate the proportion of pre-symptomatic transmission events and time-varying reproduction numbers. RESULTS: A national lockdown was implemented between April 1(st) and 22(nd). Around 200 000 people were quarantined and 266 122 RT-PCR tests conducted. Population mobility decreased progressively before lockdown. 60% (163/270) of cases were imported; 43% (89/208) of resolved infections remained asymptomatic for the duration of infection. The serial interval was 3·24 days, and 27·5% (95% confidence interval, 15·7%-40·0%) of transmissions occurred pre-symptomatically. Limited transmission amounted to a maximum reproduction number of 1·15 (95% confidence interval, 0·37-2·36). No community transmission has been detected since April 15(th). CONCLUSIONS: Vietnam has controlled SARS-CoV-2 spread through the early introduction of mass communication, meticulous contact-tracing with strict quarantine, and international travel restrictions. The value of these interventions is supported by the high proportion of asymptomatic and imported cases, and evidence for substantial pre-symptomatic transmission.


id: cord-325416-c0qj3yd9
author: Zachariah, Philip
date: 2020-05-20
txt: ./txt/cord-325416-c0qj3yd9.txt
cache: ./cache/cord-325416-c0qj3yd9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32433729/
doi: 10.1093/cid/ciaa608
abstract: nan
summary:
  title: Symptomatic Infants have Higher Nasopharyngeal SARS-CoV-2 Viral Loads but Less Severe Disease than Older Children A report published in this journal described the presence of a high nasopharyngeal (NP) viral load of severe acute respiratory coronavirus 2 (SARS-CoV-2) in a well infant [4] . While some data have suggested a higher disease severity in infants [2, 6] , how NP viral load correlates with severity across the pediatric age spectrum has not been firmly established. For each patient, we extracted age, time from reported symptom onset to the date of test, and severity of disease during hospitalization. Our report suggests symptomatic infants have higher NP viral loads at presentation but develop less severe disease as compared to older children and adolescents. A Well Infant with Coronavirus Disease 2019 (COVID-19) with High Viral Load Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China

title:
  Symptomatic Infants have Higher Nasopharyngeal SARS-CoV-2 Viral Loads but Less Severe Disease than Older Children


id: cord-325455-e464idc0
author: Atchison, Christina
date: 2020-08-12
txt: ./txt/cord-325455-e464idc0.txt
cache: ./cache/cord-325455-e464idc0.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1178
doi: 10.1093/cid/ciaa1178
summary:
  BACKGROUND: This study assesses acceptability and usability of home-based self-testing for SARS-CoV-2 antibodies using lateral flow immunoassays (LFIA). On a population level, by conducting seroprevalence surveys through widespread random sampling of the general public, and by adjusting for the sensitivity and specificity characteristics of the LFIA used, it is possible to estimate the levels of past infection with SARS-CoV-2 in the community (3) . Usability research on HIV selftesting has generally found good acceptability, the devices easy to use and high validity in interpretation of self-reported test results (7) (8) (9) . To mitigate against this, and given the scientific Our study is original because focusing on the acceptability and usability of LFIAs for self-testing for SARS-CoV-2 antibody in a home-based setting has not been done at such scale in the general population. Overall, our study has demonstrated that home-based self-testing LFIAs for use in large communitybased seroprevalence surveys of SARS-CoV-2 antibody are both acceptable and feasible.

title:
  Usability and acceptability of home-based self-testing for SARS-CoV-2 antibodies for population surveillance

abstract:
  BACKGROUND: This study assesses acceptability and usability of home-based self-testing for SARS-CoV-2 antibodies using lateral flow immunoassays (LFIA). METHODS: We carried out public involvement and pilot testing in 315 volunteers to improve usability. Feedback was obtained through online discussions, questionnaires, observations and interviews of people who tried the test at home. This informed the design of a nationally representative survey of adults in England using two LFIAs (LFIA1 and LFIA2) which were sent to 10,600 and 3,800 participants, respectively, who provided further feedback. RESULTS: Public involvement and pilot testing showed high levels of acceptability, but limitations with the usability of kits. Most people reported completing the test; however, they identified difficulties with practical aspects of the kit, particularly the lancet and pipette, a need for clearer instructions and more guidance on interpretation of results. In the national study, 99.3% (8,693/8,754) of LFIA1 and 98.4% (2,911/2,957) of LFIA2 respondents attempted the test and 97.5% and 97.8% of respondents completed it, respectively. Most found the instructions easy to understand, but some reported difficulties using the pipette (LFIA1: 17.7%) and applying the blood drop to the cassette (LFIA2: 31.3%). Most respondents obtained a valid result (LFIA1: 91.5%; LFIA2: 94.4%). Overall there was substantial concordance between participant and clinician interpreted results (kappa: LFIA1 0.72; LFIA2 0.89). CONCLUSION: Impactful public involvement is feasible in a rapid response setting. Home self-testing with LFIAs can be used with a high degree of acceptability and usability by adults, making them a good option for use in seroprevalence surveys.


id: cord-326138-16kpn9db
title: Laboratory-Acquired Infections
author: Weinstein, Robert A.
date: 2009-07-01
txt: ./txt/cord-326138-16kpn9db.txt
cache: ./cache/cord-326138-16kpn9db.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1086/599104
doi: 10.1086/599104
summary:
  Although the precise risk of infection after an exposure remains poorly defined, surveys of laboratory-acquired infections suggest that Brucella species, Shigella species, Salmonella species, Mycobacterium tuberculosis, and Neisseria meningitidis are the most common causes. Surveys of diagnostic laboratory workers in the United Kingdom conducted since 1971 have reported that tuberculosis and enteric infections (especially shigellosis) were the most common laboratory-acquired infections [7, 8] . Similar results were obtained from a survey of clinical microbiology laboratories in Utah from the period 1978-1992, with shigellosis reported to be the most common laboratory-acquired infection [10] . Although no controlled studies have been performed to assess the benefit of postexposure prophylaxis (PEP), it should be considered for laboratory workers who have high-risk exposure to Brucella species (e.g., because of direct manipulation of Brucella cultures outside of laminar-flow BSCs). Viral agents transmitted through blood and bodily fluids cause most of the laboratory-acquired infections in diagnostic laboratories and among health care workers [1] .

abstract:
  Laboratory-acquired infections due to a wide variety of bacteria, viruses, fungi, and parasites have been described. Although the precise risk of infection after an exposure remains poorly defined, surveys of laboratory-acquired infections suggest that Brucella species, Shigella species, Salmonella species, Mycobacterium tuberculosis, and Neisseria meningitidis are the most common causes. Infections due to the bloodborne pathogens (hepatitis B virus, hepatitis C virus, and human immunodeficiency virus) remain the most common reported viral infections, whereas the dimorphic fungi are responsible for the greatest number of fungal infections. Because of the increasing attention on the role of the laboratory in bioterrorism preparation, I discuss the risk of laboratory-acquired infection with uncommon agents, such as Francisella tularensis and Bacillus anthracis. Physicians who care for a sick laboratory worker need to consider the likelihood of an occupationally acquired infection while advising exposed laboratory workers about postexposure prophylaxis. In addition, physicians should be aware of the importance of alerting the laboratory if infection with a high-risk agent is suspected.


id: cord-326297-0r9pex1o
author: Hartmann, Stacy
date: 2020-08-17
txt: ./txt/cord-326297-0r9pex1o.txt
cache: ./cache/cord-326297-0r9pex1o.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32803237/
doi: 10.1093/cid/ciaa1200
summary:
  The Los Angeles County Department of Public Health (LAC DPH) set out to understand the impact of COVID-19 on healthcare facilities and HCWs by tracking and analyzing data from case-patient interviews of HCWs. As of May 31st, over three months into the pandemic, nearly 5,500 positive HCWs were reported to LAC DPH, representing 9.6% of all cases. All LAC residents who test positive for COVID-19 are interviewed by LAC DPH using a standardized form that identifies if the case-patient worked in a high-risk environment, such as a healthcare setting. From case-patient interviews and/or emailed reports, LAC DPH recorded occupational setting, occupational role, date of symptom onset, date last worked, known exposure, and if hospitalized for each HCW. At the end of April, HCWs represented 12.8% of all LAC cases, whereas only 9.6% at the end of May. When asked if they had a known exposure to COVID-19, (Table 3) , healthcare exposures within their facility accounted for nearly 44%, including contact with either a positive patient, co-worker, or both.

title:
  Coronavirus 2019 (COVID-19) Infections Among Healthcare Workers, Los Angeles County, February - May 2020

abstract:
  Across the world, healthcare workers (HCW) are at a greater risk of infection by the novel coronavirus 2019 (COVID-19) due to the nature of their work. The Los Angeles County Department of Public Health (LAC DPH) set out to understand the impact of COVID-19 on healthcare facilities and HCWs by tracking and analyzing data from case-patient interviews of HCWs. As of May 31st, over three months into the pandemic, nearly 5,500 positive HCWs were reported to LAC DPH, representing 9.6% of all cases. Cases reported working in 27 different setting types, including outpatient medical offices, correctional facilities, emergency medical services, etc., with the highest proportion from long-term care facilities (46.6%) and hospitals (27.7%). Case-patients included both clinical and non-clinical roles, with nearly half (49.4%) of positive HCWs being nurses. Over two-thirds of HCWs (68.6%) worked at some point during their infectious period and nearly half (47.9%) reported a known exposure to a positive patient and/or co-worker within their facility. Overall, compared to all LAC cases, HCWs reported lower rates of hospitalization (5.3% vs. 12.2%) and death (0.7% vs. 4.3%) from COVID-19. There are many factors that increase HCWs risk of infection, including high risk work environment, limited supply of personal protective equipment, and even pressure to help and work during a pandemic. In response to these data, LAC DPH created resources and provided guidance for healthcare facilities to best protect their patients and staff during the COVID-19 pandemic.


id: cord-326494-qhxlh43t
title: Pregnancy and Pandemic Disease
author: Beckerman, Karen Palmore
date: 2020-06-10
txt: ./txt/cord-326494-qhxlh43t.txt
cache: ./cache/cord-326494-qhxlh43t.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32520309/
doi: 10.1093/cid/ciaa741
abstract: nan
summary:
  Globally, estimates suggest it is a disease of men (57%), however women (32%) and children < age 15 (11%) together make up close to half of those living with TB. 10 They report an unexpectedly high proportion of women (37%) living with TB, The strong implication of these pregnancy data, that exposure and transmission in the population studied is both continuous and ongoing, is striking. have provided proof of concept data that routine testing during pregnancy could be an ideal method of assessing the extent of community spread of both recognized endemic infection as well as emerging infectious diseases. Today, we continue to rely on universal HIV testing of pregnant women to estimate community HIV prevalence and to prevent vertical transmission, both in resource-rich and resource-limited regions. Tuberculosis infection in women of reproductive age -a cross-sectional study at antenatal care clinics in an Ethiopian city Control of maternal HIV-1 disease during pregnancy


id: cord-327069-vjlisnui
title: Standardization of Laboratory Methods for the PERCH Study
author: Driscoll, Amanda J.
date: 2017-06-15
txt: ./txt/cord-327069-vjlisnui.txt
cache: ./cache/cord-327069-vjlisnui.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28575358/
doi: 10.1093/cid/cix081
summary:
  To build capacity at the sites, and in alignment with the priorities of the Bill & Melinda Gates Foundation, all PERCH testing was done locally, with the exception of quality assurance testing and a select subset of specialized assays, which were performed at the study reference laboratory (Canterbury Health Laboratories, Christchurch, New Zealand), which also served as the study specimen and isolate biorepository. Induced sputum, pleural fluid, and lung aspirate specimens were collected in saline in universal containers and either refrigerated at 2°C-8°C for a maximum of 24 hours, or frozen at -80°C prior to nucleic acid extraction. Organism identification was done according to standard microbiological methods that were documented in SOPs and clarified at each site at the outset; antimicrobial susceptibility testing followed the Clinical and Laboratory Standards Institute (CLSI) guidelines [15] .

abstract:
  The Pneumonia Etiology Research for Child Health study was conducted across 7 diverse research sites and relied on standardized clinical and laboratory methods for the accurate and meaningful interpretation of pneumonia etiology data. Blood, respiratory specimens, and urine were collected from children aged 1–59 months hospitalized with severe or very severe pneumonia and community controls of the same age without severe pneumonia and were tested with an extensive array of laboratory diagnostic tests. A standardized testing algorithm and standard operating procedures were applied across all study sites. Site laboratories received uniform training, equipment, and reagents for core testing methods. Standardization was further assured by routine teleconferences, in-person meetings, site monitoring visits, and internal and external quality assurance testing. Targeted confirmatory testing and testing by specialized assays were done at a central reference laboratory.


id: cord-327324-4c4a4bfz
title: Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19
author: Wilkinson, Robert J
date: 2020-06-13
txt: ./txt/cord-327324-4c4a4bfz.txt
cache: ./cache/cord-327324-4c4a4bfz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32533824/
doi: 10.1093/cid/ciaa747
abstract: nan
summary:
  title: Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 Active tuberculosis has a transcriptomic signature dominated by a neutrophil-driven type 1 and 2 interferoninducible gene profile. The exaggerated inflammation that characterizes HIV-tuberculosis-associated immune reconstitution inflammatory syndrome is triggered by Toll-like receptor and inflammasome signalling [14] . Male sex and diabetes have been identified in virtually every study as risk factors for severe COVID-19 infection, associated in the largest study to date with an adjusted hazard ratio for in-hospital death of 1.99 (male sex) and 1.50 for controlled (HbA1c < 58 mmol/mol) and 2.36 for uncontrolled DM [18] . Diabetes mellitus increases the risk of active tuberculosis: a systematic review of 13 observational studies HIV-tuberculosis-associated immune reconstitution inflammatory syndrome is characterized by Toll-like receptor and inflammasome signalling Complement pathway gene activation and rising circulating immune complexes characterize early disease in HIV-associated tuberculosis


id: cord-327862-zcg3baym
title: Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity
author: Luo, Yiqi Ruben
date: 2020-09-14
txt: ./txt/cord-327862-zcg3baym.txt
cache: ./cache/cord-327862-zcg3baym.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1389
doi: 10.1093/cid/ciaa1389
summary:
  The kinetics of IgG avidity maturation during SARS-CoV-2 infection was studied. It was found that there was a strong correlation between IgG avidity and days since symptom onset, and peak readings were significantly higher in severe than mild disease cases. 3, 4 Here we report the development of a method to characterize SARS-CoV-2 IgG avidity maturation in COVID-19 patients from initial diagnosis through convalescence. The IgG avidity assay was established on a novel label-free immunoassay platform Gator Analyzer (Gator Bio, Palo Alto, CA) to measure SARS-CoV-2 IgG avidity to the virus spike protein receptor-binding domain (RBD). The signal increase in the final step, which is proportional to the quantity of RBD-IgG-Anti-IgG immune complex on the sensing probe, was measured. As other isotypes of antibodies might bind to RBD in the second step, the measurement of the RBD-IgG-Anti-IgG immune complex enhanced the assay specificity. Magnitude and kinetics of anti-SARS-CoV-2 antibody responses and their relationship to disease severity

abstract:
  The kinetics of IgG avidity maturation during SARS-CoV-2 infection was studied. The IgG avidity assay used a novel label-free immunoassay technology. It was found that there was a strong correlation between IgG avidity and days since symptom onset, and peak readings were significantly higher in severe than mild disease cases.


id: cord-328267-tk0zc8il
title: Collateral Impact of the Covid-19 Pandemic on Tuberculosis Control in Jiangsu Province, China
author: Liu, Qiao
date: 2020-08-28
txt: ./txt/cord-328267-tk0zc8il.txt
cache: ./cache/cord-328267-tk0zc8il.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32857838/
doi: 10.1093/cid/ciaa1289
summary:
  title: Collateral Impact of the Covid-19 Pandemic on Tuberculosis Control in Jiangsu Province, China We compared tuberculosis case notifications, tuberculosis treatment outcomes, and diagnostic screening for multidrug resistance (MDR) among tuberculosis patients from 2015-2020 before and after the Covid-19 pandemic began in China. We A c c e p t e d M a n u s c r i p t Discussion This is the first data from China reporting the potential indirect impact on tuberculosis control of the Covid-19 pandemic. In addition, reductions in treatment completion and MDR screening during this time period suggest that both deterred health care seeking and community disease management are likely drivers of these trends. Our analysis suggests that collateral effects of the Covid-19 pandemic on tuberculosis control are substantial, with a reduction of 36%-52% in tuberculosis notifications in 2020 compared to 2015-2019.

abstract:
  The Covid-19 pandemic may impede global tuberculosis elimination goals. In Jiangsu Province, China, tuberculosis notifications dropped 52% in 2020 compared to 2015–2019. Treatment completion and screening for drug resistance decreased continuously in 2020. Urgent attention must be paid to tuberculosis control efforts during and after the Covid-19 pandemic.


id: cord-328667-r5w09lb6
title: The Effects of Pregnancy on Women with COVID-19: Maternal and Infant Outcomes
author: Schwartz, David A
date: 2020-05-11
txt: ./txt/cord-328667-r5w09lb6.txt
cache: ./cache/cord-328667-r5w09lb6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32392330/
doi: 10.1093/cid/ciaa559
abstract: nan
summary:
  In contrast, some pregnant women might be asymptomatic or have only mild or nonspecific symptoms from an infectious disease, resulting in their escaping detection as having infection even when the embryo or fetus is severely affected. [9] evaluated for the first time the effects of being pregnant on COVID-19 disease and pneumonia using a case-control experimental design conducted at the Maternal and Child Health Hospital of Hubei Province, a 1900-bed tertiary medical center in Wuhan, China. To accomplish this, the authors enrolled two cohorts of pregnant women with COVID-19 and pneumonia -one consisting of 16 pregnant women with pneumonia and rt-PCR confirmed SARS-CoV-2 infection, and the other with 18 pregnant women with pneumonia who were clinically and radiologically suspected of having COVID-19 but had negative rt-PCR test results. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: Maternal coronavirus infections and pregnancy outcomes Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study


id: cord-329290-vqvujry3
title: Loss of Smell and Taste Among Healthcare Personnel Screened for Coronavirus 2019
author: Kempker, Russell R
date: 2020-06-28
txt: ./txt/cord-329290-vqvujry3.txt
cache: ./cache/cord-329290-vqvujry3.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa877
doi: 10.1093/cid/ciaa877
summary:
  HCP with symptoms consistent with a viral-like illness were triaged to the employee health services staff for a virtual clinical assessment and then scheduled for SARS-CoV-2 testing. HCP with a positive SARS-CoV-2 test compared with those with a negative test had a higher mean number of symptoms and were more likely to have reported fever, chills, myalgia, and loss of smell or taste (Table 1 ). We are the first to evaluate the sensitivity of loss of smell and taste in distinguishing symptomatic HCP with and without a positive SARS-CoV-2 test and support their recent inclusion to the list of symptoms associated with COVID-19 provided by the CDC [4] . The high specificity and positive predictive value of loss of smell and/or taste for a positive SARS-CoV-2 test in our cohort highlights the utility of including these symptoms in COVID-19 screening algorithms.

abstract:
  Among 283 symptomatic healthcare personnel (HCP) tested for SARS-CoV-2, 51 (18%) were positive. Among those 51 HCP, self reported loss of smell and taste were present in 51% and 52.9%, respectively, with either present in 60.8%. These symptoms had high specificity (93% each, 96% for either) for a positive SARS-CoV-2 test.


id: cord-329311-p68kr4ga
author: Prebensen, Christian
date: 2020-09-05
txt: ./txt/cord-329311-p68kr4ga.txt
cache: ./cache/cord-329311-p68kr4ga.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32888003/
doi: 10.1093/cid/ciaa1338
summary:
  title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 Routine biochemistry was taken at admission and study-specific samples of EDTA plasma and serum were taken at three time points; baseline (enrollment), day 3 (1 day) and day 9 ( 2 days) in patients who were still hospitalized (details in Supplementary Figure 1) . SARS-CoV-2 RNAemia was detected in at least one sample in 58/123 (47%) patients, and in a significantly higher proportion of patients who were admitted to the ICU or died (80% vs. RNAemia was significantly more frequent at all time points in patients who reached the primary endpoint, whereas RNA loads were significantly higher at baseline and day 3 ( Table 1 , Supplementary Figure 2A ). In this prospective study of patients hospitalized with COVID-19 we detected SARS-CoV-2 RNAemia in 47% of included patients, and a significantly higher frequency of RNAemia and higher RNA loads in and similarly found that RNAemia was associated with ICU admission and hospital mortality [3] .

title:
  SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19

abstract:
  The clinical significance of SARS-CoV-2 RNA in the circulation is unknown. In this prospective cohort study, we detected viral RNA in the plasma of 58/123 (47%) patients hospitalized with COVID-19. RNA was detected more frequently, and levels were higher, in patients who were admitted to the ICU and/or died.


id: cord-329323-1cquorhs
author: Ko, Jean Y
date: 2020-09-18
txt: ./txt/cord-329323-1cquorhs.txt
cache: ./cache/cord-329323-1cquorhs.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa1419
doi: 10.1093/cid/ciaa1419
summary:
  Generalized Poisson regression models were used to calculate adjusted rate ratios (aRR) for hospitalization RESULTS: Among 5,416 adults, hospitalization rates were higher among those with ≥3 underlying conditions (versus without)(aRR: 5.0; 95%CI: 3.9, 6.3), severe obesity (aRR:4.4; 95%CI: 3.4, 5.7), chronic kidney disease (aRR:4.0; 95%CI: 3.0, 5.2), diabetes (aRR:3.2; 95%CI: 2.5, 4.1), obesity (aRR:2.9; 95%CI: 2.3, 3.5), hypertension (aRR:2.8; 95%CI: 2.3, 3.4), and asthma (aRR:1.4; 95%CI: 1.1, 1.7), after adjusting for age, sex, and race/ethnicity. BRFSS data were used to calculate weighted population estimates of community-dwelling adults with and without individual underlying medical conditions by age, sex, and race/ethnicity strata for the COVID-NET catchment area and served as the analytic A c c e p t e d M a n u s c r i p t 7 denominators.

title:
  Risk Factors for COVID-19-associated hospitalization: COVID-19-Associated Hospitalization Surveillance Network and Behavioral Risk Factor Surveillance System

abstract:
  BACKGROUND: Data on risk factors for COVID-19-associated hospitalization are needed to guide prevention efforts and clinical care. We sought to identify factors independently associated with COVID-19-associated hospitalizations METHODS: U.S. community-dwelling adults (≥18 years) hospitalized with laboratory-confirmed COVID-19 during March 1–June 23, 2020 were identified from the COVID-19-Associated Hospitalization Surveillance Network (COVID-NET), a multi-state surveillance system. To calculate hospitalization rates by age, sex, and race/ethnicity strata, COVID-NET data served as the numerator and Behavioral Risk Factor Surveillance System estimates served as the population denominator for characteristics of interest. Underlying medical conditions examined included hypertension, coronary artery disease, history of stroke, diabetes, obesity [BMI ≥30 kg/m (2)], severe obesity [BMI≥40 kg/m (2)], chronic kidney disease, asthma, and chronic obstructive pulmonary disease. Generalized Poisson regression models were used to calculate adjusted rate ratios (aRR) for hospitalization RESULTS: Among 5,416 adults, hospitalization rates were higher among those with ≥3 underlying conditions (versus without)(aRR: 5.0; 95%CI: 3.9, 6.3), severe obesity (aRR:4.4; 95%CI: 3.4, 5.7), chronic kidney disease (aRR:4.0; 95%CI: 3.0, 5.2), diabetes (aRR:3.2; 95%CI: 2.5, 4.1), obesity (aRR:2.9; 95%CI: 2.3, 3.5), hypertension (aRR:2.8; 95%CI: 2.3, 3.4), and asthma (aRR:1.4; 95%CI: 1.1, 1.7), after adjusting for age, sex, and race/ethnicity. Adjusting for the presence of an individual underlying medical condition, higher hospitalization rates were observed for adults aged ≥65, 45-64 (versus 18-44 years), males (versus females), and non-Hispanic black and other race/ethnicities (versus non-Hispanic whites) CONCLUSION: Our findings elucidate groups with higher hospitalization risk that may benefit from targeted preventive and therapeutic interventions


id: cord-330214-28ah3nig
title: Relationship between the ABO Blood Group and the COVID-19 Susceptibility
author: Zhao, Jiao
date: 2020-08-04
txt: ./txt/cord-330214-28ah3nig.txt
cache: ./cache/cord-330214-28ah3nig.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32750119/
doi: 10.1093/cid/ciaa1150
summary:
  To explore any relationship between the ABO blood group and the COVID-19 susceptibility, we compared ABO blood group distributions in 2,173 COVID-19 patients with local control populations, and found that blood group A was associated with an increased risk of infection, whereas group O was associated with a decreased risk. Here, we investigated the relationship between the ABO blood type and the susceptibility to COVID-19 in patients from three hospitals in Wuhan and Shenzhen, China. These results showed associations between ABO blood groups and COVID-19 susceptibility. The COVID-19 risk significantly increased for blood group A ( Figure 1 shows the estimates of ORs of the risk of ABO blood groups for COVID-19 on the pooled data from the three hospitals by random effects models. In this study, we found that ABO blood groups displayed different association risks for the infection with SARS-CoV-2 resulting in COVID-19. In the 285 patients from Shenzhen, we also found that blood group AB had an increased risk of infection.

abstract:
  To explore any relationship between the ABO blood group and the COVID-19 susceptibility, we compared ABO blood group distributions in 2,173 COVID-19 patients with local control populations, and found that blood group A was associated with an increased risk of infection, whereas group O was associated with a decreased risk.


id: cord-330742-m5xx8861
title: Age-dependent gender differences of COVID-19 in mainland China: comparative study
author: Qian, Jie
date: 2020-05-30
txt: ./txt/cord-330742-m5xx8861.txt
cache: ./cache/cord-330742-m5xx8861.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa683
doi: 10.1093/cid/ciaa683
summary:
  METHODS: We used the national surveillance database of COVID-19 in mainland China to compared gender differences in attack rate (AR), proportion of severe and critical cases (PSCC) and case fatality rate (CFR) in relation to age, affected province, and onset-to-diagnosis interval. After adjusting for age, affected province and onset-to-diagnosis interval, the female-to-male difference in AR, PSCC and CFR remained significant in multivariate logistic regression analyses. In this study, we used the surveillance data containing all confirmed cases in mainland China as of April 28, 2020 to evaluated gender-specific differences in attack rate, proportion of severe and critical cases, and case fatality in relation to age, affected province and onset-to-diagnosis interval, in order to provide evidence-based guidance for more effective and equitable interventions and treatments.

abstract:
  BACKGROUND: The ongoing pandemic of novel coronavirus disease 2019 (COVID-19) is challenging global public health system. Sex-differences in infectious diseases are a common but neglected problem. METHODS: We used the national surveillance database of COVID-19 in mainland China to compared gender differences in attack rate (AR), proportion of severe and critical cases (PSCC) and case fatality rate (CFR) in relation to age, affected province, and onset-to-diagnosis interval. RESULTS: The overall AR was significantly higher in female population than in males (63.9 versus 60.5 per million persons; P ˂ .001). By contrast, PSCC and CFR were significantly lower among female patients (16.9% and 4.0%) than among males (19.5% and 7.2%), with ORs of 0.87 and 0.57, respectively (both P ˂ .001). The female-to-male differences were age-dependent, which were significant among people aged 50–69 years for AR, and in the patients of 30-years or older for both PSCC and CFR (all P ≤ .001). The AR, PSCC and CFR varied greatly from province to province. However, female-to-male differences in AR, PSCC and CFR were significant in the epicenter, Hubei province, where 82.2% confirmed cases and 97.4% deaths occurred. After adjusting for age, affected province and onset-to-diagnosis interval, the female-to-male difference in AR, PSCC and CFR remained significant in multivariate logistic regression analyses. CONCLUSIONS: We elucidate an age-dependent gender dimorphism for COVID-19, in which the females have higher susceptibility but lower severity and fatality. Further epidemiological and biological investigations are required to better understand the sex-specific differences for effective interventions.


id: cord-330951-k54e3lbu
title: Social media and the new world of scientific communication during the COVID19 pandemic
author: Pollett, S
date: 2020-05-12
txt: ./txt/cord-330951-k54e3lbu.txt
cache: ./cache/cord-330951-k54e3lbu.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa553
doi: 10.1093/cid/ciaa553
summary:
  The human and social toll of the COVID19 pandemic has already spurred several major public health ''lessons learned'', and the theme of effective and responsible scientific communication is among them. This discussion also serves as a succinct primer on some of the pivotal epidemiological analyses (and their communication) during the early phases of the COVID19 outbreak, as seen through the lens of a Twitterfeed. The expansion of the outbreak has demanded a rapid response from public health authorities; fundamental epidemiological and scientific evidence has been acquired at break-neck speed to support those decisions. We propose that Twitter has played a fundamental -but often precarious -role in permitting real-time global communication between scientists during the COVID19 epidemic, on a scale not seen before. This discussion also serves as a succinct primer on some of the pivotal epidemiological analyses (and their communication) during the early phases of the COVID19 outbreak, as seen through the lens of a Twitter-feed.

abstract:
  The human and social toll of the COVID19 pandemic has already spurred several major public health ‘lessons learned’, and the theme of effective and responsible scientific communication is among them. We propose that Twitter has played a fundamental – but often precarious - role in permitting real-time global communication between scientists during the COVID19 epidemic, on a scale not seen before. Here, we discuss three key facets to Twitter-enabled scientific exchange during public health emergencies, including some major draw-backs. This discussion also serves as a succinct primer on some of the pivotal epidemiological analyses (and their communication) during the early phases of the COVID19 outbreak, as seen through the lens of a Twitter- feed.


id: cord-331465-humpwwk2
title: On setting expectations for a SARS-CoV-2 Vaccine
author: Canaday, David H
date: 2020-06-04
txt: ./txt/cord-331465-humpwwk2.txt
cache: ./cache/cord-331465-humpwwk2.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa726
doi: 10.1093/cid/ciaa726
summary:
  Therefore, the expectation that a SARS-CoV-2 vaccine can develop this level of protection from an immune naive state, especially in the setting of immunizing elderly individuals whose naive B and T cells are substantially diminished, needs to be set with caution. Data from several influenza studies suggest that increased CMI, specifically including both CD4+ and CD8+ T cells, helps mitigate influenza severity in older adults when infected despite vaccination [6] [7] [8] . We should expect all of the existing clinical trial candidates to have incomplete effectiveness, and we need to establish whether those that ineffectively recruit CMI have inferior disease mitigation when COVID-19 develops despite vaccination. Logically, none of the current clinical trials use a live attenuated vaccine, as we simply do not know enough about SARS-CoV-2 virology to safely put forward such a candidate. mRNA vaccines against H10N8 and H7N9 influenza viruses of pandemic potential are immunogenic and well tolerated in healthy adults in phase 1 randomized clinical trials

abstract:
  The global coronavirus pandemic is unlike any other since 1918. A century of dramatic medical advances has produced a public expectation that the medical field will rapidly provide solutions to restore normalcy. In under 6 months, since SARS-CoV-2 was identified, the massive international effort to develop a SARS-CoV-2 vaccine has generated more than 140 vaccines in different stages of development with 9 already recruiting into clinical trials posted on clinicaltrials.gov. The long-term strategy to handle COVID-19 will almost certainly rely on vaccines. But, what type of protection can we realistically expect to achieve from vaccines and when?


id: cord-331719-uijwq8gx
title: FDA Perspectives on Diagnostic Device Clinical Studies for Respiratory Infections
author: Russek-Cohen, Estelle
date: 2011-05-01
txt: ./txt/cord-331719-uijwq8gx.txt
cache: ./cache/cord-331719-uijwq8gx.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/cir056
doi: 10.1093/cid/cir056
summary:
  In the former circumstance, a clinical reference method is considered to be the best available method for establishing the presence or absence of the target organism [1] but the reference method cannot incorporate results reported by the new device; for example, a new enzymelinked immunosorbent assay (ELISA) could not be used as one of the diagnostic criteria for the reference method in a study used to evaluate the performance of the assay. In a clinical study with only 5 specimens positive for a specific pathogen (via the reference method) and an observed sensitivity of 5/5 (100%) results in a lower confidence bound of only 55.6%, meaning diagnostic performance is very uncertain. Detailed information regarding the design of studies for a CLIA waiver application, including the minimal performance criteria acceptable for a CLIA-waived device, is described in ''''FDA guidance for industry and FDA staff: recommendations for Clinical Laboratory Improvement Amendments of 1988 (CLIA) waiver applications for manufacturers of in vitro diagnostic devices'''' [9] .

abstract:
  Two pathways are described for submission to FDA for clearance of a diagnostic device: a Premarket Application (PMA), which can lead to approval of a diagnostic device, and a Premarket Notification, which can lead to clearance. The latter is often called a 510(k), named for the statute providing for this path. Recent FDA clearance of molecular-based multiplex panels represents the beginning of a new era for the diagnosis of respiratory infections. The ability to test for multiple pathogens simultaneously, accompanied by the increasing availability of molecular-based assays for newly recognized respiratory pathogens will likely have a major impact on patient care, drug development, and public health epidemiology. We provide a general overview of how FDA evaluates new diagnostics for respiratory tract infections and the agency’s expectations for sponsors developing new tests in this area.


id: cord-331731-c2r0kfaz
author: Anugwom, Chimaobi M
date: 2020-06-05
txt: ./txt/cord-331731-c2r0kfaz.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa592
doi: 10.1093/cid/ciaa592
abstract: nan
summary:
  M a n u s c r i p t Dear Editor, We read with great interest the report by Zhao et al, regarding a case of delayed immune response to SARS-CoV-2 in a patient with HIV and HCV co-infection [1] . It is unclear whether this is a simple epidemiological "misconnection" or if being chronically infected with HBV impacts the chances of clinically significant infection with SARS-CoV-2 leading to less hospital admissions, in a similar fashion as that reported by Zhao et al to HIV and HCV. Early virus clearance and delayed antibody response in a case of COVID-19 with a history of co-infection with HIV-1 and HCV Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series

title:
  Inverse association between chronic hepatitis B infection and COVID-19: immune-exhaustion or coincidence?


id: cord-331930-w2055c42
author: Tso, Eugene Y. K.
date: 2004-05-01
txt: ./txt/cord-331930-w2055c42.txt
cache: ./cache/cord-331930-w2055c42.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15127357/
doi: 10.1086/383580
abstract: nan
summary:
  title: Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome Sir-We performed a cross-sectional study to assess the physical symptoms in and abnormal laboratory findings for survivors of severe acute respiratory syndrome (SARS) at their first follow-up visit after discharge from Princess Margaret Hospital (Hong Kong, China). The median interval (‫ע‬SD) between the onset of SARS symptoms and the first follow-up visit was weeks. Symptoms reported at the first followup visit included palpitation (45.1% of patients), exertional dyspnea (41.9%), malaise (40.3%), easy forgetfulness (30.6%), chest discomfort (22.5%), hand tremor (21%), dizziness (17.7%), depression (16.1%), myalgia (12.9%), headache (9.6%), diarrhoea (8.1%), cough (8.1%), insomnia (6.5%), and hair loss over the scalp (3.2%). Laboratory findings included the following mean values (‫ע‬SD): hemoglobin of patients. However, for 1 female patient, PCR of a stool sample obtained 35 days after the onset of SARS symptoms was positive for SARS-CoV RNA.

title:
  Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome


id: cord-331978-y4uo7o8g
title: “The Art of War” in the Era of Coronavirus Disease 2019 (COVID-19)
author: Maxwell, Daniel N
date: 2020-03-04
txt: ./txt/cord-331978-y4uo7o8g.txt
cache: ./cache/cord-331978-y4uo7o8g.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa229
doi: 10.1093/cid/ciaa229
abstract: nan
summary:
  With rapidly increasing cases and local community transmission in multiple countries outside of China, including the United States, the outbreak has entered a new phase, which requires a shift in primary battle strategy from a focus on containment in China to international mitigation. As cases of COVID-19 explode internationally, a strategic shift is required away from primarily containment, keeping the virus "out there", to home-based mitigation and public health responses. Now, the task is bearing the burden of identifying, isolating, triaging and managing the rising number of cases, necessitating total engagement of the medical community, public health sector, governments and society as a whole. As Sun Tzu noted, "If in training soldiers'' commands are habitually enforced, the army will be well-disciplined." 1 The authors also highlight improvements in infection prevention and control (IPC) infrastructure, administrative controls, and public health coordination compared to their 2003 SARS experience.


id: cord-332469-zegawla5
title: The characteristics of household transmission of COVID-19
author: Li, Wei
date: 2020-04-17
txt: ./txt/cord-332469-zegawla5.txt
cache: ./cache/cord-332469-zegawla5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciaa450
doi: 10.1093/cid/ciaa450
summary:
  Secondary attack rates of SARS-CoV-2 to the contact members were computed and the risk factors for transmission within household were estimated. The secondary attack rate to contacts who were spouses of index cases was 27.8% comparing with 17.3% to other adult members in the households. Spouse relationship was another risk factor for the infection of SARS-CoV-2 to household contacts and the secondary attack rate to individuals who were spouses of index cases was 27.8%, compared to 17.3% to other members in the households (OR 2.21, 95% CI 1.18 to 4.12, p=0.013). The gender, symptoms and the time between onset of illness of index patients and hospitalization were not related to the secondary attack rates of SARS-CoV-2 to household contacts (Table 3 The results showed no infected contacts in the households with index cases who implemented quarantine immediately after appearance of symptoms, and so the secondary attack rate was zero.

abstract:
  BACKGROUND: Since December 2019, SARS-CoV-2 virus has extended to most parts of China with more than 80 thousand cases and to at least 100 countries with more than 60 thousand international cases by March 15, 2020. Here we applied household cohort study to determine the features of household transmission of COVID-19. METHODS: Total 105 index patients and 392 household contacts were enrolled. Both index patients and household members were inspected by SARS-CoV-2 RT-PCR. The information of all recruited people was extracted from medical records and confirmed or supplemented by telephone interviews. The baseline characteristics of index cases and contact patients were described. Secondary attack rates of SARS-CoV-2 to the contact members were computed and the risk factors for transmission within household were estimated. RESULTS: Secondary transmission of SARS-CoV-2 developed in 64 of 392 household contacts (16.3%). The secondary attack rate to children was 4% comparing with 17.1% to adults. The secondary attack rate to the contacts within the households with index patients quarantined by themselves since onset of symptoms was 0% comparing with 16.9% to the contacts without index patients quarantined. The secondary attack rate to contacts who were spouses of index cases was 27.8% comparing with 17.3% to other adult members in the households. CONCLUSION: The secondary attack rate of SARS-CoV-2 in household is 16.3%. Ages of household contacts and spouse relationship with index case are risk factors for transmission of SARS-CoV-2 within household. Quarantine of index patients at home since onset of symptom is useful to prevent the transmission of SARS-Co-2 within household.


